The complete sequence of the  Bacillus licheniformis  ATCC 14580 genome was determined, revealing 4,208 predicted protein-coding genes, 7 rRNA operons and 72 tRNA genes.Bacillus licheniformis

Background Bacillus licheniformis  is a Gram-positive, spore-forming bacterium widely distributed as a saprophytic organism in the environment. This species is a close relative of  Bacillus subtilis , an organism that is second only to  Escherichia coli  in the level of detail at which it has been studied. Unlike most other bacilli, which are predominantly aerobic,  B. licheniformis  is a facultative anaerobe, which may allow it to grow in additional ecological niches. Certain  B. licheniformis  isolates are capable of denitrification; the relevance of this characteristic to environmental denitrification may be small, however, as the species generally persists in soil as endospores [ 1 ]. There are numerous commercial and agricultural uses for  B. licheniformis  and its extracellular products. The species has been used for decades in the manufacture of industrial enzymes including several proteases, α-amylase, penicillinase, pentosanase, cycloglucosyltransferase, β-mannanase and several pectinolytic enzymes. The proteases from  B. licheniformis  are used in the detergent industry as well as for dehairing and bating of leather [ 2 , 3 ]. Amylases from  B. licheniformis  are deployed for the hydrolysis of starch, desizing of textiles and sizing of paper [ 3 ]. Specific  B. licheniformis  strains are also used to produce peptide antibiotics such as bacitracin and proticin in addition to a number of specialty chemicals such as citric acid, inosine, inosinic acid and poly-γ-glutamic acid [ 4 ]. Some  B. licheniformis  isolates can mitigate the affects of fungal pathogens on maize, grasses and vegetable crops [ 5 ]. As an endospore-forming bacterium, the ability of the organism to survive under unfavorable environmental conditions may enhance its potential as a natural biocontrol agent. B. licheniformis  can be differentiated from other bacilli on the basis of metabolic and physiological tests [ 6 , 7 ]; however, biochemical and phenotypic characteristics may be ambiguous among closely related species. Recent taxonomic studies indicate that  B. licheniformis  is closely related to  B. subtilis  and  Bacillus amyloliquefaciens  on the basis of comparisons of 16S rDNA and 16S-23S internal transcribed spacer (ITS) nucleotide sequences [ 8 ]. Lapidus  et al.  [ 9 ] recently constructed a physical map of the  B. licheniformis  chromosome using a PCR approach, and established a number of regions of colinearity where gene content and organization were conserved with the  B. subtilis  genome. Given that  B. licheniformis  is an industrial organism used for the manufacture of enzymes, antibiotics, and chemicals, important in nutrient cycling in the environment, and a species that is taxonomically related to  B. subtilis , perhaps the best studied of all Gram-positive bacteria, we derived the complete nucleotide sequence of the  B. licheniformis  type strain (ATCC 14580) genome. With this data in hand, functional and comparative genomics studies can be initiated that may ultimately lead to new strategies for improving industrial strains as well as better understanding of genome evolution among the species within the  subtilis-licheniformis  group.
Background
Bacillus licheniformis  is a Gram-positive, spore-forming bacterium widely distributed as a saprophytic organism in the environment. This species is a close relative of  Bacillus subtilis , an organism that is second only to  Escherichia coli  in the level of detail at which it has been studied. Unlike most other bacilli, which are predominantly aerobic,  B. licheniformis  is a facultative anaerobe, which may allow it to grow in additional ecological niches. Certain  B. licheniformis  isolates are capable of denitrification; the relevance of this characteristic to environmental denitrification may be small, however, as the species generally persists in soil as endospores [ 1 ].Bacillus licheniformisBacillus subtilisEscherichia coliB. licheniformisB. licheniformisThere are numerous commercial and agricultural uses for  B. licheniformis  and its extracellular products. The species has been used for decades in the manufacture of industrial enzymes including several proteases, α-amylase, penicillinase, pentosanase, cycloglucosyltransferase, β-mannanase and several pectinolytic enzymes. The proteases from  B. licheniformis  are used in the detergent industry as well as for dehairing and bating of leather [ 2 , 3 ]. Amylases from  B. licheniformis  are deployed for the hydrolysis of starch, desizing of textiles and sizing of paper [ 3 ]. Specific  B. licheniformis  strains are also used to produce peptide antibiotics such as bacitracin and proticin in addition to a number of specialty chemicals such as citric acid, inosine, inosinic acid and poly-γ-glutamic acid [ 4 ]. Some  B. licheniformis  isolates can mitigate the affects of fungal pathogens on maize, grasses and vegetable crops [ 5 ]. As an endospore-forming bacterium, the ability of the organism to survive under unfavorable environmental conditions may enhance its potential as a natural biocontrol agent.B. licheniformisB. licheniformisB. licheniformisB. licheniformisB. licheniformisB. licheniformis  can be differentiated from other bacilli on the basis of metabolic and physiological tests [ 6 , 7 ]; however, biochemical and phenotypic characteristics may be ambiguous among closely related species. Recent taxonomic studies indicate that  B. licheniformis  is closely related to  B. subtilis  and  Bacillus amyloliquefaciens  on the basis of comparisons of 16S rDNA and 16S-23S internal transcribed spacer (ITS) nucleotide sequences [ 8 ]. Lapidus  et al.  [ 9 ] recently constructed a physical map of the  B. licheniformis  chromosome using a PCR approach, and established a number of regions of colinearity where gene content and organization were conserved with the  B. subtilis  genome.B. licheniformisB. licheniformisB. subtilisBacillus amyloliquefacienset al.B. licheniformisB. subtilisGiven that  B. licheniformis  is an industrial organism used for the manufacture of enzymes, antibiotics, and chemicals, important in nutrient cycling in the environment, and a species that is taxonomically related to  B. subtilis , perhaps the best studied of all Gram-positive bacteria, we derived the complete nucleotide sequence of the  B. licheniformis  type strain (ATCC 14580) genome. With this data in hand, functional and comparative genomics studies can be initiated that may ultimately lead to new strategies for improving industrial strains as well as better understanding of genome evolution among the species within the  subtilis-licheniformis  group.B. licheniformisB. subtilisB. licheniformissubtilis-licheniformisResults and discussion General features of the  B. licheniformis  genome The genome of  B. licheniformis  ATCC 14580 consists of a circular chromosome of 4,222,336 base-pairs (bp) with an average G+C content of 46.2% (Table  1 ). No plasmids were found during the genome analysis, and none were found by agarose gel electrophoresis (data not shown). Using a combination of several gene-finding programs and manual inspection, 4,208 protein-coding sequences (CDSs) were predicted. These CDSs constitute 87% of the genome and have an average length of 873 bp (ranging from 78 to 10,767 bp). They are oriented on the chromosome primarily in the direction of replication (Figure  1 ) with 74.4% of the genes on the leading strand and 25.6% on the lagging strand. Among the 4,208 protein coding genes, 3,948 (94%) had significant similarity to proteins in PIR, 3,187 (76%) of these gene models contain Interpro motifs, and 2,895 (69%) contain protein motifs found in PFAM. The number of hypothetical and conserved hypothetical proteins in the  B. licheniformis  genome with hits in the PIR database was 1,318 (212 conserved hypothetical proteins). Among the list of hypothetical and conserved hypothetical gene products, 683 (52%) have protein motifs contained in PFAM (148 conserved hypothetical proteins). There are 72 tRNA genes representing all 20 amino acids and seven rRNA operons. The likely origin of replication (Figure  1 ) was identified by similarities to several features of the corresponding regions in  B. subtilis  and other bacteria. These included co-localization of four genes ( rpmH ,  dnaA ,  dnaN , and  recF ) near the origin, GC nucleotide skew ((G-C)/(G+C)) analysis, and the presence of multiple  dnaA -boxes and AT-rich sequences immediately upstream of the  dnaA  gene [ 10 - 12 ]. On the basis of these observations we assigned a cytosine residue of the  Bst BI restriction site between the  rpmH  and  dnaA  genes to be the first nucleotide of the  B. licheniformis  genome. The replication termination site was localized near 2.02 megabases (Mb) by GC skew analysis. This region lies roughly opposite the origin of replication (Figure  1 ). Unlike  B. subtilis , there was no apparent gene encoding a replication terminator protein ( rtp ) in  B. licheniformis . The  Bacillus halodurans  genome also lacks an obvious  rtp  function [ 13 ]; therefore, it seems likely that  B. subtilis  acquired the  rtp  gene following its divergence from  B. halodurans  and  B. licheniformis . Transposable elements, prophages and atypical regions The genome of  B. licheniformis  ATCC 14580 contains nine identical copies of a 1,285 bp insertion sequence element termed  IS3Bli1  [ 9 ]. This sequence shares a number of features with other  IS3  family elements [ 9 ] including direct repeats of 3-5 bp, a 10-bp left inverted repeat, and a 9 bp right inverted repeat (Figure  2 ).  IS3Bli1  encodes two predicted overlapping CDSs, designated  orfA  and  orfB  in relative translational reading frames of 0 and -1. The presence of a 'slippery heptamer' motif, AAAAAAG, before the stop codon in  orfA  may indicate that programmed translational frameshifting occurs between these two coding sequences, resulting in a single gene product [ 14 ]. The  orfB  gene product harbors the DD(35)E(7)K motif, a highly conserved pattern among insertion sequences. Eight of these  IS3Bli1  elements lie in intergenic regions, and one interrupts the  comP  gene as noted previously [ 9 ]. In addition to these insertion sequences, the genome encodes a putative transposase that is most closely related (E = 1.8 × 10 -11 ) to one identified in the  Thermoanaerobacter tengcongensis  genome [ 15 ]; however, similar transposase genes are also found in the chromosomes of  B. halodurans  [ 13 ],  Oceanobacillus iheyensis  [ 16 ],  Streptococcus agalactiae  [ 17 ] and  Streptococcus pyogenes  [ 18 ]. The presence of several bacteriophage lysogens or prophage-like elements was revealed by Smith-Waterman comparisons to other bacterial genomes and by their AT-rich signatures (Figure  3 , Table  2 ). Prophage sequences, designated NZP1 and NZP3 (similar to  B. subtilis  prophages PBSX and φ-105), were discovered by noting the presence of nearby genes that code for the large subunit of terminase, a signature protein that is highly conserved among prophages [ 19 ]. Interestingly, a terminase gene was not observed in the third putative prophage, termed NZP2 (similarity to  B. subtilis  phage SPP1); however, its absence may be the result of genome deterioration during evolution. Interestingly, we observed that regions in which the G+C content is less than 39% usually encoded proteins that have no  B. subtilis  ortholog and share identity only with hypothetical and conserved hypothetical genes. Two of these AT-rich segments correspond to the NZP2 and NZP3 prophages. An isochore plot (Figure  3 ) also revealed the presence of a region with an atypically high (62%) G+C content. This segment contains two hypothetical genes whose sizes (3,831 and 2,865 bp) greatly exceed the size of an average CDS in  B. licheniformis . The first gene encodes a protein of 1,277 amino acids for which Interpro predicts 16 collagen triple-helix repeats, and the amino acid pattern TGATGPT is repeated 75 times within the polypeptide. The second CDS is smaller, and encodes a protein with 11 collagen triple-helix repeats; the same TGATGPT motif recurs 56 times. The primary translation products from these genes do not contain canonical signal peptides for secretion, and they do not contain motifs for the twin-arginine or sortase-mediated translocation pathways. Therefore, it is not likely that they are exported to the cell