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Sadiq FA, Wenwei L, Wei C, Jianxin Z, Zhang H. Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms. MICROBIAL ECOLOGY 2022; 84:922-934. [PMID: 34676439 DOI: 10.1007/s00248-021-01904-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.
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Affiliation(s)
- Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Lu Wenwei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Chen Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Zhao Jianxin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
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2
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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3
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Yuan PB, Ling JH, Zhu JH, Peng C, Chen EZ, Zhong YX, Liu WT, Wang LJ, Yang L, Chen DQ. Proteomics profiling of ertapenem challenged major porin deficient carbapenem-resistant Klebsiella pneumoniae. J Proteomics 2022; 268:104715. [PMID: 36058541 DOI: 10.1016/j.jprot.2022.104715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 06/14/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent threat to human health. Major outer membrane proteins (OMPs) porin mutation is one important resistance mechanism of CRKP, and may also affect the inhibition activity of β-lactam and β-lactamase inhibitor combinations. The ertapenem-resistant K. pneumoniae strain 2018B120 with major porin mutations was isolated from a clinical patient. Genomic and time-series proteomic analyses were conducted to retrieve the ertapenem-challenged response of 2018B120. The abundance changing of proteins from PTS systems, ABC transporters, the autoinducer 2 (AI-2) quorum sensing system, and antioxidant systems can be observed. Overexpression of alternative porins was also noticed to balance major porins' defection. These findings added a detailed regulation network in bacterial resistance mechanisms and gave new insights into bypass adaptation mechanisms the porin deficient bacteria adopted under carbapenem antibiotics pressure. SIGNIFICANCE: Outer membrane porins deficiency is an important mechanism of carbapenem resistance in K. pneumoniae. Comprehensive genomic and proteomic profiling of an ertapenem-resistant K. pneumoniae strain 2018B120 gives a detailed systematic regulation network in bacterial resistance mechanisms. Overexpression of alternative porins to balance major porins' defection was noticed, giving new insights into bypass adaptation mechanisms of porin deficient bacteria.
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Affiliation(s)
- Pei-Bo Yuan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Hui Ling
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Hui Zhu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Peng
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - En-Zhong Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Xia Zhong
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wan-Ting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lin-Jing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ding-Qiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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4
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Sierra Cacho D, Zamorano Sánchez DS, Xiqui-Vázquez ML, Viruega Góngora VI, Ramírez-Mata A, Baca BE. CdgC, a Cyclic-di-GMP Diguanylate Cyclase of Azospirillum baldaniorum Is Involved in Internalization to Wheat Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:748393. [PMID: 34745182 PMCID: PMC8564387 DOI: 10.3389/fpls.2021.748393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Azospirillum baldaniorum is a plant growth-promoting rhizobacterium (PGPR) capable of fixing nitrogen, the synthesis of several phytohormones including indole-acetic acid, and induction of plant defenses against phytopathogens. To establish a successful and prolonged bacteria-plant interaction, A. baldaniorum can form biofilms, bacterial communities embedded in a self-made matrix formed by extracellular polymeric substances which provide favorable conditions for survival. A key modulator of biofilm formation is the second messenger bis-(3'-5')-cyclic-dimeric-GMP (c-di-GMP), which is synthesized by diguanylate cyclases (DGC) and degraded by specific phosphodiesterases. In this study, we analyzed the contribution of a previously uncharacterized diguanylate cyclase designated CdgC, to biofilm formation and bacterial-plant interaction dynamics. We showed that CdgC is capable of altering c-di-GMP levels in a heterologous host, strongly supporting its function as a DGC. The deletion of cdgC resulted in alterations in the three-dimensional structure of biofilms in a nitrogen-source dependent manner. CdgC was required for optimal colonization of wheat roots. Since we also observed that CdgC played an important role in exopolysaccharide production, we propose that this signaling protein activates a physiological response that results in the strong attachment of bacteria to the roots, ultimately contributing to an optimal bacterium-plant interaction. Our results demonstrate that the ubiquitous second messenger c-di-GMP is a key factor in promoting plant colonization by the PGPR A. baldaniorum by allowing proficient internalization in wheat roots. Understanding the molecular basis of PGPR-plant interactions will enable the design of better biotechnological strategies of agro-industrial interest.
