{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T04:59:26Z","timestamp":1780981166185,"version":"3.54.1"},"reference-count":96,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T00:00:00Z","timestamp":1780963200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Biosci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Enterococcus faecalis<\/jats:italic>\n                      survives antibiotic exposure through coordinated regulatory programs that extend beyond single resistance determinants, yet the systems-level organization of transcriptional and post-transcriptional control under clinically relevant antibiotic stress remains incompletely defined.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Here, we analyzed RNA-seq profiles of\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      V583 exposed to vancomycin or ceftriaxone and reconstructed antibiotic-activated, integrative transcriptional regulatory networks (TRNs) by projecting differentially expressed genes onto a curated TF\u2013target template and explicitly incorporating antisense ncRNA-mRNA predicted links.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Both antibiotics activated a substantial shared response dominated by envelope remodeling\/proteostasis and bioenergetic\u2013nucleotide economy, while vancomycin recruited a broader condition-specific program. Despite differing scale (Van-TRN: 533 nodes\/587 edges; Cef-TRN: 375 nodes\/431 edges), both networks displayed sparse, hub-centered hierarchies and strong nesting, with \u223c90% of ceftriaxone regulation contained within the vancomycin scaffold. From the shared ncRNA layer, we prioritized two inducible\n                      <jats:italic>cis<\/jats:italic>\n                      -antisense candidates, ncRNA3340 and ncRNA3683, exhibiting modular, multi-branch predicted folds, dual-site\n                      <jats:italic>cis<\/jats:italic>\n                      targeting, and energetics consistent with strong\n                      <jats:italic>cis<\/jats:italic>\n                      pairing and weaker but favorable\n                      <jats:italic>trans<\/jats:italic>\n                      interactions. Both ncRNAs were globally conserved across 687 clinical isolates, with low variability concentrated outside interaction-defined binding regions. Trans-target prediction points to ncRNA3340 as potentially associated with genome maintenance and cell-surface mRNAs, and ncRNA3683 with GA-like domain, glycine-alanine-rich transcripts, and a bacteriocin locus. Finally, qPCR corroborated the antibiotic-induced transcriptional changes observed for both ncRNAs.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Together, these results provide an integrated TRN framework that connects network rewiring to conserved ncRNA-centered candidate control during vancomycin and ceftriaxone stress responses, prioritizing testable ncRNA regulons for downstream functional validation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmolb.2026.1798522","type":"journal-article","created":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T04:28:00Z","timestamp":1780979280000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptional regulatory network analysis identifies conserved cis-antisense ncRNAs in the vancomycin and ceftriaxone stress response of Enterococcus faecalis"],"prefix":"10.3389","volume":"13","author":[{"given":"Javiera","family":"Pino-Gaete","sequence":"first","affiliation":[{"name":"Laboratorio de Bioingenier\u00eda; Instituto de Ciencias de La Ingenier\u00eda; Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August University G\u00f6ttingen","place":["G\u00f6ttingen, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Torres","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioingenier\u00eda; Instituto de Ciencias de La Ingenier\u00eda; Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximiliano","family":"V\u00e9liz-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00e9tica Del Desarrollo, Departamento de Biolog\u00eda, Facultad de Ciencias, Universidad de Chile","place":["Santiago, Chile"]},{"name":"Millennium Institute Center for Genome Regulation","place":["Santiago, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaime","family":"Ortega","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioingenier\u00eda; Instituto de Ciencias de La