Molecular Biology and Evolution 18:829-839 (2001)
© 2001 Society for Molecular Biology and Evolution
ARTICLE |
Pseudogenes, Junk DNA, and the Dynamics of Rickettsia Genomes
Department of Molecular Evolution, University of Uppsala, Uppsala, Sweden
Studies of neutrally evolving sequences suggest that differences in eukaryotic genome sizes result from different rates of DNA loss. However, very few pseudogenes have been identified in microbial species, and the processes whereby genes and genomes deteriorate in bacteria remain largely unresolved. The typhus-causing agent, Rickettsia prowazekii, is exceptional in that as much as 24% of its 1.1-Mb genome consists of noncoding DNA and pseudogenes. To test the hypothesis that the noncoding DNA in the R. prowazekii genome represents degraded remnants of ancestral genes, we systematically examined all of the identified pseudogenes and their flanking sequences in three additional Rickettsia species. Consistent with the hypothesis, we observe sequence similarities between genes and pseudogenes in one species and intergenic DNA in another species. We show that the frequencies and average sizes of deletions are larger than insertions in neutrally evolving pseudogene sequences. Our results suggest that inactivated genetic material in the Rickettsia genomes deteriorates spontaneously due to a mutation bias for deletions and that the noncoding sequences represent DNA in the final stages of this degenerative process.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. A. Weinert, J. J. Welch, and F. M. Jiggins Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally Proc R Soc B, October 22, 2009; 276(1673): 3619 - 3627. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-H. Kuo, N. A. Moran, and H. Ochman The consequences of genetic drift for bacterial genome complexity Genome Res., August 1, 2009; 19(8): 1450 - 1454. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-H. Kuo and H. Ochman Deletional Bias across the Three Domains of Life Gen Biol Evol, July 10, 2009; 2009(0): 145 - 152. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. D. Baldridge, N. Y. Burkhardt, R. F. Felsheim, T. J. Kurtti, and U. G. Munderloh Plasmids of the pRM/pRF Family Occur in Diverse Rickettsia Species Appl. Envir. Microbiol., February 1, 2008; 74(3): 645 - 652. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Ventura, C. Canchaya, A. Tauch, G. Chandra, G. F. Fitzgerald, K. F. Chater, and D. van Sinderen Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum Microbiol. Mol. Biol. Rev., September 1, 2007; 71(3): 495 - 548. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. A. Beare, J. E. Samuel, D. Howe, K. Virtaneva, S. F. Porcella, and R. A. Heinzen Genetic Diversity of the Q Fever Agent, Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons. J. Bacteriol., April 1, 2006; 188(7): 2309 - 2324. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Ochman and L. M. Davalos The nature and dynamics of bacterial genomes. Science, March 24, 2006; 311(5768): 1730 - 1733. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. ZAVALA-CASTRO, M. SMALL, C. KENG, D. H. BOUYER, J. ZAVALA-VELAZQUEZ, and D. H. WALKER TRANSCRIPTION OF THE RICKETTSIA FELIS OMPA GENE IN NATURALLY INFECTED FLEAS Am J Trop Med Hyg, October 1, 2005; 73(4): 662 - 666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. L. Lindroos, A. Mira, D. Repsilber, O. Vinnere, K. Naslund, M. Dehio, C. Dehio, and S. G. E. Andersson Characterization of the Genome Composition of Bartonella koehlerae by Microarray Comparative Genomic Hybridization Profiling J. Bacteriol., September 1, 2005; 187(17): 6155 - 6165. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Ochman Genomes on the shrink PNAS, August 23, 2005; 102(34): 11959 - 11960. [Full Text] [PDF]
|
|
|
|
 |
|
