1887

Abstract

identification criteria were defined to predict if genes encoding histidine protein kinases (HPKs) and response regulators (RRs) could be part of peptide-based quorum sensing (QS) two-component regulatory systems (QS-TCSs) in Firmicutes. These criteria were used to screen HPKs and RRs annotated on the completed genome sequences of species, and several (putative) QS-TCSs were identified in this way. The five peptide-based QS-TCSs that were predicted on the WCFS1 genome were further analysed to test their (QS) functionality. Four of these systems contained an upstream gene encoding a putative autoinducing peptide (AIP), of which two were preceded by a double-glycine-type leader peptide. One of these was identical to the regulatory system of C11 and was shown to regulate plantaricin production in WCFS1. The third TCS was designated for -like odule, where the gene was shown to encode a cyclic thiolactone peptide. The fourth TCS was paralogous to the system and contained a putative AIP-encoding gene but lacked the gene. Finally, a genetically separated orphan HPK and RR that showed clear peptide-based QS characteristics could form a fifth peptide-based QS-TCS. The predicted presence of multiple (peptide-based) QS-TCSs in some lactobacilli and in particular in might be a reflection of the ability of these species to persist in a diverse range of ecological niches.

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2007-12-01
2019-12-08
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Bootstrapped neighbour-joining trees showing the phylogenetic relationships of HPK (left) and RR (right) homologues of (putative) QS-TCSs from lactobacilli. Closely related (QS-)TCS from other genera belonging to the Firmicutes ( , , ) were included for improved phylogenetic assignment of some QS-TCSs. Homologues were collected using iterative BLASTP searches (PSI-BLAST) and aligned using CLUSTAL X. Bootstrap values are shown at the nodes. [ PDF] (39 kb) Gene context of the various putative QS-TCS in lactobacilli, as obtained from the ERGOdatabase. The QS system of has been included for comparison. Arrows indicate genes, and gene-context colour-coding is shown in the inset. [ PDF] (59 kb) Architecture and gene context of two-component histidine protein kinases and response regulators of WCFS1 that contain quorum-sensing-associated motifs and domains according to SMART descriptions ( http://smart.embl-heidelberg.de/smart) or PFAM families ( http://www.sanger.ac.uk/software/pfam). ( A) HPK10-subfamily type HPKs and LytTR-family type RRs. ( B) HPK7-subfamily type HPKs and LuxR-family type RRs. HATPase, histidine-kinase-like ATPase-domain; REC, CheY-homologous receiver domain; PFAM LytTR, HTH-LytTr DNA-binding domain; HTH-LuxR, helix-turn-helix Lux regulon; HTH-AraC, helix-turn-helix arabinose operon control protein. Rectangles in HPKs indicate predicted or experimentally determined transmembrane segments (see also Table 1 of the main paper). Below each HPK and RR the genomic organization of the HPK and RR and their flanking regions are shown. The description of relevant genes can be found in the text. Hairpins indicate potential transcription termination sites.

PDF

Bootstrapped neighbour-joining trees showing the phylogenetic relationships of HPK (left) and RR (right) homologues of (putative) QS-TCSs from lactobacilli. Closely related (QS-)TCS from other genera belonging to the Firmicutes ( , , ) were included for improved phylogenetic assignment of some QS-TCSs. Homologues were collected using iterative BLASTP searches (PSI-BLAST) and aligned using CLUSTAL X. Bootstrap values are shown at the nodes. [ PDF] (39 kb) Gene context of the various putative QS-TCS in lactobacilli, as obtained from the ERGOdatabase. The QS system of has been included for comparison. Arrows indicate genes, and gene-context colour-coding is shown in the inset. [ PDF] (59 kb) Architecture and gene context of two-component histidine protein kinases and response regulators of WCFS1 that contain quorum-sensing-associated motifs and domains according to SMART descriptions ( http://smart.embl-heidelberg.de/smart) or PFAM families ( http://www.sanger.ac.uk/software/pfam). ( A) HPK10-subfamily type HPKs and LytTR-family type RRs. ( B) HPK7-subfamily type HPKs and LuxR-family type RRs. HATPase, histidine-kinase-like ATPase-domain; REC, CheY-homologous receiver domain; PFAM LytTR, HTH-LytTr DNA-binding domain; HTH-LuxR, helix-turn-helix Lux regulon; HTH-AraC, helix-turn-helix arabinose operon control protein. Rectangles in HPKs indicate predicted or experimentally determined transmembrane segments (see also Table 1 of the main paper). Below each HPK and RR the genomic organization of the HPK and RR and their flanking regions are shown. The description of relevant genes can be found in the text. Hairpins indicate potential transcription termination sites.