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Affiliation(s)
- Daniel Sierra Cacho
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - David S. Zamorano Sánchez
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Maria Luisa Xiqui-Vázquez
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - Víctor Iván Viruega Góngora
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - Alberto Ramírez-Mata
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
| | - Beatriz E. Baca
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla, Mexico
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Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. Curr Genet 2021; 67:769-784. [PMID: 33837815 DOI: 10.1007/s00294-021-01184-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Here, the computational analysis of GDP-mannose 4,6-dehydratase (NoeL) proteins with great impact in modification of nod factor structure in four genomes of agriculturally important rhizobia (Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) presented. The NoeL number of amino acids was in the range of 147 (M5AMF5) to 372 (A0A023XWX0, Q89TZ1). The molecular weights were around 41 KDa. The results showed that the strain-specific purification strategy should apply as the pI of the sequences varied significantly (in the range of 5.59 to 9.12). The enzyme sequences and eight 3-dimensional structures predicted with homology modeling and machine learning representing the phylogenetic tree revealed the stability of enzymes in different conditions (Instability and Aliphatic index); however, this stability is also strain-specific. Disulphide bonds were observed in some species; however, the pattern was not detected in all members of the same species. Alpha helix was the dominant secondary structure predicted in all cytoplasmic NoeL. All models were homo-tetramer with acceptable sequence identity, GMEAN and coverage (60, - 1.80, 88, respectively). Additionally, Ramachandran maps showed that more than 94% of residues are in favored regions. We also highlight several key characterizations of NoeL from four rhizobia genomes annotation. These findings provide novel insights into the complexity and diversity of NoeL enzymes among important rhizobia and suggest considering a broader framework of biofilm for future research.
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6
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Herrera C, Moraga R, Bustamante B, Vilo C, Aguayo P, Valenzuela C, Smith CT, Yáñez J, Guzmán-Fierro V, Roeckel M, Campos VL. Characterization of Arsenite-Oxidizing Bacteria Isolated from Arsenic-Rich Sediments, Atacama Desert, Chile. Microorganisms 2021; 9:microorganisms9030483. [PMID: 33668956 PMCID: PMC7996500 DOI: 10.3390/microorganisms9030483] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/16/2022] Open
Abstract
Arsenic (As), a semimetal toxic for humans, is commonly associated with serious health problems. The most common form of massive and chronic exposure to As is through consumption of contaminated drinking water. This study aimed to isolate an As resistant bacterial strain to characterize its ability to oxidize As (III) when immobilized in an activated carbon batch bioreactor and to evaluate its potential to be used in biological treatments to remediate As contaminated waters. The diversity of bacterial communities from sediments of the As-rich Camarones River, Atacama Desert, Chile, was evaluated by Illumina sequencing. Dominant taxonomic groups (>1%) isolated were affiliated with Proteobacteria and Firmicutes. A high As-resistant bacterium was selected (Pseudomonas migulae VC-19 strain) and the presence of aio gene in it was investigated. Arsenite detoxification activity by this bacterial strain was determined by HPLC/HG/AAS. Particularly when immobilized on activated carbon, P. migulae VC-19 showed high rates of As(III) conversion (100% oxidized after 36 h of incubation). To the best of our knowledge, this is the first report of a P. migulae arsenite oxidizing strain that is promising for biotechnological application in the treatment of arsenic contaminated waters.
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Affiliation(s)
- Constanza Herrera
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Ruben Moraga
- Microbiology Laboratory, Faculty of Renewable Natural Resources, Arturo Prat University, Iquique 1100000, Chile
- Correspondence: (R.M.); (V.L.C.)
| | - Brian Bustamante
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Claudia Vilo
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Paulina Aguayo
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
- Faculty of Environmental Sciences, EULA-Chile, Universidad de Concepcion, Concepcion 4070386, Chile
- Institute of Natural Resources, Faculty of Veterinary Medicine and Agronomy, Universidad de Las Américas, Sede Concepcion, Campus El Boldal, Av. Alessandri N°1160, Concepcion 4090940, Chile
| | - Cristian Valenzuela
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Carlos T. Smith
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
| | - Jorge Yáñez
- Faculty of Chemical Sciences, Department of Analytical and Inorganic Chemistry, University of Concepción, Concepción 4070386, Chile;
| | - Victor Guzmán-Fierro
- Department of Chemical Engineering, Faculty of Engineering, University of Concepción, Concepcion 4070386, Chile; (V.G.-F.); (M.R.)
| | - Marlene Roeckel
- Department of Chemical Engineering, Faculty of Engineering, University of Concepción, Concepcion 4070386, Chile; (V.G.-F.); (M.R.)
| | - Víctor L. Campos
- Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; (C.H.); (B.B.); (C.V.); (P.A.); (C.V.); (C.T.S.)
