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Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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2
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Adiandri RS, Purwadi R, Hoerudin H, Setiadi T. Evaluation of Biosurfactant Production by Bacillus Species Using Glucose and Xylose as Carbon Sources. Curr Microbiol 2023; 80:250. [PMID: 37347358 DOI: 10.1007/s00284-023-03345-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Lignocellulosic material is one of the raw materials that can be used to reduce the cost of biosurfactant production because it is cheap, abundantly available, and contains cellulose and hemicellulose which can be hydrolyzed to glucose and xylose as carbon sources. This study aimed to evaluate biosurfactant production by Bacillus species using glucose and xylose as carbon sources, which are the most abundant sugar monomers from the hydrolysis of lignocellulosic materials. In this study, biosurfactants were produced by six bacterial isolates belonging to the Bacillus genus. The six bacterial isolates were identified molecularly through 16S rRNA sequencing. The results showed that the six bacterial isolates were identified as B. subtilis ITBCC46, B. subtilis ITBCC40, B. subtilis ITBCC31, B. siamensis ITBCC36, B. xiamenensis ITBCC43, and B. subtilis ITBCC30. All Bacillus species used in this study could be grown on glucose or xylose media. Biosurfactants produced by B. subtilis ITBCC46, B. subtilis ITBCC40, B. subtilis ITBCC31, and B. siamensis ITBCC36 could reduce surface tension below 40 mN/m (32.70 to 39.15 mN/m). All biosurfactants produced by these Bacillus species had more than 50% emulsification stability. These characteristics indicated that the biosurfactants had the desired quality.
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Affiliation(s)
- Resa Setia Adiandri
- Department of Chemical Engineering, Faculty of Industrial Technology, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung, West Java, 40132, Indonesia
- Indonesian Center for Agricultural Postharvest Research and Development, Indonesian Agency for Agricultural Research and Development, Bogor, 16124, Indonesia
| | - Ronny Purwadi
- Department of Chemical Engineering, Faculty of Industrial Technology, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung, West Java, 40132, Indonesia
- Food Engineering Department, Institut Teknologi Bandung, Jatinangor Campus, Sumedang, 45363, Indonesia
| | - Hoerudin Hoerudin
- Indonesian Center for Agricultural Postharvest Research and Development, Indonesian Agency for Agricultural Research and Development, Bogor, 16124, Indonesia
| | - Tjandra Setiadi
- Department of Chemical Engineering, Faculty of Industrial Technology, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung, West Java, 40132, Indonesia.
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Zhang YW, Shi YC, Zhang SB. Metabolic and transcriptomic analyses elucidate a novel insight into the network for biosynthesis of carbohydrate and secondary metabolites in the stems of a medicinal orchid Dendrobium nobile. PLANT DIVERSITY 2023; 45:326-336. [PMID: 37397599 PMCID: PMC10311107 DOI: 10.1016/j.pld.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/17/2022] [Accepted: 10/19/2022] [Indexed: 07/04/2023]
Abstract
Dendrobium nobile is an important medicinal and nutraceutical herb. Although the ingredients of D. nobile have been identified as polysaccharides, alkaloids, amino acids, flavonoids and bibenzyls, our understanding of the metabolic pathways that regulate the synthesis of these compounds is limited. Here, we used transcriptomic and metabolic analyses to elucidate the genes and metabolites involved in the biosynthesis of carbohydrate and several secondary metabolites in the stems of D. nobile. A total of 1005 metabolites and 31,745 genes were detected in the stems of D. nobile. The majority of these metabolites and genes were involved in the metabolism of carbohydrates (fructose, mannose, glucose, xylulose and starch), while some were involved in the metabolism of secondary metabolites (alkaloids, β-tyrosine, ferulic acid, 4-hydroxybenzoate and chrysin). Our predicted regulatory network indicated that five genes (AROG, PYK, DXS, ACEE and HMGCR) might play vital roles in the transition from carbohydrate to alkaloid synthesis. Correlation analysis identified that six genes (ALDO, PMM, BGLX, EGLC, XYLB and GLGA) were involved in carbohydrate metabolism, and two genes (ADT and CYP73A) were involved in secondary metabolite biosynthesis. Our analyses also indicated that phosphoenol-pyruvate (PEP) was a crucial bridge that connected carbohydrate to alkaloid biosynthesis. The regulatory network between carbohydrate and secondary metabolite biosynthesis established will provide important insights into the regulation of metabolites and biological systems in Dendrobium species.