surface or the extracellular medium. Interestingly, the chromosomal region (19 kb) adjacent to these genes is clearly non-colinear with the  B. subtilis  genome, and virtually all of the predicted genes encode hypothetical or conserved hypothetical proteins. There are a number of bacterial proteins listed in PIR that also contain collagen triple-helix repeat regions, including two from  Mesorhizobium loti  (accession numbers NF00607049 and NF00607035) and three from  B. cereus  (accession numbers NF01692528, NF01269899 and NF01694666). These putative orthologs share 53-76% amino-acid sequence identity with their counterparts in  B. licheniformis , and their functions are unknown. Extracellular enzymes and metabolic activities In the  Bacillus licheniformis  genome, 689 of the 4,208 gene models have signal peptides forecast by SignalP [ 20 ]. Of these, 309 have no transmembrane domain predicted by TMHMM [ 21 ] and 134 are hypothetical or conserved hypothetical genes. Based on a manual examination of the remaining 175 genes, at least 82 are likely to encode secreted proteins and enzymes. Moreover, there are 27 predicted extracellular proteins encoded by the  B. licheniformis  ATCC 14580 genome that are not found in  B. subtilis  168. In accordance with its saprophytic lifestyle, the secretome of  B. licheniformis  encodes numerous secreted enzymes that hydrolyze polysaccharides, proteins, lipids and other nutrients. Cellulose is the most abundant polysaccharide on Earth, and microorganisms that hydrolyze cellulose contribute to the global carbon cycle. Interestingly, two gene clusters involved in cellulose degradation and utilization were discovered in  B. licheniformis , and there are no counterparts in  B. subtilis  168. The enzymes encoded by the first gene cluster include two putative endoglucanases belonging to glycoside hydrolase families GH9 and GH5, a probable cellulose-1,4-β-cellobiosidase of family GH48, and a putative β-mannanase of family GH5. The β-mannanase (GH5) and endoglucanase (GH9) both harbor carbohydrate-binding motifs. With the exception of the cellulose-1,4-β-cellobiosidase (GH48), all of the gene products encoded in this cluster have secretory signal peptides, and all have homologs in  Bacillus  species other than  B. subtilis . The overall G+C content of this cluster (48%) does not appear to differ appreciably from that of the genome average (46%). The second gene cluster encodes a putative β-glucosidase (GH1) and three components of a cellobiose-specific PTS transport complex. A second β-glucosidase (GH3) gene is present at an unlinked locus in the genome. Collectively, the genes in these two clusters should enable  B. licheniformis  to utilize cellulose as a carbon and energy source, converting it to cellobiose and ultimately glucose. In this regard, we have confirmed that  B. licheniformis  ATCC 14580 is capable of growth on carboxymethyl cellulose as a sole carbon source (not shown). The chromosome of  B. licheniformis  ATCC 14580 encodes a number of additional carbohydrase activities that may allow the organism to grow on a broad range of polysaccharides. These include xylanase, endo-arabinase and pectate lyase that may be involved in degradation of hemicellulose, α-amylase and α-glucosidase for starch hydrolysis, chitinases for the breakdown of chitooligosaccharides from fungi and insects, and levanase for utilization of β-D-fructans (levans). Several of these activities are marketed as industrial enzymes. Saprophytic organisms must utilize a variety of nitrogenous compounds as nutrients for growth and metabolism. On the basis of the information encoded in its genome,  B. licheniformis  ATCC 14580 possesses the ability to acquire nitrogen from exogenous proteins, peptides, amino acids, ammonia, nitrate and nitrite. Like  B. subtilis , the repertoire of extracellular proteases produced by  B. licheniformis  includes serine proteases ( aprE ,  epr ,  vpr ), metalloprotease ( mpr ), and an assortment of endo- and exopeptidases ( yjbG ,  ydiC ,  gcp ,  ykvY ,  ampS ,  bpr  (two copies),  yfxM ,  yuiE ,  yusX ,  ywaD ,  pepT ). However,  B. licheniformis  also has the capacity to produce a number of additional proteases and peptidases that are not encoded in the  B. subtilis  genome. These include a clostripain-like protease, a zinc-metallopeptidase, a probable glutamyl endopeptidase, an aminopeptidase C homolog, two putative dipeptidases and a zinc-carboxypeptidase. B. licheniformis  also has the ability to utilize amino and imino nitrogen from arginine, asparagine and glutamine via arginine deiminase, arginase, asparaginase and glutaminase activities. Interestingly, there appear to be two genes each for arginase, asparaginase and glutaminase. Presumably, the arginine deiminase activity is expressed during anaerobic growth on arginine, whereas the arginase activities are predominant during aerobic growth. The occurrence of putative arginase genes is somewhat of an enigma in  B. licheniformis , because there are no genes encoding urease activity for the hydrolysis of urea that is generated by the arginase reaction. In addition to the absence of urease gene homologs ( ureABC ) in  B. licheniformis , the glutamine ABC transporters ( glnH ,  glnM ,  glnP ,  glnQ  gene products) are also lacking. It appears that nitrogen assimilation and transport pathways may be coordinated similarly in  B. licheniformis  and  B. subtilis  owing to the presence of key genes such as  glnA ,  glnR ,  tnrA  and  nrgA  in both species. Likewise, the pathways for nitrate/nitrite transport and metabolism in  B. licheniformis  appear to be analogous to the corresponding pathways in  B. subtilis  as suggested by the presence of  nasABC  (nitrate transport),  narGHIJ  (respiratory nitrate reductase), and  nasDEF  (NADH-dependent nitrite reductase) genes. Unlike  B. subtilis ,  B. licheniformis  evidently possesses the capability for anaerobic respiration using nitric oxide reductase. Moreover, the gene encoding this activity lies in a cluster that includes CDSs for  narK  (nitrite extrusion protein), two putative  fnr  proteins (transcriptional regulators of anaerobic growth), and a  dnrN -like gene product (nitric oxide-dependent regulator). These observations are consistent with previous findings that certain  B. licheniformis  isolates are capable of denitrification [ 22 ]. While denitrification is a process of major ecological importance, the contribution of  B. licheniformis  may be small as the species exists predominantly as endospores in soil [ 1 ]. Microbial D-hydantoinase enzymes have been applied to the industrial production of optically pure D-amino acids for synthesis of antibiotics, pesticides, sweeteners and therapeutic amino acids [ 23 ]. This enzyme catalyzes the hydrolysis of cyclic ureides such as dihydropyrimidines and 5-monosubstituted hydantoins to  N -carbamoyl amino acids. Hydantoinase activities have been detected in a variety of bacterial genera, and a cluster of six genes in  B. licheniformis  appears to confer a similar capability. This gene cluster encodes  N -methylhydantoinase (ATP-hydrolyzing), hydantoin utilization proteins A and B ( hyuAB  homologs), a possible transcriptional regulator (TetR/AcrR family), a putative pyrimidine permease, and a hypothetical protein that contains an Interpro domain (IPR004399) for phosphomethylpyrimidine kinase. Protein export, sporulation and competence pathways Kunst  et al . [ 10 ] listed 18 genes that have a major role in the secretion of extracellular enzymes by the classical (Sec) pathway in  B. subtilis  168. This list includes several chaperonins, signal peptidases, components of the signal recognition particle and protein translocase complexes. All members of this list have  B. licheniformis  counterparts. In addition to the Sec pathway, some  B. subtilis  proteins are directed into the twin-arginine (Tat) export pathway, possibly in a Sec-independent manner. Curiously, the  B. licheniformis  genome encodes three  tat  gene orthologs ( tatAY ,  tatCD , and  tatCY ), but two others ( tatAC  and  tatAD ) are conspicuously absent. Furthermore, specific proteins may be exported to the cell surface via lipoprotein signal peptides or sortase factors. Lipoprotein signal peptides are cleaved with a specific signal peptidase (Lsp) encoded by the  lspA  gene in  B. subtilis . An  lspA  homolog can be found in  B. licheniformis  as well, suggesting that this species may possess the ability to export lipoproteins via a similar mechanism. Lastly, surface proteins in Gram-positive bacteria are frequently attached to the cell wall by sortase enzymes, and genome analyses have revealed that more than one sortase is often produced by a given species. In this regard, three possible sortase gene homologs were detected in the genome of  B. licheniformis  ATCC 14580. Together these observations suggest that the central features of the protein export machinery are principally conserved in  B. subtilis  and  B. licheniformis . From the list of 139 sporulation genes tabulated by Kunst  et al . [ 10 ], all but six have obvious counterparts in  B. licheniformis . These six exceptions ( spsABCEFG ) comprise an operon involved in synthesis of a spore coat polysaccharide in  B. subtilis . In addition, the response regulator gene family ( phrACEFGI ) appears to have a low level of sequence conservation between  B. subtilis  and  B. licheniformis . Natural competence (the ability to take up and process exogenous DNA in specific growth conditions) is a feature of few  B. licheniformis  strains [ 24 ]. The reasons for variability in competence phenotype have not been explored at the genetic level, but the genome data offer several possible explanations. Although the  B. licheniformis  genome encodes all of the late competence functions ascribed in  B. subtilis  (for example,  comC ,  comEFG  operons,  comK ,  mecA ), it lacks an obvious  comS  gene, and the  comP  gene is punctuated by an insertion sequence element ( IS3Bli1 ), suggesting that the early stages of competence development have been pre-empted in  B. licheniformis  ATCC 14580. Whether these early functions can be restored by introducing the corresponding genes from  B. subtilis  is unknown. In addition to an apparent deficiency in DNA uptake, two type I restriction-modification systems were discovered that may also contribute to diminished transformation efficiencies. These are distinct from the  ydiOPS  genes of  B. subtilis , and could participate in degradation of improperly modified DNA from heterologous hosts used during construction of recombinant expression vectors. Each of these loci in  B. licheniformis  (designated as  BliI  and  BliII ) encode putative HsdS, HsdM and HsdR subunits that share significant amino-acid sequence identity to type I restriction-modification proteins in other bacteria. Curiously, the G+C-content for these loci (37%) is substantially lower than the overall genome average (46%) which may hint that they are the result of gene acquisitions. Lastly, the synthesis of a glutamyl polypeptide capsule has also been implicated as a potential barrier to transformation of  B. licheniformis  strains [ 25 ]. While laboratory strains of  B. subtilis  usually do not produce significant capsular material, the genome sequence of  B. subtilis  168 indicates that they may harbor the genes required for synthesis of polyglutamic acid. In contrast, many  B. licheniformis  isolates produce copious amounts of capsular material, giving rise to colonies with a wet or slimy appearance. Six genes were predicted ( ywtABDEF  and  ywsC  orthologs) that may be involved in the synthesis of polyglutamic acid capsular material in  B. licheniformis . Antibiotics, secondary metabolites and siderophores Bacitracin is a cyclic peptide antibiotic that is synthesized non-ribosomally by some  B. licheniformis  isolates [ 26 ]. While there is variation in the prevalence of bacitracin synthase genes among laboratory strains of this species, one study suggested that up to 50% may harbor the  bac  operon [ 27 ]. Interestingly, the  bac  operon is not present in the type strain (ATCC 14580) genome. Seemingly, the only non-ribosomal peptide synthase operon encoded by the  B. licheniformis  type strain genome is that responsible for lichenysin biosynthesis. Lichenysin structurally resembles surfactin from  B. subtilis  [ 28 ], and their respective biosynthetic operons are highly similar. Surprisingly, we found no  B. licheniformis  counterparts for the  pps  (plipastatin synthase) and polyketide