- Correspondence: (R.M.); (V.L.C.)
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7
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Wang M, Liu Q, Kang X, Zhu Z, Yang H, Xi X, Zhang X, Du Y, Guo M, Tang D, Wang L. Glycogen Metabolism Impairment via Single Gene Mutation in the glgBXCAP Operon Alters the Survival Rate of Escherichia coli Under Various Environmental Stresses. Front Microbiol 2020; 11:588099. [PMID: 33101261 PMCID: PMC7546213 DOI: 10.3389/fmicb.2020.588099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Glycogen is a highly branched polysaccharide that is widely present in all life domains. It has been identified in many bacterial species and functions as an important energy storage compound. In addition, it plays important roles in bacterial transmission, pathogenicity, and environmental viability. There are five essential enzymes (coding genes) directly involved in bacterial glycogen metabolism, which forms a single operon glgBXCAP with a suboperonic promoter in glgC gene in Escherichia coli. Currently, there is no comparative study of how the disruptions of the five glycogen metabolism genes influence bacterial phenotypes, such as growth rate, biofilm formation, and environmental survival, etc. In this study, we systematically and comparatively studied five E. coli single-gene mutants (ΔglgC, ΔglgA, ΔglgB, ΔglgP, ΔglgX) in terms of glycogen metabolism and explored their phenotype changes with a focus on environmental stress endurance, such as nutrient deprivation, low temperature, desiccation, and oxidation, etc. Biofilm formation in wild-type and mutant strains was also compared. E. coli wild-type stores the highest glycogen content after around 20-h culture while disruption of degradation genes (glgP, glgX) leads to continuous accumulation of glycogen. However, glycogen primary structure was abnormally changed in ΔglgP and ΔglgX. Meanwhile, increased accumulation of glycogen facilitates the growth of E. coli mutants but reduces glucose consumption in liquid culture and vice versa. Glycogen metabolism disruption also significantly and consistently increases biofilm formation in all the mutants. As for environmental stress endurance, glycogen over-accumulating mutants have enhanced starvation viability and reduced desiccation viability while all mutants showed decreased survival rate at low temperature. No consistent results were found for oxidative stress resistance in terms of glycogen metabolism disruptions, though ΔglgA shows highest resistance toward oxidation with unknown mechanisms. In sum, single gene disruptions in glgBXCAP operon significantly influence bacterial growth and glucose consumption during culture. Accumulation and structure of intracellular glycogen were also significantly altered. In addition, we observed significant changes in E. coli environmental viabilities due to the deletions of certain genes in the operon. Further investigations shall be focused on the molecular mechanisms behind these phenotype changes.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Xingxing Kang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Sciences, Xuzhou Medical University, Xuzhou, China
| | - Huan Yang
- School of Laboratory Medicine, Xuzhou Medical University, Xuzhou, China
| | - Xiangyu Xi
- Xuzhou Infectious Disease Hospital, Xuzhou, China
| | - Xiao Zhang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Yan Du
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Liang Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
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8
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Marizcurrena JJ, Herrera LM, Costábile A, Morales D, Villadóniga C, Eizmendi A, Davyt D, Castro-Sowinski S. Validating biochemical features at the genome level in the Antarctic bacterium Hymenobacter sp. strain UV11. FEMS Microbiol Lett 2020; 366:5545592. [PMID: 31397847 DOI: 10.1093/femsle/fnz177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022] Open
Abstract
We present experimental data that complement and validate some biochemical features at the genome level in the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11 strain. The genome was sequenced, assembled and annotated. It has 6 096 246 bp, a GC content of 60.6% and 5155 predicted genes. The secretome analysis, by combining in silico predictions with shotgun proteomics data, showed that UV11 strain produces extracellular proteases and carbohydrases with potential biotechnological uses. We observed the formation of outer membrane vesicles, mesosomes and carbon-storage compounds by using transmission electron microscopy. The in silico analysis of the genome revealed the presence of genes involved in the metabolism of glycogen-like molecules and starch. By HPLC-UV-Vis analysis and 1H-NMR spectra, we verified that strain UV11 produces xanthophyll-like carotenoids such as 2'-hydroxyflexixanthin, and the in silico analysis showed that this bacterium has genes involved in the biosynthesis of cathaxanthin, zeaxanthin and astaxanthin. We also found genes involved in the repair of UV-damaged DNA such as a photolyase, the nucleotide excision repair system and the production of ATP-dependent proteases that are important cellular components involved in the endurance to physiological stresses. This information will help us to better understand the ecological role played by Hymenobacter strains in the extreme Antarctic environment.