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Affiliation(s)
- Yu-Wen Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Cen Shi
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Bao Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China
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Han L, Zhang H, Bai X, Jiang B. The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10. BMC Microbiol 2023; 23:85. [PMID: 36991332 PMCID: PMC10061817 DOI: 10.1186/s12866-023-02818-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Burkholderia pyrrocinia strain P10 is a plant growth-promoting rhizobacterium (PGPR) that can substantially increase peanut growth. However, the mechanisms and pathways involved in the interaction between B. pyrrocinia P10 and peanut remain unclear. To clarify complex plant-PGPR interactions and the growth-promoting effects of PGPR strains, the B. pyrrocinia P10 transcriptome changes in response to the peanut root exudate (RE) were elucidated and the effects of RE components on biofilm formation and indole-3-acetic acid (IAA) secretion were analyzed. RESULTS During the early interaction phase, the peanut RE enhanced the transport and metabolism of nutrients, including carbohydrates, amino acids, nitrogen, and sulfur. Although the expression of flagellar assembly-related genes was down-regulated, the expression levels of other genes involved in biofilm formation, quorum sensing, and Type II, III, and VI secretion systems were up-regulated, thereby enabling strain P10 to outcompete other microbes to colonize the peanut rhizosphere. The peanut RE also improved the plant growth-promoting effects of strain P10 by activating the expression of genes associated with siderophore biosynthesis, IAA production, and phosphorus solubilization. Additionally, organic acids and amino acids were identified as the dominant components in the peanut RE. Furthermore, strain P10 biofilm formation was induced by malic acid, oxalic acid, and citric acid, whereas IAA secretion was promoted by the alanine, glycine, and proline in the peanut RE. CONCLUSION The peanut RE positively affects B. pyrrocinia P10 growth, while also enhancing colonization and growth-promoting effects during the early interaction period. These findings may help to elucidate the mechanisms underlying complex plant-PGPR interactions, with potential implications for improving the applicability of PGPR strains.
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Affiliation(s)
- Lizhen Han
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China.
| | - Hong Zhang
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Xue Bai
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Biao Jiang
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
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Xu F, Liu S, Naren N, Li L, Ma LZ, Zhang X. Experimental evolution of bacterial survival on metallic copper. Ecol Evol 2022. [DOI: 10.1002/ece3.9225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Feng Xu
- School of Natural Sciences Massey University Auckland New Zealand
| | - Sha Liu
- School of Natural Sciences Massey University Auckland New Zealand
| | - Naran Naren
- School of Natural Sciences Massey University Auckland New Zealand
| | - Lily Li
- School of Natural Sciences Massey University Auckland New Zealand
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Xue‐Xian Zhang
- School of Natural Sciences Massey University Auckland New Zealand
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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Sathesh-Prabu C, Tiwari R, Kim D, Lee SK. Inducible and tunable gene expression systems for Pseudomonas putida KT2440. Sci Rep 2021; 11:18079. [PMID: 34508142 PMCID: PMC8433446 DOI: 10.1038/s41598-021-97550-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
Inducible and tunable expression systems are essential for the microbial production of biochemicals. Five different carbon source- and substrate-inducible promoter systems were developed and further evaluated in Pseudomonas putida KT2440 by analyzing the expression of green fluorescent protein (GFP) as a reporter protein. These systems can be induced by low-cost compounds such as glucose, 3-hydroxypropionic acid (3HP), levulinic acid (LA), and xylose. 3HP-inducible HpdR/PhpdH was also efficiently induced by LA. LvaR/PlvaA and XutR/PxutA systems were induced even at low concentrations of LA (0.1 mM) and xylose (0.5 mM), respectively. Glucose-inducible HexR/Pzwf1 showed weak GFP expression. These inducer agents can be used as potent starting materials for both cell growth and the production of a wide range of biochemicals. The efficiency of the reported systems was comparable to that of conventional chemical-inducible systems. Hence, the newly investigated promoter systems are highly useful for the expression of target genes in the widely used synthetic biology chassis P. putida KT2440 for industrial and medical applications.
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Affiliation(s)
- Chandran Sathesh-Prabu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Rameshwar Tiwari
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Doyun Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Energy Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
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Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, Elbourne LDH, LeTourneau MK, Gang DR, Paulsen IT, Weller DM, Thomashow LS, Flynt AS, Mavrodi DV. Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. Front Microbiol 2021; 12:651282. [PMID: 33936009 PMCID: PMC8079746 DOI: 10.3389/fmicb.2021.651282] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.
