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Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.

Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I - Genome Biol Evol (2014)

Bottom Line: This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes.No evidence of coevolution between kinases and substrates at the sequence level was found.Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.

View Article: PubMed Central - PubMed

Affiliation: INRA-AgroParisTech UMR 1319, Micalis-CBAI, Thiverval-Grignon, France.

ABSTRACT
It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly and maintain relaxed substrate specificity to quickly adopt new substrates when evolutionary pressure in that direction arises. Here, we report a phylogenomic and biochemical analysis of BY-kinases, and their relationship to substrates aimed to validate this hypothesis. Our results suggest that BY-kinases are ubiquitously distributed in bacterial phyla and underwent a complex evolutionary history, affected considerably by gene duplications and horizontal gene transfer events. This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes. On the basis of similarity networks, we could classify BY kinases into three main groups with 14 subgroups. Extensive sequence conservation was observed only around the three canonical Walker motifs, whereas unique signatures proposed the functional speciation and diversification within some subgroups. The relationship between BY-kinases and their substrates was analyzed using a ubiquitous substrate (Ugd) and some Firmicute-specific substrates (YvyG and YjoA) from Bacillus subtilis. No evidence of coevolution between kinases and substrates at the sequence level was found. Seven BY-kinases, including well-characterized and previously uncharacterized ones, were used for experimental studies. Most of the tested kinases were able to phosphorylate substrates from B. subtilis (Ugd, YvyG, and YjoA), despite originating from very distant bacteria. Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.

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Motif and amino acid consensus sites in BY-kinases and related subgroups. (A) Schematic view of amino acid conserved sites in all 796 BY-kinases. Black and gray ticks represent the strong and relatively strong conserved sites in BY-kinases, respectively (see Materials and Methods). “GK” in Walker A motif, “DXDXR” in Walker A′ motif, and “DXXPX” in Walker B motif are indicated by pink, orange, and blue ticks, respectively. The three motifs Walker A, A′, and B are marked with green underlines, and the corresponding sequence logos are shown. (B) Schematic maps of the conserved sites of BY-kinase subgroups (A1 to C9). Strong and relatively strong conserved sites over the protein subgroups are indicated by black and gray ticks. Except for Walker A, A′, and B motifs, the signature motifs in each subgroup are indicated within a red box. The region marked with green underlines contained the conserved Y-R and Y-H pairs, and their weblogs are indicated in (D). (C) Sequence logos of signature motifs (defined in B) are shown. Motifs located in the same region of the BY-kinase are displayed in the same box. (D) Sequence logos of motifs are related to the Y-R and Y-H interactions in subgroup B1 (also underlined in green lines in B).
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evu056-F5: Motif and amino acid consensus sites in BY-kinases and related subgroups. (A) Schematic view of amino acid conserved sites in all 796 BY-kinases. Black and gray ticks represent the strong and relatively strong conserved sites in BY-kinases, respectively (see Materials and Methods). “GK” in Walker A motif, “DXDXR” in Walker A′ motif, and “DXXPX” in Walker B motif are indicated by pink, orange, and blue ticks, respectively. The three motifs Walker A, A′, and B are marked with green underlines, and the corresponding sequence logos are shown. (B) Schematic maps of the conserved sites of BY-kinase subgroups (A1 to C9). Strong and relatively strong conserved sites over the protein subgroups are indicated by black and gray ticks. Except for Walker A, A′, and B motifs, the signature motifs in each subgroup are indicated within a red box. The region marked with green underlines contained the conserved Y-R and Y-H pairs, and their weblogs are indicated in (D). (C) Sequence logos of signature motifs (defined in B) are shown. Motifs located in the same region of the BY-kinase are displayed in the same box. (D) Sequence logos of motifs are related to the Y-R and Y-H interactions in subgroup B1 (also underlined in green lines in B).

Mentions: To examine the conservation of residues in BY-kinase sequences, the consensus sites based on the multiple alignments with “50-10” rule (Carretero-Paulet et al. 2010) were determined. As shown in figure 5A, only seven strong conserved sites (100% identical at the position) are found in the entire data set of CD domains from 796 BY-kinases, and they are all situated in the three Walker motifs. These sites include “GK” in Walker A motif, “DXDXR” in Walker A′ motif, and “DXXPX” in Walker B motif, which was not surprising because those three motifs are included in the isBYK algorithm and also have been experimentally shown to participate directly in ATP hydrolysis and ATP-Mg interaction (Soulat et al. 2007; Lee et al. 2008; Olivares-Illana et al. 2008). This result is consistent with amino acid substitution analysis of BY-kinases and supports the notion that these enzymes evolve fast and only conserve at essential sites to maintain core enzymatic activity. In addition, we found that several regions (marked with gray bars in fig. 5A) with a relatively high degree of conservation. These include regions between the Walker A and Walker A′, regions around the Walker B motif, and the Y cluster.Fig. 5.—


Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.

Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I - Genome Biol Evol (2014)

Motif and amino acid consensus sites in BY-kinases and related subgroups. (A) Schematic view of amino acid conserved sites in all 796 BY-kinases. Black and gray ticks represent the strong and relatively strong conserved sites in BY-kinases, respectively (see Materials and Methods). “GK” in Walker A motif, “DXDXR” in Walker A′ motif, and “DXXPX” in Walker B motif are indicated by pink, orange, and blue ticks, respectively. The three motifs Walker A, A′, and B are marked with green underlines, and the corresponding sequence logos are shown. (B) Schematic maps of the conserved sites of BY-kinase subgroups (A1 to C9). Strong and relatively strong conserved sites over the protein subgroups are indicated by black and gray ticks. Except for Walker A, A′, and B motifs, the signature motifs in each subgroup are indicated within a red box. The region marked with green underlines contained the conserved Y-R and Y-H pairs, and their weblogs are indicated in (D). (C) Sequence logos of signature motifs (defined in B) are shown. Motifs located in the same region of the BY-kinase are displayed in the same box. (D) Sequence logos of motifs are related to the Y-R and Y-H interactions in subgroup B1 (also underlined in green lines in B).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4007543&req=5

evu056-F5: Motif and amino acid consensus sites in BY-kinases and related subgroups. (A) Schematic view of amino acid conserved sites in all 796 BY-kinases. Black and gray ticks represent the strong and relatively strong conserved sites in BY-kinases, respectively (see Materials and Methods). “GK” in Walker A motif, “DXDXR” in Walker A′ motif, and “DXXPX” in Walker B motif are indicated by pink, orange, and blue ticks, respectively. The three motifs Walker A, A′, and B are marked with green underlines, and the corresponding sequence logos are shown. (B) Schematic maps of the conserved sites of BY-kinase subgroups (A1 to C9). Strong and relatively strong conserved sites over the protein subgroups are indicated by black and gray ticks. Except for Walker A, A′, and B motifs, the signature motifs in each subgroup are indicated within a red box. The region marked with green underlines contained the conserved Y-R and Y-H pairs, and their weblogs are indicated in (D). (C) Sequence logos of signature motifs (defined in B) are shown. Motifs located in the same region of the BY-kinase are displayed in the same box. (D) Sequence logos of motifs are related to the Y-R and Y-H interactions in subgroup B1 (also underlined in green lines in B).
Mentions: To examine the conservation of residues in BY-kinase sequences, the consensus sites based on the multiple alignments with “50-10” rule (Carretero-Paulet et al. 2010) were determined. As shown in figure 5A, only seven strong conserved sites (100% identical at the position) are found in the entire data set of CD domains from 796 BY-kinases, and they are all situated in the three Walker motifs. These sites include “GK” in Walker A motif, “DXDXR” in Walker A′ motif, and “DXXPX” in Walker B motif, which was not surprising because those three motifs are included in the isBYK algorithm and also have been experimentally shown to participate directly in ATP hydrolysis and ATP-Mg interaction (Soulat et al. 2007; Lee et al. 2008; Olivares-Illana et al. 2008). This result is consistent with amino acid substitution analysis of BY-kinases and supports the notion that these enzymes evolve fast and only conserve at essential sites to maintain core enzymatic activity. In addition, we found that several regions (marked with gray bars in fig. 5A) with a relatively high degree of conservation. These include regions between the Walker A and Walker A′, regions around the Walker B motif, and the Y cluster.Fig. 5.—

Bottom Line: This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes.No evidence of coevolution between kinases and substrates at the sequence level was found.Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.

View Article: PubMed Central - PubMed

Affiliation: INRA-AgroParisTech UMR 1319, Micalis-CBAI, Thiverval-Grignon, France.

ABSTRACT
It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly and maintain relaxed substrate specificity to quickly adopt new substrates when evolutionary pressure in that direction arises. Here, we report a phylogenomic and biochemical analysis of BY-kinases, and their relationship to substrates aimed to validate this hypothesis. Our results suggest that BY-kinases are ubiquitously distributed in bacterial phyla and underwent a complex evolutionary history, affected considerably by gene duplications and horizontal gene transfer events. This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes. On the basis of similarity networks, we could classify BY kinases into three main groups with 14 subgroups. Extensive sequence conservation was observed only around the three canonical Walker motifs, whereas unique signatures proposed the functional speciation and diversification within some subgroups. The relationship between BY-kinases and their substrates was analyzed using a ubiquitous substrate (Ugd) and some Firmicute-specific substrates (YvyG and YjoA) from Bacillus subtilis. No evidence of coevolution between kinases and substrates at the sequence level was found. Seven BY-kinases, including well-characterized and previously uncharacterized ones, were used for experimental studies. Most of the tested kinases were able to phosphorylate substrates from B. subtilis (Ugd, YvyG, and YjoA), despite originating from very distant bacteria. Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.

Show MeSH