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OuYang M, Liu C, Sheng P, Qiu Q, OuYang K, Li Y, Zang Y, Zhao X. Characterization of acidophilic cellulase with β-glucanase and xylanase activity from the rumen metagenome and in vitro evaluation of barley digestibility. Int J Biol Macromol 2025; 306:141141. [PMID: 39984074 DOI: 10.1016/j.ijbiomac.2025.141141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 02/13/2025] [Accepted: 02/14/2025] [Indexed: 02/23/2025]
Abstract
In this study, RuCel143, an acidophilic GH5 cellulase endowed with β-glucanase and xylanase activity was identified from the rumen metagenome. Its hydrolytic efficacy was evaluated using barley in an in vitro simulation of monogastric digestion. Optimal activity for RuCel143's cellulase was observed at pH 3.5 and 40 °C, while for xylanase it was pH 4.0 and 50 °C. The cellulase exhibited strong pH tolerance, retaining 94.3 % of its initial activity after 4 h at pH 2.5. In contrast, xylanase activity increased by 80.7 % after 4 h at pH 8.0. RuCel143 exhibited good resistance to various ions and common inhibitors, with Cu2+ and Mn2+ enhancing the cellulase activity by 26.9 % and 95.6 % at 1 mM concentration, respectively. Mutation analysis involving Tyr162Ala, His235Ala, and Glu285Ala showed reduced activities to 67.4 %, 29.3 %, and 19.5 % of the wild type, respectively. Hydrolysis product analysis revealed that RuCel143 primarily produced cellobiose and xylopentaose from carboxymethyl cellulose sodium and wheat straw xylan. Comparative tests on barley, wheat, and wheat bran demonstrated RuCel143's superior performance on barley. Simulation results of in vitro monogastric digestion indicated that RuCel143 can increase the digestibility of barley from 52.6 % to 60.8 % and reduce the viscosity coefficient from 1.41 to 1.38. In summary, RuCel143 is an exceptionally acid-tolerant cellulase with both β-glucanase and xylanase activities, demonstrating unique enzymatic properties that could potentially be leveraged to improve the degradation of barley in monogastric animals.
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Affiliation(s)
- Meng OuYang
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Chanjuan Liu
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Ping Sheng
- Jiangxi Provincial Academy of Sciences, Institute of Microbiology, Nanchang, Jiangxi 330096, China
| | - Qinghua Qiu
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Kehui OuYang
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yanjiao Li
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yitian Zang
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xianghui Zhao
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
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2
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Furukawa Y, Shintani A, Narikiyo S, Sue K, Akutsu M, Muraki N. Characterization of a novel cysteine-less Cu/Zn-superoxide dismutase in Paenibacillus lautus missing a conserved disulfide bond. J Biol Chem 2023; 299:105040. [PMID: 37442237 PMCID: PMC10432803 DOI: 10.1016/j.jbc.2023.105040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Cu/Zn-superoxide dismutase (CuZnSOD) is an enzyme that binds a copper and zinc ion and also forms an intramolecular disulfide bond. Together with the copper ion as the active site, the disulfide bond is completely conserved among these proteins; indeed, the disulfide bond plays critical roles in maintaining the catalytically competent conformation of CuZnSOD. Here, we found that a CuZnSOD protein in Paenibacillus lautus (PaSOD) has no Cys residue but exhibits a significant level of enzyme activity. The crystal structure of PaSOD revealed hydrophobic and hydrogen-bonding interactions in substitution for the disulfide bond of the other CuZnSOD proteins. Also notably, we determined that PaSOD forms a homodimer through an additional domain with a novel fold at the N terminus. While the advantages of lacking Cys residues and adopting a novel dimer configuration remain obscure, PaSOD does not require a disulfide-introducing/correcting system for maturation and could also avoid misfolding caused by aberrant thiol oxidations under an oxidative environment.