Ingenier\u00eda; Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gladis","family":"Serrano","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioingenier\u00eda; Instituto de Ciencias de La Ingenier\u00eda; Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"G\u00e1lvez","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioingenier\u00eda; Instituto de Ciencias de La Ingenier\u00eda; Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Di Genova","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Computational Biology Lab, Instituto de Ciencias de La Ingenier\u00eda, Universidad de O\u2019Higgins","place":["Rancagua, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c1lvaro","family":"Glavic","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00e9tica Del Desarrollo, Departamento de Biolog\u00eda, Facultad de Ciencias, Universidad de Chile","place":["Santiago, Chile"]},{"name":"Millennium Institute Center for Genome Regulation","place":["Santiago, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Panesso-Botero","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital","place":["Houston, TX, United States"]},{"name":"Center for Infectious Diseases, Houston Methodist Research Institute","place":["Houston, TX, United States"]},{"name":"Department of Medicine, Weill Cornell Medical College, Weill Cornell Medical College","place":["New York, NY, United States"]},{"name":"Molecular Genetics and Antimicrobial Resistance Unit (UGRA), Universidad El Bosque","place":["Bogot\u00e1, Colombia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ra\u00fal","family":"Mera-Adasme","sequence":"additional","affiliation":[{"name":"Departamento de Qu\u00edmica, Facultad de Ciencias, Universidad de Tarapac\u00e1","place":["Arica, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Parra","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Laboratory for Cell Differentiation and Metabolism, Department of Biochemistry and Molecular Biology, Facultad de Ciencias Qu\u00edmicas y Farmac\u00e9uticas, Universidad de Chile","place":["Santiago, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V\u00edctor","family":"Aliaga-Tobar","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Gen\u00f3mica y Bioinform\u00e1tica, Facultad de Ciencias, Ingenier\u00eda y Tecnolog\u00eda, Universidad Mayor","place":["Santiago, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mauricio","family":"Latorre","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioingenier\u00eda; Instituto de Ciencias de La Ingenier\u00eda; Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Centro de Biolog\u00eda de Sistemas para el Estudio de Comunidades Extrem\u00f3filas de Relaves Mineros (SYSTEMIX), Universidad de O\u2019Higgins","place":["Rancagua, Chile"]},{"name":"Millennium Institute Center for Genome Regulation","place":["Santiago, Chile"]},{"name":"Center for Mathematical Modeling, University of Chile","place":["Santiago, Chile"]},{"name":"Laboratorio de Bioinform\u00e1tica y Expresi\u00f3n G\u00e9nica, INTA, Universidad de Chile","place":["Santiago, Chile"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","first-page":"e64875","DOI":"10.1371\/journal.pone.0064875","article-title":"The cell wall-targeting antibiotic stimulon of Enterococcus faecalis","volume":"8","author":"Abranches","year":"2014","journal-title":"PLoS One"},{"key":"B3","doi-asserted-by":"publisher","first-page":"e26519","DOI":"10.1371\/journal.pone.0026519","article-title":"Impact of manganese, copper and zinc ions on the transcriptome of the nosocomial pathogen Enterococcus faecalis V583","volume":"6","author":"Abrantes","year":"2011","journal-title":"PLoS One"},{"key":"B4","doi-asserted-by":"publisher","first-page":"126629","DOI":"10.1016\/j.micres.2020.126629","article-title":"Participation of two sRNA RyhB homologs from the fish pathogen Yersinia ruckeri in bacterial physiology","volume":"242","author":"Acu\u00f1a","year":"2021","journal-title":"Microbiol. Res."},{"key":"B5","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1111\/omi.12391","article-title":"Transition metals and enterococcus faecalis: homeostasis, virulence and perspectives","volume":"37","author":"Ali","year":"2022","journal-title":"Mol. Oral Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"e0124025","DOI":"10.1128\/msystems.01240-25","article-title":"Reduced glutathione levels in Enterococcus faecalis trigger metabolic and transcriptional compensatory adjustments during iron exposure","volume":"11","author":"Aliaga-Tobar","year":"2026","journal-title":"mSystems"},{"key":"B7","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq--a python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"B8","unstructured":"FASTQC. A quality control tool for high throughput sequence data\n          \n          \n            \n              Andrews\n              S.