Estudio genómico y transcriptómico de la resistencia a cadmio(II) de Serratia sp. 5b

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dc.contributor.advisorde Brito Brandão, Pedro Filipespa
dc.contributor.authorNonsocua Triviño, Kevin Stivenspa
dc.contributor.orcidNonsocua Triviño, Kevin Stiven [000900005105447X]spa
dc.contributor.researchgroupGrupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente Germinaspa
dc.date.accessioned2025-10-31T15:25:29Z
dc.date.available2025-10-31T15:25:29Z
dc.date.issued2025
dc.descriptionilustraciones, diagramas, fotografíasspa
dc.description.abstractSerratia sp. 5b es una cepa previamente aislada de suelos agrícolas contaminados con cadmio (Cd(II)), a la que se le ha determinado experimentalmente una concentración mínima inhibitoria (CMI) de 4 mM y la capacidad para reducir la concentración del metal en solución. No obstante, no se conocía su identidad taxonómica a nivel de especie ni se había determinado cuáles genes están implicados en la resistencia a Cd(II). En este estudio se integraron de forma transversal aproximaciones filogenómicas, genómicas y transcriptómicas con el propósito de identificar taxonómicamente la cepa y dilucidar los mecanismos moleculares que sustentan su resistencia al Cd(II). El análisis filogenómico, basado en 1.052 genes ortólogos de copia única, indicó que la especie de Serratia sp. 5b corresponde a Serratia surfactantfaciens, al formar un clado monofilético con soporte bootstrap del 100 %, lo cual fue ratificado por un valor ANI del 99,18 %. A nivel genómico, el ensamblaje presentó 18 contigs, una longitud total de 4,99 Mbp y una completitud estimada en 99,88 %. Se identificaron diez genes putativos relacionados con resistencia a Cd(II), dsbA, dsbB, fieF, mntH, robA, ychH, ygiW, zinT, zitB y zntA, todos ubicados en el cromosoma y sin asociación a plásmidos ni elementos genéticos móviles. Asimismo, el análisis de variantes detectó mutaciones no sinónimas en fieF y zntA, siendo este último el único con alteraciones estructurales localizadas en regiones flexibles. Por otro lado, el análisis transcriptómico reveló una respuesta génica dependiente de la concentración de Cd(II), con 428, 1.852 y 638 genes diferencialmente expresados (DEGs) al comparar las condiciones control vs 0,15 mM Cd(II), control vs 0,50 mM Cd(II), y 0,15 mM Cd(II) vs 0,50 mM Cd(II), respectivamente. Se observó una sobreexpresión progresiva de genes asociados al transporte de cationes, defensa antioxidante y reparación del ADN, destacándose zntA, zinT, mntA, znuC, trxB y recA. El análisis funcional evidenció una activación gradual de rutas implicadas en metabolismo energético, transporte activo y organización de membranas, con procesos exclusivos bajo condiciones de alta exposición. La validación experimental mediante RT-qPCR de genes seleccionados reprodujo la tendencia observada en RNA-seq, indicando la confiabilidad de los resultados transcriptómicos. En conjunto, estos hallazgos demuestran que Serratia surfactantfaciens 5b presenta una respuesta transcripcional compleja y coordinada frente a Cd(II), basada en mecanismos de exclusión, secuestro intracelular y adaptación fisiológica. (Texto tomado de la fuente).spa
dc.description.abstractSerratia sp. 5b is a strain previously isolated from cadmium (Cd(II))-contaminated agricultural soils. Experimental studies determined a minimum inhibitory concentration (MIC) of 4 mM for this strain, along with its ability to reduce the concentration of the metal in solution. However, its species-level taxonomic identity was unknown, and the genes involved in its Cd(II) resistance had not been identified. In this study, we integrated phylogenomic, genomic, and transcriptomic approaches to identify the strain at the species level and elucidate the molecular mechanisms underlying its resistance to Cd(II). Phylogenomic analysis based on 1,052 single-copy orthologous genes indicated that Serratia sp. 5b belongs to the species Serratia surfactantfaciens, as it formed a monophyletic clade with 100% bootstrap support. This finding was further supported by an ANI value of 99.18%. At the genomic level, the assembly consisted of 18 