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Burkhardt C, Baruth L, Neele Meyer-Heydecke, Klippel B, Margaryan A, Paloyan A, Panosyan HH, Antranikian G. Mining thermophiles for biotechnologically relevant enzymes: evaluating the potential of European and Caucasian hot springs. Extremophiles 2023; 28:5. [PMID: 37991546 PMCID: PMC10665251 DOI: 10.1007/s00792-023-01321-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023]
Abstract
The development of sustainable and environmentally friendly industrial processes is becoming very crucial and demanding for the rapid implementation of innovative bio-based technologies. Natural extreme environments harbor the potential for discovering and utilizing highly specific and efficient biocatalysts that are adapted to harsh conditions. This review focuses on extremophilic microorganisms and their enzymes (extremozymes) from various hot springs, shallow marine vents, and other geothermal habitats in Europe and the Caucasus region. These hot environments have been partially investigated and analyzed for microbial diversity and enzymology. Hotspots like Iceland, Italy, and the Azores harbor unique microorganisms, including bacteria and archaea. The latest results demonstrate a great potential for the discovery of new microbial species and unique enzymes that can be explored for the development of Circular Bioeconomy.Different screening approaches have been used to discover enzymes that are active at extremes of temperature (up 120 °C), pH (0.1 to 11), high salt concentration (up to 30%) as well as activity in the presence of solvents (up to 99%). The majority of published enzymes were revealed from bacterial or archaeal isolates by traditional activity-based screening techniques. However, the latest developments in molecular biology, bioinformatics, and genomics have revolutionized life science technologies. Post-genomic era has contributed to the discovery of millions of sequences coding for a huge number of biocatalysts. Both strategies, activity- and sequence-based screening approaches, are complementary and contribute to the discovery of unique enzymes that have not been extensively utilized so far.
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Affiliation(s)
- Christin Burkhardt
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Leon Baruth
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Neele Meyer-Heydecke
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Barbara Klippel
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Armine Margaryan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Ani Paloyan
- Scientific and Production Center, "Armbiotechnology" NAS RA, 14 Gyurjyan Str. 0056, Yerevan, Armenia
| | - Hovik H Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Garabed Antranikian
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany.
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Mukti IJ, Sardari RRR, Kristjansdottir T, Hreggvidsson GO, Karlsson EN. Medium development and production of carotenoids and exopolysaccharides by the extremophile Rhodothermus marinus DSM16675 in glucose-based defined media. Microb Cell Fact 2022; 21:220. [PMID: 36274123 PMCID: PMC9590192 DOI: 10.1186/s12934-022-01946-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The marine thermophilic bacterium Rhodothermus marinus can degrade many polysaccharides which makes it interesting as a future cell factory. Progress using this bacterium has, however, been hampered by limited knowledge on media and conditions for biomass production, often resulting in low cell yields and low productivity, highlighting the need to develop conditions that allow studies of the microbe on molecular level. This study presents development of defined conditions that support growth, combined with evaluation of production of carotenoids and exopolysaccharides (EPSs) by R. marinus strain DSM 16675. RESULTS Two defined media were initially prepared: one including a low addition of yeast extract (modified Wolfe's medium) and one based on specific components (defined medium base, DMB) to which two amino acids (N and Q), were added. Cultivation trials of R. marinus DSM 16675 in shake flasks, resulted in maximum cell densities (OD620 nm) of 2.36 ± 0.057, cell dry weight (CDW) 1.2 ± 0.14 mg/L, total carotenoids 0.59 × 10-3 mg/L, and EPSs 1.72 ± 0.03 mg/L using 2 g/L glucose in DMB. In Wolfe's medium (supplemented by 0.05 g/L yeast extract and 2.5 g/L glucose), maximum OD620 nm was 2.07 ± 0.05, CDW 1.05 ± 0.07 mg/L, total carotenoids 0.39 × 10-3 mg/L, and EPSs 1.74 ± 0.2 mg/L. Growth trials at 5 g/L glucose in these media either failed or resulted in incomplete substrate utilization. To improve reproducibility and increase substrate utilization, a screening of macroelements (e.g. phosphate) in DMB, was combined with use of trace elements and vitamins of the modified Wolfe's medium. The resulting defined minimal R. marinus medium, (DRM), allowed reproducible cultivations to a final OD620nm of 6.6 ± 0.05, CDW 2.85 ± 0.07 mg/L, a maximum specific growth rate (µmax) of 0.26 h-1, total carotenoids 0.77 × 10-3 mg/L and EPSs 3.4 ± 0.17 mg/L in cultivations supplemented with up to 5 g/L glucose. CONCLUSION A minimal defined medium (DRM) was designed that resulted in reproducible growth and an almost doubled formation of both total carotenoids and EPSs. Such defined conditions, are necessary for systematic studies of metabolic pathways, to determine the specific requirements for growth and fully characterize metabolite production.
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Affiliation(s)
- Israt Jahan Mukti
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
| | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden.
| | - Thordis Kristjansdottir
- Matis Ohf, Vinlandsleid 12, 113, Reykjavik, Iceland.,Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102, Reykjavik, Iceland
| | - Gudmundur O Hreggvidsson
- Matis Ohf, Vinlandsleid 12, 113, Reykjavik, Iceland.,Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102, Reykjavik, Iceland
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
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Dobruchowska JM, Bjornsdottir B, Fridjonsson OH, Altenbuchner J, Watzlawick H, Gerwig GJ, Dijkhuizen L, Kamerling JP, Hreggvidsson GO. Enzymatic depolymerization of alginate by two novel thermostable alginate lyases from Rhodothermus marinus. FRONTIERS IN PLANT SCIENCE 2022; 13:981602. [PMID: 36204061 PMCID: PMC9530828 DOI: 10.3389/fpls.2022.981602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Alginate (alginic acid) is a linear polysaccharide, wherein (1→4)-linked β-D-mannuronic acid and its C5 epimer, α-L-guluronic acid, are arranged in varying sequences. Alginate lyases catalyze the depolymerization of alginate, thereby cleaving the (1→4) glycosidic linkages between the monomers by a β-elimination mechanism, to yield unsaturated 4-deoxy-L-erythro-hex-4-enopyranosyluronic acid (Δ) at the non-reducing end of resulting oligosaccharides (α-L-erythro configuration) or, depending on the enzyme, the unsaturated monosaccharide itself. In solution, the released free unsaturated monomer product is further hydrated in a spontaneous (keto-enol tautomerization) process to form two cyclic stereoisomers. In this study, two alginate lyase genes, designated alyRm3 and alyRm4, from the marine thermophilic bacterium Rhodothermus marinus (strain MAT378), were cloned and expressed in Escherichia coli. The recombinant enzymes were characterized, and their substrate specificity and product structures determined. AlyRm3 (PL39) and AlyRm4 (PL17) are among the most thermophilic and thermostable alginate lyases described to date with temperature optimum of activity at ∼75 and 81°C, respectively. The pH optimum of activity of AlyRm3 is ∼5.5 and AlyRm4 at pH 6.5. Detailed NMR analysis of the incubation products demonstrated that AlyRm3 is an endolytic lyase, while AlyRm4 is an exolytic lyase, cleaving monomers from the non-reducing end of oligo/poly-alginates.
