Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes

Molecular Biology and Evolution
J O Andersson, S G Andersson

Abstract

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.

References

May 1, 1992·The Journal of Heredity·A T Lloyd, P M Sharp
Apr 1, 1989·Journal of Molecular Evolution·D GraurW H Li
Apr 1, 1989·Molecular Microbiology·M Skurnik, H Wolf-Watz
Jan 1, 1987·Journal of Clinical Microbiology·C I PretzmanS Bech-Nielsen
Apr 27, 1973·Science·F J TyeryarR A Ormsbee
Aug 15, 1995·Proceedings of the National Academy of Sciences of the United States of America·D A PetrovE R Lozovskaya
Jul 1, 1993·Journal of Bacteriology·C DelormeP Renault
Jul 1, 1993·Journal of Bacteriology·J J GodonP Renault
Apr 2, 1996·Proceedings of the National Academy of Sciences of the United States of America·N A Moran
May 1, 1996·Journal of Molecular Evolution·S G Andersson, P M Sharp
Nov 1, 1995·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·S G Andersson, C G Kurland
Jun 1, 1996·Molecular Biotechnology·R Staden
Nov 28, 1996·Nature·D A PetrovD L Hartl
Jan 1, 1997·Molecular Biology and Evolution·C W CunninghamJ J Bull
Dec 1, 1996·Computer Applications in the Biosciences : CABIOS·N GaltierC Gautier
Apr 1, 1997·Journal of Molecular Evolution·J G Lawrence, H Ochman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 23, 1997·Clinical Microbiology Reviews·D Raoult, V Roux
Mar 21, 1998·Molecular Biology and Evolution·D A Petrov, D L Hartl
Jun 11, 1998·Emerging Infectious Diseases·A F Azad, C B Beard
Aug 5, 1998·Proceedings of the National Academy of Sciences of the United States of America·J G Lawrence, H Ochman
Aug 26, 1998·Trends in Microbiology·S G Andersson, C G Kurland
Jan 5, 1999·Applied and Environmental Microbiology· Van Ham RCHJA Latorre
Mar 6, 1999·Current Opinion in Microbiology·S T Cole
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·R JainJ A Lake
Jun 22, 1999·FEBS Letters·A Zomorodipour, S G Andersson
Jun 26, 1999·Science·W F Doolittle
Sep 16, 1999·Molecular Biology and Evolution·J O Andersson, S G Andersson
Dec 23, 1999·Current Opinion in Genetics & Development·J O Andersson, S G Andersson
Feb 11, 2000·Science·D A PetrovK L Shaw
Sep 14, 2000·Proceedings of the National Academy of Sciences of the United States of America·R C Van HamA Latorre
May 1, 1964·Mutation Research·H J MULLER

❮ Previous
Next ❯

Citations

Jul 17, 2008·Comparative and Functional Genomics·Naomi Siew, Daniel Fischer
Mar 21, 2006·Journal of Molecular Evolution·Evgeniy S BalakirevFrancisco J Ayala
Apr 18, 2007·Journal of Molecular Evolution·Jesper LarsenJohn E Olsen
Nov 26, 2011·Antonie van Leeuwenhoek·Xiao-Yang ZhiGuo-Ping Zhao
Nov 30, 2013·Journal of Biosciences·Saubashya SurArnab Sen
Jun 1, 2008·Indian Journal of Microbiology·Kishore R Sakharkar, Vincent T K Chow
Apr 6, 2005·FEMS Microbiology Reviews·Tom CoenyeJean Swings
Dec 9, 2003·Gene·Yoko FukudaMasaru Tomita
Oct 24, 2003·Current Opinion in Microbiology·Nancy A Moran
Jan 1, 2004·Trends in Microbiology·Lisa Klasson, Siv G E Andersson
Jun 27, 2002·Journal of Molecular Biology·Paul M Harrison, Mark Gerstein
Feb 28, 2002·Veterinary Immunology and Immunopathology·Guy H Palmer
Oct 5, 2001·Trends in Genetics : TIG·A MiraN A Moran
Jul 20, 2002·Trends in Genetics : TIG·Wagied DavidsSiv G E Andersson
Aug 25, 2001·Trends in Microbiology·T Tønjum, E Seeberg
Jun 26, 2003·Trends in Microbiology·Ildefonso CasesChristos A Ouzounis
Oct 2, 2002·Current Opinion in Microbiology·Alex MiraSiv G E Andersson
Feb 3, 2005·Nature Reviews. Microbiology·Ildefonso Cases, Víctor de Lorenzo
Sep 3, 2005·Nature Reviews. Microbiology·Seth R Bordenstein, William S Reznikoff
Apr 17, 2008·Nature Reviews. Microbiology·David H Walker, Nahed Ismail
Mar 29, 2002·Molecular Microbiology·Derek H Wells, Sharon R Long
Aug 1, 2013·Briefings in Functional Genomics·Kamalika Sen, Tapash Chandra Ghosh
Jan 1, 2009·Genome Biology and Evolution·Chih-Horng Kuo, Howard Ochman
Sep 11, 2010·Genome Biology and Evolution·John P McCutcheon, Nancy A Moran
Nov 10, 2013·Genome Biology and Evolution·Pablo A NuñezEduardo P C Rocha
Oct 5, 2002·Nucleic Acids Research·Igor B RogozinEugene V Koonin
Jun 4, 2005·Nucleic Acids Research·Emmanuelle Lerat, Howard Ochman
Jul 18, 2009·Proceedings. Biological Sciences·Lucy A WeinertFrancis M Jiggins
Feb 22, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Siv G E AnderssonCharles G Kurland
Jun 9, 2009·Genome Research·Chih-Horng KuoHoward Ochman
Dec 11, 2007·Applied and Environmental Microbiology·Gerald D BaldridgeUlrike G Munderloh
Jun 7, 2011·Applied and Environmental Microbiology·Aimee M TuckerDavid O Wood
Nov 7, 2003·Applied and Environmental Microbiology·Rita V M RioSerap Aksoy
Aug 20, 2004·Journal of Bacteriology·Michael P McLeodGeorge M Weinstock
Dec 8, 2004·Journal of Clinical Microbiology·Pierre-Edouard FournierDidier Raoult
Sep 7, 2007·Microbiology and Molecular Biology Reviews : MMBR·Marco VenturaDouwe van Sinderen
Apr 24, 2010·BMC Genomics·Ingrid Lafontaine, Bernard Dujon

❮ Previous
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