1
|
Trakarnpaiboon S, Bunterngsook B, Wansuksriand R, Champreda V. Screening, Cloning, Expression and Characterization of New Alkaline Trehalose Synthase from Pseudomonas monteilii and Its Application for Trehalose Production. J Microbiol Biotechnol 2021; 31:1455-1464. [PMID: 34409951 PMCID: PMC9705850 DOI: 10.4014/jmb.2106.06032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
Trehalose is a non-reducing disaccharide in increasing demand for applications in food, nutraceutical, and pharmaceutical industries. Single-step trehalose production by trehalose synthase (TreS) using maltose as a starting material is a promising alternative process for industrial application due to its simplicity and cost advantage. Pseudomonas monteilii TBRC 1196 was identified using the developed screening method as a potent strain for TreS production. The TreS gene from P. monteilii TBRC 1196 was first cloned and expressed in Escherichia coli. Purified recombinant trehalose synthase (PmTreS) had a molecular weight of 76 kDa and showed optimal pH and temperature at 9.0 and 40°C, respectively. The enzyme exhibited >90% residual activity under mesophilic condition under a broad pH range of 7-10 for 6 h. Maximum trehalose yield by PmTreS was 68.1% with low yield of glucose (4%) as a byproduct under optimal conditions, equivalent to productivity of 4.5 g/l/h using enzyme loading of 2 mg/g substrate and high concentration maltose solution (100 g/l) in a lab-scale bioreactor. The enzyme represents a potent biocatalyst for energy-saving trehalose production with potential for inhibiting microbial contamination by alkaline condition.
Collapse
Affiliation(s)
- Srisakul Trakarnpaiboon
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin RD., Klong Luang District, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin RD., Klong Luang District, Pathumthani 12120, Thailand
| | - Rungtiva Wansuksriand
- Cassava and Starch Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, Bangkok 10900, Thailand
| | - Verawat Champreda
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin RD., Klong Luang District, Pathumthani 12120, Thailand,Corresponding author Phone: +66 2564 6700 x 3446 Fax: +66 2564 6707 E-mail:
| |
Collapse
|
2
|
|
3
|
Keshavarz-Tohid V, Vacheron J, Dubost A, Prigent-Combaret C, Taheri P, Tarighi S, Taghavi SM, Moënne-Loccoz Y, Muller D. Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov. Syst Appl Microbiol 2019; 42:468-480. [DOI: 10.1016/j.syapm.2019.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/21/2022]
|
4
|
Chunduru J, West TP. Pyrimidine nucleotide synthesis in the emerging pathogen Pseudomonas monteilii. Can J Microbiol 2018; 64:432-438. [PMID: 29486129 DOI: 10.1139/cjm-2018-0015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Regulation of pyrimidine biosynthesis by pyrimidines in the emerging, opportunistic human pathogen Pseudomonas monteilii ATCC 700476 was evident. When wild-type cells were grown on succinate in the presence of uracil or orotic acid, the activities of all 5 pyrimidine biosynthetic enzymes were depressed while the activities of 3 of the enzymes decreased in glucose-grown cells supplemented with uracil or orotic acid compared with unsupplemented cells. Pyrimidine limitation of succinate- or glucose-grown pyrimidine auxotrophic cells lacking orotate phosphoribosyltransferase activity resulted in more than a doubling of the pyrimidine biosynthetic enzyme activities relative to their activities in uracil-grown cells. Independent of carbon source, pyrimidine-limited cells of the pyrimidine auxotrophic cells deficient for dihydroorotase activity generally resulted in a slight elevation or depression of the pyrimidine biosynthetic enzyme activities compared with their activities in cells grown under saturating uracil conditions. Aspartate transcarbamoylase activity in P. monteilii was regulated at the enzyme activity level, since the enzyme was strongly inhibited by CTP, UMP, GMP, GDP, ADP, and UTP. In summary, the regulation of pyrimidine biosynthesis in P. monteilii could be used to control its growth or to differentiate it biochemically from other related species of Pseudomonas.
Collapse
Affiliation(s)
- Jayendra Chunduru
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX 75429, USA.,Department of Chemistry, Texas A&M University-Commerce, Commerce, TX 75429, USA
| | - Thomas P West
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX 75429, USA.,Department of Chemistry, Texas A&M University-Commerce, Commerce, TX 75429, USA
| |
Collapse
|
5
|
Lopes LD, Davis EW, Pereira E Silva MDC, Weisberg AJ, Bresciani L, Chang JH, Loper JE, Andreote FD. Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity. Environ Microbiol 2017; 20:62-74. [PMID: 29027341 DOI: 10.1111/1462-2920.13957] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/07/2017] [Accepted: 10/08/2017] [Indexed: 11/30/2022]
Abstract
Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P. jessenii subgroup. The remaining 18 isolates fell into two phylogenetic subclades distinct from currently recognized P. fluorescens subgroups, and probably represent new subgroups. Consistent with their phylogenetic distance from described subgroups, the genome sequences of strains in these subclades are asyntenous to the genome sequences of members of their neighbour subgroups. The tropical isolates have several functional genes also present in known fluorescent Pseudomonas spp. strains. However, members of the new subclades share exclusive genes not detected in other subgroups, pointing to the potential for novel functions. Additionally, we identified 12 potential new species among the 76 isolates from the tropical soil. The unexplored diversity found in the tropical soil is possibly related to biogeographical patterns.
