1887

Abstract

Members of the group are ubiquitously present in the environment and can adapt to a wide range of environmental fluctuations. In bacteria, these adaptive responses are generally mediated by two-component signal transduction systems (TCSs), which consist of a histidine kinase (HK) and its cognate response regulator (RR). With the use of techniques, a complete set of HKs and RRs was recovered from eight completely sequenced group genomes. By applying a bidirectional best-hits method combined with gene neighbourhood analysis, a footprint of these proteins was made. Around 40 HK-RR gene pairs were detected in each member of the group. In addition, each member contained many HK and RR genes not encoded in pairs (‘orphans’). Classification of HKs and RRs based on their enzymic domains together with the analysis of two neighbour-joining trees of these domains revealed putative interaction partners for most of the ‘orphans’. Putative biological functions, including involvement in virulence and host–microbe interactions, were predicted for the group HKs and RRs by comparing them with those of and other micro-organisms. Remarkably, appeared to lack specific HKs and RRs and was found to contain many truncated, putatively non-functional, HK and RR genes. It is hypothesized that specialization of as a pathogen could have reduced the range of environmental stimuli to which it is exposed. This may have rendered some of its TCSs obsolete, ultimately resulting in the deletion of some HK and RR genes.

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2006-10-01
2019-10-14
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Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF](13 kb) Domain organization of HKs and RRs. [PDF](18 kb) From reference codes to NCBI gi-codes. [PDF](17 kb) Nature of truncated or deleted B. anthracis TCSs in six other strains and G9241. [PDF](19 kb) HK tree. [PDF](6 Mb) This tree was constructed with all group and HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited. RR tree. [PDF](5.6 Mb) This tree was constructed with all group and RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

PDF

Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF](13 kb) Domain organization of HKs and RRs. [PDF](18 kb) From reference codes to NCBI gi-codes. [PDF](17 kb) Nature of truncated or deleted B. anthracis TCSs in six other strains and G9241. [PDF](19 kb) HK tree. [PDF](6 Mb) This tree was constructed with all group and HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited. RR tree. [PDF](5.6 Mb) This tree was constructed with all group and RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

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Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF](13 kb) Domain organization of HKs and RRs. [PDF](18 kb) From reference codes to NCBI gi-codes. [PDF](17 kb) Nature of truncated or deleted B. anthracis TCSs in six other strains and G9241. [PDF](19 kb) HK tree. [PDF](6 Mb) This tree was constructed with all group and HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited. RR tree. [PDF](5.6 Mb) This tree was constructed with all group and RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

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Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF](13 kb) Domain organization of HKs and RRs. [PDF](18 kb) From reference codes to NCBI gi-codes. [PDF](17 kb) Nature of truncated or deleted B. anthracis TCSs in six other strains and G9241. [PDF](19 kb) HK tree. [PDF](6 Mb) This tree was constructed with all group and HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited. RR tree. [PDF](5.6 Mb) This tree was constructed with all group and RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

PDF

Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF](13 kb) Domain organization of HKs and RRs. [PDF](18 kb) From reference codes to NCBI gi-codes. [PDF](17 kb) Nature of truncated or deleted B. anthracis TCSs in six other strains and G9241. [PDF](19 kb) HK tree. [PDF](6 Mb) This tree was constructed with all group and HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited. RR tree. [PDF](5.6 Mb) This tree was constructed with all group and RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

PDF

Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF](13 kb) Domain organization of HKs and RRs. [PDF](18 kb) From reference codes to NCBI gi-codes. [PDF](17 kb) Nature of truncated or deleted B. anthracis TCSs in six other strains and G9241. [PDF](19 kb) HK tree. [PDF](6 Mb) This tree was constructed with all group and HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited. RR tree. [PDF](5.6 Mb) This tree was constructed with all group and RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

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