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Affiliation(s)
- Juan José Marizcurrena
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Lorena M Herrera
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Alicia Costábile
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Danilo Morales
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Carolina Villadóniga
- Hydrolytic Enzymes Laboratory, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Agustina Eizmendi
- Organic Chemistry Department, Faculty of Chemistry, Universidad de la República, General Flores 2124, 11800 Montevideo, Uruguay
| | - Danilo Davyt
- Organic Chemistry Department, Faculty of Chemistry, Universidad de la República, General Flores 2124, 11800 Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay.,Hydrolytic Enzymes Laboratory, Faculty of Sciences, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
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9
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Park H, Do E, Kim M, Park HJ, Lee J, Han SW. A LysR-Type Transcriptional Regulator LcrX Is Involved in Virulence, Biofilm Formation, Swimming Motility, Siderophore Secretion, and Growth in Sugar Sources in Xanthomonas axonopodis Pv. glycines. FRONTIERS IN PLANT SCIENCE 2020; 10:1657. [PMID: 31998344 PMCID: PMC6965072 DOI: 10.3389/fpls.2019.01657] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/25/2019] [Indexed: 05/30/2023]
Abstract
Xanthomonas axonopodis pv. glycines (Xag) is a Gram-negative bacterium that causes bacterial pustule disease in soybean. To acclimate to new environments, the expression of genes in bacteria is controlled directly or indirectly by diverse transcriptional factors. Among them, LysR type transcriptional regulators are well-characterized and abundant in bacteria. In a previous study, comparative proteomic analysis revealed that LysR type carbohydrate-related transcriptional regulator in Xag (LcrX) was more abundant in XVM2, which is a minimal medium, compared with a rich medium. However, the functions of LcrX in Xag have not been characterized. In this study, we generated an LcrX-overexpressing strain, Xag(LcrX), and the knockout mutant strain, XagΔlcrX(EV), to elucidate the functions of LcrX. Bacterial multiplication of Xag(LcrX) in soybean was significantly impaired, indicating that LcrX is related to virulence. Comparative proteomic analysis revealed that LcrX is mainly involved in carbohydrate metabolism/transport and inorganic ion transport/metabolism. Based on the results of proteomics analysis, diverse phenotypic assays were carried out. A gel electrophoresis mobility shift assay demonstrated that LcrX specifically bound to the putative promoter regions of genes encoding putative fructose 1,6-bisphosphatase and protease. Through a 96-well plate assay under various conditions, we confirmed that the growth of Xag(LcrX) was dramatically affected in the presence of various carbon sources, while the growth of XagΔlcrX(EV) was only slightly changed. Biofilm formation activity was reduced in Xag(LcrX) but enhanced in XagΔlcrX(EV). The production of siderophores was also decreased in Xag(LcrX) but not altered in XagΔlcrX(EV). In contrast, LcrX was not associated with exopolysaccharide production, protease activity, or bacterial motility. These findings provide new insights into the functions of a carbohydrate-related transcriptional regulator in Xag.
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Affiliation(s)
- Hanbi Park
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Eunsoo Do
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Minyoung Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Hye-Jee Park
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jongchan Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Sang-Wook Han
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
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Wang L, Wang M, Wise MJ, Liu Q, Yang T, Zhu Z, Li C, Tan X, Tang D, Wang W. Recent progress in the structure of glycogen serving as a durable energy reserve in bacteria. World J Microbiol Biotechnol 2020; 36:14. [PMID: 31897771 DOI: 10.1007/s11274-019-2795-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022]
Abstract
Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, 6009, Australia
- Computer Science and Software Engineering, Faculty of Engineering and Mathematical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Ting Yang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Science, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Chengcheng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinle Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Wei Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
- The First Affiliated Hospital, Medical College of Shantou University, Shantou, 515041, Guangdong, China
- School of Public Health, Taishan Medical University, Tai'an, 271000, Shandong, China
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11
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Pujic P, Alloisio N, Fournier P, Roche D, Sghaier H, Miotello G, Armengaud J, Berry AM, Normand P. Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton. Environ Microbiol 2019; 21:3328-3345. [PMID: 30917411 DOI: 10.1111/1462-2920.14606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/13/2022]
Abstract
