Revised genome sequence of Burkholderia thailandensis MSMB43 with improved annotation.
ABSTRACT There is growing interest in discovery of novel bioactive natural products from Burkholderia thailandensis. Here we report a significantly improved genome sequence and reannotation of Burkholderia thailandensis MSMB43, which will facilitate the discovery of new natural products through genome mining and studies of the metabolic versatility of this bacterium.
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ABSTRACT: The genome of Burkholderia thailandensis codes for several LuxR-LuxI quorum-sensing systems. We used B. thailandensis quorum-sensing deletion mutants and recombinant Escherichia coli to determine the nature of the signals produced by one of the systems, BtaR2-BtaI2, and to show that this system controls genes required for the synthesis of an antibiotic. BtaI2 is an acyl-homoserine lactone (acyl-HSL) synthase that produces two hydroxylated acyl-HSLs, N-3-hydroxy-decanoyl-HSL (3OHC(10)-HSL) and N-3-hydroxy-octanoyl-HSL (3OHC(8)-HSL). The btaI2 gene is positively regulated by BtaR2 in response to either 3OHC(10)-HSL or 3OHC(8)-HSL. The btaR2-btaI2 genes are located within clusters of genes with annotations that suggest they are involved in the synthesis of polyketide or peptide antibiotics. Stationary-phase cultures of wild-type B. thailandensis, but not a btaR2 mutant or a strain deficient in acyl-HSL synthesis, produced an antibiotic effective against gram-positive bacteria. Two of the putative antibiotic synthesis gene clusters require BtaR2 and either 3OHC(10)-HSL or 3OHC(8)-HSL for activation. This represents another example where antibiotic synthesis is controlled by quorum sensing, and it has implications for the evolutionary divergence of B. thailandensis and its close relatives Burkholderia pseudomallei and Burkholderia mallei.Journal of bacteriology 05/2009; 191(12):3909-18. · 3.94 Impact Factor
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ABSTRACT: Modular polyketide synthases (PKSs) are giant bacterial enzymes that synthesize many polyketides of therapeutic value. In contrast to PKSs that provide acyltransferase (AT) activities in cis, trans-AT PKSs lack integrated AT domains and exhibit unusual enzymatic features with poorly understood functions in polyketide assembly. This has retarded insight into the assembly of products such as mupirocin, leinamycin and bryostatin 1. We show that trans-AT PKSs evolved in a fundamentally different fashion from cis-AT systems, through horizontal recruitment and assembly of substrate-specific ketosynthase (KS) domains. The insights obtained from analysis of these KS mosaics will facilitate both the discovery of novel polyketides by genome mining, as we demonstrate for the thailandamides of Burkholderia thailandensis, and the extraction of chemical information from short trans-AT PCR products, as we show using metagenomic DNA of marine sponges. Our data also suggest new strategies for dissecting polyketide biosynthetic pathways and engineering polyketide assembly.Nature Biotechnology 03/2008; 26(2):225-33. · 32.44 Impact Factor
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ABSTRACT: Comparative analysis of related biosynthetic gene clusters can provide new insights into the versatility of these pathways and allow the discovery of new natural products. The freshwater cyanobacterium Microcystis aeruginosa NIES298 produces the cytotoxic peptide microcyclamide. Here, we provide evidence that the cyclic hexapeptide is formed by a ribosomal pathway through the activity of a set of processing enzymes closely resembling those recently shown to be involved in patellamide biosynthesis in cyanobacterial symbionts of ascidians. Besides two subtilisin-type proteases and a heterocyclization enzyme, the gene cluster discovered in strain NIES298 encodes six further open reading frames, two of them without similarity to enzymes encoded by the patellamide gene cluster. Analyses of genomic data of a second cyanobacterial strain, M. aeruginosa PCC 7806, guided the discovery and structural elucidation of two novel peptides of the microcyclamide family. The identification of the microcyclamide biosynthetic genes provided an avenue by which to study the regulation of peptide synthesis at the transcriptional level. The precursor genes were strongly and constitutively expressed throughout the growth phase, excluding the autoinduction of these peptides, as has been observed for several peptide pheromone families in bacteria.Applied and environmental microbiology 04/2008; 74(6):1791-7. · 3.69 Impact Factor
Revised Genome Sequence of Burkholderia thailandensis MSMB43
with Improved Annotation
Ying Zhuo,aLin Liu,bQi Wang,aXiangyang Liu,cBiao Ren,a,eMei Liu,aPeixiang Ni,bYi-Qiang Cheng,c,dand Lixin Zhanga