\n            \n          \n          \n          2010"},{"key":"B9","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1038\/nrmicro2761","article-title":"The rise of the enterococcus: beyond vancomycin resistance","volume":"10","author":"Arias","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e00057-20","DOI":"10.1128\/mSystems.00057-20","article-title":"Inference of bacterial small RNA regulatory networks and integration with transcription factor-driven regulatory networks","volume":"5","author":"Arrieta-Ortiz","year":"2020","journal-title":"mSystems"},{"key":"B11","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1093\/bioinformatics\/btn208","article-title":"Cytoscape ESP: simple search of complex biological networks","volume":"24","author":"Ashkenazi","year":"2008","journal-title":"Bioinformatics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1093\/bioinformatics\/btp101","article-title":"ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks","volume":"25","author":"Bindea","year":"2009","journal-title":"Bioinformatics"},{"key":"B13","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B14","doi-asserted-by":"publisher","first-page":"128379","DOI":"10.1016\/j.micres.2025.128379","article-title":"Evolution of Listeria monocytogenes to a strong biofilm producer via the overexpression of Lmo1799","volume":"303","author":"Bombelli","year":"2026","journal-title":"Microbiol. Res."},{"key":"B15","doi-asserted-by":"publisher","first-page":"R110","DOI":"10.1186\/gb-2008-9-7-r110","article-title":"Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF","volume":"9","author":"Bourgogne","year":"2008","journal-title":"Genome Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"2849","DOI":"10.1093\/bioinformatics\/btn544","article-title":"IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions","volume":"24","author":"Busch","year":"2008","journal-title":"Bioinformatics"},{"key":"B17","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinforma."},{"key":"B18","doi-asserted-by":"publisher","first-page":"S11","DOI":"10.1186\/1752-0509-8-s4-s11","article-title":"cytoHubba: identifying hub objects and sub-networks from complex interactome","volume":"8","author":"Chin","year":"2014","journal-title":"BMC Syst. Biol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1128\/iai.01034-08","article-title":"Multiple functional domains of Enterococcus faecalis aggregation substance Asc10 contribute to endocarditis virulence","volume":"77","author":"Chuang","year":"2009","journal-title":"Infect. Immun."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"e00228-19","DOI":"10.1128\/mSphere.00228-19","article-title":"Genomewide profiling of the Enterococcus faecalis transcriptional response to teixobactin reveals CroRS as an essential regulator of antimicrobial tolerance","volume":"4","author":"Darnell","year":"2019","journal-title":"mSphere"},{"key":"B22","doi-asserted-by":"publisher","first-page":"6112","DOI":"10.1038\/s41598-021-85509-7","article-title":"Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli","volume":"11","author":"Deter","year":"2021","journal-title":"Sci. Rep."},{"key":"B23","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/0378-1119(93)90779-3","article-title":"The vanB gene of vancomycin-resistant Enterococcus faecalis V583 is structurally related to genes encoding D-Ala:D-Ala ligases and glycopeptide-resistance proteins VanA and VanC","volume":"124","author":"Evers","year":"1993","journal-title":"Gene"},{"key":"B24","doi-asserted-by":"publisher","first-page":"10286","DOI":"10.1073\/pnas.1702581114","article-title":"Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities","volume":"114","author":"Fang","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1696","DOI":"10.1128\/iai.01210-12","article-title":"AhrC and eep are biofilm infection-associated virulence factors in Enterococcus faecalis","volume":"81","author":"Frank","year":"2013","journal-title":"Infect. Immun."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1994","DOI":"10.1099\/mic.0.060236-0","article-title":"Global transcriptional analysis of the stringent response in Enterococcus faecalis","volume":"158","author":"Gaca","year":"2012","journal-title":"Microbiol. Read."