synthase ( pks ) operons of  B. subtilis . Collectively, these two regions represent sizeable portions (80 kb and 38 kb, respectively) of the chromosome in  B. subtilis , although they are reportedly dispensable [ 29 ]. Unexpectedly, a cluster of 11 genes was found encoding a lantibiotic, with its associated modification and transport functions. We designated this peptide of 75 amino acids as lichenicidin, and its closest homolog is mersacidin from  Bacillus  sp. strain HIL-Y85/54728 [ 30 ]. Lantibiotics are ribosomally synthesized peptides that are modified post-translationally so that the final molecules contain rare thioether amino acids such as lanthionine and/or methyl-lanthionine [ 31 ]. Like mersacidin, lichenicidin appears to be a type B lantibiotic, comprising a rigid globular peptide with no net charge (7 acidic residues, 7 basic residues) and a leader peptide with a conserved double glycine cleavage site (GG-type leader peptide). These antimicrobial compounds have attracted much attention in recent years as models for the design and genetic engineering of improved antimicrobial agents [ 32 ]. However, since several post-translational modifications and product-specific export functions are required, a dedicated expression system is a prerequisite to provide all the factors necessary to synthesize, modify and transport the lantibiotic peptide. With its history of use in industrial microbiology,  B. licheniformis  may be an attractive candidate for the development of such an expression system. Like  B. subtilis  168, the  B. licheniformis  ATCC 14580 chromosome harbors a siderophore biosynthesis gene cluster ( dhbABCEF ), and the organization of the cluster is similar to the corresponding chromosomal segment in  B. subtilis . In addition, the  B. licheniformis  genome contains a second gene cluster of four genes ( iucABCD ) that show significant similarity to proteins involved in aerobactin biosynthesis in  E. coli . Surprisingly, a gene encoding the receptor protein ( iutA  homolog) was not found in  B. licheniformis . The  B. halodurans  genome also contains genes that are homologous to  iucABCD , but like  B. licheniformis , no  iutA  homolog could be found using BLAST or Smith-Waterman searches. Comparison of the  B. licheniformis  genome with those of other bacilli The  B. licheniformis  ATCC 14580 gene models were compared to the list of essential genes in  B. subtilis  [ 33 ]. Predictably, all of the essential genes in  B. subtilis  have orthologs in  B. licheniformis , and most are present in a wide range of bacterial taxa. In pairwise BLAST comparisons, 66% of the predicted  B. licheniformis  genes have orthologs in  B. subtilis , and 55% of the gene models are represented by orthologous sequences in  B. halodurans  (E-value threshold of 1 × 10 -5 ; Figure  4 ). Using a reciprocal BLASTP analysis we found 1,719 orthologs that are common to all three species (E-value threshold of 1 × 10 -5 ). As noted by Lapidus  et al.  [ 9 ], there are broad regions of colinearity between the genomes of  B. licheniformis  and  B. subtilis  (Figure  5 ). Less conservation of genome organization exists between  B. licheniformis  and  B. halodurans , and substantial genomic segments have been inverted in  B. halodurans  with respect to  B. licheniformis  and  B. subtilis . These observations clearly support previous hypotheses [ 8 ] that  B. subtilis  and  B. licheniformis  are phylogenetically and evolutionarily closer to each other than to  B. halodurans .
Results and discussion
General features of the  B. licheniformis  genome The genome of  B. licheniformis  ATCC 14580 consists of a circular chromosome of 4,222,336 base-pairs (bp) with an average G+C content of 46.2% (Table  1 ). No plasmids were found during the genome analysis, and none were found by agarose gel electrophoresis (data not shown). Using a combination of several gene-finding programs and manual inspection, 4,208 protein-coding sequences (CDSs) were predicted. These CDSs constitute 87% of the genome and have an average length of 873 bp (ranging from 78 to 10,767 bp). They are oriented on the chromosome primarily in the direction of replication (Figure  1 ) with 74.4% of the genes on the leading strand and 25.6% on the lagging strand. Among the 4,208 protein coding genes, 3,948 (94%) had significant similarity to proteins in PIR, 3,187 (76%) of these gene models contain Interpro motifs, and 2,895 (69%) contain protein motifs found in PFAM. The number of hypothetical and conserved hypothetical proteins in the  B. licheniformis  genome with hits in the PIR database was 1,318 (212 conserved hypothetical proteins). Among the list of hypothetical and conserved hypothetical gene products, 683 (52%) have protein motifs contained in PFAM (148 conserved hypothetical proteins). There are 72 tRNA genes representing all 20 amino acids and seven rRNA operons. The likely origin of replication (Figure  1 ) was identified by similarities to several features of the corresponding regions in  B. subtilis  and other bacteria. These included co-localization of four genes ( rpmH ,  dnaA ,  dnaN , and  recF ) near the origin, GC nucleotide skew ((G-C)/(G+C)) analysis, and the presence of multiple  dnaA -boxes and AT-rich sequences immediately upstream of the  dnaA  gene [ 10 - 12 ]. On the basis of these observations we assigned a cytosine residue of the  Bst BI restriction site between the  rpmH  and  dnaA  genes to be the first nucleotide of the  B. licheniformis  genome. The replication termination site was localized near 2.02 megabases (Mb) by GC skew analysis. This region lies roughly opposite the origin of replication (Figure  1 ). Unlike  B. subtilis , there was no apparent gene encoding a replication terminator protein ( rtp ) in  B. licheniformis . The  Bacillus halodurans  genome also lacks an obvious  rtp  function [ 13 ]; therefore, it seems likely that  B. subtilis  acquired the  rtp  gene following its divergence from  B. halodurans  and  B. licheniformis .
General features of the  B. licheniformis  genome
B. licheniformisThe genome of  B. licheniformis  ATCC 14580 consists of a circular chromosome of 4,222,336 base-pairs (bp) with an average G+C content of 46.2% (Table  1 ). No plasmids were found during the genome analysis, and none were found by agarose gel electrophoresis (data not shown). Using a combination of several gene-finding programs and manual inspection, 4,208 protein-coding sequences (CDSs) were predicted. These CDSs constitute 87% of the genome and have an average length of 873 bp (ranging from 78 to 10,767 bp). They are oriented on the chromosome primarily in the direction of replication (Figure  1 ) with 74.4% of the genes on the leading strand and 25.6% on the lagging strand. Among the 4,208 protein coding genes, 3,948 (94%) had significant similarity to proteins in PIR, 3,187 (76%) of these gene models contain Interpro motifs, and 2,895 (69%) contain protein motifs found in PFAM. The number of hypothetical and conserved hypothetical proteins in the  B. licheniformis  genome with hits in the PIR database was 1,318 (212 conserved hypothetical proteins). Among the list of hypothetical and conserved hypothetical gene products, 683 (52%) have protein motifs contained in PFAM (148 conserved hypothetical proteins). There are 72 tRNA genes representing all 20 amino acids and seven rRNA operons.B. licheniformisB. licheniformisThe likely origin of replication (Figure  1 ) was identified by similarities to several features of the corresponding regions in  B. subtilis  and other bacteria. These included co-localization of four genes ( rpmH ,  dnaA ,  dnaN , and  recF ) near the origin, GC nucleotide skew ((G-C)/(G+C)) analysis, and the presence of multiple  dnaA -boxes and AT-rich sequences immediately upstream of the  dnaA  gene [ 10 - 12 ]. On the basis of these observations we assigned a cytosine residue of the  Bst BI restriction site between the  rpmH  and  dnaA  genes to be the first nucleotide of the  B. licheniformis  genome. The replication termination site was localized near 2.02 megabases (Mb) by GC skew analysis. This region lies roughly opposite the origin of replication (Figure  1 ). Unlike  B. subtilis , there was no apparent gene encoding a replication terminator protein ( rtp ) in  B. licheniformis . The  Bacillus halodurans  genome also lacks an obvious  rtp  function [ 13 ]; therefore, it seems likely that  B. subtilis  acquired the  rtp  gene following its divergence from  B. halodurans  and  B. licheniformis .B. subtilisrpmHdnaAdnaNrecFdnaAdnaABstrpmHdnaAB. licheniformisB. subtilisrtpB. licheniformisBacillus haloduransrtpB. subtilisrtpB. haloduransB. licheniformisTransposable elements, prophages and atypical regions The genome of  B. licheniformis  ATCC 14580 contains nine identical copies of a 1,285 bp insertion sequence element termed  IS3Bli1  [ 9 ]. This sequence shares a number of features with other  IS3  family elements [ 9 ] including direct repeats of 3-5 bp, a 10-bp left inverted repeat, and a 9 bp right inverted repeat (Figure  2 ).  IS3Bli1  encodes two predicted overlapping CDSs, designated  orfA  and  orfB  in relative translational reading frames of 0 and -1. The presence of a 'slippery heptamer' motif, AAAAAAG, before the stop codon in  orfA  may indicate that programmed translational frameshifting occurs between these two coding sequences, resulting in a single gene product [ 14 ]. The  orfB  gene product harbors the DD(35)E(7)K motif, a highly conserved pattern among insertion sequences. Eight of these  IS3Bli1  elements lie in intergenic regions, and one interrupts the  comP  gene as noted previously [ 9 ]. In addition to these insertion sequences, the genome encodes a putative transposase that is most closely related (E = 1.8 × 10 -11 ) to one identified in the  Thermoanaerobacter tengcongensis  genome [ 15 ]; however, similar transposase genes are also found in the chromosomes of  B. halodurans  [ 13 ],  Oceanobacillus iheyensis  [ 16 ],  Streptococcus agalactiae  [ 17 ] and  Streptococcus pyogenes  [ 18 ]. The presence of several bacteriophage lysogens or prophage-like elements was revealed by Smith-Waterman comparisons to other bacterial genomes and by their AT-rich signatures (Figure  3 , Table  2 ). Prophage sequences, designated NZP1 and NZP3 (similar to  B. subtilis  prophages PBSX and φ-105), were discovered by noting the presence of nearby genes that code for the large subunit of terminase, a signature protein that is highly conserved among prophages [ 19 ]. Interestingly, a terminase gene was not observed in the third putative prophage, termed NZP2 (similarity to  B. subtilis  phage SPP1); however, its absence may be the result of genome deterioration during evolution. Interestingly, we observed that regions in which the G+C content is less than 39% usually encoded proteins that have no  B. subtilis  ortholog and share identity only with hypothetical and conserved hypothetical genes. Two of these AT-rich segments correspond to the NZP2 and NZP3 prophages. An isochore plot (Figure  3 ) also revealed the presence of a region with an atypically high (62%) G+C content. This segment contains two hypothetical genes whose sizes (3,831 and 2,865 bp) greatly exceed the size of an average CDS in  B. licheniformis . The first gene encodes a protein of 1,277 amino acids for which Interpro predicts 16 collagen triple-helix repeats, and the amino acid pattern TGATGPT is repeated 75 times within the polypeptide. The second CDS is smaller, and encodes a protein with 11 collagen triple-helix repeats; the same TGATGPT motif recurs 56 times. The primary translation products from these genes do not contain canonical signal peptides for secretion, and they do not contain motifs for the twin-arginine or sortase-mediated translocation pathways. Therefore, it is not likely that they are exported to the cell surface or the extracellular medium. Interestingly, the chromosomal region (19 kb) adjacent to these genes is clearly non-colinear with the  B. subtilis  genome, and virtually all of the predicted genes encode hypothetical or conserved hypothetical proteins. There are a number of bacterial proteins listed in PIR that also contain collagen triple-helix repeat regions, including two from  Mesorhizobium loti  (accession numbers NF00607049 and NF00607035) and three from  B. cereus  (accession numbers NF01692528, NF01269899 and NF01694666). These putative orthologs share 53-76% amino-acid sequence identity with their counterparts in  B. licheniformis , and their functions are unknown.