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, Chinaa; Shenzhen Key Laboratory of
Transomics Biotechnologies, BGI—Shenzhen, Shenzhen, Chinab; Department of Biological Sciences and Department of Chemistry and Biochemistry, University of
Wisconsin—Milwaukee, Milwaukee, Wisconsin, USAc; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University, Ministry of Education, and
Wuhan University School of Pharmaceutical Sciences, Wuhan, Chinad; and Graduate University of Chinese Academy of Sciences, Beijing, Chinae
There is growing interest in discovery of novel bioactive natural products from Burkholderia thailandensis. Here we report a
significantly improved genome sequence and reannotation of Burkholderia thailandensis MSMB43, which will facilitate the dis-
natural products (6, 7). For example, more than 20 new com-
pounds, including our reported thailandepsins A through F, have
been isolated from B. thailandensis strain E264 in recent years (1,
2, 4, 5, 8–10, 13, 15–17). To fully enable the discovery of novel
natural products by genome mining, it is important to construct
genome sequence assemblies of the highest quality, since they are
the foundation for developing chemical separation and for engi-
neering the biosynthetic pathways. The previously reported ge-
but often fragmented secondary metabolite biosynthetic genes or
gene clusters, due to a poor-quality genome sequence. Here, we
report the resequencing of the genome of B. thailandensis
MSMB43 and we describe the sequence differences between the
previously published assembly and our assembly.
The resequencing of B. thailandensis MSMB43 was performed
with an Illumina genome analyzer (San Diego, CA), generating
?232.78 Mb of valid sequence data (about ?34.37-fold cover-
age), which was assembled into 176 contigs (N50, 102,479 bp) by
using the SOAPdenovo program (http://soap.genomics.org.cn/).
Paired-end information was then used to join the contigs into 61
draft genome sequence of B. thailandensis strain MSMB43
(GenBank accession number NZ_ABBM00000000), which con-
tained 1,230 scaffolds (12), the quality of this new draft genome
sequence is a significant improvement. In contrast to the draft
genome of B. thailandensis MSMB43, we corrected 255 sequenc-
ing errors caused by continuous nucleotides (e.g., AAAAAA), 57
of which were in the coding region.
The new draft genome includes 7,209,234 bp and contains
6,201 coding sequences (CDSs), determined by combining the
predictions from Glimmer and RAST, with a G?C content of
67.19%. The former annotation of the B. thailandensis MSMB43
genome contained 7,426 CDSs, but 590 of them were very short
(?50 amino acids). The new annotation corrected 1,204 CDSs,
which were fragmented due to the incomplete contigs. There are
single-copy genes predicted for 16S and 23S rRNA, duplicated
genes predicted for 5S rRNA, and 55 genes predicted for tRNAs.
The antiSMASH program (11) was used to predict secondary
metabolite biosynthetic genes of B. thailandensis MSMB43, re-
vealing at least 13 putative gene clusters for biosynthesis, includ-
urkholderia thailandensis is a nonpathogenic Gram-negative
bacillus that is emerging as a new source of diverse bioactive
ing lantibiotics, type I polyketide synthase (PKS)-produced
polyketides (PKs), nonribosomal peptides (NRPs), terpenes, or
hybrid PK/NRP molecules. Among those putative gene clusters,
ter of Microcystis aeroginosa NIES298 (18), and another is similar
to the FK228 (depsipeptide, an FDA-approved anticancer natural
no. 968 (3, 14). This draft genome of B. thailandensis MSMB43
will enable us to explore secondary metabolites through genome
Nucleotide sequence accession numbers. The assembled
shotgun genome sequences and annotations of B. thailandensis
MSMB43 were deposited in DDBJ/EMBL/GenBank under acces-
sion number AJXB00000000. The version described in this paper
is the first version, AJXB01000000.
We are grateful to Jay Gee for facilitating the distribution of B. thailand-
Darwin University, Australia (6).
This work was supported in part by grants from the National Natural
Science Foundation of China (31100075, 81102362, 31170095, and
31000004), the CAS Pillar Program (XDA04074000), and the Ministry of
Scienceand Technologyof China
2007DFB31620). L.Z. is an awardee of the National Distinguished Young
Scholar Program in China.
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Received 29 May 2012 Accepted 18 June 2012
Address correspondence to Lixin Zhang, Zhanglixin@im.ac.cn, or Yi-Qiang Cheng,
Y.Z., L.L., and Q.W. contributed equally to this work.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
September 2012 Volume 194 Number 17Journal of Bacteriologyp. 4749–4750jb.asm.org
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