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Singh RP, Sinha A, Deb S, Kumari K. First report on in-depth genome and comparative genome analysis of a metal-resistant bacterium Acinetobacter pittii S-30, isolated from environmental sample. Front Microbiol 2024; 15:1351161. [PMID: 38741743 PMCID: PMC11089254 DOI: 10.3389/fmicb.2024.1351161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
A newly isolated bacterium Acinetobacter pittii S-30 was recovered from waste-contaminated soil in Ranchi, India. The isolated bacterium belongs to the ESKAPE organisms which represent the major nosocomial pathogens that exhibit high antibiotic resistance. Furthermore, average nucleotide identity (ANI) analysis also showed its closest match (>95%) to other A. pittii genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO4. Whole genome sequencing and annotations revealed the occurrence of various genes involved in stress protection, motility, and metabolism of aromatic compounds. Moreover, genome annotation identified the gene clusters involved in secondary metabolite production (biosynthetic gene clusters) such as arylpolyene, acinetobactin like NRP-metallophore, betalactone, and hserlactone-NRPS cluster. The metabolic potential of A. pittii S-30 based on cluster of orthologous, and Kyoto Encyclopedia of Genes and Genomes indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux systems etc., which is relatively rare in A. pittii strains. Additionally, the presence of various carbohydrate-active enzymes such as glycoside hydrolases (GHs), glycosyltransferases (GTs), and other genes associated with lignocellulose breakdown suggests that strain S-30 has strong biomass degradation potential. Furthermore, an analysis of genetic diversity and recombination in A. pittii strains was performed to understand the population expansion hypothesis of A. pittii strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to A. pittii. Therefore, the A. pittii S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Ayushi Sinha
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
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Dinango VN, Dhouib H, Wakam LN, Kouokap LK, Youmbi DY, Eke P, Driss F, Tounsi S, Boyom FF, Frikha-Gargouri O. Bacterial endophytes inhabiting desert plants provide protection against seed rot caused by Fusarium verticillioides and promote growth in maize. PEST MANAGEMENT SCIENCE 2024; 80:1206-1218. [PMID: 37886813 DOI: 10.1002/ps.7850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/05/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Fusarium maize ear and root rot disease caused by Fusarium verticillioides has become one of the most serious fungal diseases associated with maize production. Due to their abilities to promote plant development and manage diseases, bacterial endophytes provide a more promising approach for treating this vascular disease. RESULTS This work was undertaken for the selection and identification of promising isolates as plant growth promoters and biocontrol agents against F. verticillioides in maize agroecosystems. A screening procedure consisting of in vitro and in situ tests was applied to 27 endophytic strains originating from desert plants: Euphorbia antiquorum, Calotropis procera, and Alcasia albida. In vitro studies indicated that the bacteria exhibited variable results in biocontrol, endophytism, and plant growth-promoting traits. In addition, in situ plant growth promotion and biocontrol experiments allowed the identification of the most promising bacterial endophytes. In vitro and in situ comparative study results indicated a low correlation. Our data revealed that in situ screening must be used as the method of selection of biocontrol agents against Fusarium ear and root rot disease. Based on in situ results, seven potent strains were selected and identified as Bacillus subtilis, Bacillus velezensis, Bacillus tequilensis, Stenotrophomonas maltophilia, and Klebsiella pneumoniae. CONCLUSION The results of this study showed that the selected strains seem to be promising candidates to be exploited as biofertilizers and biocontrol agents against Fusarium maize ear and root rot disease. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Vanessa Nya Dinango
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Hanen Dhouib
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Louise Nana Wakam
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
- Soil Microbiology Laboratory, Biotechnology Centre, Yaoundé, Cameroon
| | - Lanvin Kepngop Kouokap
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Diane Yimta Youmbi
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Pierre Eke
- College of Technology, Department of Crop Production Technology, University of Bamenda, Bambili, Cameroon
| | - Fatma Driss
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Slim Tounsi
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Fabrice Fekam Boyom
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Olfa Frikha-Gargouri
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
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Sharma A, Singh RN, Song XP, Singh RK, Guo DJ, Singh P, Verma KK, Li YR. Genome analysis of a halophilic Virgibacillus halodenitrificans ASH15 revealed salt adaptation, plant growth promotion, and isoprenoid biosynthetic machinery. Front Microbiol 2023; 14:1229955. [PMID: 37808307 PMCID: PMC10556750 DOI: 10.3389/fmicb.2023.1229955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 10/10/2023] Open
Abstract
Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely "Squalene." Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.
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Affiliation(s)
- Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- State Key Laboratory of Conservation and Utilization of Subtropical, College of Agriculture, Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- State Key Laboratory of Conservation and Utilization of Subtropical, College of Agriculture, Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
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Rohatgi A, Gupta P. Benzoic acid derivatives as potent antibiofilm agents against Klebsiella pneumoniae biofilm. J Biosci Bioeng 2023; 136:190-197. [PMID: 37479559 DOI: 10.1016/j.jbiosc.2023.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Klebsiella pneumoniae is responsible for a significant proportion of human urinary tract infections, and its biofilm is a major virulence. One potential approach to controlling biofilm-associated infections is targeting the adhesin MrkD1P to disrupt biofilm formation. We employed Schrodinger's Maestro tool with the OPLS 2005 force field to dock compounds with the target protein. Two benzoic acid derivatives, 3-hydroxy benzoic acid and 2,5-dihydroxybenzoic acid, had strong binding free energies (-55.57 and -18.68 kcal/mol) and were the most potent compounds. The in-vitro experiments were conducted to validate the in-silico results. The results showed that both compounds effectively inhibited biofilm formation at low concentrations (4 and 8 mg/mL, respectively) and had antibiofilm activity, restricting cell attachment. Both compounds demonstrated a strong biofilm inhibitory effect, with 97% and 89% reduction in biofilm by 3-hydroxy benzoic acid and 2,5-dihydroxybenzoic acid, respectively. These findings suggest that natural compounds can be a potential source of new drugs to combat biofilm-associated infections. The study highlights the potential of targeting adhesin MrkD1P as an effective approach to controlling biofilm-associated infections caused by K. pneumoniae. The results may have implications for the development of new therapies for biofilm-associated infections and pave the way for future research in this area.
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Affiliation(s)
- Anuj Rohatgi
- Department of Biotechnology, National Institute of Technology, Raipur 492010, India
| | - Pratima Gupta
- Department of Biotechnology, National Institute of Technology, Raipur 492010, India.
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Rosazza T, Eigentler L, Earl C, Davidson FA, Stanley‐Wall NR. Bacillus subtilis extracellular protease production incurs a context-dependent cost. Mol Microbiol 2023; 120:105-121. [PMID: 37380434 PMCID: PMC10952608 DOI: 10.1111/mmi.15110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
Microbes encounter a wide range of polymeric nutrient sources in various environmental settings, which require processing to facilitate growth. Bacillus subtilis, a bacterium found in the rhizosphere and broader soil environment, is highly adaptable and resilient due to its ability to utilise diverse sources of carbon and nitrogen. Here, we explore the role of extracellular proteases in supporting growth and assess the cost associated with their production. We provide evidence of the essentiality of extracellular proteases when B. subtilis is provided with an abundant, but polymeric nutrient source and demonstrate the extracellular proteases as a shared public good that can operate over a distance. We show that B. subtilis is subjected to a public good dilemma, specifically in the context of growth sustained by the digestion of a polymeric food source. Furthermore, using mathematical simulations, we uncover that this selectively enforced dilemma is driven by the relative cost of producing the public good. Collectively, our findings reveal how bacteria can survive in environments that vary in terms of immediate nutrient accessibility and the consequent impact on the population composition. These findings enhance our fundamental understanding of how bacteria respond to diverse environments, which has importance to contexts ranging from survival in the soil to infection and pathogenesis scenarios.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
- Mathematics, School of Science and EngineeringUniversity of DundeeDundeeUK
- Present address:
Evolutionary Biology DepartmentUniversität BielefeldKonsequenz 45Bielefeld33615Germany
| | - Chris Earl
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
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Kumari K, Rawat V, Shadan A, Sharma PK, Deb S, Singh RP. In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1. Front Microbiol 2023; 14:1140249. [PMID: 37408640 PMCID: PMC10318148 DOI: 10.3389/fmicb.2023.1140249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/29/2023] [Indexed: 07/07/2023] Open
Abstract
A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Vaishnavi Rawat
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Afreen Shadan
- Department of Microbiology, Dr. Shyama Prasad Mukerjee University, Ranchi, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
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Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. Nat Commun 2023; 14:3510. [PMID: 37316519 PMCID: PMC10267222 DOI: 10.1038/s41467-023-39121-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.
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Affiliation(s)
- Xiaofan Jin
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Jia Yan
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Xiandong Meng
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- University of California San Francisco, San Francisco, CA, USA.
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8
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New insights into the antibacterial mode of action of quercetin against uropathogen Serratia marcescens in-vivo and in-vitro. Sci Rep 2022; 12:21912. [PMID: 36536034 PMCID: PMC9763402 DOI: 10.1038/s41598-022-26621-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
In the course of a quest for therapeutic agents inhibiting uropathogens, the rise and universal blowout of antibiotic-resistant organisms is a wide problem. To overcome this matter, exploration of alternative antimicrobials is necessary. The antimicrobial potential of quercetin has been widely described against some pathogenic microorganisms, but to the best of our knowledge, no report exists against the pathogenicity of uropathogenic Serratia marcescens. Hence, the present study focused on the antibacterial mechanism of action of quercetin, a flavonoid against the uropathogen Serratia marcescens. Quercetin was evaluated for its anti-QS activity, and the attained outcomes showed that quercetin inhibited QS-mediated virulence factors such as biofilm formation, exopolysaccharides, swarming motility and prodigiosin in Serratia marcescens. The proposed mechanism of action of quercetin greatly influences cell metabolism and extracellular polysaccharide synthesis and damages the cell membrane, as revealed through global metabolome profiling. In vivo experiments revealed that treatment with quercetin prolonged the life expectancy of infected Caenorhabditis elegans and reduced the colonization of Serratia marcescens. Hence, the current study reveals the use of quercetin as a probable substitute for traditional antibiotics in the treatment of uropathogen infections driven by biofilms.
