Biomedical subjects

J Peter Gogarten

Publications and source records attributed to J Peter Gogarten.

7 recordsLinked to original sources

PubMed2003

An improved probability mapping approach to assess genome mosaicism.

BACKGROUND: Maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. However, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. Furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability. RESULTS: Quartets of orthologous proteins were complemented with homologs from selected reference genomes. The mapping of bootstrap support values from these extended datasets gives results similar to the original maximum likelihood and posterior probability mapping. The more conservative nature of the plotted support values allows to focus further analyses on those protein families that strongly disagree with the majority or plurality of genes present in the analyzed genomes. CONCLUSION: Posterior probability is a non-conservative measure for support, and posterior probability mapping only provides a quick estimation of phylogenetic information content of four genomes. This approach can be utilized as a pre-screen to select genes that might have been horizontally transferred. Better taxon sampling combined with subtree analyses prevents the inconsistencies associated with four-taxon analyses, but retains the power of visual representation. Nevertheless, a case-by-case inspection of individual multi-taxon phylogenies remains necessary to differentiate unrecognized paralogy and shared phylogenetic reconstruction artifacts from horizontal gene transfer events.

Bacterial Proteins↗

PubMed2003

Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.

Reconstructing the early evolution of photosynthesis has been guided in part by the geological record, but the complexity and great antiquity of these early events require molecular genetic techniques as the primary tools of inference. Recent genome sequencing efforts have made whole genome data available from representatives of each of the five phyla of bacteria with photosynthetic members, allowing extensive phylogenetic comparisons of these organisms. Here, we have undertaken whole genome comparisons using maximum likelihood to compare 527 unique sets of orthologous genes from all five photosynthetic phyla. Substantiating recent whole genome analyses of other prokaryotes, our results indicate that horizontal gene transfer (HGT) has played a significant part in the evolution of these organisms, resulting in genomes with mosaic evolutionary histories. A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared.

Bacteria↗

PubMed2003

Gene transfer: gene swapping craze reaches eukaryotes.

Recent studies have provided evidence for gene transfers from prokaryotes to eukaryotes and between eukaryotes. The mechanisms and frequencies of these transfers remain the subject of speculation, but the findings provide ample reason to seriously consider interspecies gene transfer as an important evolutionary process in eukaryotes.

Animals↗

PubMed2002

Whole-genome analysis of photosynthetic prokaryotes.

The process of photosynthesis has had profound global-scale effects on Earth; however, its origin and evolution remain enigmatic. Here we report a whole-genome comparison of representatives from all five groups of photosynthetic prokaryotes and show that horizontal gene transfer has been pivotal in their evolution. Excluding a small number of orthologs that show congruent phylogenies, the genomes of these organisms represent mosaics of genes with very different evolutionary histories. We have also analyzed a subset of "photosynthesis-specific" genes that were elucidated through a differential genome comparison. Our results explain incoherencies in previous data-limited phylogenetic analyses of phototrophic bacteria and indicate that the core components of photosynthesis have been subject to lateral transfer.

Bacteria↗

PubMed2002

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.

BACKGROUND: Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes. RESULTS: We adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group. CONCLUSIONS: In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny. Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes.

Journal Article↗

PubMed2002

Inteins: structure, function, and evolution.

Inteins are genetic elements that disrupt the coding sequence of genes. However, in contrast to introns, inteins are transcribed and translated together with their host protein. Inteins appear most frequently in Archaea, but they are found in organisms belonging to all three domains of life and in viral and phage proteins. Most inteins consist of two domains: One is involved in autocatalytic splicing, and the other is an endonuclease that is important in the spread of inteins. This review focuses on the evolution and technical application of inteins and only briefly summarizes recent advances in the study of the catalytic activities and structures of inteins. In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins.

Amino Acid Motifs↗

PubMed2002

Prokaryotic evolution in light of gene transfer.

Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.

Evolution, Molecular↗