ArticleBMC genomics2012
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Unique mechanistic insights into pathways associated with the synergistic activity of polymyxin B and caspofungin against multidrug-resistantComputational and structural biotechnology journal · 2022Article
- Translation of a Leaderless Reporter Is Robust During Exponential Growth and Well Sustained During Stress Conditions inFrontiers in microbiology · 2021Article
- Phenotypical profile and global transcriptomic profile of Hypervirulent Klebsiella pneumoniae due to carbapenemase-encoding plasmid acquisition.BMC genomics · 2019Article
- Decreased Antibiotic Susceptibility Driven by Global Remodeling of theMolecular & cellular proteomics : MCP · 2019Article
- Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar.Planta · 2018Article
- Translational regulation in mycobacteria and its implications for pathogenicity.Nucleic acids research · 2018Review
- Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!Microbiology spectrum · 2018Review
- Genomic insights of aromatic hydrocarbon degrading3 Biotech · 2018Article
- Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis.RNA biology · 2018Article
- Network Analyses in Plant Pathogens.Frontiers in microbiology · 2018Review
- Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH inFrontiers in microbiology · 2018Article
- Insulated transcriptional elements enable precise design of genetic circuits.Nature communications · 2017Article
- The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2).Nature communications · 2016Article
- Functional modules of sigma factor regulons guarantee adaptability and evolvability.Scientific reports · 2016Article
- Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape.PLoS genetics · 2015Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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