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Affiliation(s)
| | | | | | - Kaori Sue
- Department of Chemistry, Keio University, Yokohama, Japan
| | - Masato Akutsu
- Department of Chemistry, Keio University, Yokohama, Japan
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3
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Smrhova T, Jani K, Pajer P, Kapinusova G, Vylita T, Suman J, Strejcek M, Uhlik O. Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis. ENVIRONMENTAL MICROBIOME 2022; 17:48. [PMID: 36089611 PMCID: PMC9465906 DOI: 10.1186/s40793-022-00440-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition. RESULTS Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaClw/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs. CONCLUSIONS Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Tomas Vylita
- Institute of Balneology and Spa Sciences, Karlovy Vary, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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4
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Liyaskina EV, Rakova NA, Kitykina AA, Rusyaeva VV, Toukach PV, Fomenkov A, Vainauskas S, Roberts RJ, Revin VV. Production and сharacterization of the exopolysaccharide from strain Paenibacillus polymyxa 2020. PLoS One 2021; 16:e0253482. [PMID: 34228741 PMCID: PMC8259973 DOI: 10.1371/journal.pone.0253482] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/05/2021] [Indexed: 11/19/2022] Open
Abstract
Paenibacillus spp. exopolysaccharides (EPSs) have become a growing interest recently as a source of biomaterials. In this study, we characterized Paenibacillus polymyxa 2020 strain, which produces a large quantity of EPS (up to 68 g/L),and was isolated from wasp honeycombs. Here we report its complete genome sequence and full methylome analysis detected by Pacific Biosciences SMRT sequencing. Moreover, bioinformatic analysis identified a putative levan synthetic operon. SacC and sacB genes have been cloned and their products identified as glycoside hydrolase and levansucrase respectively. The Fourier transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectra demonstrated that the EPS is a linear β-(2→6)-linked fructan (levan). The structure and properties of levan polymer produced from sucrose and molasses were analyzed by FT-IR, NMR, scanning electron microscopy (SEM), high performance size exclusion chromatography (HPSEC), thermogravimetric analysis (TGA), cytotoxicity tests and showed low toxicity and high biocompatibility. Thus, P. polymyxa 2020 could be an exceptional cost-effective source for the industrial production of levan-type EPSs and to obtain functional biomaterials based on it for a broad range of applications, including bioengineering.
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Affiliation(s)
- Elena V. Liyaskina
- Department of Biotechnology, Bioengineering and Biochemistry of the National Research Mordovia State University, Saransk, Russia
- * E-mail: (EVL); (AF); (VVR)
| | - Nadezhda A. Rakova
- Department of Biotechnology, Bioengineering and Biochemistry of the National Research Mordovia State University, Saransk, Russia
| | - Alevtina A. Kitykina
- Department of Biotechnology, Bioengineering and Biochemistry of the National Research Mordovia State University, Saransk, Russia
| | - Valentina V. Rusyaeva
- Department of Biotechnology, Bioengineering and Biochemistry of the National Research Mordovia State University, Saransk, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Fomenkov
- New England Biolabs Inc., Ipswich, MA, United States of America
- * E-mail: (EVL); (AF); (VVR)
| | | | | | - Victor V. Revin
- Department of Biotechnology, Bioengineering and Biochemistry of the National Research Mordovia State University, Saransk, Russia
- * E-mail: (EVL); (AF); (VVR)
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5
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Mais CN, Hermann L, Altegoer F, Seubert A, Richter AA, Wernersbach I, Czech L, Bremer E, Bange G. Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex. J Biol Chem 2020; 295:9087-9104. [PMID: 32404365 PMCID: PMC7335791 DOI: 10.1074/jbc.ra120.012722] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
When faced with increased osmolarity in the environment, many bacterial cells accumulate the compatible solute ectoine and its derivative 5-hydroxyectoine. Both compounds are not only potent osmostress protectants, but also serve as effective chemical chaperones stabilizing protein functionality. Ectoines are energy-rich nitrogen and carbon sources that have an ecological impact that shapes microbial communities. Although the biochemistry of ectoine and 5-hydroxyectoine biosynthesis is well understood, our understanding of their catabolism is only rudimentary. Here, we combined biochemical and structural approaches to unravel the core of ectoine and 5-hydroxy-ectoine catabolisms. We show that a conserved enzyme bimodule consisting of the EutD ectoine/5-hydroxyectoine hydrolase and the EutE deacetylase degrades both ectoines. We determined the high-resolution crystal structures of both enzymes, derived from the salt-tolerant bacteria Ruegeria pomeroyi and Halomonas elongata These structures, either in their apo-forms or in forms capturing substrates or intermediates, provided detailed insights into the catalytic cores of the EutD and EutE enzymes. The combined biochemical and structural results indicate that the EutD homodimer opens the pyrimidine ring of ectoine through an unusual covalent intermediate, N-α-2 acetyl-l-2,4-diaminobutyrate (α-ADABA). We found that α-ADABA is then deacetylated by the zinc-dependent EutE monomer into diaminobutyric acid (DABA), which is further catabolized to l-aspartate. We observed that the EutD-EutE bimodule synthesizes exclusively the α-, but not the γ-isomers of ADABA or hydroxy-ADABA. Of note, α-ADABA is known to induce the MocR/GabR-type repressor EnuR, which controls the expression of many ectoine catabolic genes clusters. We conclude that hydroxy-α-ADABA might serve a similar function.
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Affiliation(s)
- Christopher-Nils Mais
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Lucas Hermann
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Florian Altegoer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Andreas Seubert
- Philipps-University Marburg, Faculty of Chemistry, Marburg, Germany
| | - Alexandra A Richter
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Isa Wernersbach
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Laura Czech
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Erhard Bremer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany.
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany.