},{"key":"B27","doi-asserted-by":"publisher","first-page":"e00058-18","DOI":"10.1128\/cmr.00058-18","article-title":"The enterococcus: a model of adaptability to its environment","volume":"32","author":"Garc\u00eda-Solache","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"B28","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1128\/mmbr.00032-10","article-title":"cis-antisense RNA, another level of gene regulation in bacteria","volume":"75","author":"Georg","year":"2011","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B29","doi-asserted-by":"publisher","first-page":"11512","DOI":"10.1073\/pnas.1706236114","article-title":"Maladaptive DNA repair is the ultimate contributor to the death of trimethoprim-treated cells under aerobic and anaerobic conditions","volume":"114","author":"Giroux","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B30","doi-asserted-by":"publisher","first-page":"a003798","DOI":"10.1101\/cshperspect.a003798","article-title":"Bacterial small RNA regulators: versatile roles and rapidly evolving variations","volume":"3","author":"Gottesman","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"4507","DOI":"10.1073\/pnas.1620432114","article-title":"Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans","volume":"114","author":"Graham","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B32","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1111\/mmi.14431","article-title":"Enterococcus faecalis MalR acts as a repressor of the maltose operons and additionally mediates their catabolite repression via direct interaction with seryl-phosphorylated-HPr","volume":"113","author":"Grand","year":"2020","journal-title":"Mol. Microbiol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"W70","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"16239","DOI":"10.1038\/nmicrobiol.2016.239","article-title":"GRIL-Seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation","volume":"2","author":"Han","year":"2016","journal-title":"Nat. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"127825","DOI":"10.1016\/j.micres.2024.127825","article-title":"Small RNA-Regulated expression of efflux pump affects tigecycline resistance and heteroresistance in clinical isolates of Klebsiella pneumoniae","volume":"287","author":"Han","year":"2024","journal-title":"Microbiol. Res."},{"key":"B36","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1016\/j.tim.2009.06.004","article-title":"LPxTG surface proteins of enterococci","volume":"17","author":"Hendrickx","year":"2009","journal-title":"Trends Microbiol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/978-1-60761-629-0_9","article-title":"Detection of antisense RNA transcripts by strand-specific RT-PCR","volume":"630","author":"Ho","year":"2010","journal-title":"Methods Mol. Biol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"421","DOI":"10.4161\/viru.21282","article-title":"Intrinsic and acquired resistance mechanisms in enterococcus","volume":"3","author":"Hollenbeck","year":"2012","journal-title":"Virulence"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1261\/rna.048470.114","article-title":"Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis","volume":"21","author":"Innocenti","year":"2015","journal-title":"Rna"},{"key":"B40","doi-asserted-by":"publisher","first-page":"2005","DOI":"10.1101\/2022.05.05.490712","article-title":"VanRS and CroRS cross-talk revealed by coevolutionary modeling regulates antibiotic resistance in VanA-type vancomycin-resistant Enterococcus faecalis","volume":"2022","author":"Jiang","year":"2022","journal-title":"bioRxiv"},{"key":"B41","doi-asserted-by":"publisher","first-page":"128195","DOI":"10.1016\/j.micres.2025.128195","article-title":"Xanthocillin X combats burkholderia pseudomallei by targeting UDP-N-acetylglucosamine acyltransferase","volume":"298","author":"Jiang","year":"","journal-title":"Microbiol. Res."},{"key":"B42","doi-asserted-by":"publisher","first-page":"128196","DOI":"10.1016\/j.micres.2025.128196","article-title":"Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance","volume":"297","author":"Jiang","year":"","journal-title":"Microbiol. Res."},{"key":"B43","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/0014-5793(95)01121-t","article-title":"The GA module, a Mobile albumin-binding bacterial domain, adopts a three-helix-bundle structure","volume":"374","author":"Johansson","year":"1995","journal-title":"FEBS Lett."