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Affiliation(s)
- Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Janiece R McWilliams
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jacob O Peter
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karl A Hassan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Melissa K LeTourneau
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Alex S Flynt
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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Xylose-Inducible Promoter Tools for Pseudomonas Species and Their Use in Implicating a Role for the Type II Secretion System Protein XcpQ in the Inhibition of Corneal Epithelial Wound Closure. Appl Environ Microbiol 2020; 86:AEM.00250-20. [PMID: 32414795 DOI: 10.1128/aem.00250-20] [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] [Received: 01/31/2020] [Accepted: 05/08/2020] [Indexed: 12/17/2022] Open
Abstract
Tunable control of gene expression is an invaluable tool for biological experiments. In this study, we describe a new xylose-inducible promoter system and evaluate it in both Pseudomonas aeruginosa and Pseudomonas fluorescens The Pxut promoter, derived from the P. fluorescens xut operon, was incorporated into a broad-host-range pBBR1-based plasmid and was compared to the Escherichia coli-derived PBAD promoter using gfp as a reporter. Green fluorescent protein (GFP) fluorescence from the Pxut promoter was inducible in both Pseudomonas species, but not in E. coli, which may facilitate the cloning of genes toxic to E. coli to generate plasmids. The Pxut promoter was activated at a lower inducer concentration than PBAD in P. fluorescens, and higher gfp levels were achieved using Pxut Flow cytometry analysis indicated that Pxut was leakier than PBAD in the Pseudomonas species tested but was expressed in a higher proportion of cells when induced. d-Xylose as a sole carbon source did not support the growth of P. aeruginosa or P. fluorescens and is less expensive than many other commonly used inducers, which could facilitate large-scale applications. The efficacy of this system was demonstrated by its use to reveal a role for the P. aeruginosa type II secretion system gene xcpQ in bacterial inhibition of corneal epithelial cell wound closure. This study introduces a new inducible promoter system for gene expression for use in Pseudomonas species.IMPORTANCE Pseudomonas species are enormously important in human infections, in biotechnology, and as model systems for investigating basic science questions. In this study, we have developed a xylose-inducible promoter system, evaluated it in P. aeruginosa and P. fluorescens, and found it to be suitable for the strong induction of gene expression. Furthermore, we have demonstrated its efficacy in controlled gene expression to show that a type II secretion system protein from P. aeruginosa, XcpQ, is important for host-pathogen interactions in a corneal wound closure model.
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Zhang X, Ritchie SR, Chang H, Arnold DL, Jackson RW, Rainey PB. Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecol Evol 2020; 10:5963-5975. [PMID: 32607204 PMCID: PMC7319117 DOI: 10.1002/ece3.6334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023] Open
Abstract
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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Affiliation(s)
- Xue‐Xian Zhang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Stephen R. Ritchie
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Faculty of Medical and Health SciencesUniversity of AucklandAucklandNew Zealand
| | - Hao Chang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Dawn L. Arnold
- Centre for Research in BioscienceUniversity of the West of EnglandBristolUK
| | - Robert W. Jackson
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI)UMR8231ESPCI ParisCNRSPSL Research UniversityParisFrance
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11
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Liu Y, Shang L, Zhan Y, Lin M, Liu Z, Yan Y. Genome-Wide Analysis of Sugar Transporters Identifies the gtsA Gene for Glucose Transportation in Pseudomonas stutzeri A1501. Microorganisms 2020; 8:microorganisms8040592. [PMID: 32325908 PMCID: PMC7232493 DOI: 10.3390/microorganisms8040592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas stutzeri A1501 possesses an extraordinary number of transporters which confer this rhizosphere bacterium with the sophisticated ability to metabolize various carbon sources. However, sugars are not a preferred carbon source for P. stutzeri A1501. The P. stutzeri A1501 genome has been sequenced, allowing for the homology-based in silico identification of genes potentially encoding sugar-transport systems by using established microbial sugar transporters as a template sequence. Genomic analysis revealed that there were 10 sugar transporters in P. stutzeri A1501, most of which belong to the ATP-binding cassette (ABC) family (5/10); the others belong to the phosphotransferase system (PTS), major intrinsic protein (MIP) family, major facilitator superfamily (MFS) and the sodium solute superfamily (SSS). These systems might serve for the import of glucose, galactose, fructose and other types of sugar. Growth analysis showed that the only effective medium was glucose and its corresponding metabolic system was relatively complete. Notably, the loci of glucose metabolism regulatory systems HexR, GltR/GtrS, and GntR were adjacent to the transporters ABCMalEFGK, ABCGtsABCD, and ABCMtlEFGK, respectively. Only the ABCGtsABCD expression was significantly upregulated under both glucose-sufficient and -limited conditions. The predicted structure and mutant phenotype data of the key protein GtsA provided biochemical evidence that P. stutzeri A1501 predominantly utilized the ABCGtsABCD transporter for glucose uptake. We speculate that gene absence and gene diversity in P. stutzeri A1501 was caused by sugar-deficient environmental factors and hope that this report can provide guidance for further analysis of similar bacterial lifestyles.
