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Danilo Rodrigo Pérez Pantoja

Profesor Titular

UNIVERSIDAD TECNOLÓGICA METROPOLITANA

Santiago, Chile

Líneas de Investigación


-Genómica Microbiana -Biodegradación -Metagenómica -Ingeniería Metabólica

Educación

  •  Molecular Genetics and Microbiology, PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE. Chile, 2009
  •  Biochemistry, UNIVERSIDAD DE CHILE. Chile, 1998
  •  Bioinformatics and Computational Biology, UNIVERSIDAD COMPLUTENSE DE MADRID. España, 2012
  •  Biochemist, UNIVERSIDAD DE CHILE. Chile, 2002

Experiencia Académica

  •   Profesor Asistente Full Time

    UNIVERSIDAD DE CONCEPCION

    Ciencias Biológicas

    Concepción, Chile

    2015 - 2017

  •   Investigador Full Time

    UNIVERSIDAD TECNOLOGICA METROPOLITANA

    Santiago, Chile

    2017 - 2023

  •   Investigador Postdoctoral Full Time

    Centro Nacional de Biotecnología - CSIC

    Madrid, España

    2011 - 2015

  •   Profesor Titular Full Time

    UNIVERSIDAD TECNOLOGICA METROPOLITANA

    Instituto Universitario de Investigación y Desarrollo Tecnológico (IDT)

    Santiago, Chile

    2024 - A la fecha

Experiencia Profesional

  •   Asesor Científico Other

    Bio-Iliberis R&D

    Madrid, España

    2013 - 2014

Formación de Capital Humano


TESIS DE DOCTORADO
Eduardo Hernández Ojeda
Ph.D in Materials Science and Process Engineering Thesis “Modulación de la razón G/M del alginato producido por A. vinelandii ATCC 9046, y caracterización de las propiedades del biopolímero obtenido”, 2026 (expected)
Marcelo Araya Nail
Ph.D in Microbiology Thesis “Identificación de los genes implicados en la degradación de tiramina y dopamina, en microorganismos aislados desde la microbiota intestinal de Salmónidos”, 2026 (expected)
Ricardo Corbinaud Antúnez
Ph.D. in Complex Systems Engineering Thesis “Análisis filogenético y funcional de genes responsables de la degradación de contaminantes emergentes: evolución de nuevas funcionalidades enzimáticas hacia compuestos xenobióticos como ejemplo de navegabilidad de redes genotípicas”, 2027 (expected)
Susana Calderón Toledo
Ph.D in Biochemical Engineering Thesis “Producción de PHB de Azotobacter vinelandii con sobreexpresión de hidrogenasa [NiFe] y transhidrogenasa solubles bajo limitación de oxígeno”, 2026 (expected)
Andrés Pérez Bernal
Ph.D in Biotechnology Thesis “Estudio de la biosíntesis del copolímero Poli(3-hidroxibutirato-co-3- hidroxivalerato) (PHBV) en cultivos de Azotobacter vinelandii OPNA”, 2026 (expected)
Carla Garate Castro
Ph.D in Microbiology Thesis “Regulación transcripcional de genes catabólicos para compuestos furánicos en cepas bacterianas aisladas desde la microbiota intestinal de Salmón del Atlántico”, 2024

TESIS DE MAGÍSTER
Giorgio Canessa Merino
Master in Engineering Sciences, Bioengineering Thesis “Identificación de genes potencialmente involucrados en la degradación de contaminantes emergentes del tipo parabenos en el filo actinobacteria mediante genómica comparativa”, 2025
Felipe Gallardo Agüero
Master in Engineering Sciences, Bioengineering Thesis "Papel de los genes relacionados al metabolismo de aminoácidos de cadena ramificada en la ruta biosintética del 3-metilbutanol en Burkholderiaceae”, 2025

