Abstract
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.
Highlights
The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide
Analysis of transcriptional architecture To construct the transcriptional architecture of the K. pneumoniae MGH 78578 genome, we determined the active coding regions of the genome in both exponential and stationary phase by investigating gene expression, RNAP, RpoD, and RpoS binding sites, and transcription start site (TSS) data collected under these two growth conditions (Figure 1)
RNAP, RpoD, and RpoS binding sites were identified from similar log ratio data sets from triplicate chromatin immunoprecipitation (ChIP) samples using NimbleScan software
Summary
The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. Other studies have sought to build upon the abundance of sequence data to delineate fundamental operational features of the genome, for instance the identity and binding site locations of major transcription factors, the environmental signals that stimulate transcription of certain genes, the architecture of operons, sub-operons, and transcription units, the existence of small non-coding RNAs, and other elements [24,25,26,27] Such studies often rely on the acquisition and analysis of genome-wide data sets such as chromatin immunoprecipitation combined with microarray hybridization (ChIP-chip), transcriptome profiling, proteomics, and metabolomics, resulting in a global map of the transcriptional architecture for the bacterium under defined growth conditions. This map provides a fundamental link between the genotype and phenotype for the organism
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