A novel gene,ardD, determines antirestriction activity of the non-conjugative transposon Tn5053and is located antisense within thetniAgene

Balabanov, V. P.; Kotova, V. Yu.; Kholodii, Gennady; Mindlin, S. Z.; Zavilgelsky, G. B.

doi:10.1111/1574-6968.12005

Cited by 19 publications

(18 citation statements)

References 9 publications

(18 reference statements)

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“…On the contrary, bacterial genome annotation programs systematically remove overlapping genes [ 73 , 79 – 81 ], thereby efficiently preventing their discovery. Perhaps it is not surprising that with the exception of E. coli ’s three overlapping genes, only a few further examples have been discovered rather accidentally in Streptomyces [ 82 ], Pseudomonas [ 83 , 84 ] or Xanthomonas [ 85 ]. Functional analyses of overlapping genes in bacteria are even rarer.…”

Section: Discussionmentioning

confidence: 99%

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

et al. 2015

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BackgroundGene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented.ResultsRNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the −2 reading frame of citC in enterohemorrhagic E. coli. This gene is designated novel overlapping gene, nog1. The promoter region fused to gfp exhibits specific activities and 5’ rapid amplification of cDNA ends indicated the transcriptional start 40-bp upstream of the start codon. nog1 was strand-specifically arrested in translation by a nonsense mutation silent in citC. This Nog1-mutant showed a phenotype in competitive growth against wild type in the presence of MgCl2. Small differences in metabolite concentrations were also found. Bioinformatic analyses propose Nog1 to be inner membrane-bound and to possess at least one membrane-spanning domain. A phylogenetic analysis suggests that the orphan gene nog1 arose by overprinting after Escherichia/Shigella separated from the other γ-proteobacteria.ConclusionsSince nog1 is of recent origin, non-essential, short, weakly expressed and only marginally involved in E. coli’s central metabolism, we propose that this gene is in an initial stage of evolution. While we present specific experimental evidence for the existence of a fourth overlapping gene in enterohemorrhagic E. coli, we believe that this may be an initial finding only and overlapping genes in bacteria may be more common than is currently assumed by microbiologists.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0558-z) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

et al. 2015

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“…The merA gene encodes for a reductase that reduces Hg 2+ to Hg 0 [27]. The tniA transposase gene is usually present in integrons and composite transposons conferring antibiotic resistance [29]. The S. enterica Indiana strain MHYL genome carries genes conferring resistance to β-lactams, amide alcohols, tetracyclines, aminoglycosides, and sulfonamides.…”

Section: Discussionmentioning

confidence: 99%

Genomic Sequence Analysis of the Multidrug-Resistance Region of Avian Salmonella enterica serovar Indiana Strain MHYL

Wen

et al. 2019

Microorganisms

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A series of human and animal diseases that are caused by Salmonella infections pose a serious threat to human health and huge economic losses to the livestock industry. We found antibiotic resistance (AR) genes in the genome of 133 strains of S. Indiana from a poultry production site in Shandong Province, China. Salmonella enterica subsp. enterica serovar Indiana strain MHYL had multidrug-resistance (MDR) genes on its genome. Southern blot analysis was used to locate genes on the genomic DNA. High-throughput sequencing technology was used to determine the gene sequence of the MHYL genome. Areas containing MDR genes were mapped based on the results of gene annotation. The AR genes blaTEM, strA, tetA, and aac(6′)-Ib-cr were found on the MHYL genome. The resistance genes were located in two separate MDR regions, RR1 and RR2, containing type I integrons, and Tn7 transposons and multiple IS26 complex transposons with transposable functions. Portions of the MDR regions were determined to be highly homologous to the structure of plasmid pAKU_1 in S. enterica serovar Paratyphi A (accession number: AM412236), SGI11 in S. enterica serovar Typhimurium (accession number: KM023773), and plasmid pS414 in S. Indiana (accession No.: KC237285).

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“…Nevertheless, statistical analysis of bacterial genomes has shown that ORFs overlapping annotated genes in alternative reading frames are longer than expected, leading to the hypothesis of a potential selection pressure due to overlapping protein-coding genes (Mir et al, 2012). Besides this, functionality of at least a few non-trivially overlapping genes has been demonstrated (e.g., Behrens et al, 2002;Balabanov et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC)

et al. 2020

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Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA. An active σ 70 promoter, transcription start site (TSS), Shine-Dalgarno motif and rho-independent terminator were experimentally validated, providing evidence that this open reading frame has all the structural features of a functional gene. Furthermore, ribosomal profiling revealed translation of the mRNA, the protein was detected in Western blots and a pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop (pH-regulated overlapping protein-coding gene), thus adding another example to the growing list of overlapping, protein coding genes in bacteria.

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A novel gene,ardD, determines antirestriction activity of the non-conjugative transposon Tn5053and is located antisense within thetniAgene

Cited by 19 publications

References 9 publications

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

Genomic Sequence Analysis of the Multidrug-Resistance Region of Avian Salmonella enterica serovar Indiana Strain MHYL

A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC)

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