- Gene duplications in the E. - coli , a detailed analysis of the extent of gene duplications in this microorganism is needed.. - Results: The genomes of the E. - coli enteroaggregative strain 042 and other pathogenic strains contain duplications of the gene that codes for the global regulator Hha. - To determine whether the presence of additional copies of the hha gene correlates with the presence of other genes, we performed a comparative genomic analysis between E. - The results showed that strains harboring additional copies of the hha gene also encode the yeeR irmA ( aec69 ) gene cluster, which, in turn, is also duplicated in strain 042 and several other strains.. - Duplications in the genomes of the enteroaggregative strain 042, the uropathogenic strain CFT073 and the enterohemorrhagic strain O145:H28 have been identified by a BLASTp protein similarity search. - This algorithm was also used to evaluate the distribution of the identified duplicates among the genomes of a set of 28 representative E. - Most duplicated genes have no known function. - Conclusions: Several duplicated genes are widely distributed among pathogenic E. - As mentioned above, enteroaggregative Escherichia coli (EAEC) strains are one of the groups of diarrheal E. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - coli strains, the chromosome of this strain encodes four paralogues of the hha gene:. - coli strains, encode a paralogue of the hha gene (the ydgT gene). - The presence of the novel chromosomal hha paralogues hha2 and hha3 has been associated with pathogenic E. - In this work, we first aimed to gain insight into the biological role of the novel hha2 and hha3 genes of strain 042. - For the gene duplication analysis between strains and for the identification of the presence/absence of putative duplicated encoded proteins/coding regions, we also employed BLASTp. - To identify those genes that are truly exclusive to the hha + set, we used a restrictive strategy of excluding the pangenome of the hha − set from the core genome of the hha + set. - showed that 72% of the strains expressing hha2/hha3 also express the yeeR or irmA (aec69) genes (P-value <. - We then analyzed the map positions of the hha2/hha3 genes and the flu yeeR irmA (aec69) aec70 aec71 gene cluster in the chromo- somes of seven E. - This study also showed that in most of the viru- lent E. - three copies of hns-like genes (hns, stpA and hns2) [27], two copies of yeeR and irmA (aec69), three copies of flu and four copies of the aec71 gene suggests that gene duplication may play a relevant role in this and perhaps other patho- genic E. - Gene duplications in the EAEC strain 042 genome. - Most of the duplicated genes are clustered in. - Schematic representation of the genetic cluster comprising the flu, yeeR, yeeS and yeeT genes in E.. - One of the copies of this region includes the hha2 gene. - Duplicated genes in regions 1 and 2 are repressed by the H-NS/Hha system. - We assessed whether the duplicated genes of the three regions of strain 042 show H-NS- or Hha-dependent regulation (Table 1). - 2 Map position of the hha (red bar), hha2 (orange bar), hha3 (green bar) and genes from the flu yeeR aec gene cluster (violet bar) in the chromosomes of E. - We used the DNA sequences of the selected 28 E. - coli genomes to perform a gene duplication ana- lysis (see the methods for details) and annotated the number of copies of each of the duplicated genes from strain 042 that were detected in each of the other. - 3 a Genes duplicated in the E. - coli strain 042. - The X axis corresponds to the linear map of the chromosome. - The different spots indicate the map positions of the different copies of the gene. - Numbers correspond to the different duplicated genes, which have been numbered by their order starting from the origin of the chromosomal map. - With respect to region 1, 10 out of the 14 duplicated genes in strain 042 were duplicated in most of the genomes analyzed. - With respect to region 2, the 15 duplicated genes are duplicated in either some or most of the genomes studied (Fig. - Six of the genes. - from that region (listed as 55 to 60), which appear as a single linkage group and belong to the same putative transcriptional unit, are present in several copies (4 to 6) in the genomes of most of the strains. - With regard to region 3, duplications of the eight genes identified in strain 042 are a specific feature of that strain. - Several of these genes are either absent or present in a single copy in most of the ge- nomes studied (Fig. - The rest of the genes are not present in the genome of the commensal strain.. - Gene duplications in the genomes of strains CFT073 (UPEC) and O145:H28 (EHEC). - A total of 154 duplicated genes could be identified in the genome of strain O145:H28. - The duplicated genes can also be grouped into six regions (Fig. - In this strain, several of the identified genes are present in more than two copies (Fig. - The genomic DNA se- quences of the 28 E. - coli strains were used to perform gene duplication analysis, and the number of copies of each of the duplicated genes from strains CFT073 and O145:H28 that were detected in each genome of the 28 E. - The duplicated genes from strain CF703 region 5 be- long to that group. - These genes are duplicated only in all the EHEC Table 1 Comparative expression of the duplicated genes from. - regions 1 to 3 of strain 