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Liang J, Huang H, Wang Y, Li L, Yi J, Wang S. A Cytoplasmic NAD(P)H-Dependent Polysulfide Reductase with Thiosulfate Reductase Activity from the Hyperthermophilic Bacterium Thermotoga maritima. Microbiol Spectr 2022; 10:e0043622. [PMID: 35762779 PMCID: PMC9431562 DOI: 10.1128/spectrum.00436-22] [Citation(s) in RCA: 2] [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: 02/03/2022] [Accepted: 06/05/2022] [Indexed: 11/22/2022] Open
Abstract
Thermotoga maritima is an anaerobic hyperthermophilic bacterium that efficiently produces H2 by fermenting carbohydrates. High concentration of H2 inhibits the growth of T. maritima, and S0 could eliminate the inhibition and stimulate the growth through its reduction. The mechanism of T. maritima sulfur reduction, however, has not been fully understood. Herein, based on its similarity with archaeal NAD(P)H-dependent sulfur reductases (NSR), the ORF THEMA_RS02810 was identified and expressed in Escherichia coli, and the recombinant protein was characterized. The purified flavoprotein possessed NAD(P)H-dependent S0 reductase activity (1.3 U/mg for NADH and 0.8 U/mg for NADPH), polysulfide reductase activity (0.32 U/mg for NADH and 0.35 U/mg for NADPH), and thiosulfate reductase activity (2.3 U/mg for NADH and 2.5 U/mg for NADPH), which increased 3~4-folds by coenzyme A stimulation. Quantitative RT-PCR analysis showed that nsr was upregulated together with the mbx, yeeE, and rnf genes when the strain grew in S0- or thiosulfate-containing medium. The mechanism for sulfur reduction in T. maritima was discussed, which may affect the redox balance and energy metabolism of T. maritima. Genome search revealed that NSR homolog is widely distributed in thermophilic bacteria and archaea, implying its important role in the sulfur cycle of geothermal environments. IMPORTANCE The reduction of S0 and thiosulfate is essential in the sulfur cycle of geothermal environments, in which thermophiles play an important role. Despite previous research on some sulfur reductases of thermophilic archaea, the mechanism of sulfur reduction in thermophilic bacteria is still not clearly understood. Herein, we confirmed the presence of a cytoplasmic NAD(P)H-dependent polysulfide reductase (NSR) from the hyperthermophile T. maritima, with S0, polysulfide, and thiosulfate reduction activities, in contrast to other sulfur reductases. When grown in S0- or thiosulfate-containing medium, its expression was upregulated. And the putative membrane-bound MBX and Rnf may also play a role in the metabolism, which might influence the redox balance and energy metabolism of T. maritima. This is distinct from the mechanism of sulfur reduction in mesophiles such as Wolinella succinogenes. NSR homologs are widely distributed among heterotrophic thermophiles, suggesting that they may be vital in the sulfur cycle in geothermal environments.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Haiyan Huang
- Department of Pathogen Biology, School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Yubo Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Lexin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
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Wang Y, Wang J, Zhang Z, Yang J, Turunen O, Xiong H. High-temperature behavior of hyperthermostable Thermotoga maritima xylanase XYN10B after designed and evolved mutations. Appl Microbiol Biotechnol 2022; 106:2017-2027. [PMID: 35171339 DOI: 10.1007/s00253-022-11823-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 11/24/2022]
Abstract
A hyperthermostable xylanase XYN10B from Thermotoga maritima (PDB code 1VBR, GenBank accession number KR078269) was subjected to site-directed and error-prone PCR mutagenesis. From the selected five mutants, the two site-directed mutants (F806H and F806V) showed a 3.3-3.5-fold improved enzyme half-life at 100 °C. The mutant XYNA generated by error-prone PCR showed slightly improved stability at 100 °C and a lower Km. In XYNB and XYNC, the additional mutations over XYNA decreased the thermostability and temperature optimum, while elevating the Km. In XYNC, two large side-chains were introduced into the protein's interior. Micro-differential scanning calorimetry (DSC) showed that the melting temperature (Tm) dropped in XYNB and XYNC from 104.9 °C to 93.7 °C and 78.6 °C, respectively. The detrimental mutations showed that extremely thermostable enzymes can tolerate quite radical mutations in the protein's interior and still retain high thermostability. The analysis of mutations (F806H and F806V) in a hydrophobic area lining the substrate-binding region indicated that active site hydrophobicity is important for high activity at extreme temperatures. Although polar His at 806 provided higher stability, the hydrophobic Phe at 806 provided higher activity than His. This study generates an understanding of how extreme thermostability and high activity are formed in GH10 xylanases. KEY POINTS: • Characterization and molecular dynamics simulations of TmXYN10B and its mutants • Explanation of structural stability of GH10 xylanase.
