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Given the high frequency with which RNA is found in DNA, it is unknown which bacterial DNA polymerases are responsible for catalyzing RNA-dependent DNA synthesis. In this work, we establish bacterial DNA polymerase I (Pol I), a robust reverse transcriptase (RT), as the primary bypass enzyme. We tested several bacterial Pol I enzymes and found that all possess RT activity, with Bacillus subtilis Pol I showing robust RNA-dependent DNA synthesis activity similar to the Moloney murine leukemia virus RT. In contrast, template RNA slowed or blocked DNA synthesis by B. subtilis replicative C-family DNA polymerases PolC and DnaE. We tested several substrates with increasing patches of consecutive ribonucleotides in DNA and found that a single ribonucleotide slows synthesis by PolC, while DnaE can traverse a patch of five consecutive ribonucleotides. Therefore, DnaE activity would allow for ribonucleotide bypass of short patches, while Pol I could bypass longer stretches up to 40 nt in length. We conclude that Pol I and DnaE are responsible for RNA-templated DNA replication, establishing the DNA polymerase hierarchy for navigating RNA tracts that become integrated into genomic DNA.<\/jats:p>","DOI":"10.1093\/nar\/gkag971","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T11:46:12Z","timestamp":1790941572000},"source":"Crossref","is-referenced-by-count":0,"title":["DNA polymerase I and DnaE mediate RNA-templated DNA synthesis over embedded ribonucleotides"],"prefix":"10.1093","volume":"54","author":[{"given":"Frances C","family":"Lowder","sequence":"first","affiliation":[{"name":"Department of Molecular, Cellular, and Developmental Biology, University of Michigan , Ann Arbor, MI 48109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail H","family":"Kendal","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular, and Developmental Biology, University of Michigan , Ann Arbor, MI 48109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9600-7623","authenticated-orcid":false,"given":"Lyle A","family":"Simmons","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular, and Developmental Biology, University of Michigan , Ann Arbor, MI 48109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,8]]},"reference":[{"key":"2026100805075989600_B1","doi-asserted-by":"publisher","first-page":"181","DOI":"10.3109\/10409238.2014.981647","article-title":"Ribonucleotides in bacterial DNA","volume":"50","author":"Schroeder","year":"2015","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"2026100805075989600_B2","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1073\/pnas.59.2.598","article-title":"Mechanism of DNA chain growth. 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