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Expression patterns of protein kinases correlate with gene architecture and evolutionary rates.

Ogurtsov AY, Mariño-Ramírez L, Johnson GR, Landsman D, Shabalina SA, Spiridonov NA - PLoS ONE (2008)

Bottom Line: The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages.Structure and evolutionary divergence of tissue-specific PK genes is related to the proliferative activity of the tissue where these genes are predominantly expressed.Our data provide evidence that physiological requirements for transcription intensity, ubiquitous expression, and tissue-specific regulation shape gene structure and affect rates of evolution.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

ABSTRACT

Background: Protein kinase (PK) genes comprise the third largest superfamily that occupy approximately 2% of the human genome. They encode regulatory enzymes that control a vast variety of cellular processes through phosphorylation of their protein substrates. Expression of PK genes is subject to complex transcriptional regulation which is not fully understood.

Principal findings: Our comparative analysis demonstrates that genomic organization of regulatory PK genes differs from organization of other protein coding genes. PK genes occupy larger genomic loci, have longer introns, spacer regions, and encode larger proteins. The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages. On average, PK genes evolve slower than other protein coding genes. Breadth of PK expression negatively correlates with rate of non-synonymous substitutions in protein coding regions. This rate is lower for high expression and ubiquitous PKs, relative to low expression PKs, and correlates with divergence in untranslated regions. Conversely, rate of silent mutations is uniform in different PK groups, indicating that differing rates of non-synonymous substitutions reflect variations in selective pressure. Brain and testis employ a considerable number of tissue-specific PKs, indicating high complexity of phosphorylation-dependent regulatory network in these organs. There are considerable differences in genomic organization between PKs up-regulated in the testis and brain. PK genes up-regulated in the highly proliferative testicular tissue are fast evolving and small, with short introns and transcribed regions. In contrast, genes up-regulated in the minimally proliferative nervous tissue carry long introns, extended transcribed regions, and evolve slowly.

Conclusions/significance: PK genomic architecture, the size of gene functional domains and evolutionary rates correlate with the pattern of gene expression. Structure and evolutionary divergence of tissue-specific PK genes is related to the proliferative activity of the tissue where these genes are predominantly expressed. Our data provide evidence that physiological requirements for transcription intensity, ubiquitous expression, and tissue-specific regulation shape gene structure and affect rates of evolution.

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Characteristic transcription factor binding sites over-represented in evolutionarily conserved regions of PK genes predominantly expressed in nervous tissue.
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pone-0003599-g007: Characteristic transcription factor binding sites over-represented in evolutionarily conserved regions of PK genes predominantly expressed in nervous tissue.

Mentions: PK genes up-regulated in the nervous tissue had significantly longer 5′-spacers and introns then genes down-regulated in the nervous tissue. These extended gene loci may harbor binding sites for nervous tissue-specific transcription factors. To identify brain-specific regulatory elements, we analyzed conserved synteny regions of PK genes predominantly expressed in the nervous tissue with the DiRE program. Whole gene loci, including promoters, UTRs, introns, and distant intergenic and spacer regions were included in this analysis. Conserved synteny regions of PK genes with similar overall expression levels and low expression in the brain tissue were used as a background set. Typical transcription factor binding sites overrepresented in evolutionarily conserved brain-specific PK genes are shown in Figure 7, and the top 30 overrepresented motifs are presented in Table S2. As seen from the Table, binding sites for POU, Pit, Pbx, Pax, Olf, Meis and other neuron-specific transcription factors that perform specific functions in the central nervous system were highly overrepresented in evolutionarily conserved in regions of PK genes predominantly expressed in the nervous tissue.


Expression patterns of protein kinases correlate with gene architecture and evolutionary rates.

Ogurtsov AY, Mariño-Ramírez L, Johnson GR, Landsman D, Shabalina SA, Spiridonov NA - PLoS ONE (2008)

Characteristic transcription factor binding sites over-represented in evolutionarily conserved regions of PK genes predominantly expressed in nervous tissue.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2572838&req=5

pone-0003599-g007: Characteristic transcription factor binding sites over-represented in evolutionarily conserved regions of PK genes predominantly expressed in nervous tissue.
Mentions: PK genes up-regulated in the nervous tissue had significantly longer 5′-spacers and introns then genes down-regulated in the nervous tissue. These extended gene loci may harbor binding sites for nervous tissue-specific transcription factors. To identify brain-specific regulatory elements, we analyzed conserved synteny regions of PK genes predominantly expressed in the nervous tissue with the DiRE program. Whole gene loci, including promoters, UTRs, introns, and distant intergenic and spacer regions were included in this analysis. Conserved synteny regions of PK genes with similar overall expression levels and low expression in the brain tissue were used as a background set. Typical transcription factor binding sites overrepresented in evolutionarily conserved brain-specific PK genes are shown in Figure 7, and the top 30 overrepresented motifs are presented in Table S2. As seen from the Table, binding sites for POU, Pit, Pbx, Pax, Olf, Meis and other neuron-specific transcription factors that perform specific functions in the central nervous system were highly overrepresented in evolutionarily conserved in regions of PK genes predominantly expressed in the nervous tissue.

Bottom Line: The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages.Structure and evolutionary divergence of tissue-specific PK genes is related to the proliferative activity of the tissue where these genes are predominantly expressed.Our data provide evidence that physiological requirements for transcription intensity, ubiquitous expression, and tissue-specific regulation shape gene structure and affect rates of evolution.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

ABSTRACT

Background: Protein kinase (PK) genes comprise the third largest superfamily that occupy approximately 2% of the human genome. They encode regulatory enzymes that control a vast variety of cellular processes through phosphorylation of their protein substrates. Expression of PK genes is subject to complex transcriptional regulation which is not fully understood.

Principal findings: Our comparative analysis demonstrates that genomic organization of regulatory PK genes differs from organization of other protein coding genes. PK genes occupy larger genomic loci, have longer introns, spacer regions, and encode larger proteins. The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages. On average, PK genes evolve slower than other protein coding genes. Breadth of PK expression negatively correlates with rate of non-synonymous substitutions in protein coding regions. This rate is lower for high expression and ubiquitous PKs, relative to low expression PKs, and correlates with divergence in untranslated regions. Conversely, rate of silent mutations is uniform in different PK groups, indicating that differing rates of non-synonymous substitutions reflect variations in selective pressure. Brain and testis employ a considerable number of tissue-specific PKs, indicating high complexity of phosphorylation-dependent regulatory network in these organs. There are considerable differences in genomic organization between PKs up-regulated in the testis and brain. PK genes up-regulated in the highly proliferative testicular tissue are fast evolving and small, with short introns and transcribed regions. In contrast, genes up-regulated in the minimally proliferative nervous tissue carry long introns, extended transcribed regions, and evolve slowly.

Conclusions/significance: PK genomic architecture, the size of gene functional domains and evolutionary rates correlate with the pattern of gene expression. Structure and evolutionary divergence of tissue-specific PK genes is related to the proliferative activity of the tissue where these genes are predominantly expressed. Our data provide evidence that physiological requirements for transcription intensity, ubiquitous expression, and tissue-specific regulation shape gene structure and affect rates of evolution.

Show MeSH
Related in: MedlinePlus