Collapse
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
| | - 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
| | - 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
| | - Luana Bresciani
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - 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
| |
Collapse
|
6
|
Yonezuka K, Shimodaira J, Tabata M, Ohji S, Hosoyama A, Kasai D, Yamazoe A, Fujita N, Ezaki T, Fukuda M. Phylogenetic analysis reveals the taxonomically diverse distribution of the Pseudomonas putida group. J GEN APPL MICROBIOL 2017; 63:1-10. [DOI: 10.2323/jgam.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kenta Yonezuka
- Department of Bioengineering, Nagaoka University of Technology
| | - Jun Shimodaira
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Michiro Tabata
- Department of Bioengineering, Nagaoka University of Technology
| | - Shoko Ohji
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Akira Hosoyama
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Nobuyuki Fujita
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Takayuki Ezaki
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology
| |
Collapse
|
7
|
Alcaraz LD, Martínez-Sánchez S, Torres I, Ibarra-Laclette E, Herrera-Estrella L. The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant. PLoS One 2016; 11:e0148979. [PMID: 26859489 PMCID: PMC4747601 DOI: 10.1371/journal.pone.0148979] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/26/2016] [Indexed: 02/01/2023] Open
Abstract
The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant.
Collapse
Affiliation(s)
- Luis David Alcaraz
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70–275, 04510, Ciudad Universitaria, Ciudad de México, México
| | - Shamayim Martínez-Sánchez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70–275, 04510, Ciudad Universitaria, Ciudad de México, México
| | - Ignacio Torres
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, 58190, Morelia, Michoacán, México
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C, 91070, Carretera antigua a Coatepec 351, El Haya Xalapa, Veracruz, México
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Km 9.6 Carretera Irapuato-León, 36821, Irapuato, Guanajuato, México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Km 9.6 Carretera Irapuato-León, 36821, Irapuato, Guanajuato, México
| |
Collapse
|
8
|
Dueholm MS, Marques IG, Karst SM, D'Imperio S, Tale VP, Lewis D, Nielsen PH, Nielsen JL. Survival and activity of individual bioaugmentation strains. BIORESOURCE TECHNOLOGY 2015; 186:192-199. [PMID: 25817029 DOI: 10.1016/j.biortech.2015.02.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/25/2015] [Accepted: 02/27/2015] [Indexed: 06/04/2023]
Abstract
Successful application of bioaugmentation for enhanced degradation of environmental pollutants is often limited by the lack of methods to monitor the survival and activity of individual bioaugmentation strains. However, recent advancements in sequencing technologies and molecular techniques now allow us to address these limitations. Here a complementing set of general applicable molecular methods are presented that provides detailed information on the performance of individual bioaugmentation strains under in situ conditions. The approach involves genome sequencing to establish highly specific qPCR and RT-qPCR tools for cell enumerations and expression of involved genes, stable isotope probing to follow growth on the target compounds and GFP-tagging to visualize the bioaugmentation strains directly in samples, all in combination with removal studies of the target compounds. The concept of the approach is demonstrated through a case study involving degradation of aromatic hydrocarbons in activated sludge augmented with the bioaugmentation strain Pseudomonas monteilii SB3078.
Collapse
Affiliation(s)
- Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Irina G Marques
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Seth D'Imperio
- Novozymes Biologicals, Inc., 5400 Corporate Circle, Salem, VA 24153, United States
| | - Vaibhav P Tale
- Novozymes Biologicals, Inc., 5400 Corporate Circle, Salem, VA 24153, United States
| | - Derrick Lewis
- Novozymes Biologicals, Inc., 5400 Corporate Circle, Salem, VA 24153, United States
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark.
| |
Collapse
|
9
|
Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2. GENOME ANNOUNCEMENTS 2014; 2:2/5/e01049-14. [PMID: 25323719 PMCID: PMC4200157 DOI: 10.1128/genomea.01049-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Pseudomonas bauzanensis W13Z2 is a halotolerant polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from petroleum-contaminated drill cuttings in the Bohai Sea. Here, we report the 8.6-Mb draft genome sequence of this strain, which will provide insights into the diversity of Pseudomonas and the mechanism of PAHs degradation in drill cuttings.
Collapse
|