PDF

Bootstrapped neighbour-joining trees showing the phylogenetic relationships of HPK (left) and RR (right) homologues of (putative) QS-TCSs from lactobacilli. Closely related (QS-)TCS from other genera belonging to the Firmicutes ( , , ) were included for improved phylogenetic assignment of some QS-TCSs. Homologues were collected using iterative BLASTP searches (PSI-BLAST) and aligned using CLUSTAL X. Bootstrap values are shown at the nodes. [ PDF] (39 kb) Gene context of the various putative QS-TCS in lactobacilli, as obtained from the ERGOdatabase. The QS system of has been included for comparison. Arrows indicate genes, and gene-context colour-coding is shown in the inset. [ PDF] (59 kb) Architecture and gene context of two-component histidine protein kinases and response regulators of WCFS1 that contain quorum-sensing-associated motifs and domains according to SMART descriptions ( http://smart.embl-heidelberg.de/smart) or PFAM families ( http://www.sanger.ac.uk/software/pfam). ( A) HPK10-subfamily type HPKs and LytTR-family type RRs. ( B) HPK7-subfamily type HPKs and LuxR-family type RRs. HATPase, histidine-kinase-like ATPase-domain; REC, CheY-homologous receiver domain; PFAM LytTR, HTH-LytTr DNA-binding domain; HTH-LuxR, helix-turn-helix Lux regulon; HTH-AraC, helix-turn-helix arabinose operon control protein. Rectangles in HPKs indicate predicted or experimentally determined transmembrane segments (see also Table 1 of the main paper). Below each HPK and RR the genomic organization of the HPK and RR and their flanking regions are shown. The description of relevant genes can be found in the text. Hairpins indicate potential transcription termination sites.

PDF

Bootstrapped neighbour-joining trees showing the phylogenetic relationships of HPK (left) and RR (right) homologues of (putative) QS-TCSs from lactobacilli. Closely related (QS-)TCS from other genera belonging to the Firmicutes ( , , ) were included for improved phylogenetic assignment of some QS-TCSs. Homologues were collected using iterative BLASTP searches (PSI-BLAST) and aligned using CLUSTAL X. Bootstrap values are shown at the nodes. [ PDF] (39 kb) Gene context of the various putative QS-TCS in lactobacilli, as obtained from the ERGOdatabase. The QS system of has been included for comparison. Arrows indicate genes, and gene-context colour-coding is shown in the inset. [ PDF] (59 kb) Architecture and gene context of two-component histidine protein kinases and response regulators of WCFS1 that contain quorum-sensing-associated motifs and domains according to SMART descriptions ( http://smart.embl-heidelberg.de/smart) or PFAM families ( http://www.sanger.ac.uk/software/pfam). ( A) HPK10-subfamily type HPKs and LytTR-family type RRs. ( B) HPK7-subfamily type HPKs and LuxR-family type RRs. HATPase, histidine-kinase-like ATPase-domain; REC, CheY-homologous receiver domain; PFAM LytTR, HTH-LytTr DNA-binding domain; HTH-LuxR, helix-turn-helix Lux regulon; HTH-AraC, helix-turn-helix arabinose operon control protein. Rectangles in HPKs indicate predicted or experimentally determined transmembrane segments (see also Table 1 of the main paper). Below each HPK and RR the genomic organization of the HPK and RR and their flanking regions are shown. The description of relevant genes can be found in the text. Hairpins indicate potential transcription termination sites.

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