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Pan X, Cai J. Comparative transcriptome analysis of doramectin-producing Streptomyces avermitilis N72 and its mutant strains. World J Microbiol Biotechnol 2024; 40:228. [PMID: 38822927 DOI: 10.1007/s11274-024-04028-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
Doramectin, an essential animal anthelmintic, is synthesized through the fermentation process of Streptomyces avermitilis. This study delves into the transcriptomic profiles of two strains, namely the doramectin-producing wild-type S. avermitilis N72 and its highly doramectin-producing mutant counterpart, S. avermitilis XY-62. Comparative analysis revealed 860 up-regulated genes and 762 down-regulated genes in the mutant strain, notably impacting the expression of key genes pivotal in doramectin biosynthesis, including aveA1, aveA2, aveA3, aveA4, aveE, and aveBI. These findings shed light on the molecular mechanisms underpinning the heightened doramectin production in S. avermitilis XY-62, presenting promising avenues for optimizing doramectin production processes.
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Affiliation(s)
- Xiaojun Pan
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan,, 430068, China
| | - Jun Cai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan,, 430068, China.
- College of Bioengineering and Food, Hubei University of Technology, No. 28 Nanli Road, Wuhan, Hubei Province, China.
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2
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Hernández-Martínez G, Ares MA, Rosales-Reyes R, Soria-Bustos J, Yañez-Santos JA, Cedillo ML, Girón JA, Martínez-Laguna Y, Leng F, Ibarra JA, De la Cruz MA. The nucleoid protein HU positively regulates the expression of type VI secretion systems in Enterobacter cloacae. mSphere 2024; 9:e0006024. [PMID: 38647313 DOI: 10.1128/msphere.00060-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
Enterobacter cloacae is an emerging pathogen isolated in healthcare-associated infections. A major virulence factor of this bacterium is the type VI secretion system (T6SS). The genome of E. cloacae harbors two T6SS gene clusters (T6SS-1 and T6SS-2), and the functional characterization of both systems showed that these two T6SSs are not expressed under the same conditions. Here, we report that the major histone-like protein HU positively regulates the expression of both T6SSs and, therefore, the function that each T6SS exerts in E. cloacae. Single deletions of the genes encoding the HU subunits (hupA and hupB) decreased mRNA levels of both T6SS. In contrast, the hupA hupB double mutant dramatically affected the T6SS expression, diminishing its transcription. The direct binding of HU to the promoter regions of T6SS-1 and T6SS-2 was confirmed by electrophoretic mobility shift assay. In addition, single and double mutations in the hup genes affected the ability of inter-bacterial killing, biofilm formation, adherence to epithelial cells, and intestinal colonization, but these phenotypes were restored when such mutants were trans-complemented. Our data broaden our understanding of the regulation of HU-mediated T6SS in these pathogenic bacteria. IMPORTANCE T6SS is a nanomachine that functions as a weapon of bacterial destruction crucial for successful colonization in a specific niche. Enterobacter cloacae expresses two T6SSs required for bacterial competition, adherence, biofilm formation, and intestinal colonization. Expression of T6SS genes in pathogenic bacteria is controlled by multiple regulatory systems, including two-component systems, global regulators, and nucleoid proteins. Here, we reported that the HU nucleoid protein directly activates both T6SSs in E. cloacae, affecting the T6SS-related phenotypes. Our data describe HU as a new regulator involved in the transcriptional regulation of T6SS and its impact on E. cloacae pathogenesis.
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Affiliation(s)
- Gabriela Hernández-Martínez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental de la Facultad de Medicina, Universidad Autónoma de México, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Pathogen and Microbiome Division, Translational Genomics Research Institute (TGen) North, Flagstaff, Arizona, USA
- Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca, Hidalgo, Mexico
| | | | - María L Cedillo
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Ygnacio Martínez-Laguna
- Centro de Investigación en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - J Antonio Ibarra
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A De la Cruz
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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3
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Da Silva AG, Bach E, Ellwanger JH, Chies JAB. Tips and tools to obtain and assess mosquito viromes. Arch Microbiol 2024; 206:132. [PMID: 38436750 DOI: 10.1007/s00203-023-03813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 03/05/2024]
Abstract
Due to their vectorial capacity, mosquitoes (Diptera: Culicidae) receive special attention from health authorities and entomologists. These cosmopolitan insects are responsible for the transmission of many viral diseases, such as dengue and yellow fever, causing huge impacts on human health and justifying the intensification of research focused on mosquito-borne diseases. In this context, the study of the virome of mosquitoes can contribute to anticipate the emergence and/or the reemergence of infectious diseases. The assessment of mosquito viromes also contributes to the surveillance of a wide variety of viruses found in these insects, allowing the early detection of pathogens with public health importance. However, the study of mosquito viromes can be challenging due to the number and complexities of steps involved in this type of research. Therefore, this article aims to describe, in a straightforward and simplified way, the steps necessary for obtention and assessment of mosquito viromes. In brief, this article explores: the capture and preservation of specimens; sampling strategies; treatment of samples before DNA/RNA extraction; extraction methodologies; enrichment and purification processes; sequencing choices; and bioinformatics analysis.
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Affiliation(s)
- Amanda Gonzalez Da Silva
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Evelise Bach
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Joel Henrique Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Postgraduate Program in Genetics and Molecular Biology (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), UFRGS. Av. Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil.
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4
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Jeckel H, Nosho K, Neuhaus K, Hastewell AD, Skinner DJ, Saha D, Netter N, Paczia N, Dunkel J, Drescher K. Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations. Nat Microbiol 2023; 8:2378-2391. [PMID: 37973866 PMCID: PMC10686836 DOI: 10.1038/s41564-023-01518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
Development of microbial communities is a complex multiscale phenomenon with wide-ranging biomedical and ecological implications. How biological and physical processes determine emergent spatial structures in microbial communities remains poorly understood due to a lack of simultaneous measurements of gene expression and cellular behaviour in space and time. Here we combined live-cell microscopy with a robotic arm for spatiotemporal sampling, which enabled us to simultaneously acquire phenotypic imaging data and spatiotemporal transcriptomes during Bacillus subtilis swarm development. Quantitative characterization of the spatiotemporal gene expression patterns revealed correlations with cellular and collective properties, and phenotypic subpopulations. By integrating these data with spatiotemporal metabolome measurements, we discovered a spatiotemporal cross-feeding mechanism fuelling swarm development: during their migration, earlier generations deposit metabolites which are consumed by later generations that swarm across the same location. These results highlight the importance of spatiotemporal effects during the emergence of phenotypic subpopulations and their interactions in bacterial communities.
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Affiliation(s)
- Hannah Jeckel
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kazuki Nosho
- Biozentrum, University of Basel, Basel, Switzerland
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Alasdair D Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dominic J Skinner
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| | - Dibya Saha
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Knut Drescher
- Biozentrum, University of Basel, Basel, Switzerland.
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5
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Ingel B, Castro C, Burbank L, Her N, De Anda NI, Way H, Wang P, Roper MC. Xylella fastidiosa Requires the Type II Secretion System for Pathogenicity and Survival in Grapevine. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:636-646. [PMID: 37188464 DOI: 10.1094/mpmi-03-23-0027-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Xylella fastidiosa is a xylem-limited bacterial pathogen that causes Pierce's disease (PD) of grapevine. In host plants, this bacterium exclusively colonizes the xylem, which is primarily non-living at maturity. Understanding how X. fastidiosa interfaces with this specialized conductive tissue is at the forefront of investigation for this pathosystem. Unlike many bacterial plant pathogens, X. fastidiosa lacks a type III secretion system and cognate effectors that aid in host colonization. Instead, X. fastidiosa utilizes plant cell-wall hydrolytic enzymes and lipases as part of its xylem colonization strategy. Several of these virulence factors are predicted to be secreted via the type II secretion system (T2SS), the main terminal branch of the Sec-dependent general secretory pathway. In this study, we constructed null mutants in xpsE and xpsG, which encode for the ATPase that drives the T2SS and the major structural pseudopilin of the T2SS, respectively. Both mutants were non-pathogenic and unable to effectively colonize Vitis vinifera grapevines, demonstrating that the T2SS is required for X. fastidiosa infection processes. Furthermore, we utilized mass spectrometry to identify type II-dependent proteins in the X. fastidiosa secretome. In vitro, we identified six type II-dependent proteins in the secretome that included three lipases, a β-1,4-cellobiohydrolase, a protease, and a conserved hypothetical protein. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Brian Ingel
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Claudia Castro
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Lindsey Burbank
- USDA Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, U.S.A
| | - Nancy Her
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - N Itzel De Anda
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Hannah Way
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Peng Wang
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
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6
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Espindula E, Sperb ER, Moz B, Pankievicz VCS, Tuleski TR, Tadra-Sfeir MZ, Bonato P, Scheid C, Merib J, de Souza EM, Passaglia LMP. Effects on gene expression during maize-Azospirillum interaction in the presence of a plant-specific inhibitor of indole-3-acetic acid production. Genet Mol Biol 2023; 46:e20230100. [PMID: 37725833 PMCID: PMC10510588 DOI: 10.1590/1678-4685-gmb-2023-0100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/27/2023] [Indexed: 09/21/2023] Open
Abstract
Amongst the sustainable alternatives to increase maize production is the use of plant growth-promoting bacteria (PGPB). Azospirillum brasilense is one of the most well-known PGPB being able to fix nitrogen and produce phytohormones, especially indole-3-acetic acid - IAA. This work investigated if there is any contribution of the bacterium to the plant's IAA levels, and how it affects the plant. To inhibit plant IAA production, yucasin, an inhibitor of the TAM/YUC pathway, was applied. Plantlets' IAA concentration was evaluated through HPLC and dual RNA-Seq was used to analyze gene expression. Statistical differences between the group treated with yucasin and the other groups showed that A. brasilense inoculation was able to prevent the phenotype caused by yucasin concerning the number of lateral roots. Genes involved in the auxin and ABA response pathways, auxin efflux transport, and the cell cycle were regulated by the presence of the bacterium, yucasin, or both. Genes involved in the response to biotic/abiotic stress, plant disease resistance, and a D-type cellulose synthase changed their expression pattern among two sets of comparisons in which A. brasilense acted as treatment. The results suggest that A. brasilense interferes with the expression of many maize genes through an IAA-independent pathway.