The early Frankia-Alnus symbiotic molecular exchanges were analyzed in detail by protein and RNA omics. For this, Frankia cells were placed in the presence of Alnus roots but separated by a dialysis membrane for 64 h. The bacterial cells were then harvested and analyzed by high-throughput proteomics and transcriptomics (RNA-seq). The most upregulated gene clusters were found to be the potassium transporter operon kdp and an ABC transporter operon of uncharacterized function. The most upregulated proteins were found to be acyl dehydrogenases and the potassium transporter Kdp. These suggest a preadaptation to the impending stresses linked to the penetration into isotonic host tissues and a possible rearrangement of the membrane. Another cluster among the 60 most upregulated ones that comprised two cellulases and a cellulose synthase was conserved among the Frankia and other actinobacteria such as Streptomyces. Cellulase activity was detected on CMC all along the length of the root but not away from it. Frankia alni ACN14a was found to be unable to respire or grow on glucose as sole carbon source. The cellulose synthase was found active at the tip of hyphae in response to Alnus root exudates, resulting in a calcofluor stained tip.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
| | - Nicole Alloisio
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
| | - David Roche
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Haitham Sghaier
- National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, Ariana, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
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12
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Luan G, Zhang S, Wang M, Lu X. Progress and perspective on cyanobacterial glycogen metabolism engineering. Biotechnol Adv 2019; 37:771-786. [DOI: 10.1016/j.biotechadv.2019.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/09/2019] [Accepted: 04/07/2019] [Indexed: 12/20/2022]
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13
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Velmourougane K, Prasanna R, Supriya P, Ramakrishnan B, Thapa S, Saxena AK. Transcriptome profiling provides insights into regulatory factors involved in Trichoderma viride-Azotobacter chroococcum biofilm formation. Microbiol Res 2019; 227:126292. [PMID: 31421719 DOI: 10.1016/j.micres.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 06/15/2019] [Indexed: 12/14/2022]
Abstract
Azotobacter chroococcum (Az) and Trichoderma viride (Tv) represent agriculturally important and beneficial plant growth promoting options which contribute towards nutrient management and biocontrol, respectively. When Az and Tv are co-cultured, they form a biofilm, which has proved promising as an inoculant in several crops; however, the basic aspects related to regulation of biofilm formation were not investigated. Therefore, whole transcriptome sequencing (Illumina NextSeq500) and gene expression analyses were undertaken, related to biofilm formation vis a vis Tv and Az growing individually. Significant changes in the transcriptome profiles of biofilm were recorded and validated through qPCR analyses. In-depth evaluation also identified several genes (phoA, phoB, glgP, alg8, sipW, purB, pssA, fadD) specifically involved in biofilm formation in Az, Tv and Tv-Az. Genes coding for RNA-dependent RNA polymerase, ABC transporters, translation elongation factor EF-1, molecular chaperones and double homeobox 4 were either up-regulated or down-regulated during biofilm formation. To our knowledge, this is the first report on the modulation of gene expression in an agriculturally beneficial association, as a biofilm. Our results provide insights into the regulatory factors involved during biofilm formation, which can help to improve the beneficial effects and develop more effective and promising plant- microbe associations.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Puram Supriya
- Centre for Agricultural Bioinformatics, ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Shobit Thapa
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kusmaur, PO Kaitholi, Mau Nath Bhanjan, Uttar Pradesh 275101, India
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14
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Polar flagellum of the alphaproteobacterium Azospirillum brasilense Sp245 plays a role in biofilm biomass accumulation and in biofilm maintenance under stationary and dynamic conditions. World J Microbiol Biotechnol 2019; 35:19. [PMID: 30656428 DOI: 10.1007/s11274-019-2594-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
Bacteria Azospirillum brasilense may swim and swarm owing to the rotation of a constitutive polar flagellum (Fla) and inducible lateral flagella (Laf). They also construct sessile biofilms on various interfaces. As compared to the wild-type strain Sp245, the previously characterized Fla- Laf- flhB1 mutant Sp245.1063 accumulated less biomass in mature biofilms, which also were susceptible to the forces of hydrodynamic shear. In this study, we compared biofilms formed by strain Sp245 and its previously constructed derivatives on the interfaces between a minimal (malate-salt medium, or MSM) or rich (LB) liquid growth medium and a hydrophilic (glass) or hydrophobic (polystyrene) solid surface under static or dynamic conditions. In all experimental settings, the alterations in Sp245.1063's mature biofilm traits were partially (in MSM) or completely (in LB) rescued in the complemented mutant Sp245.1063 (pRK415-150177), which received the pRK415-borne coding sequence for the putative FlhB1 protein of the flagellar type III secretion system. Although Laf were not found in the biofilms of azospirilla, Fla was present on the biofilm cells of the complemented mutant Sp245.1063 (pRK415-150177) and other studied strains, which had normal flagellation on liquid and solid nutritional media. Accordingly, mature biofilms of these strains contained more biomass and were significantly more resistant to shaking at 140 rpm, as compared to the biofilms of the flagella-free mutant bacteria. These data proved that the polar flagellum of A. brasilense Sp245 plays a significant positive role in biofilm biomass increase and in biofilm stabilization.