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Affiliation(s)
- Justyna M. Dobruchowska
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | | | | | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Stuttgart, Germany
| | | | - Gerrit J. Gerwig
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Johannis P. Kamerling
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Gudmundur O. Hreggvidsson
- Matís Ltd., Reykjavík, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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Bergsten P, Vannier P, Mougeolle A, Rigaud L, Marteinsson VT. Rhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island Surtsey. Int J Syst Evol Microbiol 2022; 72. [PMID: 35072600 DOI: 10.1099/ijsem.0.005214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel thermophilic heterotrophic bacteria were isolated from the subsurface of the volcanic island Surtsey off the south coast of Iceland. The strains were isolated from tephra core and borehole fluid samples collected below 70 m depth. The Gram-negative bacteria were rod-shaped (0.3-0.4 µm wide, 1.5-7 µm long), aerobic, non-sporulating and non-motile. Optimal growth was observed at 70 °C, at pH 7-7.5 and with 1% NaCl. Phylogenetic analysis identified the strains as members of the genus Rhodothermus. The type strain, ISCAR-7401T, was genetically distinct from its closest relatives Rhodothermus marinus DSM 4252T and Rhodothermus profundi PRI 2902T based on 16S rRNA gene sequence similarity (95.81 and 96.01%, respectively), genomic average nucleotide identity (73.73 and 72.61%, respectively) and digital DNA-DNA hybridization (17.6 and 16.9%, respectively). The major fatty acids of ISCAR-7401T were iso-C17:0, anteiso-C15:0, anteiso-C17:0 and iso-C15:0 (>10 %). The major isoprenoid quinone was MK-7 while phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminophospholipid and a phospholipid were the predominant polar lipid components. Based on comparative chemotaxonomic, genomic and phylogenetic analyses, we propose that the isolated strain represents a novel species of the genus Rhodothermus with the name Rhodothermus bifroesti sp. nov. The type strain is ISCAR-7401T (=DSM 112103T=CIP 111906T).
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Affiliation(s)
- Pauline Bergsten
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Pauline Vannier
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
| | - Alan Mougeolle
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
| | - Louise Rigaud
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
| | - Viggó Thór Marteinsson
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
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Santiago LD, DeLeon-Rodriguez N, LaSanta-Pagán K, Hatt JK, Kurt Z, Massol-Deyá A, Konstantinidis KT. Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. comprising a new bacterial family. Syst Appl Microbiol 2021; 45:126288. [PMID: 34933230 DOI: 10.1016/j.syapm.2021.126288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR's capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.
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Affiliation(s)
- Lizbeth-Dávila Santiago
- Department of Biology, University of Puerto Rico, Mayagüez, Puerto Rico; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Natasha DeLeon-Rodriguez
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Arturo Massol-Deyá
- Department of Biology, University of Puerto Rico, Mayagüez, Puerto Rico; Casa Pueblo, Adjuntas, Puerto Rico.
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.
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A Survey of Spontaneous Antibiotic-Resistant Mutants of the Halophilic, Thermophilic Bacterium Rhodothermus marinus. Antibiotics (Basel) 2021; 10:antibiotics10111384. [PMID: 34827322 PMCID: PMC8614978 DOI: 10.3390/antibiotics10111384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Rhodothermus marinus is a halophilic extreme thermophile, with potential as a model organism for studies of the structural basis of antibiotic resistance. In order to facilitate genetic studies of this organism, we have surveyed the antibiotic sensitivity spectrum of R. marinus and identified spontaneous antibiotic-resistant mutants. R. marinus is naturally insensitive to aminoglycosides, aminocylitols and tuberactinomycins that target the 30S ribosomal subunit, but is sensitive to all 50S ribosomal subunit-targeting antibiotics examined, including macrolides, lincosamides, streptogramin B, chloramphenicol, and thiostrepton. It is also sensitive to kirromycin and fusidic acid, which target protein synthesis factors. It is sensitive to rifampicin (RNA polymerase inhibitor) and to the fluoroquinolones ofloxacin and ciprofloxacin (DNA gyrase inhibitors), but insensitive to nalidixic acid. Drug-resistant mutants were identified using rifampicin, thiostrepton, erythromycin, spiramycin, tylosin, lincomycin, and chloramphenicol. The majority of these were found to have mutations that are similar or identical to those previously found in other species, while several novel mutations were identified. This study provides potential selectable markers for genetic manipulations and demonstrates the feasibility of using R. marinus as a model system for studies of ribosome and RNA polymerase structure, function, and evolution.
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Björnsdóttir SH, Pétursdóttir SK, Gudmundsdóttir EE, Olgudóttir E, Stefansson SK, Róbertsdóttir T, Sigurpálsson ÁH, Ólafsdóttir SK, Fridjónsson ÓH, Hreggvidsson GÓ. Rhodocaloribacter litoris gen. nov., sp. nov., isolated from an intertidal hot spring. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672921 DOI: 10.1099/ijsem.0.005073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Red-pigmented strains of non-sporeforming, aerobic, chemoorganotrophic bacteria were isolated from intertidal hot springs in Laugarvík, NW-Iceland. Cells stained Gram-negative and formed pleomorphic rods that often had swollen ends and occurred singly or in filaments. Growth was observed at 40-65 °C (optimum at 60 °C), pH 6-9 (optimum at 6.5-8) and 0.5-5% (optimum at 1-2%) (w/v) NaCl. Strain ISCAR-4553T contained MK-7 as the main respiratory quinone and saturated iso and anteiso branched chains of 17 and 15 carbons as the main cellular fatty acids (83.4%). The G+C content of the DNA is 67.3 mol%. The highest 16S rRNA gene sequence similarity was with the genus Roseithermus (92.0%) and followed by Rhodothermus, Rubrivirga and Rubricoccus (88-90%). Genome and phenotype comparisons supported the affiliation of the novel isolates and the genus Roseithermus to the family Rhodothermaceae of the phylum Rhodothermaeota. The described isolates are proposed to be classified as representatives of a novel species belonging to a novel genus, with the name Rhodocaloribacter litoris gen. nov., sp. nov. The type strain is ISCAR-4553T (=DSM 110790T = ATCC TSD-179T).
