1
|
Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
Collapse
Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| |
Collapse
|
2
|
Curci N, Strazzulli A, Iacono R, De Lise F, Maurelli L, Di Fenza M, Cobucci-Ponzano B, Moracci M. Xyloglucan Oligosaccharides Hydrolysis by Exo-Acting Glycoside Hydrolases from Hyperthermophilic Microorganism Saccharolobus solfataricus. Int J Mol Sci 2021; 22:3325. [PMID: 33805072 PMCID: PMC8037949 DOI: 10.3390/ijms22073325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
In the field of biocatalysis and the development of a bio-based economy, hemicellulases have attracted great interest for various applications in industrial processes. However, the study of the catalytic activity of the lignocellulose-degrading enzymes needs to be improved to achieve the efficient hydrolysis of plant biomasses. In this framework, hemicellulases from hyperthermophilic archaea show interesting features as biocatalysts and provide many advantages in industrial applications thanks to their stability in the harsh conditions encountered during the pretreatment process. However, the hemicellulases from archaea are less studied compared to their bacterial counterpart, and the activity of most of them has been barely tested on natural substrates. Here, we investigated the hydrolysis of xyloglucan oligosaccharides from two different plants by using, both synergistically and individually, three glycoside hydrolases from Saccharolobus solfataricus: a GH1 β-gluco-/β-galactosidase, a α-fucosidase belonging to GH29, and a α-xylosidase from GH31. The results showed that the three enzymes were able to release monosaccharides from xyloglucan oligosaccharides after incubation at 65 °C. The concerted actions of β-gluco-/β-galactosidase and the α-xylosidase on both xyloglucan oligosaccharides have been observed, while the α-fucosidase was capable of releasing all α-linked fucose units from xyloglucan from apple pomace, representing the first GH29 enzyme belonging to subfamily A that is active on xyloglucan.
Collapse
Affiliation(s)
- Nicola Curci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
| | - Federica De Lise
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Luisa Maurelli
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| |
Collapse
|
3
|
Zayulina KS, Kochetkova TV, Piunova UE, Ziganshin RH, Podosokorskaya OA, Kublanov IV. Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis. Front Microbiol 2020; 10:2972. [PMID: 31998263 PMCID: PMC6965361 DOI: 10.3389/fmicb.2019.02972] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 01/16/2023] Open
Abstract
A novel hyperthermophilic, anaerobic filamentous archaeon, Thermofilum adornatum strain 1910bT, is capable of growing with cellulose as its sole carbon and energy source. This strain was isolated from a terrestrial hot spring in Kamchatka, Russia. The isolate 1910bT grew optimally at a temperature of 80°C and a pH of 5.5-6.0, producing cell-bound inducible cellulases. During genome analysis, genes, encoding various glycosidases (GHs) involved in oligo- and polysaccharide hydrolysis and genes for the fermentation of sugars were identified. No homologs of currently known cellulase families were found among the GHs encoded by the 1910bT genome, suggesting that novel proteins are involved. To figure this out, a proteomic analysis of cells grown on cellulose or pyruvate (as a control) was performed. Both in-depth genomic and proteomic analyses revealed four proteins (Cel25, Cel30, Cel40, and Cel45) that were the most likely to be involved in the cellulose hydrolysis in this archaeon. Two of these proteins (Cel30 and Cel45) were hypothetical according to genome analysis, while the other two (Cel25 and Cel40) have GH3 and GH1 domains, respectively. The respective genes were heterologously expressed in Escherichia coli BL21 (DE3), and enzymatic activities of recombinant proteins were measured with carboxymethyl cellulose (CMC), Avicel and cellobiose as substrates. It was revealed that the Cel30 and Cel25 proteins were likely exoglucanases with side beta-glucosidase and endoglucanase activities, that Cel40 was a multifunctional glucanase capable of hydrolyzing beta-1,4-glucosides of various lengths, and that Cel45 was an endoglucanase with side exoglucanase activity. Taking into account that the cellulolytic activity of T. adornatum 1910bT surface protein fractions was inducible, that recombinant Cel25 and Cel30 were much less active than Cel40 and Cel45, and that their gene expressions were (almost) non-induced by CMC, we suggest that Cel40 and Cel45 play a major role in the degradation of cellulose, while Cel25 and Cel30 act only as accessory enzymes.