Transposable elements, prophages and atypical regions
The genome of  B. licheniformis  ATCC 14580 contains nine identical copies of a 1,285 bp insertion sequence element termed  IS3Bli1  [ 9 ]. This sequence shares a number of features with other  IS3  family elements [ 9 ] including direct repeats of 3-5 bp, a 10-bp left inverted repeat, and a 9 bp right inverted repeat (Figure  2 ).  IS3Bli1  encodes two predicted overlapping CDSs, designated  orfA  and  orfB  in relative translational reading frames of 0 and -1. The presence of a 'slippery heptamer' motif, AAAAAAG, before the stop codon in  orfA  may indicate that programmed translational frameshifting occurs between these two coding sequences, resulting in a single gene product [ 14 ]. The  orfB  gene product harbors the DD(35)E(7)K motif, a highly conserved pattern among insertion sequences. Eight of these  IS3Bli1  elements lie in intergenic regions, and one interrupts the  comP  gene as noted previously [ 9 ]. In addition to these insertion sequences, the genome encodes a putative transposase that is most closely related (E = 1.8 × 10 -11 ) to one identified in the  Thermoanaerobacter tengcongensis  genome [ 15 ]; however, similar transposase genes are also found in the chromosomes of  B. halodurans  [ 13 ],  Oceanobacillus iheyensis  [ 16 ],  Streptococcus agalactiae  [ 17 ] and  Streptococcus pyogenes  [ 18 ].B. licheniformisIS3Bli1IS3IS3Bli1orfAorfBorfAorfBIS3Bli1comPThermoanaerobacter tengcongensisB. haloduransOceanobacillus iheyensisStreptococcus agalactiaeStreptococcus pyogenesThe presence of several bacteriophage lysogens or prophage-like elements was revealed by Smith-Waterman comparisons to other bacterial genomes and by their AT-rich signatures (Figure  3 , Table  2 ). Prophage sequences, designated NZP1 and NZP3 (similar to  B. subtilis  prophages PBSX and φ-105), were discovered by noting the presence of nearby genes that code for the large subunit of terminase, a signature protein that is highly conserved among prophages [ 19 ]. Interestingly, a terminase gene was not observed in the third putative prophage, termed NZP2 (similarity to  B. subtilis  phage SPP1); however, its absence may be the result of genome deterioration during evolution. Interestingly, we observed that regions in which the G+C content is less than 39% usually encoded proteins that have no  B. subtilis  ortholog and share identity only with hypothetical and conserved hypothetical genes. Two of these AT-rich segments correspond to the NZP2 and NZP3 prophages.B. subtilisB. subtilisB. subtilisAn isochore plot (Figure  3 ) also revealed the presence of a region with an atypically high (62%) G+C content. This segment contains two hypothetical genes whose sizes (3,831 and 2,865 bp) greatly exceed the size of an average CDS in  B. licheniformis . The first gene encodes a protein of 1,277 amino acids for which Interpro predicts 16 collagen triple-helix repeats, and the amino acid pattern TGATGPT is repeated 75 times within the polypeptide. The second CDS is smaller, and encodes a protein with 11 collagen triple-helix repeats; the same TGATGPT motif recurs 56 times. The primary translation products from these genes do not contain canonical signal peptides for secretion, and they do not contain motifs for the twin-arginine or sortase-mediated translocation pathways. Therefore, it is not likely that they are exported to the cell surface or the extracellular medium. Interestingly, the chromosomal region (19 kb) adjacent to these genes is clearly non-colinear with the  B. subtilis  genome, and virtually all of the predicted genes encode hypothetical or conserved hypothetical proteins. There are a number of bacterial proteins listed in PIR that also contain collagen triple-helix repeat regions, including two from  Mesorhizobium loti  (accession numbers NF00607049 and NF00607035) and three from  B. cereus  (accession numbers NF01692528, NF01269899 and NF01694666). These putative orthologs share 53-76% amino-acid sequence identity with their counterparts in  B. licheniformis , and their functions are unknown.B. licheniformisB. subtilisMesorhizobium lotiB. cereusB. licheniformisExtracellular enzymes and metabolic activities In the  Bacillus licheniformis  genome, 689 of the 4,208 gene models have signal peptides forecast by SignalP [ 20 ]. Of these, 309 have no transmembrane domain predicted by TMHMM [ 21 ] and 134 are hypothetical or conserved hypothetical genes. Based on a manual examination of the remaining 175 genes, at least 82 are likely to encode secreted proteins and enzymes. Moreover, there are 27 predicted extracellular proteins encoded by the  B. licheniformis  ATCC 14580 genome that are not found in  B. subtilis  168. In accordance with its saprophytic lifestyle, the secretome of  B. licheniformis  encodes numerous secreted enzymes that hydrolyze polysaccharides, proteins, lipids and other nutrients. Cellulose is the most abundant polysaccharide on Earth, and microorganisms that hydrolyze cellulose contribute to the global carbon cycle. Interestingly, two gene clusters involved in cellulose degradation and utilization were discovered in  B. licheniformis , and there are no counterparts in  B. subtilis  168. The enzymes encoded by the first gene cluster include two putative endoglucanases belonging to glycoside hydrolase families GH9 and GH5, a probable cellulose-1,4-β-cellobiosidase of family GH48, and a putative β-mannanase of family GH5. The β-mannanase (GH5) and endoglucanase (GH9) both harbor carbohydrate-binding motifs. With the exception of the cellulose-1,4-β-cellobiosidase (GH48), all of the gene products encoded in this cluster have secretory signal peptides, and all have homologs in  Bacillus  species other than  B. subtilis . The overall G+C content of this cluster (48%) does not appear to differ appreciably from that of the genome average (46%). The second gene cluster encodes a putative β-glucosidase (GH1) and three components of a cellobiose-specific PTS transport complex. A second β-glucosidase (GH3) gene is present at an unlinked locus in the genome. Collectively, the genes in these two clusters should enable  B. licheniformis  to utilize cellulose as a carbon and energy source, converting it to cellobiose and ultimately glucose. In this regard, we have confirmed that  B. licheniformis  ATCC 14580 is capable of growth on carboxymethyl cellulose as a sole carbon source (not shown). The chromosome of  B. licheniformis  ATCC 14580 encodes a number of additional carbohydrase activities that may allow the organism to grow on a broad range of polysaccharides. These include xylanase, endo-arabinase and pectate lyase that may be involved in degradation of hemicellulose, α-amylase and α-glucosidase for starch hydrolysis, chitinases for the breakdown of chitooligosaccharides from fungi and insects, and levanase for utilization of β-D-fructans (levans). Several of these activities are marketed as industrial enzymes. Saprophytic organisms must utilize a variety of nitrogenous compounds as nutrients for growth and metabolism. On the basis of the information encoded in its genome,  B. licheniformis  ATCC 14580 possesses the ability to acquire nitrogen from exogenous proteins, peptides, amino acids, ammonia, nitrate and nitrite. Like  B. subtilis , the repertoire of extracellular proteases produced by  B. licheniformis  includes serine proteases ( aprE ,  epr ,  vpr ), metalloprotease ( mpr ), and an assortment of endo- and exopeptidases ( yjbG ,  ydiC ,  gcp ,  ykvY ,  ampS ,  bpr  (two copies),  yfxM ,  yuiE ,  yusX ,  ywaD ,  pepT ). However,  B. licheniformis  also has the capacity to produce a number of additional proteases and peptidases that are not encoded in the  B. subtilis  genome. These include a clostripain-like protease, a zinc-metallopeptidase, a probable glutamyl endopeptidase, an aminopeptidase C homolog, two putative dipeptidases and a zinc-carboxypeptidase. B. licheniformis  also has the ability to utilize amino and imino nitrogen from arginine, asparagine and glutamine via arginine deiminase, arginase, asparaginase and glutaminase activities. Interestingly, there appear to be two genes each for arginase, asparaginase and glutaminase. Presumably, the arginine deiminase activity is expressed during anaerobic growth on arginine, whereas the arginase activities are predominant during aerobic growth. The occurrence of putative arginase genes is somewhat of an enigma in  B. licheniformis , because there are no genes encoding urease activity for the hydrolysis of urea that is generated by the arginase reaction. In addition to the absence of urease gene homologs ( ureABC ) in  B. licheniformis , the glutamine ABC transporters ( glnH ,  glnM ,  glnP ,  glnQ  gene products) are also lacking. It appears that nitrogen assimilation and transport pathways may be coordinated similarly in  B. licheniformis  and  B. subtilis  owing to the presence of key genes such as  glnA ,  glnR ,  tnrA  and  nrgA  in both species. Likewise, the pathways for nitrate/nitrite transport and metabolism in  B. licheniformis  appear to be analogous to the corresponding pathways in  B. subtilis  as suggested by the presence of  nasABC  (nitrate transport),  narGHIJ  (respiratory nitrate reductase), and  nasDEF  (NADH-dependent nitrite reductase) genes. Unlike  B. subtilis ,  B. licheniformis  evidently possesses the capability for anaerobic respiration using nitric oxide reductase. Moreover, the gene encoding this activity lies in a cluster that includes CDSs for  narK  (nitrite extrusion protein), two putative  fnr  proteins (transcriptional regulators of anaerobic growth), and a  dnrN -like gene product (nitric oxide-dependent regulator). These observations are consistent with previous findings that certain  B. licheniformis  isolates are capable of denitrification [ 22 ]. While denitrification is a process of major ecological importance, the contribution of  B. licheniformis  may be small as the species exists predominantly as endospores in soil [ 1 ]. Microbial D-hydantoinase enzymes have been applied to the industrial production of optically pure D-amino acids for synthesis of antibiotics, pesticides, sweeteners and therapeutic amino acids [ 23 ]. This enzyme catalyzes the hydrolysis of cyclic ureides such as dihydropyrimidines and 5-monosubstituted hydantoins to  N -carbamoyl amino acids. Hydantoinase activities have been detected in a variety of bacterial genera, and a cluster of six genes in  B. licheniformis  appears to confer a similar capability. This gene cluster encodes  N -methylhydantoinase (ATP-hydrolyzing), hydantoin utilization proteins A and B ( hyuAB  homologs), a possible transcriptional regulator (TetR/AcrR family), a putative pyrimidine permease, and a hypothetical protein that contains an Interpro domain (IPR004399) for phosphomethylpyrimidine kinase.
