Genome sequence of Bacillus licheniformis WX-02.
ABSTRACT Bacillus licheniformis is an important bacterium that has been used extensively for large-scale industrial production of exoenzymes and peptide antibiotics. B. licheniformis WX-02 produces poly-gamma-glutamate increasingly when fermented under stress conditions. Here its genome sequence (4,270,104 bp, with G+C content of 46.06%), which comprises a circular chromosome, is announced.
- SourceAvailable from: Zakry Fitri Ab Aziz[Show abstract] [Hide abstract]
ABSTRACT: In this study, computational methods were used to predict information hidden in the small subunit 16S rRNA gene from newly isolated plant growth-promoting rhizobacteria B. cereus strain UPMLH24. In the present study, the computational methods employed revealed that the small subunit 16S rRNA gene sequence from B. cereus strain UPMLH24 contained a number of small open reading frames that encoded several functional proteins. Computational predictions classified seven phyla of organisms associated with small open reading frames of novel B. cereus strain UPMLH24. The data generated from computational predictions in the present study could form the basis for further research to advance new hypotheses in the microbiology of rhizobacteria. In recent years, bioinformatics has emerged as a powerful tool for the rapid investigation of molecular sequences and has taken the center stage in molecular biology research as a tool for transforming the voluminous molecular sequence data into new knowledge and information. Advances in this field have expanded the horizons in biological research. Bioinformatics uses mathematical and statistical concepts to develop computer algorithm in accordance with theories and concepts in biology. With databases of DNA and protein sequences becoming increasingly available in public databases, bioinformatics has evolved into an essential tool in the development of new concepts, theories and experimental approaches in biological research. The small subunit of the 16S ribosomal RNA gene (16S rRNA) is a highly conserved region found in almost all organisms. In prokaryotes, the 16S rRNA genes occur in at least one copy in the genome. Ribosomal RNAs (16S, 23S, 5S) and ribosomal proteins play very important roles in the formation of ribosomes and in the control of protein translation 1 . The 16S rRNA gene is widely studied as a molecular signature and is commonly adopted as the standard for identification and phylogenetic analysis 2,3 since it contains conserved regions and other more variable sequences that vary according to species or familiesJournal of Pure and Applied Microbiology 11/2014; 8:2801-2816. · 0.07 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Lichenysin is a biodegradable surfactant with huge potential for recovering crude oil from the oil reservoir. The current production of lichenysin is made through fermentation from wild strain of Bacillus licheniformis, which is limited by low yield. The aim of this work was to improve lichenysin-producing capability of a wide strain B. licheniformis WX-02. Lichenysin produced from WX-02 was first extracted, purified, and identified. Through the substitution of the promoter of lichenysin biosynthesis operon, the mutants B. licheniformis WX02-P43lch, WX02-Pxyllch, and WX02-Psrflch were constructed with the constitutive promoter (P43), the xylose-inducible promoter (P xyl ), and the surfactin operon promoter (P srf ), respectively. A consistent change trend was observed between lichenysin production and lchAA gene transcription, confirming the strength of the promoters as an important factor for lichenysin synthesis. Among the three mutants, WX02-Psrflch produced the highest lichenysin yield. The production by the mutant WX02-Psrflch was further improved with the optimization of the major medium components including glucose, NH4NO3, and Na2HPO4/KH2PO4. Under 30 g/L glucose, 5 g/L NH4NO3, and 80 mM/60 mM Na2HPO4/KH2PO4, the strain WX02-Psrflch produced 2,149 mg/L lichenysin, a 16.8-fold improvement compared to that of wild strain WX-02.Applied Microbiology and Biotechnology 08/2014; · 3.81 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Staphylococcus aureus strain LZ-01, isolated from the Lanzhou reaches of the Yellow River, is capable of reducing Cr(VI) to Cr(III) aerobically. We employed transcriptome sequencing analysis to identify genes involved in Cr(VI) stress responses in S. aureus LZ-01. Our results showed that 512 of the 2,370 predicted genes displayed up-regulation (>2-fold), and 49 genes were down-regulated (<50 %) after Cr(VI) exposure. Among up-regulated genes, 128 genes were annotated to encode proteins involved in cellular processes; 68 were categorized to transport and binding proteins; 26 were involved in DNA repair and 32 were associated with regulatory functions. To further elucidate the Cr(VI) resistance and reduction mechanism, we carried out physiological tests and quantitative PCR analysis. Both RNA-seq and qRT-PCR data showed genes encoding a thioredoxin reductase and main subunits of cytochrome c oxidase complex were up-regulated upon Cr(VI) treatment. Either cadmium or NaN3 treatment could inhibit Cr(VI) reduction which indicates that thioredoxin and cytochrome are involved in Cr(VI) reduction strain LZ-01. 29 ABC-type metal/multidrug transporters and efflux pumps were up-regulated, suggesting that they are involved in Cr(VI) resistance by pumping chromium ions out of cells. The up-regulation of 26 DNA repair genes demonstrate that Cr(VI) is toxic to DNA and those DNA protection proteins need to be responded for Cr(VI) stress. Based on these results, the mechanism of strain LZ-01 resists and reduces Cr(VI) is revealed.Ecotoxicology 08/2014; · 2.50 Impact Factor
