Abstract and poster presented at ASM 2001

 

We plan to submit manuscripts describing our results. Until then, this section might give you a background on what to look for in the publications.

 

 

 

ABSTRACT: [back to top] 

The relative evolutionary distances within groups of homologous genes were utilized to test for lateral gene transfer. Using the WIT (aka ERGO) database (http://ergo.IntegratedGenomics.com/ERGO) (Overbeek et al., 2000), gene sequences for 40 ribosomal proteins, 20 aminoacyl-tRNA synthetases, and 9 enzymes in the aromatic amino acid biosynthetic pathway were obtained from the genomic sequences of 7 archaea, 31 bacteria, and one eukaryote. Evolutionary distances (Ed) were calculated by comparisons of all genes within a group. In the absence of lateral gene transfer, the Ed from one group of homologous genes was expected to be linearly correlated to the Ed for other groups of homologous genes. Gene which may have been obtained by lateral gene transfer (LGT) could then be identified by the absence of a correlation with the Ed for other genes from the same taxa. This method detected many LGTs proposed by analyses of phylogenetic trees and predicted a direction of transfer. In general, LGT was found to be less common among the ribosomal protein genes and more common among the aminoacyl-tRNA synthetase and aromatic amino acid biosynthetic genes.

 

INTRODUCTION: [back to top] 

Prior to the development of genomics, evidence for horizontal or lateral gene transfer in the evolution of prokaryotes was limited to a few special cases, such as antibiotic resistance, catabolic resistance and endosymbiosis. With recent advancements in comparative genome studies, the role of lateral gene transfer (LGT) in evolutionary history of prokaryotes is more evident than before (Nelson et al., 1999). Some researchers speculate that the rate of lateral gene transfer (LGT) is frequent enough to distort the phylogenetic relationships among organisms previously inferred from highly conserved genes (Doolittle, 1999). Other investigators argue that the rate of LGT is relatively minor compared to the rate of linear or vertical inheritance of genetic information (Glansdorff, 2000). Our work examines an alternative method of predicting LGT occurrences. For this method, the relative evolutionary distances (Ed) were calculated among groups of homologous genes. In the absence of LGT, the Ed from one group of homologous genes was expected to be linearly correlated to the Ed for other groups of homologous genes. Evidence for LGT was obtained by the absence of this correlation (see Figure 1 and 2 ).

Figure 1 (top left): Hypothetical tree containing representations of the three domains – Archaea (A), Bacteria (sub-groups B1 and B2) and Eukaryota (E) – which illustrates a LGT event  (broken line) between Archaea and Bacteria sub-group B1.

Figure 2 (top right): example plot of intra-domain and inter-domain phylogenetic relationships inferred by hypothetical Ed’s from Figure 1. Comparisons of taxa participating in vertical and lateral gene transfer events are projected on this plot by solid circles and open circles, respectively; y-axis represents the experimental gene Ed and x-axis resents the control gene Ed; (i) reflects distance of  the donating taxa from B2; (ii) reflects distance of receiving taxa from B2; (iii) reflects age of transfer.

 

In Figure 1, solid lines reflect the normal evolutionary relationship among genes without the occurrence of LGT, and the accompanying plot shows a correlation in the Ed for a pair of genes (solid circles). If a LGT occurred between the Archaea and the Bacteria sub-group B1, as imagined by the broken arrow, the plot reflects this relationship caused by LGT. The open circles show that there is an increase in the distance between the Bacterial subgroups B1 and B2. Furthermore, the inter-domain comparisons of Bacteria sub-group B1 with Archaea or Eukaryote domain plots fall below their expected position, suggesting that B1 received the gene from these lineages. Finally, the lowest distance to the plot’s x-axis (y=0) is indicative of the donor taxa. Therefore the plot suggests Archaea as the possible ancestor of the gene in the Bacteria sub-group B1.

This novel method is used here to examine three groups of gene families represented by up to 40 organisms. A total of 60 genes supplied evidence for developing visual models and quantitative thresholds for projecting LGT, which can be used in both large and small-scale applications. In addition, the phylogenetic relationships that were inferred for aminoacyl-tRNA synthetases were compared to those inferences reported by gene trees (Woese et al, 2000).

 

REFERENCES: [ back to top ]

 

CONTACT INFORMATION: [ back to top ]

Kamyar Farahi

Department of Microbiology, University of Georgia

major professor: William B. Whitman

mailing address: 541 Biological Sciences Bldg., Athens, GA 30602-0002 (USA) 

telephone: 706.542.4692

e-mail: kfarahi@uga.edu

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