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Huang S, Xue Y, Zhou C, Ma Y. An efficient CRISPR/Cas9-based genome editing system for alkaliphilic Bacillus sp. N16-5 and application in engineering xylose utilization for D-lactic acid production. Microb Biotechnol 2022; 15:2730-2743. [PMID: 36309986 PMCID: PMC9618316 DOI: 10.1111/1751-7915.14131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022] Open
Abstract
Alkaliphiles are considered more suitable chassis than traditional neutrophiles due to their excellent resistance to microbial contamination. Alkaliphilic Bacillus sp. N16-5, an industrially interesting strain with great potential for the production of lactic acid and alkaline polysaccharide hydrolases, can only be engineered genetically by the laborious and time-consuming homologous recombination. In this study, we reported the successful development of a CRISPR/Cas9-based genome editing system with high efficiency for single-gene deletion, large gene fragment deletion and exogenous DNA chromosomal insertion. Moreover, based on a catalytically dead variant of Cas9 (dCas9), we also developed a CRISPRi system to efficiently regulate gene expression. Finally, this efficient genome editing system was successfully applied to engineer the xylose metabolic pathway for the efficient bioproduction of D-lactic acid. Compared with the wild-type Bacillus sp. N16-5, the final engineered strain with XylR deletion and AraE overexpression achieved 34.3% and 27.7% increases in xylose consumption and D-lactic acid production respectively. To our knowledge, this is the first report on the development and application of CRISPR/Cas9-based genome editing system in alkaliphilic Bacillus, and this study will significantly facilitate functional genomic studies and genome manipulation in alkaliphilic Bacillus, laying a foundation for the development of more robust microbial chassis.
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Affiliation(s)
- Shiyong Huang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
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Joshi JR, Brown K, Charkowski AO, Heuberger AL. Protease Inhibitors from Solanum chacoense Inhibit Pectobacterium Virulence by Reducing Bacterial Protease Activity and Motility. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:825-834. [PMID: 36104309 DOI: 10.1094/mpmi-04-22-0072-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Potato is a major staple crop, and necrotrophic bacterial pathogens such as Pectobacterium spp. are a major threat to global food security. Most lines of cultivated potato (Solanum tuberosum) are susceptible to Pectobacterium spp., but some lines of wild potato are resistant, including Solanum chacoense M6. Despite the discovery of resistance in wild potatoes, specific resistance genes are yet to be discovered. Crude protein extract from M6 had a global effect on Pectobacterium brasiliense Pb1692 (Pb1692) virulence phenotypes. Specifically, M6 protein extracts resulted in reduced Pectobacterium exo-protease activity and motility, induced cell elongation, and affected bacterial virulence and metabolic gene expression. These effects were not observed from protein extracts of susceptible potato S. tuberosum DM1. A proteomics approach identified protease inhibitors (PIs) as candidates for S. chacoense resistance, and genomic analysis showed higher abundance and diversity of PIs in M6 than in DM1. We cloned five PIs that are unique or had high abundance in M6 compared with DM1 and purified the proteins (g18987, g28531, g39249, g40384, g6571). Four of the PIs significantly reduced bacterial protease activity, with strongest effects from g28531 and g6571. Three PIs (g18987, g28531, g6571) inhibited disease when co-inoculated with Pectobacterium pathogens into potato tubers. Two PIs (g28531, g6571) also significantly reduced Pb1692 motility and are promising as resistance genes. These results show that S. chacoense PIs contribute to bacterial disease resistance by inhibiting exo-proteases, motility, and tuber maceration and by modulating cell morphology and metabolism. [Formula: see text] Copyright © 2022 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)
- Janak R Joshi
- Department of Horticulture and Landscape Architecture, Colorado State University, 1173 Campus Delivery, Fort Collins, CO 80523, U.S.A
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Kitty Brown
- Analytical Resource Center-Bioanalysis and Omics, Colorado State University, 2021 Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Amy O Charkowski
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, 1173 Campus Delivery, Fort Collins, CO 80523, U.S.A
- Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, CO 80523, U.S.A
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Karuppiah V, Seralathan M. Quorum sensing inhibitory potential of vaccenic acid against Chromobacterium violaceum and methicillin-resistant Staphylococcus aureus. World J Microbiol Biotechnol 2022; 38:146. [PMID: 35759150 DOI: 10.1007/s11274-022-03335-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022]
Abstract
Quorum sensing (QS) is a potential target for inhibiting bacterial antibiotic resistance and associated pathogenicity. The present study aimed to investigate vaccenic acid anti-QS and antibiofilm potential against Chromobacterium violaceum and methicillin-resistant Staphylococcus aureus (MRSA). In the broth microdilution method, we determined the minimum inhibitory concentration (MIC) of vaccenic acid against C. violaceum and MRSA. Then, we determined the vaccenic acid anti-QS potential against C. violaceum via a violacein inhibition assay. Vaccenic acid at a sub-MIC concentration significantly inhibited violacein pigment production. Vaccenic acid also inhibits C. violaceum and MRSA biofilm formation at sub-MIC concentrations. The effect of vaccenic acid antivirulence potential was evaluated by phenotypic virulence assays. The results showed that vaccenic acid at a sub-MIC concentration significantly inhibited the virulence production of C. violaceum (chitinase and motility) and MRSA (hemolysin and staphyloxanthin production). Quantitative PCR analysis revealed the downregulation of QS associated genes upon vaccenic acid treatment. This resulted in the downregulation of genes involved in QS mechanisms such as cviI, cviR, and SarA and pigment production such as vioB and crtM. The results of the present study suggest that vaccenic acid is a promising agent to combat C. violaceum and MRSA.
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Affiliation(s)
- Vijayakumar Karuppiah
- Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai, Cuddalore, Tamil Nadu, 608 502, India.
- PAR Life Sciences and Research Private Limited, Woraiyur, Trichy, Tamil Nadu, 620003, India.
| | - Muhilvannan Seralathan
- PAR Life Sciences and Research Private Limited, Woraiyur, Trichy, Tamil Nadu, 620003, India
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12
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Maldonado Desena F, De la Cruz Ceferino N, Gómez Cornelio S, Alvarez Villagomez C, Herrera Candelario JL, De la Rosa García S. Bacteria Halotolerant from Karst Sinkholes as a Source of Biosurfactants and Bioemulsifiers. Microorganisms 2022; 10:microorganisms10071264. [PMID: 35888984 PMCID: PMC9319531 DOI: 10.3390/microorganisms10071264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Halotolerant bacteria with biosurfactant (BS) and bioemulsifiers (BE) activity can coexist in Karstic sinkholes with marine influence. Two sinkholes in the Yucatan peninsula were selected to isolate bacteria with BE and BS activity stable in NaCl. The optimal time, the effect of nitrogen and carbon source in the medium, and the conditions (agitation, pH and salinity) for the production of BS and BE compounds in planktonic and sessile (stimulate the formation of biofilms in cell roller) culture were determined. Eighty strains showed the highest emulsification activity (EI24 ≥ 50%) and drop-collapse ≥ 4 mm. 87% of the strains are moderately halotolerant, and 21% bordered the limit of extreme halotolerance. Twenty-four strains maintained or improved their BS and BE activity under salinity conditions at 5% and 10%, being the most active genera Bacillus, Paenibacillus and Lysinibacillus, identified by sequencing of the 16S rRNA gene. The results show that the nitrogen source positively affects the BS and BE activity, regardless of the type of culture. The sessile culture markedly stimulated BS activity with significant differences. However, we did not find a greater influence on the culture conditions. The results suggest that halotolerant bacteria from sinkholes could be implemented in bioremediation and other biotechnological applications.
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Affiliation(s)
- Félix Maldonado Desena
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carr. Villahermosa-Cardenas Km 0.5, Ranchería Emialiano Zapata, Villahermosa 86150, Tabasco, Mexico; (F.M.D.); (N.D.l.C.C.); (C.A.V.); (J.L.H.C.)
| | - Navila De la Cruz Ceferino
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carr. Villahermosa-Cardenas Km 0.5, Ranchería Emialiano Zapata, Villahermosa 86150, Tabasco, Mexico; (F.M.D.); (N.D.l.C.C.); (C.A.V.); (J.L.H.C.)
| | - Sergio Gómez Cornelio
- Ingeniería en Biotecnología, Universidad Politécnica del Centro, Carretera Federal, Villahermosa-Teapa Km 22.5, Tumbulushal Centro, Villahermosa 86290, Tabasco, Mexico;
| | - Carina Alvarez Villagomez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carr. Villahermosa-Cardenas Km 0.5, Ranchería Emialiano Zapata, Villahermosa 86150, Tabasco, Mexico; (F.M.D.); (N.D.l.C.C.); (C.A.V.); (J.L.H.C.)
| | - José Luis Herrera Candelario
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carr. Villahermosa-Cardenas Km 0.5, Ranchería Emialiano Zapata, Villahermosa 86150, Tabasco, Mexico; (F.M.D.); (N.D.l.C.C.); (C.A.V.); (J.L.H.C.)
| | - Susana De la Rosa García
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carr. Villahermosa-Cardenas Km 0.5, Ranchería Emialiano Zapata, Villahermosa 86150, Tabasco, Mexico; (F.M.D.); (N.D.l.C.C.); (C.A.V.); (J.L.H.C.)
