Bioinformatic analysis of the Type VI Secretion System and its potential toxins in the Acinetobacter genus

Several Acinetobacter strains are important nosocomial pathogens, with Acinetobacter baumannii as the species of greatest concern worldwide due to its multi-drug resistance and recent appearance of hyper-virulent strains in the clinical setting. Acinetobacter colonization of the environment and the host is associated with a multitude of factors which remain poorly characterized. Among them, the secretion systems (SS) encoded by Acinetobacter species confer adaptive advantages depending on the niche occupied. Different SS have been characterized in this group of microorganisms, including T6SS used by several Acinetobacter species to outcompete other bacteria and in some A. baumannii strains for Galleria mellonella colonization. Therefore, to better understand the distribution of the T6SS in this genus we carried out an in depth comparative genomic analysis of the T6SS in 191 sequenced strains. To this end, we analyzed the gene content, sequence similarity, synteny and operon structure of each T6SS loci. The presence of a single conserved T6SS-main cluster (T6SS-1), with two different genetic organizations, was detected in the genomes of several ecologically diverse species. Furthermore, a second main cluster (T6SS-2) was detected in a subgroup of 3 species of environmental origin. Detailed analysis also showed an impressive genetic versatility in T6SS-associated islands, carrying VgrG, PAAR and putative toxin-encoding genes. This in silico study represents the first detailed intra species comparative analysis of T6SS-associated genes in the Acinetobacter genus, that should contribute to the future experimental characterization of T6SS proteins and effectors.Para citar este articulo: Repizo GD, Espariz M, Seravalle JL and Salcedo SP (2019) Bioinformatic Analysis of the Type VI Secretion System and Its Potential Toxins in the Acinetobacter Genus. Front. Microbiol. 10:2519. doi: 10.3389/fmicb.2019.02519Fil: Repizo, Guillermo Daniel. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Repizo, Guillermo Daniel. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Seravalle, Joana L. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Seravalle, Joana L. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Salcedo, Susana P. University of Lyon. Laboratory of Molecular Microbiology and Structural Biochemistry; France

Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case

Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. In this study, first, a whole-genome in silico approach was used to accurately demarcate B. pumilus group strains, as a case of highly phylogenetically related taxa, at the species level. In order to achieve that and consequently to validate or correct taxonomic identities of genomes in public databases, an average nucleotide identity correlation, a core-based phylogenomic and a gene function repertory analyses were performed. Eventually, more than 50% such genomes were found to be misclassified. Hierarchical clustering of gene functional repertoires was also used to infer ecotypes among B. pumilus group species. Furthermore, for the first time the machine-learning algorithm Random Forest was used to rank genes in order of their importance for species classification. We found that ybbP, a gene involved in the synthesis of cyclic di-AMP, was the most important gene for accurately predicting species identity among B. pumilus group strains. Finally, principal component analysis was used to classify strains based on the distances between their ybbP genes. The methodologies described could be utilized more broadly to identify other highly phylogenetically related species in metagenomic or epidemiological assessments.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular de Rosario (IBR-CONICET). Rosario; Argentin

Draft genome sequences of four Enterococcus faecium strains isolated from Argentine cheese

We report the draft genome sequences of four Enterococcus faecium strains isolated from Argentine regional cheeses. These strains were selected based on their technological properties, i.e., their ability to produce aroma compounds (diacetyl, acetoin, and 2,3-butanediol) from citrate. The goal of our study is to provide further genetic evidence for the rational selection of entero-cocci strains based on their pheno- and genotype in order to be used in cheese production.Fil: Martino, Gabriela Paula. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET). Laboratorio de Fisiología y Genética de Bacterias Lácticas; Argentina.Fil: Martino, Gabriela Paula. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina.Fil: Quintana, Ingrid M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET). Laboratorio de Fisiología y Genética de Bacterias Lácticas; Argentina.Fil: Quintana, Ingrid M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET). Laboratorio de Fisiología y Genética de Bacterias Lácticas; Argentina.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina.Fil: Blancato, Victor. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET). Laboratorio de Fisiología y Genética de Bacterias Lácticas; Argentina.Fil: Blancato, Victor. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina.Fil: Gallina Nizo, Gabriel. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina.Fil: Gallina Nizo, Gabriel. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; Argentina.Fil: Esteban, Luis. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina.Fil: Esteban, Luis. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; Argentina.Fil: Magni, Christian. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET). Laboratorio de Fisiología y Genética de Bacterias Lácticas; Argentina.Fil: Magni, Christian. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio de Biotecnología e Inocuidad de los Alimentos; Argentina

Analysis of CcpA and PTS^Man effects on expression of the <i>aguBDAC</i> operon.