Collapse
Affiliation(s)
- Kseniya S. Zayulina
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Kochetkova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ulyana E. Piunova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga A. Podosokorskaya
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
4
|
Strazzulli A, Cobucci-Ponzano B, Iacono R, Giglio R, Maurelli L, Curci N, Schiano-di-Cola C, Santangelo A, Contursi P, Lombard V, Henrissat B, Lauro FM, Fontes CMGA, Moracci M. Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments. FEBS J 2019; 287:1116-1137. [PMID: 31595646 DOI: 10.1111/febs.15080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/23/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
Abstract
The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy), to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here, we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T = 85 °C and pH 5.5; T = 92 °C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in silico analysis led to 14 934 and 17 652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarchaeota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~ 2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ -dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity. DATABASES: The sequencing reads are available in the NCBI Sequence Read Archive (SRA) database under the accession numbers SRR7545549 (Pool1) and SRR7545550 (Pool2). The sequences of GH5_Pool2 and GH109_Pool2 are available in GenBank database under the accession numbers MK869723 and MK86972, respectively. The environmental data relative to Pool1 and Pool2 (NCBI BioProject PRJNA481947) are available in the Biosamples database under the accession numbers SAMN09692669 (Pool1) and SAMN09692670 (Pool2).
Collapse
Affiliation(s)
- Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | | | - Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Rosa Giglio
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Nicola Curci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Corinna Schiano-di-Cola
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Annalisa Santangelo
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, INRA, AFMB, USC 1408, Aix Marseille Univ, France
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, INRA, AFMB, USC 1408, Aix Marseille Univ, France.,Department Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Carlos M G A Fontes
- NZYTech LDA, Estrada Do Paco Do Lumiar, Lisbon, Portugal.,CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Portugal
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| |
Collapse
|
5
|
Fusco FA, Ronca R, Fiorentino G, Pedone E, Contursi P, Bartolucci S, Limauro D. Biochemical characterization of a thermostable endomannanase/endoglucanase from Dictyoglomus turgidum. Extremophiles 2017; 22:131-140. [DOI: 10.1007/s00792-017-0983-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/20/2017] [Indexed: 11/21/2022]
|
6
|
Stark H, Wolf J, Albersmeier A, Pham TK, Hofmann JD, Siebers B, Kalinowski J, Wright PC, Neumann-Schaal M, Schomburg D. Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus. FEBS J 2017; 284:2078-2095. [PMID: 28497654 DOI: 10.1111/febs.14105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/27/2017] [Accepted: 05/08/2017] [Indexed: 11/28/2022]
Abstract
The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It has been well characterised concerning the utilisation of numerous carbohydrates as carbon source. However, its amino acid metabolism, especially the degradation of single amino acids, is not as well understood. In this work, we performed metabolic modelling as well as metabolome, transcriptome and proteome analysis on cells grown on caseinhydrolysate as carbon source in order to draw a comprehensive picture of amino acid metabolism in S. solfataricus P2. We found that 10 out of 16 detectable amino acids are imported from the growth medium. Overall, uptake of glutamate, methionine, leucine, phenylalanine and isoleucine was the highest of all observed amino acids. Our simulations predict an incomplete degradation of leucine and tyrosine to organic acids, and in accordance with this, we detected the export of branched-chain and aromatic organic acids as well as amino acids, ammonium and trehalose into the culture supernatants. The branched-chain amino acids as well as phenylalanine and tyrosine are degraded to organic acids via oxidative Stickland reactions. Such reactions are known for prokaryotes capable of anaerobic growth, but so far have never been observed in an obligate aerobe. Also, 3-methyl-2-butenoate and 2-methyl-2-butenoate are for the first time found as products of modified Stickland reactions for the degradation of branched-chain amino acids. This work presents the first detailed description of branched-chain and aromatic amino acid catabolism in S. solfataricus.
Collapse
Affiliation(s)
- Helge Stark
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Germany
| | - Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Germany
| | | | - Trong K Pham
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, UK
| | - Julia D Hofmann
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Germany
| | - Phillip C Wright
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, UK
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Germany
| |
Collapse
|
7
|
Dong M, Yang Y, Tang X, Shen J, Xu B, Li J, Wu Q, Zhou J, Ding J, Han N, Mu Y, Huang Z. NaCl-, protease-tolerant and cold-active endoglucanase from Paenibacillus sp. YD236 isolated from the feces of Bos frontalis. Springerplus 2016; 5:746. [PMID: 27376014 PMCID: PMC4909688 DOI: 10.1186/s40064-016-2360-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
Bos frontalis, which consumes
bamboo and weeds, may have evolved unique gastrointestinal microorganisms that digest cellulase. A Paenibacillus sp. YD236 strain was isolated from B. frontalis feces, from which a GH8 endoglucanase gene, pglue8 (1107 bp, 54.5 % GC content), encoding a 368-residue polypeptide (PgluE8, 40.4 kDa) was cloned. PgluE8 efficiently hydrolyzed barley-β-d-glucan followed by CMC-Na, soluble starch, laminarin, and glucan from black yeast optimally at pH 5.5 and 50 °C, and retained 78.6, 41.6, and 34.5 % maximum activity when assayed at 20, 10, and 0 °C, respectively. Enzyme activity remained above 176.6 % after treatment with 10.0 mM β-mercaptoethanol, and was 83.0, 78, and 56 % after pre-incubation in 30 % (w/v) NaCl, 16.67 mg/mL trypsin, and 160.0 mg/mL protease K, respectively. Cys23 and Cys364 residues were critical for PgluE8 activity. pglue8, identified from B. frontalis feces for the first time in this study, is a potential alternative for applications including food processing, washing, and animal feed preparation.