- Correspondence:
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13
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Singh RP, Pandey DM, Jha PN, Ma Y. ACC deaminase producing rhizobacterium Enterobacter cloacae ZNP-4 enhance abiotic stress tolerance in wheat plant. PLoS One 2022; 17:e0267127. [PMID: 35522667 PMCID: PMC9075627 DOI: 10.1371/journal.pone.0267127] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 04/02/2022] [Indexed: 11/19/2022] Open
Abstract
Plant growth promoting rhizobacterium (PGPR) designated as ZNP-4, isolated from the rhizosphere of Ziziphus nummularia, was identified as Enterobacter cloacae following 16S rRNA sequence analysis. The isolated strain exhibited various plant growth promoting (PGP) traits. The 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) activity was evaluated under diverse physiological conditions that could be useful for minimizing the abiotic stress-induced inhibitory effects on wheat plants. The strain showed resistance to salt (NaCl) and metal (ZnSO4) stress. The effect of E. cloacae ZNP-4 on the augmentation of plant growth was studied under salinity stress of 150 mM (T1 treatment) & 200 mM (T2 treatment) NaCl. The inoculation of strain ZNP-4 significantly improved the various growth parameters of wheat plant such as shoot length (41%), root length (31%), fresh weight (28%), dry weight (29%), photosynthetic pigments chlorophyll a (62%) and chlorophyll b (34%). Additionally, the strain was found to be efficient for minimizing the imposed Zn stress in terms of improving plant growth, biomass and photosynthetic pigments in pots containing different levels of metal stress of 150 mg kg-1 (treatment T1) and 250 mg kg-1 (treatment T2). Isolate ZNP-4 also improved the proline content and decreased malondialdehyde (MDA) level under both salinity and metal stress, therefore maintaining the membrane integrity. Furthermore, bacterial inoculation increased the activities of antioxidative enzymes such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POX). The positive effects of PGPR occurred concurrently with the decrease in abiotic stress-induced reactive oxygen species (ROS) molecules such as hydrogen peroxide (H2O2) and superoxide (O2-) contents. Overall, the observed results indicate that use of bacteria with such beneficial traits could be used as bio-fertilizers for many crops growing under stress conditions.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
- * E-mail: (RPS); (YM)
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Rajasthan
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
- * E-mail: (RPS); (YM)
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14
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Manikandan A, Johnson I, Jaivel N, Krishnamoorthy R, SenthilKumar M, Raghu R, Gopal NO, Mukherjee PK, Anandham R. Gamma-induced mutants of Bacillus and Streptomyces display enhanced antagonistic activities and suppression of the root rot and wilt diseases in pulses. Biomol Concepts 2022; 13:103-118. [DOI: 10.1515/bmc-2022-0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
This study aims to increase Bacillus and Streptomyces antagonistic activity against the root rot and wilt diseases of pulses caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. udum, respectively. To increase antagonistic action, Bacillus subtilis BRBac4, Bacillus siamensis BRBac21, and Streptomyces cavourensis BRAcB10 were subjected to random mutagenesis using varying doses of gamma irradiation (0.5–3.0 kGy). Following the irradiation, 250 bacterial colonies were chosen at random for each antagonistic strain and their effects against pathogens were evaluated in a plate assay. The ERIC, BOX, and random amplified polymorphic studies demonstrated a clear distinction between mutant and wild-type strains. When mutants were compared to wild-type strains, they showed improved plant growth-promoting characteristics and hydrolytic enzyme activity. The disease suppression potential of the selected mutants, B. subtilis BRBac4-M6, B. siamensisi BRBac21-M10, and S. cavourensis BRAcB10-M2, was tested in green gram, black gram, and red gram. The combined inoculation of B. siamensis BRBac21-M10 and S. cavourensis BRAcB10-M2 reduced the incidence of root rot and wilt disease. The same treatment also increased the activity of the defensive enzymes peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase. These findings suggested that gamma-induced mutation can be exploited effectively to improve the biocontrol characteristics of Bacillus and Streptomyces. Following the field testing, a combined bio-formulation of these two bacteria may be utilised to address wilt and root-rot pathogens in pulses.
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Affiliation(s)
- Ariyan Manikandan
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU) , Coimbatore 641003 , Tamil Nadu , India
| | - Iruthayasamy Johnson
- Department of Plant Pathology, Tamil Nadu Agricultural University (TNAU) , Coimbatore , Tamil Nadu , India
| | - Nanjundan Jaivel
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU) , Coimbatore 641003 , Tamil Nadu , India
| | - Ramasamy Krishnamoorthy
- Department of Crop Management, Vanavarayar Institute of Agriculture , Pollachi , Tamil Nadu , India
| | - Murugaiyan SenthilKumar
- Department of Crop Management, Agricultural College and Research Institute, Tamil Nadu Agricultural University (TNAU) , Eachangkottai , Tamil Nadu , India
| | - Rajasekaran Raghu
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU) , Coimbatore 641003 , Tamil Nadu , India
| | - Nellaiappan Olaganathan Gopal
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU) , Coimbatore 641003 , Tamil Nadu , India
| | - Prasun K. Mukherjee
- Environmental Biotechnology Section Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre , Trombay , Mumbai 400085 , India
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU) , Coimbatore 641003 , Tamil Nadu , India
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15
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Hickey A, Pardo LM, Reen FJ, McGlacken GP. Pyrones Identified as LuxR Signal Molecules in Photorhabdus and Their Synthetic Analogues Can Alter Multicellular Phenotypic Behavior of Bacillus atropheaus. ACS OMEGA 2021; 6:33141-33148. [PMID: 34901665 PMCID: PMC8655920 DOI: 10.1021/acsomega.1c05508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
Individual bacteria communicate by the release and interpretation of small molecules, a phenomenon known as quorum sensing (QS). We hypothesized that QS compounds extruded by Photorhabdus could be interpreted by Bacillus-a form of interspecies communication. We interrogate the structure-activity relationship within the recently discovered pyrone QS network and reveal the exquisite structural features required for targeted phenotypic behavior. The interruption of QS is an exciting, nonbiocidal approach to tackling infection, and understanding its nuances can only be achieved by studies such as this.
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Affiliation(s)
- Aobha Hickey
- School
of Chemistry, Analytical and Biological Chemistry Research
Facility, School of Microbiology, Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork T12 YN60, Ireland
| | - Leticia M. Pardo
- School
of Chemistry, Analytical and Biological Chemistry Research
Facility, School of Microbiology, Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork T12 YN60, Ireland
| | - F. Jerry Reen
- School
of Chemistry, Analytical and Biological Chemistry Research
Facility, School of Microbiology, Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork T12 YN60, Ireland
| | - Gerard P. McGlacken
- School
of Chemistry, Analytical and Biological Chemistry Research
Facility, School of Microbiology, Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork T12 YN60, Ireland
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16
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Opdensteinen P, Dietz SJ, Gengenbach BB, Buyel JF. Expression of Biofilm-Degrading Enzymes in Plants and Automated High-Throughput Activity Screening Using Experimental Bacillus subtilis Biofilms. Front Bioeng Biotechnol 2021; 9:708150. [PMID: 34621728 PMCID: PMC8490750 DOI: 10.3389/fbioe.2021.708150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Biofilm-forming bacteria are sources of infections because they are often resistant to antibiotics and chemical removal. Recombinant biofilm-degrading enzymes have the potential to remove biofilms gently, but they can be toxic toward microbial hosts and are therefore difficult to produce in bacteria. Here, we investigated Nicotiana species for the production of such enzymes using the dispersin B-like enzyme Lysobacter gummosus glyco 2 (Lg2) as a model. We first optimized transient Lg2 expression in plant cell packs using different subcellular targeting methods. We found that expression levels were transferable to differentiated plants, facilitating the scale-up of production. Our process yielded 20 mg kg−1 Lg2 in extracts but 0.3 mg kg−1 after purification, limited by losses during depth filtration. Next, we established an experimental biofilm assay to screen enzymes for degrading activity using different Bacillus subtilis strains. We then tested complex and chemically defined growth media for reproducible biofilm formation before converting the assay to an automated high-throughput screening format. Finally, we quantified the biofilm-degrading activity of Lg2 in comparison with commercial enzymes against our experimental biofilms, indicating that crude extracts can be screened directly. This ability will allow us to combine high-throughput expression in plant cell packs with automated activity screening.
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Affiliation(s)
- P Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - S J Dietz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - B B Gengenbach
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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17
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Harwood CR, Kikuchi Y. The ins and outs of Bacillus proteases: activities, functions and commercial significance. FEMS Microbiol Rev 2021; 46:6354784. [PMID: 34410368 PMCID: PMC8767453 DOI: 10.1093/femsre/fuab046] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
Because the majority of bacterial species divide by binary fission, and do not have distinguishable somatic and germline cells, they could be considered to be immortal. However, bacteria ‘age’ due to damage to vital cell components such as DNA and proteins. DNA damage can often be repaired using efficient DNA repair mechanisms. However, many proteins have a functional ‘shelf life’; some are short lived, while others are relatively stable. Specific degradation processes are built into the life span of proteins whose activities are required to fulfil a specific function during a prescribed period of time (e.g. cell cycle, differentiation process, stress response). In addition, proteins that are irreparably damaged or that have come to the end of their functional life span need to be removed by quality control proteases. Other proteases are involved in performing a variety of specific functions that can be broadly divided into three categories: processing, regulation and feeding. This review presents a systematic account of the proteases of Bacillus subtilis and their activities. It reviews the proteases found in, or associated with, the cytoplasm, the cell membrane, the cell wall and the external milieu. Where known, the impacts of the deletion of particular proteases are discussed, particularly in relation to industrial applications.
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Affiliation(s)
- Colin R Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University NE2 4AX, Newcastle upon Tyne, UK
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, JAPAN
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18
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Nagpal S, Sharma P, Sirari A, Kumawat KC, Wati L, Gupta SC, Mandahal KS. Chickpea (Cicer arietinum L.) as model legume for decoding the co-existence of Pseudomonas fluorescens and Mesorhizobium sp. as bio-fertilizer under diverse agro-climatic zones. Microbiol Res 2021; 247:126720. [PMID: 33592359 DOI: 10.1016/j.micres.2021.126720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 11/18/2022]
Abstract
Microbial co-inoculation strategy utilizes a combination of microbes to stimulate plant growth concomitant with an increased phytopathogen tolerance. In the present study, 15 endophytic bacterial isolates from rhizosphere and roots of wild chickpea accessions (Cicer pinnatifidum, C. judiacum, C. bijugum and C. reticulatum) were characterized for morphological, biochemical and physiological traits. Two promising isolates were identified as Pseudomonas fluorescens strain LRE-2 (KR303708.1) and Pseudomonas argentinensis LPGPR-1 (JX239745.1) based on 16S rRNA gene sequencing. Biocompatibility of selected endophytes with Mesorhizobium sp. CH1233, a standard isolate used as a national check in All India Coordinated Research Project (AICRP) was assessed to develop functional combinations capable of producing Indole acetic acid, gibberellins, siderophores and improving seed vigour (in vitro). In vivo synergistic effect of promising combinations was further evaluated under national AICRP, (Chickpea) at two different agro-climatic zones [North-West plain (Ludhiana and Hisar) and Central zones (Sehore)] for three consecutive Rabi seasons (2015-18) to elucidate their effect on symbiotic, soil quality and yield parameters. On the pooled mean basis across locations over the years, combination of Mrh+LRE-2 significantly enhanced symbiotic, soil quality traits and grain yield over Mrh alone and highly positive correlation was obtained between the nodulation traits and grain yield. Superior B: C ratio (1.12) and additional income of Rs 6,505.18 ha-1 was obtained by application of Mrh+LRE-2 over Mrh alone and un-inoculated control. The results demonstrate that dual combination of Mrh and Pseudomonas sp. from wild Cicer relatives can be exploited as a potential bio-fertilizer for increasing soil fertility and improving chickpea productivity under sustainable agriculture.