MEMORIA PROFESIONAL
Mauricio Guajardo Parra
Professional Certificate in Biotechnology Engineering Thesis “Selección funcional de genes de tolerancia desde genoteca plurigenómica construida a partir de microorganismos tolerantes a inhibidores derivados de material lignocelulósico”, 2019
Marcelo Araya Nail
Professional Certificate in Biotechnology Engineering Thesis “Construcción de una genoteca plurigenómica a partir de microorganismos tolerantes a inhibidores derivados de material lignocelulósico y selección funcional de genes de tolerancia”, 2020
Sandra Galaz Farías
Professional Certificate in Biotechnology Engineering Thesis “Identificación de los genes responsables de la degradación de guaiacol en bacterias Gram negativas”, 2022
Ricardo Corbinaud Antúnez
Professional Certificate in Biotechnology Engineering Thesis “Identificación de genes responsables de la degradación de ácido siríngico en cepas de Pseudomonas”, 2022
Catalina Galdames Gutiérrez
Professional Certificate in Biotechnology Engineering Thesis “Análisis transcripcional de genes potencialmente codificantes de la enzima 4-metoxibenzoato o-desmetilasa en la cepa Pseudomonas putida DSM 1868”, 2023
Fabián González Toro
Professional Certificate in Biotechnology Engineering Thesis “Análisis filogenómico y pangenómico de la degradación de furaldehídos por cepas bacterianas del género Pseudomonas”, 2023
Karina Sotelo Bastías
Professional Certificate in Biotechnology Engineering Thesis “Expresión heteróloga en Escherichia coli de una enzima fenol hidroxilasa con amplio rango de sustratos”, 2024
Nicolás López Muñoz
Professional Certificate in Biotechnology Engineering Thesis “Identificación de genes codificantes de esterasas que hidrolizan ésteres aromáticos catalogados como contaminantes emergentes”, 2025


Premios y Distinciones

  •   Premio Medalla de Honor Hermann Niemeyer

    SOCIEDAD DE BIOQUIMICA DE CHILE

    Chile, 2004

    Premio al mejor estudiante de los programas de Doctorado en Bioquímica y Biología Molecular


 

Article (34)

Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well
The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA-LexA interplay
Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution
Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics
Draft Genome Sequences of Two Pseudomonas Strains That Are Able To Use Furan Derivatives as Their Sole Carbon Source
Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments
Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells
Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat
Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay
The interplay of EIIANtr with C-source regulation of the Pu promoter of Pseudomonas putida mt-2
The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates
Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid
Genomic features of "Candidatus Venteria ishoeyi", a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile
Plasmid and clonal interference during post horizontal gene transfer evolution
DNA damage elicits a different SOS response in Pseudomonas putida and Escherichia coli
High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2
Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds
Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134
Pseudomonas putida mt-2 tolerates reactive oxygen species generated during matric stress by inducing a major oxidative defense response
The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in m-xylene biodegradation
A second chromosomal copy of the catA gene endows Pseudomonas putidamt-2 with an enzymatic safety valve for excess of catechol
Endogenous Stress Caused by Faulty Oxidation Reactions Fosters Evolution of 2,4-Dinitrotoluene-Degrading Bacteria
The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress
Why are chlorinated pollutants so difficult to degrade aerobically? Redox stress limits 1,3-dichloprop-1-ene metabolism by Pseudomonas pavonaceae
Aromatic compounds degradation plays a role in colonization of Arabidopsis thaliana and Acacia caven by Cupriavidus pinatubonensis JMP134
Strict and direct transcriptional repression of the pobA gene by benzoate avoids 4-hydroxybenzoate degradation in the pollutant degrader bacterium Cupriavidus necator JMP134
Modified 3-Oxoadipate Pathway for the Biodegradation of Methylaromatics in Pseudomonas reinekei MT1
The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader
Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134
Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways
Efficient turnover of chlorocatechols is essential for growth of Ralstonia eutropha JMP134(pJP4) in 3-chlorobenzoic acid
Importance of different tfd genes for degradation of chloroaromatics by Ralstonia eutropha JMP134
Novel insights into the interplay between peripheral reactions encoded by xyl genes and the chlorocatechol pathway encoded by tfd genes for the degradation of chlorobenzoates by Ralstonia eutropha JMP134
Role of tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II)F(II) gene modules in catabolism of 3-chlorobenzoate by Ralstonia eutropha JMP134(pJP4)

Abstract (1)

Genome sequencing and characterization of novel proteobacterial strains having the ability to use furan aldehydes as only carbon source

BookSection (4)

Prokaryotic Metatranscriptomics
Aerobic Degradation of Aromatic Hydrocarbons
Aerobic Degradation of Chloroaromatics
Phylogenomics of Aerobic Bacterial Degradation of Aromatics

EditorialMaterial (1)

Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2

Proyecto (10)