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Affiliation(s)
- Eliandro Espindula
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de
Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e
Biologia Molecular, Porto Alegre, RS, Brazil
| | - Edilena Reis Sperb
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de
Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e
Biologia Molecular, Porto Alegre, RS, Brazil
| | - Brenda Moz
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de
Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e
Biologia Molecular, Porto Alegre, RS, Brazil
| | - Vânia Carla Silva Pankievicz
- Universidade Federal do Paraná (UFPR), Centro Politécnico,
Departamento de Bioquímica e Biologia Molecular, Curitiba, PR, Brazil
| | - Thalita Regina Tuleski
- Universidade Federal do Paraná (UFPR), Centro Politécnico,
Departamento de Bioquímica e Biologia Molecular, Curitiba, PR, Brazil
| | - Michelle Zibetti Tadra-Sfeir
- Universidade Federal do Paraná (UFPR), Centro Politécnico,
Departamento de Bioquímica e Biologia Molecular, Curitiba, PR, Brazil
| | - Paloma Bonato
- Universidade Federal do Paraná (UFPR), Centro Politécnico,
Departamento de Bioquímica e Biologia Molecular, Curitiba, PR, Brazil
| | - Camila Scheid
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA),
Programa de Pós-Graduação em Biociências, Porto Alegre, RS, Brazil
| | - Josias Merib
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA),
Departamento de Farmacociências, Programa de Pós-Graduação em Biociências, Porto
Alegre, Brazil
| | - Emanuel Maltempi de Souza
- Universidade Federal do Paraná (UFPR), Centro Politécnico,
Departamento de Bioquímica e Biologia Molecular, Curitiba, PR, Brazil
| | - Luciane Maria Pereira Passaglia
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de
Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e
Biologia Molecular, Porto Alegre, RS, Brazil
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Verbeelen T, Van Houdt R, Leys N, Ganigué R, Mastroleo F. RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies. STAR Protoc 2023; 4:102358. [PMID: 37347668 PMCID: PMC10331297 DOI: 10.1016/j.xpro.2023.102358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/25/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
RNA-sequencing for whole transcriptome analysis requires high-quality RNA in adequate amounts, which can be difficult to generate with low-biomass-producing bacteria where sample volume is limited. We present an RNA extraction protocol for low-biomass-producing autotrophic bacteria Nitrosomonas europaea and Nitrobacter winogradskyi cultures. We describe steps for sample collection, lysozyme-based enzymatic lysis, and a commercial silica-column-based RNA extraction. We then detail evaluation of RNA yield and quality for downstream applications such as RNA-Seq. For complete details on the use and execution of this protocol, please refer to Verbeelen et al.1.
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Affiliation(s)
- Tom Verbeelen
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), 9000 Ghent, Belgium
| | - Felice Mastroleo
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium.
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8
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Chang PE, Wu YH, Tai CY, Lin IH, Wang WD, Tseng TS, Chuang HW. Examining the Transcriptomic and Biochemical Signatures of Bacillus subtilis Strains: Impacts on Plant Growth and Abiotic Stress Tolerance. Int J Mol Sci 2023; 24:13720. [PMID: 37762026 PMCID: PMC10531026 DOI: 10.3390/ijms241813720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Rhizobacteria from various ecological niches display variations in physiological characteristics. This study investigates the transcriptome profiling of two Bacillus subtilis strains, BsCP1 and BsPG1, each isolated from distinct environments. Gene expression linked to the synthesis of seven types of antibiotic compounds was detected in both BsCP1 and BsPG1 cultures. Among these, the genes associated with plipastatin synthesis were predominantly expressed in both bacterial strains. However, genes responsible for the synthesis of polyketide, subtilosin, and surfactin showed distinct transcriptional patterns. Additionally, genes involved in producing exopolysaccharides (EPS) showed higher expression levels in BsPG1 than in BsCP1. Consistently with this, a greater quantity of EPS was found in the BsPG1 culture compared to BsCP1. Both bacterial strains exhibited similar effects on Arabidopsis seedlings, promoting root branching and increasing seedling fresh weight. However, BsPG1 was a more potent enhancer of drought, heat, and copper stress tolerance than BsCP1. Treatment with BsPG1 had a greater impact on improving survival rates, increasing starch accumulation, and stabilizing chlorophyll content during the post-stress stage. qPCR analysis was used to measure transcriptional changes in Arabidopsis seedlings in response to BsCP1 and BsPG1 treatment. The results show that both bacterial strains had a similar impact on the expression of genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Likewise, genes associated with stress response, root development, and disease resistance showed comparable responses to both bacterial strains. However, treatment with BsCP1 and BsPG1 induced distinct activation of genes associated with the ABA signaling pathway. The results of this study demonstrate that bacterial strains from different ecological environments have varying abilities to produce beneficial metabolites for plant growth. Apart from the SA and JA signaling pathways, ABA signaling triggered by PGPR bacterial strains could play a crucial role in building an effective resistance to various abiotic stresses in the plants they colonize.
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Affiliation(s)
| | | | | | | | | | - Tong-Seung Tseng
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan (C.-Y.T.); (I.-H.L.)
| | - Huey-wen Chuang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan (C.-Y.T.); (I.-H.L.)
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9
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Zhang J, Liu Y, Li C, Xiao Q, Zhang D, Chen Y, Rosenecker J, Ding X, Guan S. Recent Advances and Innovations in the Preparation and Purification of In Vitro-Transcribed-mRNA-Based Molecules. Pharmaceutics 2023; 15:2182. [PMID: 37765153 PMCID: PMC10536309 DOI: 10.3390/pharmaceutics15092182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic poses a disruptive impact on public health and the global economy. Fortunately, the development of COVID-19 vaccines based on in vitro-transcribed messenger RNA (IVT mRNA) has been a breakthrough in medical history, benefiting billions of people with its high effectiveness, safety profile, and ease of large-scale production. This success is the result of decades of continuous RNA research, which has led to significant improvements in the stability and expression level of IVT mRNA through various approaches such as sequence optimization and improved preparation processes. IVT mRNA sequence optimization has been shown to have a positive effect on enhancing the mRNA expression level. The innovation of IVT mRNA purification technology is also indispensable, as the purity of IVT mRNA directly affects the success of downstream vaccine preparation processes and the potential for inducing unwanted side effects in therapeutic applications. Despite the progress made, challenges related to IVT mRNA sequence design and purification still require further attention to enhance the quality of IVT mRNA in the future. In this review, we discuss the latest innovative progress in IVT mRNA design and purification to further improve its clinical efficacy.
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Affiliation(s)
- Jingjing Zhang
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Yuheng Liu
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Chao Li
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Qin Xiao
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Dandan Zhang
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Yang Chen
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
| | - Joseph Rosenecker
- Department of Pediatrics, Ludwig-Maximilians University of Munich, 80337 Munich, Germany;
| | - Xiaoyan Ding
- Department of Pediatrics, Ludwig-Maximilians University of Munich, 80337 Munich, Germany;
| | - Shan Guan
- National Engineering Research Center of Immunological Products, Third Military Medical University, Chongqing 400038, China; (J.Z.); (Y.L.); (C.L.); (Q.X.); (D.Z.); (Y.C.)
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10
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Jagare L, Rozenberga M, Silamikelis I, Ansone L, Elbere I, Briviba M, Megnis K, Konrade I, Birka I, Straume Z, Klovins J. Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients. J Med Microbiol 2023; 72. [PMID: 37335601 DOI: 10.1099/jmm.0.001719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Introduction. Although the presence of micro-organisms in the blood of healthy humans is a relatively new concept, there is a growing amount of evidence that blood might have its own microbiome.Gap Statement. Previous research has targeted the taxonomic composition of the blood microbiome using DNA-based sequencing methods, while little information is known about the presence of microbial transcripts obtained from the blood and their relation to conditions connected with increased gut permeability.Aim. To detect potentially alive and active micro-organisms and investigate differences in taxonomic composition between healthy people and patients with irritable bowel syndrome (IBS), we used the metatranscriptomics approach.Methodology. We collected blood samples from 23 IBS patients and 26 volunteers from the general population, and performed RNAseq on the isolated RNA. Reads corresponding to microbial genomes were identified with Kraken 2's standard plus protozoa and fungi database, and re-estimated at genus level with Bracken 2.7. We looked for trends in the taxonomic composition, making a comparison between the IBS and control groups, accounting for other different factors.Results. The dominant genera in the blood microbiome were found to be Cutibacterium, Bradyrhizobium, Escherichia, Pseudomonas, Micrococcus, Delftia, Mediterraneibacter, Staphylococcus, Stutzerimonas and Ralstonia. Some of these are typical environmental bacteria and could partially represent contamination. However, analysis of sequences from the negative controls suggested that some genera which are characteristic of the gut microbiome (Mediterraneibacter, Blautia, Collinsella, Klebsiella, Coprococcus, Dysosmobacter, Anaerostipes, Faecalibacterium, Dorea, Simiaoa, Bifidobacterium, Alistipes, Prevotella, Ruminococcus) are less likely to be a result of contamination. Differential analysis of microbes between groups showed that some taxa associated with the gut microbiome (Blautia, Faecalibacterium, Dorea, Bifidobacterium, Clostridium, Christensenella) are more prevalent in IBS patients compared to the general population. No significant correlations with any other factors were identified.Conclusion. Our findings support the existence of the blood microbiome and suggest the gut and possibly the oral microbiome as its origin, while the skin microbiome is a possible but less certain source. The blood microbiome is likely influenced by states of increased gut permeability such as IBS.
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Affiliation(s)
- Lauma Jagare
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Maija Rozenberga
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ivars Silamikelis
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Monta Briviba
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ilze Konrade
- Riga Stradins University, Dzirciema iela 16, Riga, LV-1007, Latvia
| | - Ilze Birka
- Pauls Stradins Clinical University Hospital, Pilsonu iela 13, Riga, LV-1002, Latvia
| | - Zane Straume
- Ogre Regional Hospital, Slimnicas iela 2, Ogre, LV-5001, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
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Sánchez-Estrada R, Méndez-Guerrero O, García-Morales L, González-Y-Merchand JA, Cerna-Cortes JF, Menendez MC, García MJ, León-Solís LE, Rivera-Gutiérrez S. Organization and Characterization of the Promoter Elements of the rRNA Operons in the Slow-Growing Pathogen Mycobacterium kumamotonense. Genes (Basel) 2023; 14:genes14051023. [PMID: 37239384 DOI: 10.3390/genes14051023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The slow-growing, nontuberculous mycobacterium Mycobacterium kumamotonense possesses two rRNA operons, rrnA and rrnB, located downstream from the murA and tyrS genes, respectively. Here, we report the sequence and organization of the promoter regions of these two rrn operons. In the rrnA operon, transcription can be initiated from the two promoters, named P1 rrnA and PCL1, while in rrnB, transcription can only start from one, called P1 rrnB. Both rrn operons show a similar organization to the one described in Mycobacterium celatum and Mycobacterium smegmatis. Furthermore, by qRT-PCR analyses of the products generated from each promoter, we report that stress conditions such as starvation, hypoxia, and cellular infection affect the contribution of each operon to the synthesis of pre-rRNA. It was found that the products from the PCL1 promoter of rrnA play a pivotal role in rRNA synthesis during all stress conditions. Interestingly, the main participation of the products of transcription from the P1 promoter of rrnB was found during hypoxic conditions at the NRP1 phase. These results provide novel insights into pre-rRNA synthesis in mycobacteria, as well as the potential ability of M. kumamotonense to produce latent infections.