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Affiliation(s)
- Sharon Nagpal
- Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Asmita Sirari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - K C Kumawat
- Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Leela Wati
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - S C Gupta
- RAK, College of Agriculture, Sehore, Madhya Pradesh, 466001, India
| | - Kamalpreet Singh Mandahal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
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19
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Quorum sensing modulatory and biofilm inhibitory activity of Plectranthus barbatus essential oil: a novel intervention strategy. Arch Microbiol 2021; 203:1767-1778. [PMID: 33474610 DOI: 10.1007/s00203-020-02171-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/07/2020] [Accepted: 12/27/2020] [Indexed: 01/05/2023]
Abstract
The essential oil (EO) from the roots of Plectranthus barbatus Andr. (Syn. Coleus forskohlii Briq.) was evaluated for quorum sensing (QS) inhibitory activity. P. barbatus EO was screened for inhibition of QS regulated violacein production in Chromobacterium violaceum (ATCC 12472) wild-type strain. At inhibitory (6.25% v/v) and sub-inhibitory concentrations (3.125% v/v) of the EO, dose-dependent response in the inhibition of violacein production was observed in C. violaceum. Similarly, sub-MIC (6.25% v/v) of P. barbatus EO disrupted QS regulated biofilm formation by 27.87% and inhibited swarming and twitching motility in Pseudomonas aeruginosa PA01 implying its anti-infective and QS modulatory activity. Fluorescence microscopy studies confirmed the disruption of biofilm formation by EO in P. aeruginosa PAO1. Promising antibacterial activity was recorded at concentrations as low as 3.12% v/v for Listeria monocytogenes (ATCC 13932) and at 6.25% v/v for both Salmonella enterica subsp. enterica serovar Typhimurium (ATCC 25241) and Escherichia coli (ATCC 11775). Furthermore, significant dose-dependent inhibition was observed for biofilm formation and motility in all the tested pathogens in different treated concentrations. GC-MS analysis revealed α-pinene, endo-borneol, bornyl acetate, 1-Hexyl-2-Nitrocyclohexane as the major phytoconstituents. P. barbatus EO or its constituent compounds with QS modulatory, antimicrobial and biofilm inhibitory property could be potential new-age dietary source based intervention and preservation technologies.
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20
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Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle. Appl Environ Microbiol 2020; 86:AEM.02038-20. [PMID: 33097507 DOI: 10.1128/aem.02038-20] [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] [Received: 08/25/2020] [Accepted: 10/04/2020] [Indexed: 12/19/2022] Open
Abstract
Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings.IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.
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21
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Sidrim JJ, Ocadaque CJ, Amando BR, de M Guedes GM, Costa CL, Brilhante RS, A Cordeiro RD, Rocha MF, Scm Castelo-Branco D. Rhamnolipid enhances Burkholderia pseudomallei biofilm susceptibility, disassembly and production of virulence factors. Future Microbiol 2020; 15:1109-1121. [PMID: 32954847 DOI: 10.2217/fmb-2020-0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: This study evaluated the effect of the biosurfactant rhamnolipid on the antimicrobial susceptibility, biofilm growth dynamics and production of virulence factors by Burkholderia pseudomallei. Materials & methods: The effects of rhamnolipid on planktonic and biofilm growth and its interaction with antibacterial drugs were evaluated. Then, its effects on growing and mature biofilms and on protease and siderophore production were assessed. Results: Rhamnolipid did not inhibit B. pseudomallei growth, but significantly enhanced the activity of meropenem and amoxicillin-clavulanate against mature biofilms. Rhamnolipid significantly reduced the biomass of mature biofilms, significantly increased protease production by growing and mature biofilms and siderophore release by growing biofilms. Conclusion: Rhamnolipid enhances the antimicrobial activity against B. pseudomallei, assists biofilm disassembly and alters protease and siderophore production by bacterial biofilms.
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Affiliation(s)
- José Jc Sidrim
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Laboratory of Emerging and Reemerging Pathogens, Federal University of Ceara, Rua Coronel, Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Crister J Ocadaque
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceara, Rua Coronel Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Bruno R Amando
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceara, Rua Coronel Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Glaucia M de M Guedes
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Laboratory of Emerging and Reemerging Pathogens, Federal University of Ceara, Rua Coronel, Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Cecília L Costa
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceara, Rua Coronel Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Raimunda Sn Brilhante
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Laboratory of Emerging and Reemerging Pathogens, Federal University of Ceara, Rua Coronel, Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Rossana de A Cordeiro
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Laboratory of Emerging and Reemerging Pathogens, Federal University of Ceara, Rua Coronel, Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
| | - Marcos Fg Rocha
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Laboratory of Emerging and Reemerging Pathogens, Federal University of Ceara, Rua Coronel, Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil.,School of Veterinary Medicine, Postgraduate Program in Veterinary Sciences, State University of Ceará, Av. Dr. Silas Munguba 1700 - Itaperi - CEP:60714-903, Fortaleza, Ceará, Brazil
| | - Débora Scm Castelo-Branco
- Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Laboratory of Emerging and Reemerging Pathogens, Federal University of Ceara, Rua Coronel, Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil.,Department of Pathology & Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceara, Rua Coronel Nunes de Melo, 1315 - Rodolfo Teófilo - CEP 60430-275, Fortaleza, Ceará, Brazil
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Bridier A, Piard JC, Briandet R, Bouchez T. Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms. MICROBIAL ECOLOGY 2020; 80:47-59. [PMID: 31844910 DOI: 10.1007/s00248-019-01470-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bacterial interactions in the diversification process. On the basis of colony morphology, three variants of P. putida KT2440 were obtained from co-culture after 168 h of growth whereas no variant was identified from the axenic KT2440 biofilm. The variants exhibited distinct phenotypes and produced biofilms with specific architecture in comparison with the ancestor. The variants better competed with the P. putida PCL1480 strain in the dual-strain biofilms after 24 h of co-culture in comparison with the ancestor. Moreover, the synergistic interaction of KT2440 ancestor and the variants led to an improved biofilm production and to higher competitive ability versus the PCL1480 strain, highlighting the key role of diversification in the adaptation of P. putida KT2440 in the mixed community. Whole genome sequencing revealed mutations in polysaccharides biosynthesis protein, membrane transporter, or lipoprotein signal peptidase genes in variants.
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Affiliation(s)
- Arnaud Bridier
- ANSES, Fougères Laboratory, AB2R, 10B rue Claude Bourgelat, 35300, Fougères, France.
- IRSTEA, UR PROSE, 1 rue Pierre-Gilles de Gennes, 92761, Antony Cedex, France.
| | - J C Piard
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - R Briandet
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - T Bouchez
- IRSTEA, UR PROSE, 1 rue Pierre-Gilles de Gennes, 92761, Antony Cedex, France
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23
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Krueger LA, Spangler DA, Sims MD. Titration of supplemental Bacillus subtilis subsp. subtilis American Type Culture Collection PTA-125135 to broiler chickens fed diets of 2 different metabolizable energy concentrations. Poult Sci 2020; 99:3987-3996. [PMID: 32731986 PMCID: PMC7597919 DOI: 10.1016/j.psj.2020.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/30/2020] [Accepted: 04/25/2020] [Indexed: 11/30/2022] Open
Abstract
Bacillus subtilis subsp. subtilis American Type Culture Collection deposit number PTA-125135 has recently been studied by our laboratory as a potential probiotic strain for avian species. The objective of the present study was to evaluate growth performance and feed efficiency in broiler chickens in response to a dose titration of the Bacillus strain in feed. In addition to a nonsupplemented control, Bacillus spores were supplemented into broiler chicken diets at 4 levels, which were 8.1 × 104, 1.6 × 105, 2.4 × 105, and 3.2 × 105 CFU per g of feed. The titration was applied to two different dietary regimes of standard or low metabolizable energy (ME), which differed in ME by 22, 56, and 110 kcal/kg in starter, grower, and finisher dietary phases, respectively. All diets contained 249 g per metric ton of a previously patented synbiotic feed additive. Performance data were collected at day 14, 26, and 40 of age, and the effects of Bacillus and ME treatments were evaluated by factorial ANOVA. Treatment group means were further examined for significant (P < 0.05) pairwise differences among treatments and for significant (P < 0.05) linear and quadratic effects. At day 14 of age, significant linear effects for decreased feed conversion ratio (FCR) with higher CFU of Bacillus supplementation were observed within the standard ME diet. At day 26, a linear trend was observed for increased mortality with increased dose within the standard ME diet only. Bacillus supplementation at day 26 also significantly affected FCR and mortality-adjusted FCR, where supplementation with 3.2 × 105 CFU per g feed produced lower FCR and mortality-adjusted FCR than supplementation with 1.6 × 105 CFU per g feed. We conclude from linear effects related to feed efficiency observed at day 14 and from the significant separation of Bacillus treatment means within the titrated range of supplementation at day 26 that further evaluation for effects on performance should be made of doses at 2.4 × 105, 3.2 × 105, and greater CFU per g in feed.
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Affiliation(s)
| | | | - M D Sims
- Virginia Diversified Research Corporation, Harrisonburg, VA, USA
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25
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Poudel S, Giannone RJ, Farmer AT, Campagna SR, Bible AN, Morrell-Falvey JL, Elkins JG, Hettich RL. Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility. Front Microbiol 2019; 10:2594. [PMID: 31798553 PMCID: PMC6878767 DOI: 10.3389/fmicb.2019.02594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/25/2019] [Indexed: 11/15/2022] Open
Abstract
Paenibacillus polymyxa is a Gram-positive bacterium commonly found associated with plant roots. P. polymyxa can exhibit two forms of flagellar motility: swimming in liquid culture and swarming on a surface. Here, swimming cells were compared to swarming cells using an integrated proteomic and lipidomic approach, yielding information about how lipid modifications and protein/enzyme pathways are tailored for these specific phenotypes. Observed differences in both phospholipid composition and metabolism between the two conditions suggest membrane remodeling in response to the surrounding environment. Key enzymes involved in glycerophospholipid metabolism were abundant in swimming bacteria, while enzymes associated with glycerol-3-phosphate metabolism were more abundant in swarming bacteria. Several glycoside hydrolases were either unique to or more abundant during swarming. This likely reflects the degradation of their own exopolysaccharides to both enhance swarming and supply the necessary chemical energy to compensate for increased flagellar synthesis. The observed upregulation of biosynthetic gene clusters (polyketides, lantibiotics, and surfactin) in swarming bacteria suggest the importance of signaling, antimicrobial activity, and surfactin production during this mode of motility – the latter of which is confirmed via RT-PCR.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Abigail T Farmer
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Shawn R Campagna
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jennifer L Morrell-Falvey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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26
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Kumawat KC, Sharma P, Singh I, Sirari A, Gill BS. Co-existence of Leclercia adecarboxylata (LSE-1) and Bradyrhizobium sp. (LSBR-3) in nodule niche for multifaceted effects and profitability in soybean production. World J Microbiol Biotechnol 2019; 35:172. [PMID: 31673798 DOI: 10.1007/s11274-019-2752-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/18/2019] [Indexed: 01/06/2023]
Abstract
The present study was designed with the objective of improving growth and nodulation of soybean [Glycine max (L.) Merill] with co-inoculation of native Bradyrhizobium sp. (LSBR-3) (KF906140) and non-rhizobial nodule endophytic diazotroph Leclercia adecarboxylata (LSE-1) (KX925974) with multifunctional plant growth promoting (PGP) traits in cereal based cropping system (Rice-Wheat). A total of 40 endophytic bacteria from cultivated and wild sp. of soybean were screened for multifarious PGP traits and pathogenicity test. Based on PGP traits, antagonistic activities and bio-safety test; L. adecarboxylata (LSE-1) was identified with 16 S rRNA gene sequencing along with the presence of nifH (nitrogen fixation) and ipdc (IAA production) genes. Dual inoculant LSE-1 and LSBR-3 increased indole acetic acid (IAA), P & Zn-solubilization, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity, siderophore, biofilm formation and exo-polysaccharides in contrast to single inoculation treatment. Further, assessment of dual inoculant LSBR-3 + LSE-1 improved growth parameters, nodulation, soil enzymes activities, nutrient accumulation and yield as compared to single as well as un-inoculated control treatment under field conditions. Single inoculant LSBR-3 improved yield by 8.84% over control. Further, enhancement of 4.15% grain yield was noticed with LSBR-3 + LSE-1 over LSBR-3 alone treatment. Application of LSBR-3 + LSE-1 gave superior B:C ratio (1.29) and additional income approximately 116 USD ha-1 in contrast to control treatment. The present results thus, is the first report of novel endophytic diazotroph L. adecarboxylata (LSE-1) as PGPR from Indian conditions particularly in Punjab region for exploiting as potential PGPR along with Bradyrhizobium sp. (LSBR-3) in soybean.
