A Paenibacillus elgii strain isolated from soil samples from Cerrado, Brazil, showed antimicrobial activity. Its genome sequence was acquired (GS20 FLX Titanium 454 platform) and comprises 108 contigs (N50, 198,427 bp) and 6,810 predicted sequences.
ABSTRACT
A Paenibacillus elgii strain isolated from soil samples from Cerrado, Brazil, showed antimicrobial activity. Its genome sequence was acquired (GS20 FLX Titanium 454 platform) and comprises 108 contigs (N50, 198,427 bp) and 6,810 predicted sequences. Here, we shed some light on the antimicrobial genes of the strain, including a nonribosomal peptide synthetase (NRPS) module identified as part of a pelgipeptin gene cluster.
GENOME ANNOUNCEMENT
The Paenibacillus genus was defined after an extensive comparison between DNA sequences encoding 16S rRNA (1). Since then, different species of this genus have been described as biological control agents and producers of molecules with surfactant properties and several lipopeptides with antimicrobial activity (2–4). Lipopeptides are cyclic or linear peptides carrying a variable fatty acid in their N-terminal region. These molecules are a product of nonribosomal synthesis. Differently from the ribosomal synthesis, nonribosomal peptide synthetases (NRPS) use a mixture of d- and l-amino acids and nonproteinogenic amino acids as building blocks (2).
Paenibacillus elgii strain AC13 is a spore-forming monoderm bacterium isolated from soil samples from the Brazilian Cerrado. This strain exhibits long-rod cells and motility by peritrichous flagella; growth occurs at pH values ranging from 4.7 to 8.0 at temperatures of 28°C and 37°C. Paenibacillus elgii strain AC13 also produces at least two groups of antimicrobial compounds (5–7).
The DNA of strain AC13 was isolated from an overnight culture on Luria-Bertani medium (37°C). Approximately 0.5 g of cells was collected, and DNA was extracted using a modified cetyltrimethylammonium bromide (CTAB) protocol (8). Cells were lysed using a solution containing 10% sodium dodecyl sulfate (SDS), 10% CTAB in 0.7 M NaCl, and 1 mg ml−1 lysozyme. Proteins were removed enzymatically with 100 ng ml−1 (wt/vol) proteinase K, followed by a phenol-chloroform-isoamyl alcohol (25:24:1 [vol/vol/vol]) extraction (9). The DNA was suspended in distilled water and quantified. The genome sequence was acquired using a GS20 FLX Titanium 454 platform with 20× coverage yielding 455,876 reads. The assembly was performed using the Newbler software (version 2.3) yielding 126 contigs, of which 108 contigs had more than 100 bp, with an N50 value of 198,427 bp, 53.4% G+C content, and 7,809,407 bp.
Genomic sequence annotation was performed using the Prokaryotic Genome Annotation Pipeline (PGAP), a modified NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) protocol (10–16). The genome contained 7,149 total genes and 6,810 coding sequences (CDS), including 111 RNA genes, of which there were 7 5S rRNA genes, 7 partial 16S rRNA genes, 1 partial 23S rRNA gene, and 92 tRNA genes.
Forty putative NRPS genes were identified, and some of them might be part of the pelgipeptin synthase gene cluster that was identified in P. elgii strain B69 (17, 18). Other antimicrobial genes were identified, including a fusaricidin coding sequence, nine genes involved in polyketide gene cluster, eight genes related to bacteriocins, and genes for two ABC transporters related to lantibiotics.
The average nucleotide identity (ANI) comparison with other Paenibacillus genomes available at the NCBI genome database and the Joint Genome Institute (19) revealed ANI values of 70.23% with P. antarcticus CECT 5836, 70.3% with P. panacisoli DSM 21345, 70.46% with P. polymyxa CR1, 70.76% with P. crassostreae LPB0068, 70.78% with P. larvae BRL-230010, 70.95% with P. alvei TS-15, 74.96% with P. mucilaginosus K02, 96.45% with P. elgii B69, and 97.62% with P. elgii type strain M63, indicating that AC13 is a new Paenibacillus elgii strain.
Accession number(s).