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15
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Wang L, Yan J, Wise MJ, Liu Q, Asenso J, Huang Y, Dai S, Liu Z, Du Y, Tang D. Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence. Front Microbiol 2018; 9:782. [PMID: 29755430 PMCID: PMC5932413 DOI: 10.3389/fmicb.2018.00782] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/06/2018] [Indexed: 12/15/2022] Open
Abstract
Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Yan
- Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Michael J Wise
- School of Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia.,The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - James Asenso
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yue Huang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Shiyun Dai
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | | | - Yan Du
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Center for Experimental Animals, Xuzhou Medical University, Xuzhou, China
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16
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Velmourougane K, Prasanna R, Singh SB, Kumar R, Saha S. Sequence of inoculation influences the nature of extracellular polymeric substances and biofilm formation in Azotobacter chroococcum and Trichoderma viride. FEMS Microbiol Ecol 2017; 93:3814244. [DOI: 10.1093/femsec/fix066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/10/2017] [Indexed: 11/13/2022] Open
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17
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Velmourougane K, Prasanna R, Saxena AK. Agriculturally important microbial biofilms: Present status and future prospects. J Basic Microbiol 2017; 57:548-573. [PMID: 28407275 DOI: 10.1002/jobm.201700046] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nath Bhanjan, Uttar Pradesh, India
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18
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Metabolic adaptations of Azospirillum brasilense to oxygen stress by cell-to-cell clumping and flocculation. Appl Environ Microbiol 2015; 81:8346-57. [PMID: 26407887 DOI: 10.1128/aem.02782-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/18/2015] [Indexed: 11/20/2022] Open
Abstract
The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists.
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Wang L, Regina A, Butardo VM, Kosar-Hashemi B, Larroque O, Kahler CM, Wise MJ. Influence of in situ progressive N-terminal is still controversial truncation of glycogen branching enzyme in Escherichia coli DH5α on glycogen structure, accumulation, and bacterial viability. BMC Microbiol 2015; 15:96. [PMID: 25947105 PMCID: PMC4433092 DOI: 10.1186/s12866-015-0421-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/01/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Glycogen average chain length (ACL) has been linked with bacterial durability, but this was on the basis of observations across different species. We therefore wished to investigate the relationship between bacterial durability and glycogen ACL by varying glycogen average chain length in a single species. It has been shown that progressive shortening of the N-terminus of glycogen branching enzyme (GBE) leads to a lengthening of oligosaccharide inter-α-1,6-glycosidic chain lengths, so we sought to harness this to create a set of Escherichia coli DH5α strains with a range of glycogen average chain lengths, and assess these strains for durability related attributes, such as starvation, cold and desiccation stress resistance, and biofilm formation. RESULTS A series of Escherichia coli DH5α mutants were created with glgB genes that were in situ progressively N-terminus truncated. N-terminal truncation shifted the distribution of glycogen chain lengths from 5-11 DP toward 13-50 DP, but the relationship between glgB length and glycogen ACL was not linear. Surprisingly, removal of the first 270 nucleotides of glgB (glgBΔ270) resulted in comparatively high glycogen accumulation, with the glycogen having short ACL. Complete knockout of glgB led to the formation of amylose-like glycogen containing long, linear α1,4-glucan chains with significantly reduced branching frequency. Physiologically, the set of mutant strains had reduced bacterial starvation resistance, while minimally increasing bacterial desiccation resistance. Finally, although there were no obvious changes in cold stress resistance or biofilm forming ability, one strain (glgBΔ180) had significantly increased biofilm formation in favourable media. CONCLUSIONS Despite glgB being the first gene of an operon, it is clear that in situ mutation is a viable means to create more biologically relevant mutant strains. Secondly, there was the suggestion in the data that impairments of starvation, cold and desiccation resistance were worse for the strain lacking glgB, though the first of these was not statistically significant. The results provide prima facie evidence linking abiotic stress tolerance with shorter glycogen ACL. However, further work needs to be done, perhaps in a less labile species. Further work is also required to tease out the complex relationship between glycogen abundance and glycogen structure.