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Affiliation(s)
- Ricardo Sánchez-Estrada
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Oscar Méndez-Guerrero
- Departamento de Química Inorgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Lázaro García-Morales
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Jorge Alberto González-Y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Jorge Francisco Cerna-Cortes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - María Carmen Menendez
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, C. Arzobispo Morcillo, 4, 28029 Madrid, Spain
| | - María Jesús García
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, C. Arzobispo Morcillo, 4, 28029 Madrid, Spain
| | - Lizbel Esperanza León-Solís
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomas, Delegación Miguel Hidalgo, Ciudad de México 11340, Mexico
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12
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Guo H, Long GJ, Liu XZ, Ma YF, Zhang MQ, Gong LL, Dewer Y, Hull JJ, Wang MM, Wang Q, He M, He P. Functional characterization of tyrosine melanin genes in the white-backed planthopper and utilization of a spray-based nanoparticle-wrapped dsRNA technique for pest control. Int J Biol Macromol 2023; 230:123123. [PMID: 36603718 DOI: 10.1016/j.ijbiomac.2022.123123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
As a significant pest of rice the white-backed planthopper (WBPH) Sogatella furcifera is a focus of pest management. However, traditional chemical-based control methods risk the development of pesticide resistance as well as severe ecological repercussions. Although nanoparticle-encapsulated dsRNAs provide a promising alternative method for sustainable pest management, gene targets specific to WBPH have yet to be optimized. Genes in the tyrosine-melanin pathway impact epidermal melanization and sclerotization, two processes essential for insect development and metabolism, have been proposed as good candidate targets for pest management. Seven genes (aaNAT, black, DDC, ebony, tan, TH, and yellow-y) in this group were identified from WBPH genome and functionally characterized by using RNAi for their impact on WBPH body color, development, and mortality. Knockdown of SfDDC, Sfblack, SfaaNAT, and Sftan caused cuticles to turn black, whereas Sfyellow-y and Sfebony knockdown resulted in yellow coloration. SfTH knockdown resulted in pale-colored bodies and high mortality. Additionally, an Escherichia coli expression system for large-scale dsRNA production was coupled with star polycation nanoparticles to develop a sprayable RNAi method targeting SfTH that induced high WBPH mortality rates on rice seedlings. These findings lay the groundwork for the development of large-scale dsRNA nanoparticle sprays as a WBPH control method.
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Affiliation(s)
- Huan Guo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Gui-Jun Long
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Xuan-Zheng Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Yun-Feng Ma
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Meng-Qi Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Lang-Lang Gong
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Youssef Dewer
- Phytotoxicity Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, 7 Nadi El-Seid Street, Dokki, 12618 Giza, Egypt
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ, 85138, USA
| | - Mei-Mei Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Qin Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China
| | - Ming He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China.
| | - Peng He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, PR China.
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13
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Guo H, Liu XZ, Long GJ, Gong LL, Zhang MQ, Ma YF, Hull JJ, Dewer Y, He M, He P. Functional characterization of developmentally critical genes in the white-backed planthopper: Efficacy of nanoparticle-based dsRNA sprays for pest control. PEST MANAGEMENT SCIENCE 2023; 79:1048-1061. [PMID: 36325939 DOI: 10.1002/ps.7271] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/30/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR), zinc finger homeodomain-2 (zfh-2), Abdominal-A (Abd-A), and Abdominal-B (Abd-B) regulate the growth and development of the insect abdomen. However, their potential roles in pest control have not been fully assessed. The development of insecticide resistance to multiple chemistries in the white-backed planthopper (WBPH), a major pest of rice, has prompted interest in novel pest control approaches that are ecologically friendly. Although pest management approaches based on double-stranded RNA (dsRNA)-mediated RNA interference (RNAi) have potential, their susceptibility to degradation limits large-scale field applications. These limitations, however, can be overcome with nanoparticle-dsRNA complexes that have greater environmental stability and improved cellular uptake. RESULTS In this study, at 5 days post-injection, transcripts for the four gene targets were reduced relative to controls and all of the experimental groups exhibited significant phenotypic defects and increased mortality. To evaluate the potential of these gene targets for field applications, a nanocarrier-dsRNA spray delivery system was assessed for RNAi efficacy. At 11 days post-spray, significant phenotypic defects and increased mortality were observed in all experimental groups. CONCLUSION Taken together, the results confirm the suitability of the target genes (SfEGFR, Sfzfh-2, SfAbd-A, and SfAbd-B) for pest management and demonstrate the efficacy of the nanocarrier spray system for inducing RNAi-mediated knockdown. As such, the study lays the foundation for the further development and optimization of this technology for large-scale field applications. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Huan Guo
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Xuan-Zheng Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Gui-Jun Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Lang-Lang Gong
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Meng-Qi Zhang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Yun-Feng Ma
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ, USA
| | - Youssef Dewer
- Phytotoxicity Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, Giza, Egypt
| | - Ming He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
| | - Peng He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, P. R. China
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Wang LX, Ji CH, Ning CC, Liu YC, Li ZY, Sun YQ, Xia XZ, Cai XP, Meng QL, Qiao J. A Regulatory sRNA rli41 is Implicated in Cell Adhesion, Invasion and Pathogenicity in Listeria monocytogenes. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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Verbeelen T, Van Houdt R, Leys N, Ganigué R, Mastroleo F. Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples. iScience 2022; 25:105311. [PMID: 36345334 PMCID: PMC9636042 DOI: 10.1016/j.isci.2022.105311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g., as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs. Lysis through ultrasonication results in a high RNA yield but in a low RNA quality Enzymatic lysis using lysozyme provides high-yield, high-quality RNA samples RNA from low-biomass bacterial samples is suitable for downstream RNA-seq
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León-Montes N, Nava-Galeana J, Rodríguez-Valverde D, Soria-Bustos J, Rosales-Reyes R, Rivera-Gutiérrez S, Hirakawa H, Ares MA, Bustamante VH, De la Cruz MA. The Two-Component System CpxRA Represses Salmonella Pathogenicity Island 2 by Directly Acting on the ssrAB Regulatory Operon. Microbiol Spectr 2022; 10:e0271022. [PMID: 36073960 PMCID: PMC9603713 DOI: 10.1128/spectrum.02710-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023] Open
Abstract
The acquisition of Salmonella pathogenicity island 2 (SPI-2) conferred on Salmonella the ability to survive and replicate within host cells. The ssrAB bicistronic operon, located in SPI-2, encodes the SsrAB two-component system (TCS), which is the central positive regulator that induces the expression of SPI-2 genes as well as other genes located outside this island. On the other hand, CpxRA is a two-component system that regulates expression of virulence genes in many bacteria in response to different stimuli that perturb the cell envelope. We previously reported that the CpxRA system represses the expression of SPI-1 and SPI-2 genes under SPI-1-inducing conditions by decreasing the stability of the SPI-1 regulator HilD. Here, we show that under SPI-2-inducing conditions, which mimic the intracellular environment, CpxRA represses the expression of SPI-2 genes by the direct action of phosphorylated CpxR (CpxR-P) on the ssrAB regulatory operon. CpxR-P recognized two sites located proximal and distal from the promoter located upstream of ssrA. Consistently, we found that CpxRA reduces the replication of Salmonella enterica serovar Typhimurium inside murine macrophages. Therefore, our results reveal CpxRA as an additional regulator involved in the intracellular lifestyle of Salmonella, which in turn adds a new layer to the intricate regulatory network controlling the expression of Salmonella virulence genes. IMPORTANCE SPI-2 encodes a type III secretion system (T3SS) that is a hallmark for the species Salmonella enterica, which is essential for the survival and replication within macrophages. Expression of SPI-2 genes is positively controlled by the two-component system SsrAB. Here, we determined a regulatory mechanism involved in controlling the overgrowth of Salmonella inside macrophages. In this mechanism, CpxRA, a two-component system that is activated by extracytoplasmic stress, directly represses expression of the ssrAB regulatory operon; as a consequence, expression of SsrAB target genes is decreased. Our findings reveal a novel mechanism involved in the intracellular lifestyle of Salmonella, which is expected to sense perturbations in the bacterial envelope that Salmonella faces inside host cells, as the synthesis of the T3SS-2 itself.
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Affiliation(s)
- Nancy León-Montes
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jessica Nava-Galeana
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Víctor H. Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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Li M, Chen Q, Wu C, Li Y, Wang S, Chen X, Qiu B, Li Y, Mao D, Lin H, Yu D, Cao Y, Huang Z, Cui C, Zhong Z. A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571. Genes (Basel) 2022; 13:genes13101895. [PMID: 36292780 PMCID: PMC9601964 DOI: 10.3390/genes13101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICEAc) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICEAc, but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICEAc and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host’s flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICEAc by 18.5%. We propose the feasibility of constructing a minimal ICEAc element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.
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Affiliation(s)
- Mingxu Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qianqian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanhui Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyang Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Sanle Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuelian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bowen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongmei Mao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Lin
- Animal, Plant and Food Inspection Center, Nanjing Customs, No. 39, Chuangzhi Road, Nanjing 210019, China
| | - Daogeng Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou 571737, China
| | - Yajun Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Chunhong Cui
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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18
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Gárriz A, Williamson SA, Shah AD, Evans RG, Deveson Lucas DS, Powell DR, Walton SL, Marques FZ, Reina RD. Transcriptomic analysis of pre-ovipositional embryonic arrest in a non-squamate reptile (Chelonia mydas). Mol Ecol 2022; 31:4319-4331. [PMID: 35762848 PMCID: PMC9540450 DOI: 10.1111/mec.16583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/29/2022]
Abstract
After gastrulation, oviductal hypoxia maintains turtle embryos in an arrested state prior to oviposition. Subsequent exposure to atmospheric oxygen upon oviposition initiates recommencement of embryonic development. Arrest can be artificially extended for several days after oviposition by incubation of the egg under hypoxic conditions, with development recommencing in an apparently normal fashion after subsequent exposure to normoxia. To examine the transcriptomic events associated with embryonic arrest in green sea turtles (Chelonia mydas), RNA‐sequencing analysis was performed on embryos from freshly laid eggs and eggs incubated in either normoxia (oxygen tension ~159 mmHg) or hypoxia (<8 mmHg) for 36 h after oviposition (n = 5 per group). The patterns of gene expression differed markedly among the three experimental groups. Normal embryonic development in normoxia was associated with upregulation of genes involved in DNA replication, the cell cycle, and mitosis, but these genes were commonly downregulated after incubation in hypoxia. Many target genes of hypoxia inducible factors, including the gene encoding insulin‐like growth factor binding protein 1 (igfbp1), were downregulated by normoxic incubation but upregulated by incubation in hypoxia. Notably, some of the transcriptomic effects of hypoxia in green turtle embryos resembled those reported to be associated with hypoxia‐induced embryonic arrest in diverse taxa, including the nematode Caenorhabditis elegans and zebrafish (Danio rerio). Hypoxia‐induced preovipositional embryonic arrest appears to be a unique adaptation of turtles. However, our findings accord with the proposition that the mechanisms underlying hypoxia‐induced embryonic arrest per se are highly conserved across diverse taxa.
