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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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Distribution and functional classification of genes surrounding the BY-kinases. For each of the five neighboring genes (located upstream and downstream of the BY-kinase), the functional COG category was determined. For each surrounded position, the bar indicates the frequency of each functional gene type (represented here by COG category) among the overall categories of the same position. Bar in the right part represents the COG distribution in all genomes harboring BY-kinases. COG categories are shown in different colors (see the COG color legend) and are associated with the corresponding capital letters: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division, and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification; protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, extracellular structures; Y, nuclear structure; Z, cytoskeleton.
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evu056-F6: Distribution and functional classification of genes surrounding the BY-kinases. For each of the five neighboring genes (located upstream and downstream of the BY-kinase), the functional COG category was determined. For each surrounded position, the bar indicates the frequency of each functional gene type (represented here by COG category) among the overall categories of the same position. Bar in the right part represents the COG distribution in all genomes harboring BY-kinases. COG categories are shown in different colors (see the COG color legend) and are associated with the corresponding capital letters: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division, and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification; protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, extracellular structures; Y, nuclear structure; Z, cytoskeleton.

Mentions: Experimentally characterized BY-kinases are usually encoded by genes located in operons involved in synthesis and export of capsular or extracellular polysaccharides and have been described as polysaccharide copolymerases in previous studies (Cuthbertson et al. 2009; Grangeasse et al. 2012). We sought to shed more light on the function of BY-kinases by screening the genomic neighborhoods of their genes. As shown in figure 6, the genomic context of BY-kinase genes was not conserved and varied considerably in different genomes. However, by comparing the COG classification between the immediate neighbor genes of BY-kinase genes and the entire genome, we found the location of BY-kinase genes was not entirely random. For the proteins encoded by the three immediate neighbor genes, 45.4% in average were involved in cell wall/membrane/envelop biogenesis (COG category M), 9.4% in average were involved in carbohydrate transport and metabolism (COG category G), and about 20% in average were belong to proteins without hits in COG, independently of the neighbor position from −3 to +3 except −1. The high frequency of neighbor genes encode proteins for cell wall/membrane/envelop biogenesis (COG category M) is not related to their proportion within the genomes, because the overall distribution of COG category M genes from all genomes is lower than 5%. This finding suggests a functional enrichment of BY-kinase regions in capsular biosynthesis proteins, which is consistent with the initial definition of BY-kinases as a component of the polysaccharide biosynthesis pathway. The same conclusion can be achieved by the analysis of genomic-context network associated to BY-kinase genes (supplementary fig. S6, Supplementary Material online), for example, BY-kinase (COG0489) was strongly linked to COG category M (COG3944), which corresponds to capsular biosynthesis proteins. Moreover, at position −1, proteins related to signal transduction (COG category T) appear to be among the most frequent neighbors of BY-kinase genes (fig. 6), and protein tyrosine phosphatases (COG0394) were linked with high frequency to BY-kinases (COG3206, another COG which BY-kinases were defined to) (supplementary fig. S6, Supplementary Material online). This result was consistent with previous report that BY-kinase genes are often colocalized with phosphatase-encoding genes (Mijakovic et al. 2003) and indicates that dephosphorylation performed by these phosphatases also plays a major role in the regulatory mechanisms mediated by BY-kinases. However, the genes flanking BY-kinases genes are also involved in many other biological processes (supplementary fig. S6, Supplementary Material online), which was not surprising because it was known that BY-kinases Wzc from E. coli and PtkA from B. subtilis participate in many processes besides capsular biosynthesis (Klein et al. 2003; Lacour et al. 2006, 2008). The variety of the immediate genomic environment supports the notion that BY-kinases may play a complex role in bacterial physiology and may contribute to several distinct signaling pathways in the same bacterium.Fig. 6.—


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)

Distribution and functional classification of genes surrounding the BY-kinases. For each of the five neighboring genes (located upstream and downstream of the BY-kinase), the functional COG category was determined. For each surrounded position, the bar indicates the frequency of each functional gene type (represented here by COG category) among the overall categories of the same position. Bar in the right part represents the COG distribution in all genomes harboring BY-kinases. COG categories are shown in different colors (see the COG color legend) and are associated with the corresponding capital letters: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division, and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification; protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, extracellular structures; Y, nuclear structure; Z, cytoskeleton.
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Related In: Results  -  Collection

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evu056-F6: Distribution and functional classification of genes surrounding the BY-kinases. For each of the five neighboring genes (located upstream and downstream of the BY-kinase), the functional COG category was determined. For each surrounded position, the bar indicates the frequency of each functional gene type (represented here by COG category) among the overall categories of the same position. Bar in the right part represents the COG distribution in all genomes harboring BY-kinases. COG categories are shown in different colors (see the COG color legend) and are associated with the corresponding capital letters: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division, and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification; protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, extracellular structures; Y, nuclear structure; Z, cytoskeleton.
Mentions: Experimentally characterized BY-kinases are usually encoded by genes located in operons involved in synthesis and export of capsular or extracellular polysaccharides and have been described as polysaccharide copolymerases in previous studies (Cuthbertson et al. 2009; Grangeasse et al. 2012). We sought to shed more light on the function of BY-kinases by screening the genomic neighborhoods of their genes. As shown in figure 6, the genomic context of BY-kinase genes was not conserved and varied considerably in different genomes. However, by comparing the COG classification between the immediate neighbor genes of BY-kinase genes and the entire genome, we found the location of BY-kinase genes was not entirely random. For the proteins encoded by the three immediate neighbor genes, 45.4% in average were involved in cell wall/membrane/envelop biogenesis (COG category M), 9.4% in average were involved in carbohydrate transport and metabolism (COG category G), and about 20% in average were belong to proteins without hits in COG, independently of the neighbor position from −3 to +3 except −1. The high frequency of neighbor genes encode proteins for cell wall/membrane/envelop biogenesis (COG category M) is not related to their proportion within the genomes, because the overall distribution of COG category M genes from all genomes is lower than 5%. This finding suggests a functional enrichment of BY-kinase regions in capsular biosynthesis proteins, which is consistent with the initial definition of BY-kinases as a component of the polysaccharide biosynthesis pathway. The same conclusion can be achieved by the analysis of genomic-context network associated to BY-kinase genes (supplementary fig. S6, Supplementary Material online), for example, BY-kinase (COG0489) was strongly linked to COG category M (COG3944), which corresponds to capsular biosynthesis proteins. Moreover, at position −1, proteins related to signal transduction (COG category T) appear to be among the most frequent neighbors of BY-kinase genes (fig. 6), and protein tyrosine phosphatases (COG0394) were linked with high frequency to BY-kinases (COG3206, another COG which BY-kinases were defined to) (supplementary fig. S6, Supplementary Material online). This result was consistent with previous report that BY-kinase genes are often colocalized with phosphatase-encoding genes (Mijakovic et al. 2003) and indicates that dephosphorylation performed by these phosphatases also plays a major role in the regulatory mechanisms mediated by BY-kinases. However, the genes flanking BY-kinases genes are also involved in many other biological processes (supplementary fig. S6, Supplementary Material online), which was not surprising because it was known that BY-kinases Wzc from E. coli and PtkA from B. subtilis participate in many processes besides capsular biosynthesis (Klein et al. 2003; Lacour et al. 2006, 2008). The variety of the immediate genomic environment supports the notion that BY-kinases may play a complex role in bacterial physiology and may contribute to several distinct signaling pathways in the same bacterium.Fig. 6.—

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