TY - JOUR
T1 - The spectrum of replication errors in the absence of error correction assayed across the whole genome of escherichia coli
AU - Niccum, Brittany A.
AU - Lee, Heewook
AU - MohammedIsmail, Wazim
AU - Tang, Haixu
AU - Foster, Patricia L.
N1 - Publisher Copyright:
© 2018 by the Genetics Society of America.
PY - 2018/8
Y1 - 2018/8
N2 - When the DNA polymerase that replicates the Escherichia coli chromosome, DNA polymerase III, makes an error, there are two primary defenses against mutation: proofreading by the e subunit of the holoenzyme and mismatch repair. In proofreadingdeficient strains, mismatch repair is partially saturated and the cell’s response to DNA damage, the SOS response, may be partially induced. To investigate the nature of replication errors, we used mutation accumulation experiments and whole-genome sequencing to determine mutation rates and mutational spectra across the entire chromosome of strains deficient in proofreading, mismatch repair, and the SOS response. We report that a proofreading-deficient strain has a mutation rate 4000-fold greater than wild-type strains. While the SOS response may be induced in these cells, it does not contribute to the mutational load. Inactivating mismatch repair in a proofreading-deficient strain increases the mutation rate another 1.5-fold. DNA polymerase has a bias for converting G:C to A:T base pairs, but proofreading reduces the impact of these mutations, helping to maintain the genomic G:C content. These findings give an unprecedented view of how polymerase and error-correction pathways work together to maintain E. coli’s low mutation rate of 1 per 1000 generations.
AB - When the DNA polymerase that replicates the Escherichia coli chromosome, DNA polymerase III, makes an error, there are two primary defenses against mutation: proofreading by the e subunit of the holoenzyme and mismatch repair. In proofreadingdeficient strains, mismatch repair is partially saturated and the cell’s response to DNA damage, the SOS response, may be partially induced. To investigate the nature of replication errors, we used mutation accumulation experiments and whole-genome sequencing to determine mutation rates and mutational spectra across the entire chromosome of strains deficient in proofreading, mismatch repair, and the SOS response. We report that a proofreading-deficient strain has a mutation rate 4000-fold greater than wild-type strains. While the SOS response may be induced in these cells, it does not contribute to the mutational load. Inactivating mismatch repair in a proofreading-deficient strain increases the mutation rate another 1.5-fold. DNA polymerase has a bias for converting G:C to A:T base pairs, but proofreading reduces the impact of these mutations, helping to maintain the genomic G:C content. These findings give an unprecedented view of how polymerase and error-correction pathways work together to maintain E. coli’s low mutation rate of 1 per 1000 generations.
KW - DNA proofreading
KW - DNA replication fidelity
KW - Mismatch repair
KW - Mutation accumulation
KW - Mutation hotspots
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U2 - 10.1534/genetics.117.300515
DO - 10.1534/genetics.117.300515
M3 - Article
C2 - 29907648
AN - SCOPUS:85050772153
SN - 0016-6731
VL - 209
SP - 1043
EP - 1054
JO - Genetics
JF - Genetics
IS - 4
ER -