Limits...
Association between translation efficiency and horizontal gene transfer within microbial communities.

Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E - Nucleic Acids Res. (2011)

Bottom Line: These results remain significant after controlling for diverse ecological and evolutionary parameters.Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them.Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Mathematics and Computer Science, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Blavatnik School of Computer Science, School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.

ABSTRACT
Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an additional central barrier to HGT-the lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism. Analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools. Those genes that are better adapted to the tRNA pools of the target genomes tend to undergo more frequent HGT. At the community (or environment) level, organisms that share a common ecological niche tend to have similar tRNA pools. These results remain significant after controlling for diverse ecological and evolutionary parameters. Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them. Similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome. Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.

Show MeSH

Related in: MedlinePlus

(A) The number of HGT events (six) as a function of RVtAI across five bins of equal size: a Whisker plot with the means marked with red circles. (B) Correlations with the number of HGT events when controlling for all the other factors; P denotes asymptotic P-value, pe denotes empirical P-value (‘Materials and Methods’ section). (C) Correlation given increasing number of factors (A) estimated mean expression levels, (B) variance in GC content and (C) variance in amino acid bias.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3113575&req=5

Figure 1: (A) The number of HGT events (six) as a function of RVtAI across five bins of equal size: a Whisker plot with the means marked with red circles. (B) Correlations with the number of HGT events when controlling for all the other factors; P denotes asymptotic P-value, pe denotes empirical P-value (‘Materials and Methods’ section). (C) Correlation given increasing number of factors (A) estimated mean expression levels, (B) variance in GC content and (C) variance in amino acid bias.

Mentions: To better understand how different features of a COG explain the number of times it has been horizontally transferred, we computed a combined and more robust measure of tAI robustness, RVtAI, (a combination of the two previous measures, where higher RVtAI means less robustness to changes in the tRNA pool, see ‘Materials and Methods’ section). As can be seen in Figure 1A, the correlation between the RVtAI of a COG and the number of times that COG was horizontally transferred is very high (r = −0.4340; P < 10−16). Specifically, the 20% of the COGs with the lowest RVtAI scores have been horizontally transferred over 7-fold more frequently than the 20% of the COGs with the top RVtAI (Figure 1A) demonstrating again the strong relation between robustness to tRNA pools and HGT.Figure 1.


Association between translation efficiency and horizontal gene transfer within microbial communities.

Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E - Nucleic Acids Res. (2011)

(A) The number of HGT events (six) as a function of RVtAI across five bins of equal size: a Whisker plot with the means marked with red circles. (B) Correlations with the number of HGT events when controlling for all the other factors; P denotes asymptotic P-value, pe denotes empirical P-value (‘Materials and Methods’ section). (C) Correlation given increasing number of factors (A) estimated mean expression levels, (B) variance in GC content and (C) variance in amino acid bias.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113575&req=5

Figure 1: (A) The number of HGT events (six) as a function of RVtAI across five bins of equal size: a Whisker plot with the means marked with red circles. (B) Correlations with the number of HGT events when controlling for all the other factors; P denotes asymptotic P-value, pe denotes empirical P-value (‘Materials and Methods’ section). (C) Correlation given increasing number of factors (A) estimated mean expression levels, (B) variance in GC content and (C) variance in amino acid bias.
Mentions: To better understand how different features of a COG explain the number of times it has been horizontally transferred, we computed a combined and more robust measure of tAI robustness, RVtAI, (a combination of the two previous measures, where higher RVtAI means less robustness to changes in the tRNA pool, see ‘Materials and Methods’ section). As can be seen in Figure 1A, the correlation between the RVtAI of a COG and the number of times that COG was horizontally transferred is very high (r = −0.4340; P < 10−16). Specifically, the 20% of the COGs with the lowest RVtAI scores have been horizontally transferred over 7-fold more frequently than the 20% of the COGs with the top RVtAI (Figure 1A) demonstrating again the strong relation between robustness to tRNA pools and HGT.Figure 1.

Bottom Line: These results remain significant after controlling for diverse ecological and evolutionary parameters.Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them.Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Mathematics and Computer Science, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Blavatnik School of Computer Science, School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.

ABSTRACT
Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an additional central barrier to HGT-the lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism. Analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools. Those genes that are better adapted to the tRNA pools of the target genomes tend to undergo more frequent HGT. At the community (or environment) level, organisms that share a common ecological niche tend to have similar tRNA pools. These results remain significant after controlling for diverse ecological and evolutionary parameters. Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them. Similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome. Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.

Show MeSH
Related in: MedlinePlus