},{"key":"B44","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1006\/jmbi.1996.0856","article-title":"Solution structure of the albumin-binding GA module: a versatile bacterial protein domain","volume":"266","author":"Johansson","year":"1997","journal-title":"J. Mol. Biol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B46","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief. Bioinform"},{"key":"B47","doi-asserted-by":"publisher","first-page":"e02461-16","DOI":"10.1128\/aac.02461-16","article-title":"Requirement of the CroRS two-component system for resistance to cell wall-targeting antimicrobials in Enterococcus faecium","volume":"61","author":"Kellogg","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"B48","doi-asserted-by":"publisher","first-page":"3377","DOI":"10.1093\/bioinformatics\/btv372","article-title":"Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams","volume":"31","author":"Kerpedjiev","year":"2015","journal-title":"Bioinformatics"},{"key":"B49","doi-asserted-by":"publisher","first-page":"e00199","DOI":"10.1128\/mBio.00199-11","article-title":"Reciprocal regulation of cephalosporin resistance in Enterococcus faecalis","volume":"2","author":"Kristich","year":"2011","journal-title":"mBio"},{"key":"B50","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B51","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1016\/j.bbrc.2011.02.109","article-title":"CutC is induced late during copper exposure and can modify intracellular copper content in Enterococcus faecalis","volume":"406","author":"Latorre","year":"2011","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B52","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1039\/c3mt00288h","article-title":"Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels","volume":"6","author":"Latorre","year":"2014","journal-title":"Metallomics"},{"key":"B53","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.3389\/fmicb.2018.01580","article-title":"The role of Fur in the transcriptional and iron homeostatic response of Enterococcus faecalis","volume":"9","author":"Latorre","year":"2018","journal-title":"Front. Microbiol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B55","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1016\/j.molcel.2011.08.023","article-title":"Engineering biological systems with synthetic RNA molecules","volume":"43","author":"Liang","year":"2011","journal-title":"Mol. Cell"},{"key":"B56","doi-asserted-by":"publisher","first-page":"8488","DOI":"10.1073\/pnas.1314810111","article-title":"Visual account of protein investment in cellular functions","volume":"111","author":"Liebermeister","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B57","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1007\/s10534-012-9539-5","article-title":"Transcriptomic response of Enterococcus faecalis to iron excess","volume":"25","author":"L\u00f3pez","year":"2012","journal-title":"Biometals"},{"key":"B58","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol. Biol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"B60","doi-asserted-by":"publisher","first-page":"W435","DOI":"10.1093\/nar\/gkx279","article-title":"IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions","volume":"45","author":"Mann","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B61","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1073\/pnas.0401799101","article-title":"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure","volume":"101","author":"Mathews","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B62","doi-asserted-by":"publisher","first-page":"3599","DOI":"10.1128\/iai.01900-14","article-title":"Involvement of Enterococcus faecalis small RNAs in stress response and virulence","volume":"82","author":"Michaux","year":"2014","journal-title":"Infect. Immun."},{"key":"B63","doi-asserted-by":"publisher","first-page":"600325","DOI":"10.3389\/fcimb.2020.600325","article-title":"Single-nucleotide RNA maps for the two major nosocomial pathogens Enterococcus faecalis and Enterococcus faecium","volume":"10","author":"Michaux","year":"2020","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"5216","DOI":"10.1128\/jb.175.16.5216-5223.1993","article-title":"Generation of restriction map of Enterococcus faecalis OG1 and investigation of growth requirements and regions encoding biosynthetic function","volume":"175","author":"Murray","year":"1993","journal-title":"J. Bacteriol."