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Barona Duque K, Gaviria D. Modelamiento in silico de la liasa organomercurial (MerB) de Pseudomonas fluorescens. REVISTA COLOMBIANA DE QUÍMICA 2022. [DOI: 10.15446/rev.colomb.quim.v51n1.98381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El modelamiento in silico ha sido de gran contribución en los procesos proteómicos, desarrollando estructuras de las secuencias proteicas ya existentes, que por motivos de altos costos y las diferentes tecnologías necesarias para el desarrollo de estas metodologías, se encuentran deficientes en el número de modelamientos de proteínas disponibles. Entre aquellas secuencias con carencia de estructura proteica se encuentra la proteína liasa organomercurial (MerB) de Pseudomonas fluorescens, importante en la resistencia al mercurio. En el presente artículo se analizó tanto estructural como funcionalmente la proteína MerB en Pseudomonas fluorescens, utilizando la herramienta de la química estructural “modelamiento por homología” mediante plataformas bioinformáticas, con el fin de obtener un modelo que represente la estructura 3D más precisa y que capturen las mejores variantes estructurales entre todas las posibles conformaciones de las proteínas en la familia. En este trabajo, se desarrolló un método comparativo de la secuencia estudiada con las reportadas en las bases de datos para las proteínas MerB del género Pseudomonas. Se propone un modelo tridimensional para la enzima (MerB) en P. fluorescens, mediante el modelamiento por homología, se muestra la caracterización en la estructura secundaria, terciaria, la caracterización del dominio catalítico y los motivos estructurales presentes.
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Li X, Yang Z, Wang Z, Li W, Zhang G, Yan H. Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity. Front Microbiol 2022; 12:755874. [PMID: 35095786 PMCID: PMC8792951 DOI: 10.3389/fmicb.2021.755874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas stutzeri is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 P. stutzeri complex genomes covering at least six well-defined species among all sequenced Pseudomonas genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the P. stutzeri complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster (ect) was present in all genomes of P. stutzeri species complex strains but distributed at very low frequency (43 out of 9548) in other Pseudomonas genomes, suggesting a possible origin of the ancestors of P. stutzeri species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the P. stutzeri complex, shedding new light on its genomic diversity and evolutionary history.
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Affiliation(s)
- Xiangyang Li
- School of Sciences, Kaili University, Kaili, China
- Bacterial Genome Data Mining and Bioinformatic Analysis Center, Kaili University, Kaili, China
- *Correspondence: Xiangyang Li,
| | - Zilin Yang
- School of Sciences, Kaili University, Kaili, China
| | - Zhao Wang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Weipeng Li
- School of Big Data Engineering, Kaili University, Kaili, China
| | - Guohui Zhang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Hongguang Yan
- School of Life and Health Science, Kaili University, Kaili, China
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Draft Genome Sequence of Geobacter sp. Strain SVR, Isolated from Antimony Mine Soil. Microbiol Resour Announc 2020; 9:9/26/e00461-20. [PMID: 32586864 PMCID: PMC7317101 DOI: 10.1128/mra.00461-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We report here the draft genome sequence of Geobacter sp. strain SVR, isolated from antimony mine soil in Hyogo Prefecture, Japan. The genome sequence data in this study will provide useful information for understanding bacterial antimonate reduction. We report here the draft genome sequence of Geobacter sp. strain SVR, isolated from antimony mine soil in Hyogo Prefecture, Japan. The genome sequence data in this study will provide useful information for understanding bacterial antimonate reduction.
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Aguila-Torres P, Maldonado J, Gaete A, Figueroa J, González A, Miranda R, González-Stegmaier R, Martin C, González M. Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia. Mar Drugs 2020; 18:md18050252. [PMID: 32414006 PMCID: PMC7281626 DOI: 10.3390/md18050252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
Pesticides cause severe environmental damage to marine ecosystems. In the last ten years, cypermethrin has been extensively used as an antiparasitic pesticide in the salmon farming industry located in Northern Patagonia. The objective of this study was the biochemical and genomic characterization of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from cypermethrin-contaminated marine sediment samples collected in southern Chile (MS). Eleven strains were isolated by cypermethrin enrichment culture techniques and were identified by 16S rDNA gene sequencing analyses. The highest growth rate on cypermethrin was observed in four isolates (MS13, MS15a, MS16, and MS19) that also exhibited high levels of biosurfactant production. Genome sequence analyses of these isolates revealed the presence of genes encoding components of bacterial secondary metabolism, and the enzymes esterase, pyrethroid hydrolase, and laccase, which have been associated with different biodegradation pathways of cypermethrin. These novel cypermethrin-degrading and biosurfactant-producing bacterial isolates have a biotechnological potential for biodegradation of cypermethrin-contaminated marine sediments, and their genomes contribute to the understanding of microbial lifestyles in these extreme environments.
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Affiliation(s)
- Patricia Aguila-Torres
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt 5504335, Chile;
- Correspondence: (P.A.-T.); (M.G.); Tel.: +56-65-2277118 (P.A.-T.); +56-2-29781440 (M.G.)
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7810000, Chile; (J.M.); (A.G.)
- Center for Genome Regulation, Santiago 7810000, Chile
- Laboratorio de Biología de Sistemas de Plantas, Departamento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7810000, Chile; (J.M.); (A.G.)
- Center for Genome Regulation, Santiago 7810000, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (J.F.); (R.G.-S.)
| | - Alex González
- Laboratorio de Microbiología Ambiental y extremófilos, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno 5290000, Chile;
| | - Richard Miranda
- Escuela de Ingeniería Civil Industrial, Universidad Austral de Chile, Puerto Montt 5500000, Chile;
| | - Roxana González-Stegmaier
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (J.F.); (R.G.-S.)
- Laboratorio Medicina Traslacional, Instituto Clínico Oncológico, Fundación Arturo López Pérez, Santiago 8320000, Chile
| | - Carolina Martin
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt 5504335, Chile;
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7810000, Chile; (J.M.); (A.G.)
- Center for Genome Regulation, Santiago 7810000, Chile
- Correspondence: (P.A.-T.); (M.G.); Tel.: +56-65-2277118 (P.A.-T.); +56-2-29781440 (M.G.)
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