Abstract
BackgroundAs one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. We carried out a systematic reannotation by combining automated annotation tools with manual efforts to provide a comprehensive understanding of virulence for the CFT073 genome.ResultsThe reannotation excluded 608 coding sequences from the RefSeq annotation. Meanwhile, a total of 299 coding sequences were newly added, about one third of them are found in genomic island (GI) regions while more than one fifth of them are located in virulence related regions pathogenicity islands (PAIs). Furthermore, there are totally 341 genes were relocated with their translational initiation sites (TISs), which resulted in a high quality of gene start annotation. In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs) has been updated from 6 in RefSeq to 46 in the reannotation. Based on the adjustment in the reannotation, subsequent analysis were conducted by both general and case studies on new virulence factors or new virulence-associated genes that are crucial during the urinary tract infections (UTIs) process, including invasion, colonization, nutrition uptaking and population density control. Furthermore, miscellaneous RNAs collected in the reannotation are believed to contribute to the virulence of strain CFT073. The reannotation including the nucleotide data, the original RefSeq annotation, and all reannotated results is freely available via http://mech.ctb.pku.edu.cn/CFT073/.ConclusionAs a result, the reannotation presents a more comprehensive picture of mechanisms of uropathogenicity of UPEC strain CFT073. The new genes change the view of its uropathogenicity in many respects, particularly by new genes in GI regions and new virulence-associated factors. The reannotation thus functions as an important source by providing new information about genomic structure and organization, and gene function. Moreover, we expect that the detailed analysis will facilitate the studies for exploration of novel virulence mechanisms and help guide experimental design.
Highlights
As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research
All of such Open reading frame (ORF) were filtered by running blastp against Swiss-Prot [15] and rps-blast against the conserved domain database (CDD) [16]
Using a combination of approaches and in-depth analysis, the reannotation of the Escherichia coli CFT073 genome presents a substantial update across the complete genome
Summary
As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. The current RefSeq annotation of this pathogen is outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. Uropathogenic Escherichia coli (UPEC) strains lead to 7090% of the estimated annual 150 million communityacquired urinary tract infections (UTIs) [1]. The difference in the CFT073 genome is mostly caused by five unique cryptic inserted prophage genomes that contain a large portion of virulence or virulence-associated genes, referred to as pathogenicity islands (PAIs) [3]. Regarding virulence and virulence-associated genes, the annotation includes 12 types of fimbriae, 7 autotransporters, and toxin operons such as hlyCABD and upxBDA [2]. The annotation presents an overview of the complexity of the pathogen's lifestyle, and has served as a guide for experimental design
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