RnhP is a plasmid‐borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610

RNA‐DNA hybrids form throughout the chromosome during normal growth and under stress conditions. When left unresolved, RNA‐DNA hybrids can slow replication fork progression, cause DNA breaks, and increase mutagenesis. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degr...

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Bibliographic Details
Published in:Molecular microbiology 2021-01, Vol.115 (1), p.99-115
Main Authors: Nye, Taylor M., McLean, Emma K., Burrage, Andrew M., Dennison, Devon D., Kearns, Daniel B., Simmons, Lyle A.
Format: Article
Language:English
Subjects:
Amino Acid Sequence - genetics
Bacillus subtilis
Bacillus subtilis - genetics
Bacillus subtilis - metabolism
Bacillus subtilis ribonuclease
Cell division
Chromosomes
Deoxyribonucleic acid
DNA
DNA - genetics
DNA biosynthesis
DNA damage
DNA Replication - genetics
Enzymes
Genomes
Genomic Instability - genetics
Growth rate
Hybrids
Mutagenesis
NCIB 310
Okazaki fragments
Plasmids - genetics
Replication
Ribonuclease H
Ribonuclease H - genetics
Ribonuclease H - metabolism
Ribonuclease H1
Ribonuclease H2
Ribonucleic acid
RNA
RNA - metabolism
RNase HI
RNA‐DNA hybrid
SOS response
Stability
Substrate Specificity - genetics
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Summary:RNA‐DNA hybrids form throughout the chromosome during normal growth and under stress conditions. When left unresolved, RNA‐DNA hybrids can slow replication fork progression, cause DNA breaks, and increase mutagenesis. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degrade the RNA portion. Here we show that, in addition to chromosomally encoded RNase HII and RNase HIII, Bacillus subtilis NCIB 3610 encodes a previously uncharacterized RNase HI protein, RnhP, on the endogenous plasmid pBS32. Like other RNase HI enzymes, RnhP incises Okazaki fragments, ribopatches, and a complementary RNA‐DNA hybrid. We show that while chromosomally encoded RNase HIII is required for pBS32 hyper‐replication, RnhP compensates for the loss of RNase HIII activity on the chromosome. Consequently, loss of RnhP and RNase HIII impairs bacterial growth. We show that the decreased growth rate can be explained by laggard replication fork progression near the terminus region of the right replichore, resulting in SOS induction and inhibition of cell division. We conclude that all three functional RNase H enzymes are present in B. subtilis NCIB 3610 and that the plasmid‐encoded RNase HI contributes to chromosome stability, while the chromosomally encoded RNase HIII is important for chromosome stability and plasmid hyper‐replication. We have discovered an RNase HI (RnhP) encoded on the 84 Kbp endogenous plasmid of ancestral Bacillus subtilis strain NCIB 3610. RnhP has an overlapping function with RNase HIII and it serves to resolve several types of RNA‐DNA hybrids that can impact genome integrity. While neither RNase HIII nor RhnP contributes to plasmid maintenance, chromosome‐encoded RNase HIII is required for plasmid hyper‐replication.
ISSN:0950-382X
1365-2958
DOI:10.1111/mmi.14601