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6
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Richter AA, Kobus S, Czech L, Hoeppner A, Zarzycki J, Erb TJ, Lauterbach L, Dickschat JS, Bremer E, Smits SHJ. The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine. J Biol Chem 2020; 295:2822-2838. [PMID: 31969391 DOI: 10.1074/jbc.ra119.011277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/19/2020] [Indexed: 12/17/2022] Open
Abstract
Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by l-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed l-2,4-diaminobutyrate (DAB), yielding N-γ-acetyl-l-2,4-diaminobutyrate (N-γ-ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus (Pl). We found that (Pl)EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N-γ-ADABA but not the ectoine catabolic intermediate N-α-acetyl-l-2,4-diaminobutyric acid. High-resolution crystal structures of (Pl)EctA (at 1.2-2.2 Å resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N-γ-ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of (Pl)EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.
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Affiliation(s)
- Alexandra A Richter
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany; Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Lukas Lauterbach
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany; Institute of Biochemistry, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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7
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Richter AA, Mais CN, Czech L, Geyer K, Hoeppner A, Smits SHJ, Erb TJ, Bange G, Bremer E. Biosynthesis of the Stress-Protectant and Chemical Chaperon Ectoine: Biochemistry of the Transaminase EctB. Front Microbiol 2019; 10:2811. [PMID: 31921013 PMCID: PMC6915088 DOI: 10.3389/fmicb.2019.02811] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria frequently adapt to high osmolarity surroundings through the accumulation of compatible solutes. Ectoine is a prominent member of these types of stress protectants and is produced via an evolutionarily conserved biosynthetic pathway beginning with the L-2,4-diaminobutyrate (DAB) transaminase (TA) EctB. Here, we studied EctB from the thermo-tolerant Gram-positive bacterium Paenibacillus lautus (Pl) and show that this tetrameric enzyme is highly tolerant to salt, pH, and temperature. During ectoine biosynthesis, EctB converts L-glutamate and L-aspartate-beta-semialdehyde into 2-oxoglutarate and DAB, but it also catalyzes the reverse reaction. Our analysis unravels that EctB enzymes are mechanistically identical to the PLP-dependent gamma-aminobutyrate TAs (GABA-TAs) and only differ with respect to substrate binding. Inspection of the genomic context of the ectB gene in P. lautus identifies an unusual arrangement of juxtapositioned genes for ectoine biosynthesis and import via an Ehu-type binding-protein-dependent ABC transporter. This operon-like structure suggests the operation of a highly coordinated system for ectoine synthesis and import to maintain physiologically adequate cellular ectoine pools under osmotic stress conditions in a resource-efficient manner. Taken together, our study provides an in-depth mechanistic and physiological description of EctB, the first enzyme of the ectoine biosynthetic pathway.
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Affiliation(s)
- Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Christopher-Nils Mais
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kyra Geyer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany.,Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
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8
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Gumkowski JD, Martinie RJ, Corrigan PS, Pan J, Bauerle MR, Almarei M, Booker SJ, Silakov A, Krebs C, Boal AK. Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme. Biochemistry 2019; 58:3169-3184. [PMID: 31246421 DOI: 10.1021/acs.biochem.9b00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly. The cfr gene has been identified as a mobile genetic element in diverse bacteria and in the genome of select Bacillales and Clostridiales species. Despite the importance of Cfr, few representatives have been purified and characterized in vitro. Here we show that Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays. C. difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The C-terminal domain can be truncated with minimal impact on C. difficile Cfr activity, but the rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation. These findings indicate an important purpose for the observed C-terminal iron in the native fusion protein. Bioinformatic analysis of the C. difficile Cfr Cys-rich domain shows that it is widespread (∼1400 homologues) as a stand-alone gene in pathogenic or commensal Bacilli and Clostridia, with >10% encoded adjacent to a predicted radical SAM RNA methylase. Although the domain is not essential for in vitro C. difficile Cfr activity, the genomic co-occurrence and high abundance in the human microbiome suggest a possible functional role for a specialized rubredoxin in certain radical SAM RNA methylases that are relevant to human health.