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Affiliation(s)
- K C Kumawat
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Inderjeet Singh
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Asmita Sirari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - B S Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
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Razzaq A, Shamsi S, Ali A, Ali Q, Sajjad M, Malik A, Ashraf M. Microbial Proteases Applications. Front Bioeng Biotechnol 2019; 7:110. [PMID: 31263696 PMCID: PMC6584820 DOI: 10.3389/fbioe.2019.00110] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
The use of chemicals around the globe in different industries has increased tremendously, affecting the health of people. The modern world intends to replace these noxious chemicals with environmental friendly products for the betterment of life on the planet. Establishing enzymatic processes in spite of chemical processes has been a prime objective of scientists. Various enzymes, specifically microbial proteases, are the most essentially used in different corporate sectors, such as textile, detergent, leather, feed, waste, and others. Proteases with respect to physiological and commercial roles hold a pivotal position. As they are performing synthetic and degradative functions, proteases are found ubiquitously, such as in plants, animals, and microbes. Among different producers of proteases, Bacillus sp. are mostly commercially exploited microbes for proteases. Proteases are successfully considered as an alternative to chemicals and an eco-friendly indicator for nature or the surroundings. The evolutionary relationship among acidic, neutral, and alkaline proteases has been analyzed based on their protein sequences, but there remains a lack of information that regulates the diversity in their specificity. Researchers are looking for microbial proteases as they can tolerate harsh conditions, ways to prevent autoproteolytic activity, stability in optimum pH, and substrate specificity. The current review focuses on the comparison among different proteases and the current problems faced during production and application at the industrial level. Deciphering these issues would enable us to promote microbial proteases economically and commercially around the world.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Sadia Shamsi
- School of Medicine, Medical Sciences and Nutrition, The Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Arfan Ali
- 1-FB, Genetics, Four Brothers Group, Lahore, Pakistan
| | - Qurban Ali
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sajjad
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
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28
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Biofilm formation and potential virulence factors of Salmonella strains isolated from ready-to-eat shrimps. PLoS One 2018; 13:e0204345. [PMID: 30235341 PMCID: PMC6147607 DOI: 10.1371/journal.pone.0204345] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
Abstract
Salmonella species is an important foodborne pathogen with the non-typhoidal serovars such as Enteritidis and Typhimurium as the most predominant strains. This study examines the biofilm formation, phenotypic virulence factors and cell surface characteristics of Salmonella strains from ready-to-eat shrimps. The ready-to-eat shrimps were obtained from open markets between November 2016 and October 2017 in Edo and Delta States, Nigeria. The occurrence of Salmonella strains in this study was 210/1440 (14.58%) of the ready-to-eat shrimp’s samples. The identified strains comprise of Salmonella Enteritidis 11, Salmonella Typhimurium 14 and other Salmonella spp. 20. The 45 identified Salmonella strains revealed the following virulence properties: swimming and swarming motility 45(100%); S-layer 39(86.67%); haemolytic activity 40(88.89%); lipase activity 43(95.56%); protease activity 43(95.56%); gelatinase production 43(95.56%); and DNA degrading activity 41(91.11%). The variation in the formation of biofilm-based on the diversity of Salmonella species was observed with higher percentage of Salmonella Typhimurium strains as strong biofilms producers under different environmental conditions. For surface hydrophobicity using bacterial adherence to hydrocarbons, 25(55.56%) were hydrophilic while 20(44.44%) were moderately hydrophobic from the 45 Salmonella isolates. Using salting aggregation test for surface hydrophobicity, all selected isolates 45(100%) was hydrophilic. Autoaggregation index for the 12 selected Salmonella isolates ranged from 15.2–47.2%, while the autoaggragation index for the 12 selected test bacteria ranged from 26.2–71.3%. Coaggragation between the 12 selected test bacteria and 12 Salmonella isolates ranged from 12.5–81.0%. The occurrence of pathogenic species of Salmonella from ready-to-eat shrimps could be detrimental to the consumers. Findings on the physiological conditions of biofilms formed by the foodborne pathogenic Salmonella and the cell surface characteristics therein are crucial for the advancement of methods for controlling Salmonella from ready-to-eat foods.
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29
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Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis. J Bacteriol 2018; 200:JB.00267-18. [PMID: 29941421 DOI: 10.1128/jb.00267-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022] Open
Abstract
Horizontal gene transfer (HGT) is a driving force for bacterial evolution that occurs via conjugation, transduction, and transformation. Whereas conjugation and transduction depend on nonbacterial vehicles, transformation is considered a naturally occurring process in which naked DNA molecules are taken up by a competent recipient cell. Here, we report that HGT occurred between two Bacillus subtilis strains cocultured on a minimum medium agar plate for 10 h. This process was almost completely resistant to DNase treatment and appeared to require close proximity between cells. The deletion of comK in the recipient completely abolished gene transfer, indicating that the process involved transformation. This process was also highly efficient, reaching 1.75 × 106 transformants/μg DNA compared to 5.3 × 103 and 1.86 × 105 transformants/μg DNA for DNA-to-cell transformation by the same agar method and the standard two-step procedure, respectively. Interestingly, when three distantly localized chromosomal markers were selected simultaneously, the efficiency of cell-to-cell transformation still reached 6.26 × 104 transformants/μg DNA, whereas no transformants were obtained when free DNA was used as the donor. Stresses, such as starvation and exposure to antibiotics, further enhanced transformation efficiency by affecting the donor cells, suggesting that stress served as an important signal for promoting this type of HGT. Taken together, our results defined a bona fide process of cell-to-cell natural transformation (CTCNT) in B. subtilis and related species. This finding reveals the previously unrecognized role of donor cells in bacterial natural transformation and improves our understanding of how HGT drives bacterial evolution at a mechanistic level.IMPORTANCE Because DNA is easily prepared, studies of bacterial natural genetic transformation traditionally focus on recipient cells. However, such laboratory artifacts cannot explain how this process occurs in nature. In most cases, competence is only transient and involves approximately 20 to 50 genes, and it is unreasonable for bacteria to spend so many genetic resources on unpredictable and uncertain environmental DNA. Here, we characterized a donor cell-dependent CTCNT process in B. subtilis and related species that was almost completely resistant to DNase treatment and was more efficient than classical natural transformation using naked DNA as a donor, i.e., DNA-to-cell transformation, suggesting that DNA donor cells were also important in the transformation process in natural environments.
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30
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Sarwar A, Brader G, Corretto E, Aleti G, Abaidullah M, Sessitsch A, Hafeez FY. Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity. PLoS One 2018; 13:e0198107. [PMID: 29864153 PMCID: PMC5986119 DOI: 10.1371/journal.pone.0198107] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/14/2018] [Indexed: 11/28/2022] Open
Abstract
Bacillus spp. produce a broad spectrum of lipopeptide biosurfactants, among which surfactin, iturin and fengycin are widely studied families. The goals of this study were to characterize the biosurfactant activity of Bacillus spp. and to investigate their motility and biofilm formation capabilities. In addition, we extracted lipopeptides from these bacteria to assess their antifungal activities and analyzed these products by mass spectrometry (MS). B. amyloliquefaciens FZB42, Bacillus sp. NH 217 and B. subtilis NH-100 exhibited excellent biosurfactant and surface spreading activities, whereas B. atrophaeus 176s and Paenibacillus polymyxa C1225 showed moderate activity, and B. subtilis 168 showed no activity. Strains FZB42, NH-100, NH-217, 176s and CC125 exhibited excellent biofilm formation capabilities. Lipopeptide extracts displayed good antifungal activity against various phytopathogens and their associated diseases, such as Fusarium moniliforme (rice bakanae disease), Fusarium oxysporum (root rot), Fusarium solani (root rot) and Trichoderma atroviride (ear rot and root rot). Lipopeptide extracts of these strains also showed hemolytic activity, demonstrating their strong potential to produce surfactants. LCMS-ESI analyses identified the presence of surfactin, iturin and fengycin in the extracts of Bacillus strains. Thus, the strains assayed in this study show potential as biocontrol agents against various Fusarium and Trichoderma species.
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Affiliation(s)
- Ambrin Sarwar
- Department of Biosciences, Faculty of Sciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Günter Brader
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse, Tulln, Austria
| | - Erika Corretto
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse, Tulln, Austria
| | - Gajendar Aleti
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse, Tulln, Austria
| | - Muhammad Abaidullah
- Department of Biosciences, Faculty of Sciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Angela Sessitsch
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse, Tulln, Austria
| | - Fauzia Yusuf Hafeez
- Department of Biosciences, Faculty of Sciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
- * E-mail:
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31
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Song Y, Liu D, Liu M, Yang H, Fan Y, Sun W, Xue Y, Zhang T, Ma Y. Transcriptional regulation of the mannan utilization genes in the alkaliphilic Bacillus sp. N16-5. FEMS Microbiol Lett 2018; 365:4816728. [DOI: 10.1093/femsle/fnx280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yajian Song
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Duoduo Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengya Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Haixu Yang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanli Fan
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenyuan Sun
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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32
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Tauber JP, Gallegos-Monterrosa R, Kovács ÁT, Shelest E, Hoffmeister D. Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during inter-kingdom interactions. MICROBIOLOGY-SGM 2017; 164:65-77. [PMID: 29205129 DOI: 10.1099/mic.0.000582] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Production of basidiomycete atromentin-derived pigments like variegatic acid (pulvinic acid-type) and involutin (diarylcyclopentenone) from the brown-rotter Serpula lacrymans and the ectomycorrhiza-forming Paxillus involutus, respectively, is induced by complex nutrition, and in the case of S. lacrymans, bacteria. Pigmentation in S. lacrymans was stimulated by 13 different bacteria and cell-wall-damaging enzymes (lytic enzymes and proteases), but not by lysozyme or mechanical damage. The use of protease inhibitors with Bacillus subtilis or heat-killed bacteria during co-culturing with S. lacrymans significantly reduced pigmentation indicating that enzymatic hyphal damage and/or released peptides, rather than mechanical injury, was the major cause of systemic pigment induction. Conversely, no significant pigmentation by bacteria was observed from P. involutus. We found additional putative transcriptional composite elements of atromentin synthetase genes in P. involutus and other ectomycorrhiza-forming species that were absent from S. lacrymans and other brown-rotters. Variegatic and its precursor xerocomic acid, but not involutin, in return inhibited swarming and colony biofilm spreading of Bacillus subtilis, but did not kill B. subtilis. We suggest that dissimilar pigment regulation by fungal lifestyle was a consequence of pigment bioactivity and additional promoter motifs. The focus on basidiomycete natural product gene induction and regulation will assist in future studies to determine global regulators, signalling pathways and associated transcription factors of basidiomycetes.