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Affiliation(s)
- Snædís H Björnsdóttir
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | | | | | | | - Sigmar K Stefansson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | - Tara Róbertsdóttir
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | - Ásbjörn H Sigurpálsson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | | | | | - Gudmundur Ó Hreggvidsson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland.,Matis, Vínlandsleið 12, IS-113 Reykjavík, Iceland
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8
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Braga LPP, Pereira RV, Martins LF, Moura LMS, Sanchez FB, Patané JSL, da Silva AM, Setubal JC. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics 2021; 22:652. [PMID: 34507539 PMCID: PMC8434746 DOI: 10.1186/s12864-021-07957-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. RESULTS Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. CONCLUSIONS The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.
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Affiliation(s)
- Lucas Palma Perez Braga
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Beltrame Sanchez
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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Yang H, Jung H, Oh K, Jeon JM, Cho KS. Characterization of the Bacterial Community Associated with Methane and Odor in a Pilot-Scale Landfill Biocover under Moderately Thermophilic Conditions. J Microbiol Biotechnol 2021; 31:803-814. [PMID: 33879637 PMCID: PMC9705922 DOI: 10.4014/jmb.2103.03005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/09/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022]
Abstract
A pilot-scale biocover was constructed at a sanitary landfill and the mitigation of methane and odor compounds was compared between the summer and non-summer seasons. The average inlet methane concentrations were 22.0%, 16.3%, and 31.3%, and the outlet concentrations were 0.1%, 0.1%, and 0.2% during winter, spring, and summer, respectively. The odor removal efficiency was 98.0% during summer, compared to 96.6% and 99.6% during winter and spring, respectively. No deterioration in methane and odor removal performance was observed even when the internal temperature of the biocover increased to more than 40°C at midday during summer. During summer, the packing material simultaneously degraded methane and dimethyl sulfide (DMS) under both moderately thermophilic (40-50°C) and mesophilic conditions (30°C). Hyphomicrobium and Brevibacillus, which can degrade methane and DMS at 40°C and 50°C, were isolated. The diversity of the bacterial community in the biocover during summer did not decrease significantly compared to other seasons. The thermophilic environment of the biocover during summer promoted the growth of thermotolerant and thermophilic bacterial populations. In particular, the major methane-oxidizing species were Methylocaldum spp. during summer and Methylobacter spp. during the nonsummer seasons. The performance of the biocover remained stable under moderately thermophilic conditions due to the replacement of the main species and the maintenance of bacterial diversity. The information obtained in this study could be used to design biological processes for methane and odor removal during summer and/or in subtropical countries.
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Affiliation(s)
- Hyoju Yang
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hyekyeng Jung
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyungcheol Oh
- Green Environmental Complex Center, Suncheon 57992, Republic of Korea
| | - Jun-Min Jeon
- Green Environmental Complex Center, Suncheon 57992, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea,Corresponding author Phone: +82-2-32772393 E-mail:
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Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus. Protein J 2021; 40:184-191. [PMID: 33651244 PMCID: PMC7923407 DOI: 10.1007/s10930-021-09970-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2021] [Indexed: 11/15/2022]
Abstract
Substrate binding proteins (SBPs) bind to specific ligands in the periplasmic regions of cells and then bind to membrane proteins to participate in transport or signal transduction. Typically, SBPs consist of two α/β domains and recognize the substrate by a flexible hinge region between the two domains. Conversely, the short-length SBPs are often observed in protein databases, which are located around methyl-accepting chemotaxis protein genes. We previously determined the crystal structure of Rhodothermus marinus SBP (named as RmSBP), consisting of a single α/β domain; however, the substrate recognition mechanism is still unclear. To better understand the functions of short length RmSBP, we performed a comprehensive study, involving comparative structure analysis, computational substrate docking, and X-ray crystallographic data. RmSBP shares a high level of similarity in the α/β domain region with other SBPs, but it has a distinct topology in the C-terminal domain. The substrate binding model suggested that conformational changes in the peripheral region of RmSBP was required to recognize the substrate. We determined the crystal structures of RmSBP at pH 5.5, 6.0, and 7.5. RmSBP showed structural flexibility in the β1–α2 loop, β5–β6 loop, and extended C-terminal domains, based on the electron density map and temperature B-factor analysis. These results provide information that will further our understanding on the functions of the short length SBP.
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Zhu P, Li Y, Gao Y, Yin M, Wu Y, Liu L, Du N, Liu J, Yu X, Wang L, Guo W. Insight into the effect of nitrogen-rich substrates on the community structure and the co-occurrence network of thermophiles during lignocellulose-based composting. BIORESOURCE TECHNOLOGY 2021; 319:124111. [PMID: 32971335 DOI: 10.1016/j.biortech.2020.124111] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Thermophilic microorganisms play vital roles in the composting process. To elucidate how raw materials affect thermophilic microbial community composition and their interactions, the succession of thermophilic bacterial and fungal communities were monitored in reed straw co-composting with four common nitrogen-rich substrates. The results of high-throughput sequencing showed that raw materials and composting process significantly changed bacterial and fungal community composition. Firmicutes and Actinobacteria drove the assembly of bacterial communities, while Ascomycetes drove the assembly of fungal communities. Network analysis indicated that during the composting process, the addition of nitrogen-rich sources abundant in easily degradable substances promoted the complexity of thermophilic microbial network. Moreover, microorganisms mainly exhibited synergistic effects, and inter-kingdom competition was more intense than intra-kingdom competition. Notably, rare species play essential roles in maintaining the network construction. Our findings provided novel insights into thermophilic microbial community assembly and their co-occurrence networks during the composting process.
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Affiliation(s)
- Pengcheng Zhu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Yichen Li
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Yufei Gao
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Meiqi Yin
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Yuxin Wu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Lele Liu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Ning Du
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Jian Liu
- Environmental Research Institute, Shandong University, Qingdao 266237, PR China
| | - Xiaona Yu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Weihua Guo
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, PR China.
