Abstract：
:The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extremophile bacterium Deinococcus radiodurans ΔmutS1 and the model soil bacterium Pseudomonas fluorescens wild-type and MMR- (Methyl-dependent Mismatch Repair-deficient) strains, we report the mutational features of these two important bacteria. We find that P. fluorescens has one of the highest MMR repair efficiencies among tested bacteria. We also discover that MMR of D. radiodurans preferentially repairs deletions, contrary to all other bacteria examined. We then, for the first time, quantify genome-wide efficiency and specificity of MMR in repairing different genomic regions and mutation types, by evaluating the P. fluorescens and D. radiodurans mutation data sets, along with previously reported ones of Bacillus subtilis subsp. subtilis, Escherichia coli, Vibrio cholerae, and V. fischeri. MMR in all six bacteria shares two general features: 1) repair efficiency is influenced by the neighboring base composition for both transitions and transversions, not limited to transversions as previously reported; and 2) MMR only recognizes indels <4 bp in length. This study demonstrates the power of mutation accumulation lines in quantifying DNA repair and mutagenesis patterns.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Long H,Miller SF,Williams E,Lynch Mdoi
10.1093/molbev/msy134subject
Has Abstractpub_date
2018-10-01 00:00:00pages
2414-2421issue
10eissn
0737-4038issn
1537-1719pii
5043854journal_volume
35pub_type
杂志文章abstract：:In a striking contrast, matK is one of the most rapidly evolving plastid genes and also one of the few plastid genes to be retained in all nonphotosynthetic plants examined to date. DNA sequences of this region were obtained from photosynthetic and nonphotosynthetic plants of Orobanchaceae and their relatives. The res...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026295
更新日期：2000-12-01 00:00:00
abstract：:Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models, the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
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更新日期：2008-08-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026285
更新日期：2000-12-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a004043
更新日期：2002-12-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040661
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msn190
更新日期：2008-11-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a025728
更新日期：1997-12-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msp210
更新日期：2010-01-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msm262
更新日期：2008-02-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 信件
doi：10.1093/molbev/msm010
更新日期：2007-04-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msn177
更新日期：2008-11-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msi230
更新日期：2005-12-01 00:00:00
abstract：:Previous studies on human mitochondrial genomes showed that the ratio of intra-specific diversities at nonsynonymous-to-synonymous positions was two to ten times higher than the ratio of interspecific divergences at these positions, suggesting an excess of slightly deleterious nonsynonymous polymorphisms. However, suc...
journal_title：Molecular biology and evolution
pub_type： 信件
doi：10.1093/molbev/msq287
更新日期：2011-01-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msj023
更新日期：2006-01-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msaa024
更新日期：2020-06-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msaa147
更新日期：2020-10-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msr073
更新日期：2011-09-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msi095
更新日期：2005-04-01 00:00:00
abstract：:Cryptophytes are photosynthetic protists that have acquired their plastids through the secondary symbiotic uptake of a red alga. A remarkable feature of cryptophytes is that they maintain a reduced form of the red algal nucleus, the nucleomorph, between the second and third plastid membranes (periplastidial compartmen...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026271
更新日期：2000-11-01 00:00:00
abstract：:Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We pres...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msx307
更新日期：2018-02-01 00:00:00
abstract：:The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
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更新日期：2009-09-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msq229
更新日期：2011-01-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a003893
更新日期：2001-06-01 00:00:00
abstract：:Human histatins are a family of low-M(r), neutral to very basic, histidine-rich salivary polypeptides. They probably function as part of the nonimmune host defense system in the oral cavity. A 39-kb region of DNA containing the HIS1 and HIS2 genes was isolated from two human genomic phage libraries as a series of over...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040022
更新日期：1993-05-01 00:00:00
abstract：:Serotonin is a neurotransmitter that plays an important role in regulating behavior and personality in humans and other mammals. Polymorphisms in genes coding for the serotonin receptor subtype 1A (HTR1A), the serotonin transporter (SLC6A4), and the serotonin degrading enzyme monoamine oxidase A (MAOA) are associated ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
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更新日期：2019-07-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msz242
更新日期：2020-02-01 00:00:00
abstract：:The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msk016
更新日期：2006-06-01 00:00:00
abstract：:Evolutionary parsimony is an easy-to-use method of phylogenetic inference that is based on nucleic acid sequences and that does not require the assumption that evolutionary processes in the various sites on the molecule are identical. It does, however, require a parameter constraint, known as the "balanced transversio...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040784
更新日期：1992-11-01 00:00:00
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journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msm021
更新日期：2007-04-01 00:00:00
abstract：:Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptati...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msz194
更新日期：2019-12-01 00:00:00