Towards more robust Escherichia coli strains for lignocellulosic biomass conversion by metabolic engineering involving transfer of the biodetoxification potential evolved by microbial communities from pulp-mill waste sludge
Genomics and Applied Microbiology for Biodegradation and Bioproducts (GAMBIO)
METAGENOMIC EXPLORATION OF HARSH ENVIRONMENTS FOR INCREASING TOLERANCE TO LIGNOCELLULOSE-DERIVED INHIBITORS IN E. COLI
ST-Flow - Standardization and Orthogonalization of the Gene Expression Flow for Robust Engineering of NTN (new-to-nature) Biological Properties
PROACTIVE - Programmed acceleration of evolution of the biodegradative gene inventory
BACSIN - Bacterial abiotic celular stress and survival improvement network
Desarrollo y Reprogramación de Sistemas Microbianos
EXPRESION DE GENES MICROBIANOS INVOLUCRADOS EN EL CATABOLISMO DE COMPUESTOS AROMATICOS, LIGNINA Y HEMICELULOSAS, A NIVEL DE LABORATORIO Y EN EL AMBIENTE
UN MODELO PARA CONOCER LAS BASES MOLECULARES DE LA ADAPTACION DE BACTERIAS AEROBICAS A LA DEGRADACION DE CONTAMINANTES CLOROAROMATICOS=> EXPRESION DE OPERONES CATABOLICOS DE RALSTONIA EUTROPHA
MEJORAMIENTO DE LA CAPACIDAD DE BACTERIAS PARA DEGRADAR CONTAMINANTES CLOROFENOLITICOS MEDIANTE PRESION SELECTIVA Y TRANSFERENCIA DE GENES CATABOLICOS Y EVALUACION DE SU ACTIVIDAD EN MICROCOSMOS DE TRATAMIENTO DE EFLUENTES INDUS

Review (2)

Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales
Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134
2
Luz Vásquez

Profesor Asociado

Genética Molecular y Microbiología

Pontificia Universidad Católica de Chile

Santiago, Chile

2
Michael Seeger

Full Professor

Chemistry

UNIVERSIDAD TÉCNICA FEDERICO SANTA MARÍA

Valparaíso, Chile

2
Rodrigo De la Iglesia

Profesor Asociado

Genética Molecular y Microbiología

PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE

Santiago, Chile

21
Bernardo González

Full Professor

UNIVERSIDAD ADOLFO IBAÑEZ

Santiago, Chile

7
Thomas Ledger

Associate Professor

UNIVERSIDAD ADOLFO IBÁÑEZ

Santiago, Chile

1
Beatriz Diez

PROFESORA TITULAR

Universidad Mayor de Chile

Santiago, Chile

1
Katia Soto

Académica

Universidad de Chile

Santiago, Chile

1
Nicole Trefault

Profesora Titular

Centro GEMA, Genomica, Ecologia y Medio Ambiente

UNIVERSIDAD MAYOR

Santiago, Chile

1
Alexis Salas

Associate Professor

Pharmacology

UNIVERSIDAD DE CONCEPCIÓN

Concepción, Chile

1
Daniel Garrido

Associate Professor

Chemical and Bioprocess Engineering

Pontificia Universidad Católica de Chile

Santiago, Chile

1
Ana Zúñiga

postdoctoral research fellow

Centre de Biologie Structurale

Montpellier, Francia

43
Danilo Pérez

Profesor Titular

Instituto Universitario de Investigación y Desarrollo Tecnológico (IDT)

UNIVERSIDAD TECNOLÓGICA METROPOLITANA

Santiago, Chile

1
VERONICA MORGANTE

Gerente de Operaciones

Multiplex Spa

SANTIAGO, Chile

1
María Alcamán

Investigador-Docente

Ingenieria

Universidad del Desarrollo

Concepcion, Chile

1
Rodrigo Maldonado

Académico Investigador

Universidad Finis Terrae

Santiago, Chile

1
Lucy Belmar

Profesor asistente adjunto

Facultad de Ciencias de la Vida

Universidad Andrés Bello

Santiago, Chile

1
Loreine Agullo

INVESTIGADOR POSDTOCTORAL

FACULTAD DE CIENCIAS

PONTIFICIA UNIVERSIDAD CATOLICA DE VALPARAISO

VALPARAISO, Chile

1
Cedric Little

Associated Professor and Director of Research Centre

Engineering and Sciences

Universidad Adolfo Ibáñez

Viña del Mar, Chile

8
Raúl Donoso

Investigador

PIDi

Universidad Tecnológica Metropolitana

Santiago, Chile

1
Leda Guzman

Profesor Adjunto

Instituto de Química

Pontificia Universidad Católica de Valparaíso

Valparaíso, Chile

2
Marlene Manzano

Coordinador de Investigacion

Universidad Mayor

Santiago, Chile

1
Roberto Durán

Investigador (Programa Asistentes Científicos)

Departamento de Química

Universidad Técnica Federico Santa María

Valparaíso, Chile

2
Carlos Farkas

PostDoctoral Fellow

CancerCare Manitoba

University of Manitoba

Winnipeg, Canada