Extracellular enzymes and metabolic activities
In the  Bacillus licheniformis  genome, 689 of the 4,208 gene models have signal peptides forecast by SignalP [ 20 ]. Of these, 309 have no transmembrane domain predicted by TMHMM [ 21 ] and 134 are hypothetical or conserved hypothetical genes. Based on a manual examination of the remaining 175 genes, at least 82 are likely to encode secreted proteins and enzymes. Moreover, there are 27 predicted extracellular proteins encoded by the  B. licheniformis  ATCC 14580 genome that are not found in  B. subtilis  168. In accordance with its saprophytic lifestyle, the secretome of  B. licheniformis  encodes numerous secreted enzymes that hydrolyze polysaccharides, proteins, lipids and other nutrients.Bacillus licheniformisB. licheniformisB. subtilisB. licheniformisCellulose is the most abundant polysaccharide on Earth, and microorganisms that hydrolyze cellulose contribute to the global carbon cycle. Interestingly, two gene clusters involved in cellulose degradation and utilization were discovered in  B. licheniformis , and there are no counterparts in  B. subtilis  168. The enzymes encoded by the first gene cluster include two putative endoglucanases belonging to glycoside hydrolase families GH9 and GH5, a probable cellulose-1,4-β-cellobiosidase of family GH48, and a putative β-mannanase of family GH5. The β-mannanase (GH5) and endoglucanase (GH9) both harbor carbohydrate-binding motifs. With the exception of the cellulose-1,4-β-cellobiosidase (GH48), all of the gene products encoded in this cluster have secretory signal peptides, and all have homologs in  Bacillus  species other than  B. subtilis . The overall G+C content of this cluster (48%) does not appear to differ appreciably from that of the genome average (46%). The second gene cluster encodes a putative β-glucosidase (GH1) and three components of a cellobiose-specific PTS transport complex. A second β-glucosidase (GH3) gene is present at an unlinked locus in the genome. Collectively, the genes in these two clusters should enable  B. licheniformis  to utilize cellulose as a carbon and energy source, converting it to cellobiose and ultimately glucose. In this regard, we have confirmed that  B. licheniformis  ATCC 14580 is capable of growth on carboxymethyl cellulose as a sole carbon source (not shown). The chromosome of  B. licheniformis  ATCC 14580 encodes a number of additional carbohydrase activities that may allow the organism to grow on a broad range of polysaccharides. These include xylanase, endo-arabinase and pectate lyase that may be involved in degradation of hemicellulose, α-amylase and α-glucosidase for starch hydrolysis, chitinases for the breakdown of chitooligosaccharides from fungi and insects, and levanase for utilization of β-D-fructans (levans). Several of these activities are marketed as industrial enzymes.B. licheniformisB. subtilisBacillusB. subtilisB. licheniformisB. licheniformisB. licheniformisSaprophytic organisms must utilize a variety of nitrogenous compounds as nutrients for growth and metabolism. On the basis of the information encoded in its genome,  B. licheniformis  ATCC 14580 possesses the ability to acquire nitrogen from exogenous proteins, peptides, amino acids, ammonia, nitrate and nitrite. Like  B. subtilis , the repertoire of extracellular proteases produced by  B. licheniformis  includes serine proteases ( aprE ,  epr ,  vpr ), metalloprotease ( mpr ), and an assortment of endo- and exopeptidases ( yjbG ,  ydiC ,  gcp ,  ykvY ,  ampS ,  bpr  (two copies),  yfxM ,  yuiE ,  yusX ,  ywaD ,  pepT ). However,  B. licheniformis  also has the capacity to produce a number of additional proteases and peptidases that are not encoded in the  B. subtilis  genome. These include a clostripain-like protease, a zinc-metallopeptidase, a probable glutamyl endopeptidase, an aminopeptidase C homolog, two putative dipeptidases and a zinc-carboxypeptidase.B. licheniformisB. subtilisB. licheniformisaprEeprvprmpryjbGydiCgcpykvYampSbpryfxMyuiEyusXywaDpepTB. licheniformisB. subtilisB. licheniformis  also has the ability to utilize amino and imino nitrogen from arginine, asparagine and glutamine via arginine deiminase, arginase, asparaginase and glutaminase activities. Interestingly, there appear to be two genes each for arginase, asparaginase and glutaminase. Presumably, the arginine deiminase activity is expressed during anaerobic growth on arginine, whereas the arginase activities are predominant during aerobic growth. The occurrence of putative arginase genes is somewhat of an enigma in  B. licheniformis , because there are no genes encoding urease activity for the hydrolysis of urea that is generated by the arginase reaction. In addition to the absence of urease gene homologs ( ureABC ) in  B. licheniformis , the glutamine ABC transporters ( glnH ,  glnM ,  glnP ,  glnQ  gene products) are also lacking.B. licheniformisB. licheniformisureABCB. licheniformisglnHglnMglnPglnQIt appears that nitrogen assimilation and transport pathways may be coordinated similarly in  B. licheniformis  and  B. subtilis  owing to the presence of key genes such as  glnA ,  glnR ,  tnrA  and  nrgA  in both species. Likewise, the pathways for nitrate/nitrite transport and metabolism in  B. licheniformis  appear to be analogous to the corresponding pathways in  B. subtilis  as suggested by the presence of  nasABC  (nitrate transport),  narGHIJ  (respiratory nitrate reductase), and  nasDEF  (NADH-dependent nitrite reductase) genes. Unlike  B. subtilis ,  B. licheniformis  evidently possesses the capability for anaerobic respiration using nitric oxide reductase. Moreover, the gene encoding this activity lies in a cluster that includes CDSs for  narK  (nitrite extrusion protein), two putative  fnr  proteins (transcriptional regulators of anaerobic growth), and a  dnrN -like gene product (nitric oxide-dependent regulator). These observations are consistent with previous findings that certain  B. licheniformis  isolates are capable of denitrification [ 22 ]. While denitrification is a process of major ecological importance, the contribution of  B. licheniformis  may be small as the species exists predominantly as endospores in soil [ 1 ].B. licheniformisB. subtilisglnAglnRtnrAnrgAB. licheniformisB. subtilisnasABCnarGHIJnasDEFB. subtilisB. licheniformisnarKfnrdnrNB. licheniformisB. licheniformisMicrobial D-hydantoinase enzymes have been applied to the industrial production of optically pure D-amino acids for synthesis of antibiotics, pesticides, sweeteners and therapeutic amino acids [ 23 ]. This enzyme catalyzes the hydrolysis of cyclic ureides such as dihydropyrimidines and 5-monosubstituted hydantoins to  N -carbamoyl amino acids. Hydantoinase activities have been detected in a variety of bacterial genera, and a cluster of six genes in  B. licheniformis  appears to confer a similar capability. This gene cluster encodes  N -methylhydantoinase (ATP-hydrolyzing), hydantoin utilization proteins A and B ( hyuAB  homologs), a possible transcriptional regulator (TetR/AcrR family), a putative pyrimidine permease, and a hypothetical protein that contains an Interpro domain (IPR004399) for phosphomethylpyrimidine kinase.NB. licheniformisNhyuABProtein export, sporulation and competence pathways Kunst  et al . [ 10 ] listed 18 genes that have a major role in the secretion of extracellular enzymes by the classical (Sec) pathway in  B. subtilis  168. This list includes several chaperonins, signal peptidases, components of the signal recognition particle and protein translocase complexes. All members of this list have  B. licheniformis  counterparts. In addition to the Sec pathway, some  B. subtilis  proteins are directed into the twin-arginine (Tat) export pathway, possibly in a Sec-independent manner. Curiously, the  B. licheniformis  genome encodes three  tat  gene orthologs ( tatAY ,  tatCD , and  tatCY ), but two others ( tatAC  and  tatAD ) are conspicuously absent. Furthermore, specific proteins may be exported to the cell surface via lipoprotein signal peptides or sortase factors. Lipoprotein signal peptides are cleaved with a specific signal peptidase (Lsp) encoded by the  lspA  gene in  B. subtilis . An  lspA  homolog can be found in  B. licheniformis  as well, suggesting that this species may possess the ability to export lipoproteins via a similar mechanism. Lastly, surface proteins in Gram-positive bacteria are frequently attached to the cell wall by sortase enzymes, and genome analyses have revealed that more than one sortase is often produced by a given species. In this regard, three possible sortase gene homologs were detected in the genome of  B. licheniformis  ATCC 14580. Together these observations suggest that the central features of the protein export machinery are principally conserved in  B. subtilis  and  B. licheniformis . From the list of 139 sporulation genes tabulated by Kunst  et al . [ 10 ], all but six have obvious counterparts in  B. licheniformis . These six exceptions ( spsABCEFG ) comprise an operon involved in synthesis of a spore coat polysaccharide in  B. subtilis . In addition, the response regulator gene family ( phrACEFGI ) appears to have a low level of sequence conservation between  B. subtilis  and  B. licheniformis . Natural competence (the ability to take up and process exogenous DNA in specific growth conditions) is a feature of few  B. licheniformis  strains [ 24 ]. The reasons for variability in competence phenotype have not been explored at the genetic level, but the genome data offer several possible explanations. Although the  B. licheniformis  genome encodes all of the late competence functions ascribed in  B. subtilis  (for example,  comC ,  comEFG  operons,  comK ,  mecA ), it lacks an obvious  comS  gene, and the  comP  gene is punctuated by an insertion sequence element ( IS3Bli1 ), suggesting that the early stages of competence development have been pre-empted in  B. licheniformis  ATCC 14580. Whether these early functions can be restored by introducing the corresponding genes from  B. subtilis  is unknown. In addition to an apparent deficiency in DNA uptake, two type I restriction-modification systems were discovered that may also contribute to diminished transformation efficiencies. These are distinct from the  ydiOPS  genes of  B. subtilis , and could participate in degradation of improperly modified DNA from heterologous hosts used during construction of recombinant expression vectors. Each of these loci in  B. licheniformis  (designated as  BliI  and  BliII ) encode putative HsdS, HsdM and HsdR subunits that share significant amino-acid sequence identity to type I restriction-modification proteins in other bacteria. Curiously, the G+C-content for these loci (37%) is substantially lower than the overall genome average (46%) which may hint that they are the result of gene acquisitions. Lastly, the synthesis of a glutamyl polypeptide capsule has also been implicated as a potential barrier to transformation of  B. licheniformis  strains [ 25 ]. While laboratory strains of  B. subtilis  usually do not produce significant capsular material, the genome sequence of  B. subtilis  168 indicates that they may harbor the genes required for synthesis of polyglutamic acid. In contrast, many  B. licheniformis  isolates produce copious amounts of capsular material, giving rise to colonies with a wet or slimy appearance. Six genes were predicted ( ywtABDEF  and  ywsC  orthologs) that may be involved in the synthesis of polyglutamic acid capsular material in  B. licheniformis .