 E. Lerat and H. Ochman Recognizing the pseudogenes in bacterial genomes Nucleic Acids Res., June 2, 2005; 33(10): 3125 - 3132. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Belda, A. Moya, and F. J. Silva Genome Rearrangement Distances and Gene Order Phylogeny in {gamma}-Proteobacteria Mol. Biol. Evol., June 1, 2005; 22(6): 1456 - 1467. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P.-E. Fournier, Y. Zhu, H. Ogata, and D. Raoult Use of Highly Variable Intergenic Spacer Sequences for Multispacer Typing of Rickettsia conorii Strains J. Clin. Microbiol., December 1, 2004; 42(12): 5757 - 5766. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Daubin and N. A. Moran Comment on "The Origins of Genome Complexity" Science, November 5, 2004; 306(5698): 978a - 978a. [Full Text] [PDF]
|
|
|
|
 |
|
 K. R. Sakharkar, P. K. Dhar, and V. T. K. Chow Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis Int J Syst Evol Microbiol, November 1, 2004; 54(6): 1937 - 1941. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Gomez-Valero, A. Latorre, and F. J. Silva The Evolutionary Fate of Nonfunctional DNA in the Bacterial Endosymbiont Buchnera aphidicola Mol. Biol. Evol., November 1, 2004; 21(11): 2172 - 2181. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. P. McLeod, X. Qin, S. E. Karpathy, J. Gioia, S. K. Highlander, G. E. Fox, T. Z. McNeill, H. Jiang, D. Muzny, L. S. Jacob, et al. Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae J. Bacteriol., September 1, 2004; 186(17): 5842 - 5855. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. V. M. Rio, C. Lefevre, A. Heddi, and S. Aksoy Comparative Genomics of Insect-Symbiotic Bacteria: Influence of Host Environment on Microbial Genome Composition Appl. Envir. Microbiol., November 1, 2003; 69(11): 6825 - 6832. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Waters, M. J. Hohn, I. Ahel, D. E. Graham, M. D. Adams, M. Barnstead, K. Y. Beeson, L. Bibbs, R. Bolanos, M. Keller, et al. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism PNAS, October 28, 2003; 100(22): 12984 - 12988. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Amiri, W. Davids, and S. G. E. Andersson Birth and Death of Orphan Genes in Rickettsia Mol. Biol. Evol., October 1, 2003; 20(10): 1575 - 1587. [Abstract] [Full Text]
|
|
|
|
|
|
D. Raoult, H. Ogata, S. Audic, C. Robert, K. Suhre, M. Drancourt, and J.-M. Claverie Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome Genome Res., August 1, 2003; 13(8): 1800 - 1809. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. P.C. Rocha An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome Reduction Genome Res., June 1, 2003; 13(6): 1123 - 1132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. D. Read, G. S. A. Myers, R. C. Brunham, W. C. Nelson, I. T. Paulsen, J. Heidelberg, E. Holtzapple, H. Khouri, N. B. Federova, H. A. Carty, et al. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae Nucleic Acids Res., April 15, 2003; 31(8): 2134 - 2147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Goffin and J.-M. Ghuysen Biochemistry and Comparative Genomics of SxxK Superfamily Acyltransferases Offer a Clue to the Mycobacterial Paradox: Presence of Penicillin-Susceptible Target Proteins versus Lack of Efficiency of Penicillin as Therapeutic Agent Microbiol. Mol. Biol. Rev., December 1, 2002; 66(4): 702 - 738. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. B. Rogozin, K. S. Makarova, D. A. Natale, A. N. Spiridonov, R. L. Tatusov, Y. I. Wolf, J. Yin, and E. V. Koonin Congruent evolution of different classes of non-coding DNA in prokaryotic genomes Nucleic Acids Res., October 1, 2002; 30(19): 4264 - 4271. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Amiri, C. M. Alsmark, and S. G. E. Andersson Proliferation and Deterioration of Rickettsia Palindromic Elements Mol. Biol. Evol., August 1, 2002; 19(8): 1234 - 1243. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Mira and H. Ochman Gene Location and Bacterial Sequence Divergence Mol. Biol. Evol., August 1, 2002; 19(8): 1350 - 1358. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Ogata, S. Audic, P. Renesto-Audiffren, P.-E. Fournier, V. Barbe, D. Samson, V. Roux, P. Cossart, J. Weissenbach, J.-M. Claverie, et al. Mechanisms of Evolution in Rickettsia conorii and R. prowazekii Science, September 14, 2001; 293(5537): 2093 - 2098. [Abstract] [Full Text] [PDF]
|
|