Collapse
Affiliation(s)
- Mingjie Dong
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Yunjuan Yang
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Xianghua Tang
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Jidong Shen
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Bo Xu
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Junjun Li
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Qian Wu
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Junpei Zhou
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Junmei Ding
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Nanyu Han
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Yuelin Mu
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| | - Zunxi Huang
- School of Life Science, Yunnan Normal University, Kunming, 650500 People's Republic of China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, No.1 Yuhua District, Chenggong, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500 Yunnan People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 People's Republic of China
| |
Collapse
|
8
|
Piñar G, Dalnodar D, Voitl C, Reschreiter H, Sterflinger K. Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms. PLoS One 2016; 11:e0148279. [PMID: 26885815 DOI: 10.1371/journal.pone.0148279] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/15/2016] [Indexed: 11/19/2022] Open
Abstract
Background The prosperity of Hallstatt (Salzkammergut region, Austria) is based on the richness of salt in the surrounding mountains and salt mining, which is documented as far back as 1500 years B.C. Substantial archaeological evidence of Bronze and Iron Age salt mining has been discovered, with a wooden staircase (1108 B.C.) being one of the most impressive and well preserved finds. However, after its discovery, fungal mycelia have been observed on the surface of the staircase, most probably due to airborne contamination after its find. Objective As a basis for the further preservation of this valuable object, the active micro-flora was examined to investigate the presence of potentially biodegradative microorganisms. Results Most of the strains isolated from the staircase showed to be halotolerant and halophilic microorganisms, due to the saline environment of the mine. Results derived from culture-dependent assays revealed a high fungal diversity, including both halotolerant and halophilic fungi, the most dominant strains being members of the genus Phialosimplex (synonym: Aspergillus). Additionally, some typical cellulose degraders, namely Stachybotrys sp. and Cladosporium sp. were detected. Numerous bacterial strains were isolated and identified as members of 12 different genera, most of them being moderately halophilic species. The most dominant isolates affiliated with species of the genera Halovibrio and Marinococcus. Halophilic archaea were also isolated and identified as species of the genera Halococcus and Halorubrum. Molecular analyses complemented the cultivation assays, enabling the identification of some uncultivable archaea of the genera Halolamina, Haloplanus and Halobacterium. Results derived from fungi and bacteria supported those obtained by cultivation methods, exhibiting the same dominant members in the communities. Conclusion The results clearly showed the presence of some cellulose degraders that may become active if the requirements for growth and the environmental conditions turn suitable; therefore, these microorganisms must be regarded as a threat to the wood.
Collapse
|
9
|
Jachlewski S, Jachlewski WD, Linne U, Bräsen C, Wingender J, Siebers B. Isolation of Extracellular Polymeric Substances from Biofilms of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius. Front Bioeng Biotechnol 2015; 3:123. [PMID: 26380258 PMCID: PMC4550784 DOI: 10.3389/fbioe.2015.00123] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
Extracellular polymeric substances (EPS) are the major structural and functional components of microbial biofilms. The aim of this study was to establish a method for EPS isolation from biofilms of the thermoacidophilic archaeon, Sulfolobus acidocaldarius, as a basis for EPS analysis. Biofilms of S. acidocaldarius were cultivated on the surface of gellan gum-solidified Brock medium at 78°C for 4 days. Five EPS extraction methods were compared, including shaking of biofilm suspensions in phosphate buffer, cation-exchange resin (CER) extraction, and stirring with addition of EDTA, crown ether, or NaOH. With respect to EPS yield, impact on cell viability, and compatibility with subsequent biochemical analysis, the CER extraction method was found to be the best suited isolation procedure resulting in the detection of carbohydrates and proteins as the major constituents and DNA as a minor component of the EPS. Culturability of CER-treated cells was not impaired. Analysis of the extracellular proteome using two-dimensional gel electrophoresis resulted in the detection of several hundreds of protein spots, mainly with molecular masses of 25–116 kDa and pI values of 5–8. Identification of proteins suggested a cytoplasmic origin for many of these proteins, possibly released via membrane vesicles or biofilm-inherent cell lysis during biofilm maturation. Functional analysis of EPS proteins, using fluorogenic substrates as well as zymography, demonstrated the activity of diverse enzyme classes, such as proteases, lipases, esterases, phosphatases, and glucosidases. In conclusion, the CER extraction method, as previously applied to bacterial biofilms, also represents a suitable method for isolation of water soluble EPS from the archaeal biofilms of S. acidocaldarius, allowing the investigation of composition and function of EPS components in these types of biofilms.