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Liew KJ, Bruce NC, Sani RK, Chong CS, Yaakop AS, Shamsir MS, Goh KM. Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan. Microorganisms 2020; 8:E976. [PMID: 32610703 PMCID: PMC7409140 DOI: 10.3390/microorganisms8070976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022] Open
Abstract
The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Neil C. Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK;
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia;
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor 84600, Malaysia
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
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Complete Genome Sequences of Rhodothermus marinus Strains AA2-13 and AA3-38, Isolated from Arima Onsen Hot Spring in Japan. Microbiol Resour Announc 2020; 9:9/2/e01475-19. [PMID: 31919149 PMCID: PMC6952675 DOI: 10.1128/mra.01475-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated Rhodothermus marinus strains AA2-13 and AA3-38 from Arima Onsen, a hot spring in Japan, and sequenced their genomes. The average nucleotide identity between their genomes was 99.2%, and that with the genome of R. marinus strain DSM 4252T (isolated from Iceland) was ∼95.2%, suggesting close relationships among these strains. We isolated Rhodothermus marinus strains AA2-13 and AA3-38 from Arima Onsen, a hot spring in Japan, and sequenced their genomes. The average nucleotide identity between their genomes was 99.2%, and that with the genome of R. marinus strain DSM 4252T (isolated from Iceland) was ∼95.2%, suggesting close relationships among these strains.
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14
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Husser MC, Vo PQN, Sinha H, Ahmadi F, Shih SCC. An Automated Induction Microfluidics System for Synthetic Biology. ACS Synth Biol 2018. [PMID: 29516725 DOI: 10.1021/acssynbio.8b00025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The expression of a recombinant gene in a host organism through induction can be an extensively manual and labor-intensive procedure. Several methods have been developed to simplify the protocol, but none has fully replaced the traditional IPTG-based induction. To simplify this process, we describe the development of an autoinduction platform based on digital microfluidics. This system consists of a 600 nm LED and a light sensor to enable the real-time monitoring of the optical density (OD) samples coordinated with the semicontinuous mixing of a bacterial culture. A hand-held device was designed as a microbioreactor to culture cells and to measure the OD of the bacterial culture. In addition, it serves as a platform for the analysis of regulated protein expression in E. coli without the requirement of standardized well-plates or pipetting-based platforms. Here, we report for the first time, a system that offers great convenience without the user to physically monitor the culture or to manually add inducer at specific times. We characterized our system by looking at several parameters (electrode designs, gap height, and growth rates) required for an autoinducible system. As a first step, we carried out an automated induction optimization assay using a RFP reporter gene to identify conditions suitable for our system. Next, we used our system to identify active thermophilic β-glucosidase enzymes that may be suitable candidates for biomass hydrolysis. Overall, we believe that this platform may be useful for synthetic biology applications that require regulating and analyzing expression of heterologous genes for strain optimization.
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Affiliation(s)
- Mathieu C. Husser
- Department of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Philippe Q. N. Vo
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Hugo Sinha
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Fatemeh Ahmadi
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Steve C. C. Shih
- Department of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
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Abstract
YcfD from Escherichia coli is a homologue of the human ribosomal oxygenases NO66 and MINA53, which catalyse histidyl-hydroxylation of the 60S subunit and affect cellular proliferation (Ge et al., Nat Chem Biol 12:960–962, 2012). Bioinformatic analysis identified a potential homologue of ycfD in the thermophilic bacterium Rhodothermus marinus (ycfDRM). We describe studies on the characterization of ycfDRM, which is a functional 2OG oxygenase catalysing (2S,3R)-hydroxylation of the ribosomal protein uL16 at R82, and which is active at significantly higher temperatures than previously reported for any other 2OG oxygenase. Recombinant ycfDRM manifests high thermostability (Tm 84 °C) and activity at higher temperatures (Topt 55 °C) than ycfDEC (Tm 50.6 °C, Topt 40 °C). Mass spectrometric studies on purified R. marinus ribosomal proteins demonstrate a temperature-dependent variation in uL16 hydroxylation. Kinetic studies of oxygen dependence suggest that dioxygen availability can be a limiting factor for ycfDRM catalysis at high temperatures, consistent with incomplete uL16 hydroxylation observed in R. marinus cells. Overall, the results that extend the known range of ribosomal hydroxylation, reveal the potential for ycfD-catalysed hydroxylation to be regulated by temperature/dioxygen availability, and that thermophilic 2OG oxygenases are of interest from a biocatalytic perspective.
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16
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Memarpoor-Yazdi M, Karbalaei-Heidari HR, Doroodmand MM. Enantioselective hydrolysis of ibuprofen ethyl ester by a thermophilic immobilized lipase, ELT, from Rhodothermus marinus. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Edrada-Ebel R, Ævarsson A, Polymenakou P, Hentschel U, Carettoni D, Day J, Green D, Hreggviðsson GÓ, Harvey L, McNeil B. SeaBioTech: From Seabed to Test-Bed: Harvesting the Potential of Marine Biodiversity for Industrial Biotechnology. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Ron EYC, Plaza M, Kristjansdottir T, Sardari RRR, Bjornsdottir SH, Gudmundsson S, Hreggvidsson GO, Turner C, van Niel EWJ, Nordberg-Karlsson E. Characterization of carotenoids in Rhodothermus marinus. Microbiologyopen 2017; 7. [PMID: 29045010 PMCID: PMC5822342 DOI: 10.1002/mbo3.536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/13/2022] Open
Abstract
Rhodothermus marinus, a marine aerobic thermophile, was first isolated from an intertidal hot spring in Iceland. In recent years, the R. marinus strain PRI 493 has been genetically modified, which opens up possibilities for targeted metabolic engineering of the species, such as of the carotenoid biosynthetic pathway. In this study, the carotenoids of the R. marinus type‐strain DSM 4252T, strain DSM 4253, and strain PRI 493 were characterized. Bioreactor cultivations were used for pressurized liquid extraction and analyzed by ultra‐high performance supercritical fluid chromatography with diode array and quadropole time‐of‐flight mass spectrometry detection (UHPSFC‐DAD‐QTOF/MS). Salinixanthin, a carotenoid originally found in Salinibacter ruber and previously detected in strain DSM 4253, was identified in all three R. marinus strains, both in the hydroxylated and nonhydroxylated form. Furthermore, an additional and structurally distinct carotenoid was detected in the three strains. MS/MS fragmentation implied that the mass difference between salinixanthin and the novel carotenoid structure corresponded to the absence of a 4‐keto group on the ß‐ionone ring. The study confirmed the lack of carotenoids for the strain SB‐71 (ΔtrpBΔpurAcrtBI’::trpB) in which genes encoding two enzymes of the proposed pathway are partially deleted. Moreover, antioxidant capacity was detected in extracts of all the examined R. marinus strains and found to be 2–4 times lower for the knock‐out strain SB‐71. A gene cluster with 11 genes in two operons in the R. marinusDSM 4252T genome was identified and analyzed, in which several genes were matched with carotenoid biosynthetic pathway genes in other organisms.
