Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei

Han Song; Junghyun Hwang; Jaehee Myung; Hyoseok Seo; Hyojeong Yi; Hee Sun Sim; Bong Su Kim; William C. Nierman; Heenam Stanley Kim

doi:10.1007/s10059-009-0029-8

Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei

Han Song, Junghyun Hwang, Jaehee Myung, Hyoseok Seo, Hyojeong Yi, Hee Sun Sim, Bong Su Kim, William C. Nierman, Heenam Stanley Kim

School of Biosystem and Biomedical Science

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

Original language	English
Pages (from-to)	237-241
Number of pages	5
Journal	Molecules and cells
Volume	27
Issue number	2
DOIs	https://doi.org/10.1007/s10059-009-0029-8
Publication status	Published - 2009 Feb

Bibliographical note

Funding Information:
This work was supported by the grants M102KK010005-08K1101-00530 from the 21C Frontier Microbial Genomics and Applications Center Program and RO1-2008-000-11047-0 from the Basic Research Program, both of which from the Ministry of Education, Science and Technology in the Republic of Korea, and by the Korea Foundation for International Cooperation of Science and Technology through a grant provided by the Korean Ministry of Science and Technology in K20601000002-07E0100-00240 to H.S.K. Sequencing and annotation of most of the Bp and Bm strains was supported by NIAID N01-AI30071 to W.C.N.

Keywords

Burkholderia mallei
Burkholderia pseudomallei
Pathogen
Phase variation
Simple sequence repeats

ASJC Scopus subject areas

Molecular Biology
Cell Biology

Access to Document

10.1007/s10059-009-0029-8

Cite this

@article{0d55632d29b445b9a6fcd921e4f099ef,

title = "Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei",

abstract = "Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.",

keywords = "Burkholderia mallei, Burkholderia pseudomallei, Pathogen, Phase variation, Simple sequence repeats",

author = "Han Song and Junghyun Hwang and Jaehee Myung and Hyoseok Seo and Hyojeong Yi and Sim, {Hee Sun} and Kim, {Bong Su} and Nierman, {William C.} and Kim, {Heenam Stanley}",

note = "Funding Information: This work was supported by the grants M102KK010005-08K1101-00530 from the 21C Frontier Microbial Genomics and Applications Center Program and RO1-2008-000-11047-0 from the Basic Research Program, both of which from the Ministry of Education, Science and Technology in the Republic of Korea, and by the Korea Foundation for International Cooperation of Science and Technology through a grant provided by the Korean Ministry of Science and Technology in K20601000002-07E0100-00240 to H.S.K. Sequencing and annotation of most of the Bp and Bm strains was supported by NIAID N01-AI30071 to W.C.N.",

year = "2009",

month = feb,

doi = "10.1007/s10059-009-0029-8",

language = "English",

volume = "27",

pages = "237--241",

journal = "Molecules and cells",

issn = "1016-8478",

publisher = "Korean Society for Molecular and Cellular Biology",

number = "2",

}

TY - JOUR

T1 - Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei

AU - Song, Han

AU - Hwang, Junghyun

AU - Myung, Jaehee

AU - Seo, Hyoseok

AU - Yi, Hyojeong

AU - Sim, Hee Sun

AU - Kim, Bong Su

AU - Nierman, William C.

AU - Kim, Heenam Stanley

N1 - Funding Information: This work was supported by the grants M102KK010005-08K1101-00530 from the 21C Frontier Microbial Genomics and Applications Center Program and RO1-2008-000-11047-0 from the Basic Research Program, both of which from the Ministry of Education, Science and Technology in the Republic of Korea, and by the Korea Foundation for International Cooperation of Science and Technology through a grant provided by the Korean Ministry of Science and Technology in K20601000002-07E0100-00240 to H.S.K. Sequencing and annotation of most of the Bp and Bm strains was supported by NIAID N01-AI30071 to W.C.N.

PY - 2009/2

Y1 - 2009/2

N2 - Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

AB - Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

KW - Burkholderia mallei

KW - Burkholderia pseudomallei

KW - Pathogen

KW - Phase variation

KW - Simple sequence repeats

UR - http://www.scopus.com/inward/record.url?scp=66149124100&partnerID=8YFLogxK

U2 - 10.1007/s10059-009-0029-8

DO - 10.1007/s10059-009-0029-8

M3 - Article

C2 - 19277507

AN - SCOPUS:66149124100

SN - 1016-8478

VL - 27

SP - 237

EP - 241

JO - Molecules and cells

JF - Molecules and cells

IS - 2

ER -

Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this