{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T14:34:14Z","timestamp":1790346854858,"version":"4.1.0"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T00:00:00Z","timestamp":1684800000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host's environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replaced Escherichia coli's chromosomal folA gene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons of folA genes from trimethoprim-sensitive Listeria grayi and trimethoprim-resistant Neisseria sicca. The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5\u2032-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5\u2032-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host's environment in shaping the codon bias compatibility of horizontally transferred genes.<\/jats:p>","DOI":"10.1093\/molbev\/msad123","type":"journal-article","created":{"date-parts":[[2023,5,23]],"date-time":"2023-05-23T21:05:27Z","timestamp":1684875927000},"source":"Crossref","is-referenced-by-count":13,"title":["The Fitness Effects of Codon Composition of the Horizontally Transferred Antibiotic Resistance Genes Intensify at Sub-lethal Antibiotic Levels"],"prefix":"10.1093","volume":"40","author":[{"given":"Michael","family":"Shaferman","sequence":"first","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melis","family":"Gencel","sequence":"additional","affiliation":[{"name":"Departement de Biochimie, Universite de Montreal , Montreal, Quebec , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noga","family":"Alon","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khawla","family":"Alasad","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barak","family":"Rotblat","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva , Israel"},{"name":"Ben-Gurion University of the Negev, National Institute for Biotechnology in the Negev (NIBN) , Beer-Sheva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian W R","family":"Serohijos","sequence":"additional","affiliation":[{"name":"Departement de Biochimie, Universite de Montreal , Montreal, Quebec , Canada"},{"name":"Centre Robert-Cedergren en Bio-informatique et Genomique, Universite de Montreal , Montreal, Quebec , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lital","family":"Alfonta","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva , Israel"},{"name":"Department of Chemistry, Ben-Gurion University of the Negev , Beer-Sheva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shimon","family":"Bershtein","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,23]]},"reference":[{"key":"2023060914134906300_msad123-B1","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1038\/s41419-020-03182-6","article-title":"4EBP1\/2 are active under standard cell culture conditions to regulate the translation of specific mRNAs","volume":"11","author":"Alasad","year":"2020","journal-title":"Cell Death Dis"},{"key":"2023060914134906300_msad123-B2","doi-asserted-by":"crossref","first-page":"2141","DOI":"10.1093\/molbev\/msq103","article-title":"Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage","volume":"27","author":"Amoros-Moya","year":"2010","journal-title":"Mol Biol Evol"},{"key":"2023060914134906300_msad123-B3","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/msb.2013.32","article-title":"Efficient translation initiation dictates codon usage at gene 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