Bacterial proteins belonging to the YczE family are predicted to be membrane proteins of yet unknown function. In many bacterial species, the yczE gene coding for the YczE protein is divergently transcribed with respect to an adjacent transcriptional regulator of the MocR family. According to in-silico predictions, proteins named YczR are supposed to regulate the expression of yczE genes. These regulators linked to the yczE genes are predicted to constitute a subfamily within the MocR family. To put forward hypotheses amenable to experimental testing about the possible function of the YczE proteins, a phylogenetic profile strategy was applied. This strategy consists in searching for those genes that, within a set of genomes, co-occur exclusively with a certain gene of interest. Co-occurrence can be suggestive of a functional link. A set of 30 Mycobacterium complete proteomes were collected. Of these, only sixteen contained YczE proteins. In all cases, each yczE gene was divergently transcribed with respect to a yczR gene. Two orthology clustering procedure were applied to find proteins co-occurring exclusively with the YczE proteins. Results suggests that YczE may be involved in the membrane translocation and metabolism of sulfur-containing compounds.

A comprehensive computational analysis of Mycobacterium genomes pinpoints the genes co-occurring with ycze, a membrane protein coding gene under the putative control of a mocr, and predicts its function / Milano, Teresa; Angelaccio, Sebastiana; Tramonti, Angela; DI SALVO, Martino Luigi; Nogues, Isabel; Contestabile, Roberto; Pascarella, Stefano. - In: INTERDISCIPLINARY SCIENCES: COMPUTATIONAL LIFE SCIENCES. - ISSN 1913-2751. - ELETTRONICO. - (2018), pp. 111-125. [10.1007/s12539-017-0266-z]

A comprehensive computational analysis of Mycobacterium genomes pinpoints the genes co-occurring with ycze, a membrane protein coding gene under the putative control of a mocr, and predicts its function

Teresa Milano
Methodology
;
Sebastiana Angelaccio
Writing – Review & Editing
;
Angela Tramonti
Writing – Original Draft Preparation
;
Martino Luigi Di Salvo
Membro del Collaboration Group
;
Roberto Contestabile
Membro del Collaboration Group
;
Stefano Pascarella
Supervision
2018

Abstract

Bacterial proteins belonging to the YczE family are predicted to be membrane proteins of yet unknown function. In many bacterial species, the yczE gene coding for the YczE protein is divergently transcribed with respect to an adjacent transcriptional regulator of the MocR family. According to in-silico predictions, proteins named YczR are supposed to regulate the expression of yczE genes. These regulators linked to the yczE genes are predicted to constitute a subfamily within the MocR family. To put forward hypotheses amenable to experimental testing about the possible function of the YczE proteins, a phylogenetic profile strategy was applied. This strategy consists in searching for those genes that, within a set of genomes, co-occur exclusively with a certain gene of interest. Co-occurrence can be suggestive of a functional link. A set of 30 Mycobacterium complete proteomes were collected. Of these, only sixteen contained YczE proteins. In all cases, each yczE gene was divergently transcribed with respect to a yczR gene. Two orthology clustering procedure were applied to find proteins co-occurring exclusively with the YczE proteins. Results suggests that YczE may be involved in the membrane translocation and metabolism of sulfur-containing compounds.
Mycobacterium; Ycz; sulfur compounds; ABC transporter; phylogenetic profile; MocR
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A comprehensive computational analysis of Mycobacterium genomes pinpoints the genes co-occurring with ycze, a membrane protein coding gene under the putative control of a mocr, and predicts its function / Milano, Teresa; Angelaccio, Sebastiana; Tramonti, Angela; DI SALVO, Martino Luigi; Nogues, Isabel; Contestabile, Roberto; Pascarella, Stefano. - In: INTERDISCIPLINARY SCIENCES: COMPUTATIONAL LIFE SCIENCES. - ISSN 1913-2751. - ELETTRONICO. - (2018), pp. 111-125. [10.1007/s12539-017-0266-z]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1016014
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