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Affiliation(s)
- Emanuel Y C Ron
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Merichel Plaza
- Division of Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | - Charlotta Turner
- Division of Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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19
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Memarpoor-Yazdi M, Karbalaei-Heidari HR, Khajeh K. Production of the renewable extremophile lipase: Valuable biocatalyst with potential usage in food industry. FOOD AND BIOPRODUCTS PROCESSING 2017. [DOI: 10.1016/j.fbp.2016.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Duan XC, Lu AM, Gu B, Cai ZP, Ma HY, Wei S, Laborda P, Liu L, Voglmeir J. Functional characterization of the UDP-xylose biosynthesis pathway in Rhodothermus marinus. Appl Microbiol Biotechnol 2015; 99:9463-72. [PMID: 26033773 DOI: 10.1007/s00253-015-6683-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 05/07/2015] [Indexed: 10/23/2022]
Abstract
UDP-glucuronic acid dehydrogenase (UGD) and UDP-xylose synthase (UXS) are the two enzymes responsible for the biosynthesis of UDP-xylose from UDP-glucose. Several UGDs from bacterial sources, which oxidize UDP-glucose to glucuronic acid, have been found and functionally characterized whereas only few reports on bacterial UXS isoforms exist. Rhodothermus marinus, a halothermophilic bacterium commonly found in hot springs, proved to be a valuable source of carbohydrate active enzymes of biotechnological interest, such as xylanases, mannanases, and epimerases. However, no enzymes of R. marinus involved in the biosynthesis or modification of nucleotide sugars have been reported yet. Herein, we describe the cloning and characterization of two putative UGD (RmUGD1 and RmUGD2) and one UXS (RmUXS) isoform from this organism. All three enzymes could be expressed in recombinant form and purified to near homogeneity. UPLC- and NMR-based activity tests showed that RmUGD1 and RmUXS are indeed active enzymes, whereas no enzymatic activity could be detected by RmUGD2. Both RmUGD1 and RmUXS showed a temperature optimum of 60 °C, with almost no loss of activity after 1 h exposure at 70 °C. No metal ions were required for enzymatic activities. Zn(2+) ions strongly inhibited both enzymes. RmUGD1 showed higher salt tolerance and had a higher pH optimum than RmUXS. Furthermore, RmUGD1 was inhibited by UDP-xylose at higher concentrations. By coupling recombinant RmUXS and RmUGD1, UDP-xylose could be successfully synthesized directly from UDP-glucose. The high activity of the herein described enzymes make RmUGD1 and RmUXS the first thermo-tolerant biocatalysts for the synthesis of UDP-glucuronic acid and UDP-xylose.
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Affiliation(s)
- Xu C Duan
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Ai M Lu
- College of Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bin Gu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Zhi P Cai
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Hong Y Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Shuang Wei
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Pedro Laborda
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.
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22
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Jorge CD, Borges N, Santos H. A novel pathway for the synthesis of inositol phospholipids uses cytidine diphosphate (CDP)-inositol as donor of the polar head group. Environ Microbiol 2015; 17:2492-504. [PMID: 25472423 DOI: 10.1111/1462-2920.12734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 11/28/2022]
Abstract
We describe a novel biosynthetic pathway for glycerophosphoinositides in Rhodothermus marinus in which inositol is activated by cytidine triphosphate (CTP); this is unlike all known pathways that involve activation of the lipid group instead. This work was motivated by the detection in the R. marinus genome of a gene with high similarity to CTP:L-myo-inositol-1-phosphate cytidylyltransferase, the enzyme that synthesizes cytidine diphosphate (CDP)-inositol, a metabolite only known in the synthesis of di-myo-inositol phosphate. However, this solute is absent in R. marinus. The fate of radiolabelled CDP-inositol was investigated in cell extracts to reveal that radioactive inositol was incorporated into the chloroform-soluble fraction. Mass spectrometry showed that the major lipid product has a molecular mass of 810 Da and contains inositol phosphate and alkyl chains attached to glycerol by ether bonds. The occurrence of ether-linked lipids is rare in bacteria and has not been described previously in R. marinus. The relevant synthase was identified by functional expression of the candidate gene in Escherichia coli. The enzyme catalyses the transfer of L-myo-inositol-1-phosphate from CDP-inositol to dialkylether glycerol yielding dialkylether glycerophosphoinositol. Database searching showed homologous proteins in two bacterial classes, Sphingobacteria and Alphaproteobacteria. This is the first report of the involvement of CDP-inositol in phospholipid synthesis.
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Affiliation(s)
- Carla D Jorge
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República-EAN, Apartado 127, Oeiras, 2780-157, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República-EAN, Apartado 127, Oeiras, 2780-157, Portugal
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República-EAN, Apartado 127, Oeiras, 2780-157, Portugal
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Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass. Appl Environ Microbiol 2014; 80:7423-32. [PMID: 25261509 DOI: 10.1128/aem.02795-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022] Open
Abstract
Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction.
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24
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Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer SW. Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:15. [PMID: 24479406 PMCID: PMC3923250 DOI: 10.1186/1754-6834-7-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/15/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND The development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. Certain ionic liquids (ILs) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrated to reduce the recalcitrance of biomass for enzymatic hydrolysis. However, current commercial cellulase cocktails are strongly inhibited by most of the ILs that are effective biomass pretreatment solvents. Fortunately, recent research has shown that IL-tolerant cocktails can be formulated and are functional on lignocellulosic biomass. This study sought to expand the list of known IL-tolerant cellulases to further enable IL-tolerant cocktail development by developing a combined in vitro/in vivo screening pipeline for metagenome-derived genes. RESULTS Thirty-seven predicted cellulases derived from a thermophilic switchgrass-adapted microbial community were screened in this study. Eighteen of the twenty-one enzymes that expressed well in E. coli were active in the presence of the IL 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) concentrations of at least 10% (v/v), with several retaining activity in the presence of 40% (v/v), which is currently the highest reported tolerance to [C2mim][OAc] for any cellulase. In addition, the optimum temperatures of the enzymes ranged from 45 to 95°C and the pH optimum ranged from 5.5 to 7.5, indicating these enzymes can be used to construct cellulase cocktails that function under a broad range of temperature, pH and IL concentrations. CONCLUSIONS This study characterized in detail twenty-one cellulose-degrading enzymes derived from a thermophilic microbial community and found that 70% of them were [C2mim][OAc]-tolerant. A comparison of optimum temperature and [C2mim][OAc]-tolerance demonstrates that a positive correlation exists between these properties for those enzymes with a optimum temperature >70°C, further strengthening the link between thermotolerance and IL-tolerance for lignocelluolytic glycoside hydrolases.
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Affiliation(s)
- John M Gladden
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Joint BioEnergy Institute (JBEI), 1 Cyclotron Road, Berkeley, CA 94720, USA.
