A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

被引：169

作者：

Perkins, Timothy T. ^{[1
]}

Kingsley, Robert A. ^{[1
]}

Fookes, Maria C. ^{[1
]}

Gardner, Paul P. ^{[1
]}

James, Keith D. ^{[1
]}

Yu, Lu ^{[1
]}

Assefa, Samuel A. ^{[1
]}

He, Miao ^{[1
]}

Croucher, Nicholas J. ^{[1
]}

Pickard, Derek J. ^{[1
]}

Maskell, Duncan J. ^{[2
]}

Parkhill, Julian ^{[1
]}

Choudhary, Jyoti ^{[1
]}

Thomson, Nicholas R. ^{[1
]}

Dougan, Gordon ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge, England

[2] Univ Cambridge, Dept Vet Med, Cambridge, England

来源：

PLOS GENETICS | 2009年 / 5卷 / 07期

基金：

英国惠康基金;

关键词：

ENTERICA SEROVAR TYPHIMURIUM; COMPLETE GENOME SEQUENCE; ESCHERICHIA-COLI K-12; IRON TRANSPORT; OMPR MUTANTS; GENE; RIBOSWITCHES; BINDING; PORIN; REPERTOIRE;

D O I：

10.1371/journal.pgen.1000569

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

High-density, strand-specific cDNA sequencing (ssRNA-seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping sequence data to the entire S. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously unannotated, and 3'- or 5'-untranslated regions (UTR). An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.

引用

页数：13

共 64 条

[1] Type III secretion chaperone FlgN regulates flagellar assembly via a negative feedback loop containing its chaperone substrates FlgK and FlgL [J].