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Affiliation(s)
- Angela Gárriz
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Sean A Williamson
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Anup D Shah
- Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Roger G Evans
- Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Victoria 3800, Australia.,Pre-clinical Critical Care Unit, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Deanna S Deveson Lucas
- Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sarah L Walton
- Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - Francine Z Marques
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Richard D Reina
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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19
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Cowles KN, Block AK, Barak JD. Xanthomonas hortorum pv. gardneri TAL effector AvrHah1 is necessary and sufficient for increased persistence of Salmonella enterica on tomato leaves. Sci Rep 2022; 12:7313. [PMID: 35508535 PMCID: PMC9068798 DOI: 10.1038/s41598-022-11456-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/25/2022] [Indexed: 01/16/2023] Open
Abstract
Salmonella enterica is ubiquitous in the plant environment, persisting in the face of UV stress, plant defense responses, desiccation, and nutrient limitation. These fluctuating conditions of the leaf surface result in S. enterica population decline. Biomultipliers, such as the phytopathogenic bacterium Xanthomonas hortorum pv. gardneri (Xhg), alter the phyllosphere to the benefit of S. enterica. Specific Xhg-dependent changes to this niche that promote S. enterica persistence remain unclear, and this work focuses on identifying factors that lead to increased S. enterica survival on leaves. Here, we show that the Xhg transcription activator-like effector AvrHah1 is both necessary and sufficient for increased survival of S. enterica on tomato leaves. An Xhg avrHah1 mutant fails to influence S. enterica survival while addition of avrHah1 to X. vesicatoria provides a gain of function. Our results indicate that although Xhg stimulates a robust immune response from the plant, AvrHah1 is not required for these effects. In addition, we demonstrate that cellular leakage that occurs during disease is independent of AvrHah1. Investigation of the interaction between S. enterica, Xhg, and the plant host provides information regarding how an inhospitable environment changes during infection and can be transformed into a habitable niche.
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Affiliation(s)
- Kimberly N Cowles
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna K Block
- Center for Medical, Agricultural, and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL, USA
| | - Jeri D Barak
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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20
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Crowley MA, Bankhead T. Potential Regulatory Role in Mammalian Host Adaptation for a Small Intergenic Region of Lp17 in the Lyme Disease Spirochete. Front Cell Infect Microbiol 2022; 12:892220. [PMID: 35586252 PMCID: PMC9108270 DOI: 10.3389/fcimb.2022.892220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The bacterial agent of Lyme disease, Borrelia burgdorferi, relies on an intricate gene regulatory network to transit between the disparate Ixodes tick vector and mammalian host environments. We recently reported that a B. burgdorferi mutant lacking a transcriptionally active intergenic region of lp17 displayed attenuated murine tissue colonization and pathogenesis due to altered expression of multiple antigens. In this study, a more detailed characterization of the putative regulatory factor encoded by the intergenic region was pursued. In cis complemented strains featuring mutations aimed at eliminating potential protein translation were capable of full tissue colonization, suggesting that the functional product encoded by the intergenic region is not a protein as previously predicted. In trans complementation of the intergenic region resulted in elevated transcription of the sequence compared to wild type and was found to completely abolish infectivity in both immunocompetent "and immunodeficient mice. Quantitative analysis of transcription of the intergenic region by wild-type B. burgdorferi showed it to be highly induced during murine infection relative to in vitro culture. Lastly, targeted deletion of this intergenic region resulted in significant changes to the transcriptome, including genes with potential roles in transmission and host adaptation. The findings reported herein strongly suggest that this segment of lp17 serves a potentially critical role in the regulation of genes required for adaptation and persistence of the pathogen in a mammalian host.
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Affiliation(s)
| | - Troy Bankhead
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
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21
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Grivokostopoulos NC, Makariti IP, Hilaj N, Apostolidou Z, Skandamis PN. Internalization of Salmonella in Leafy Greens and Impact on Acid Tolerance. Appl Environ Microbiol 2022; 88:e0224921. [PMID: 35108086 PMCID: PMC8939352 DOI: 10.1128/aem.02249-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/26/2022] [Indexed: 11/20/2022] Open
Abstract
Salmonella colonizes the surface or the inner part of leafy greens, while the ability of internalized bacteria to evade common disinfection practices may pose a considerable risk. Hereby, we aimed to assess how the colonization and internalization of Salmonella spp. (i) vary with the type of leafy green, the storage conditions (temperature, time), and Salmonella serovar at phenotypic and gene transcriptional level (regarding stress- and virulence- or type III secretion system [T3SS]-associated genes) and (ii) potentially impact the survival of the pathogen against subsequent exposure at lethal pH (2.7), mimicking the gastric acidity. Internalized Salmonella reached 3.0 to 5.0 log CFU/g depending on storage conditions and vegetable, with spinach and chicory allowing the highest (P < 0.05) internalization. Prolonged storage (48 h) at 20°C increased the recovery of internalized Salmonella in spinach and green amaranth by 1.0 to 1.5 log units. Colonization of Salmonella on/in leafy vegetables induced the transcription (maximum fold change [FCmax], ∼2,000) of T3SS-related genes. Interserovar variation regarding the internalization ability of Salmonella was observed only in lettuce and green amaranth in a time- and temperature-dependent manner. Attached cells exhibited higher survival rates against low pH than the internalized subpopulation; however, habituation at 20°C in lettuce and amaranth induced acid tolerance to internalized cells, manifested by the 1.5 to 2.0 log CFU/g survivors after 75 min at pH 2.7. Habituation of Salmonella in vegetable extracts sensitized it toward acid, while indigenous microbiota had limited impact on acid resistance of the organism. These findings reveal physiological aspects of Salmonella colonizing leafy vegetables that could be useful in fresh produce microbial risk assessment. IMPORTANCE Consumption of leafy greens has been increasingly associated with foodborne illnesses, and their contamination could occur at pre- and/or postharvest level. Human pathogens may become passively or actively internalized in plant tissues, thereby escaping decontamination procedures. Plant colonization may impact bacterial physiology such as stress resistance and virulence. In this study, it was demonstrated that internalization of Salmonella spp., at the postharvest level, varied with type of vegetable, serovar, and storage conditions. Attached and internalized subpopulations of Salmonella on/in leafy greens showed distinct physiological responses regarding transcriptional changes of stress- and virulence-associated genes, as well as survival capacity against subsequent exposure to lethal pH (2.7). These findings could contribute to a better understanding and potential (re)definition of the risk of enteric pathogens colonizing leafy greens, as well as to the design of intervention strategies aiming to improve the microbiological safety of fresh produce.
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Affiliation(s)
- N. C. Grivokostopoulos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - I. P. Makariti
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - N. Hilaj
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Z. Apostolidou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - P. N. Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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22
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Khan D, Ziegler DJ, Kalichuk JL, Hoi V, Huynh N, Hajihassani A, Parkin IAP, Robinson SJ, Belmonte MF. Gene expression profiling reveals transcription factor networks and subgenome bias during Brassica napus seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:477-489. [PMID: 34786793 DOI: 10.1111/tpj.15587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 05/22/2023]
Abstract
We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole-genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive-lethal phenotype. Global mRNA profiling revealed lower accumulation of Cn subgenome transcripts relative to the An subgenome. Subgenome-specific transcription factor networks identified distinct transcription factor families enriched in each of the An and Cn subgenomes early in seed development. Analysis of laser-microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the An subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cn subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the An and Cn genomes of the whole B. napus seed can identify valuable targets for seed development research and that -omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.
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Affiliation(s)
- Deirdre Khan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Dylan J Ziegler
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Jenna L Kalichuk
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Vanessa Hoi
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Nina Huynh
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Abolfazl Hajihassani
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
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23
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He FB, Khan H, Huttunen M, Kolehmainen P, Melén K, Maljanen S, Qu M, Jiang M, Kakkola L, Julkunen I. Filovirus VP24 Proteins Differentially Regulate RIG-I and MDA5-Dependent Type I and III Interferon Promoter Activation. Front Immunol 2022; 12:694105. [PMID: 35069519 PMCID: PMC8767557 DOI: 10.3389/fimmu.2021.694105] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Filovirus family consists of highly pathogenic viruses that have caused fatal outbreaks especially in many African countries. Previously, research focus has been on Ebola, Sudan and Marburg viruses leaving other filoviruses less well studied. Filoviruses, in general, pose a significant global threat since they are highly virulent and potentially transmissible between humans causing sporadic infections and local or widespread epidemics. Filoviruses have the ability to downregulate innate immunity, and especially viral protein 24 (VP24), VP35 and VP40 have variably been shown to interfere with interferon (IFN) gene expression and signaling. Here we systematically analyzed the ability of VP24 proteins of nine filovirus family members to interfere with retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated antigen 5 (MDA5) induced IFN-β and IFN-λ1 promoter activation. All VP24 proteins were localized both in the cell cytoplasm and nucleus in variable amounts. VP24 proteins of Zaire and Sudan ebolaviruses, Lloviu, Taï Forest, Reston, Marburg and Bundibugyo viruses (EBOV, SUDV, LLOV, TAFV, RESTV, MARV and BDBV, respectively) were found to inhibit both RIG-I and MDA5 stimulated IFN-β and IFN-λ1 promoter activation. The inhibition takes place downstream of interferon regulatory factor 3 phosphorylation suggesting the inhibition to occur in the nucleus. VP24 proteins of Mengla (MLAV) or Bombali viruses (BOMV) did not inhibit IFN-β or IFN-λ1 promoter activation. Six ebolavirus VP24s and Lloviu VP24 bound tightly, whereas MARV and MLAV VP24s bound weakly, to importin α5, the subtype that regulates the nuclear import of STAT complexes. MARV and MLAV VP24 binding to importin α5 was very weak. Our data provides new information on the innate immune inhibitory mechanisms of filovirus VP24 proteins, which may contribute to the pathogenesis of filovirus infections.
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Affiliation(s)
- Felix B. He
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
| | - Hira Khan
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
| | - Moona Huttunen
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
| | - Pekka Kolehmainen
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
| | - Krister Melén
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sari Maljanen
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
| | - Mengmeng Qu
- Research Center for Clinical & Translational Medicine, Fifth Medical Center for General Hospital of People’s Liberation Army (PLA), Beijing, China
| | - Miao Jiang
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Laura Kakkola
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine/Virology, University of Turku, Turku, Finland
- Turku University Hospital, Clinical Microbiology, Turku, Finland
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24
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Mehta D, Chirmade T, Tungekar AA, Gani K, Bhambure R. Cloning and expression of antibody fragment (Fab) I: Effect of expression construct and induction strategies on light and heavy chain gene expression. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Cárdenas Espinosa MJ, Schmidgall T, Wagner G, Kappelmeyer U, Schreiber S, Heipieper HJ, Eberlein C. An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene. PLoS One 2021; 16:e0260002. [PMID: 34780548 PMCID: PMC8592408 DOI: 10.1371/journal.pone.0260002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/30/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.