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25
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Hjorleifsdottir S, Aevarsson A, Hreggvidsson GO, Fridjonsson OH, Kristjansson JK. Isolation, growth and genome of the Rhodothermus RM378 thermophilic bacteriophage. Extremophiles 2013; 18:261-70. [PMID: 24318108 DOI: 10.1007/s00792-013-0613-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/21/2013] [Indexed: 01/04/2023]
Abstract
Several bacteriophages that infect different strains of the thermophilic bacterium Rhodothermus marinus were isolated and their infection pattern was studied. One phage, named RM378 was cultivated and characterized. The RM378 genome was also sequenced and analyzed. The phage was grouped as a member of the Myoviridae family with A2 morphology. It had a moderately elongated head, with dimensions of 85 and 95 nm between opposite apices and a 150 nm long tail, attached with a connector to the head. RM378 showed a virulent behavior that followed a lytic cycle of infection. It routinely gave lysates with 10(11) pfu/ml, and sometimes reached titers as high as 10(13) pfu/ml. The titer remained stable up to 65 °C but the phage lost viability when incubated at higher temperatures. Heating for 30 min at 96 °C lowered the titer by 10(4). The RM378 genome consisted of ds DNA of 129.908 bp with a GC ratio of 42.0% and contained about 120 ORFs. A few structural proteins, such as the major head protein corresponding to the gp23 in T4, could be identified. Only 29 gene products as probable homologs to other proteins of known function could be predicted, with most showing only low similarity to known proteins in other bacteriophages. These and other studies based on sequence analysis of a large number of phage genomes showed RM378 to be distantly related to all other known T4-like phages.
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Dick JM, Shock EL. A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring. PLoS One 2013; 8:e72395. [PMID: 24023738 PMCID: PMC3759468 DOI: 10.1371/journal.pone.0072395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022] Open
Abstract
Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the composition of biomass and the environmental conditions.
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Affiliation(s)
- Jeffrey M. Dick
- Department of Chemistry and Department of Applied Geology, Curtin University, Perth, Western Australia, Australia
- * E-mail:
| | - Everett L. Shock
- School of Earth and Space Exploration and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America
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A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One 2012; 7:e37010. [PMID: 22649505 PMCID: PMC3359315 DOI: 10.1371/journal.pone.0037010] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 04/11/2012] [Indexed: 11/19/2022] Open
Abstract
Generation of biofuels from sugars in lignocellulosic biomass is a promising alternative to liquid fossil fuels, but efficient and inexpensive bioprocessing configurations must be developed to make this technology commercially viable. One of the major barriers to commercialization is the recalcitrance of plant cell wall polysaccharides to enzymatic hydrolysis. Biomass pretreatment with ionic liquids (ILs) enables efficient saccharification of biomass, but residual ILs inhibit both saccharification and microbial fuel production, requiring extensive washing after IL pretreatment. Pretreatment itself can also produce biomass-derived inhibitory compounds that reduce microbial fuel production. Therefore, there are multiple points in the process from biomass to biofuel production that must be interrogated and optimized to maximize fuel production. Here, we report the development of an IL-tolerant cellulase cocktail by combining thermophilic bacterial glycoside hydrolases produced by a mixed consortia with recombinant glycoside hydrolases. This enzymatic cocktail saccharifies IL-pretreated biomass at higher temperatures and in the presence of much higher IL concentrations than commercial fungal cocktails. Sugars obtained from saccharification of IL-pretreated switchgrass using this cocktail can be converted into biodiesel (fatty acid ethyl-esters or FAEEs) by a metabolically engineered strain of E. coli. During these studies, we found that this biodiesel-producing E. coli strain was sensitive to ILs and inhibitors released by saccharification. This cocktail will enable the development of novel biomass to biofuel bioprocessing configurations that may overcome some of the barriers to production of inexpensive cellulosic biofuels.
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Gladden JM, Eichorst SA, Hazen TC, Simmons BA, Singer SW. Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnol Bioeng 2011; 109:1140-5. [PMID: 22125273 DOI: 10.1002/bit.24388] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/11/2011] [Accepted: 11/17/2011] [Indexed: 11/11/2022]
Abstract
Bacteria modulate glycoside hydrolase expression in response to the changes in the composition of lignocellulosic biomass. The response of switchgrass-adapted thermophilic bacterial consortia to perturbation with a variety of biomass substrates was characterized to determine if bacterial consortia also responded to changes in biomass composition. Incubation of the switchgrass-adapted consortia with these alternative substrates produced shifts in glycoside hydrolase activities and bacterial community composition. Substantially increased endoglucanase activity was observed upon incubation with microcrystalline cellulose and trifluororacetic acid-pretreated switchgrass. In contrast, culturing the microbial consortia with ionic liquid-pretreated switchgrass increased xylanase activity dramatically. Microbial community analyses of these cultures indicated that the increased endoglucanase activity correlated with an increase in bacteria related to Rhodothermus marinus. Inclusion of simple organic substrates in the culture medium abrogated glycoside hydrolase activity and enriched for bacteria related to Thermus thermophilus. These results demonstrate that the composition of biomass substrates influences the glycoside hydrolase activities and community composition of biomass-deconstructing bacterial consortia.
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Affiliation(s)
- John M Gladden
- Joint BioEnergy Institute, Emeryville, California 94608, USA
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Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Appl Environ Microbiol 2011; 77:5804-12. [PMID: 21724886 DOI: 10.1128/aem.00032-11] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
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Generation of targeted deletions in the genome of Rhodothermus marinus. Appl Environ Microbiol 2011; 77:5505-12. [PMID: 21705543 DOI: 10.1128/aem.02070-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to develop an approach for chromosomal engineering of the thermophile Rhodothermus marinus. A selection strategy for R. marinus had previously been developed; this strategy was based on complementing a restriction-negative trpB strain with the R. marinus trpB gene. The current work identified an additional selective marker, purA, which encodes adenylosuccinate synthase and confers adenine prototrophy. In a two-step procedure, the available Trp(+) selection was used during the deletion of purA from the R. marinus chromosome. The alternative Ade(+) selection was in turn used while deleting the endogenous trpB gene. Since both deletions are unmarked, the purA and trpB markers may be reused. Through the double deletant SB-62 (ΔtrpB ΔpurA), the difficulties that are associated with spontaneous revertants and unintended chromosomal integration of marker-containing molecules are circumvented. The selection efficiency in R. marinus strain SB-62 (ΔtrpB ΔpurA) was demonstrated by targeting putative carotenoid biosynthesis genes, crtBI, using a linear molecule containing a marked deletion with 717 and 810 bp of 5' and 3' homologous sequences, respectively. The resulting Trp(+) transformants were colorless rather than orange-red. The correct replacement of an internal crtBI fragment with the trpB marker was confirmed by Southern hybridization analysis of the transformants. Thus, it appears that target genes in the R. marinus chromosome can be readily replaced with linear molecules in a single step by double-crossover recombination.
