PMID- 25539726
OWN - NLM
STAT- MEDLINE
DCOM- 20150916
LR  - 20181113
IS  - 1759-6653 (Electronic)
IS  - 1759-6653 (Linking)
VI  - 7
IP  - 1
DP  - 2014 Dec 23
TI  - Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch 
      repair-deficient Pseudomonas fluorescens ATCC948.
PG  - 262-71
LID - 10.1093/gbe/evu284 [doi]
AB  - High levels of genetic diversity exist among natural isolates of the bacterium 
      Pseudomonas fluorescens, and are especially elevated around the replication 
      terminus of the genome, where strain-specific genes are found. In an effort to 
      understand the role of genetic variation in the evolution of Pseudomonas, we 
      analyzed 31,106 base substitutions from 45 mutation accumulation lines of P. 
      fluorescens ATCC948, naturally deficient for mismatch repair, yielding a 
      base-substitution mutation rate of 2.34 x 10(-8) per site per generation (SE: 
      0.01 x 10(-8)) and a small-insertion-deletion mutation rate of 1.65 x 10(-9) per 
      site per generation (SE: 0.03 x 10(-9)). We find that the spectrum of mutations 
      in prophage regions, which often contain virulence factors and antibiotic 
      resistance, is highly similar to that in the intergenic regions of the host 
      genome. Our results show that the mutation rate varies around the chromosome, 
      with the lowest mutation rate found near the origin of replication. Consistent 
      with observations from other studies, we find that site-specific mutation rates 
      are heavily influenced by the immediately flanking nucleotides, indicating that 
      mutations are context dependent.
CI  - (c) The Author(s) 2014. Published by Oxford University Press on behalf of the 
      Society for Molecular Biology and Evolution.
FAU - Long, Hongan
AU  - Long H
AD  - Department of Biology, Indiana University, Bloomington longhongan@gmail.com.
FAU - Sung, Way
AU  - Sung W
AD  - Department of Biology, Indiana University, Bloomington.
FAU - Miller, Samuel F
AU  - Miller SF
AD  - Department of Biology, Indiana University, Bloomington.
FAU - Ackerman, Matthew S
AU  - Ackerman MS
AD  - Department of Biology, Indiana University, Bloomington.
FAU - Doak, Thomas G
AU  - Doak TG
AD  - Department of Biology, Indiana University, Bloomington National Center for Genome 
      Analysis Support, Indiana University, Bloomington.
FAU - Lynch, Michael
AU  - Lynch M
AD  - Department of Biology, Indiana University, Bloomington.
LA  - eng
SI  - BioProject/PRJNA264995
GR  - R01 GM036827/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20141223
PL  - England
TA  - Genome Biol Evol
JT  - Genome biology and evolution
JID - 101509707
SB  - IM
MH  - DNA Mismatch Repair/*genetics
MH  - DNA Replication/genetics
MH  - Drug Resistance, Bacterial/genetics
MH  - *Genetic Variation
MH  - Host-Pathogen Interactions/*genetics
MH  - Humans
MH  - INDEL Mutation/genetics
MH  - *Mutation Rate
MH  - Pseudomonas fluorescens/genetics
PMC - PMC4316635
OTO - NOTNLM
OT  - mutation hotspots
OT  - neutral evolution
OT  - nonrandom mutations
OT  - phage evolution
EDAT- 2014/12/30 06:00
MHDA- 2015/09/17 06:00
PMCR- 2014/12/23
CRDT- 2014/12/26 06:00
PHST- 2014/12/26 06:00 [entrez]
PHST- 2014/12/30 06:00 [pubmed]
PHST- 2015/09/17 06:00 [medline]
PHST- 2014/12/23 00:00 [pmc-release]
AID - evu284 [pii]
AID - 10.1093/gbe/evu284 [doi]
PST - epublish
SO  - Genome Biol Evol. 2014 Dec 23;7(1):262-71. doi: 10.1093/gbe/evu284.