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Affiliation(s)
- James P Tauber
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University, Winzerlaer Str. 2, 07745 Jena, Germany
| | - Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Neugasse 23, 07743 Jena, Germany
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Neugasse 23, 07743 Jena, Germany.,Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, 2800 Kgs. Lyngby, Denmark
| | - Ekaterina Shelest
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.,Present address: German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University, Winzerlaer Str. 2, 07745 Jena, Germany
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Singh RP, Jha PN. The PGPR Stenotrophomonas maltophilia SBP-9 Augments Resistance against Biotic and Abiotic Stress in Wheat Plants. Front Microbiol 2017; 8:1945. [PMID: 29062306 PMCID: PMC5640710 DOI: 10.3389/fmicb.2017.01945] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/21/2017] [Indexed: 11/20/2022] Open
Abstract
Certain plant growth promoting bacteria have ability to ameliorate abiotic and/or biotic stressors, which can be exploited to enhance plant growth and productivity of the plants under stress conditions. Therefore, the present study aimed to examine the role of a rhizospheric bacterial isolate SBP-9 isolated from Sorghum bicolor (i) in promoting the wheat plant growth under salinity stress, and (ii) in enhancing the defense response in wheat against fungal pathogen "Fusarium graminearum." The test isolate possessed plant growth promoting (PGP) traits including ACC deaminase (ACCD), gibberellic acid, indole acetic acid (IAA), siderophore, and inorganic phosphate solubilization. Under salt (NaCl) stress, inoculation of this isolate to wheat plant significantly increased plant growth in terms of various growth parameters such as shoot length/root length (20-39%), fresh weight/dry weight (28-42%), and chlorophyll content (24-56%) following inoculation of test isolate SBP-9. Bacterial inoculation decreased the level of proline, and malondialdehyde, whereas elevated the antioxidative enzymatic activities of superoxide-dismutase (SOD; 28-41%), catalase (CAT; 24-56%), and peroxidase (POX; 26-44%). Furthermore, it also significantly decreased the Na+ accumulation in both shoot and roots in the range of 25-32%, and increased the K+ uptake by 20-28%, thereby favoring the K+/Na+ ratio. On the other hand, the test isolate also enhanced the level of defense enzymes like β-1, 3 glucanase, phenylalanine ammonia lyase (PAL), peroxidae (PO), and polyphenol oxidase (PPO), which can protect plants from the infection of pathogens. The result of colonization test showed an ability of the test isolate to successfully colonize the wheat plants. These results indicate that Stenotrophomonas maltophilia SBP-9 has potential to promote the wheat growth under biotic and abiotic (salt) stressors directly or indirectly and can be further tested at field level for exploitation as bioinoculant.
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Affiliation(s)
| | - Prabhat N. Jha
- Department of Biological Science, Birla Institute of Technology and Science, Pilani, Pilani, India
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Han LL, Shao HH, Liu YC, Liu G, Xie CY, Cheng XJ, Wang HY, Tan XM, Feng H. Transcriptome profiling analysis reveals metabolic changes across various growth phases in Bacillus pumilus BA06. BMC Microbiol 2017; 17:156. [PMID: 28693413 PMCID: PMC5504735 DOI: 10.1186/s12866-017-1066-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/04/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacillus pumilus can secret abundant extracellular enzymes, and may be used as a potential host for the industrial production of enzymes. It is necessary to understand the metabolic processes during cellular growth. Here, an RNA-seq based transcriptome analysis was applied to examine B. pumilus BA06 across various growth stages to reveal metabolic changes under two conditions. RESULTS Based on the gene expression levels, changes to metabolism pathways that were specific to various growth phases were enriched by KEGG analysis. Upon entry into the transition from the exponential growth phase, striking changes were revealed that included down-regulation of the tricarboxylic acid cycle, oxidative phosphorylation, flagellar assembly, and chemotaxis signaling. In contrast, the expression of stress-responding genes was induced when entering the transition phase, suggesting that the cell may suffer from stress during this growth stage. As expected, up-regulation of sporulation-related genes was continuous during the stationary growth phase, which was consistent with the observed sporulation. However, the expression pattern of the various extracellular proteases was different, suggesting that the regulatory mechanism may be distinct for various proteases. In addition, two protein secretion pathways were enriched with genes responsive to the observed protein secretion in B. pumilus. However, the expression of some genes that encode sporulation-related proteins and extracellular proteases was delayed by the addition of gelatin to the minimal medium. CONCLUSIONS The transcriptome data depict global alterations in the genome-wide transcriptome across the various growth phases, which will enable an understanding of the physiology and phenotype of B. pumilus through gene expression.
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Affiliation(s)
- Lin-Li Han
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Huan-Huan Shao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Yong-Cheng Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Gang Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Chao-Ying Xie
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Xiao-Jie Cheng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Hai-Yan Wang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Xue-Mei Tan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Hong Feng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
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Zhu F, Yang X, Wu Y, Wang Y, Tang XF, Tang B. Release of an HtrA-Like Protease from the Cell Surface of Thermophilic Brevibacillus sp. WF146 via Substrate-Induced Autoprocessing of the N-terminal Membrane Anchor. Front Microbiol 2017; 8:481. [PMID: 28377763 PMCID: PMC5359297 DOI: 10.3389/fmicb.2017.00481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/08/2017] [Indexed: 01/07/2023] Open
Abstract
High-temperature requirement A (HtrA)-like proteases participate in protein quality control in prokaryotes and eukaryotes by degrading damaged proteins; however, little is known about HtrAs produced by thermophiles. HtrAw is an HtrA-like protease of thermophilic Brevibacillus sp. WF146. The intact form of HtrAw (iHtrAw) consisting of a transmembrane segment-containing N-terminal domain, a trypsin-like protease domain, and a C-terminal PDZ domain was produced in Escherichia coli. Purified iHtrAw itself is unable to cleave the N-terminal domain, but requires protein substrates to autoprocess the N-terminal domain intermolecularly, yielding a short form (sHtrAw). Mutation at the substrate-binding site in the PDZ domain affects the conversion of iHtrAw to sHtrAw. Deletion analysis revealed that the N-terminal domain is not necessary for enzyme folding, activity, and thermostability. Compared with other known HtrAs, HtrAw contains an additional Ca2+-binding Dx[DN]xDG motif important for enzyme stability and/or activity. When produced in an htrA/htrB double deletion mutant of Bacillus subtilis, iHtrAw localized predominantly to the cell pellet, and the amount of sHtrAw in the culture supernatant increased at elevated temperatures. Moreover, HtrAw increased the heat resistance of the B. subtilis mutant. In strain WF146, HtrAw exists in both a cell-associated intact form and a cell-free short form; an increase in growth temperature enhanced HtrAw production and the amount of cell-free short form. Release of the short form of HtrAw from the membrane may have the advantage of allowing the enzyme to freely access and degrade damaged proteins surrounding the bacterium living at high temperatures.
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Affiliation(s)
- Fengtao Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Xing Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Yan Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Yasi Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Xiao-Feng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan UniversityWuhan, China; Hubei Provincial Cooperative Innovation Center of Industrial FermentationWuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan UniversityWuhan, China; Hubei Provincial Cooperative Innovation Center of Industrial FermentationWuhan, China
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Dong Q, Luo J, Qiu W, Cai L, Anjum SI, Li B, Hou M, Xie G, Sun G. Inhibitory Effect of Camptothecin against Rice Bacterial Brown Stripe Pathogen Acidovorax avenae subsp. avenae RS-2. Molecules 2016; 21:molecules21080978. [PMID: 27472315 PMCID: PMC6274382 DOI: 10.3390/molecules21080978] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 12/28/2022] Open
Abstract
Camptothecin (CPT) has anticancer, antiviral, and antifungal properties. However, there is a dearth of information about antibacterial activity of CPT. Therefore, in this study, we investigated the inhibitory effect of CPT on Acidovorax avenae subsp. avenae strain RS-2, the pathogen of rice bacterial brown stripe, by measuring cell growth, DNA damage, cell membrane integrity, the expression of secretion systems, and topoisomerase-related genes, as well as the secretion of effector protein Hcp. Results indicated that CPT solutions at 0.05, 0.25, and 0.50 mg/mL inhibited the growth of strain RS-2 in vitro, while the inhibitory efficiency increased with an increase in CPT concentration, pH, and incubation time. Furthermore, CPT treatment affected bacterial growth and replication by causing membrane damage, which was evidenced by transmission electron microscopic observation and live/dead cell staining. In addition, quantitative real-time PCR analysis indicated that CPT treatment caused differential expression of eight secretion system-related genes and one topoisomerase-related gene, while the up-regulated expression of hcp could be justified by the increased secretion of Hcp based on the ELISA test. Overall, this study indicated that CPT has the potential to control the bacterial brown stripe pathogen of rice.
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Affiliation(s)
- Qiaolin Dong
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ju Luo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Wen Qiu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China.
| | - Li Cai
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Syed Ishtiaq Anjum
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China.
- Department of Zoology Kohat University of Science and Technology Kohat, Khyber Pakhtunkhwa 26000, Pakistan.
| | - Bin Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China.
| | - Mingsheng Hou
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guanlin Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China.
