Genome reannotation of Escherichia coli CFT073 with new insights into virulence

Abstract

Background: 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. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence.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.

Results: The 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/.

Conclusion: As 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.

Figure 1

Differences between RefSeq annotation and the reannotation in cdiAB region. In the reannotation, three pseudogenes (c0342, c0343 and c0344) are merged into two genes, and are found to be homologues of contact-dependent growth inhibitor encoding genes cdiAB.

Figure 2

Conservative structure of mch operon and mcm operon in different E. coli strains. The Fur boxes are marked by the orange lines; the content in brackets under gene name indicates the ID of this novel gene. The line in the bottom shows the partial structure of PAI-CFT073-serX, the numbers on the genes note the positions in the genome.

Figure 3

Structural domains of c0139's product in the reannotation and autotransporter virulence factor antigen 43. The domain in blue has the ability to form a β-barrel, also termed autotransporter domain, and is a key component in self-exportation; the domain in green is the passenger domain, which varies widely with different ATs; the segment in red is signal peptide, which guides the whole protein during the translocation; and the dashed line indicates the cleavage site in which protease cuts AT and releases the passenger segment.