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: Mining the genome sequence of Burkholderia thailandensis MSMB43 revealed a cryptic biosynthetic gene cluster resembling that of FR901464 (4), a prototype spliceosome inhibitor produced by Pseudomonas sp. No. 2663. Transcriptional analysis revealed a cultivation condition in which a regulatory gene of the cryptic gene cluster is adequately expressed. Consequently, three new compounds, named thailanstatins A (1), B (2), and C (3), were isolated from the fermentation broth of B. thailandensis MSMB43. Thailanstatins are proposed to be biosynthesized by a hybrid polyketide synthase-nonribosomal peptide synthetase pathway. They differ from 4 by lacking an unstable hydroxyl group and by having an extra carboxyl moiety; those differences endow thailanstatins with a significantly greater stability than 4 as tested in phosphate buffer at pH 7.4. In vitro assays showed that thailanstatins inhibit pre-mRNA splicing as potently as 4, with half-maximal inhibitory concentrations in the single to sub-μM range. Cell culture assays indicated that thailanstatins also possess potent antiproliferative activities in representative human cancer cell lines, with half-maximal growth inhibitory concentrations in the single nM range. This work provides new chemical entities for research and development and new structure-activity information for chemical optimization of related spliceosome inhibitors.Journal of Natural Products 03/2013; · 3.95 Impact Factor
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ABSTRACT: The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.Standards in Genomic Sciences 12/2012; 7(2):321-340. · 3.17 Impact Factor
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ABSTRACT: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques. The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related. We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters.PLoS ONE 09/2013; 8(9):e74319. · 3.53 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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2. Carr G, Seyedsayamdost MR, Chandler JR, Greenberg EP, Clardy J.
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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