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Expression breadth and expression abundance behave differently in correlations with evolutionary rates.

ABSTRACT: BACKGROUND: One of the main objectives of the molecular evolution and evolutionary systems biology field is to reveal the underlying principles that dictate protein evolutionary rates. Several studies argue that expression abundance is the most critical component in determining the rate of evolution, especially in unicellular organisms. However, the expression breadth also needs to be considered for multicellular organisms. RESULTS: In the present paper, we analyzed the relationship between the two expression variables and rates using two different genome-scale expression datasets, microarrays and ESTs. A significant positive correlation between the expression abundance (EA) and expression breadth (EB) was revealed by Kendall's rank correlation tests. A novel random shuffling approach was applied for EA and EB to compare the correlation coefficients obtained from real data sets to those estimated based on random chance. A novel method called a Fixed Group Analysis (FGA) was designed and applied to investigate the correlations between expression variables and rates when one of the two expression variables was evenly fixed. CONCLUSIONS: In conclusion, all of these analyses and tests consistently showed that the breadth rather than the abundance of gene expression is tightly linked with the evolutionary rate in multicellular organisms.

SUBMITTER: Park SG

PROVIDER: S-EPMC2924872 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Expression breadth and expression abundance behave differently in correlations with evolutionary rates.

Park Seung Gu SG Choi Sun Shim SS

BMC evolutionary biology 20100807

<h4>Background</h4>One of the main objectives of the molecular evolution and evolutionary systems biology field is to reveal the underlying principles that dictate protein evolutionary rates. Several studies argue that expression abundance is the most critical component in determining the rate of evolution, especially in unicellular organisms. However, the expression breadth also needs to be considered for multicellular organisms.<h4>Results</h4>In the present paper, we analyzed the relationship ...[more]

PMID: 20691101

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Project description:Lameness affects dairy cows worldwide and is usually associated with pain. Behavioral differences in lame compared to non-lame tie-stall-housed dairy cows might be less pronounced than in free-stall-housed, since the principle demands to a cow's locomotor system and thus the impact of lameness on behavior seem to be lower in tie stalls. Behavioral differences between lame and non-lame cows might be used to estimate the impact of lameness on the well-being of tied dairy cows. In the current study, lame cows were categorized as locomotion scoring between 2.25 and 3.25 on a 1-5 scale. The aim was to compare the eating, rumination and lying behavior of lame cows against non-lame tied dairy cows, in order to draw conclusions on the association of lameness, behavior and well-being in tied dairy cows. The eating and rumination behavior of 26, the lying behavior of 30, and the relative upright and lying activities of 25 matched case-control pairs were analyzed, considering the matching criteria farm, breed-type, and parity-group. Lame cows had fewer [mean of the pairwise differences (case-control) (meandiff) = -2.6 bouts, CI95% (-3.8--1.4) bouts, p = 0.001], but longer lying bouts [meandiff = 26.7 min per bout, CI95% (10.1-43.4) min per bout, p = 0.006]. The lying time was shorter [meandiff = -64.7 min, CI95% (-104.4--24.9) min, p = 0.006] in lame cows compared to their non-lame controls. Lame cows had a shorter eating time [meandiff = -27.7 min, CI95% (-51.5--4.0) min, p = 0.042] and spent a larger proportion of their upright time ruminating [meandiff = 7.2%, CI95% (3.2-11.1)%, p = 0.001] instead of eating. The results of the current study indicate that the eating, rumination, and lying behavior of lame tied dairy cows is altered. These findings indicate that slight and moderate lameness (locomotion score between 2.25 and 3.25 on a 1-5 scale) are likely to be associated with an impaired well-being in affected tied dairy cows. This underlines the need to continuously reduce the lameness prevalence and severity in tied dairy herds.

Project description: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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Expression breadth and expression abundance behave differently in correlations with evolutionary rates.

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Expression breadth and expression abundance behave differently in correlations with evolutionary rates.

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