042 in the hha null (deletion of the hha and hha2 alleles) and hns mutants. - 4 Distribution of the detected duplicated genes in other E. - Note that a significant number of the duplicated genes are absent in strain MG1655. - 5 Genes duplicated in the E. - Each group of spots connected by a horizontal dotted line corresponds to a single gene, which is shown to be duplicated in different positions of the chromosome. - See Additional file 1: Table S4 for the function of each of the duplicated genes. - coli strains was previously re- ported Nevertheless, detailed information about the extent of gene duplications in the genomes of the different types of pathogenic E. - 10 − 10 ) and found that most duplicates cluster together in specific regions of the 042 genome. - It is worth mentioning that, as a general rule, duplications result in the presence of copies of the duplicated gene in both strands of the E. - It is also remarkable that a significant number of the duplicated genes are or- ganized in putative transcriptional units (Fig. - coli strains belonging to different pathotypes provides relevant information that can contribute to our under- standing of the virulence mechanisms of this pathogen and better establish the relationships among the E. - Genes 55 to 60 from strain 042 region 2 are duplicated in all except three of the 26 pathogenic E. - Given that detailed information about the function of the products encoded by a large number of these genes is missing, assigning functions to them and to many other genes of unknown function is a critical issue for better understanding the ability of E. - In addition to identifying a set of duplicated genes that is widespread in the different E. - Examples are the duplicated genes in region 3. - 6 Genes duplicated in the E. - Each group of spots connected by a horizontal dotted line corresponds to a single gene, which is shown to be duplicated in different positions of the chromosome.. - of strain 042 or the duplicated genes in regions 5 and 4 from the UPEC strain CFT073 and the EHEC strain 0145:H28, respectively. - The study of the function of these genes can also contribute to a better understanding of the mechanisms underlying virulence in these pathotypes. - Some of the duplicated genes in region 5 from the UPEC strain CFT073 encode putative fimbrial pro- teins, which might play a role in UPEC pathogenesis.. - The correlation we observed between hha duplication and the presence of the duplicated yeeR irmA (aec69) gene cluster suggested that Hha (and H-NS) could modulate the expression of duplicated E. - The analysis of the comparative expression of duplicated genes in the wt 042 strain and its isogenic hha null and hns derivatives shows that under specific growth condi- tions (LB medium, 37 °C), H-NS/Hha proteins downreg- ulate the expression of a significant number of duplicated genes. - These data highlight a novel role for the H-NS/Hha proteins in silencing several of the genes that are duplicated in strain 042. - Hence, it can be hy- pothesized that to avoid fitness costs, duplications of genes targeted by global regulators may require the du- plication of the genes that encode them. - The duplicated genes that map in the region 1 of strain 042 are of phage origin and can hence be considered as HGT DNA. - It is remarkable that most of the duplicated genes in the EAEC strain 042 are also duplicated in UPEC strains. - A distinctive fea- ture of EHEC strains is that some of the duplicated genes are present in more than two copies.. - coli infections, such as those caused by ETEC, the effectiveness of the existing vaccines must be. - If any of the gene products encoded by the identified duplicated genes are antigenic, they could be candidates for developing novel improved E. - Duplications of the hha gene can be correlated with the presence of genes belonging to the flu yeeR aec gene cluster, which is also duplicated in several pathogenic E.. - The analysis of gene duplications in the E.. - coli strains, irrespective of the pathotype. - and (iii) some duplicated genes are strain specific. - Locus tag and gene function of each of the duplicated genes in regions 1, 2 and 3 of strain 042. - Locus tag and gene function of each of the duplicated genes in regions and 6 of strain CFT073. - Locus tag and gene function of each of the duplicated genes in regions and 6 of strain O145:H8. - The locus tags of the different copies are shown. - Five-set Venn diagram of the exclusive core-genome of the hha 2/3 + set ( E. - Genes duplicated in the E. - Distribution of the strain CFT073 duplicated genes in other E. - Distribution of strain O145:H28 duplicated genes in other E. - (DOC 2532 kb) Additional file 2: DNA sequences of the genes comprising the three shared families identified in the exclusive core genome of the hha2/. - Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study.. - Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.. - Autoactivation of the AggR regulator of enteroaggregative Escherichia coli in vitro and in vivo. - The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins. - Molecular evolution of the H-NS protein: interaction with Hha-like proteins is restricted to. - Antigen 43, the major phase-variable protein of the Escherichia coli outer membrane, can exist as a family of proteins encoded by multiple alleles
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