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Affiliation(s)
| | - Tabea Schmidgall
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Georg Wagner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephan Schreiber
- Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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26
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Valdez-Salazar HA, Ares MA, Fernández FJ, Ibarra JA, Torres J, Bustamante VH, De la Cruz MA. Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes. PeerJ 2021; 9:e12270. [PMID: 34760355 PMCID: PMC8567857 DOI: 10.7717/peerj.12270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
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Affiliation(s)
- Hilda A Valdez-Salazar
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Posgrado en Biología Experimental, DCBS., Universidad Autónoma Metropolitana (UAM) Iztapalapa, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco J Fernández
- Laboratorio de Ingeniería Genética y Metabolismo Secundario, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - J Antonio Ibarra
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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27
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Díaz-Pascual F, Lempp M, Nosho K, Jeckel H, Jo JK, Neuhaus K, Hartmann R, Jelli E, Hansen MF, Price-Whelan A, Dietrich LEP, Link H, Drescher K. Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies. eLife 2021; 10:e70794. [PMID: 34751128 PMCID: PMC8579308 DOI: 10.7554/elife.70794] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
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Affiliation(s)
| | - Martin Lempp
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Kazuki Nosho
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Jeanyoung K Jo
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Konstantin Neuhaus
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Eric Jelli
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
| | | | - Alexa Price-Whelan
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Lars EP Dietrich
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Hannes Link
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology
and Infection Medicine, Eberhard Karls Universität
TübingenTübingenGermany
| | - Knut Drescher
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
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28
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Rodríguez-Valverde D, León-Montes N, Soria-Bustos J, Martínez-Cruz J, González-Ugalde R, Rivera-Gutiérrez S, González-y-Merchand JA, Rosales-Reyes R, García-Morales L, Hirakawa H, Fox JG, Girón JA, De la Cruz MA, Ares MA. cAMP Receptor Protein Positively Regulates the Expression of Genes Involved in the Biosynthesis of Klebsiella oxytoca Tilivalline Cytotoxin. Front Microbiol 2021; 12:743594. [PMID: 34659176 PMCID: PMC8515920 DOI: 10.3389/fmicb.2021.743594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 01/09/2023] Open
Abstract
Klebsiella oxytoca is a resident of the human gut. However, certain K. oxytoca toxigenic strains exist that secrete the nonribosomal peptide tilivalline (TV) cytotoxin. TV is a pyrrolobenzodiazepine that causes antibiotic-associated hemorrhagic colitis (AAHC). The biosynthesis of TV is driven by enzymes encoded by the aroX and NRPS operons. In this study, we determined the effect of environmental signals such as carbon sources, osmolarity, and divalent cations on the transcription of both TV biosynthetic operons. Gene expression was enhanced when bacteria were cultivated in tryptone lactose broth. Glucose, high osmolarity, and depletion of calcium and magnesium diminished gene expression, whereas glycerol increased transcription of both TV biosynthetic operons. The cAMP receptor protein (CRP) is a major transcriptional regulator in bacteria that plays a key role in metabolic regulation. To investigate the role of CRP on the cytotoxicity of K. oxytoca, we compared levels of expression of TV biosynthetic operons and synthesis of TV in wild-type strain MIT 09-7231 and a Δcrp isogenic mutant. In summary, we found that CRP directly activates the transcription of the aroX and NRPS operons and that the absence of CRP reduced cytotoxicity of K. oxytoca on HeLa cells, due to a significant reduction in TV production. This study highlights the importance of the CRP protein in the regulation of virulence genes in enteric bacteria and broadens our knowledge on the regulatory mechanisms of the TV cytotoxin.
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Affiliation(s)
- Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Nancy León-Montes
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jessica Martínez-Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ricardo González-Ugalde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A. González-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lázaro García-Morales
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jorge A. Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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du Toit JP, Lea-Smith DJ, Git A, Hervey JRD, Howe CJ, Pott RWM. Expression of Alternative Nitrogenases in Rhodopseudomonas palustris Is Enhanced Using an Optimized Genetic Toolset for Rapid, Markerless Modifications. ACS Synth Biol 2021; 10:2167-2178. [PMID: 34431288 DOI: 10.1021/acssynbio.0c00496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The phototrophic bacterium Rhodopseudomonas palustris is emerging as a promising biotechnological chassis organism, due to its resilience to a range of harsh conditions, a wide metabolic repertoire, and the ability to quickly regenerate ATP using light. However, realization of this promise is impeded by a lack of efficient, rapid methods for genetic modification. Here, we present optimized tools for generating chromosomal insertions and deletions employing electroporation as a means of transformation. Generation of markerless strains can be completed in 12 days, approximately half the time for previous conjugation-based methods. This system was used for overexpression of alternative nitrogenase isozymes with the aim of improving biohydrogen productivity. Insertion of the pucBa promoter upstream of vnf and anf nitrogenase operons drove robust overexpression up to 4000-fold higher than wild-type. Transcript quantification was facilitated by an optimized high-quality RNA extraction protocol employing lysis using detergent and heat. Overexpression resulted in increased nitrogenase protein levels, extending to superior hydrogen productivity in bioreactor studies under nongrowing conditions, where promoter-modified strains better utilized the favorable energy state created by reduced competition from cell division. Robust heterologous expression driven by the pucBa promoter is thus attractive for energy-intensive biosyntheses suited to the capabilities of R. palustris. Development of this genetic modification toolset will accelerate the advancement of R. palustris as a biotechnological chassis organism, and insights into the effects of nitrogenase overexpression will guide future efforts in engineering strains for improved hydrogen production.
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Affiliation(s)
- Jan-Pierre du Toit
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, 7600, South Africa
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - John R. D. Hervey
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Christopher J. Howe
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Robert W. M. Pott
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, 7600, South Africa
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Loss of RND-type multidrug efflux pumps triggers iron starvation and lipid A modifications in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2021; 65:e0059221. [PMID: 34252310 DOI: 10.1128/aac.00592-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transporters belonging to the Resistance-Nodulation-Division (RND) superfamily of proteins are invariably present in the genomes of Gram-negative bacteria and are largely responsible for the intrinsic antibiotic resistance of these organisms. The number of genes encoding RND transporters per genome vary from one to sixteen and correlates with environmental versatilities of bacterial species. Pseudomonas aeruginosa PAO1 strain, a ubiquitous nosocomial pathogen, possesses twelve RND pumps, which are implicated in development of clinical multidrug resistance and known to contribute to virulence, quorum sensing and many other physiological functions. In this study, we analyzed how P. aeruginosa physiology adapts to the lack of RND-mediated efflux activities. A combination of transcriptomics, metabolomics, genetic and analytical approaches showed that the P. aeruginosa PΔ6 strain lacking six best characterized RND pumps activates a specific adaptation response that involves significant changes in abundance and activities of several transport systems, quorum sensing, iron acquisition and lipid A modifications. Our results demonstrate that these cells accumulate large quantities of pseudomonas quorum signal (PQS), which triggers iron starvation and activation of siderophore biosynthesis and acquisition pathways. The accumulation of iron in turn activates lipid A modification and membrane protection pathways. A transcriptionally regulated RND pump MuxABC-OpmB contributes to these transformations by controlling concentrations of coumarins. Our results suggest that these changes reduce the permeability barrier of the outer membrane and are needed to protect the cell envelope of efflux-deficient P. aeruginosa.
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Bacillus anthracis chain length, a virulence determinant, is regulated by membrane localized serine/threonine protein kinase PrkC. J Bacteriol 2021; 203:JB.00582-20. [PMID: 33753466 PMCID: PMC8117516 DOI: 10.1128/jb.00582-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anthrax is a zoonotic disease caused by Bacillus anthracis, a spore-forming pathogen that displays a chaining phenotype. It has been reported that the chaining phenotype acts as a virulence factor in B. anthracis In this study, we identify a serine/threonine protein kinase of B. anthracis, PrkC, the only kinase localized at the bacteria-host interface, as a determinant of B. anthracis chain length. In vitro, prkC disruption strain (BAS ΔprkC) grew as shorter chains throughout the bacterial growth cycle. A comparative analysis between the parent strain and BAS ΔprkC indicated that the levels of proteins, BslO and Sap, associated with the regulation of the bacterial chain length, were upregulated in BAS ΔprkC BslO is a septal murein hydrolase that catalyzes daughter cell separation and Sap is an S-layer structural protein required for the septal localization of BslO. PrkC disruption also has a significant effect on bacterial growth, cell wall thickness, and septa formation. Upregulation of ftsZ in BAS ΔprkC was also observed. Altogether, our results indicate that PrkC is required for maintaining optimum growth, cell wall homeostasis and most importantly - for the maintenance of the chaining phenotype.IMPORTANCEChaining phenotype acts as a virulence factor in Bacillus anthracis This is the first study that identifies a 'signal transduction protein' with an ability to regulate the chaining phenotype in Bacillus anthracis We show that the disruption of the lone surface-localized serine/threonine protein kinase, PrkC, leads to the shortening of the bacterial chains. We report upregulation of the de-chaining proteins in the PrkC disruption strain. Apart from this, we also report for the first time that PrkC disruption results in an attenuated cell growth, a decrease in the cell wall thickness and aberrant cell septa formation during the logarithmic phase of growth - a growth phase where PrkC is expressed maximally.
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Yao Y, Rao S, Habimana O. Active Microbiome Structure and Functional Analyses of Freshwater Benthic Biofilm Samples Influenced by RNA Extraction Methods. Front Microbiol 2021; 12:588025. [PMID: 33935982 PMCID: PMC8085529 DOI: 10.3389/fmicb.2021.588025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/24/2021] [Indexed: 02/01/2023] Open
Abstract
Advances in high-throughput sequencing technologies have enabled extensive studies of freshwater biofilms and significant breakthroughs in biofilm meta-omics. To date, however, no standardized protocols have been developed for the effective isolation of RNA from freshwater benthic biofilms. In this study, we compared column-based kit RNA extraction with five RNAzol-based extractions, differentiated by various protocol modifications. The RNA products were then evaluated to determine their integrity, purity and yield and were subjected to meta-transcriptomic sequencing and analysis. Significant discrepancies in the relative abundance of active communities and structures of eukaryotic, bacterial, archaebacterial, and viral communities were observed as direct outcomes of the tested RNA extraction methods. The column isolation-based group was characterized by the highest relative abundance of Archaea and Eukaryota, while the organic isolation-based groups commonly had the highest relative abundances of Prokaryota (bacteria). Kit extraction methods provided the best outcomes in terms of high-quality RNA yield and integrity. However, these methods were deemed questionable for studies of active bacterial communities and may contribute a significant degree of bias to the interpretation of downstream meta-transcriptomic analyses.