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Affiliation(s)
- James D Gumkowski
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Ryan J Martinie
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Patrick S Corrigan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Juan Pan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Matthew R Bauerle
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Mohamed Almarei
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Squire J Booker
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Howard Hughes Medical Institute , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Alexey Silakov
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Carsten Krebs
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Amie K Boal
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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9
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van Gestel J, Ackermann M, Wagner A. Microbial life cycles link global modularity in regulation to mosaic evolution. Nat Ecol Evol 2019; 3:1184-1196. [PMID: 31332330 DOI: 10.1038/s41559-019-0939-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 06/03/2019] [Indexed: 11/09/2022]
Abstract
Microbes are exposed to changing environments, to which they can respond by adopting various lifestyles such as swimming, colony formation or dormancy. These lifestyles are often studied in isolation, thereby giving a fragmented view of the life cycle as a whole. Here, we study lifestyles in the context of this whole. We first use machine learning to reconstruct the expression changes underlying life cycle progression in the bacterium Bacillus subtilis, based on hundreds of previously acquired expression profiles. This yields a timeline that reveals the modular organization of the life cycle. By analysing over 380 Bacillales genomes, we then show that life cycle modularity gives rise to mosaic evolution in which life stages such as motility and sporulation are conserved and lost as discrete units. We postulate that this mosaic conservation pattern results from habitat changes that make these life stages obsolete or detrimental. Indeed, when evolving eight distinct Bacillales strains and species under laboratory conditions that favour colony growth, we observe rapid and parallel losses of the sporulation life stage across species, induced by mutations that affect the same global regulator. We conclude that a life cycle perspective is pivotal to understanding the causes and consequences of modularity in both regulation and evolution.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland. .,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,The Santa Fe Institute, Santa Fe, NM, USA.
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10
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Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep 2019; 9:364. [PMID: 30674920 PMCID: PMC6344544 DOI: 10.1038/s41598-018-36247-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Ectoine synthase (EctC) is the signature enzyme for the production of ectoine, a compatible solute and chemical chaperone widely synthesized by bacteria as a cellular defense against the detrimental effects of osmotic stress. EctC catalyzes the last step in ectoine synthesis through cyclo-condensation of the EctA-formed substrate N-gamma-acetyl-L-2,4-diaminobutyric acid via a water elimination reaction. We have biochemically and structurally characterized the EctC enzyme from the thermo-tolerant bacterium Paenibacillus lautus (Pl). EctC is a member of the cupin superfamily and forms dimers, both in solution and in crystals. We obtained high-resolution crystal structures of the (Pl)EctC protein in forms that contain (i) the catalytically important iron, (ii) iron and the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid, and (iii) iron and the enzyme reaction product ectoine. These crystal structures lay the framework for a proposal for the EctC-mediated water-elimination reaction mechanism. Residues involved in coordinating the metal, the substrate, or the product within the active site of ectoine synthase are highly conserved among a large group of EctC-type proteins. Collectively, the biochemical, mutational, and structural data reported here yielded detailed insight into the structure-function relationship of the (Pl)EctC enzyme and are relevant for a deeper understanding of the ectoine synthase family as a whole.
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11
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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12
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Yadav S, Dubey SK. Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence. BIORESOURCE TECHNOLOGY 2018; 262:124-131. [PMID: 29702421 DOI: 10.1016/j.biortech.2018.04.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study cellulose degradation and whole genome sequence of Paenibacillus lautus BHU3 isolate. The 16S rRNA gene sequence analysis revealed genetic relatedness (99%) of Iso 7 with Paenibacillus lautus, Iso 8 with Paenibacillus lactis, and Iso 9 with Bacillus amyloliquefaciens. Clear zone formation followed by CMCase and FPase assays exhibited cellulolytic potential in the order: P. lautus > P. lactis > B. amyloliquefaciens. The most potent isolate, Paenibacillus lautus strain BHU3 was subjected to whole genome analysis with reference to the genomic basis of cellulose degradation. Results showed that P. lautus strain BHU3 contains 6234 protein coding genes of which, 316 were associated with the carbohydrate metabolism. Further, genomic CAZymes analysis indicated that the P. lautus strain BHU3 comprising a range of glycoside hydrolase (GH) family genes (143), may play the vital role(s) in enhancing the cellulolytic attributes, and could be the useful tool for lignocellulosic biomass degradation and waste management.
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Affiliation(s)
- Suman Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Suresh Kumar Dubey
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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13
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Prieto-Barajas CM, Alfaro-Cuevas R, Valencia-Cantero E, Santoyo G. Effect of seasonality and physicochemical parameters on bacterial communities in two hot spring microbial mats from Araró, Mexico. REV MEX BIODIVERS 2017. [DOI: 10.1016/j.rmb.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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14
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Kobayashi K, Kanesaki Y, Yoshikawa H. Genetic Analysis of Collective Motility of Paenibacillus sp. NAIST15-1. PLoS Genet 2016; 12:e1006387. [PMID: 27764113 PMCID: PMC5072692 DOI: 10.1371/journal.pgen.1006387] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/26/2016] [Indexed: 11/18/2022] Open
Abstract
Bacteria have developed various motility mechanisms to adapt to a variety of solid surfaces. A rhizosphere isolate, Paenibacillus sp. NAIST15-1, exhibited unusual motility behavior. When spotted onto 1.5% agar media, Paenibacillus sp. formed many colonies, each of which moved around actively at a speed of 3.6 μm/sec. As their density increased, each moving colony began to spiral, finally forming a static round colony. Despite its unusual motility behavior, draft genome sequencing revealed that both the composition and organization of flagellar genes in Paenibacillus sp. were very similar to those in Bacillus subtilis. Disruption of flagellar genes and flagellar stator operons resulted in loss of motility. Paenibacillus sp. showed increased transcription of flagellar genes and hyperflagellation on hard agar media. Thus, increased flagella and their rotation drive Paenibacillus sp. motility. We also identified a large extracellular protein, CmoA, which is conserved only in several Paenibacillus and related species. A cmoA mutant could neither form moving colonies nor move on hard agar media; however, motility was restored by exogenous CmoA. CmoA was located around cells and enveloped cell clusters. Comparison of cellular behavior between the wild type and cmoA mutant indicated that extracellular CmoA is involved in drawing water out of agar media and/or smoothing the cell surface interface. This function of CmoA probably enables Paenibacillus sp. to move on hard agar media.
