{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T13:29:02Z","timestamp":1787232542341,"version":"build-2736575974"},"reference-count":24,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2021\/10577-0"],"award-info":[{"award-number":["2021\/10577-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2021\/00610-0"],"award-info":[{"award-number":["2021\/00610-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2026,8,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Phosphonates are alternative phosphorus sources widely present in environmental settings and in commercially relevant compounds such as pesticides and antibiotics. In\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      , uptake and assimilation of phosphonates are mediated by the 14-gene\n                      <jats:italic toggle=\"yes\">phnCDEFGHIJKLMNOP<\/jats:italic>\n                      operon. In the laboratory, strain K-12 and its derivatives,\n                      <jats:italic toggle=\"yes\">phnE<\/jats:italic>\n                      , encoding the phosphonate permease, carry an 8 bp insertion that causes a frameshift and premature termination. Early studies reported unusually high frequencies of\n                      <jats:italic toggle=\"yes\">phn<\/jats:italic>\n                      revertants selected on phosphonates as the sole phosphorus source. Separately, high cell density has been proposed to suppress mutation emergence in multiple systems. Here, we reexamined the frequency of\n                      <jats:italic toggle=\"yes\">phn<\/jats:italic>\n                      revertants in\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      K-12. When phosphate impurities were rigorously eliminated from the medium, estimated revertant frequencies decreased by orders of magnitude, contradicting earlier reports. Revertant frequency was not significantly affected by bacterial density on selective plates. Furthermore, under phosphate-limiting conditions, the presence of a functional\n                      <jats:italic toggle=\"yes\">phnE<\/jats:italic>\n                      allele did not confer a measurable fitness advantage. Finally, an\n                      <jats:italic toggle=\"yes\">in silico<\/jats:italic>\n                      survey revealed that approximately 15% of\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      strains lack functional\n                      <jats:italic toggle=\"yes\">phn<\/jats:italic>\n                      genes, suggesting that loss of phosphonate utilization may be favored in specific ecological or physiological contexts.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Phosphonates are an important phosphorus reservoir in many environments, and their utilization by\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      depends on the\n                      <jats:italic toggle=\"yes\">phn<\/jats:italic>\n                      operon. This study reexamines the unusually high frequencies of\n                      <jats:italic toggle=\"yes\">phnE<\/jats:italic>\n                      revertants reported for laboratory K-12 strains. By controlling for phosphate contamination in selective media, we show that reversion frequencies are substantially lower than previously estimated and largely independent of cell density. We further find that restoration of\n                      <jats:italic toggle=\"yes\">phnE<\/jats:italic>\n                      function does not confer a detectable fitness advantage under phosphate limitation. Consistent with this observation, genomic analyses reveal that loss of\n                      <jats:italic toggle=\"yes\">phn<\/jats:italic>\n                      function is common among natural\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      isolates. Together, these findings suggest that loss of\n                      <jats:italic toggle=\"yes\">phn<\/jats:italic>\n                      function may represent an adaptive strategy in a substantial fraction of natural populations.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/jb.00073-26","type":"journal-article","created":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T16:29:51Z","timestamp":1784046591000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["<i>phnE<\/i>\n                    frameshift reversion frequency: beyond density effects to genomic prevalence"],"prefix":"10.1128","volume":"208","author":[{"given":"Lu\u00edsa Andrea","family":"Villanueva da Fonseca","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/036rp1748","id-type":"ROR","asserted-by":"publisher"}],"name":"Departamento de Microbiologia, Instituto de Ci\u00eancias Biom\u00e9dicas Universidade de S\u00e3o Paulo","place":["S\u00e3o Paulo, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Caldas Leite","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/036rp1748","id-type":"ROR","asserted-by":"publisher"}],"name":"Departamento de Microbiologia, Instituto de Ci\u00eancias Biom\u00e9dicas Universidade de S\u00e3o Paulo","place":["S\u00e3o Paulo, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5394-9074","authenticated-orcid":true,"given":"Beny","family":"Spira","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/036rp1748","id-type":"ROR","asserted-by":"publisher"}],"name":"Departamento de Microbiologia, Instituto de Ci\u00eancias Biom\u00e9dicas Universidade de S\u00e3o Paulo","place":["S\u00e3o Paulo, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1023\/a:1000530927928"},{"key":"e_1_3_3_3_2","first-page":"1357","volume-title":"Escherichia coli and Salmonella: cellular and molecular biology","author":"Wanner BL","year":"1996","unstructured":"Wanner BL. 1996. Phosphorus assimilation and control of the phosphate regulon, p 1357\u20131381. In Escherichia coli and Salmonella: cellular and molecular biology. Vol. 1."},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/bies.201800091"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12010-019-03161-4"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.h3783"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-019-1445-3"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.78.091707.100215"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.173.8.2665-2672.1991"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.18.6118-6123.2004"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.06094-11"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4742"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-020-00913-1"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(71)90051-9"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF03175618"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mrgentox.2015.04.008"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/162.1.5"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/128.4.695"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-021-01751-6"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56851-5"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa010"},{"key":"e_1_3_3_22_2","volume-title":"A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria","author":"Miller JH","year":"1992","unstructured":"Miller JH. 1992. A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y."},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac60119a033"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-018-1191-4"},{"key":"e_1_3_3_25_2","unstructured":"JASP Team. 2025. JASP (Version 0.95.4)."}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jb.00073-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jb.00073-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T13:02:48Z","timestamp":1787230968000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/jb.00073-26"}},"subtitle":[],"editor":[{"given":"Melissa M.","family":"Kendall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,20]]},"references-count":24,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,20]]}},"alternative-id":["10.1128\/jb.00073-26"],"URL":"https:\/\/doi.org\/10.1128\/jb.00073-26","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,20]]},"assertion":[{"value":"2026-02-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-02","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00073-26"}}