<p>β-galactosidase activity of P<i>aguB</i>-<i>lacZ</i> transcriptional fusion in wild type (JH2-2), <i>ccpA</i>⁻ (CL14), <i>mpt</i>⁻ (JH98) and <i>ccpA</i>⁻<i>mpt</i>⁻ (CL98) strains. Cells were grown in LBA with or without 30 mM glucose (Glu), lactose (Lac), maltose (Mal) or fructose (Fru). Error bars represent standard deviation of at least triplicate measurements.</p

CcpA interaction with the <i>aguR-aguBDAC</i> intergenic region.

<p>For band shift assays, <i>agu</i> or <i>agu^mut</i> amplicons (2.69 nM each) were incubated with increasing concentrations of CcpA (0.025–0.7 mM), 5 mM of P-Ser-HPr and 20 mM FBP. The arrow indicates position of the retarded complex (C). Consensus, wild type and mutated sequence of <i>cre</i> sites are indicated.</p

Acinetobacter baumannii NCIMB8209: a rare environmental strain displaying extensive insertion sequence-mediated genome remodeling resulting in the loss of exposed cell structures and defensive mechanisms

Acinetobacter baumannii represents nowadays an important nosocomial pathogen of poorly defined reservoirs outside the clinical setting. Here, we con ducted whole-genome sequencing analysis of the Acinetobacter sp. NCIMB8209 col lection strain, isolated in 1943 from the aerobic degradation (retting) of desert gu ayule shrubs. Strain NCIMB8209 contained a 3.75-Mb chromosome and a plasmid of 134 kb. Phylogenetic analysis based on core genes indicated NCIMB8209 affiliation to A. baumannii, a result supported by the identification of a chromosomal blaOXA 51-like gene. Seven genomic islands lacking antimicrobial resistance determinants, 5 regions encompassing phage-related genes, and notably, 93 insertion sequences (IS) were found in this genome. NCIMB8209 harbors most genes linked to persistence and virulence described in contemporary A. baumannii clinical strains, but many of the genes encoding components of surface structures are interrupted by IS. More over, defense genetic islands against biological aggressors such as type 6 secretion systems or CRISPR-cas are absent from this genome. These findings correlate with a low capacity of NCIMB8209 to form biofilm and pellicle, low motility on semisolid medium, and low virulence toward Galleria mellonella and Caenorhabditis elegans. Searching for catabolic genes and concomitant metabolic assays revealed the ability of NCIMB8209 to grow on a wide range of substances produced by plants, including aromatic acids and defense compounds against external aggressors. All the above features strongly suggest that NCIMB8209 has evolved specific adaptive features to a particular environmental niche. Moreover, they also revealed that the remarkable genetic plasticity identified in contemporary A. baumannii clinical strains represents an intrinsic characteristic of the species.Fil: Repizo, Guillermo Daniel. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Repizo, Guillermo Daniel. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Seravalle, Joana L. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Seravalle, Joana L. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Díaz Miloslavich, Juan Ignacio. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Díaz Miloslavich, Juan Ignacio. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Steimbrüch, Bruno A. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Steimbrüch, Bruno A. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina.Fil: Shuman, Howard A. University of Chicago. Department of Microbiology; United States.Fil: Viale, Alejandro M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR -CONICET); Argentina.Fil: Viale, Alejandro M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Microbiología; Argentina

Ammonium production and final pH values of <i>E. faecalis</i> strains grown in the presence or absence of agmatine.

<p>Ammonium production and final pH values of <i>E. faecalis</i> strains grown in the presence or absence of agmatine.</p

Proposed species names and assembly data for strains used for pipeline construction and testing.

<p>Proposed species names and assembly data for strains used for pipeline construction and testing.</p

Analysis of functional repertoires among clusters of <i>Bacillus pumilus</i> group strains.

<p>Numbers of biological functions of proteins encoded in each cluster, all <i>B</i>. <i>pumilus</i> group strains or all 26 strains under analysis are indicated.</p

Gene context analysis of the AgDI system from different sources.

<p>Gene context analysis of the AgDI system from different sources.</p