Genome Sequence of Bacillus licheniformis WX-02
Wuming Yangtse, Yinhua Zhou, Yang Lei, Yimin Qiu, Xuetuan Wei, Zhixia Ji, Gaofu Qi, Yangchun Yong, Lingling Chen,
and Shouwen Chen
State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
Bacillus licheniformis is an important bacterium that has been used extensively for large-scale industrial production of exoen-
zymes and peptide antibiotics. B. licheniformis WX-02 produces poly-gamma-glutamate increasingly when fermented under
is used to produce enzymatic agents (12), peptide antibiotics (7),
acetoin (8), and poly-?-glutamic acid (?-PGA) (1, 2), etc. B. li-
cheniformis WX-02 was isolated from saline soil in Yingcheng
produce larger amounts of ?-PGA under stress conditions than
under normal ones; the stresses refer to high salt, high tempera-
ture, caustic alkali, ultrasonic shock, and so on. The yield of
?-PGA can be raised 5.28 times against that of the control group
when the salt concentration reaches 8% (13). In order to explore
the mechanism of high production of ?-PGA under adverse cir-
licheniformis WX-02 has been maintained at the China Center for
Type Culture Collection and designated B. licheniformis CCTCC
Whole-genome sequencing was performed using a Solexa
genome analyzer (BGI; Shenzhen, China) using a shotgun
strategy, which produced paired reads totaling ?555 Mb with
were processed and assembled into 45 contigs and 29 scaffolds
(5). Gaps between contigs were closed by combinatorial PCR
and sequencing amplicons by primer walking. Finally, this as-
sembling process produced 3 large scaffolds in one potential
circular chromosome. Open reading frames were identified using
&group?programs&subgroup?gfindb), Prodigal (http://compbio
.ornl.gov/prodigal/), and Glimmer (http://www.ncbi.nlm.nih.gov
/genomes/MICROBES/glimmer_3.cgi) and BLAST against the Ref-
Seq database. tRNA and rRNA genes were identified by the
tRNAScan and RNAmmer software programs, respectively (4, 6).
The genome of strain CCTCC M208065 is 4,270,104 bp long with a
GC content of 46.06%, containing 4,320 open reading frames, 72
M208065 shares great similarity (94.8%) with that of ATCC 14580,
about 76 kb in this genome sharing very low homology with the
ment encodes the DNA replication initiator protein, conjugation
protein, RNA polymerase sigma factors, transcriptional regulators,
acillus licheniformis is a Gram-positive bacterium which in-
in regulation of ?-PGA synthesis (3, 11). The comP gene in the
ATCC 14580 strain is inactivated by two insertional fragments,
the comP gene between these two strains might be associated with
idence is needed to verify this.
paper is the first version, AHIF01000000.
(grant no. 30970036 and no. 31170046).
We are grateful to Sun Ming for his kind and generous suggestions.
1. Birrer GA, Cromwick AM, Gross RA. 1994. ?-Poly (glutamic acid)
formation by Bacillus licheniformis 9945A: physiological and biochemical
studies. Int. J. Biol. Macromol. 16:265–275.
2. Buescher JM, Margaritis A. 2007. Microbial biosynthesis of polyglutamic
acid biopolymer and applications in the biopharmaceutical, biomedical
and food industries. Crit. Rev. Biotechnol. 27:1–19.
3. Hoffmann K, et al. 2010. Facilitation of direct conditional knockout of
essential genes in Bacillus licheniformis DSM13 by comparative genetic
analysis and manipulation of genetic competence. Appl. Environ. Micro-
4. Lagesen K, et al. 2007. RNAmmer: consistent annotation of rRNA genes
in genomic sequences. Nucleic Acids Res. 35:3100–3108.
5. Li R, et al. 2009. SOAP2: an improved ultrafast tool for short read align-
ment. Bioinformatics 25:1966–1967.
6. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-
tion of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:
7. McInerney MJ, Javaheri M, Nagle DP. 1990. Properties of the biosur-
factant produced by Bacillus licheniformis strain JF-2. J. Ind. Microbiol.
8. Perego P, Converti A, Del Borghi M. 2003. Effects of temperature,
inoculum size and starch hydrolyzate concentration on butanediol pro-
duction by Bacillus licheniformis. Bioresour. Technol. 89:125–131.
Received 5 April 2012 Accepted 10 April 2012
Address correspondence to Shouwen Chen, email@example.com.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
July 2012 Volume 194 Number 13Journal of Bacteriologyp. 3561–3562jb.asm.org
9. Pötter M, Oppermann-Sanio FB, Steinbüchel A. 2001. Cultivation of
bacteria producing polyamino acids with liquid manure as carbon and
nitrogen source. Appl. Environ. Microbiol. 67:617–622.
10. Rey MW, et al. 2004. Complete genome sequence of the industrial bac-
species. Genome Biol. 5:R77. doi:10.1186/gb-2004-5-10-r77.
11. Stanley NR, Lazazzera BA. 2005. Defining the genetic differences be-
tween wild and domestic strains of Bacillus subtilis that affect poly-?-DL-
glutamic acid production and biofilm formation. Mol. Microbiol. 57:
12. Veith B, et al. 2004. The complete genome sequence of Bacillus licheni-
biol. Biotechnol. 7:204–211.
13. Wei X, Ji Z, Chen S. 2010. Isolation of halotolerant Bacillus licheniformis
jb.asm.orgJournal of Bacteriology