Collapse
Affiliation(s)
- Silke Jachlewski
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Witold D Jachlewski
- Aquatic Microbiology, Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Uwe Linne
- Core Facility for Mass Spectrometry and Elemental Analysis, Department of Chemistry and SYNMIKRO, Philipps-University of Marburg , Marburg , Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Jost Wingender
- Aquatic Microbiology, Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| |
Collapse
|
10
|
Leis B, Heinze S, Angelov A, Pham VTT, Thürmer A, Jebbar M, Golyshin PN, Streit WR, Daniel R, Liebl W. Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon. Front Bioeng Biotechnol 2015; 3:95. [PMID: 26191525 PMCID: PMC4486847 DOI: 10.3389/fbioe.2015.00095] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/17/2015] [Indexed: 01/27/2023] Open
Abstract
Extreme habitats serve as a source of enzymes that are active under extreme conditions and are candidates for industrial applications. In this work, six large-insert mixed genomic libraries were screened for hydrolase activities in a broad temperature range (8-70°C). Among a variety of hydrolytic activities, one fosmid clone, derived from a library of pooled isolates of hyperthermophilic archaea from deep sea vents, displayed hydrolytic activity on carboxymethyl cellulose substrate plates at 70°C but not at lower temperatures. Sequence analysis of the fosmid insert revealed a gene encoding a novel glycoside hydrolase family 12 (GHF12) endo-1,4-β-glucanase, termed Cel12E. The enzyme shares 45% sequence identity with a protein from the archaeon Thermococcus sp. AM4 and displays a unique multidomain architecture. Biochemical characterization of Cel12E revealed a remarkably thermostable protein, which appears to be of archaeal origin. The enzyme displayed maximum activity at 92°C and was active on a variety of linear 1,4-β-glucans like carboxymethyl cellulose, β-glucan, lichenan, and phosphoric acid swollen cellulose. The protein is able to bind to various insoluble β-glucans. Product pattern analysis indicated that Cel12E is an endo-cleaving β-glucanase. Cel12E expands the toolbox of hyperthermostable archaeal cellulases with biotechnological potential.
Collapse
Affiliation(s)
- Benedikt Leis
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Simon Heinze
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Angel Angelov
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Vu Thuy Trang Pham
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Georg-August University Göttingen, Göttingen, Germany
| | - Mohamed Jebbar
- Laboratoire de Microbiologie des Environnements Extrêmes-UMR 6197 (CNRS-Ifremer-UBO), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, Plouzané, France
| | | | - Wolfgang R. Streit
- Fakultät für Mathematik, Informatik und Naturwissenschaften Biologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Georg-August University Göttingen, Göttingen, Germany
| | - Wolfgang Liebl
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| |
Collapse
|
11
|
Contursi P, Fusco S, Cannio R, She Q. Molecular biology of fuselloviruses and their satellites. Extremophiles 2014; 18:473-89. [DOI: 10.1007/s00792-014-0634-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
|
12
|
|
13
|
Lalithambika S, Peterson L, Dana K, Blum P. Carbohydrate hydrolysis and transport in the extreme thermoacidophile Sulfolobus solfataricus. Appl Environ Microbiol 2012; 78:7931-8. [PMID: 22941087 DOI: 10.1128/AEM.01758-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extremely thermoacidophilic microbes, such as Sulfolobus solfataricus, are strict chemoheterotrophs despite their geologic niche. To clarify their ecophysiology, the overlapping roles of endoglucanases and carbohydrate transporters were examined during growth on soluble cellodextrins as the sole carbon and energy source. Strain-specific differences in genome structure implied a unique role for one of three endogenous endoglucanases. Plasmid-based endoglucanase expression promoted the consumption of oligosaccharides, including cellohexaose (G6) through cellonanaose (G9). Protein transporters required for cellodextrin uptake were identified through mutagenesis and complementation of an ABC transporter cassette, including a putative oligosaccharide binding protein. In addition, ablation of the binding protein compromised growth on glucose and alpha-linked oligosaccharides while inactivation of a previously described glucose transporter had no apparent impact. These data demonstrate that S. solfataricus employs a redundant mechanism for soluble cellodextrin catabolism having both substrate uptake and extracytoplasmic hydrolytic components.
