Danilo Pérez Pantoja

Danilo Pérez Pantoja
Universidad Tecnológica Metropolitana · Institutional Program for the Promotion of Research, Development and Innovation

PhD in Molecular Genetics and Microbiology

About

79
Publications
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Introduction
RESEARCH INTERESTS: Microbial Genomics and Metabolic Engineering for Biodegradation of Pollutants and Bioconversion of Lignocellulose

Publications

Publications (79)
Article
Full-text available
The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first...
Article
Full-text available
Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis fro...
Article
Full-text available
We report the complete 8.94-Mb genome sequence of the type strain of Cupriavidus basilensis (DSM 11853 = CCUG 49340 = RK1), formed by two chromosomes and six putative plasmids, which offers insights into its chloroaromatic-biodegrading capabilities.
Article
Full-text available
In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phen...
Article
Full-text available
Furans represent a class of promising chemicals, since they constitute valuable intermediates in conversion of biomass into sustainable products intended to replace petroleum-derivatives. Conversely, generation of furfural and 5-hydroxymethylfurfural (HMF) as by-products in lignocellulosic hydrolysates is undesirable due its inhibitory effect over...
Article
The dnt pathway of Burkholderia sp. R34 is in the midst of an evolutionary journey from its ancestral, natural substrate (naphthalene) towards a new xenobiotic one (2,4 dinitrotoluene, DNT). The gene cluster encoding the leading multicomponent ring dioxygenase (DntA) has activity on the old and the new substrate, but it is induced by neither. Inste...
Article
Despite its environmental robustness Pseudomonas putida strain KT2440 is very sensitive to DNA damage and displays poor homologous recombination efficiencies. To gain an insight into this deficiency isogenic ∆recA and ∆lexA1 derivatives of prophage‐free strain P. putida EM173 were generated and responses of the recA and lexA1 promoters to DNA damag...
Preprint
Full-text available
Abstract The search for microorganisms that degrade hydrocarbons is highly relevant because it enables the bioremediation of these substances cheaply and without dangerous by-products. In this work, we studied the microbial communities of an exploratory oil well, abandoned a century ago, located in the Cahuita National Park of Costa Rica. Cahuita w...
Article
Full-text available
Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from...
Article
Full-text available
Rhodococcus ruber R1 was isolated from a pulp mill wastewater treatment plant because of its ability to use methoxylated aromatics as growth substrates. We report the 5.56-Mb genome sequence of strain R1, which can provide insights into the biodegradation of lignin-derived phenolic monomers and potentially support processes for lignocellulose conve...
Article
Full-text available
Pseudomonas sp. strains ALS1279 and ALS1131 were isolated from wastewater treatment facilities on the basis of their ability to use furfural, a key lignocellulose-derived inhibitor, as their only carbon source. Here, we present the draft genome sequences of both strains, which can shed light on catabolic pathways for furan compounds in pseudomonads...
Article
Full-text available
Members of the genus Cylindrospermopsis represent an important environmental and health concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of the...
Article
Full-text available
Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (H13CO3) and nitrogen (15NH4Cl and K15NO3) assimilation rates. The microbial mat community included 31 phyla,...
Data
Total transcripts (cDNA) assigned to phototrophic processes. (a) Transcripts associated with photosystems PSI (psaA gene) and PSII (psbA gene) in oxygenic photosynthesis. (b) Transcripts (pufM, fmoA, pscA and bchC genes) associated with anoxygenic photosynthesis. Each bar represents a different temperature and daily period. Transcripts were normali...
Data
Diurnal carbon and nitrogen assimilation rates recorded at 58 and 48°C in Porcelana microbial mats. Nitrogen fixation data from Alcamán et al. (2015). The black bars represent the C or N assimilation rates in the dark.
Data
Process and pathways analyzed with principal genes associated and encoding protein. All this was used as diagnostic for phototrophy, autotrophy, and nitrogen cycle transformations.
Data
Taxonomic assignment of Chloroflexi by metagenomic (DNA; white bars) and metatranscriptomic reads (cDNA day: gray bars; cDNA night: black bars) at the Order (a) and genus (b) levels at the three temperatures studied.
Data
Total transcripts (cDNA) associated with the autotrophic carbon fixation pathways. CC, Calvin–Benson–Basham cycle (rbcL gene); 3HP, 3-hydroxypropionate bi-cycle (mcr gene); HH, hydroxypropionate-hydroxybutyrate cycle (atoB gene). Transcripts were normalized by RPKM.
Data
Total transcripts (cDNA) associated with specific carbon fixation pathways. (a) 3-Hydroxypropionate bi-cycle (mcr, prpE, and mcl genes) and (b) hydroxypropionate-hydroxybutyrate atoB, crt, abfD, sucD genes) cycle. Transcripts were normalized by RPKM.
Data
Results of high throughput sequencing: raw reads, quality reads, percentage of reads corresponding to ribosomal RNA, non-ribosomal genes, non-redundant (NR) hits and percentage of the latter that could be taxonomically assigned. Numbers of sequences are shown in millions.
