Pablo Vinuesa | Universidad Nacional Autónoma de México (original) (raw)

Papers by Pablo Vinuesa

Figure S1. Subsystem category distribution of the S. diarizonae strain SBO13 genome. The genome o... more Figure S1. Subsystem category distribution of the S. diarizonae strain SBO13 genome. The genome of diarizonae SBO13 was annotated using the Rapid Annotation System technology (RAST) server and classified in 27 categories and 571 subsystems. Total proteins annotated with a putative function covered a 56% of the subsystems (green bar). The pie chart represents the percentage distribution of the subsystems categories. (PDF 377 kb)

of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infectio... more of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Table S9. Presence/absence of slrP, sseK2, sseK3, GI6 and SPI-7 in S. enterica subsp. diarizonae ... more Table S9. Presence/absence of slrP, sseK2, sseK3, GI6 and SPI-7 in S. enterica subsp. diarizonae draft genomes available at EnteroBase. (XLSX 39 kb)

Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and represe... more Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and representative genomes from other Salmonella species and subspecies (XLSX 19 kb)

Table S7. Phophages carried by the S. enterica subsp. diarizonae SBO13 and SBO27 (XLSX 10 kb)

The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin rece... more The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor-related receptor (IRR) are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight ‘twist ’ rotation of the last two fibronectin type III domains in or...

Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, g... more Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, generated with PacBio RS II single-molecule real-time technology, consisting of a single circular chromosome of 4.13Mb.We annotated mobile genetic ele-ments and natural product biosynthesis clusters, including a novel class-II lasso peptide with a 7-residue macrolactam ring.

We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated... more We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed...

This article cites 57 articles, 28 of which can be accessed free

Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted ... more Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted in the identification of strain KIM-G1. Its rough colony appearance, flocculation in liquid culture, and Ndv � Fix � phenotype were indicative of a lipopolysaccharide (LPS) defect. Electrophoretic analysis of cell-associated polysaccharides showed that KIM-G1 produces only rough LPS. Composition analysis of purified LPS oligosaccharides from KIM-G1 indicated that it produces an intact LPS core trisaccharide (�-D-GalA-134[�-D-GalA-135]-Kdo) and tetrasaccharide (�-D-Gal-136[�-D-GalA-134]-�-D-Man-135Kdo), strongly suggesting that the transposon insertion disrupted a locus involved in O-antigen biosynthesis. Five monosaccharides (Glc, Man, GalA, 3-O-Me-6-deoxytalose, and Kdo) were identified as the components of the repeating O unit of the smooth parent strain, KIM5s. Strain KIM-G1 was complemented with a 7.2-kb DNA fragment from KIM5s that, when provided in trans on a broad-host-range vecto...

This chapter presents a review of critical factors that have to be considered and evaluated in mu... more This chapter presents a review of critical factors that have to be considered and evaluated in multilocus sequence analysis (MLSA) in order to make robust estimates of bacterial species phylogenies. The theoretical arguments in favour of the conditional data combination will be presented. I will briefly review criteria for marker selection, and will provide practical advice on the computational aspects, potential pitfalls, and software choices available for each step in a MLSA. For this purpose, a detailed case study using atpD, glnII, recA and rpoB sequences of symbiotic root nodule bacteria of the genus Bradyrhizobium will be presented. I will discuss and illustrate the use of phylogenetic congruence analysis, and a strategy to evaluate the additivity of the phylogenetic signals in the different partitions. The importance of using multiple isolates per species/ lineage, proper model selection and thorough tree searches to get a good estimate of a multispecies phylogeny will be emp...

Journal of Virology

In this study, we describe seven vegetative phage genomes homologous to the historic phage B3 tha... more In this study, we describe seven vegetative phage genomes homologous to the historic phage B3 that infect Pseudomonas aeruginosa. Like other phage groups, the B3-like group contains conserved (core) and variable (accessory) open reading frames (ORFs) grouped at fixed regions in their genomes; however, in either case, many ORFs remain without assigned functions. We constructed lysogens of the seven B3-like phages in strain Ps33 of P. aeruginosa, a novel clinical isolate, and assayed the exclusion phenotype against a variety of temperate and virulent superinfecting phages. In addition to the classic exclusion conferred by the phage immunity repressor, the phenotype observed in B3-like lysogens suggested the presence of other exclusion genes. We set out to identify the genes responsible for this exclusion phenotype. Phage Ps56 was chosen as the study subject since it excluded numerous temperate and virulent phages. Restriction of the Ps56 genome, cloning of several fragments, and resec...

BMC Genomics

An amendment to this paper has been published and can be accessed via the original article.