Protein export, sporulation and competence pathways
Kunst  et al . [ 10 ] listed 18 genes that have a major role in the secretion of extracellular enzymes by the classical (Sec) pathway in  B. subtilis  168. This list includes several chaperonins, signal peptidases, components of the signal recognition particle and protein translocase complexes. All members of this list have  B. licheniformis  counterparts. In addition to the Sec pathway, some  B. subtilis  proteins are directed into the twin-arginine (Tat) export pathway, possibly in a Sec-independent manner. Curiously, the  B. licheniformis  genome encodes three  tat  gene orthologs ( tatAY ,  tatCD , and  tatCY ), but two others ( tatAC  and  tatAD ) are conspicuously absent. Furthermore, specific proteins may be exported to the cell surface via lipoprotein signal peptides or sortase factors. Lipoprotein signal peptides are cleaved with a specific signal peptidase (Lsp) encoded by the  lspA  gene in  B. subtilis . An  lspA  homolog can be found in  B. licheniformis  as well, suggesting that this species may possess the ability to export lipoproteins via a similar mechanism. Lastly, surface proteins in Gram-positive bacteria are frequently attached to the cell wall by sortase enzymes, and genome analyses have revealed that more than one sortase is often produced by a given species. In this regard, three possible sortase gene homologs were detected in the genome of  B. licheniformis  ATCC 14580. Together these observations suggest that the central features of the protein export machinery are principally conserved in  B. subtilis  and  B. licheniformis .et alB. subtilisB. licheniformisB. subtilisB. licheniformistattatAYtatCDtatCYtatACtatADlspAB. subtilislspAB. licheniformisB. licheniformisB. subtilisB. licheniformisFrom the list of 139 sporulation genes tabulated by Kunst  et al . [ 10 ], all but six have obvious counterparts in  B. licheniformis . These six exceptions ( spsABCEFG ) comprise an operon involved in synthesis of a spore coat polysaccharide in  B. subtilis . In addition, the response regulator gene family ( phrACEFGI ) appears to have a low level of sequence conservation between  B. subtilis  and  B. licheniformis .et alB. licheniformisspsABCEFGB. subtilisphrACEFGIB. subtilisB. licheniformisNatural competence (the ability to take up and process exogenous DNA in specific growth conditions) is a feature of few  B. licheniformis  strains [ 24 ]. The reasons for variability in competence phenotype have not been explored at the genetic level, but the genome data offer several possible explanations. Although the  B. licheniformis  genome encodes all of the late competence functions ascribed in  B. subtilis  (for example,  comC ,  comEFG  operons,  comK ,  mecA ), it lacks an obvious  comS  gene, and the  comP  gene is punctuated by an insertion sequence element ( IS3Bli1 ), suggesting that the early stages of competence development have been pre-empted in  B. licheniformis  ATCC 14580. Whether these early functions can be restored by introducing the corresponding genes from  B. subtilis  is unknown. In addition to an apparent deficiency in DNA uptake, two type I restriction-modification systems were discovered that may also contribute to diminished transformation efficiencies. These are distinct from the  ydiOPS  genes of  B. subtilis , and could participate in degradation of improperly modified DNA from heterologous hosts used during construction of recombinant expression vectors. Each of these loci in  B. licheniformis  (designated as  BliI  and  BliII ) encode putative HsdS, HsdM and HsdR subunits that share significant amino-acid sequence identity to type I restriction-modification proteins in other bacteria. Curiously, the G+C-content for these loci (37%) is substantially lower than the overall genome average (46%) which may hint that they are the result of gene acquisitions. Lastly, the synthesis of a glutamyl polypeptide capsule has also been implicated as a potential barrier to transformation of  B. licheniformis  strains [ 25 ]. While laboratory strains of  B. subtilis  usually do not produce significant capsular material, the genome sequence of  B. subtilis  168 indicates that they may harbor the genes required for synthesis of polyglutamic acid. In contrast, many  B. licheniformis  isolates produce copious amounts of capsular material, giving rise to colonies with a wet or slimy appearance. Six genes were predicted ( ywtABDEF  and  ywsC  orthologs) that may be involved in the synthesis of polyglutamic acid capsular material in  B. licheniformis .B. licheniformisB. licheniformisB. subtiliscomCcomEFGcomKmecAcomScomPIS3Bli1B. licheniformisB. subtilisydiOPSB. subtilisB. licheniformisBliIBliIIB. licheniformisB. subtilisB. subtilisB. licheniformisywtABDEFywsCB. licheniformisAntibiotics, secondary metabolites and siderophores Bacitracin is a cyclic peptide antibiotic that is synthesized non-ribosomally by some  B. licheniformis  isolates [ 26 ]. While there is variation in the prevalence of bacitracin synthase genes among laboratory strains of this species, one study suggested that up to 50% may harbor the  bac  operon [ 27 ]. Interestingly, the  bac  operon is not present in the type strain (ATCC 14580) genome. Seemingly, the only non-ribosomal peptide synthase operon encoded by the  B. licheniformis  type strain genome is that responsible for lichenysin biosynthesis. Lichenysin structurally resembles surfactin from  B. subtilis  [ 28 ], and their respective biosynthetic operons are highly similar. Surprisingly, we found no  B. licheniformis  counterparts for the  pps  (plipastatin synthase) and polyketide synthase ( pks ) operons of  B. subtilis . Collectively, these two regions represent sizeable portions (80 kb and 38 kb, respectively) of the chromosome in  B. subtilis , although they are reportedly dispensable [ 29 ]. Unexpectedly, a cluster of 11 genes was found encoding a lantibiotic, with its associated modification and transport functions. We designated this peptide of 75 amino acids as lichenicidin, and its closest homolog is mersacidin from  Bacillus  sp. strain HIL-Y85/54728 [ 30 ]. Lantibiotics are ribosomally synthesized peptides that are modified post-translationally so that the final molecules contain rare thioether amino acids such as lanthionine and/or methyl-lanthionine [ 31 ]. Like mersacidin, lichenicidin appears to be a type B lantibiotic, comprising a rigid globular peptide with no net charge (7 acidic residues, 7 basic residues) and a leader peptide with a conserved double glycine cleavage site (GG-type leader peptide). These antimicrobial compounds have attracted much attention in recent years as models for the design and genetic engineering of improved antimicrobial agents [ 32 ]. However, since several post-translational modifications and product-specific export functions are required, a dedicated expression system is a prerequisite to provide all the factors necessary to synthesize, modify and transport the lantibiotic peptide. With its history of use in industrial microbiology,  B. licheniformis  may be an attractive candidate for the development of such an expression system. Like  B. subtilis  168, the  B. licheniformis  ATCC 14580 chromosome harbors a siderophore biosynthesis gene cluster ( dhbABCEF ), and the organization of the cluster is similar to the corresponding chromosomal segment in  B. subtilis . In addition, the  B. licheniformis  genome contains a second gene cluster of four genes ( iucABCD ) that show significant similarity to proteins involved in aerobactin biosynthesis in  E. coli . Surprisingly, a gene encoding the receptor protein ( iutA  homolog) was not found in  B. licheniformis . The  B. halodurans  genome also contains genes that are homologous to  iucABCD , but like  B. licheniformis , no  iutA  homolog could be found using BLAST or Smith-Waterman searches.
Antibiotics, secondary metabolites and siderophores
Bacitracin is a cyclic peptide antibiotic that is synthesized non-ribosomally by some  B. licheniformis  isolates [ 26 ]. While there is variation in the prevalence of bacitracin synthase genes among laboratory strains of this species, one study suggested that up to 50% may harbor the  bac  operon [ 27 ]. Interestingly, the  bac  operon is not present in the type strain (ATCC 14580) genome. Seemingly, the only non-ribosomal peptide synthase operon encoded by the  B. licheniformis  type strain genome is that responsible for lichenysin biosynthesis. Lichenysin structurally resembles surfactin from  B. subtilis  [ 28 ], and their respective biosynthetic operons are highly similar. Surprisingly, we found no  B. licheniformis  counterparts for the  pps  (plipastatin synthase) and polyketide synthase ( pks ) operons of  B. subtilis . Collectively, these two regions represent sizeable portions (80 kb and 38 kb, respectively) of the chromosome in  B. subtilis , although they are reportedly dispensable [ 29 ].B. licheniformisbacbacB. licheniformisB. subtilisB. licheniformisppspksB. subtilisB. subtilisUnexpectedly, a cluster of 11 genes was found encoding a lantibiotic, with its associated modification and transport functions. We designated this peptide of 75 amino acids as lichenicidin, and its closest homolog is mersacidin from  Bacillus  sp. strain HIL-Y85/54728 [ 30 ]. Lantibiotics are ribosomally synthesized peptides that are modified post-translationally so that the final molecules contain rare thioether amino acids such as lanthionine and/or methyl-lanthionine [ 31 ]. Like mersacidin, lichenicidin appears to be a type B lantibiotic, comprising a rigid globular peptide with no net charge (7 acidic residues, 7 basic residues) and a leader peptide with a conserved double glycine cleavage site (GG-type leader peptide). These antimicrobial compounds have attracted much attention in recent years as models for the design and genetic engineering of improved antimicrobial agents [ 32 ]. However, since several post-translational modifications and product-specific export functions are required, a dedicated expression system is a prerequisite to provide all the factors necessary to synthesize, modify and transport the lantibiotic peptide. With its history of use in industrial microbiology,  B. licheniformis  may be an attractive candidate for the development of such an expression system.BacillusB. licheniformisLike  B. subtilis  168, the  B. licheniformis  ATCC 14580 chromosome harbors a siderophore biosynthesis gene cluster ( dhbABCEF ), and the organization of the cluster is similar to the corresponding chromosomal segment in  B. subtilis . In addition, the  B. licheniformis  genome contains a second gene cluster of four genes ( iucABCD ) that show significant similarity to proteins involved in aerobactin biosynthesis in  E. coli . Surprisingly, a gene encoding the receptor protein ( iutA  homolog) was not found in  B. licheniformis . The  B. halodurans  genome also contains genes that are homologous to  iucABCD , but like  B. licheniformis , no  iutA  homolog could be found using BLAST or Smith-Waterman searches.B. subtilisB. licheniformisdhbABCEFB. subtilisB. licheniformisiucABCDE. coliiutAB. licheniformisB. haloduransiucABCDB. licheniformisiutAComparison of the  B. licheniformis  genome with those of other bacilli The  B. licheniformis  ATCC 14580 gene models were compared to the list of essential genes in  B. subtilis  [ 33 ]. Predictably, all of the essential genes in  B. subtilis  have orthologs in  B. licheniformis , and most are present in a wide range of bacterial taxa. In pairwise BLAST comparisons, 66% of the predicted  B. licheniformis  genes have orthologs in  B. subtilis , and 55% of the gene models are represented by orthologous sequences in  B. halodurans  (E-value threshold of 1 × 10 -5 ; Figure  4 ). Using a reciprocal BLASTP analysis we found 1,719 orthologs that are common to all three species (E-value threshold of 1 × 10 -5 ). As noted by Lapidus  et al.  [ 9 ], there are broad regions of colinearity between the genomes of  B. licheniformis  and  B. subtilis  (Figure  5 ). Less conservation of genome organization exists between  B. licheniformis  and  B. halodurans , and substantial genomic segments have been inverted in  B. halodurans  with respect to  B. licheniformis  and  B. subtilis . These observations clearly support previous hypotheses [ 8 ] that  B. subtilis  and  B. licheniformis  are phylogenetically and evolutionarily closer to each other than to  B. halodurans .
