Nucleotide sequence of the<i>hemX</i>gene, the third member of the Uro operon of<i>Escherichia coli</i>K12

Săsárman, A; Echelard, Yann; Letowski, Jaroslav; Tardif, Danielle; Drolet, Marc

doi:10.1093/nar/16.24.11835

Cited by 7 publications

(3 citation statements)

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“…While this result is expected, given that the authors used TMHMM, a predictor of α-helices, to select potential TIMPs (see Green fluorescent protein (GFP) expression studies) before analysis, we note that the other more global study by Dr H. Mori and colleagues using GFP to determine protein subcellular localization ( http://ecoli.naist.jp/GFP/gfp_top.jsp ) also ranked highly in terms of ‘Agreement’ ( A =0.84), despite the fact that no bioinformatic prefiltering was seemingly used. Of the 471 ‘Membrane’ proteins (without specified status as TIMPs or TOMPs) analyzed by GFP in this study, we found that 395 of them (83%) are likely TIMPs based on the ‘Majority Consensus’, another 46 (10%) are predicted as cytoplasmic (although 10 contain one or two putative α-helices), one is predicted as OM and other as EC while the remaining 28 (5%) had no prediction, although Phobius predicted α-helices in 14, including the poorly characterized proteins HemY and HemX suggested to be a uroporphyrinogen III methylase ( Sasarman et al , 1988 ). This overlap of common hits between the GFP studies, bioinformatic predictors and knowledge databases provides strong evidence for both novel and corroborative TIMP annotations (see Table S1 for a detailed list), suggesting that an integrative approach can achieve high precision for detecting TIMPs (i.e.…”

Section: Deciphering the E Coli Cell-envelope Promentioning

confidence: 95%

Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

2009

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The bacterial cell-envelope consists of a complex arrangement of lipids, proteins and carbohydrates that serves as the interface between a microorganism and its environment or, with pathogens, a human host. Escherichia coli has long been investigated as a leading model system to elucidate the fundamental mechanisms underlying microbial cell-envelope biology. This includes extensive descriptions of the molecular identities, biochemical activities and evolutionary trajectories of integral transmembrane proteins, many of which play critical roles in infectious disease and antibiotic resistance. Strikingly, however, only half of the c. 1200 putative cell-envelope-related proteins of E. coli currently have experimentally attributed functions, indicating an opportunity for discovery. In this review, we summarize the state of the art of computational and proteomic approaches for determining the components of the E. coli cell-envelope proteome, as well as exploring the physical and functional interactions that underlie its biogenesis and functionality. We also provide a comprehensive comparative benchmarking analysis on the performance of different bioinformatic and proteomic methods commonly used to determine the subcellular localization of bacterial proteins.

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Section: Deciphering the E Coli Cell-envelope Promentioning

confidence: 95%

Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

2009

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“…Urogen III methylase may be coded by hemX (47). Following cyaA, two potential ORF's overlap in opposite directions.…”

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confidence: 99%

Analysis of the Escherichia coli Genome: DNA Sequence of the Region from 84.5 to 86.5 Minutes

Daniels

Plunkett

Burland

et al. 1992

Science

254

159

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The DNA sequence of 91.4 kilobases of the Escherichia coli K-12 genome, spanning the region between rrnC at 84.5 minutes and rrnA at 86.5 minutes on the genetic map (85 to 87 percent on the physical map), is described. Analysis of this sequence identified 82 potential coding regions (open reading frames) covering 84 percent of the sequenced interval. The arrangement of these open reading frames, together with the consensus promoter sequences and terminator-like sequences found by computer searches, made it possible to assign them to proposed transcriptional units. More than half the open reading frames correlated with known genes or functions suggested by similarity to other sequences. Those remaining encode still unidentified proteins. The sequenced region also contains several RNA genes and two types of repeated sequence elements were found. Intergenic regions include three "gray holes," 0.6 to 0.8 kilobases, with no recognizable functions.

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“…This region has previously been found in other groups of bacteria (Sasarman et al . ; McNicholas et al . ).…”

Section: Resultsmentioning

confidence: 99%

Use of essential gene, encoding prophobilinogen deaminase from extreme psychrophilic Colwellia sp. C1, to generate temperature-sensitive strain of Francisella novicida

Pankowski

2016

Lett Appl Microbiol

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The issue of biosafety is often raised when it comes to work with pathogenic organisms. The main concern is caused by the risk of researchers being exposed to infectious doses of dangerous microbes. This paper analyses essential genes identified in partial genomic sequence of the psychrophilic bacterium Collwelia sp. C1. These sequences can be used as a mean of generating temperature-sensitive strains of pathogenic bacteria. Such strains are incapable of surviving at the temperature of human body. This means they could be applied as vaccines or for safer work with dangerous organisms.

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Nucleotide sequence of thehemXgene, the third member of the Uro operon ofEscherichia coliK12

Abstract: In a recent paper (1), we described the cloning and sequencing of the hemp gene, the second member of the Uro operon. Sequencing the DNA past the stop codon of the hemD gene revealed the presence of another ORF of at least

Cited by 7 publications

References 1 publication

Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

Analysis of the Escherichia coli Genome: DNA Sequence of the Region from 84.5 to 86.5 Minutes

Use of essential gene, encoding prophobilinogen deaminase from extreme psychrophilic Colwellia sp. C1, to generate temperature-sensitive strain of Francisella novicida

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