The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

<p>Abstract</p> <p>Background</p> <p>Despite the prevalence of horizontal gene transfer (HGT) in bacteria, to this date there were few studies on HGT in the context of gene expression, operons and protein-protein interactions. Using the recently available data set on the <it>E. coli </it>protein-protein interaction network, we sought to explore the impact of HGT on genome structure and protein networks.</p> <p>Results</p> <p>We classified the <it>E. coli </it>genes into three categories based on their evolutionary conservation: a set of 2158 <it>Core </it>genes that are shared by all <it>E. coli </it>strains, a set of 1044 <it>Non-core </it>genes that are strain-specific, and a set of 1053 genes that were putatively acquired by horizontal transfer. We observed a clear correlation between gene expressivity (measured by Codon Adaptation Index), evolutionary rates, and node connectivity between these categories of genes. Specifically, we found the <it>Core </it>genes are the most highly expressed and the most slowly evolving, while the <it>HGT </it>genes are expressed at the lowest level and evolve at the highest rate. <it>Core </it>genes are the most likely and <it>HGT </it>genes are the least likely to be member of the operons. In addition, we found the <it>Core </it>genes on average are more highly connected than <it>Non-core </it>and <it>HGT </it>genes in the protein interaction network, however the <it>HGT </it>genes displayed a significantly higher mean node degree than the <it>Core </it>and <it>Non-core </it>genes in the defence COG functional category. Interestingly, <it>HGT </it>genes are more likely to be connected to <it>Core </it>genes than expected by chance, which suggest a model of differential attachment in the expansion of cellular networks.</p> <p>Conclusion</p> <p>Results from our analysis shed light on the mode and mechanism of the integration of horizontally transferred genes into operons and protein interaction networks.</p

The Journey to smORFland

The genome sequences completed so far contain more than 20 000 genes with unknown function and no similarity to genes in other genomes. The origin and evolution of the orphan genes is an enigma. Here, we discuss the suggestion that some orphan genes may represent pseudogenes or short fragments of genes that were functional in the genome of a common ancestor. These may be the remains of unsuccessful duplication or horizontal gene transfer events, in which the acquired sequences have entered the fragmentation process and thereby lost their similarity to genes in other species. This scenario is supported by a recent case study of orphan genes in several closely related species of Rickettsia, where full-length ancestral genes were reconstructed from sets of short, overlapping orphan genes. One of these was found to display similarity to genes encoding proteins with ankyrin-repeat domains

Causes of Substitution Frequency Variation in Pathogenic Bacteria

Estimating substitution frequencies at sites that influence (Ka) and do not influence (Ks) the amino acid sequence is important for understanding the dynamics of molecular sequence evolution and the selective pressures that have shaped genetic variation. The aim of this work was to gain a deeper understanding of the driving forces of substitution frequency variation in human pathogens. Rickettsia prowazekii, the causative agent of epidemic typhus and Helicobacter pylori, which has been implicated in gastric diseases were used as model systems. A specific focus was on the evolution of orphan genes in Rickettsia. Additionally, adaptive sequence evolution and factors influencing protein evolutionary rates in H. pylori were studied. The comparative sequence analyses of orphan genes using Typhus Group (TG) and Spotted Fever Group (SFG) Rickettsia, indicate that orphan genes in the SFG correspond to pseudogenes in the TG and that pseudogenes in the SFG correspond to extensively degraded gene remnants in the TG. The analysis also showed that ancestral gene sequences could be reconstructed from extant gene remnants of closely related species. The studies of split genes in R. conorii indicate that many of the small fragmented ORFs are probably pseudogenes. Analysis of the H. pylori carbamoyl phosphate synthetase provided an opportunity to understand natural selection acting on a protein undergoing adaptive evolution. Factors such as network properties, protein-protein interactions, gene essentiality and chromosomal position on protein evolutionary rates in H. pylori were studied, of which antigenicity and gene location were identified as the strongest factors. In conclusion, high Ka/Ks ratios in human pathogens may reflect either adaptive sequence evolution or gene deterioration. Distinguishing between the two is an important task in molecular evolution and also of great relevance for medical microbiology and functional genomics research

Distribution of evolutionary rates for various strains overlaid on a phylogenetic tree using as reference for genome comparisons

<p><b>Copyright information:</b></p><p>Taken from "The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment"</p><p>http://www.biomedcentral.com/1471-2148/8/23</p><p>BMC Evolutionary Biology 2008;8():23-23.</p><p>Published online 24 Jan 2008</p><p>PMCID:PMC2259305.</p><p></p> genes evolve slower than and genes (P-value < 0.001)

Number of genes in the genome organizations: operons, protein interaction network (PIN)

<p><b>Copyright information:</b></p><p>Taken from "The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment"</p><p>http://www.biomedcentral.com/1471-2148/8/23</p><p>BMC Evolutionary Biology 2008;8():23-23.</p><p>Published online 24 Jan 2008</p><p>PMCID:PMC2259305.</p><p></p> Genes are classified into three evolutionary categories , -and genes. genes predominantly occur in both operons and protein interaction networks (P-value < 0.001)

Gene expressivity (CAI) values and log2 gene expression values between , and genes in different genome organizations

<p><b>Copyright information:</b></p><p>Taken from "The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment"</p><p>http://www.biomedcentral.com/1471-2148/8/23</p><p>BMC Evolutionary Biology 2008;8():23-23.</p><p>Published online 24 Jan 2008</p><p>PMCID:PMC2259305.</p><p></p> Box plot of CAI values between , and genes in operons; Box plot of gene CAI values between , and genes in protein interaction network (PIN); Box plot of log2 gene expression values between , and genes in operons; Box plot of log2 gene expression values between , and genes in protein interaction network (PIN)

Comparative and Functional Genomics Conference Review The journey to smORFland

Abstract The genome sequences completed so far contain more than 20 000 genes with unknown function and no similarity to genes in other genomes. The origin and evolution of the orphan genes is an enigma. Here, we discuss the suggestion that some orphan genes may represent pseudogenes or short fragments of genes that were functional in the genome of a common ancestor. These may be the remains of unsuccessful duplication or horizontal gene transfer events, in which the acquired sequences have entered the fragmentation process and thereby lost their similarity to genes in other species. This scenario is supported by a recent case study of orphan genes in several closely related species of Rickettsia, where full-length ancestral genes were reconstructed from sets of short, overlapping orphan genes. One of these was found to display similarity to genes encoding proteins with ankyrin-repeat domains