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Affiliation(s)
- Yaqun Liu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570100, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Liguo Shang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Zhu Liu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570100, China;
- Correspondence: (Z.L.); (Y.Y.)
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
- Correspondence: (Z.L.); (Y.Y.)
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12
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Improving glucose and xylose assimilation in Azotobacter vinelandii by adaptive laboratory evolution. World J Microbiol Biotechnol 2020; 36:46. [DOI: 10.1007/s11274-020-02822-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 11/25/2022]
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13
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Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1. Sci Rep 2020; 10:3787. [PMID: 32123183 PMCID: PMC7051946 DOI: 10.1038/s41598-020-59731-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
Transcription is of the most crucial steps of gene expression in bacteria, whose regulation guarantees the bacteria's ability to adapt to varying environmental conditions. Discovering the molecular basis and genomic principles of the transcriptional regulation is thus one of the most important tasks in cellular and molecular biology. Here, a comprehensive phylogenetic footprinting framework was implemented to predict maximal regulons of Lactococcus lactis subsp. lactis IO-1, a lactic acid bacterium known for its high potentials in nisin Z production as well as efficient xylose consumption which have made it a promising biotechnological strain. A total set of 321 regulons covering more than 90% of all the bacterium's operons have been elucidated and validated according to available data. Multiple novel biologically-relevant members were introduced amongst which arsC, mtlA and mtl operon for BusR, MtlR and XylR regulons can be named, respectively. Moreover, the effect of riboflavin on nisin biosynthesis was assessed in vitro and a negative correlation was observed. It is believed that understandings from such networks not only can be useful for studying transcriptional regulatory potentials of the target organism but also can be implemented in biotechnology to rationally design favorable production conditions.
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14
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Lopes LD, Pereira E Silva MDC, Weisberg AJ, Davis EW, Yan Q, Varize CDS, Wu CF, Chang JH, Loper JE, Andreote FD. Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population. Environ Microbiol 2018; 20:4401-4414. [PMID: 30033663 DOI: 10.1111/1462-2920.14363] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 11/28/2022]
Abstract
Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.
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Affiliation(s)
- Lucas Dantas Lopes
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Michele de C Pereira E Silva
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, 97331, USA
| | - Qing Yan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Camila de S Varize
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Chih-Feng Wu
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, 97331, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, 97331, USA
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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15
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Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metab Eng 2018; 48:94-108. [DOI: 10.1016/j.ymben.2018.05.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 01/02/2023]
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16
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Liu Y, Gokhale CS, Rainey PB, Zhang XX. Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25. Mol Microbiol 2017; 105:589-605. [PMID: 28557013 DOI: 10.1111/mmi.13720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
Abstract
The two-component system CbrAB is the principal regulator for cellular metabolic balance in Pseudomonas fluorescens SBW25 and is necessary for growth on many substrates including xylose. To understand the regulatory linkage between CbrAB and genes for xylose utilization (xut), we performed transposon mutagenesis of ΔcbrB to select for Xut+ suppressors. This led to identification of crc and hfq. Subsequent genetic and biochemical analysis showed that Crc and Hfq are key mediators of succinate-provoked carbon catabolite repression (CCR). Specifically, Crc/Hfq sequentially bind to mRNAs of both the transcriptional activator and structural genes involved in xylose catabolism. However, in the absence of succinate, repression is relieved through competitive binding by two ncRNAs, CrcY and CrcZ, whose expression is activated by CbrAB. These findings provoke a model for CCR in which it is assumed that crc and hfq are functionally complementary, whereas crcY and crcZ are genetically redundant. Inactivation of either crcY or crcZ produced no effects on bacterial fitness in laboratory media, however, results of mathematical modelling predict that the co-existence of crcY and crcZ requires separate functional identity. Finally, we provide empirical evidence that CCR is advantageous in nutrient-complex environments where preferred carbon sources are present at high concentrations but fluctuate in their availability.
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Affiliation(s)
- Yunhao Liu
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand.,New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, 75231 Paris Cedex 05, France
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand
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17
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Liu S, Zhang XX. Small colony variants are more susceptible to copper-mediated contact killing for Pseudomonas aeruginosa and Staphylococcus aureus. J Med Microbiol 2016; 65:1143-1151. [DOI: 10.1099/jmm.0.000348] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sha Liu
- Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand
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