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Affiliation(s)
- Yuan Yao
- The School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - Subramanya Rao
- The School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - Olivier Habimana
- The School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, China
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de Matos GF, Rouws LFM, Simões-Araújo JL, Baldani JI. Evolution and function of nitrogen fixation gene clusters in sugarcane associated Bradyrhizobium strains. Environ Microbiol 2021; 23:6148-6162. [PMID: 33928743 DOI: 10.1111/1462-2920.15533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/01/2022]
Abstract
Bradyrhizobium spp. are well known to mediate biological nitrogen fixation (BNF) as microsymbionts inhabiting nodules on leguminous plants. However, they may also contribute to plant growth via free-living N2 fixation (FLNF) in association with non-legumes. Notably, several Bradyrhizobium strains from sugarcane roots display FLNF activity. Among them, Bradyrhizobium sacchari is a legume symbiotic species, whereas strains AG48 and M12 are non-symbiotic. In the present study, a phylogenomic approach was applied to study peculiarities of these and other Bradyrhizobium strains with respect to N fixation (nif) gene content in order to reveal genetic features that enable FNLF in Bradyrhizobium spp. All FLNF strains carry an ancestral 'non-symbiotic' nif-gene cluster (NSC). B. sacchari also contains a second 'symbiotic' nif-gene cluster (SC), a characteristic observed in only three of 156 evaluated genomes. B. sacchari stood out and presented a high level of sequence divergence between individual nif-gene homologues and we discuss scenarios for the evolutionary origin of these clusters. The transcript level of NSC nifH gene increased during FLNF, when compared to symbiotic conditions. The data suggest that sugarcane roots harbor diverse Bradyrhizobium spp. that are genetically adapted to a dynamic environment where leguminous and non-leguminous host plants are alternately available.
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Affiliation(s)
- Gustavo Feitosa de Matos
- Curso de Pós-graduação em Fitotecnia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 7, Seropédica, RJ, 23891-000, Brazil
| | | | | | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, 23891-000, Brazil
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Liu X, Zhao F, Liu H, Xie Y, Zhao D, Li C. Transcriptomics and metabolomics reveal the adaption of Akkermansia muciniphila to high mucin by regulating energy homeostasis. Sci Rep 2021; 11:9073. [PMID: 33907216 PMCID: PMC8079684 DOI: 10.1038/s41598-021-88397-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
In gut, Akkermansia muciniphila (A. muciniphila) probably exerts its probiotic activities by the positive modulation of mucus thickness and gut barrier integrity. However, the potential mechanisms between A. muciniphila and mucin balance have not been fully elucidated. In this study, we cultured the bacterium in a BHI medium containing 0% to 0.5% mucin, and transcriptome and gas chromatography mass spectrometry (GC-MS) analyses were performed. We found that 0.5% (m/v) mucin in a BHI medium induced 1191 microbial genes to be differentially expressed, and 49 metabolites to be changed. The metabolites of sorbose, mannose, 2,7-anhydro-β-sedoheptulose, fructose, phenylalanine, threonine, lysine, ornithine, asparagine, alanine and glutamic acid were decreased by 0.5% mucin, while the metabolites of leucine, valine and N-acetylneuraminic acid were increased. The association analysis between transcriptome and metabolome revealed that A. muciniphila gave strong responses to energy metabolism, amino sugar and nucleotide sugar metabolism, and galactose metabolism pathways to adapt to high mucin in the medium. This finding showed that only when mucin reached a certain concentration in a BHI medium, A. muciniphila could respond to the culture environment significantly at the level of genes and metabolites, and changed its metabolic characteristics by altering the effect on carbohydrates and amino acids.
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Affiliation(s)
- Xinyue Liu
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Meat Production, College of Food Science and Technology, Nanjing Agricultural University, Weigang 1#, Nanjing, 210095, People's Republic of China
| | - Fan Zhao
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Meat Production, College of Food Science and Technology, Nanjing Agricultural University, Weigang 1#, Nanjing, 210095, People's Republic of China
| | - Hui Liu
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Meat Production, College of Food Science and Technology, Nanjing Agricultural University, Weigang 1#, Nanjing, 210095, People's Republic of China
| | - Yunting Xie
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Meat Production, College of Food Science and Technology, Nanjing Agricultural University, Weigang 1#, Nanjing, 210095, People's Republic of China
| | - Di Zhao
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Meat Production, College of Food Science and Technology, Nanjing Agricultural University, Weigang 1#, Nanjing, 210095, People's Republic of China
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Key Laboratory of Meat Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Meat Production, College of Food Science and Technology, Nanjing Agricultural University, Weigang 1#, Nanjing, 210095, People's Republic of China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Leus IV, Adamiak J, Trinh AN, Smith RD, Smith L, Richardson S, Ernst RK, Zgurskaya HI. Inactivation of AdeABC and AdeIJK efflux pumps elicits specific nonoverlapping transcriptional and phenotypic responses in Acinetobacter baumannii. Mol Microbiol 2020; 114:1049-1065. [PMID: 32858760 DOI: 10.1111/mmi.14594] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Multidrug resistant (MDR) strains of Acinetobacter baumannii present a serious clinical challenge. The development of antibiotic resistance in this species is enabled by efflux pumps of the Resistance-Nodulation-Division (RND) superfamily of proteins creating an efficient permeability barrier for antibiotics. At least three RND pumps, AdeABC, AdeIJK, and AdeFGH are encoded in the A. baumannii genome and are reported to contribute to antibiotic resistance in clinical isolates. In this study, we analyzed the contributions of AdeABC and AdeIJK in antibiotic resistance and growth physiology of the two MDR strains, AYE and AB5075. We found that not only the two pumps have nonoverlapping substrate specificities, their inactivation leads to specific nonoverlapping changes in gene expression as determined by RNA sequencing and confirmed by gene knockouts and growth phenotypes. Our results suggest that inactivation of AdeIJK elicits broader changes in the abundances of mRNAs and this response is modified in the absence of AdeB. In contrast, inactivation of AdeB leads to a focused cellular response, which is not sensitive to the activity of AdeIJK. We identified additional efflux pumps and transcriptional regulators that contribute to MDR phenotype of clinical A. baumannii isolates.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Justyna Adamiak
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Anhthu N Trinh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Richard D Smith
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Lauren Smith
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Sophie Richardson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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Imrat, Labala RK, Velhal S, Bhagat S, Patel V, Jeyaram K. Small double-stranded RNA with anti-HIV activity abundantly produced by Bacillus subtilis MTCC5480 isolated from fermented soybean. Int J Biol Macromol 2020; 161:828-835. [PMID: 32553954 DOI: 10.1016/j.ijbiomac.2020.06.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/27/2022]
Abstract
Anti-viral RNA therapy is on high demand nowadays due to the emergence of several new viral infections. The small non-coding regulatory RNAs (dsRNA) from the microbial sources are not yet explored for anti-viral activity. In this study, we assessed the anti-HIV activity of the small dsRNA produced by 12 different microbial species isolated from naturally fermented foods of North-East India. For this, we selectively extracted the dsRNA from the microbial culture, confirmed its double-stranded nature by immunoblotting, and deep sequenced the cDNA library using Illumina platform. Further, we used conventional algorithms to predict the potential targets of the dsRNA sequences within the 3'-UTR region of HIV-1. A small dsRNA fragment with 34 bases in size with a sequence of 3'-UUGGUACACGAGAUGGUUCGACUCGAUGAAGGGC-5' produced abundantly (9.17% of the total dsRNA fraction) by Bacillus subtilis MTCC5480 showed a much higher base complementarity values than previously reported miRNAs analysed against HIV-1. We separated the dsRNA fraction and validated the anti-HIV activity against human peripheral blood mononuclear cells (PBMC) infected with JRCSF strain of HIV-1 virus and the EC50 value ranges from 0.2-0.3 μM. This small dsRNA abundantly produced by B. subtilis could be studied further for its application as an anti-viral therapeutic agent.
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Affiliation(s)
- Imrat
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India; Department of Biotechnology, Gauhati University, Guwahati 781014, Assam, India
| | - Rajendra Kumar Labala
- Distributed Information Sub-Centre (DISC), Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India
| | - Shilpa Velhal
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Sharad Bhagat
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Vainav Patel
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India; Institute of Bioresources and Sustainable Development (IBSD), Mizoram Center, Nursery Veng, Khatla, Aizawl 796005, Mizoram, India.
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Grapevine phenolic compounds influence cell surface adhesion of Xylella fastidiosa and bind to lipopolysaccharide. PLoS One 2020; 15:e0240101. [PMID: 33007036 PMCID: PMC7531785 DOI: 10.1371/journal.pone.0240101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/19/2020] [Indexed: 12/14/2022] Open
Abstract
Bacterial phytopathogen Xylella fastidiosa specifically colonizes the plant vascular tissue through a complex process of cell adhesion, biofilm formation, and dispersive movement. Adaptation to the chemical environment of the xylem is essential for bacterial growth and progression of infection. Grapevine xylem sap contains a range of plant secondary metabolites such as phenolics, which fluctuate in response to pathogen infection and plant physiological state. Phenolic compounds are often involved in host-pathogen interactions and influence infection dynamics through signaling activity, antimicrobial properties, and alteration of bacterial phenotypes. The effect of biologically relevant concentrations of phenolic compounds coumaric acid, gallic acid, epicatechin, and resveratrol on growth of X. fastidiosa was assessed in vitro. None of these compounds inhibited bacterial growth, but epicatechin and gallic acid reduced cell-surface adhesion. Cell-cell aggregation decreased with resveratrol treatment, but the other phenolic compounds tested had minimal effect on aggregation. Expression of attachment (xadA) and aggregation (fimA) related genes were altered by presence of the phenolic compounds, consistent with observed phenotypes. All four of the phenolic compounds bound to purified X. fastidiosa lipopolysaccharide (LPS), a major cell-surface component. Information regarding the impact of chemical environment on pathogen colonization in plants is important for understanding the infection process and factors associated with host susceptibility.
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Soria-Bustos J, Ares MA, Gómez-Aldapa CA, González-Y-Merchand JA, Girón JA, De la Cruz MA. Two Type VI Secretion Systems of Enterobacter cloacae Are Required for Bacterial Competition, Cell Adherence, and Intestinal Colonization. Front Microbiol 2020; 11:560488. [PMID: 33072020 PMCID: PMC7541819 DOI: 10.3389/fmicb.2020.560488] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Enterobacter cloacae has emerged as an opportunistic pathogen in healthcare-associated infections. Analysis of the genomic sequences of several E. cloacae strains revealed the presence of genes that code for expression of at least one type VI secretion system (T6SS). Here, we report that E. cloacae strain ATCC 13047 codes for two functional T6SS named T6SS-1 and T6SS-2. T6SS-1 and T6SS-2 were preferentially expressed in tryptic soy broth and tissue culture medium (DMEM), respectively. Mutants in T6SS-1-associated genes clpV1 and hcp1 significantly affected their ability of inter- and intra-bacterial killing indicating that T6SS-1 is required for bacterial competition. In addition, the Hcp effector protein was detected in supernatants of E. cloacae cultures and a functional T6SS-1 was required for the secretion of this protein. A clpV2 mutant was impaired in both biofilm formation and adherence to epithelial cells, supporting the notion that these phenotypes are T6SS-2 dependent. In vivo data strongly suggest that both T6SSs are required for intestinal colonization because single and double mutants in clpV1 and clpV2 genes were defective in gut colonization in mice. We conclude that the two T6SSs are involved in the pathogenesis scheme of E. cloacae with specialized functions in the interaction with other bacteria and with host cells.
