Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC.

BMC Genomics
Stefan EngelenAntoine Danchin

Abstract

Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves...Continue Reading

References

Mar 30, 1976·Molecular & General Genetics : MGG·E LoveN C Brown
Sep 20, 1977·Journal of Molecular Evolution·C R Woese, G E Fox
Jan 1, 1987·Journal of Molecular Evolution·E Zuckerkandl
Dec 1, 1971·Proceedings of the National Academy of Sciences of the United States of America·M L GefterC Barnoux
May 1, 1996·Molecular Biology and Evolution·J R Lobry
Oct 24, 1997·Science·R L TatusovD J Lipman
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·M PellegriniT O Yeates
Apr 27, 1999·Molecular Microbiology·E P RochaA Viari
Apr 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·B R Morton
Aug 14, 1999·Nucleic Acids Research·D D LeipeE V Koonin
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Nov 15, 2001·Protein Engineering·F Pazos, A Valencia
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
May 9, 2002·Genome Research·Qiyu BaoHuanming Yang
Apr 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·K KobayashiN Ogasawara
Jul 9, 2003·Nature Genetics·Eduardo P C Rocha, Antoine Danchin
Aug 20, 2003·Acta Crystallographica. Section D, Biological Crystallography·Daniela DeriuMarkus G Grütter
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Apr 15, 1962·Proceedings of the National Academy of Sciences of the United States of America·N SUEOKA
Nov 1, 2003·The Journal of Biological Chemistry·Emmanuelle Le ChatelierLaurent Jannière
Nov 7, 2003·Nucleic Acids Research·Eduardo P C Rocha, Antoine Danchin
Jul 15, 2005·Molecular Biology and Evolution·Gang FangAntoine Danchin
Aug 17, 2005·PLoS Computational Biology·Daniel Barker, Mark Pagel
Jan 7, 2006·Nucleic Acids Research·Monica RileyBarry L Wanner
Apr 24, 2007·Annual Review of Microbiology·Agamemnon J Carpousis
Jun 26, 2007·Nucleic Acids Research·Undine MecholdAntoine Danchin
Oct 23, 2008·Nucleic Acids Research·Lars J JensenChristian von Mering
Dec 25, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ronald J EvansThale C Jarvis
Feb 14, 2009·Progress in Molecular Biology and Translational Science·Antoine Danchin
Apr 21, 2009·Current Opinion in Cell Biology·Nina Y Yao, Mike O'Donnell

❮ Previous
Next ❯

Citations

Oct 10, 2013·Nucleic Acids Research·Kestutis TiminskasČeslovas Venclovas
Feb 23, 2013·Microbiology·Eugeni BeldaAntoine Danchin
Dec 12, 2012·Trends in Genetics : TIG·Carlos G Acevedo-RochaAntoine Danchin
Jul 21, 2016·Microbial Biotechnology·Antoine Danchin, Gang Fang
Feb 26, 2016·Environmental Microbiology·Eugeni BeldaClaudine Médigue
Dec 30, 2016·Microbial Biotechnology·Antoine Danchin
Mar 11, 2020·Microbial Biotechnology·Antoine DanchinConghui You
Dec 28, 2017·Microbial Biotechnology·Rainer BorrissDavid Vallenet
May 29, 2018·Microbial Biotechnology·Antoine DanchinJean-Daniel Zucker

❮ Previous
Next ❯

Datasets Mentioned

BETA
BSU05910

Methods Mentioned

BETA
phylogenetic profile
phylogenetic profiles
gene neighbourhood
phosphotransferase

Software Mentioned

MicroScope
BlastP
JMP
PhyloProfile
Syntonizer
STRING

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.