Collapse
|
14
|
Klose H, Röder J, Girfoglio M, Fischer R, Commandeur U. Hyperthermophilic endoglucanase for in planta lignocellulose conversion. Biotechnol Biofuels 2012; 5:63. [PMID: 22928996 PMCID: PMC3497586 DOI: 10.1186/1754-6834-5-63] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/06/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND The enzymatic conversion of lignocellulosic plant biomass into fermentable sugars is a crucial step in the sustainable and environmentally friendly production of biofuels. However, a major drawback of enzymes from mesophilic sources is their suboptimal activity under established pretreatment conditions, e.g. high temperatures, extreme pH values and high salt concentrations. Enzymes from extremophiles are better adapted to these conditions and could be produced by heterologous expression in microbes, or even directly in the plant biomass. RESULTS Here we show that a cellulase gene (sso1354) isolated from the hyperthermophilic archaeon Sulfolobus solfataricus can be expressed in plants, and that the recombinant enzyme is biologically active and exhibits the same properties as the wild type form. Since the enzyme is inactive under normal plant growth conditions, this potentially allows its expression in plants without negative effects on growth and development, and subsequent heat-inducible activation. Furthermore we demonstrate that the recombinant enzyme acts in high concentrations of ionic liquids and can therefore degrade α-cellulose or even complex cell wall preparations under those pretreatment conditions. CONCLUSION The hyperthermophilic endoglucanase SSO1354 with its unique features is an excellent tool for advanced biomass conversion. Here we demonstrate its expression in planta and the possibility for post harvest activation. Moreover the enzyme is suitable for combined pretreatment and hydrolysis applications.
Collapse
Affiliation(s)
- Holger Klose
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Juliane Röder
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Michele Girfoglio
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- Institute of Protein Biochemistry, CNR, Via P. Castellino 111, 80131, Naples, Italy
| | - Rainer Fischer
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstrasse 6, 52074, Aachen, Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| |
Collapse
|
15
|
Girfoglio M, Rossi M, Cannio R. Cellulose degradation by Sulfolobus solfataricus requires a cell-anchored endo-β-1-4-glucanase. J Bacteriol 2012; 194:5091-100. [PMID: 22821975 DOI: 10.1128/JB.00672-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A sequence encoding a putative extracellular endoglucanase (sso1354) was identified in the complete genome sequence of Sulfolobus solfataricus. The encoded protein shares signature motifs with members of glycoside hydrolases family 12. After an unsuccessful first attempt at cloning the full-length coding sequences in Escherichia coli, an active but unstable recombinant enzyme lacking a 27-residue N-terminal sequence was generated. This 27-amino-acid sequence shows significant similarity with corresponding regions in the sugar binding proteins AraS, GlcS, and TreS of S. solfataricus that are responsible for anchoring them to the plasma membrane. A strategy based on an effective vector/host genetic system for Sulfolobus and on expression control by the promoter of the S. solfataricus gene which encodes the glucose binding protein allowed production of the enzyme in sufficient quantities for study. In fact, the enzyme expressed in S. solfataricus was stable and highly thermoresistant and showed optimal activity at low pH and high temperature. The protein was detected mainly in the plasma membrane fraction, confirming the structural similarity to the sugar binding proteins. The results of the protein expression in the two different hosts showed that the SSO1354 enzyme is endowed with an endo-β-1-4-glucanase activity and specifically hydrolyzes cellulose. Moreover, it also shows significant but distinguishable specificity toward several other sugar polymers, such as lichenan, xylan, debranched arabinan, pachyman, and curdlan.
Collapse
|
16
|
Sharma A, Kawarabayasi Y, Satyanarayana T. Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles 2012; 16:1-19. [PMID: 22080280 DOI: 10.1007/s00792-011-0402-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/05/2011] [Indexed: 01/05/2023]
Abstract
Acidophiles are ecologically and economically important group of microorganisms, which thrive in acidic natural (solfataric fields, sulfuric pools) as well as artificial man-made (areas associated with human activities such as mining of coal and metal ores) environments. They possess networked cellular adaptations to regulate pH inside the cell. Several extracellular enzymes from acidophiles are known to be functional at much lower pH than the cytoplasmic pH. Enzymes like amylases, proteases, ligases, cellulases, xylanases, α-glucosidases, endoglucanases, and esterases stable at low pH are known from various acidophilic microbes. The possibility of improving them by genetic engineering and directed evolution will further boost their industrial applications. Besides biocatalysts, other biomolecules such as plasmids, rusticynin, and maltose-binding protein have also been reported from acidophiles. Some strategies for circumventing the problems encountered in expressing genes encoding proteins from extreme acidophiles have been suggested. The investigations on the analysis of crystal structures of some acidophilic proteins have thrown light on their acid stability. Attempts are being made to use thermoacidophilic microbes for biofuel production from lignocellulosic biomass. The enzymes from acidophiles are mainly used in polymer degradation.