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Affiliation(s)
- Liang Wang
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia.
| | - Ahmed Regina
- CSIRO Agriculture Flagship, Canberra, Australia.
| | - Vito M Butardo
- International Rice Research Institute, Los Baños, Philippines.
| | | | | | - Charlene M Kahler
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia.
| | - Michael J Wise
- School of Chemistry and Biochemistry, University of Western Australia, Perth, Australia.
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Valenzuela C, Moraga R, Leon C, Smith CT, Mondaca MA, Campos VL. Arsenite oxidation by Pseudomonas arsenicoxydans immobilized on zeolite and its potential biotechnological application. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 94:667-673. [PMID: 25673523 DOI: 10.1007/s00128-015-1495-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
Pseudomonas arsenicoxydans has been recently described as a new arsenite oxidizing bacterial species. Arsenite detoxification activity by this species was determined by HPLC/HG/AAS. P. arsenicoxydans showed a high rate of As(III) conversion, particularly when immobilized (it oxidizes 100 % of 500 μg arsenite present in the medium after 48 of incubation). Arsenite oxidizing activity, mediated by a constitutive periplasmic enzyme, was determined following the transfer of reducing equivalents from arsenite to 2,4-dichlorophenolindophenol (DCIP) showing that approximately 75 % (0.173 µmol DCIP min(-1) mg(-1)) of the total activity (0.231 µmol DCIP min(-1) mg(-1)) was detected in the periplasmic fraction. Using PCR with primers specific for arsenite oxidase gene showed the presence of a gene encoding for arsenite oxidase in P. arsenicoxydans. Results show the potential biotechnological application of P. arsenicoxydans as a candidate for detoxification of As(III).
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Affiliation(s)
- Cristian Valenzuela
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepcion, P.O. Box 160-C, Correo 3, Concepción, Chile
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21
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Choix FJ, Bashan Y, Mendoza A, de-Bashan LE. Enhanced activity of ADP glucose pyrophosphorylase and formation of starch induced by Azospirillum brasilense in Chlorella vulgaris. J Biotechnol 2014; 177:22-34. [DOI: 10.1016/j.jbiotec.2014.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 11/16/2022]
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22
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Fibach-Paldi S, Burdman S, Okon Y. Key physiological properties contributing to rhizosphere adaptation and plant growth promotion abilities of Azospirillum brasilense. FEMS Microbiol Lett 2011; 326:99-108. [DOI: 10.1111/j.1574-6968.2011.02407.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 08/30/2011] [Accepted: 09/03/2011] [Indexed: 12/29/2022] Open
Affiliation(s)
- Sharon Fibach-Paldi
- Department of Plant Pathology and Microbiology and The Otto Warburg Minerva Center for Agricultural Biotechnology; The Robert H. Smith Faculty of Agriculture, Food and Environment; The Hebrew University of Jerusalem; Rehovot; Israel
| | - Saul Burdman
- Department of Plant Pathology and Microbiology and The Otto Warburg Minerva Center for Agricultural Biotechnology; The Robert H. Smith Faculty of Agriculture, Food and Environment; The Hebrew University of Jerusalem; Rehovot; Israel
| | - Yaacov Okon
- Department of Plant Pathology and Microbiology and The Otto Warburg Minerva Center for Agricultural Biotechnology; The Robert H. Smith Faculty of Agriculture, Food and Environment; The Hebrew University of Jerusalem; Rehovot; Israel
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23
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Campos VL, León C, Mondaca MA, Yañez J, Zaror C. Arsenic mobilization by epilithic bacterial communities associated with volcanic rocks from Camarones River, Atacama Desert, northern Chile. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2011; 61:185-192. [PMID: 20859623 DOI: 10.1007/s00244-010-9601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 08/23/2010] [Indexed: 05/29/2023]
Abstract
The arsenic biogeochemical cycle is greatly dependent on microbial transformations that affect both the distribution and mobility of arsenic species in the environment. In this study, a microbial biofilm from volcanic rocks was characterized on the basis of its bacterial composition and ability to mobilize arsenic under circumneutral pH. Biofilm microstructure was analyzed by scanning electron microscopy (SEM)-energy-dispersive spectroscopy (EDS). Strains were isolated from biofilms and identified by 16S rDNA sequences analysis. Arsenic oxidation and reduction capacity was assayed with high-performance liquid chromatography coupled to gaseous formation performing the detection by atomic absortion in a quartz bucket (HPLC/HG/QAAS), and polymerase chain reaction was used to detect aox and ars genes. Bacterial communities associated with volcanic rocks were studied by denaturing gradient gel electrophoresis (DGGE). The SEM-EDS studies showed the presence of biofilm after 45 days of incubation. The relative closest GenBank matches of the DNA sequences, of isolated arsenic-resistant strains, showed the existence of four different genus: Burkholderia, Pseudomonas, Erwinia, and Pantoea. Four arsenite-resistant strains were isolates, and only three strains were able to oxidize >97% of the As(III) present (500 uM). All arsenate-resistant isolates were able to reduce between 69 and 86% of total As(V) (1000 uM). Analysis of 16S rDNA sequences obtained by DGGE showed the presence of four bacterial groups (∝-proteobacteria, γ-proteobacteria, Firmicutes, and Actinobacteria). Experiments demonstrate that epilithic bacterial communities play a key role in the mobilization of arsenic and metalloids speciation.