Data
Taxonomic assignment of Cyanobacteria by metagenomic (DNA; white bars) and metatranscriptomic reads (cDNA day: gray bars; cDNA night: black bars) at the three temperatures studied. (a) Proportion of cyanobacterial reads in different Orders. (b) Proportion of Stigonematales reads in different genera.
Data
Total reads assigned to Proteobacteria by 16S rRNA sequences recovered from metagenomes. Rhodospirillales (alphaproteobacteria) and Burkholderiales (betaproteobacteria) were the most abundant orders at the lowest temperature. Note that the vertical scale is logarithmic.
Data
Total transcripts (cDNA) assigned to nitrogen cycle pathways: ammonia transporter (amt gene), nitrate assimilation (narB gene), ammonia assimilation (glnA gene), ammonia oxidation (amoA gene), N2 fixation (nifH gene), DNRA (nrfA gene), and denitrification (nosZ gene). Transcripts were normalized by RPKM.
Data
Total percentage of Bacteria and Archaea phyla present in the entire temperature gradient of Porcelana hot spring at noon and night (N) periods.
Data
Best hits and % similarity in the SILVA database of the most relevant organisms found in Porcelana mat.
Article
Full-text available
The molecular mechanisms behind the mutagenic effect of reactive oxygen species (ROS) released by defective metabolization of xenobiotic 2,4‐dinitrotoluene (DNT) by a still‐evolving degradation pathway were studied. To this end, the genes required for biodegradation of DNT from Burkholderia cepacia R34 were implanted in Escherichia coli and the eff...
Article
The presence of some sugars (e.g. glucose) down‐regulates the activity of the Pu promoter of plasmid pWW0 of Pseudomonas putida mt‐2, which drives the upper TOL operon for biodegradation of m‐xylene. Genetic evidence produced 20 years ago documented an effect of the EIIANtr (PtsN) protein of the nitrogen‐related phosphoenolpyruvate‐dependent phosph...
Article
Full-text available
During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the...
Preprint
Full-text available
During evolution of biodegradation pathways for xenobiotic compounds, the transition towards novel substrates of Rieske non-heme iron oxygenases borne by environmental bacteria is frequently associated with faulty reactions. Such reactions release reactive oxygen species (ROS), endowed with high mutagenic potential. The present work studies how the...
Article
Full-text available
The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (ca. 6°S and ca. 36°S). Studies show that primeval sulfuretums held diverse prokaryotic life, and, while rare today, still sustain species-rich giant sulfur-oxidizing bacterial commun...
Data
Phylogenetic analysis for the amino acid sequence of phytoene synthase identified in “Ca. V. ishoeyi”. The aligning of the amino acid sequence of the phytoene synthase (ps) identified in “Ca. V. ishoeyi” and 25 amino acid sequences of the Squalene/Phytoene synthase (Sps) and Phytoene synthases taken from the top 50 blastp match, and a sequence of A...
Data
S5A. Gene and product names of the Terpene type gene cluster. S5B. Gene and product names of the gene cluster, related with the potential biosynthesis of a non-classified secondary metabolite. (PDF)
Data
Genes identified in “Ca. V. ishoeyi”: S3A. In the tricarboxylic acid cycle; S3B. Involved in glycolysis; S3C. Involved in the Calvin-Benson-Bassham cycle. (PDF)
Data
S4A. List of CRISPR repeats identified in “Ca. V. ishoeyi”. The table shows: scaffolds containing start and end of CRISPR repeat regions, Direct Repeat (DR) sequences, length of the DR, and number of spacers. S4B. CRISPR-associated protein encoding genes identified in “Ca. V. ishoeyi”. (PDF)
Data
Amplification products of 16S rDNA genes and whole genome amplification (WGA) from seven bacterial filaments (MDA1-7) isolated by micromanipulation and visualized using agarose gel electrophoresis. The top of the figure shows the amplification products of the full length (~1.5 kbp) 16S rDNA PCR products of the seven micro-manipulated bacterial fila...
Data
Identification of amplified filaments by SeqMatch function (Ribosomal Database Project, RDPII). (PDF)
Data
Genes coding for sulfur oxidation enzymes in “Ca. V. ishoeyi”. (PDF)
Article
Full-text available
Background Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactiv...
Article
The metabolic versatility of the soil bacterium Pseudomonas putida is reflected by its ability to execute strong redox reactions (e.g., mono- and di-oxygenations) on aromatic substrates. Biodegradation of aromatics occurs via the pathway encoded in the archetypal TOL plasmid pWW0, yet the effect of running such oxidative route on redox balance agai...
Chapter
Microorganisms are key players in the global carbon cycle. In addition, it appears that most xenobiotic industrial chemicals can be degraded by microorganisms, either by a combination of cometabolic steps or by serving as growth substrate, leading to the mineralization of at least part of the molecule. Here, we present the principles of the microbi...
Chapter
Aromatic hydrocarbons are widely distributed in nature. They are found as lignin components, aromatic amino acids and xenobiotic compounds, among others. Microorganisms, mostly bacteria, degrade an impressive variety of such chemical structures. The major principle of aromatic hydrocarbon biodegradation is that a broad range of aromatic hydrocarbon...