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Bleicher L, Prates ET, Gomes TCF, Silveira RL, Nascimento AS, Rojas AL, Golubev A, Martínez L, Skaf MS, Polikarpov I. Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations. J Phys Chem B 2011; 115:7940-9. [DOI: 10.1021/jp200330z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Bleicher
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Erica T. Prates
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Thiago C. F. Gomes
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Alessandro S. Nascimento
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Adriana L. Rojas
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
- Structural Biology Unit, Center for Cooperative Research in Biosciences bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alexander Golubev
- Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg, 188300, Russia
| | - Leandro Martínez
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
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Taylor MP, van Zyl L, Tuffin IM, Leak DJ, Cowan DA. Genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts. Microb Biotechnol 2011; 4:438-48. [PMID: 21310009 PMCID: PMC3815256 DOI: 10.1111/j.1751-7915.2010.00246.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. The application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose-derived carbohydrates. Fundamental to the success of this work has been the development of reliable genetic and molecular systems. These technical tools are now available to assist in the development of other (hyper)thermophilic strains with diverse phenotypes such as hemicellulolytic and cellulolytic properties, branched chain alcohol production and other 'valuable bioproduct' synthetic capabilities. Here we present an insight into the historical limitations, recent developments and current status of a number of genetic systems for thermophiles. We also highlight the value of reliable genetic methods for increasing our knowledge of thermophile physiology. We argue that the development of robust genetic systems is paramount in the evolution of future thermophilic based bioprocesses and make suggestions for future approaches and genetic targets that will facilitate this process.
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Affiliation(s)
- M P Taylor
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Modderdam Road, Bellville 7535, Cape Town, South Africa
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Forget NL, Murdock SA, Juniper SK. Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes. GEOBIOLOGY 2010; 8:417-432. [PMID: 20533949 DOI: 10.1111/j.1472-4669.2010.00247.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Seafloor iron oxide deposits are a common feature of submarine hydrothermal systems. Morphological study of these deposits has led investigators to suggest a microbiological role in their formation, through the oxidation of reduced Fe in hydrothermal fluids. Fe-oxidizing bacteria, including the recently described Zetaproteobacteria, have been isolated from a few of these deposits but generally little is known about the microbial diversity associated with this habitat. In this study, we characterized bacterial diversity in two Fe oxide samples collected on the seafloor of Volcanoes 1 and 19 on the South Tonga Arc. We were particularly interested in confirming the presence of Zetaproteobacteria at these two sites and in documenting the diversity of groups other than Fe oxidizers. Our results (small subunit rRNA gene sequence data) showed a surprisingly high bacterial diversity, with 150 operational taxonomic units belonging to 19 distinct taxonomic groups. Both samples were dominated by Zetaproteobacteria Fe oxidizers. This group was most abundant at Volcano 1, where sediments were richer in Fe and contained more crystalline forms of Fe oxides. Other groups of bacteria found at these two sites include known S- and a few N-metabolizing bacteria, all ubiquitous in marine environments. The low similarity of our clones with the GenBank database suggests that new species and perhaps new families were recovered. The results of this study suggest that Fe-rich hydrothermal sediments, while dominated by Fe oxidizers, can be exploited by a variety of autotrophic and heterotrophic micro-organisms.
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Affiliation(s)
- N L Forget
- Department of Biology, University of Victoria, Petch Building 116, 3800 Finnerty Rd, Victoria, BC, Canada.
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Marteinsson VT, Bjornsdottir SH, Bienvenu N, Kristjansson JK, Birrien JL. Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean. Int J Syst Evol Microbiol 2010; 60:2729-2734. [DOI: 10.1099/ijs.0.012724-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nine thermophilic strains of aerobic, non-sporulating, heterotrophic bacteria were isolated after enrichment of chimney material sampled from a deep-sea hydrothermal field at a depth of 2634 m on the East-Pacific Rise (1 °N). The bacteria stained Gram-negative. They were rod-shaped and measured approximately 0.5 μm in width and 1.5–3.5 μm in length. They grew at 55–80 °C, pH 6–8 and 1–6 % NaCl. Optimal growth was observed at 70–75 °C, pH 7.0 and 1–3 % NaCl. The organisms were identified as members of the genus Rhodothermus, having a 16S rRNA gene similarity of 98.1 % with Rhodothermus
marinus DSM 4252T. The novel isolates differed morphologically, physiologically and chemotaxonomically from R. marinus, e.g. in lack of pigmentation, response to hydrostatic pressure, maximum growth temperature and DNA G+C content. DNA–DNA hybridization revealed a reassociation value of 37.2 % between strain PRI 2902T and R. marinus DSM 4252T, which strongly suggested that they represent different species. Furthermore, AFLP fingerprinting separated the novel strains from R. marinus reference strains. It is therefore concluded that the strains described here should be classified as representatives of a novel species for which the name Rhodothermus profundi sp. nov. is proposed; the type strain is PRI 2902T (=DSM 22212T =JCM 15944T).
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Affiliation(s)
| | - Snaedis H. Bjornsdottir
- Institute of Biology, University of Iceland, Sturlugata 7, IS-101, Reykjavik, Iceland
- Matis Vinlandsleid 12, IS-113, Reykjavik, Iceland
| | - Nadège Bienvenu
- UMR 6197, Centre National de la Recherche Scientifique, Université de Bretagne Occidentale, Ifremer, IUEM, BP70, 29282 Plouzané, France
| | | | - Jean-Louis Birrien
- UMR 6197, Centre National de la Recherche Scientifique, Université de Bretagne Occidentale, Ifremer, IUEM, BP70, 29282 Plouzané, France
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The alternative complex III of Rhodothermus marinus and its structural and functional association with caa3 oxygen reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1477-82. [DOI: 10.1016/j.bbabio.2010.02.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 11/21/2022]
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Energy conservation by Rhodothermus marinus respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:509-15. [PMID: 20100453 DOI: 10.1016/j.bbabio.2010.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 01/11/2010] [Accepted: 01/15/2010] [Indexed: 11/21/2022]
Abstract
A sodium ion efflux, together with a proton influx and an inside-positive DeltaPsi, was observed during NADH-respiration by Rhodothermus marinus membrane vesicles. Proton translocation was monitored by fluorescence spectroscopy and sodium ion transport by (23)Na-NMR spectroscopy. Specific inhibitors of complex I (rotenone) and of the dioxygen reductase (KCN) inhibited the proton and the sodium ion transport, but the KCN effect was totally reverted by the addition of menaquinone analogues, indicating that both transports were catalyzed by complex I. We concluded that the coupling ion of the system is the proton and that neither the catalytic reaction nor the establishment of the delta-pH are dependent on sodium, but the presence of sodium increases proton transport. Moreover, studies of NADH oxidation at different sodium concentrations and of proton and sodium transport activities allowed us to propose a model for the mechanism of complex I in which the presence of two different energy coupling sites is suggested.