The Paenibacillus elgii strain AC13 whole-genome shotgun project sequencing has been deposited at DDBJ/ENA/GenBank under the accession number PYHP00000000. The version described in this paper is version PYHP01000000.
ACKNOWLEDGMENTS
We thank the UCB sequencing center staff and the GenBank staff for their assistance in genomic sequence data registration.
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) provided financial support for our postgraduate students and to the project CNPq number 560915/2010-1.
Footnotes
Citation Ortega DB, Costa RA, Pires AS, Araújo TF, Araújo JF, Kurokawa AS, Magalhães BS, Reis AMM, Franco OL, Kruger RH, Pappas GJ, Jr, Barreto CC. 2018. Draft genome sequence of the antimicrobial-producing strain Paenibacillus elgii AC13. Genome Announc 6:e00573-18. https://doi.org/10.1128/genomeA.00573-18.
REFERENCES
- 1.Ash C, Priest FG, Collins MD. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64:253–260. doi: 10.1007/BF00873085. [DOI] [PubMed] [Google Scholar]
- 2.Cochrane SA, Vederas JC. 2016. Lipopeptides from Bacillus and Paenibacillus spp.: a gold mine of antibiotic candidates. Med Res Rev 36:4–31. doi: 10.1002/med.21321. [DOI] [PubMed] [Google Scholar]
- 3.Grady EN, MacDonald J, Liu L, Richman A, Yuan Z-C. 2016. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 15:203. doi: 10.1186/s12934-016-0603-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Wu X-C, Shen X-B, Ding R, Qian C-D, Fang H-H, Li O. 2010. Isolation and partial characterization of antibiotics produced by Paenibacillus elgii B69. FEMS Microbiol Lett 310:32–38. doi: 10.1111/j.1574-6968.2010.02040.x. [DOI] [PubMed] [Google Scholar]
- 5.Kurokawa AS. 2006. Exploração biotecnológica de microrganismos do solo de Cerrado através da construção de bibliotecas metagenômicas e técnicas de cultivo. Universidade Católica de Brasília, Brasília, Brazil. [Google Scholar]
- 6.de Araújo JF. 2011. Diversidade bacteriana do solo em diferentes fitofisionomias do bioma cerrado e perspectivas biotecnológicas. Universidade Católica de Brasília, Brasília, Brazil. [Google Scholar]
- 7.Costa RA. 2017. Paenibacillus elgii: ciclo celular, produção de peptídeos não ribossomais e potencial biotecnológico. Universidade Católica de Brasília, Brasília, Brazil. [Google Scholar]
- 8.Wilson K. 1987. Preparation of genomic DNA from bacteria, p 2.4.1–2.4.5. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. (ed), Current protocols in molecular biology. Greene Publishing & Wiley Interscience, New York, NY. [DOI] [PubMed] [Google Scholar]
- 9.Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. [Google Scholar]
- 10.Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. OMICS 12:137–141. doi: 10.1089/omi.2008.0017. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O’Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T. 2009. The National Center for Biotechnology Information’s Protein Clusters Database. Nucleic Acids Res 37:D216–D223. doi: 10.1093/nar/gkn734. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. 2013. TIGRFAMs and genome properties in 2013. Nucleic Acids Res 41:D387–D395. doi: 10.1093/nar/gks1234. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285. doi: 10.1093/nar/gkv1344. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Lowe TM, Chan PP. 2016. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57. doi: 10.1093/nar/gkw413. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD. 2015. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 43:D130–D137. doi: 10.1093/nar/gku1063. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Borodovsky M, Lomsadze A. 2011. Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. Curr Protoc Bioinformatics Chapter 4:Unit 4.5.1–4.5.17. doi: 10.1002/0471250953.bi0405s35. [DOI] [PubMed] [Google Scholar]
- 17.Donadio S, Monciardini P, Sosio M. 2007. Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat Prod Rep 24:1073–1109. doi: 10.1039/b514050c. [DOI] [PubMed] [Google Scholar]
- 18.Qian C-D, Liu T-Z, Zhou S-L, Ding R, Zhao W-P, Li O, Wu X-C. 2012. Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii. BMC Microbiol 12:197. doi: 10.1186/1471-2180-12-197. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. doi: 10.1099/ijs.0.64483-0. [DOI] [PubMed] [Google Scholar]