contigs, with a total length of 4.99 Mbp and an estimated completeness of 99.88%. Ten putative genes associated with Cd(II) resistance were identified—dsbA, dsbB, fieF, mntH, robA, ychH, ygiW, zinT, zitB, and zntA—all of which were located on the chromosome and showed no association with plasmids or mobile genetic elements. Variant analysis revealed non-synonymous mutations in fieF and zntA, the latter being the only gene with structural alterations located in flexible protein regions. Transcriptomic analysis revealed a Cd(II) concentration-dependent gene expression response, with 428, 1,852, and 638 differentially expressed genes (DEGs) identified when comparing control vs. 0.15 mM Cd(II), control vs. 0.50 mM Cd(II), and 0.15 mM vs. 0.50 mM Cd(II), respectively. A progressive overexpression was observed in genes associated with cation transport, antioxidant defense, and DNA repair, particularly zntA, zinT, mntA, znuC, trxB, and recA. Functional enrichment analysis revealed a gradual activation of pathways involved in energy metabolism, active transport, and membrane organization, with exclusive processes emerging under high Cd(II) exposure. Experimental validation by RT-qPCR of selected genes reproduced the expression trends observed in the RNA-seq data, confirming the reliability of the transcriptomic results. Together, these findings demonstrate that Serratia surfactantfaciens 5b exhibits a complex and coordinated transcriptional response to Cd(II), based on mechanisms involving exclusion, intracellular sequestration, and physiological adaptation.eng
dc.description.degreelevelMaestríaspa
dc.description.degreenameMagíster en Ciencias – Microbiologíaspa
dc.description.researchareaMicrobiología ambientalspa
dc.format.extent115 páginasspa
dc.format.mimetypeapplication/pdf
dc.identifier.instnameUniversidad Nacional de Colombiaspa
dc.identifier.reponameRepositorio Institucional Universidad Nacional de Colombiaspa
dc.identifier.repourlhttps://repositorio.unal.edu.co/spa
dc.identifier.urihttps://repositorio.unal.edu.co/handle/unal/89091
dc.language.isospa
dc.publisherUniversidad Nacional de Colombiaspa
dc.publisher.branchUniversidad Nacional de Colombia - Sede Bogotáspa
dc.publisher.departmentInstituto de Biotecnología IBUNspa
dc.publisher.facultyFacultad de Cienciasspa
dc.publisher.placeBogotá, Colombiaspa
dc.publisher.programBogotá - Ciencias - Maestría en Ciencias - Microbiologíaspa
dc.relation.indexedAgrosaviaspa
dc.relation.indexedAgrovocspa
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dc.rights.accessrightsinfo:eu-repo/semantics/openAccess
dc.rights.licenseAtribución-NoComercial-CompartirIgual 4.0 Internacional
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/
dc.subject.agrovocBacteria gram negativaspa
dc.subject.agrovocGram-negative bacteriaeng
dc.subject.agrovocGenoma bacterianospa
dc.subject.agrovocbacterial genomeseng
dc.subject.agrovocTranscripción génicaspa
dc.subject.agrovocgene transcriptioneng
dc.subject.ddc570 - Biología::579 - Historia natural microorganismos, hongos, algasspa
dc.subject.proposalCadmiospa
dc.subject.proposalGenesspa
dc.subject.proposalDNAspa
dc.subject.proposalRNAspa
dc.subject.proposalSecuenciaciónspa
dc.subject.proposalSerratialat
dc.subject.proposalCadmiumeng
dc.subject.proposalDNAeng
dc.subject.proposalRNAeng
dc.subject.proposalSequencingeng
dc.subject.proposalResistanceeng
dc.subject.proposalGeneseng
dc.subject.proposalResistenciaspa
dc.subject.proposalSurfactantfacienslat
dc.titleEstudio genómico y transcriptómico de la resistencia a cadmio(II) de Serratia sp. 5bspa
dc.title.translatedGenomic and transcriptomic study of cadmium(II) resistance in Serratia sp. 5beng
dc.typeTrabajo de grado - Maestríaspa
dc.type.coarhttp://purl.org/coar/resource_type/c_bdcc
dc.type.coarversionhttp://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.contentText
dc.type.driverinfo:eu-repo/semantics/masterThesis
dc.type.redcolhttp://purl.org/redcol/resource_type/TM
dc.type.versioninfo:eu-repo/semantics/acceptedVersion
dcterms.audience.professionaldevelopmentEstudiantesspa
dcterms.audience.professionaldevelopmentInvestigadoresspa
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