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Patterns and Processes of Molecular Evolution in Rickettsia
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
2002 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Species of the genus Rickettsia are obligate intracellular parasites of the a-proteobacterial subdivision. It has been suggested that obligate intracellular bacteria have evolved from free-living bacteria with much larger genome sizes. Transitions to intracellular growth habitats are normally associated with radical genomic alterations, particularly genome rearrangements and gene losses.

This thesis presents a comparative study of evolutionary processes such as gene rearrangements, deletions and duplications in a variety of Rickettsia species. The results show that early intrachromosomal recombination events mediated by duplicated genes and short repeats have resulted in deletions as well as rearrangements. For example, an exceptional organization of the elongation factor genes was found in all species examined, suggesting that this rearrangement event occurred at the early stage of the evolution of Rickettsia. Likewise, it was found that a repetitive element, the so-called Rickettsia Palindromic Element (RPE) flourished prior to species divergence in Rickettsia. Finally, a phylogenetic analysis shows that the duplication events that gave rise to the five genes encoding ATP/ADP transporters occurred long before the divergence of the two major groups of Rickettsia. Taken together, this suggests that Rickettsia have been intracellular parasites for an extensive period of time.

A detailed analysis of the patterns of nucleotide changes in genes and intergenic regions among the different species provides evidence for a gradual accumulation of short deletions. This suggests that different distributions of genes and repeated sequences in modern Rickettsia species reflect species-specific differences in rates of deterioration rather than variation in rates of intra-genomic sequence proliferation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2002. , p. 40
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 689
Keywords [en]
Developmental biology
Keywords [sv]
Utvecklingsbiologi
National Category
Developmental Biology
Research subject
Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-1789ISBN: 91-554-5248-5 (print)OAI: oai:DiVA.org:uu-1789DiVA, id: diva2:161381
Public defence
2002-03-22, Lindahlsalen, Uppsala, 10:00
Opponent
Available from: 2002-03-06 Created: 2002-03-06Bibliographically approved
List of papers
1. A chimeric disposition of the elongation factor genes in Rickettsia prowazekii
Open this publication in new window or tab >>A chimeric disposition of the elongation factor genes in Rickettsia prowazekii
Show others...
1996 In: J. Bacteriol., Vol. 178, p. 6192-6199Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-89688 (URN)
Available from: 2002-03-06 Created: 2002-03-06Bibliographically approved
2. Proliferation and deterioration of Rickettsia palindromic elements
Open this publication in new window or tab >>Proliferation and deterioration of Rickettsia palindromic elements
2002 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 19, no 8, p. 1234-1243Article in journal (Refereed) Published
Abstract [en]

It has been suggested that Rickettsia Palindromic Elements (RPEs) have evolved as selfish DNA that mediate protein sequence evolution by being targeted to genes that code for RNA and proteins. Here, we have examined the phylogenetic depth of two RPEs that are located close to the genes encoding elongation factors Tu (tuf) and G (fus) in Rickettsia. An exceptional organization of the elongation factor genes was found in all 11 species examined, with complete or partial RPEs identified downstream of the tuf gene (RPE-tuf) in six species and of the fus gene (RPE-fus) in 10 species. A phylogenetic reconstruction shows that both RPE-tuf and RPE-fus have evolved in a manner that is consistent with the expected species divergence. The analysis provides evidence for independent loss of RPE-tuf in several species, possibly mediated by short repetitive sequences flanking the site of excision. The remaining RPE-tuf sequences evolve as neutral sequences in different stages of deterioration. Likewise, highly fragmented remnants of the RPE-fus sequence were identified in two species. This suggests that genome-specific differences in the content of RPEs are the result of recent loss rather than recent proliferation.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-89689 (URN)12140235 (PubMedID)
Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
3. In the phylogenetic footsteps of ATP- ADP translocases
Open this publication in new window or tab >>In the phylogenetic footsteps of ATP- ADP translocases
Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-89690 (URN)
Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2010-01-13Bibliographically approved
4. Evolution of intergenic DNA in Rickettsia
Open this publication in new window or tab >>Evolution of intergenic DNA in Rickettsia
Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-89691 (URN)
Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2010-01-13Bibliographically approved
5. Loss of gene function: Clues from expressed gene fragments in Rickettsia
Open this publication in new window or tab >>Loss of gene function: Clues from expressed gene fragments in Rickettsia
2002 (English)In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 18, no 7, p. 331-334Article in journal (Refereed) Published
Abstract [en]

Many obligate intracellular pathogens have small genomes with high fractions of pseudogenes. A recent analysis of gene expression patterns in Rickettsia conorii shows that short open reading frames inside deteriorating genes are occasionally transcribed into RNA. Here, we show that substitution frequencies at nonsynonymous sites are similar for expressed and unexpressed parts of the fragmented genes. We conclude that the observed expression is a temporary stage in the gene degradation process, suggesting that the expressed gene fragments are not functional.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-89692 (URN)10.1016/S0168-9525(02)02685-9 (DOI)
Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
6. Genome deterioration: Loss of repeated sequences and accumulation of junk DNA
Open this publication in new window or tab >>Genome deterioration: Loss of repeated sequences and accumulation of junk DNA
2002 (English)In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 115, no 1, p. 1-12Article in journal (Refereed) Published
Abstract [en]

A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and 'junk' DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-89693 (URN)12188042 (PubMedID)
Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
7. Rickettsia: The highly rearranged cousin of mitochondria
Open this publication in new window or tab >>Rickettsia: The highly rearranged cousin of mitochondria
2001 In: Recent Res. Dev. Microbiol., Vol. 5, p. 321-329Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-89694 (URN)
Available from: 2002-03-06 Created: 2002-03-06Bibliographically approved

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