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Singh RP, Jha PN. The Multifarious PGPR Serratia marcescens CDP-13 Augments Induced Systemic Resistance and Enhanced Salinity Tolerance of Wheat (Triticum aestivum L.). PLoS One 2016; 11:e0155026. [PMID: 27322827 PMCID: PMC4913913 DOI: 10.1371/journal.pone.0155026] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/22/2016] [Indexed: 11/24/2022] Open
Abstract
The present study demonstrates the plant growth promoting (PGP) potential of a bacterial isolate CDP-13 isolated from ‘Capparis decidua’ plant, and its ability to protect plants from the deleterious effect of biotic and abiotic stressors. Based on 16S rRNA gene sequence analysis, the isolate was identified as Serratia marcescens. Among the PGP traits, the isolate was found to be positive for ACC deaminase activity, phosphate solubilization, production of siderophore, indole acetic acid production, nitrogen fixation, and ammonia production. CDP-13 showed growth at an increased salt (NaCl) concentration of up to 6%, indicating its potential to survive and associate with plants growing in saline soil. The inoculation of S. marcescens enhanced the growth of wheat plant under salinity stress (150–200 mM). It significantly reduced inhibition of plant growth (15 to 85%) caused by salt stressors. Application of CDP-13 also modulated concentration (20 to 75%) of different osmoprotectants (proline, malondialdehyde, total soluble sugar, total protein content, and indole acetic acid) in plants suggesting its role in enabling plants to tolerate salt stressors. In addition, bacterial inoculation also reduced the disease severity caused by fungal infection, which illustrated its ability to confer induced systemic resistance (ISR) in host plants. Treatment of wheat plants with the test organism caused alteration in anti-oxidative enzymes activities (Superoxide dismutase, Catalase, and Peroxidase) under various salinity levels, and therefore minimizes the salinity-induced oxidative damages to the plants. Colonization efficiency of strain CDP-13 was confirmed by CFU count, epi-fluorescence microscopy, and ERIC-PCR-based DNA fingerprinting approach. Hence, the study indicates that bacterium CDP-13 enhances plant growth, and has potential for the amelioration of salinity stress in wheat plants. Likewise, the results also provide insights into biotechnological approaches to using PGPR as an alternative to chemicals and pesticides.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
- * E-mail:
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Ge D, Xue Y, Ma Y. Two unexpected promiscuous activities of the iron-sulfur protein IspH in production of isoprene and isoamylene. Microb Cell Fact 2016; 15:79. [PMID: 27169371 PMCID: PMC4864966 DOI: 10.1186/s12934-016-0476-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background Bacillus species, possessing the methylerythritol phosphate (MEP) pathway for the synthesis of isoprenoid feedstock, are the highest producers of isoprene among bacteria; however, the enzyme responsible for isoprene synthesis has not been identified. The iron–sulfur protein IspH is the final enzyme of the MEP pathway and catalyses the reductive dehydration of (E)-4-hydroxy-3-methyl-2-butenyl diphosphate (HMBPP) to form isopentenyl diphosphate and dimethylallyl diphosphate (DMAPP). In this study, we demonstrated two unexpected promiscuous activities of IspH from alkaliphilic Bacillus sp. N16-5, which can produce high levels of isoprene. Results Bacillus sp. N16-5 IspH could catalyse the formation of isoprene from HMBPP and the conversion of DMAPP into a mixture of 2-methyl-2-butene and 3-methyl-1-butene. Both reactions require an electron transfer system, such as that used for HMBPP dehydration. Isoprene and isoamylene synthesis in Bacillus sp. N16-5 was investigated and the reaction system was reconstituted in vitro, including IspH, ferredoxin and ferredoxin-NADP+-reductase proteins and NADPH. The roles of specific IspH protein residues were also investigated by site-directed mutagenesis experiments; two variants (H131N and E133Q) were found to have lost the HMBPP reductase activity but could still catalyse the formation of isoprene. Overexpression of IspH H131N in Bacillus sp. N16-5 resulted in a twofold enhancement of isoprene production, and the yield of isoprene from the strain expressing E133Q was increased 300 % compared with the wild-type strain. Conclusions IspH from Bacillus sp. N16-5 is a promiscuous enzyme that can catalyse formation of isoprene and isoamylene. This enzyme, especially the H131N and E133Q variants, could be used for the production of isoprene from HMBPP. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0476-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deyong Ge
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,College of Medicine, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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A Novel Manno-Oligosaccharide Binding Protein Identified in Alkaliphilic Bacillus sp. N16-5 Is Involved in Mannan Utilization. PLoS One 2016; 11:e0150059. [PMID: 26978267 PMCID: PMC4792470 DOI: 10.1371/journal.pone.0150059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/09/2016] [Indexed: 11/19/2022] Open
Abstract
ManH, a novel substrate-binding protein of an ABC transporter, was identified from the mannan utilization gene cluster of Bacillus sp. N16-5. We cloned, overexpressed, and purified ManH and measured its binding affinity to different substrates by isothermal titration calorimetry. ManH binds to mannotriose, mannotetraose, mannopentose, and galactosyl-mannotriose with dissociation constants in the micromolar range. Deletion of manH led to decreased growth ability of the strain when cultivated in medium with manno-oligosaccharides or mannan as the carbon source. ManH belongs to a manno-oligosaccharide transporter and plays an important role in mannan utilization by Bacillus sp. N16-5.
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Alleviation of salinity-induced damage on wheat plant by an ACC deaminase-producing halophilic bacterium Serratia sp. SL- 12 isolated from a salt lake. Symbiosis 2016. [DOI: 10.1007/s13199-016-0387-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Efficient fermentative production of polymer-grade D-lactate by an engineered alkaliphilic Bacillus sp. strain under non-sterile conditions. Microb Cell Fact 2016; 15:3. [PMID: 26754255 PMCID: PMC4709905 DOI: 10.1186/s12934-015-0408-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/30/2015] [Indexed: 11/17/2022] Open
Abstract
Background Polylactic acid (PLA) is one important chemical building block that is well known as a biodegradable and a biocompatible plastic. The traditional lactate fermentation processes need CaCO3 as neutralizer to maintain the desired pH, which results in an amount of insoluble CaSO4 waste during the purification process. To overcome such environmental issue, alkaliphilic organisms have the great potential to be used as an organic acid producer under NaOH-neutralizing agent based fermentation. Additionally, high optical purity property in d-lactic acid is now attracting more attention from both scientific and industrial communities because it can improve mechanical properties of PLA by blending l- or d-polymer together. However, the use of low-price nitrogen source for d-lactate fermentation by alkaliphilic organisms combined with NaOH-neutralizing agent based process has not been studied. Therefore, our goal was the demonstrations of newly simplify high-optical-purity d-lactate production by using low-priced peanut meal combined with non-sterile NaOH-neutralizing agent based fermentation. Results In this study, we developed a process for high-optical-purity d-lactate production using an engineered alkaliphilic Bacillus strain. First, the native l-lactate dehydrogenase gene (ldh) was knocked out, and the d-lactate dehydrogenase gene from Lactobacillus delbrueckii was introduced to construct a d-lactate producer. The key gene responsible for exopolysaccharide biosynthesis (epsD) was subsequently disrupted to increase the yield and simplify the downstream process. Finally, a fed-batch fermentation under non-sterile conditions was conducted using low-priced peanut meal as a nitrogen source and NaOH as a green neutralizer. The d-lactate titer reached 143.99 g/l, with a yield of 96.09 %, an overall productivity of 1.674 g/l/h including with the highest productivity at 16 h of 3.04 g/l/h, which was even higher than that of a sterile fermentation. Moreover, high optical purities (approximately 99.85 %) of d-lactate were obtained under both conditions. Conclusions Given the use of a cheap nitrogen source and a non-sterile green fermentation process, this study provides a more valuable and favorable fermentation process for future polymer-grade d-lactate production.
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Singh RP, Jha PN. A Halotolerant Bacterium Bacillus licheniformis HSW-16 Augments Induced Systemic Tolerance to Salt Stress in Wheat Plant ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2016; 7:1890. [PMID: 28018415 PMCID: PMC5159429 DOI: 10.3389/fpls.2016.01890] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/30/2016] [Indexed: 05/08/2023]
Abstract
Certain plant growth promoting bacteria can protect associated plants from harmful effects of salinity. We report the isolation and characterization of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase bacterium Bacillus licheniformis HSW-16 capable of ameliorating salt (NaCl) stress in wheat plants. The bacterium was isolated from the water of Sambhar salt lake, Rajasthan, India. The presence of ACC deaminase activity was confirmed by enzyme assay and analysis of AcdS gene, a structural gene for ACC deaminase. Inoculation of B. licheniformis HSW-16 protected wheat plants from growth inhibition caused by NaCl and increased plant growth (6-38%) in terms of root length, shoot length, fresh weight, and dry weight. Ionic analysis of plant samples showed that the bacterial inoculation decreased the accumulation of Na+ content (51%), and increased K+ (68%), and Ca2+ content (32%) in plants at different concentration of NaCl. It suggested that bacterial inoculation protected plants from the effect of NaCl by decreasing the level of Na+ in plants. Production of exopolysaccharide by the B. licheniformis HSW-16 can also protect from Na+ by binding this ion. Moreover, application of test isolate resulted in an increase in certain osmolytes such as total soluble sugar, total protein content, and a decrease in malondialdehyde content, illustrating their role in the protection of plants. The ability of B. licheniformis HSW-16 to colonize plant root surface was examined by staining the bacterium with acridine orange followed by fluorescence microscopy and polymerase chain reaction-based DNA finger printing analysis. These results suggested that B. licheniformis HSW-16 could be used as a bioinoculant to improve the productivity of plants growing under salt stress.
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Maturation of Fibrinolytic Bacillopeptidase F Involves both Hetero- and Autocatalytic Processes. Appl Environ Microbiol 2015; 82:318-27. [PMID: 26497454 DOI: 10.1128/aem.02673-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
Bacillopeptidase F (Bpr) is a fibrinolytic serine protease produced by Bacillus subtilis. Its precursor is composed of a signal peptide, an N-terminal propeptide, a catalytic domain, and a long C-terminal extension (CTE). Several active forms of Bpr have been previously reported, but little is known about the maturation of this enzyme. Here, a gene encoding a Bpr (BprL) was cloned from B. subtilis LZW and expressed in B. subtilis WB700, and three fibrinolytic mature forms with apparent molecular masses of 45, 75, and 85 kDa were identified in the culture supernatant. After treatment with urea, the 75-kDa mature form had the same molecular mass as the 85-kDa mature form, from which we infer that they adopt different conformations. Mutational analysis revealed that while the 85-kDa mature form is generated via heterocatalytic processing of a BprL proform by an unidentified protease of B. subtilis, the production of the 75- and 45-kDa mature forms involves both hetero- and autocatalytic events. From in vitro analysis of BprL and its sequential C-terminal truncation variants, it appears that partial removal of the CTE is required for the initiation of autoprocessing of the N-terminal propeptide, which is composed of a core domain (N*) and a 15-residue linker peptide, thereby yielding the 45-kDa mature form. These data suggest that the differential processing of BprL, either heterocatalytically or autocatalytically, leads to the formation of multiple mature forms with different molecular masses or conformations.