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Affiliation(s)
- Kazuo Kobayashi
- Graduate School of Biological Sciences, Nara Institute of Science & Technology, Ikoma, Japan
- * E-mail:
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Japan
| | - Hirofumi Yoshikawa
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Japan
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Japan
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15
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Azizi M, Hemmat J, Seifati SM, Torktaz I, Karimi S. Characterization of a thermostable endoglucanase produced by Isoptericola variabilis sp. IDAH9. Braz J Microbiol 2016; 46:1225-34. [PMID: 26691485 PMCID: PMC4704623 DOI: 10.1590/s1517-838246420140846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/21/2015] [Indexed: 01/04/2023] Open
Abstract
This study aimed to isolate and evaluate the cellulase activity of cellulolytic
bacteria in hot springs of Dehloran, Ilam province, Iran. Water and sludge samples
were collected from the hot springs and the bacterial enrichment was performed in a
medium containing rice barn and carboxymethyl cellulose (CMC). The cultures were
incubated at 50 °C in aerobic conditions. The bacteria were isolated on CMC agar (1%)
medium. Cellulase assay of the isolates was measured by the evaluation of
endoglucanase enzyme activity, which is also called as carboxymethyl cellulase
(CMCase). The isolated thermotolerant bacteria were then identified and optimized for
the production of CMCase. Moreover, stabilizing elements of the enzyme were
identified with in silico approach. The chosen isolate was
identified as Isoptericola variabilis sp. IDAH9. The identified
strain produced the most thermostable CMCase at a concentration of 5.6 g/L of
ammonium sulfate, 9 g/L CMCase or 12 g/L rice bran, 0/6% Tween-80, and 0.2% sucrose.
The produced enzyme showed 80% of the residual activity after 1 h of incubation at 65
°C. In silico data indicated that the remaining residual activity
was due to the redundant stabilizing elements in the protein structure. Consequently,
I. variabilis can be isolated from the extreme environment and
has a thermostable endoglucanase which may be used for various applications after
studying them.
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Affiliation(s)
- Maryam Azizi
- Biotechnology Department, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Jafar Hemmat
- Biotechnology Department, Iranian Research Organization for Science and Technology, Tehran, Iran
| | | | - Ibrahim Torktaz
- Biotechnology Department, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Soodabeh Karimi
- Biotechnology Department, Iranian Research Organization for Science and Technology, Tehran, Iran
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16
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Chen SQ, Cai XH, Xie JL, Wei W, Wei DZ. Structural and biochemical properties of a novel pullulanase ofPaenibacillus lautusDSM 3035. STARCH-STARKE 2016. [DOI: 10.1002/star.201500333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Si-Qi Chen
- State Key Laboratory of Bioreactor Engineering; Newworld Institute of Biotechnology; East China University of Science and Technology; Shanghai P. R. China
| | - Xiang-Hai Cai
- State Key Laboratory of Bioreactor Engineering; Newworld Institute of Biotechnology; East China University of Science and Technology; Shanghai P. R. China
| | - Jing-Li Xie
- State Key Laboratory of Bioreactor Engineering; Newworld Institute of Biotechnology; East China University of Science and Technology; Shanghai P. R. China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering; Newworld Institute of Biotechnology; East China University of Science and Technology; Shanghai P. R. China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering; Newworld Institute of Biotechnology; East China University of Science and Technology; Shanghai P. R. China
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Brumm P, Land ML, Hauser LJ, Jeffries CD, Chang YJ, Mead DA. Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 2015; 10:81. [PMID: 26500717 PMCID: PMC4617443 DOI: 10.1186/s40793-015-0075-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes and average nucleotide identity, Geobacillus sp. Y412MC52 and the related Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus. The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of 3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057 bp and an average G + C content of 45 %. Y412MC52 possesses arabinan, arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of hemicellulose from biomass. Transport and utilization clusters are also present for other carbohydrates including starch, cellobiose, and α- and β-galactooligosaccharides.