Comparison of the  B. licheniformis  genome with those of other bacilli
B. licheniformisThe  B. licheniformis  ATCC 14580 gene models were compared to the list of essential genes in  B. subtilis  [ 33 ]. Predictably, all of the essential genes in  B. subtilis  have orthologs in  B. licheniformis , and most are present in a wide range of bacterial taxa. In pairwise BLAST comparisons, 66% of the predicted  B. licheniformis  genes have orthologs in  B. subtilis , and 55% of the gene models are represented by orthologous sequences in  B. halodurans  (E-value threshold of 1 × 10 -5 ; Figure  4 ). Using a reciprocal BLASTP analysis we found 1,719 orthologs that are common to all three species (E-value threshold of 1 × 10 -5 ).B. licheniformisB. subtilisB. subtilisB. licheniformisB. licheniformisB. subtilisB. haloduransAs noted by Lapidus  et al.  [ 9 ], there are broad regions of colinearity between the genomes of  B. licheniformis  and  B. subtilis  (Figure  5 ). Less conservation of genome organization exists between  B. licheniformis  and  B. halodurans , and substantial genomic segments have been inverted in  B. halodurans  with respect to  B. licheniformis  and  B. subtilis . These observations clearly support previous hypotheses [ 8 ] that  B. subtilis  and  B. licheniformis  are phylogenetically and evolutionarily closer to each other than to  B. halodurans .et al.B. licheniformisB. subtilisB. licheniformisB. haloduransB. haloduransB. licheniformisB. subtilisB. subtilisB. licheniformisB. haloduransConclusions In comparisons of shared regions, the genomes of  B. licheniformis  ATCC 14580 and  B. subtilis  168 are approximately 84.6% identical at the nucleotide level and show extensive organizational similarity. Accordingly, their genome sequences represent potentially useful instruments for comparative and evolutionary studies among species within the  subtilis-licheniformis  group, and they may offer new information regarding the evolution and ecology of these closely related species. Despite the broad colinearity of  B. licheniformis  and  B. subtilis  genomes, there are local regions that are individually unique. These include chromosome segments that comprise prophage and insertion sequence elements, DNA restriction-modification systems, antibiotic synthases, and a number of extracellular enzymes and metabolic activities that are not present in  B. subtilis . It is tempting to speculate that the presence of these genes forecasts the ability of  B. licheniformis  to grow on an expanded array of substrates and/or in additional ecological niches compared to  B. subtilis . Together, the similarities and differences may hint at overlapping but non-identical environmental niches for these taxa. The  subtilis-licheniformis  group of bacilli includes many strains that are used to manufacture industrial enzymes, antibiotics and biochemicals. The availability of a complete genome from  B. licheniformis  should permit a thorough comparison of the biochemical pathways and regulatory networks in  B. subtilis  and  B. licheniformis , thereby offering new opportunities and strategies for improvement of industrial strains. When considering the safety of  B. licheniformis  as an industrial organism it should be noted that the species is considered neither a human pathogen nor a toxigenic microorganism [ 34 ]; however, there are reports in the literature implicating it as a causal agent of food poisoning. In these isolated cases, specific strains were shown to produce a toxin similar to cereulide, the emetic toxin of  B. cereus  [ 35 ]. Cereulide is a cyclic depsipeptide synthesized non-ribosomally [ 36 ]. Importantly, the only non-ribosomal peptide synthase genes found in the  B. licheniformis  ATCC 14580 genome are those that involved in synthesis of lichenysin. Similarly, we detected no homologs of the  B. cereus  hemolytic and non-hemolytic enterotoxins (Swiss-Prot accession numbers P80567, P80568, P80172, and P81242). In a comparison of the genotypic and phenotypic characteristics among 182 soil isolates of  B. licheniformis , Manachini  et al.  [ 37 ] observed that while this bacterial species appears to be phenotypically homogeneous, clear genotypic differences are evident between isolates. They postulated the existence of three genomovars for  B. licheniformis . Similarly, De Clerck and De Vos [ 38 ] proposed that this species consists of two lineages that can be distinguished using several molecular genotyping methods. The genome sequence data presented in this work should provide a solid foundation on which to conduct future studies to elucidate the genotypic variation among  B. licheniformis  isolates.
Conclusions
In comparisons of shared regions, the genomes of  B. licheniformis  ATCC 14580 and  B. subtilis  168 are approximately 84.6% identical at the nucleotide level and show extensive organizational similarity. Accordingly, their genome sequences represent potentially useful instruments for comparative and evolutionary studies among species within the  subtilis-licheniformis  group, and they may offer new information regarding the evolution and ecology of these closely related species.B. licheniformisB. subtilissubtilis-licheniformisDespite the broad colinearity of  B. licheniformis  and  B. subtilis  genomes, there are local regions that are individually unique. These include chromosome segments that comprise prophage and insertion sequence elements, DNA restriction-modification systems, antibiotic synthases, and a number of extracellular enzymes and metabolic activities that are not present in  B. subtilis . It is tempting to speculate that the presence of these genes forecasts the ability of  B. licheniformis  to grow on an expanded array of substrates and/or in additional ecological niches compared to  B. subtilis . Together, the similarities and differences may hint at overlapping but non-identical environmental niches for these taxa.B. licheniformisB. subtilisB. subtilisB. licheniformisB. subtilisThe  subtilis-licheniformis  group of bacilli includes many strains that are used to manufacture industrial enzymes, antibiotics and biochemicals. The availability of a complete genome from  B. licheniformis  should permit a thorough comparison of the biochemical pathways and regulatory networks in  B. subtilis  and  B. licheniformis , thereby offering new opportunities and strategies for improvement of industrial strains. When considering the safety of  B. licheniformis  as an industrial organism it should be noted that the species is considered neither a human pathogen nor a toxigenic microorganism [ 34 ]; however, there are reports in the literature implicating it as a causal agent of food poisoning. In these isolated cases, specific strains were shown to produce a toxin similar to cereulide, the emetic toxin of  B. cereus  [ 35 ]. Cereulide is a cyclic depsipeptide synthesized non-ribosomally [ 36 ]. Importantly, the only non-ribosomal peptide synthase genes found in the  B. licheniformis  ATCC 14580 genome are those that involved in synthesis of lichenysin. Similarly, we detected no homologs of the  B. cereus  hemolytic and non-hemolytic enterotoxins (Swiss-Prot accession numbers P80567, P80568, P80172, and P81242).subtilis-licheniformisB. licheniformisB. subtilisB. licheniformisB. licheniformisB. cereusB. licheniformisB. cereusIn a comparison of the genotypic and phenotypic characteristics among 182 soil isolates of  B. licheniformis , Manachini  et al.  [ 37 ] observed that while this bacterial species appears to be phenotypically homogeneous, clear genotypic differences are evident between isolates. They postulated the existence of three genomovars for  B. licheniformis . Similarly, De Clerck and De Vos [ 38 ] proposed that this species consists of two lineages that can be distinguished using several molecular genotyping methods. The genome sequence data presented in this work should provide a solid foundation on which to conduct future studies to elucidate the genotypic variation among  B. licheniformis  isolates.B. licheniformiset al.B. licheniformisB. licheniformisMaterials and methods Shotgun DNA sequencing and genome assembly The genome of  B. licheniformis  ATCC 14580 was sequenced by a combination of the whole-genome shotgun method [ 39 ] and fosmid end sequencing [ 40 ]. Plasmid libraries were constructed using randomly sheared and  Mbo I-digested genomic DNA that was enriched for fragments of 2-3 kb by preparative agarose gel electrophoresis. Approximately 49,000 random clones were sequenced using dye-terminator chemistry (Applied Biosystems) with ABI 377 and ABI 3700 automated sequencers yielding approximately 6× coverage of the genome. A combination of methods was used for gap closure, including sequencing on fosmids [ 40 ] and primer-walking on selected clones and PCR-amplified DNA fragments. We also incorporated data from both ends of approximately 1,975 fosmid clones with an average insert size of 40 kb to aid in validating the final assembly. In total, the number of input reads was 62,685, with 78.6% of these incorporated into the assembled genome sequence. Individual nucleotides were called using TraceTuner 2.0 (Paracel), and sequence reads were assembled into contigs using the Paracel Genome Assembler using optimized parameters and the quality score set to >20. Phrap, Crossmatch and Consed were used for sequence finishing [ 41 ]. Prediction and annotation of CDSs Protein-coding regions in the assembled genome sequence were identified using a combination of previously described software tools including EasyGene [ 42 ], Glimmer [ 43 ] and FrameD [ 44 ]. EasyGene was used as the primary gene finder in these studies. It searches for protein matches in the raw genome data to derive a good training set, and an HMM with states for coding regions as well as ribosome-binding sites (RBSs) is estimated from the dataset. This HMM is used to score all the predicted CDSs in the genome, and the score is converted to a measure of significance (R-value) which is the expected number of CDSs that would be predicted in 1 Mb of random DNA. Gene models with R-values lower than 10 and a log-odds score of greater than -10 were included/considered significant. The principal advantage of this significance measure is that it properly takes into account the length distribution of random CDSs. EasyGene has been shown to match or exceed other gene finders currently available [ 42 ]. Glimmer was used as a secondary gene finder to aid in identification of small genes (< 100 bp) that were sometimes missed by EasyGene. Glimmer models were post-processed with RBSFINDER [ 45 ] to pinpoint the positions of start codons by searching for consensus Shine-Dalgarno sequences. According to the RBS states in the EasyGene HMM model, the bases with the highest probability were AA AAGGAG  (the bases in bold type had distinctly higher probabilities compared to the initial AA). This motif concurs with the consensus Shine-Dalgarno sequence for  B. subtilis  (AAAGGAGG) [ 46 ]. RBSFINDER identified the core AAGGAG motif in around 80% of the cases for Glimmer gene predictions and adjusted the start codon accordingly. Manual inspection and alignments to  B. subtilis  homologs were also used to determine the incidence of specific genes. During the gene-finding process, possible errors and frameshifts were detected by both visual inspection of the CDSs to look for interrupted or truncated genes and by deploying FrameD software [ 44 ]. Frameshifts were resolved by re-sequencing of PCR-amplified segments or subclones. After re-sequencing and manual editing a total of 27 frameshifts remain in the genome assembly (excluding those contained in the  IS3Bli1  elements). It is not known at present whether these represent pseudogenes or instances of programmed translational frameshifting. The positions of rRNA operons in the genome assembly were confirmed by long-range PCR amplification using primers that annealed to genes flanking the rRNA genes. These PCR fragments were sequenced to high redundancy and the consensus sequences were manually inserted into the assembly. Among the seven rRNA operons, the nucleotide sequences of 16S and 23S genes are at least 99% identical, differing by only one to three nucleotides in pairwise comparisons. Protein-coding sequences were annotated in an automated fashion with the following software applications. Predicted proteins were compared to the nonredundant database PIR-NREF [ 47 ] and the  B. subtilis  genome [ 48 ] using BLASTP with a E-value threshold of 1 × 10 -5 . InterProScan was used to predict putative function [ 49 ]. The InterPro analysis included comparison to PFAM [ 50 ], TIGRFAM [ 51 ], Interpro [ 52 ] signal peptide prediction using SignalP [ 20 ] and transmembrane domain prediction using TMHMM [ 21 ]. These CDSs were assigned to functional categories based on the Cluster of Orthologous Groups (COG) database [ 53 ] with manual verification as described [ 54 , 55 ]. Phage gene boundaries were predicted using gene finding algorithms and by homology to known bacteriophage genes. Transfer RNA genes were identified using tRNAscan-SE [ 56 ].  B. licheniformis  genes that shared significant homology with  B. subtilis  counterparts were named using the nomenclature in the SubtiList database [ 48 ] with updated gene names from the BSORF [ 57 ] and UniProt [ 58 ] databases. Comparative analyses VisualGenome software (Rational Genomics) was used for comparisons of ortholog distribution among  B. licheniformis ,  B. subtilis  and  B. halodurans  genomes with precomputed BLAST results stored in a local database. Accession of genome sequence information The GenBank accession number for the  B. licheniformis  ATCC 14580 genome is CP000002. An interactive web portal for viewing and searching the assembled genome based on the generic genome browser developed by Stein  et al.  [ 59 ] is available at [ 60 ].
