Debunking the dogma that RecBCD nuclease destroys phage

Clarence Zheng; Curtis Furukawa; Jerry Liu; Srishti Sankaran; Han Lin; Nidhi Munugeti; Meranda Wang; Gerald R Smith

doi:10.1093/genetics/iyae199

Debunking the dogma that RecBCD nuclease destroys phage

Genetics. 2024 Nov 28:iyae199. doi: 10.1093/genetics/iyae199. Online ahead of print.

Authors

Clarence Zheng¹, Curtis Furukawa², Jerry Liu³, Srishti Sankaran⁴, Han Lin⁵, Nidhi Munugeti⁶, Meranda Wang⁷, Gerald R Smith⁸

Affiliations

¹ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA.
² Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 916 145th Pl, NE Bellevue, WA 98007.
³ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 16347 NE 12th Pl, Bellevue, WA 98008.
⁴ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA Brown University, Providence, RI.
⁵ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 4654 SE Bakken Ct, Port Orchard, WA 98366.
⁶ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 1117 141st Pl NE, Bellevue, WA, 98005.
⁷ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 13450 NE 12th Pl, Bellevue, WA 98005.
⁸ Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109.

PMID: 39605281
DOI: 10.1093/genetics/iyae199

Abstract

For decades, it has been repeatedly claimed that the potent bacterial helicase-nuclease RecBCD (exonuclease V) destroys foreign (non-self) DNA, such as that of phages, but repairs and recombines cellular (self) DNA. While this would constitute a strong host-survival mechanism, no phage destroyed by RecBCD is ever specified in those claims. To determine which phages are destroyed by RecBCD, we searched for phage isolates that grow on Escherichia coli ΔrecBCD but not on recBCD+. In contrast to the prevailing claim, we found none among >80 new isolates from nature and >80 from previous collections. Based on these and previous observations, we conclude that RecBCD repairs broken DNA that can recombine but destroys DNA that cannot recombine and recycles the nucleotides.

Keywords: E. coli; RecBCD helicase-nuclease; environmental phages; phage destruction dogma.

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