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Affiliation(s)
- Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Carlos A Gómez-Aldapa
- Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km 4.5 Mineral de la Reforma, Hidalgo, Mexico
| | - Jorge A González-Y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S, Bernal A. Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. Front Genet 2020; 11:837. [PMID: 32849823 PMCID: PMC7432306 DOI: 10.3389/fgene.2020.00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 07/10/2020] [Indexed: 01/05/2023] Open
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)+ balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
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Affiliation(s)
- David Botero
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Jonathan Monk
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - María Juliana Rodríguez Cubillos
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | | | - Mariana Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Vivian Bernal-Galeano
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Silvia Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Adriana Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, LIMMA, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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40
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Rasouli F, Kiani-Pouya A, Zhang H, Shabala S. Developing and validating protocols for mechanical isolation of guard-cell enriched epidermal peels for omics studies. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:803-814. [PMID: 32513383 DOI: 10.1071/fp20085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Stomata, which are microscopic valves on the leaf surface formed by two guard cells (GC), play a critical role in the regulation of leaf water and gas exchange and, hence, determine plant adaptive potential. However, little data is available on GC biochemistry, protein abundance and gene expression, mainly due to technical difficulties and challenges in isolating sufficient amounts of high-quality pure GC. In the present study we applied some modifications to the mechanical isolation of guard-cell to generalise this method for diverse growth conditions as well as plant species. Epidermal peel fragments enriched in guard cells were mechanically isolated from quinoa, spinach and sugar beet leaves grown at two conditions (normal and salt stress). Multiple analysis was performed to confirm the suitability and superiority of the modified technique to the original method. At the first step, the viability and purity of GC-enriched epidermal fragments were assessed under the microscope. Then, the RNA integrity, gene expression, and 1D SDS-PAGE tests were performed to validate the suitability of this technique for omics studies. The data revealed a wide range of proteins as well as a high integrity of RNA extracted from guard cell samples. The expression level of several GC-specific genes and mesophyll-dominant genes were investigated using a comparative analysis of transcriptome datasets of GC and whole-leaf samples. We found that Rubisco and photosynthesis-related proteins such as chlorophyll a/b binding protein were substantially higher in the whole leaf compared with the GCs. More importantly, GC-specific genes such as OST1, SLAC1, MYB60, FAMA and HT1 were highly expressed in the GCs, confirming that our guard cell preparation was highly enriched in GC gene transcripts. Real-time quantitative reverse transcription PCR further confirmed the efficacy of the GC isolation technique for exploring responses of GC to diverse types of stress at the molecular level.
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Affiliation(s)
- Fatemeh Rasouli
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas. 7001, Australia; and Shanghai Centre for Plant Stress Biology and CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Ali Kiani-Pouya
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas. 7001, Australia; and Shanghai Centre for Plant Stress Biology and CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Heng Zhang
- Shanghai Centre for Plant Stress Biology and CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas. 7001, Australia; and International Research Centre for Environmental Membrane Biology, Foshan University, 528000 Foshan, China; and Corresponding author.
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41
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la Cruz MAD, Ares MA, Rodríguez-Valverde D, Vallejo-Cardona AA, Flores-Valdez MA, Núñez IDC, Aceves-Sánchez MDJ, Lira-Chávez J, Rodríguez-Campos J, Bravo-Madrigal J. Transcriptional and Mycolic Acid Profiling in Mycobacterium bovis BCG In Vitro Show an Effect for c-di-GMP and Overlap between Dormancy and Biofilms. J Microbiol Biotechnol 2020; 30:811-821. [PMID: 32238759 PMCID: PMC9728378 DOI: 10.4014/jmb.1911.11043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/12/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis produces mycolic acids which are relevant for persistence, recalcitrance to antibiotics and defiance to host immunity. c-di-GMP is a second messenger involved in transition from planktonic cells to biofilms, whose levels are controlled by diguanylate cyclases (DGC) and phosphodiesterases (PDE). The transcriptional regulator dosR, is involved in response to low oxygen, a condition likely happening to a subset of cells within biofilms. Here, we found that in M. bovis BCG, expression of both BCG1416c and BCG1419c genes, which code for a DGC and a PDE, respectively, decreased in both stationary phase and during biofilm production. The kasA, kasB, and fas genes, which are involved in mycolic acid biosynthesis, were induced in biofilm cultures, as was dosR, therefore suggesting an inverse correlation in their expression compared with that of genes involved in c-di-GMP metabolism. The relative abundance within trehalose dimycolate (TDM) of α-mycolates decreased during biofilm maturation, with methoxy mycolates increasing over time, and keto species remaining practically stable. Moreover, addition of synthetic c-di-GMP to mid-log phase BCG cultures reduced methoxy mycolates, increased keto species and practically did not affect α-mycolates, showing a differential effect of c-di-GMP on keto- and methoxy-mycolic acid metabolism.
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Affiliation(s)
- Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional (CMN) Siglo XXI, Instituto Mexicano de Seguro Social (IMSS), Ciudad de México, México
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional (CMN) Siglo XXI, Instituto Mexicano de Seguro Social (IMSS), Ciudad de México, México
| | - Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional (CMN) Siglo XXI, Instituto Mexicano de Seguro Social (IMSS), Ciudad de México, México
| | - Alba Adriana Vallejo-Cardona
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México,Alba Adriana Vallejo-Cardona Phone: +52-33-33-45-52-00 E-mail:
| | - Mario Alberto Flores-Valdez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México,Corresponding authors Mario Alberto Flores-Valdez Phone: +52-33-33-45-52-00 E-mail:
| | - Iris Denisse Cota Núñez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
| | - Michel de Jesús Aceves-Sánchez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
| | - Jonahtan Lira-Chávez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
| | - Jacobo Rodríguez-Campos
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C, Unidad de Servicios Analíticos y Metrológicos, Av. Normalistas No. 800. Colinas de la Normal, C.P. 44270 Guadalajara, Jalisco, México
| | - Jorge Bravo-Madrigal
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
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42
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Townsend K, Ness J, Hoguet J, Stacy NI, Komoroske LM, Lynch JM. Testing the Stability of Plasma Protein and Whole Blood RNA in Archived Blood of Loggerhead Sea Turtles, Caretta caretta. Biopreserv Biobank 2020; 18:358-366. [PMID: 32589445 DOI: 10.1089/bio.2020.0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sample storage conditions can affect accuracy and reproducibility of biological measurements. Storing samples rapidly at the lowest available temperatures is considered ideal but is not always feasible when sampling in remote and logistically challenging field conditions, as is often the case with sea turtles. The objective of this study was to examine the stability of plasma proteins and quality of whole blood RNA from loggerhead sea turtle samples collected as part of an eighteen-year-long curated specimen collection. These biological variables are often used to assess sea turtle health; therefore, it is necessary to maintain the integrity of these components during storage. Protein electrophoresis was conducted on heparinized plasma from individual turtles collected in 2018 (n = 3), 2008 (n = 3), and 2001 (n = 3). Plasma was also pooled from four turtles sampled in 2018 and subjected to various storage temperatures. Whole blood was collected in blood collection tubes containing sodium heparin or PAXgene tubes with an RNA preservative. These were subjected to different storage treatments that can possibly occur during logistically difficult field sampling. Following various treatments, plasma proteins showed minor differences across collection years and no differences among storage treatments were observed, even when exposed to 38°C for three hours. RNA quality was assessed from whole blood using an RNA integrity number (RIN). RINs were poor from sodium heparin tubes that were frozen and from PAXgene tubes after an extended thaw. High-quality RNA was obtained from sodium heparin tubes that were never frozen and from PAXgene tubes with freezing delayed by up to 11 days. Overall, these results indicate that plasma proteins remain stable over time and when exposed to undesirable storage conditions, and RNA degrades rapidly in sea turtle blood after freezing and when not properly preserved. These aspects are important to consider when planning sampling protocols and logistics for optimal long-term sample preservation.
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Affiliation(s)
- Kelly Townsend
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina, USA.,Elmhurst College, Elmhurst, Illinois, USA
| | - Jennifer Ness
- Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Jennifer Hoguet
- Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Jennifer M Lynch
- Chemical Sciences Division, National Institute of Standards and Technology, Waimanalo, Hawaii, USA.,Center for Marine Debris Research, Hawaii Pacific University, Waimanalo, Hawaii, USA
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43
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Gárriz A, Williamson SA, Evans RG, Reina RD. A method for the collection of early-stage sea turtle embryos. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Early-stage turtle embryos, immediately after oviposition, are very small (<5 mm diameter), hindering research on the initial period of embryonic development. For example, assessing whether turtle eggs had been fertilized and contained a viable embryo at oviposition, especially under field conditions, is complicated by the microscopic size of embryos that may have died at an early stage of development. Further, little is known about the molecular pathways that promote and regulate early developmental processes in turtles, such as pre-ovipositional embryonic arrest. To enable further investigation of the processes critical to early embryonic development in turtle species, a reliable method is required for extraction of early-stage embryos from the egg. Therefore, our aim was to develop a novel and reproducible method for extracting early-stage sea turtle embryos. Herein, we describe the technique for extracting Chelonia mydas embryos before and after white spot formation. Once the embryos were collected, the total RNA of 10 embryos was extracted to validate the method. The total RNA concentration was above 5 ng µl-1 and the RNA integrity number varied between 7.0 and 10.0, which is considered acceptable for further RNA-sequencing analyses. This extraction technique could be employed when investigating fertilization rates of turtle nests and for further investigation of the molecular biology of embryonic development in turtles. Furthermore, the technique should be adaptable to other turtle species or any oviparous species with similar eggs.
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Affiliation(s)
- A Gárriz
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - SA Williamson
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - RG Evans
- Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - RD Reina
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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44
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Espindula E, Sperb ER, Bach E, Passaglia LMP. The combined analysis as the best strategy for Dual RNA-Seq mapping. Genet Mol Biol 2020; 42:e20190215. [PMID: 32442239 PMCID: PMC7249662 DOI: 10.1590/1678-4685-gmb-2019-0215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/26/2019] [Indexed: 01/01/2023] Open
Abstract
In Dual RNA-Seq experiments the simultaneous extraction of RNA and analysis of gene expression data from both interacting organisms could be a challenge. One alternative is separating the reads during in silico data analysis. There are two main mapping methods used: sequential and combined. Here we present a combined approach in which the libraries were aligned to a concatenated genome to sort the reads before mapping them to the respective annotated genomes. A comparison of this method with the sequential analysis was performed. Two RNA-Seq libraries available in public databases consisting of a eukaryotic (Zea mays) and a prokaryotic (Herbaspirillum seropediceae) organisms were mixed to simulate a Dual RNA-Seq experiment. Libraries from real Dual RNA-Seq experiments were also used. The sequential analysis consistently attributed more reads to the first reference genome used in the analysis (due to cross-mapping) than the combined approach. More importantly, the combined analysis resulted in lower numbers of cross-mapped reads. Our results highlight the necessity of combining the reference genomes to sort reads previously to the counting step to avoid losing information in Dual RNA-Seq experiments. Since most studies first map the RNA-Seq libraries to the eukaryotic genome, much prokaryotic information has probably been lost.