Collapse
|
17
|
Wang H, Squina F, Segato F, Mort A, Lee D, Pappan K, Prade R. High-temperature enzymatic breakdown of cellulose. Appl Environ Microbiol 2011; 77:5199-206. [PMID: 21685160 DOI: 10.1128/AEM.00199-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulose is an abundant and renewable biopolymer that can be used for biofuel generation; however, structural entrapment with other cell wall components hinders enzyme-substrate interactions, a key bottleneck for ethanol production. Biomass is routinely subjected to treatments that facilitate cellulase-cellulose contacts. Cellulases and glucosidases act by hydrolyzing glycosidic bonds of linear glucose β-1,4-linked polymers, producing glucose. Here we describe eight high-temperature-operating cellulases (TCel enzymes) identified from a survey of thermobacterial and archaeal genomes. Three TCel enzymes preferentially hydrolyzed soluble cellulose, while two preferred insoluble cellulose such as cotton linters and filter paper. TCel enzymes had temperature optima ranging from 85°C to 102°C. TCel enzymes were stable, retaining 80% of initial activity after 120 h at 85°C. Two modes of cellulose breakdown, i.e., with endo- and exo-acting glucanases, were detected, and with two-enzyme combinations at 85°C, synergistic cellulase activity was observed for some enzyme combinations.
Collapse
|
18
|
Liang C, Fioroni M, Rodríguez-Ropero F, Xue Y, Schwaneberg U, Ma Y. Directed evolution of a thermophilic endoglucanase (Cel5A) into highly active Cel5A variants with an expanded temperature profile. J Biotechnol 2011; 154:46-53. [PMID: 21501637 DOI: 10.1016/j.jbiotec.2011.03.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/03/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022]
Abstract
Cel5A is a highly active endoglucanase from Thermoanaerobacter tengcongensis MB4, displaying an optimal temperature range between 75 and 80°C. After three rounds of error-prone PCR and screening of 4700 mutants, five variants of Cel5A with improved activities were identified by Congo Red based screening method. Compared with the wild type, the best variants 3F6 and C3-13 display 135±6% and 193±8% of the wild type specific activity for the substrate carboxymethyl cellulose (CMC), besides improvements in the relative expression level in Escherichia coli system. Remarkable are especially the improvements in activities at reduced temperatures (50% of maximum activity at 50°C and about 45°C respectively, while 65°C for the wild type). Molecular Dynamics simulations performed on the 3F6 and C3-13 variants show a decreased number of intra-Cel5A hydrogen bonds compared to the wild type, implying a more flexible protein skeleton which correlates well to the higher catalytic activity at lower temperatures. To investigate functions of each individual amino acid position site-directed (saturation) mutagenesis were generated and screened. Amino acid positions Val249 and Ile321 were found to be crucial for improving activity and residue Ile13 (encoded by rare codon AUA) yields an improved expression level in E. coli.
Collapse
Affiliation(s)
- Chaoning Liang
- State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | | | | | | | | | | |
Collapse
|
19
|
Liang C, Xue Y, Fioroni M, Rodríguez-ropero F, Zhou C, Schwaneberg U, Ma Y. Cloning and characterization of a thermostable and halo-tolerant endoglucanase from Thermoanaerobacter tengcongensis MB4. Appl Microbiol Biotechnol 2011; 89:315-26. [DOI: 10.1007/s00253-010-2842-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 08/10/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
|
20
|
Kim TW, Chokhawala HA, Nadler D, Blanch HW, Clark DS. Binding modules alter the activity of chimeric cellulases: Effects of biomass pretreatment and enzyme source. Biotechnol Bioeng 2010; 107:601-11. [DOI: 10.1002/bit.22856] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
21
|
Abstract
Domestic ethanol production in the USA relies on starch feedstocks using a first generation bioprocess. Enzymes that contribute to this industry remain of critical value in new and established markets as commodity additives and for in planta production. A transition to non-food feedstocks is both desirable and essential to enable larger scale production. This objective would relieve dependence on foreign oil and strengthen the national economy. Feedstocks derived from corn stover, wheat straw, perennial grasses and timber require pretreatment to increase the accessibility of the cellulosic and hemicellulosic substrates to commodity enzymes for saccharification, which is followed by fermentation-based conversion of monosaccharides to ethanol. Hot acid pretreatment is the industrial standard method used to achieve deconstruction of lignocellulosic biomass. Therefore, enzymes that tolerate both acid and heat may contribute toward the improvement of lignocellulosic biomass processing. These enzymes are produced naturally by extremely thermophilic microbes, sometimes called extremophiles. This review summarizes information on enzymes from selected (acido)thermophiles that mediate saccharification of alpha- and beta-linked carbohydrates of relevance to biomass processing.