Chapter
Aromatic compounds are widely distributed in nature. They are found as lignin components, aromatic amino acids, and xenobiotic compounds, among others. Microorganisms, mostly bacteria, degrade an impressive variety of such chemical structures. Various aerobic aromatic catabolic pathways have been reported in bacteria, which typically consist of act...
Chapter
Metatranscriptomics, the determination of RNA transcripts found in a microbiome, is a very active field nowadays. Improvements both in sequencing technologies and in software for analysis have made metatranscriptomics a very amenable technique, soon to be routinely used. In this chapter, we illustrate the steps needed to perform a metatranscriptomi...
Article
Full-text available
Background: Soil bacteria typically thrive in water-limited habitats that cause an inherent matric stress to the cognate cells. Matric stress gives rise to accumulation of intracellular reactive oxygen species (ROS), which in turn may induce oxidative stress, and even promote mutagenesis. However, little is known about the impact of ROS induced by...
Article
Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures...
Article
Full-text available
Cupriavidus pinatubonensis JMP134, like many other environmental bacteria uses a range of aromatic compounds as carbon sources. Previous reports have shown the preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to ot...
Article
Pseudomonas putida mt-2 encompasses two alternative and potentially conflicting routes for benzoate metabolism, one meta pathway encoded by xyl genes of the pWW0 plasmid and mastered by the Pm promoter and XylS, and one chromosomally-encoded ortho pathway initiated by Pben and the BenR protein. Any cross-activation of Pben promoter by XylS ought to...
Article
Pseudomonas putida mt-2 harbors two different routes for catabolism of catechol, namely one meta pathway encoded by the xyl genes of the TOL plasmid pWW0 and one ortho pathway determined by the chromosomal ben and cat genes. P. putida mt-2 has a second chromosomal copy of the catA gene (named catA2) located downstream of the ben operon that encodes...
Article
Full-text available
Environmental strain Burkholderia sp. DNT mineralizes the xenobiotic compound 2,4-dinitrotoluene (DNT) owing to the catabolic dnt genes borne by plasmid DNT, but the process fails to promote significant growth. To investigate this lack of physiological return of such an otherwise complete metabolic route, cells were exposed to DNT under various gro...
Article
Full-text available
Chlorinated pollutants are hardly biodegradable under oxic conditions, but they can often be metabolized by anaerobic bacteria through organohalide respiration reactions. In an attempt to identify bottlenecks limiting aerobic catabolism of 1,3-dichloroprop-1-ene (1,3-DCP; a widely used organohalide) in Pseudomonas pavonaceae, the possible physiolog...
Article
Glucose catabolism of Pseudomonas putida is carried out exclusively through the Entner-Doudoroff (ED) pathway due to the absence of 6-phosphofructokinase. In order to activate the Embden-Meyerhof-Parnas (EMP) route we transferred the pfkA gene from Escherichia coli to a P. putida wild-type strain as well as to an eda mutant, i.e. lacking 2-keto-3-d...
Article
Full-text available
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
Article
Full-text available
Plant rhizosphere and internal tissues may constitute a relevant habitat for soil bacteria displaying high catabolic versatility towards xenobiotic aromatic compounds. Root exudates contain various molecules that are structurally related to aromatic xenobiotics and have been shown to stimulate bacterial degradation of aromatic pollutants in the rhi...
Article
The relevance of the β-proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomi...
Article
As other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4-hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, defective in the first step of benzoate degradation, is unable to metabolize 4-hydroxybenzoate...
Data
Functional distribution of unique genes. COG categories are as follows: Information storage and processing: A, RNA processing, modification; B, chromatin structure; J, translation, ribosomal structure/biogenesis; K, transcription; L, DNA replication, recombination, repair. Cellular processes: D, cell division, chromosome partitioning; M, cell envel...
Data
Functional annotation of key metabolic genes of C. necator JMP134. (0.27 MB DOC)
Article
Full-text available
Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common t...
Article
Full-text available
Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes i...
Chapter
Microorganisms are key players in the global carbon cycle. In addition, it appears that most xenobiotic industrial chemicals can be degraded by microorganisms, either by a combination of cometabolic steps or by serving as growth substrate, leading to the mineralization of at least part of the molecule. Here, we present the principles of the microbi...
Chapter
Aromatic hydrocarbons are widely distributed in nature. They are found as lignin components, aromatic amino acids and xenobiotic compounds, among others. Microorganisms, mostly bacteria, degrade an impressive variety of such chemical structures. The major principle of aromatic hydrocarbon biodegradation is that a broad range of peripheral reactions...