Applied Microbiology and Biotechnology

Bioinformatic mining of the Streptomyces thermocarboxydus K155 genome predicted the presence of f... more Bioinformatic mining of the Streptomyces thermocarboxydus K155 genome predicted the presence of four synthases for the production of geosmin, hopene, albaflavenone, and a type B-type A diterpenoid system like that described for labdane-related diterpenoids (LRD). The lrd cluster was comprised by an operon of four genes (lrdABDC). This cluster seemed to be silent in the wild-type strain, as neither labdane nor terpene-like compounds were detected by UPLC-TOF-MS and GC-MS analyses in both culture supernatants and mycelial extracts. Heterologous expression of the lrdABDC cluster in a defective cyslabdan producer (Streptomyces cyslabdanicus K04-0144Δcld) generated 8,17-epoxy-7-hydroxy labda-12,14-diene and cyslabdan. The same cluster expressed in the strains Streptomyces coelicolor M1152, Streptomyces peucetius var. caesius, and Streptomyces avermitilis SUKA22 produced the general intermediary labda-8(17), 12(E),14-triene [(E)-biformene]. Besides (E)-biformene, S. coelicolor M1152 and S. avermitilis SUKA22 produced two and three different labdane-type diterpenoids, underlying the relevance of the genetic background of the Streptomyces host in product formation.

International Journal of Systematic and Evolutionary Microbiology

Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the Internatio... more Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.

BMC Genomics

Background: Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environm... more Background: Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown. Results: We report here the genome features of two diarizonae strains, SBO13 and SBO27, isolated from endocervical tissue collected post-abortion and from cerebrospinal fluid of a newborn child, respectively, in the city of Santa Cruz, Bolivia. Although isolated six years apart, SBO27 in 2008 and SBO13 in 2014, both strains belong to the same sequence type 1256 (ST1256) and show a high degree of genome conservation sharing more than 99% of their genes, including the conservation of a~10 kb plasmid. A prominent feature of the two genomes is the presence of 24 genomic islands (GIs), in addition to 10 complete Salmonella pathogenicity islands (SPI) and fragments of SPI-7, a pathogenicity island first reported in the human-adapted serovar Typhi. Some of the GIs identified in SBO13 and SBO27 harbor genes putatively encoding auto-transporters involved in adhesion, lipopolysaccharide modifying enzymes, putative toxins, pili-related proteins, efflux pumps, and several putative membrane cation transport relatedgenes, among others. These two Bolivian isolates also share genes encoding the type-III secretion system effector proteins SseK2, SseK3 and SlrP with other diarizonae sequence types (ST) mainly-associated with infections in humans. The sseK2, sseK3 and slrP genes were either absent or showing frameshift mutations in a significant proportion of genomes from environmental diarizonae isolates.

Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Vi... more Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the world's countries, and showed that its phylogeography is locally clustered within countries, cities, and individuals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage...

Molecular Phylogenetics and Evolution

Slo1 and Slo3 encode close paralogues of the Slo potassium (K+) channels family. Despite their ev... more Slo1 and Slo3 encode close paralogues of the Slo potassium (K+) channels family. Despite their evolutionary relatedness, Slo1 and Slo3 channels show marked functional differences and evolutionary dynamics. Whereas Slo1 is a highly conserved and widely expressed channel, Slo3 is a rapidly evolving channel restricted to sperm. However, the molecular mechanisms behind the structural-functional differences of Slo1 and Slo3 channels are unknown. In this study, we explored the functional divergence of Slo1 and Slo3 subfamilies in vertebrates and examined the structure-function relationships of our predictions using experimental data. We found that ∼25% of sites between Slo1 and Slo3 underwent altered functional constraints, affecting some residues with important roles in Slo1 channel gating. Because functional divergence was principally generated by accelerated evolution of Slo3 after gene duplication, we explored selective forces behind Slo3 diversification. We observed that Slo3 subjected was principally subjected to relaxation of purifying selection, but we also identified several sites evolving under positive selection in the cytosolic domain of this channel . Concerning Slo1, this channel presented strong purifying selection. Whether residues evolving under different selection in Slo1 and Slo3 are responsible for functional differences observed between these channels, as well as among Slo3 orthologs, remains to be established.

Genome announcements, Jan 27, 2017

We present here the high-quality complete genome sequences of eight strains of Rhizobium-nodulati... more We present here the high-quality complete genome sequences of eight strains of Rhizobium-nodulating Phaseolus vulgaris Comparative analyses showed that some of them belonged to different genomic and evolutionary lineages with common symbiotic properties. Two novel symbiotic plasmids (pSyms) with P. vulgaris specificity are reported here.

Table S7. Phophages carried by the S. enterica subsp. diarizonae SBO13 and SBO27 (XLSX 10 kb)

This article cites 57 articles, 28 of which can be accessed free

Journal of Virology

BMC Genomics

An amendment to this paper has been published and can be accessed via the original article.

Applied Microbiology and Biotechnology

International Journal of Systematic and Evolutionary Microbiology

BMC Genomics

Molecular Phylogenetics and Evolution

Genome announcements, Jan 27, 2017