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Hur JM, Park DH. Making soy sauce from defatted soybean meal without the mejus process by submerged cultivation using thermophilic bacteria. Journal of Food Science and Technology 2015; 52:5030-8. [PMID: 26243923 DOI: 10.1007/s13197-014-1536-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/10/2014] [Accepted: 08/25/2014] [Indexed: 11/24/2022]
Abstract
The diversity of thermophilic bacteria was not significantly altered while growing in a defatted soybean meal (DFSM) slurry at 60 °C for 10, 20, and 30 days. Five species of thermophilic bacteria, which belong to the genera Aeribacillus (temperature gradient gel electrophoresis [TGGE] band no. 1), Saccharococcus (TGGE band no. 2), Geobacillus (TGGE band no. 3), Bacillus (TGGE band no. 4), and Anoxybacillus (TGGE band no. 5), were detected in the fermenting DFSM slurry. The cell-free culture fluid obtained from the fermenting DFSM slurry on day 14 hydrolyzed starch and soy protein at 60 °C but not at 30 °C. Soy sauce (test soy sauce) was prepared from the fermented DFSM slurry after a 30 day cultivation at 60 °C and a 60 day ripening at 45 °C. Free amino acid (AA) and organic acid contents in the soy sauce increased in proportion to the fermentation period, whereas ammonium decreased proportionally. Mg and Ca contained in the soy sauce decreased proportionally during fermentation and were lower than those in the non-fermented DFSM extract (control). Spectral absorbance of soy sauce prepared from the fermented DFSM slurry was maximal at 430 nm and increased slightly in proportion to the fermentation period. The aroma and flavor of the test soy sauce were significantly different from those of traditional Korean soy sauce. Conclusively, soy sauce may be prepared directly from the fermented DFSM slurry without meju-preparing process and fermentation period may be a factor for control of soy sauce quality.
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Affiliation(s)
- Jeong Min Hur
- Department of Chemical and Biological Engineering, Seokyeong University, 124 Seokyeong-Ro, Sungbuk-gu Seoul, 136-704 South Korea
| | - Doo Hyun Park
- Department of Chemical and Biological Engineering, Seokyeong University, 124 Seokyeong-Ro, Sungbuk-gu Seoul, 136-704 South Korea
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Singh RP, Jha P, Jha PN. The plant-growth-promoting bacterium Klebsiella sp. SBP-8 confers induced systemic tolerance in wheat (Triticum aestivum) under salt stress. JOURNAL OF PLANT PHYSIOLOGY 2015; 184:57-67. [PMID: 26217911 DOI: 10.1016/j.jplph.2015.07.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 05/20/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) with 1-aminocyclopropane-1-carboxylatedeaminase (ACCD) activity can protect plants from the deleterious effects of abioticstressors. An ACCD bacterial strain, SBP-8, identified as Klebsiella sp., also having other plant-growth-promoting activities, was isolated from Sorghum bicolor growing in the desertregion of Rajasthan, India. ACCD activity of SBP-8 was characterized at biochemical, physiological, and molecular levels. The presence of AcdS, a structural gene for ACCD, was confirmed by the polymerase chain reaction. Strain SBP-8 showed optimum growth and ACCD activity at increased salt (NaCl) concentrations of up to 6%, indicating its potential to survive and associate with plants growing in saline soil. Inoculation of wheat plants with SBP-8 when grow in the presence of salt (150-200 mM) and temperature (30-40 °C) stressors resulted inamelioration of stress conditions by increasing plant biomass and chlorophyll content, and are duction in plant growth inhibition (10-100%) occurred due to salt and temperature stressors. Moreover, strain SBP-8 also caused Na(+) exclusion (65%) and increased uptake of K(+) (84.21%) in the host plant. This property can protect plants from adverse effects of Na(+) on plant growth and physiology. Thus, SBP-8 improves growth of the host plant and protects from salt stressors through more than one mechanism including an effect of ACCD activity and on K(+)/Na(+) ratio in plants. The colonization efficiency of strain SBP-8 was confirmedby CFU (colony-forming unit) count, microscopy, and ERIC-PCR based DNA-finger-printing approach. Therefore, and the use of efficient colonizing plant-growth-promoting bacteria may provideinsights into possible biotechnological approaches to decrease the impact of salinity and other stressors.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani 333031, Rajasthan, India
| | - Prameela Jha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani 333031, Rajasthan, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani 333031, Rajasthan, India.
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CodY regulates expression of the Bacillus subtilis extracellular proteases Vpr and Mpr. J Bacteriol 2015; 197:1423-32. [PMID: 25666135 DOI: 10.1128/jb.02588-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED CodY is a global transcriptional regulator in low-G+C Gram-positive bacteria that is responsive to GTP and branched-chain amino acids. By interacting with its two cofactors, it is able to sense the nutritional and energetic status of the cell and respond by regulating expression of adaptive genetic programs. In Bacillus subtilis, more than 200 genes, including those for peptide transporters, intracellular proteolytic enzymes, and amino acid degradative pathways, are controlled by CodY. In this study, we demonstrated that expression of two extracellular proteases, Vpr and Mpr, is negatively controlled by CodY. By gel mobility shift and DNase I footprinting assays, we showed that CodY binds to the regulatory regions of both genes, in the vicinity of their transcription start points. The mpr gene is also characterized by the presence of a second, higher-affinity CodY-binding site located at the beginning of its coding sequence. Using strains carrying vpr- or mpr-lacZ transcriptional fusions in which CodY-binding sites were mutated, we demonstrated that repression of both protease genes is due to the direct effect by CodY and that the mpr internal site is required for regulation. The vpr promoter is a rare example of a sigma H-dependent promoter that is regulated by CodY. In a codY null mutant, Vpr became one of the more abundant proteins of the B. subtilis exoproteome. IMPORTANCE CodY is a global transcriptional regulator of metabolism and virulence in low-G+C Gram-positive bacteria. In B. subtilis, more than 200 genes, including those for peptide transporters, intracellular proteolytic enzymes, and amino acid degradative pathways, are controlled by CodY. However, no role for B. subtilis CodY in regulating expression of extracellular proteases has been established to date. In this work, we demonstrate that by binding to the regulatory regions of the corresponding genes, B. subtilis CodY negatively controls expression of Vpr and Mpr, two extracellular proteases. Thus, in B. subtilis, CodY can now be seen to regulate the entire protein utilization pathway.
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Yin L, Xue Y, Ma Y. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation. PLoS One 2015; 10:e0128649. [PMID: 26030352 PMCID: PMC4452262 DOI: 10.1371/journal.pone.0128649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/29/2015] [Indexed: 11/29/2022] Open
Abstract
The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress.
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Affiliation(s)
- Liang Yin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YM)
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Effect of incubation temperature on variations in bacterial communities grown in fermenting meju and the nutritional quality of soy sauce. Food Sci Biotechnol 2014. [DOI: 10.1007/s10068-014-0262-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Morohoshi S, Matsuura K, Haruta S. Secreted protease mediates interspecies interaction and promotes cell aggregation of the photosynthetic bacterium Chloroflexus aggregans. FEMS Microbiol Lett 2014; 362:1-5. [PMID: 25673656 DOI: 10.1093/femsle/fnu046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interspecies interactions were studied in hot spring microbial mats where diverse species of bacterial cells are densely packed. The anoxygenic photosynthetic bacterium, Chloroflexus aggregans, has been widely found in the microbial mats as a major component in terrestrial hot springs in Japan at the temperature from 50 to 70°C. C. aggregans shows cellular motility to form a microbial mat-like dense cell aggregate. The aggregating ability of C. aggregans was affected by another bacterial species, strain BL55a (related to Bacillus licheniformis) isolated from the microbial mats containing C. aggregans. Cell aggregation rate of C. aggregans was promoted by the addition of culture supernatants of strain BL55a. Similar effects were also detected from other bacterial isolates, specifically Geobacillus sp. and Aeribacillus sp. Protease activity was detected from the culture supernatants from all of these isolates. The promoting effect of strain BL55a was suppressed by a serine protease inhibitor, phenylmethylsulfonyl fluoride. A purified serine protease, subtilisin obtained from B. licheniformis, showed a promoting effect on the cell aggregation. These results suggest that an extracellular protease, secreted from co-existing bacterial species promoted the aggregating motility of C. aggregans. This is the first report that exogenous protease affects bacterial cellular motility.
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Affiliation(s)
- Sho Morohoshi
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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Wang Y, Chen Z, Zhao R, Jin T, Zhang X, Chen X. Deleting multiple lytic genes enhances biomass yield and production of recombinant proteins by Bacillus subtilis. Microb Cell Fact 2014; 13:129. [PMID: 25176138 PMCID: PMC4243946 DOI: 10.1186/s12934-014-0129-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/23/2014] [Indexed: 02/01/2023] Open
Abstract
Background Bacillus subtilis is widely used in agriculture and industrial biotechnology; however, cell autolysis significantly decreases its yield in liquid cultures. Numerous factors mediate the lysis of B. subtilis, such as cannibalism factors, prophages, and peptidoglycan (PG) hydrolases. The aim of this work was to use molecular genetic techniques to develop a new strategy to prevent cell lysis and enhance biomass as well as the production of recombinant proteins. Results Five genes or genetic elements representing three different functional categories were studied as follows: lytC encoding PG hydrolases, the prophage genes xpf and yqxG-yqxH-cwlA (yGlA), and skfA and sdpC that encode cannibalism factors. Cell lysis was reduced and biomass was enhanced by deleting individually skfA, sdpC, xpf, and lytC. We constructed the multiple deletion mutant LM2531 (skfA sdpC lytC xpf) and found that after 4 h of culture, its biomass yield was significantly increased compared with that of prototypical B. subtilis 168 (wild-type) strain and that 15% and 92% of the cells were lysed in cultures of LM2531 and wild-type, respectively. Moreover, two expression vectors were constructed for producing recombinant proteins (β-galactosidase and nattokinase) under the control of the P43 promoter. Cultures of LM2531 and wild-type transformants produced 13741 U/ml and 7991 U/ml of intracellular β-galactosidase, respectively (1.72-fold increase). Further, the level of secreted nattokinase produced by strain LM2531 increased by 2.6-fold compared with wild-type (5226 IU/ml vs. 2028 IU/ml, respectively). Conclusions Our novel, systematic multigene deletion approach designed to inhibit cell lysis significantly increased the biomass yield and the production of recombinant proteins by B. subtilis. These findings show promise for guiding efforts to manipulate the genomes of other B. subtilis strains that are used for industrial purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0129-9) contains supplementary material, which is available to authorized users.
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