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Affiliation(s)
| | | | | | | | - Yun-Juan Chang
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
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18
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Brumm P, Land ML, Hauser LJ, Jeffries CD, Chang YJ, Mead DA. Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 2015. [PMID: 26500717 DOI: 10.1186/s40793-015-0075-0 10.1186/s40793-016-0133-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes and average nucleotide identity, Geobacillus sp. Y412MC52 and the related Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus. The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of 3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057 bp and an average G + C content of 45 %. Y412MC52 possesses arabinan, arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of hemicellulose from biomass. Transport and utilization clusters are also present for other carbohydrates including starch, cellobiose, and α- and β-galactooligosaccharides.
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Affiliation(s)
| | | | | | | | - Yun-Juan Chang
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
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19
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Brumm PJ, Monsma S, Keough B, Jasinovica S, Ferguson E, Schoenfeld T, Lodes M, Mead DA. Complete Genome Sequence of Thermus aquaticus Y51MC23. PLoS One 2015; 10:e0138674. [PMID: 26465632 PMCID: PMC4605624 DOI: 10.1371/journal.pone.0138674] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/02/2015] [Indexed: 12/29/2022] Open
Abstract
Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser Basin of Yellowstone National Park. Remarkably, this T. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. Y51MC23 is a Gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C. Growth studies suggest that Y51MC23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular proteases and peptidases as well as transporter systems for amino acids and peptides. The genome was assembled de novo using a 350 bp fragment library (paired end sequencing) and an 8 kb long span mate pair library. A closed and finished genome was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on megaplasmids were identified on the chromosome. The Y51MC23 genome contains two full and two partial prophage as well as numerous CRISPR loci. The high identity and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is interesting, given the 8,800 km separation of the two hot springs from which they were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple morphologies present in cultures. The use of fluorescence microscopy reveals new details about these unusual morphological features, including the presence of multiple types of large and small spheres, often forming a confluent layer of spheres. Many of the spheres appear to be formed not from cell envelope or outer membrane components as previously believed, but from a remodeled peptidoglycan cell wall. These complex morphological forms may serve multiple functions in the survival of the organism, including food and nucleic acid storage as well as colony attachment and organization.
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Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLC, Fitchburg, Wisconsin, United States of America
- * E-mail:
| | - Scott Monsma
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | - Brendan Keough
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | | | - Erin Ferguson
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | | | - Michael Lodes
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | - David A. Mead
- Lucigen Corporation, Middleton, Wisconsin, United States of America
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20
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Gao G, Smith DI. Mate-Pair Sequencing as a Powerful Clinical Tool for the Characterization of Cancers with a DNA Viral Etiology. Viruses 2015; 7:4507-28. [PMID: 26262638 PMCID: PMC4576192 DOI: 10.3390/v7082831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/16/2015] [Accepted: 07/29/2015] [Indexed: 01/18/2023] Open
Abstract
DNA viruses are known to be associated with a variety of different cancers. Human papillomaviruses (HPV) are a family of viruses and several of its sub-types are classified as high-risk HPVs as they are found to be associated with the development of a number of different cancers. Almost all cervical cancers appear to be driven by HPV infection and HPV is also found in most cancers of the anus and at least half the cancers of the vulva, penis and vagina, and increasingly found in one sub-type of head and neck cancers namely oropharyngeal squamous cell carcinoma. Our understanding of HPVs role in cancer development comes from extensive studies done on cervical cancer and it has just been assumed that HPV plays an identical role in the development of all other cancers arising in the presence of HPV sequences, although this has not been proven. Most invasive cervical cancers have the HPV genome integrated into one or more sites within the human genome. One powerful tool to examine all the sites of HPV integration in a cancer but that also provides a comprehensive view of genomic alterations in that cancer is the use of next generation sequencing of mate-pair libraries produced from the DNA isolated. We will describe how this powerful technology can provide important information about the genomic organization within an individual cancer genome, and how this has demonstrated that HPVs role in oropharyngeal squamous cell carcinoma is distinct from that in cervical cancer. We will also describe why the sequencing of mate-pair libraries could be a powerful clinical tool for the management of patients with a DNA viral etiology and how this could quickly transform the care of these patients.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.
| | - David I Smith
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.
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21
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Brumm PJ, De Maayer P, Mead DA, Cowan DA. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. Front Microbiol 2015; 6:430. [PMID: 26029180 PMCID: PMC4428132 DOI: 10.3389/fmicb.2015.00430] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
Abstract
In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.