},{"key":"B65","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.micres.2019.04.004","article-title":"Quorum-dependent expression of rsmX and rsmY, small non-coding RNAs, in Pseudomonas syringae","author":"Nakatsu","year":"2019","journal-title":"Microbiol. Res."},{"key":"B66","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1146\/annurev-biophys-070816-034058","article-title":"Integration of bacterial small RNAs in regulatory networks","volume":"46","author":"Nitzan","year":"2017","journal-title":"Annu. Rev. Biophys."},{"key":"B67","doi-asserted-by":"publisher","first-page":"20435","DOI":"10.1073\/pnas.1009784107","article-title":"Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA","volume":"107","author":"Papenfort","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B68","doi-asserted-by":"publisher","first-page":"14249","DOI":"10.1073\/pnas.0503838102","article-title":"Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains","volume":"102","author":"Pichon","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B69","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1128\/aac.22.5.816","article-title":"Pharmacokinetic characteristics of intravenous ceftriaxone in normal adults","volume":"22","author":"Pollock","year":"1982","journal-title":"Antimicrob. Agents Chemother."},{"key":"B70","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"B71","doi-asserted-by":"publisher","first-page":"3001","DOI":"10.1099\/mic.0.053314-0","article-title":"Lipoproteins of enterococcus faecalis: bioinformatic identification, expression analysis and relation to virulence","volume":"157","author":"Reffuveille","year":"2011","journal-title":"Microbiol. Read."},{"key":"B72","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1099\/mic.0.055319-0","article-title":"The prolipoprotein diacylglyceryl transferase (lgt) of Enterococcus faecalis contributes to virulence","volume":"158","author":"Reffuveille","year":"2012","journal-title":"Microbiol. Read."},{"key":"B73","doi-asserted-by":"publisher","first-page":"3064","DOI":"10.1128\/iai.00161-08","article-title":"Characterization of the ers regulon of Enterococcus faecalis","volume":"76","author":"Riboulet-Bisson","year":"2008","journal-title":"Infect. Immun."},{"key":"B74","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/j.ijfoodmicro.2008.06.022","article-title":"Ers a Crp\/fnr-Like transcriptional regulator of Enterococcus faecalis","volume":"131","author":"Riboulet-Bisson","year":"2009","journal-title":"Int. J. Food Microbiol."},{"key":"B75","doi-asserted-by":"publisher","first-page":"e00361-18","DOI":"10.1128\/mBio.00361-18","article-title":"Structural and regulatory changes in PBP4 trigger decreased \u03b2-Lactam susceptibility in Enterococcus faecalis","volume":"9","author":"Rice","year":"2018","journal-title":"mBio"},{"key":"B76","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.1105\/tpc.109.066001","article-title":"Real-time quantitative RT-PCR: design, calculations, and statistics","volume":"21","author":"Rieu","year":"2009","journal-title":"Plant Cell"},{"key":"B77","doi-asserted-by":"publisher","first-page":"e45","DOI":"10.1093\/nar\/gkp045","article-title":"Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data","volume":"37","author":"Ruijter","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B78","doi-asserted-by":"publisher","first-page":"5536","DOI":"10.1038\/s41467-019-13483-w","article-title":"The Escherichia coli transcriptome mostly consists of independently regulated modules","volume":"10","author":"Sastry","year":"2019","journal-title":"Nat. Commun."},{"key":"B79","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1016\/j.mib.2006.08.007","article-title":"Transcriptional regulatory networks in bacteria: from input signals to output responses","volume":"9","author":"Seshasayee","year":"2006","journal-title":"Curr. Opin. Microbiol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"B81","doi-asserted-by":"publisher","first-page":"e23948","DOI":"10.1371\/journal.pone.0023948","article-title":"Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583","volume":"6","author":"Shioya","year":"2011","journal-title":"PLoS One"},{"key":"B82","doi-asserted-by":"publisher","first-page":"4280","DOI":"10.1111\/febs.12856","article-title":"Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis","volume":"281","author":"\u0160kerlov\u00e1","year":"2014","journal-title":"Febs J."