Collapse
Affiliation(s)
- P S Miller
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | |
Collapse
|
22
|
Abstract
Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones. The method performs satisfactorily, yielding a 35-fold cross-validation procedure, a sensitivity of 100% and specificity 98.41% with the Matthews' correlation coefficient being equal to 0.964. This particular method is currently the only available method for the prediction of secretory SPs in archaea, and performs consistently and significantly better compared with other available predictors that were trained on sequences of eukaryotic or bacterial origin. Searching 48 completely sequenced archaeal genomes we identified 9437 putative SPs. The method, PRED-SIGNAL, and the results are freely available for academic users at http://bioinformatics.biol.uoa.gr/PRED-SIGNAL/ and we anticipate that it will be a valuable tool for the computational analysis of archaeal genomes.
Collapse
Affiliation(s)
- P G Bagos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece.
| | | | | | | | | |
Collapse
|
23
|
Maurelli L, Giovane A, Esposito A, Moracci M, Fiume I, Rossi M, Morana A. Evidence that the xylanase activity from Sulfolobus solfataricus Oα is encoded by the endoglucanase precursor gene (sso1354) and characterization of the associated cellulase activity. Extremophiles 2008; 12:689-700. [DOI: 10.1007/s00792-008-0175-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 05/26/2008] [Indexed: 10/22/2022]
|
24
|
Birbir M, Calli B, Mertoglu B, Bardavid RE, Oren A, Ogmen MN, Ogan A. Extremely halophilic Archaea from Tuz Lake, Turkey, and the adjacent Kaldirim and Kayacik salterns. World J Microbiol Biotechnol 2007; 23:309-16. [DOI: 10.1007/s11274-006-9223-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
25
|
Morana A, Paris O, Maurelli L, Rossi M, Cannio R. Gene cloning and expression in Escherichia coli of a bi-functional β-d-xylosidase/α-l-arabinosidase from Sulfolobus solfataricus involved in xylan degradation. Extremophiles 2006; 11:123-32. [PMID: 17033733 DOI: 10.1007/s00792-006-0020-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
An open reading frame encoding a putative bi-functional beta-D-xylosidase/alpha-L-arabinosidase (Sso3032) was identified on the genome sequence of Sulfolobus solfataricus P2, the predicted gene product showing high amino-acid sequence similarity to bacterial and eukaryal individual beta-D-xylosidases and alpha-L-arabinosidases as well as bi-functional enzymes such as the protein from Thermoanaerobacter ethanolicus and barley. The sequence was PCR amplified from genomic DNA of S. solfataricus P2 and heterologous gene expression obtained in Escherichia coli, under optimal conditions for overproduction. Specific assays performed at 75 degrees C revealed the presence in the transformed E. coli cell extracts of this archaeal activity involved in sugar hydrolysis and specific for both substrates. The recombinant protein was purified by thermal precipitation of the host proteins and ethanol fractionation and other properties, such as high thermal activity and thermostability could be determined. The protein showed a homo-tetrameric structure with a subunit of molecular mass of 82.0 kDa which was in perfect agreement with that deduced from the cloned gene. Northern blot analysis of the xarS gene indicates that it is specifically induced by xylan and repressed by monosaccharides like D-glucose and L-arabinose.
Collapse
Affiliation(s)
- Alessandra Morana
- Istituto di Biochimica delle Proteine, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | | | | | | | | |
Collapse
|
26
|
Huang Y, Krauss G, Cottaz S, Driguez H, Lipps G. A highly acid-stable and thermostable endo-beta-glucanase from the thermoacidophilic archaeon Sulfolobus solfataricus. Biochem J 2005; 385:581-8. [PMID: 15456402 PMCID: PMC1134732 DOI: 10.1042/bj20041388] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The thermoacidophilic archaeon Sulfolobus solfataricus P2 encodes three hypothetic endo-beta-glucanases, SSO1354, SSO1949 and SSO2534. We cloned and expressed the gene sso1949 encoding the 334 amino acids containing protein SSO1949, which can be classified as a member of glycoside hydrolase family 12. The purified recombinant enzyme hydrolyses carboxymethylcellulose as well as cello-oligomers, with cellobiose and cellotriose as main reaction products. By following the hydrolysis of a fluorescently labelled cellohexaoside under a wide variety of conditions, we show that SSO1949 is a unique extremophilic enzyme. This archaeal enzyme has a pH optimum of approx. pH 1.8 and a temperature optimum of approx. 80 degrees C. Furthermore, the enzyme is thermostable, with a half-life of approx. 8 h at 80 degrees C and pH 1.8. The thermostability is strongly pH-dependent. At neutral pH, the thermal inactivation rate is nearly two orders of magnitude higher than at pH 1.8. Homology modelling suggests that the catalytic domain of SSO1949 has a similar fold to other mesophilic, acidophilic and neutral cellulases. The presence of a signal peptide indicates that SSO1949 is a secreted protein, which enables S. solfataricus to use cellulose as an external carbon source. It appears that SSO1949 is perfectly adapted to the extreme environment in solfataric pools. A cellulolytic enzyme with such a combination of stability and activity at high temperatures and low pH has not been described so far and could be a valuable tool for the large-scale hydrolysis of cellulose under acidic conditions.
