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Terán LC, Mortera P, Tubio G, Alarcón SH, Blancato VS, Espariz M, Esteban L, Magni C. Genomic analysis revealed conserved acid tolerance mechanisms from native micro-organisms in fermented feed. J Appl Microbiol 2021; 132:1152-1165. [PMID: 34487594 DOI: 10.1111/jam.15292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/28/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022]
Abstract
AIMS Fermented feed is an agricultural practice used in many regions of the world to improve the growth performance of farm animals. This study aimed to identify and evaluate the lactic acid bacteria and yeast involved in the production of fermented feed. METHODS AND RESULTS We isolated and described two micro-organisms from autochthonous microbiota origin present in a regional feed product, Lactobacillus paracasei IBR07 (Lacticaseibacillus paracasei) and Kazachstania unispora IBR014 (Saccharomyces unisporum). Genome sequence analyses were performed to characterize both micro-organisms. Potential pathways involved in the acid response, tolerance and persistence were predicted in both genomes. Although L. paracasei and K. unispora are considered safe for animal feed, we analysed the presence of virulence factors, antibiotic resistance and pathogenicity islands. Furthermore, the Galleria mellonella model was used to support the safety of both isolates. CONCLUSIONS We conclude that IBR07 and IBR014 strains are good candidates to be used as starter cultures for feed fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY The data presented here will be helpful to explore other biotechnological aspects and constitute a starting point for further studies to establish the consumption benefit of fermented feed in farm animal production.
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Affiliation(s)
- Lucrecia C Terán
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Centro de Referencia para Lactobacilos, CERELA-CONICET, San Miguel de Tucuman, Tucumán, Argentina
| | - Pablo Mortera
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Gisela Tubio
- Instituto de Procesos Biotecnológicos y Químicos Rosario, IPROByQ (CONICET-UNR), Rosario, Argentina
| | - Sergio H Alarcón
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Instituto de Química de Rosario, IQUIR (CONICET-UNR), Rosario, Argentina
| | - Victor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, FBioyF-UNR, Rosario, Argentina
| | - Luis Esteban
- Química Biológica, Facultad de Ciencias Médicas, UNR, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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Mideros-Mora C, Miguel-Romero L, Felipe-Ruiz A, Casino P, Marina A. Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases. Nat Commun 2020; 11:769. [PMID: 32034139 PMCID: PMC7005713 DOI: 10.1038/s41467-020-14540-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/17/2020] [Indexed: 02/01/2023] Open
Abstract
Histidine is a versatile residue playing key roles in enzyme catalysis thanks to the chemistry of its imidazole group that can serve as nucleophile, general acid or base depending on its protonation state. In bacteria, signal transduction relies on two-component systems (TCS) which comprise a sensor histidine kinase (HK) containing a phosphorylatable catalytic His with phosphotransfer and phosphatase activities over an effector response regulator. Recently, a pH-gated model has been postulated to regulate the phosphatase activity of HisKA HKs based on the pH-dependent rotamer switch of the phosphorylatable His. Here, we have revisited this model from a structural and functional perspective on HK853-RR468 and EnvZ-OmpR TCS, the prototypical HisKA HKs. We have found that the rotamer of His is not influenced by the environmental pH, ruling out a pH-gated model and confirming that the chemistry of the His is responsible for the decrease in the phosphatase activity at acidic pH.
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Affiliation(s)
- Cristina Mideros-Mora
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain.,Universidad UTE, Facultad de Ciencias de la Salud Eugenio Espejo, Rumipamba s/n, Quito, Ecuador
| | - Laura Miguel-Romero
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain.,Institute of Infection, Inmmunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alonso Felipe-Ruiz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain
| | - Patricia Casino
- Departament de Bioquímica i Biología molecular, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain. .,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain. .,CIBER de enfermedades raras (CIBERER-ISCIII), Madrid, Spain.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain. .,CIBER de enfermedades raras (CIBERER-ISCIII), Madrid, Spain.
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Buckley SJ, Timms P, Davies MR, McMillan DJ. In silico characterisation of the two-component system regulators of Streptococcus pyogenes. PLoS One 2018; 13:e0199163. [PMID: 29927994 PMCID: PMC6013163 DOI: 10.1371/journal.pone.0199163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/02/2018] [Indexed: 12/14/2022] Open
Abstract
Bacteria respond to environmental changes through the co-ordinated regulation of gene expression, often mediated by two-component regulatory systems (TCS). Group A Streptococcus (GAS), a bacterium which infects multiple human body sites and causes multiple diseases, possesses up to 14 TCS. In this study we examined genetic variation in the coding sequences and non-coding DNA upstream of these TCS as a method for evaluating relationships between different GAS emm-types, and potential associations with GAS disease. Twelve of the 14 TCS were present in 90% of the genomes examined. The length of the intergenic regions (IGRs) upstream of TCS coding regions varied from 39 to 345 nucleotides, with an average nucleotide diversity of 0.0064. Overall, IGR allelic variation was generally conserved with an emm-type. Subsequent phylogenetic analysis of concatenated sequences based on all TCS IGR sequences grouped genomes of the same emm-type together. However grouping with emm-pattern and emm-cluster-types was much weaker, suggesting epidemiological and functional properties associated with the latter are not due to evolutionary relatedness of emm-types. All emm5, emm6 and most of the emm18 genomes, all historically considered rheumatogenic emm-types clustered together, suggesting a shared evolutionary history. However emm1, emm3 and several emm18 genomes did not cluster within this group. These latter emm18 isolates were epidemiologically distinct from other emm18 genomes in study, providing evidence for local variation. emm-types associated with invasive disease or nephritogenicity also did not cluster together. Considering the TCS coding sequences (cds), correlation with emm-type was weaker than for the IGRs, and no strong correlation with disease was observed. Deletion of the malate transporter, maeP, was identified that serves as a putative marker for the emm89.0 subtype, which has been implicated in invasive outbreaks. A recombination-related, subclade-forming DNA motif was identified in the putative receiver domain of the Spy1556 response regulator that correlated with throat-associated emm-pattern-type A-C strains.
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Affiliation(s)
- Sean J. Buckley
- Inflammation and Healing Biomedical Research Cluster, and School of Health and Sports Sciences, Faculty of Science, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Peter Timms
- Inflammation and Healing Biomedical Research Cluster, and School of Health and Sports Sciences, Faculty of Science, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Mark R. Davies
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - David J. McMillan
- Inflammation and Healing Biomedical Research Cluster, and School of Health and Sports Sciences, Faculty of Science, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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