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Affiliation(s)
- Phillip J. Brumm
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
| | - Pieter De Maayer
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, South Africa
| | - David A. Mead
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
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Brumm P, Land ML, Hauser LJ, Jeffries CD, Chang YJ, Mead DA. Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 2015. [PMID: 26500717 PMCID: PMC4617443 DOI: 10.1186/s40793-015-0075-0+10.1186/s40793-016-0133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes and average nucleotide identity, Geobacillus sp. Y412MC52 and the related Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus. The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of 3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057 bp and an average G + C content of 45 %. Y412MC52 possesses arabinan, arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of hemicellulose from biomass. Transport and utilization clusters are also present for other carbohydrates including starch, cellobiose, and α- and β-galactooligosaccharides.
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Affiliation(s)
| | | | | | | | - Yun-Juan Chang
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
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23
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Affiliation(s)
- David J Studholme
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
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24
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Widderich N, Höppner A, Pittelkow M, Heider J, Smits SHJ, Bremer E. Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. PLoS One 2014; 9:e93809. [PMID: 24714029 PMCID: PMC3979721 DOI: 10.1371/journal.pone.0093809] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Ectoine and hydroxyectoine are well-recognized members of the compatible solutes and are widely employed by microorganisms as osmostress protectants. The EctABC enzymes catalyze the synthesis of ectoine from the precursor L-aspartate-β-semialdehyde. A subgroup of the ectoine producers can convert ectoine into 5-hydroxyectoine through a region-selective and stereospecific hydroxylation reaction. This compatible solute possesses stress-protective and function-preserving properties different from those of ectoine. Hydroxylation of ectoine is carried out by the EctD protein, a member of the non-heme-containing iron (II) and 2-oxoglutarate-dependent dioxygenase superfamily. We used the signature enzymes for ectoine (EctC) and hydroxyectoine (EctD) synthesis in database searches to assess the taxonomic distribution of potential ectoine and hydroxyectoine producers. Among 6428 microbial genomes inspected, 440 species are predicted to produce ectoine and of these, 272 are predicted to synthesize hydroxyectoine as well. Ectoine and hydroxyectoine genes are found almost exclusively in Bacteria. The genome context of the ect genes was explored to identify proteins that are functionally associated with the synthesis of ectoines; the specialized aspartokinase Ask_Ect and the regulatory protein EctR. This comprehensive in silico analysis was coupled with the biochemical characterization of ectoine hydroxylases from microorganisms that can colonize habitats with extremes in salinity (Halomonas elongata), pH (Alkalilimnicola ehrlichii, Acidiphilium cryptum), or temperature (Sphingopyxis alaskensis, Paenibacillus lautus) or that produce hydroxyectoine very efficiently over ectoine (Pseudomonas stutzeri). These six ectoine hydroxylases all possess similar kinetic parameters for their substrates but exhibit different temperature stabilities and differ in their tolerance to salts. We also report the crystal structure of the Virgibacillus salexigens EctD protein in its apo-form, thereby revealing that the iron-free structure exists already in a pre-set configuration to incorporate the iron catalyst. Collectively, our work defines the taxonomic distribution and salient biochemical properties of the ectoine hydroxylase protein family and contributes to the understanding of its structure.
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Affiliation(s)
- Nils Widderich
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Emeritus Group R.K. Thauer, Marburg, Germany
| | - Astrid Höppner
- X-Ray Facility and Crystal Farm, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marco Pittelkow
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- * E-mail: (SHGS); (EB)
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (SHGS); (EB)
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Xie JB, Du Z, Bai L, Tian C, Zhang Y, Xie JY, Wang T, Liu X, Chen X, Cheng Q, Chen S, Li J. Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes. PLoS Genet 2014; 10:e1004231. [PMID: 24651173 PMCID: PMC3961195 DOI: 10.1371/journal.pgen.1004231] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/26/2014] [Indexed: 11/18/2022] Open
Abstract
We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ(70)-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.
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Affiliation(s)
- Jian-Bo Xie
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Zhenglin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Lanqing Bai
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Changfu Tian
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Yunzhi Zhang
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Jiu-Yan Xie
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Tianshu Wang
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Xiaomeng Liu
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Xi Chen
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (QC); (SC)
| | - Sanfeng Chen
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
- * E-mail: (QC); (SC)
| | - Jilun Li
- Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, P. R. China
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Moreno Switt AI, Andrus AD, Ranieri ML, Orsi RH, Ivy R, den Bakker HC, Martin NH, Wiedmann M, Boor KJ. Genomic comparison of sporeforming bacilli isolated from milk. BMC Genomics 2014; 15:26. [PMID: 24422886 PMCID: PMC3902026 DOI: 10.1186/1471-2164-15-26] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/08/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6°C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under these conditions. To gain a better understanding of genomic features of these important spoilage organisms and to identify candidate genomic features that may facilitate cold growth in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers representing isolates that can and cannot grow in milk at 6°C. RESULTS The genomes for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and Viridibacillus into three distinct well supported clades and further classified the Paenibacillus strains characterized here into three distinct clades, including (i) clade I, which contains one strain able to grow at 6°C in skim milk broth and one strain not able to grow under these conditions, (ii) clade II, which contains three strains able to grow at 6°C in skim milk broth, and (iii) clade III, which contains two strains unable to grow under these conditions. While all Paenibacillus genomes were found to include multiple copies of genes encoding β-galactosidases, clade II strains showed significantly higher numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of strains able to grow at 6°C and strains unable to grow at this temperature identified numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at 6°C, including peptidases with cold-adapted features (flexibility and disorder regions in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone DnaJ). CONCLUSIONS Through a comparative genomics approach we identified a number of genomic features that may relate to the ability of selected Paenibacillus strains to cause spoilage of refrigerated fluid milk. With additional experimental evidence, these data will facilitate identification of targets to detect and control Gram positive spore formers in fluid milk.