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Affiliation(s)
- V L Campos
- Microbiology Department, Biologic Science Faculty, University of Concepción, P.O. Box 160-C, Correo 3, Concepción, Chile.
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Sant'anna FH, Andrade DS, Trentini DB, Weber SS, Schrank IS. Tools for genetic manipulation of the plant growth-promoting bacterium Azospirillum amazonense. BMC Microbiol 2011; 11:107. [PMID: 21575234 PMCID: PMC3111374 DOI: 10.1186/1471-2180-11-107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/16/2011] [Indexed: 12/16/2022] Open
Abstract
Background Azospirillum amazonense has potential to be used as agricultural inoculant since it promotes plant growth without causing pollution, unlike industrial fertilizers. Owing to this fact, the study of this species has gained interest. However, a detailed understanding of its genetics and physiology is limited by the absence of appropriate genetic tools for the study of this species. Results Conjugation and electrotransformation methods were established utilizing vectors with broad host-replication origins (pVS1 and pBBR1). Two genes of interest - glnK and glnB, encoding PII regulatory proteins - were isolated. Furthermore, glnK-specific A. amazonense mutants were generated utilizing the pK19MOBSACB vector system. Finally, a promoter analysis protocol based on fluorescent protein expression was optimized to aid genetic regulation studies on this bacterium. Conclusion In this work, genetic tools that can support the study of A. amazonense were described. These methods could provide a better understanding of the genetic mechanisms of this species that underlie its plant growth promotion.
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Affiliation(s)
- Fernando H Sant'anna
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Campus do Vale, Porto Alegre, RS, Brazil
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Velázquez-Hernández ML, Baizabal-Aguirre VM, Cruz-Vázquez F, Trejo-Contreras MJ, Fuentes-Ramírez LE, Bravo-Patiño A, Cajero-Juárez M, Chávez-Moctezuma MP, Valdez-Alarcón JJ. Gluconacetobacter diazotrophicus levansucrase is involved in tolerance to NaCl, sucrose and desiccation, and in biofilm formation. Arch Microbiol 2010; 193:137-49. [PMID: 21103984 DOI: 10.1007/s00203-010-0651-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 10/07/2010] [Accepted: 10/29/2010] [Indexed: 11/24/2022]
Abstract
Gluconacetobacter diazotrophicus is a nitrogen-fixing bacterium and endophyte of sugarcane, which expresses levansucrase, a fructosyltransferase exoenzyme with sucrose hydrolytic and levan biosynthetic activities. As a result of their physical properties, the levan can provide protection against stress caused by abiotic or biotic factors and participate in the formation of biofilms. In this study, we investigated the construction and function of a levansucrase-defective mutant of G. diazotrophicus. The lsdA mutant showed a decreased tolerance (65.5%) to 50-150 mM NaCl and a decrease of 89% in 876 mM (30%) sucrose, a reduction (99%) in tolerance to desiccation after 18 h, and a decrease (36.9-58.5%) in the ability to form cell aggregates on abiotic surfaces. Complementation of the mutant with the complete lsdA gene leads to a recovery of the ability to grow on sucrose-containing medium and to form slimy colonies, the ability to form the cell aggregates on abiotic surfaces and the tolerance to NaCl. This report demonstrates the importance of levansucrase in environmental adaptation of G. diazotrophicus under high osmotic stress and in biofilm formation.
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Affiliation(s)
- M Lourdes Velázquez-Hernández
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Michoacán, México
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