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Affiliation(s)
- P. L. Starokadomskyy
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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38
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Costa KC, Navarro JB, Shock EL, Zhang CL, Soukup D, Hedlund BP. Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles 2009; 13:447-59. [PMID: 19247786 DOI: 10.1007/s00792-009-0230-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 02/04/2009] [Indexed: 11/24/2022]
Abstract
A coordinated study of water chemistry, sediment mineralogy, and sediment microbial community was conducted on four >73 degrees C springs in the northwestern Great Basin. Despite generally similar chemistry and mineralogy, springs with short residence time (approximately 5-20 min) were rich in reduced chemistry, whereas springs with long residence time (>1 day) accumulated oxygen and oxidized nitrogen species. The presence of oxygen suggested that aerobic metabolisms prevail in the water and surface sediment. However, Gibbs free energy calculations using empirical chemistry data suggested that several inorganic electron donors were similarly favorable. Analysis of 298 bacterial 16S rDNAs identified 36 species-level phylotypes, 14 of which failed to affiliate with cultivated phyla. Highly represented phylotypes included Thermus, Thermotoga, a member of candidate phylum OP1, and two deeply branching Chloroflexi. The 276 archaeal 16S rDNAs represented 28 phylotypes, most of which were Crenarchaeota unrelated to the Thermoprotei. The most abundant archaeal phylotype was closely related to "Candidatus Nitrosocaldus yellowstonii", suggesting a role for ammonia oxidation in primary production; however, few other phylotypes could be linked with energy calculations because phylotypes were either related to chemoorganotrophs or were unrelated to known organisms.
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Affiliation(s)
- Kyle C Costa
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
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Wang X, Yang H, Ruan L, Liu X, Li F, Xu X. Cloning and characterization of a thermostable superoxide dismutase from the thermophilic bacterium Rhodothermus sp. XMH10. J Ind Microbiol Biotechnol 2007; 35:133-9. [DOI: 10.1007/s10295-007-0274-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
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Ruan L, Luo T, Li F, Xu X. Identification of differentially expressed genes from Rhodothermus sp. XMH10 in response to low temperature using random arbitrarily primed PCR. Curr Microbiol 2007; 55:543-8. [PMID: 17917777 DOI: 10.1007/s00284-007-9029-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 07/05/2007] [Indexed: 11/29/2022]
Abstract
Most research on the adaptation of thermophiles is focused on their adaptation to heat stress; only a few studies are focused on their cold adaptation. In this report, the thermophilic bacterium Rhodothermus sp. XMH10 was examined to gain a better understanding of gene expression in response to low temperature. Random arbitrarily primed polymerase chain reaction (RAP-PCR) was used to isolate and identify differentially expressed genes of bacteria grown at 45 degrees C (lowest) compared to those at 75 degrees C (optimal). Fifty-three differential cDNA fragments in total were isolated. Among them, 35 different cDNAs were analyzed by Northern blot, and 17 were confirmed to be differentially expressed at the transcriptional levels. These genes reflected a profile of differential expression and were involved in many physiological processes such as metabolism, cell membrane alterations, and regulatory adaptive response; most of them have never been previously reported. This study provides some new information on the adaptation of thermophilic bacteria to environmental temperature stress.
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Affiliation(s)
- Lingwei Ruan
- School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
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Bjornsdottir SH, Fridjonsson OH, Kristjansson JK, Eggertsson G. Cloning and expression of heterologous genes in Rhodothermus marinus. Extremophiles 2006; 11:283-93. [PMID: 17124556 DOI: 10.1007/s00792-006-0037-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 10/01/2006] [Indexed: 10/23/2022]
Abstract
The construction of a shuttle cloning system for Rhodothermus marinus and Escherichia coli is described. It is based on the shuttle vector pRM3000, which contains a multiple cloning site as well as the shuttle marker trpB and TrpB(-) recipients of both species. The vector is stable and in 25 +/- 2 and 91 +/- 3 copies in R. marinus SB-1 and E. coli SDH-1, respectively. Three different R. marinus regulatory sequences of the dnaJ, dnaK and recA genes were integrated into pRM3000 to make the expression vectors pRM5100, pRM5200 and pRM5300, respectively. Genes encoding alpha- and beta-galactosidase (agaT and bgaT) from Thermus brockianus were cloned in R. marinus. Expression of both recombinant genes in R. marinus was demonstrated. The agaT gene was used as a reporter to study transcription from the expression vectors. Induced expression by ten- and twentyfold was observed from the dnaK and dnaJ regulatory sequences, respectively, after a temperature shift from 63 to 77 degrees C. This is the first report of cloning and expression of heterologous genes in R. marinus and the first study of promoter activity in the species.
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Jorge CD, Sampaio MM, Hreggvidsson GO, Kristjánson JK, Santos H. A highly thermostable trehalase from the thermophilic bacterium Rhodothermus marinus. Extremophiles 2006; 11:115-22. [PMID: 16944251 DOI: 10.1007/s00792-006-0021-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
Trehalases play a central role in the metabolism of trehalose and can be found in a wide variety of organisms. A periplasmic trehalase (alpha,alpha-trehalose glucohydrolase, EC 3.2.1.28) from the thermophilic bacterium Rhodothermus marinus was purified and the respective encoding gene was identified, cloned and overexpressed in Escherichia coli. The recombinant trehalase is a monomeric protein with a molecular mass of 59 kDa. Maximum activity was observed at 88 degrees C and pH 6.5. The recombinant trehalase exhibited a K(m) of 0.16 mM and a V(max) of 81 micromol of trehalose (min)(-1) (mg of protein)(-1) at the optimal temperature for growth of R. marinus (65 degrees C) and pH 6.5. The enzyme was highly specific for trehalose and was inhibited by glucose with a K(i) of 7 mM. This is the most thermostable trehalase ever characterized. Moreover, this is the first report on the identification and characterization of a trehalase from a thermophilic bacterium.
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Affiliation(s)
- Carla D Jorge
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, Apartado 127, 2780-156, Oeiras, Portugal
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Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbø CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci U S A 2005; 102:18147-52. [PMID: 16330755 PMCID: PMC1312414 DOI: 10.1073/pnas.0509073102] [Citation(s) in RCA: 252] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.
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Affiliation(s)
- E F Mongodin
- The Institute for Genomic Research, Rockville, MD 20850, USA
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