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Consequently, all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids (RDHs).\n            <jats:italic>Escherichia coli<\/jats:italic>\n            lacking RNase HI (\n            <jats:italic>rnhA<\/jats:italic>\n            ) and RNase HII (\n            <jats:italic>rnhB<\/jats:italic>\n            ) enzymes, the \u2206\n            <jats:italic>rnhA<\/jats:italic>\n            \u2206\n            <jats:italic>rnhB<\/jats:italic>\n            double mutant, accumulates RDHs in its DNA. These RDHs can convert into RNA-containing DNA lesions (R-lesions) of unclear nature that compromise genomic stability. The \u2206\n            <jats:italic>rnhAB<\/jats:italic>\n            double mutant has severe phenotypes, like growth inhibition, replication stress, sensitivity to ultraviolet radiation, SOS induction, increased chromosomal fragmentation, and defects in nucleoid organization. In this study, we found that RNase HI deficiency also alters wild-type levels of DNA supercoiling. Despite these severe chromosomal complications, \u2206\n            <jats:italic>rnhAB<\/jats:italic>\n            double mutant survives, suggesting that dedicated pathways operate to avoid or repair R-lesions. To identify these pathways, we systematically searched for mutants synthetic lethal (colethal) with the\n            <jats:italic>rnhAB<\/jats:italic>\n            defect using an unbiased color screen and a candidate gene approach. We identified both novel and previously reported\n            <jats:italic>rnhAB<\/jats:italic>\n            -colethal and -coinhibited mutants, characterized them, and sorted them into avoidance or repair pathways. These mutants operate in various parts of nucleic acid metabolism, including replication fork progression, R-loop prevention and removal, nucleoid organization, tRNA modification, recombinational repair, and chromosome-dimer resolution, demonstrating the pleiotropic nature of RNase H deficiency.\n          <\/jats:p>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              Ribonucleotides (rNs) are structurally very similar to deoxyribonucleotides. Consequently, rN contamination of DNA is common and pervasive across all domains of life. Failure to remove rNs from DNA has severe consequences, and all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids. RNase H deficiency leads to complications in bacteria, yeast, and mouse, and diseases like progressive external ophthalmoplegia (mitochondrial defects in RNASEH1) and Aicardi-Gouti\u00e8res syndrome (defects in RNASEH2) in humans.\n              <jats:italic>Escherichia coli \u2206rnhAB<\/jats:italic>\n              mutant, deficient in RNases H, has severe chromosomal complications. Despite substantial problems, nearly half of the mutant population survives. We have identified novel and previously confirmed pathways in various parts of nucleic acid metabolism that ensure survival with RNase H deficiency.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/jb.00280-23","type":"journal-article","created":{"date-parts":[[2023,10,11]],"date-time":"2023-10-11T13:06:23Z","timestamp":1697029583000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["Synthetic lethal mutants in\n            <i>Escherichia coli<\/i>\n            define pathways necessary for survival with RNase H deficiency"],"prefix":"10.1128","volume":"205","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5482-7576","authenticated-orcid":false,"given":"Sneha","family":"Das","sequence":"first","affiliation":[{"name":"Department of Microbiology, University of Illinois Urbana-Champaign , Urbana, Illinois, 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