Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

Genome Biology
Morgan N PriceAdam P Arkin

Abstract

Most bacterial genes were acquired by horizontal gene transfer from other bacteria instead of being inherited by continuous vertical descent from an ancient ancestor. To understand how the regulation of these acquired genes evolved, we examined the evolutionary histories of transcription factors and of regulatory interactions from the model bacterium Escherichia coli K12. Although most transcription factors have paralogs, these usually arose by horizontal gene transfer rather than by duplication within the E. coli lineage, as previously believed. In general, most neighbor regulators - regulators that are adjacent to genes that they regulate - were acquired by horizontal gene transfer, whereas most global regulators evolved vertically within the gamma-Proteobacteria. Neighbor regulators were often acquired together with the adjacent operon that they regulate, and so the proximity might be maintained by repeated transfers (like 'selfish operons'). Many of the as yet uncharacterized (putative) regulators have also been acquired together with adjacent genes, and so we predict that these are neighbor regulators as well. When we analyzed the histories of regulatory interactions, we found that the evolution of regulation by duplicatio...Continue Reading

References

Mar 1, 1992·Molecular Phylogenetics and Evolution·M A Ragan
Jun 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·K BuitingB Horsthemke
Dec 23, 1999·Current Opinion in Genetics & Development·J Lawrence
Apr 3, 2001·Genome Research·I K JordanE V Koonin
Apr 6, 2002·Bioinformatics·Heiko A SchmidtArndt von Haeseler
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
May 4, 2002·Science·Sergei Maslov, Kim Sneppen
Jun 11, 2002·International Journal of Systematic and Evolutionary Microbiology·Mark A Ragan, Robert L Charlebois
Nov 9, 2002·Bioinformatics·Kevin HoweRichard Durbin
Nov 26, 2002·Molecular Biology and Evolution·J Peter GogartenJeffrey G Lawrence
Feb 13, 2003·Nucleic Acids Research·M Madan Babu, Sarah A Teichmann
Jul 4, 2003·Genome Research·Victor Kunin, Christos A Ouzounis
Oct 16, 2003·Journal of Theoretical Biology·Andreas Wagner
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 27, 2004·Nature Genetics·Sarah A Teichmann, M Madan Babu
May 18, 2004·Trends in Genetics : TIG·Csaba Pál, Laurence D Hurst
Jun 3, 2004·Genome Research·Vincent Daubin, Howard Ochman
Jun 5, 2004·Nucleic Acids Research·Stephen E Halford, John F Marko
Jun 23, 2004·Nature Genetics·Yoji NakamuraTakashi Gojobori
Oct 13, 2004·Nucleic Acids Research·Sarath Chandra Janga, Gabriel Moreno-Hagelsieb
Dec 21, 2004·Nucleic Acids Research·Ingrid M KeselerPeter D Karp
Feb 11, 2005·Nucleic Acids Research·Morgan N PriceAdam P Arkin
Mar 1, 2005·Trends in Genetics : TIG·Ruth HershbergHanah Margalit
Apr 1, 2005·PLoS Biology·Emmanuelle LeratNancy A Moran
Jun 3, 2005·Genome Research·Morgan N PriceEric J Alm
Jun 21, 2005·Genome Research·Victor KuninChristos A Ouzounis
Sep 24, 2005·Proceedings of the National Academy of Sciences of the United States of America·Robert G BeikoMark A Ragan
Nov 29, 2005·Nature Genetics·Csaba PálMartin J Lercher
Jan 10, 2006·BMC Bioinformatics·Heladia SalgadoJulio Collado-Vides
Apr 13, 2006·BMC Bioinformatics·Paramvir S Dehal, Jeffrey L Boore
May 3, 2006·Current Opinion in Structural Biology·Mikhail S Gelfand
May 3, 2006·Genome Research·Weilong Hao, G Brian Golding
Jun 23, 2006·PLoS Genetics·Morgan N PriceEric J Alm
Jul 15, 2006·Nucleic Acids Research·Irma Lozada-ChávezJulio Collado-Vides
Jul 25, 2006·Genome Biology·Ruth Hershberg, Hanah Margalit
Jan 31, 2007·Proceedings of the National Academy of Sciences of the United States of America·W Ford Doolittle, Eric Bapteste
Mar 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·M Cosentino LagomarsinoH Isambert

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Citations

Jun 2, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sergei MaslovKim Sneppen
Oct 25, 2008·Nucleic Acids Research·Eugene V Koonin, Yuri I Wolf
Mar 7, 2009·Nucleic Acids Research·Tasha A DesaiChristopher V Rao
Oct 30, 2009·Proceedings. Biological Sciences·Luis Boto
Jul 3, 2009·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mark A Ragan, Robert G Beiko
Nov 4, 2008·Journal of Bacteriology·Julio Collado-VidesAlberto Santos-Zavaleta
Aug 18, 2012·International Journal of Evolutionary Biology·M Pilar Francino
Sep 29, 2011·BMC Evolutionary Biology·Francisco J FernandezM Cristina Vega
Oct 9, 2012·BMC Evolutionary Biology·Olga V TsoyMikhail S Gelfand
Aug 12, 2009·BMC Evolutionary Biology·Tobias WarneckeLaurence D Hurst
Nov 28, 2009·Genome Biology·Jeffrey M SkerkerAdam P Arkin
Feb 20, 2010·PLoS Computational Biology·Sara BallouzMark M Tanaka
Feb 8, 2011·PLoS Genetics·Todd J Treangen, Eduardo P C Rocha
Nov 7, 2008·PloS One·Francisco M Camas, Juan F Poyatos
Jul 4, 2012·Annual Review of Microbiology·Emily J Capra, Michael T Laub
Apr 28, 2009·Molecular BioSystems·Marco Cosentino LagomarsinoDaniel Remondini
Jan 1, 2013·Molecular Phylogenetics and Evolution·F Jerry ReenFergal O'Gara
Jul 23, 2011·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Li WangWei Qian
Feb 19, 2011·Mathematical Biosciences·Baldiri SalvadoRui Alves
Oct 9, 2015·Biophysical Journal·Mahendra Kumar PrajapatSupreet Saini
Apr 18, 2013·Molecular Systems Biology·Morgan N PriceAdam P Arkin
Dec 21, 2013·Molecular Microbiology·Elena Espinosa, Josep Casadesús
Oct 2, 2015·Molecular Biology and Evolution·D Domman, M Horn
Sep 22, 2015·BMC Bioinformatics·Abdulkadir ElmasMichael S Samoilov
Dec 5, 2008·FEMS Microbiology Reviews·Chih-Horng Kuo, Howard Ochman
Dec 17, 2008·FEMS Microbiology Reviews·Enrique BallezaJulio Collado-Vides
Jun 30, 2011·FEMS Microbiology Reviews·Jane Wiedenbeck, Frederick M Cohan
Jan 13, 2011·FEMS Microbiology Reviews·Elizabeth Skippington, Mark A Ragan
Jul 5, 2015·BMC Genomics·Jiangtao GuoHuaiqiu Zhu
Dec 18, 2014·BMC Research Notes·Marc del Grande, Gabriel Moreno-Hagelsieb

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Software Mentioned

BLAST
DPInteract
MicrobesOnline tree browser
MUSCLE
Basic Local Alignment Search Tool
EcoCyc
MicrobesOnline
MEME
phyml
Basic Local Alignment Search Tool ( BLAST )

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