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Affiliation(s)
- Eliandro Espindula
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Edilena Reis Sperb
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Evelise Bach
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Universidade Federal do Rio Grande do Sul (UFRGS), Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
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45
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Kannappan A, Durgadevi R, Srinivasan R, Lagoa RJL, Packiavathy IASV, Pandian SK, Veera Ravi A. 2-Hydroxy-4-methoxybenzaldehyde from Hemidesmus indicus is antagonistic to Staphylococcus epidermidis biofilm formation. BIOFOULING 2020; 36:549-563. [PMID: 32586125 DOI: 10.1080/08927014.2020.1777989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 05/21/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Staphylococcus epidermidis (SE) is an opportunistic nosocomial pathogen that accounts for recalcitrant device-related infections worldwide. Owing to the growing interest in plants and their secondary metabolites targeting bacterial adhesion, this study was intended to uncover the anti-biofilm potential of Hemidesmus indicus and its major constituent 2-hydroxy-4-methoxybenzaldehyde (HMB) against SE. The minimum biofilm inhibitory concentration (MBIC) of H. indicus root extract and HMB were found to be 500 and 250 µg ml-1, respectively. The results of time-dependent biofilm inhibition and mature biofilm disruption assays confirmed that HMB targets initial cell adhesion. Furthermore, interference by HMB in the expression of adhesin genes (icaA, aap and bhp) and biofilm components was associated with an increased susceptibility of SE to oxidative stress and antibiotics. To conclude, this study reports for the first time HMB as a potential drug against SE biofilms.
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Affiliation(s)
- Arunachalam Kannappan
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Ravindran Durgadevi
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ramanathan Srinivasan
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | | | | | | | - Arumugam Veera Ravi
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
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Chimal-Cázares F, Hernández-Martínez G, Pacheco S, Ares MA, Soria-Bustos J, Sánchez-Gutiérrez M, Izquierdo-Vega JA, Ibarra JA, González-Y-Merchand JA, Gorvel JP, Méresse S, De la Cruz MA. Molecular Characterization of SehB, a Type II Antitoxin of Salmonella enterica Serotype Typhimurium: Amino Acid Residues Involved in DNA-Binding, Homodimerization, Toxin Interaction, and Virulence. Front Microbiol 2020; 11:614. [PMID: 32328049 PMCID: PMC7160566 DOI: 10.3389/fmicb.2020.00614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/19/2020] [Indexed: 11/22/2022] Open
Abstract
Salmonella enterica serotype Typhimurium is a bacterium that causes gastroenteritis and diarrhea in humans. The genome of S. Typhimurium codes for diverse virulence factors, among which are the toxin-antitoxin (TA) systems. SehAB is a type II TA, where SehA is the toxin and SehB is the antitoxin. It was previously reported that the absence of the SehB antitoxin affects the growth of S. Typhimurium. In addition, the SehB antitoxin can interact directly with the SehA toxin neutralizing its toxic effect as well as repressing its own expression. We identified conserved residues on SehB homologous proteins. Point mutations were introduced at both N- and C-terminal of SehB antitoxin to analyze the effect of these changes on its transcription repressor function, on its ability to form homodimers and on the virulence of S. Typhimurium. All changes in amino acid residues at both the N- and C-terminal affected the repressor function of SehB antitoxin and they were required for DNA-binding activity. Mutations in the amino acid residues at the N-terminal showed a lower capacity for homodimer formation of the SehB protein. However, none of the SehB point mutants were affected in the interaction with the SehA toxin. In terms of virulence, the eight single-amino acid mutations were attenuated for virulence in the mouse model. In agreement with our results, the eight amino acid residues of SehB antitoxin were required for its repressor activity, affecting both homodimerization and DNA-binding activity, supporting the notion that both activities of SehB antitoxin are required to confer virulence to Salmonella enterica.
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Affiliation(s)
- Fernando Chimal-Cázares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Gabriela Hernández-Martínez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sabino Pacheco
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | - Jose Antonio Ibarra
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A González-Y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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47
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Ohr and OhrR Are Critical for Organic Peroxide Resistance and Symbiosis in Azorhizobium caulinodans ORS571. Genes (Basel) 2020; 11:genes11030335. [PMID: 32245101 PMCID: PMC7141136 DOI: 10.3390/genes11030335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Azorhizobium caulinodans is a symbiotic nitrogen-fixing bacterium that forms both root and stem nodules on Sesbania rostrata. During nodule formation, bacteria have to withstand organic peroxides that are produced by plant. Previous studies have elaborated on resistance to these oxygen radicals in several bacteria; however, to the best of our knowledge, none have investigated this process in A. caulinodans. In this study, we identified and characterised the organic hydroperoxide resistance gene ohr (AZC_2977) and its regulator ohrR (AZC_3555) in A. caulinodans ORS571. Hypersensitivity to organic hydroperoxide was observed in an ohr mutant. While using a lacZ-based reporter system, we revealed that OhrR repressed the expression of ohr. Moreover, electrophoretic mobility shift assays demonstrated that OhrR regulated ohr by direct binding to its promoter region. We showed that this binding was prevented by OhrR oxidation under aerobic conditions, which promoted OhrR dimerization and the activation of ohr. Furthermore, we showed that one of the two conserved cysteine residues in OhrR, Cys11, was critical for the sensitivity to organic hydroperoxides. Plant assays revealed that the inactivation of Ohr decreased the number of stem nodules and nitrogenase activity. Our data demonstrated that Ohr and OhrR are required for protecting A. caulinodans from organic hydroperoxide stress and play an important role in the interaction of the bacterium with plants. The results that were obtained in our study suggested that a thiol-based switch in A. caulinodans might sense host organic peroxide signals and enhance symbiosis.
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48
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Yen E, Kaneko-Tarui T, Maron JL. Technical Considerations and Protocol Optimization for Neonatal Salivary Biomarker Discovery and Analysis. Front Pediatr 2020; 8:618553. [PMID: 33575231 PMCID: PMC7870796 DOI: 10.3389/fped.2020.618553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/31/2020] [Indexed: 12/04/2022] Open
Abstract
Non-invasive techniques to monitor and diagnose neonates, particularly those born prematurely, are a long-sought out goal of Newborn Medicine. In recent years, technical advances, combined with increased assay sensitivity, have permitted the high-throughput analysis of multiple biomarkers simultaneously from a single sample source. Multiplexed transcriptomic and proteomic platforms, along with more comprehensive assays such as RNASeq, allow for interrogation of ongoing physiology and pathology in unprecedented ways. In the fragile neonatal population, saliva is an ideal biofluid to assess clinical status serially and offers many advantages over more invasively obtained blood samples. Importantly, saliva samples are amenable to analysis on emerging proteomic and transcriptomic platforms, even at quantitatively limited volumes. However, biomarker targets are often degraded in human saliva, and as a mixed source biofluid containing both human and microbial targets, saliva presents unique challenges for the investigator. Here, we provide insight into technical considerations and protocol optimizations developed in our laboratory to quantify and discover neonatal salivary biomarkers with improved reproducibility and reliability. We will detail insights learned from years of experimentation on neonatal saliva within our laboratory ranging from salivary collection techniques to processing to downstream analyses, highlighting the need for consistency in approach and a global understanding of both the potential benefits and limitations of neonatal salivary biomarker analyses. Importantly, we will highlight the need for robust and stringent research in this population to provide the field with standardized approaches and workflows to impact neonatal care successfully.
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Affiliation(s)
- Elizabeth Yen
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, United States.,Division of Newborn Medicine, Tufts Children's Hospital, Boston, MA, United States
| | - Tomoko Kaneko-Tarui
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, United States
| | - Jill L Maron
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, United States.,Division of Newborn Medicine, Tufts Children's Hospital, Boston, MA, United States
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49
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Leonard S, Meyer S, Lacour S, Nasser W, Hommais F, Reverchon S. APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data. Nucleic Acids Res 2019; 47:e88. [PMID: 31147705 PMCID: PMC6735904 DOI: 10.1093/nar/gkz485] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 12/02/2022] Open
Abstract
Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate for the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm to detect small transcripts from paired-end bacterial RNA-seq data. In contrast to previous approaches that start from the read coverage distribution, APERO analyzes boundaries of individual sequenced fragments to infer the 5′ and 3′ ends of all transcripts. Since sRNAs are about the same size as individual fragments (50–350 nucleotides), this algorithm provides a significantly higher accuracy and robustness, e.g., with respect to spontaneous internal breaking sites. To demonstrate this improvement, we develop a comparative assessment on datasets from Escherichia coli and Salmonella enterica, based on experimentally validated sRNAs. We also identify the small transcript repertoire of Dickeya dadantii including putative intergenic RNAs, 5′ UTR or 3′ UTR-derived RNA products and antisense RNAs. Comparisons to annotations as well as RACE-PCR experimental data confirm the precision of the detected transcripts. Altogether, APERO outperforms all existing methods in terms of sRNA detection and boundary precision, which is crucial for comprehensive genome annotations. It is freely available as an open source R package on https://github.com/Simon-Leonard/APERO
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Affiliation(s)
- Simon Leonard
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Stephan Lacour
- Univ. Grenoble Alpes, CNRS, Inria, LiPhy (UMR5588), 38000 Grenoble, France
| | - William Nasser
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
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50
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Ding H, Grüll MP, Mulligan ME, Lang AS, Beatty JT. Induction of Rhodobacter capsulatus Gene Transfer Agent Gene Expression Is a Bistable Stochastic Process Repressed by an Extracellular Calcium-Binding RTX Protein Homologue. J Bacteriol 2019; 201:e00430-19. [PMID: 31501287 PMCID: PMC6832060 DOI: 10.1128/jb.00430-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/06/2019] [Indexed: 01/28/2023] Open
Abstract
Bacteriophage-like gene transfer agents (GTAs) have been discovered in both of the prokaryotic branches of the three-domain phylogenetic tree of life. The production of a GTA (RcGTA) by the phototrophic alphaproteobacterium Rhodobacter capsulatus is regulated by quorum sensing and a phosphorelay homologous to systems in other species that control essential functions such as the initiation of chromosome replication and cell division. In wild-type strains, RcGTA is produced in <3% of cells in laboratory cultures. Mutants of R. capsulatus that exhibit greatly elevated production of RcGTA were created decades ago by chemical mutagenesis, but the nature and molecular consequences of the mutation were unknown. We show that the number of cells in a population that go on to express RcGTA genes is controlled by a stochastic process, in contrast to a genetic process. We used transposon mutagenesis along with a fluorescent protein reporter system and genome sequence data to identify a gene, rcc00280, that encodes an RTX family calcium-binding protein homologue. The Rc280 protein acts as an extracellular repressor of RcGTA gene expression by decreasing the percentage of cells that induce the production of RcGTA.IMPORTANCE GTAs catalyze horizontal gene transfer (HGT), which is important for genomic evolution because the majority of genes found in bacterial genomes have undergone HGT at some point in their evolution. Therefore, it is important to determine how the production of GTAs is regulated to understand the factors that modulate the frequency of gene transfer and thereby specify the tempo of evolution. This work describes a new type of genetic regulation in which an extracellular calcium-binding protein homologue represses the induction of the Rhodobacter capsulatus GTA, RcGTA.
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Affiliation(s)
- Hao Ding
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc P Grüll
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Martin E Mulligan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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