Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features

BMC Genomics

Research Article

Bernhard O Palsson¹  Donghyuk Kim¹  Joo-Hyun Seo¹  Pep Charusanti¹  Jay Sung-Joong Hong²  Byung-Kwan Cho³  Tzu-Wen Huang⁴  Shih-Feng Tsai⁵ 

[1] Department of Bioengineering, University of California, 92093, San Diego, La Jolla, CA, USA;Department of Bioengineering, University of California, 92093, San Diego, La Jolla, CA, USA;Central Research Institute, Samsung Petrochemical, Samsung Advanced Institute of Technology, 6th floor, Building 2, Nongseo-dong, Giheung-gu, 446-712, Yongin, Gyeonggi-do, Republic of Korea;Department of Bioengineering, University of California, 92093, San Diego, La Jolla, CA, USA;Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, 305-701, Yuseong-gu, Daejeon, Korea;Department of Bioengineering, University of California, 92093, San Diego, La Jolla, CA, USA;Institute of Molecular and Genomic Medicine, National Health Research Institutes, 350, Miaoli, Taiwan;Institute of Molecular and Genomic Medicine, National Health Research Institutes, 350, Miaoli, Taiwan;

关键词: Klebsiella pneumoniae;    Infectious disease;    Transcriptional architecture;    Omics data;    Systems biology;   

DOI  :  10.1186/1471-2164-13-679

 received in 2012-08-03, accepted in 2012-11-21,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. The development of next-generation sequencing technologies now permits rapid sequencing of many K. pneumoniae isolates, but sequence information alone does not provide important structural and operational information for its genome.ResultsHere we take a systems biology approach to annotate the K. pneumoniae MGH 78578 genome at the structural and operational levels. Through the acquisition and simultaneous analysis of multiple sample-matched –omics data sets from two growth conditions, we detected 2677, 1227, and 1066 binding sites for RNA polymerase, RpoD, and RpoS, respectively, 3660 RNA polymerase-guided transcript segments, and 3585 transcription start sites throughout the genome. Moreover, analysis of the transcription start site data identified 83 probable leaderless mRNAs, while analysis of unannotated transcripts suggested the presence of 119 putative open reading frames, 15 small RNAs, and 185 antisense transcripts that are not currently annotated.ConclusionsThese findings highlight the strengths of systems biology approaches to the refinement of sequence-based annotations, and to provide new insight into fundamental genome-level biology for this important human pathogen.

【 授权许可】

Unknown   
© Seo et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.