Collapse
Affiliation(s)
- Yiwei Huang
- *Institute of Biochemistry, University of Bayreuth, Universitätstrasse 30, 95447 Bayreuth, Germany
| | - Gerhard Krauss
- *Institute of Biochemistry, University of Bayreuth, Universitätstrasse 30, 95447 Bayreuth, Germany
| | - Sylvain Cottaz
- †Centre de Recherches sur les Macromolécules Végétales, FR CNRS 2607, BP 53, 38041 Grenoble cedex 9, France
| | - Hugues Driguez
- †Centre de Recherches sur les Macromolécules Végétales, FR CNRS 2607, BP 53, 38041 Grenoble cedex 9, France
| | - Georg Lipps
- *Institute of Biochemistry, University of Bayreuth, Universitätstrasse 30, 95447 Bayreuth, Germany
- To whom correspondence should be addressed (email )
| |
Collapse
|
27
|
Perevalova AA, Svetlichny VA, Kublanov IV, Chernyh NA, Kostrikina NA, Tourova TP, Kuznetsov BB, Bonch-Osmolovskaya EA. Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus. Int J Syst Evol Microbiol 2005; 55:995-999. [PMID: 15879224 DOI: 10.1099/ijs.0.63378-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain Z-1312T, was isolated from a freshwater hot spring of the Uzon caldera (Kamchatka Peninsula, Russia). The cells were regular cocci, 1–4 μm in diameter, with one long flagellum. The cell envelope was composed of a globular layer attached to the cytoplasmic membrane. The temperature range for growth was 63–89 °C, with an optimum between 80 and 82 °C. The pH range for growth at 80 °C was 4·8–6·8, with an optimum at pH 6·0. Strain Z-1312Tgrew by hydrolysis and/or fermentation of a wide range of polymeric and monomeric substrates, including agarose, amygdalin, arabinose, arbutin, casein hydrolysate, cellulose (filter paper, microcrystalline cellulose, carboxymethyl cellulose), dextran, dulcitol, fructose, lactose, laminarin, lichenan, maltose, pectin, peptone, ribose, starch and sucrose. No growth was detected on glucose, xylose, mannitol or sorbitol. Growth products when sucrose or starch were used as the substrate were acetate, H2and CO2. Elemental sulfur, thiosulfate and nitrate added as potential electron acceptors for anaerobic respiration did not stimulate growth when tested with starch as the substrate. H2at 100 % in the gas phase did not inhibit growth on starch or peptone. The G+C content of the DNA was 42·5 mol%. 16S rRNA gene sequence analysis placed the isolated strain Z-1312Tas a member of the genusDesulfurococcus, where it represented a novel species, for which the nameDesulfurococcus fermentanssp. nov. (type strain Z-1312T=DSM 16532T=VKM V-2316T) is proposed.
Collapse
Affiliation(s)
- A A Perevalova
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - V A Svetlichny
- Lehrstuhl für Mikrobiologie, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - I V Kublanov
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - N A Chernyh
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - N A Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - T P Tourova
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - B B Kuznetsov
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, Moscow 117312, Russia
| | - E A Bonch-Osmolovskaya
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| |
Collapse
|
28
|
Abstract
Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are the subject of current experimental evaluation. Topics covered include cultivation methods, recent achievements in genomics, which are of key importance for the development of new biotechnological tools, and the application of wild-type biomasses, engineered microorganisms, enzymes and specific metabolites in particular bioprocesses of industrial interest.
Collapse
Affiliation(s)
- Chiara Schiraldi
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Faculty of Medicine, II University of Naples, via Costantinopoli 16, 80138 Naples, Italy
| | - Mariateresa Giuliano
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Faculty of Medicine, II University of Naples, via Costantinopoli 16, 80138 Naples, Italy
| | - Mario De Rosa
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Faculty of Medicine, II University of Naples, via Costantinopoli 16, 80138 Naples, Italy
| |
Collapse
|