},{"key":"B83","doi-asserted-by":"publisher","first-page":"xtae030","DOI":"10.1093\/femsmc\/xtae030","article-title":"Arginine impacts aggregation, biofilm formation, and antibiotic susceptibility in Enterococcus faecalis","volume":"5","author":"Snell","year":"2024","journal-title":"FEMS Microbes"},{"key":"B84","doi-asserted-by":"publisher","first-page":"4890","DOI":"10.1093\/nar\/gkr037","article-title":"Antisense RNA protects mRNA from RNase E degradation by RNA\u2013RNA duplex formation during phage infection","volume":"39","author":"Stazic","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"B85","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1002\/pro.3819","article-title":"Molecular mechanisms of vancomycin resistance","volume":"29","author":"Stogios","year":"2020","journal-title":"Protein Sci."},{"key":"B86","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1016\/j.molcel.2011.08.022","article-title":"Regulation by small RNAs in bacteria: expanding frontiers","volume":"43","author":"Storz","year":"2011","journal-title":"Mol. Cell"},{"key":"B87","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s12864-015-2307-5","article-title":"Comprehensive prediction of lncRNA-RNA interactions in human transcriptome","volume":"17","author":"Terai","year":"2016","journal-title":"BMC Genomics"},{"key":"B88","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1128\/aac.45.3.973-975.2001","article-title":"Restoration of vancomycin susceptibility in Enterococcus faecalis by antiresistance determinant gene transfer","volume":"45","author":"Torres Viera","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"B89","doi-asserted-by":"publisher","first-page":"127997","DOI":"10.1016\/j.micres.2024.127997","article-title":"Listeria monocytogenes colonises established multispecies biofilms and resides within them without altering biofilm composition or gene expression","volume":"292","author":"Voglauer","year":"2025","journal-title":"Microbiol. Res."},{"key":"B90","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","article-title":"RSeQC: quality control of RNA-Seq experiments","volume":"28","author":"Wang","year":"2012","journal-title":"Bioinformatics"},{"key":"B91","doi-asserted-by":"publisher","first-page":"127396","DOI":"10.1016\/j.micres.2023.127396","article-title":"AlgU controls environmental stress adaptation, biofilm formation, motility, pyochelin synthesis and antagonism potential in Pseudomonas protegens SN15-2","volume":"272","author":"Wang","year":"2023","journal-title":"Microbiol. Res."},{"key":"B92","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1016\/j.cell.2009.01.043","article-title":"Regulatory RNAs in bacteria","volume":"136","author":"Waters","year":"2009","journal-title":"Cell"},{"key":"B93","doi-asserted-by":"publisher","first-page":"127709","DOI":"10.1016\/j.micres.2024.127709","article-title":"Molecular insights into FucR transcription factor to control the metabolism of (L)-fucose in Bifidobacterium longum subsp. infantis","volume":"283","author":"Yang","year":"2024","journal-title":"Microbiol. Res."},{"key":"B94","doi-asserted-by":"publisher","first-page":"e1003711","DOI":"10.1371\/journal.ppat.1003711","article-title":"DNA damage repair and bacterial pathogens","volume":"9","author":"\u017dgur-Bertok","year":"2013","journal-title":"PLOS Pathog."},{"key":"B95","doi-asserted-by":"publisher","first-page":"eadg0188","DOI":"10.1126\/sciadv.adg0188","article-title":"Drugging evolution of antibiotic resistance at a regulatory network hub","volume":"9","author":"Zhai","year":"2023","journal-title":"Sci. Adv."},{"key":"B96","doi-asserted-by":"publisher","first-page":"127528","DOI":"10.1016\/j.micres.2023.127528","article-title":"Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates","volume":"278","author":"Zhuang","year":"2024","journal-title":"Microbiol. Res."}],"container-title":["Frontiers in Molecular Biosciences"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmolb.2026.1798522\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T04:28:12Z","timestamp":1780979292000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmolb.2026.1798522\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,9]]},"references-count":96,"alternative-id":["10.3389\/fmolb.2026.1798522"],"URL":"https:\/\/doi.org\/10.3389\/fmolb.2026.1798522","relation":{},"ISSN":["2296-889X"],"issn-type":[{"value":"2296-889X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,9]]},"article-number":"1798522"}}