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Affiliation(s)
- Andrea I Moreno Switt
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Alexis D Andrus
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Matthew L Ranieri
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Renato H Orsi
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Reid Ivy
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Henk C den Bakker
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Kathryn J Boor
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Li Y, Pan Y, She Q, Chen L. A novel carboxyl-terminal protease derived from Paenibacillus lautus CHN26 exhibiting high activities at multiple sites of substrates. BMC Biotechnol 2013; 13:89. [PMID: 24161150 PMCID: PMC4231363 DOI: 10.1186/1472-6750-13-89] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/17/2013] [Indexed: 01/11/2023] Open
Abstract
Background Carboxyl-terminal protease (CtpA) plays essential functions in posttranslational protein processing in prokaryotic and eukaryotic cells. To date, only a few bacterial ctpA genes have been characterized. Here we cloned and characterized a novel CtpA. The encoding gene, ctpAp (ctpA of Paenibacillus lautus), was derived from P. lautus CHN26, a Gram-positive bacterium isolated by functional screening. Recombinant protein was obtained from protein over-expression in Escherichia coli and the biochemical properties of the enzyme were investigated. Results Screening of environmental sediment samples with a skim milk-containing medium led to the isolation of a P. lautus CHN26 strain that exhibited a high proteolytic activity. A gene encoding a carboxyl-terminal protease (ctpAp) was cloned from the isolate and characterized. The deduced mature protein contains 466 aa with a calculated molecular mass of 51.94 kDa, displaying 29-38% amino acid sequence identity to characterized bacterial CtpA enzymes. CtpAp contains an unusual catalytic dyad (Ser309-Lys334) and a PDZ substrate-binding motif, characteristic for carboxyl-terminal proteases. CtpAp was expressed as a recombinant protein and characterized. The purified enzyme showed an endopeptidase activity, which effectively cleaved α S1- and β- casein substrates at carboxyl-terminus as well as at multiple internal sites. Furthermore, CtpAp exhibited a high activity at room temperature and strong tolerance to conventional protease inhibitors, demonstrating that CtpAp is a novel endopeptidase. Conclusions Our work on CtpA represents the first investigation of a member of Family II CtpA enzymes. The gene was derived from a newly isolated P. lautus CHN26 strain exhibiting a high protease activity in the skim milk assay. We have demonstrated that CtpAp is a novel endopeptidase with distinct cleavage specificities, showing a strong potential in biotechnology and industry applications.
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Affiliation(s)
| | | | | | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Engineering Centre for Quality Control and Risk Assessment of Aquatic Products, College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai 201306, People's Republic of China.
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Abbott DW, Thomas D, Pluvinage B, Boraston AB. An ancestral member of the polysaccharide lyase family 2 displays endolytic activity and magnesium dependence. Appl Biochem Biotechnol 2013; 171:1911-23. [PMID: 24013861 DOI: 10.1007/s12010-013-0483-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
Polysaccharide lyases (PLs) are enzymes that cleave glycosidic linkages in hexuronate polysaccharides, such as homogalacturonan (HG), using a β-elimination mechanism. Traditionally, PL activities on HG have been associated with catalytic calcium cofactors, unusually high pH optima, and arginine Brønstead bases. Recently, however, PL families that harness transition metal cofactors, utilize lysine and histidine Brønstead bases, and display more neutral pH optima have been described. One such family is PL2, which has members found primarily in phytopathogenic (e.g., Dickeya spp. and Pectobacterium spp.) or enteropathogenic (e.g., Yersinia spp.) bacterial species. PL2 is divided into two major subfamilies that are correlated with either an endolytic or exolytic activity. This study has focused on the activity of a PL2 member, which is not classified within either subfamily and helps to illuminate the origin of enzyme activities within the family. In addition, the role of Mg(2+) as a preferential catalytic metal for an intracellular PL2 (PaePL2) is described. The implications for the relationship between catalytic metal selectivity and the cellular location of pectate lyase-mediated catalysis are discussed.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Station, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada,
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