Materials and methods
Shotgun DNA sequencing and genome assembly The genome of  B. licheniformis  ATCC 14580 was sequenced by a combination of the whole-genome shotgun method [ 39 ] and fosmid end sequencing [ 40 ]. Plasmid libraries were constructed using randomly sheared and  Mbo I-digested genomic DNA that was enriched for fragments of 2-3 kb by preparative agarose gel electrophoresis. Approximately 49,000 random clones were sequenced using dye-terminator chemistry (Applied Biosystems) with ABI 377 and ABI 3700 automated sequencers yielding approximately 6× coverage of the genome. A combination of methods was used for gap closure, including sequencing on fosmids [ 40 ] and primer-walking on selected clones and PCR-amplified DNA fragments. We also incorporated data from both ends of approximately 1,975 fosmid clones with an average insert size of 40 kb to aid in validating the final assembly. In total, the number of input reads was 62,685, with 78.6% of these incorporated into the assembled genome sequence. Individual nucleotides were called using TraceTuner 2.0 (Paracel), and sequence reads were assembled into contigs using the Paracel Genome Assembler using optimized parameters and the quality score set to >20. Phrap, Crossmatch and Consed were used for sequence finishing [ 41 ].
Shotgun DNA sequencing and genome assembly
The genome of  B. licheniformis  ATCC 14580 was sequenced by a combination of the whole-genome shotgun method [ 39 ] and fosmid end sequencing [ 40 ]. Plasmid libraries were constructed using randomly sheared and  Mbo I-digested genomic DNA that was enriched for fragments of 2-3 kb by preparative agarose gel electrophoresis. Approximately 49,000 random clones were sequenced using dye-terminator chemistry (Applied Biosystems) with ABI 377 and ABI 3700 automated sequencers yielding approximately 6× coverage of the genome. A combination of methods was used for gap closure, including sequencing on fosmids [ 40 ] and primer-walking on selected clones and PCR-amplified DNA fragments. We also incorporated data from both ends of approximately 1,975 fosmid clones with an average insert size of 40 kb to aid in validating the final assembly. In total, the number of input reads was 62,685, with 78.6% of these incorporated into the assembled genome sequence. Individual nucleotides were called using TraceTuner 2.0 (Paracel), and sequence reads were assembled into contigs using the Paracel Genome Assembler using optimized parameters and the quality score set to >20. Phrap, Crossmatch and Consed were used for sequence finishing [ 41 ].B. licheniformisMboPrediction and annotation of CDSs Protein-coding regions in the assembled genome sequence were identified using a combination of previously described software tools including EasyGene [ 42 ], Glimmer [ 43 ] and FrameD [ 44 ]. EasyGene was used as the primary gene finder in these studies. It searches for protein matches in the raw genome data to derive a good training set, and an HMM with states for coding regions as well as ribosome-binding sites (RBSs) is estimated from the dataset. This HMM is used to score all the predicted CDSs in the genome, and the score is converted to a measure of significance (R-value) which is the expected number of CDSs that would be predicted in 1 Mb of random DNA. Gene models with R-values lower than 10 and a log-odds score of greater than -10 were included/considered significant. The principal advantage of this significance measure is that it properly takes into account the length distribution of random CDSs. EasyGene has been shown to match or exceed other gene finders currently available [ 42 ]. Glimmer was used as a secondary gene finder to aid in identification of small genes (< 100 bp) that were sometimes missed by EasyGene. Glimmer models were post-processed with RBSFINDER [ 45 ] to pinpoint the positions of start codons by searching for consensus Shine-Dalgarno sequences. According to the RBS states in the EasyGene HMM model, the bases with the highest probability were AA AAGGAG  (the bases in bold type had distinctly higher probabilities compared to the initial AA). This motif concurs with the consensus Shine-Dalgarno sequence for  B. subtilis  (AAAGGAGG) [ 46 ]. RBSFINDER identified the core AAGGAG motif in around 80% of the cases for Glimmer gene predictions and adjusted the start codon accordingly. Manual inspection and alignments to  B. subtilis  homologs were also used to determine the incidence of specific genes. During the gene-finding process, possible errors and frameshifts were detected by both visual inspection of the CDSs to look for interrupted or truncated genes and by deploying FrameD software [ 44 ]. Frameshifts were resolved by re-sequencing of PCR-amplified segments or subclones. After re-sequencing and manual editing a total of 27 frameshifts remain in the genome assembly (excluding those contained in the  IS3Bli1  elements). It is not known at present whether these represent pseudogenes or instances of programmed translational frameshifting. The positions of rRNA operons in the genome assembly were confirmed by long-range PCR amplification using primers that annealed to genes flanking the rRNA genes. These PCR fragments were sequenced to high redundancy and the consensus sequences were manually inserted into the assembly. Among the seven rRNA operons, the nucleotide sequences of 16S and 23S genes are at least 99% identical, differing by only one to three nucleotides in pairwise comparisons. Protein-coding sequences were annotated in an automated fashion with the following software applications. Predicted proteins were compared to the nonredundant database PIR-NREF [ 47 ] and the  B. subtilis  genome [ 48 ] using BLASTP with a E-value threshold of 1 × 10 -5 . InterProScan was used to predict putative function [ 49 ]. The InterPro analysis included comparison to PFAM [ 50 ], TIGRFAM [ 51 ], Interpro [ 52 ] signal peptide prediction using SignalP [ 20 ] and transmembrane domain prediction using TMHMM [ 21 ]. These CDSs were assigned to functional categories based on the Cluster of Orthologous Groups (COG) database [ 53 ] with manual verification as described [ 54 , 55 ]. Phage gene boundaries were predicted using gene finding algorithms and by homology to known bacteriophage genes. Transfer RNA genes were identified using tRNAscan-SE [ 56 ].  B. licheniformis  genes that shared significant homology with  B. subtilis  counterparts were named using the nomenclature in the SubtiList database [ 48 ] with updated gene names from the BSORF [ 57 ] and UniProt [ 58 ] databases.
Prediction and annotation of CDSs
Protein-coding regions in the assembled genome sequence were identified using a combination of previously described software tools including EasyGene [ 42 ], Glimmer [ 43 ] and FrameD [ 44 ]. EasyGene was used as the primary gene finder in these studies. It searches for protein matches in the raw genome data to derive a good training set, and an HMM with states for coding regions as well as ribosome-binding sites (RBSs) is estimated from the dataset. This HMM is used to score all the predicted CDSs in the genome, and the score is converted to a measure of significance (R-value) which is the expected number of CDSs that would be predicted in 1 Mb of random DNA. Gene models with R-values lower than 10 and a log-odds score of greater than -10 were included/considered significant. The principal advantage of this significance measure is that it properly takes into account the length distribution of random CDSs. EasyGene has been shown to match or exceed other gene finders currently available [ 42 ]. Glimmer was used as a secondary gene finder to aid in identification of small genes (< 100 bp) that were sometimes missed by EasyGene. Glimmer models were post-processed with RBSFINDER [ 45 ] to pinpoint the positions of start codons by searching for consensus Shine-Dalgarno sequences. According to the RBS states in the EasyGene HMM model, the bases with the highest probability were AA AAGGAG  (the bases in bold type had distinctly higher probabilities compared to the initial AA). This motif concurs with the consensus Shine-Dalgarno sequence for  B. subtilis  (AAAGGAGG) [ 46 ]. RBSFINDER identified the core AAGGAG motif in around 80% of the cases for Glimmer gene predictions and adjusted the start codon accordingly. Manual inspection and alignments to  B. subtilis  homologs were also used to determine the incidence of specific genes. During the gene-finding process, possible errors and frameshifts were detected by both visual inspection of the CDSs to look for interrupted or truncated genes and by deploying FrameD software [ 44 ]. Frameshifts were resolved by re-sequencing of PCR-amplified segments or subclones. After re-sequencing and manual editing a total of 27 frameshifts remain in the genome assembly (excluding those contained in the  IS3Bli1  elements). It is not known at present whether these represent pseudogenes or instances of programmed translational frameshifting. The positions of rRNA operons in the genome assembly were confirmed by long-range PCR amplification using primers that annealed to genes flanking the rRNA genes. These PCR fragments were sequenced to high redundancy and the consensus sequences were manually inserted into the assembly. Among the seven rRNA operons, the nucleotide sequences of 16S and 23S genes are at least 99% identical, differing by only one to three nucleotides in pairwise comparisons. Protein-coding sequences were annotated in an automated fashion with the following software applications. Predicted proteins were compared to the nonredundant database PIR-NREF [ 47 ] and the  B. subtilis  genome [ 48 ] using BLASTP with a E-value threshold of 1 × 10 -5 . InterProScan was used to predict putative function [ 49 ]. The InterPro analysis included comparison to PFAM [ 50 ], TIGRFAM [ 51 ], Interpro [ 52 ] signal peptide prediction using SignalP [ 20 ] and transmembrane domain prediction using TMHMM [ 21 ]. These CDSs were assigned to functional categories based on the Cluster of Orthologous Groups (COG) database [ 53 ] with manual verification as described [ 54 , 55 ]. Phage gene boundaries were predicted using gene finding algorithms and by homology to known bacteriophage genes. Transfer RNA genes were identified using tRNAscan-SE [ 56 ].  B. licheniformis  genes that shared significant homology with  B. subtilis  counterparts were named using the nomenclature in the SubtiList database [ 48 ] with updated gene names from the BSORF [ 57 ] and UniProt [ 58 ] databases.AAGGAGB. subtilisB. subtilisIS3Bli1B. subtilisB. licheniformisB. subtilisComparative analyses VisualGenome software (Rational Genomics) was used for comparisons of ortholog distribution among  B. licheniformis ,  B. subtilis  and  B. halodurans  genomes with precomputed BLAST results stored in a local database.
Comparative analyses
VisualGenome software (Rational Genomics) was used for comparisons of ortholog distribution among  B. licheniformis ,  B. subtilis  and  B. halodurans  genomes with precomputed BLAST results stored in a local database.B. licheniformisB. subtilisB. haloduransAccession of genome sequence information The GenBank accession number for the  B. licheniformis  ATCC 14580 genome is CP000002. An interactive web portal for viewing and searching the assembled genome based on the generic genome browser developed by Stein  et al.  [ 59 ] is available at [ 60 ].
Accession of genome sequence information
The GenBank accession number for the  B. licheniformis  ATCC 14580 genome is CP000002. An interactive web portal for viewing and searching the assembled genome based on the generic genome browser developed by Stein  et al.  [ 59 ] is available at [ 60 ].B. licheniformiset al.