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Helicobacter pylori has been recognized as the major cause of stomach cancer (gastric cancer), but the mechanism by which it destabilizes the human genome to cause cancer remains unclear. Our recent studies have identified a unique family of toxic restriction enzymes that excise a base (A: adenine) from their recognition sequence (5\u2032-GTAC). At the resulting abasic sites (5\u2032-GT_C), its inherent endonuclease activity or that of a separate endonuclease may yield atypical strand breaks that resist repair by ligation. Here, we present evidence demonstrating involvement of its H. pylori member, HpPabI, in stomach carcinogenesis: (i) Association of intact HpPabI gene with gastric cancer in the global H. pylori Genome Project and the open genomes; (ii) Frequent mutations at A in 5\u2032-GTAC in the gastric cancer genomes as well as in H. pylori genomes; (iii) Its induction of chromosomal double-strand breaks in infected human cells and of mutagenesis in bacterial test systems. In addition, its unique regions that interact with DNA exhibit signs of diversifying selection. Our further analysis revealed similar oncogenic bacterium\u2013restriction\u2013enzyme pairs for other types of cancer. These results set another stage for cancer research and medicine around oncogenic restriction enzymes.<\/jats:p>","DOI":"10.1093\/pnasnexus\/pgaf244","type":"journal-article","created":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T07:10:01Z","timestamp":1754377801000},"source":"Crossref","is-referenced-by-count":1,"title":["<i>Helicobacter pylori<\/i>\n                    base-excision restriction enzyme in stomach carcinogenesis"],"prefix":"10.1093","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2320-1529","authenticated-orcid":false,"given":"Masaki","family":"Fukuyo","sequence":"first","affiliation":[{"name":"Department of Molecular Oncology, Graduate School of Medicine, Chiba University , Chiba 260-8670 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noriko","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Kyorin University School of Medicine , Mitaka, Tokyo 181-8611 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,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7102-784X","authenticated-orcid":false,"given":"Takeshi","family":"Terabayashi","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Faculty of Medicine, Oita University , Yufu, Oita ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4759-4267","authenticated-orcid":false,"given":"Yukako","family":"Katsura","sequence":"additional","affiliation":[{"name":"Center for the Evolutionary Origins of Human Behavior, Kyoto University , Inuyama, Aichi 484-0081 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0180-5372","authenticated-orcid":false,"given":"Naoki","family":"Osada","sequence":"additional","affiliation":[{"name":"Graduate School of Information Science and Technology, Hokkaido University , Sapporo 060-0814 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6980-5515","authenticated-orcid":false,"given":"Atsushi","family":"Kaneda","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, Graduate School of Medicine, Chiba University , Chiba 260-8670 ,","place":["Japan"]},{"name":"Health and Disease Omics Center, Chiba University , Chiba 260-8670 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1065-2198","authenticated-orcid":false,"given":"M Constanza","family":"Camargo","sequence":"additional","affiliation":[{"name":"Division of Cancer Epidemiology and Genetics, National Cancer Institute , Rockville, MD 20878 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles S","family":"Rabkin","sequence":"additional","affiliation":[{"name":"Division of Cancer Epidemiology and Genetics, National Cancer 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Medicine , Mitaka, Tokyo 181-8611 ,","place":["Japan"]},{"name":"Laboratory of Genome Informatics, National Institute for Basic Biology , Okazaki 444-8585 ,","place":["Japan"]},{"name":"Research Institute for Micro-Nano Technology, Hosei University , Koganei, Tokyo 184-0003 ,","place":["Japan"]},{"name":"Department of Medical Genome Sciences, University of Tokyo , Minato-ku, Tokyo 108-8639 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,8,5]]},"reference":[{"key":"2026020603513821700_pgaf244-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/s41572-023-00431-8","article-title":"Helicobacter pylori infection","volume":"9","author":"Malfertheiner","year":"2023","journal-title":"Nat Rev Dis Primers"},{"key":"2026020603513821700_pgaf244-B2","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/s12915-018-0550-3","article-title":"A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk","volume":"16","author":"Berthenet","year":"2018","journal-title":"BMC Biol"},{"key":"2026020603513821700_pgaf244-B3","first-page":"000680","article-title":"Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates","volume":"7","author":"Tuan","year":"2021","journal-title":"Microb Genom"},{"key":"2026020603513821700_pgaf244-B4","first-page":"000676","article-title":"Genomic differentiation within East Asian Helicobacter pylori","volume":"8","author":"You","year":"2022","journal-title":"Microb Genom"},{"key":"2026020603513821700_pgaf244-B5","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1016\/S0016-5085(03)00266-X","article-title":"Chronic Helicobacter pylori infections induce gastric mutations in 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