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| 2. |
- Andersson, Siv G E, et al.
(författare)
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Comparative genomics of microbial pathogens and symbionts.
- 2002
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Ingår i: Bioinformatics. - 1367-4803 .- 1367-4811. ; 18 Suppl 2, s. S17-
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Tidskriftsartikel (refereegranskat)abstract
- We are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. Here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. A particular focus is on intracellular pathogens and symbionts of the genera Rickettsia, Bartonella and BUCHNERA: Extensive gene loss and restricted access to phage and plasmid pools may provide an explanation for why single host pathogens are normally less successful than multihost pathogens. We note that species-specific genes tend to be shorter than orthologous genes, suggesting that a fraction of these may represent fossil-orfs, as also supported by multiple sequence alignments among species. The results of our genome comparisons are placed in the context of phylogenomic analyses of alpha and gamma proteobacteria. We highlight artefacts caused by different rates and patterns of mutations, suggesting that atypical phylogenetic placements can not a priori be taken as evidence for horizontal gene transfer events. The flexibility in genome structure among free-living microbes contrasts with the extreme stability observed for the small genomes of aphid endosymbionts, in which no rearrangements or inflow of genetic material have occurred during the past 50 millions years (1). Taken together, the results suggest that genomic stability correlate with the content of repeated sequences and mobile genetic elements, and thereby indirectly with bacterial lifestyles.
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| 3. |
- Canbäck, Björn, et al.
(författare)
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A phylogenomic study of endosymbiotic bacteria
- 2004
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 21:6, s. 1110-1122
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Tidskriftsartikel (refereegranskat)abstract
- Endosymbiotic bacteria of aphids, Buchnera aphidicola, and tsetse flies, Wigglesworthia glossinidia, are descendents of free-living γ-Proteobacteria. The acceleration of sequence evolution in the endosymbiont genomes is here estimated from a phylogenomic analysis of the γ-Proteobacteria. The tree topologies associated with the most highly conserved genes suggest that the endosymbionts form a sister group with Escherichia coli, Salmonella sp., and Yersinia pestis. Our results indicate that deviant tree topologies result from high substitution rates and biased nucleotide patterns, rather than from lateral gene transfer, as previously suggested. A reinvestigation of the relative rate increase in the endosymbiont genomes reveals variability among genes that correlate with host-associated metabolic dependencies. The conclusion is that host-level selection has retarded both the loss of genes and the acceleration of sequence evolution in endocellular symbionts.
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| 5. |
- Tamas, Ivica, et al.
(författare)
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50 million years of genomic stasis in endosymbiotic bacteria.
- 2002
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 296:5577, s. 2376-9
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Tidskriftsartikel (refereegranskat)abstract
- Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts.
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| 6. |
- Tamas, Ivica, 1967-
(författare)
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Comparative Genomics of Endosymbiotic Bacteria
- 2002
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genomes of intracellular bacteria are thought to be the products of reductive evolution. They have evolved from ancestral genomes of free-living bacteria through a process of massive gene loss. This doctoral thesis focuses on the comparison of the only two completely sequenced genomes of obligate symbionts presently available: Buchnera (Ap) and Buchnera (Sg). The sequencing of the complete genome of Buchnera (Sg) is a part of this work.A major finding presented is that these genomes are remarkably conserved in both genome content and gene order, which contrasts with the current view of bacterial genomes as rapidly evolving entities. On the basis of the data obtained, there are no signs of inversions, translocations, duplications or horizontally transferred genes. Furthermore, the Buchnera genomes are the first bacterial genomes identified with a loss of recA, a major gene involved in homologous recombination. This single deletion event has probably contributed to the observed genomic stasis. In addition, the recF gene involved in DNA-repair and SOS induction has also been eliminated, and mutations have started to accumulate in genes related to base-excision repair in Buchnera (Sg). In contrast to the remarkable stability in structure, surprisingly high rates of nucleotide substitutions causing amino acids replacements and substitutions at synonymous sites were identified. Therefore, the genetic changes introduced into these two genomes since their divergence is almost exclusively due to the nucleotide sequence substitutions.A number of pseudogenes in different stages of gene degradation have been observed in the Buchnera (Sg) genome, suggesting that genome reduction is still an ongoing, albeit slow process. Almost half of the weakly mutated genes with single or a few frameshift mutations are associated with DNA-repair, cell envelope or cysteine biosynthesis. A comparative study of a set of genes involved in peptidoglycan biosynthesis in four additional lineages of Buchnera has shown that some of the single nucleotide deletions were acquired already 30-50 million years ago. Nevertheless, the substitution patterns of these genes are typical of Buchnera genes, suggesting that they may have maintained a functional role despite the accumulation of frameshift mutations.The two Buchnera genomes are the first ever completely sequenced bacterial genomes for which a divergence date is available (50-70 myr). This was made possible by the availability of a fossil record for the aphid host and the exclusively vertical transmission of Buchnera via maternal inheritance. Thus, the analysis of the two genomes provides a first insight into the pace of molecular evolution in prokaryotes. Substitution rates were estimated to 9 x 10-9 synonymous substitutions per site and per year and 1.65 x 10-9 nonsynonymous substitutions per site and per year on the average for all orthologous genes identified in the genomes. The rate of gene loss was found to be surprisingly low, with about one complete gene elimination per 5-10 million years.
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| 7. |
- Tamas, Ivica, et al.
(författare)
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Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts
- 2008
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 105:39, s. 14934-14939
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Tidskriftsartikel (refereegranskat)abstract
- Among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160-790 kb) and most A + T-rich (>70%) bacterial genomes known to date. These genomes are riddled with poly(A) tracts, and 5-50% of genes contain tracts of 10 As or more. Here, we demonstrate transcriptional slippage at poly(A) tracts within genes of Buchnera aphidicola associated with aphids and Blochmannia pennsylvanicus associated with ants. Several tracts contain single frameshift deletions; these apparent pseudogenes showed patterns of constraint consistent with purifying selection on the encoded proteins. Transcriptional slippage yielded a heterogeneous population of transcripts with variable numbers of As in the tract. Across several frameshifted genes, including B. aphidicola cell wall biosynthesis genes and a B. pennsylvanicus histidine biosynthesis gene, 12-50% of transcripts contained corrected reading frames that could potentially yield full-length proteins. In situ immunostaining confirmed the production of the cell wall biosynthetic enzyme UDP-N-acetylmuramyl pentapeptide synthase encoded by the frameshifted murF gene. Simulation studies indicated an overrepresentation of poly(A) tracts in endosymbiont genomes relative to other A + T-rich bacterial genomes. Polymerase infidelity at poly(A) tracts rescues the functionality of genes with frameshift mutations and, conversely, reduces the efficiency of expression for in-frame genes carrying poly(A) regions. These features of homopolymeric tracts could be exploited to manipulate gene expression in small synthetic genomes.
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