DOI: 10.1093/gbe/evp005. Coevolution of DNA Uptake Sequences and Bacterial Proteomes

Coevolution of DNA Uptake Sequences and Bacterial Proteomes

10.1093/gbe/evp005

Crossref journal-article

Oxford University Press (OUP)

Genome Biology and Evolution (286)

Bibliography

Findlay, W. A., & Redfield, R. J. (2009). Coevolution of DNA Uptake Sequences and Bacterial Proteomes. Genome Biology and Evolution, 1, 45â55.

Authors 2

W. A. Findlay (first)
R. J. Redfield (additional)

References 31 Referenced 14

10.1073/pnas.87.14.5509 / Proc Natl Acad Sci USA / Protein database searches for multiple alignments by Altschul (1990)
10.1128/JB.01408-06 / J Bacteriol / New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators by Ambur (2007)
10.1099/mic.0.2006/004200-0 / Microbiology / The outer membrane secretin PilQ from Neisseria meningitidis binds DNA by Assalkhou (2007)
10.1371/journal.pone.0000741 / PLoS ONE / Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences by Bakkali (2007)
10.1073/pnas.0306366101 / Proc Natl Acad Sci USA / Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae by Bakkali (2004)
10.1016/0378-1119(80)90071-2 / Gene / An eleven-base-pair sequence determines the specificity of DNA uptake in Haemophilus transformation by Danner (1980)
10.1093/nar/gkh255 / Nucleic Acids Res / Biased distribution of DNA uptake sequences towards genome maintenance genes by Davidsen (2004)
10.1093/nar/gkh834 / Nucleic Acids Res / Solving the riddle of codon usage preferences: a test for translational selection by dos Reis (2004)
10.1038/299111a0 / Nature / Molecular drive: a cohesive mode of species evolution by Dover (1982)
10.1016/S0168-9525(02)02789-0 / Trends Genet / Molecular drive by Dover (2002)
10.1016/S0378-1119(99)00297-8 / Gene / Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms by Frank (1999)
10.1093/nar/gkg004 / Nucleic Acids Res / HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes by Garcia-Vallve (2003)
10.1073/pnas.85.18.6982 / Proc Natl Acad Sci USA / Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae by Goodman (1988)
10.1093/genetics/138.1.227 / Genetics / Selection intensity for codon bias by Hartl (1994)
10.1073/pnas.89.22.10915 / Proc Natl Acad Sci USA / Amino acid substitution matrices from protein blocks by Henikoff (1992)
10.1007/BF01868974 / J Membr Biol / Transformation in Haemophilus: a problem in membrane biology by Kahn (1984)
10.1093/nar/24.21.4263 / Nucleic Acids Res / Frequent oligonucleotides and peptides of the Haemophilus influenzae genome by Karlin (1996)
10.1186/gb-2007-8-2-r22 / Genome Biol / Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake by Kingsford (2007)
10.1038/35047500 / Nat Rev Genet / Rewiring the keyboard: evolvability of the genetic code by Knight (2001)
10.1007/PL00006158 / J Mol Evol / Amelioration of bacterial genomes: rates of change and exchange by Lawrence (1997)
10.1093/nar/28.1.292 / Nucleic Acids Res / Codon usage tabulated from international DNA sequence databases: status for the year 2000 by Nakamura (2000)
10.1042/BST0340519 / Biochem Soc Trans / Why have sex? The population genetics of sex and recombination by Otto (2006)
10.1186/1471-2105-7-257 / BMC Bioinformatics / Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes by Pasamontes (2006)
10.1186/1471-2148-6-82 / BMC Evol Biol / Evolution of competence and DNA uptake specificity in the Pasteurellaceae by Redfield (2006)
10.1128/JB.118.2.369-373.1974 / J Bacteriol / Specificity in deoxyribonucleic acid uptake by transformable Haemophilus influenzae by Scocca (1974)
10.1093/nar/gki242 / Nucleic Acids Res / Variation in the strength of selected codon usage bias among bacteria by Sharp (2005)
10.1016/S0923-2508(99)00130-8 / Res Microbiol / DNA uptake signal sequences in naturally transformable bacteria by Smith (1999)
10.1126/science.7542802 / Science / Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome by Smith (1995)
10.1093/nar/22.22.4673 / Nucleic Acids Res / Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice by Thompson (1994)
10.1186/gb-2008-9-3-r60 / Genome Biol / The impact of the neisserial DNA uptake sequences on genome evolution and stability by Treangen (2008)
10.1186/1745-6150-3-12 / Biol Direct / An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae by van Passel (2008)

Dates

Type	When
Created	16 years, 4 months ago (May 5, 2009, 11:04 p.m.)
Deposited	3 years, 11 months ago (Oct. 4, 2021, 8:18 p.m.)
Indexed	1 year, 11 months ago (Sept. 13, 2023, 4:05 p.m.)
Issued	16 years, 8 months ago (Jan. 1, 2009)
Published	16 years, 8 months ago (Jan. 1, 2009)
Published Online	16 years, 4 months ago (May 5, 2009)
Published Print	16 years, 8 months ago (Jan. 1, 2009)

Funders 0

None

BibTeX

@article{Findlay_2009, title={Coevolution of DNA Uptake Sequences and Bacterial Proteomes}, volume={1}, ISSN={1759-6653}, url={http://dx.doi.org/10.1093/gbe/evp005}, DOI={10.1093/gbe/evp005}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Findlay, W. A. and Redfield, R. J.}, year={2009}, month=jan, pages={45–55} }

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