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Affiliation(s)
- Yawei Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430048, China
| | - Jing Wang
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Zhongqiang Zhang
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Jiangke Yang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430048, China
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland.
| | - Hairong Xiong
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China.
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LaFrance BJ, Cassidy-Amstutz C, Nichols RJ, Oltrogge LM, Nogales E, Savage DF. The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein. Sci Rep 2021; 11:22810. [PMID: 34815415 PMCID: PMC8610991 DOI: 10.1038/s41598-021-01932-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/30/2021] [Accepted: 10/29/2021] [Indexed: 11/09/2022] Open
Abstract
Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based 'organelles' found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~ 25-50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure-function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model Thermotoga maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryo-EM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the Thermotoga maritima encapsulin, the decameric cargo protein with fivefold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier-it also plays a significant role in the structure and function of the cargo enzyme.
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Affiliation(s)
- Benjamin J LaFrance
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Robert J Nichols
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
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Medeiros Almeida V, Chaudhuri A, Cangussu Cardoso MV, Matsuyama BY, Monteiro Ferreira G, Goulart Trossini GH, Salinas RK, Loria JP, Marana SR. Role of a high centrality residue in protein dynamics and thermal stability. J Struct Biol 2021; 213:107773. [PMID: 34320379 DOI: 10.1016/j.jsb.2021.107773] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/24/2021] [Revised: 07/02/2021] [Accepted: 07/21/2021] [Indexed: 11/27/2022]
Abstract
Centralities determined from Residue Interaction Networks (RIN) in proteins have been used to predict aspects of their structure and dynamics. Here, we correlate the Eigenvector Centrality (Ec) with the rate constant for thermal denaturation (kden) of the HisF protein from Thermotoga maritima based on 12 single alanine substitution mutants. The molecular basis for this correlation was further explored by studying a mutant containing a replacement of a high Ec residue, Y182A, which displayed increased kden at 80 °C. The crystallographic structure of this mutant showed few changes, mostly in two flexible loops. The 1H-15N -HSQC showed only subtle changes of cross peak positions for residues located near the mutation site and scattered throughout the structure. However, the comparison of the RIN showed that Y182 is the vertex of a set of high centrality residues that spreads throughout the HisF structure, which is lacking in the mutant. Cross-correlation displacements of Cα calculated from a molecular dynamics simulation at different temperatures showed that the Y182A mutation reduced the correlated movements in the HisF structure above 70 °C. 1H-15N NMR chemical shift covariance using temperature as perturbation were consistent with these results. In conclusion the increase in temperature drives the structure of the mutant HisF-Y182A into a less connected state, richer in non-concerted motions, located predominantly in the C-terminal half of the protein where Y182 is placed. Conversely, wild-type HisF responds to increased temperature as a single unit. Hence the replacement of a high Ec residue alters the distribution of thermal energy through HisF structure.
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Affiliation(s)
- Vitor Medeiros Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Apala Chaudhuri
- Departament of Chemistry, Yale University, New Haven, CT, United States
| | | | - Bruno Yasui Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Roberto Kopke Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - J Patrick Loria
- Departament of Chemistry, Yale University, New Haven, CT, United States; Departament of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Sandro Roberto Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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Marjanovic A, Ramírez-Palacios CJ, Masman MF, Drenth J, Otzen M, Marrink SJ, Janssen DB. Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. Protein Eng Des Sel 2021; 34:gzab016. [PMID: 34258615 PMCID: PMC8277567 DOI: 10.1093/protein/gzab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/02/2021] [Revised: 06/03/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes.
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Affiliation(s)
- Antonija Marjanovic
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Carlos J Ramírez-Palacios
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Marcelo F Masman
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jeroen Drenth
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marleen Otzen
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Bunn BM, Xu M, Webb CM, Viswanathan R. Biocatalysts from cyanobacterial hapalindole pathway afford antivirulent isonitriles against MRSA. J Biosci 2021; 46:37. [PMID: 33952728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The emergence of resistance to frontline antibiotics has called for novel strategies to combat serious pathogenic infections. Methicillin-resistant Staphylococcus aureus [MRSA] is one such pathogen. As opposed to traditional antibiotics, bacteriostatic anti-virulent agents disarm MRSA, without exerting pressure, that cause resistance. Herein, we employed a thermophilic Thermotoga maritima tryptophan synthase (TmTrpB1) enzyme followed by an isonitrile synthase and Fe(II)-α-ketoglutarate-dependent oxygenase, in sequence as biocatalysts to produce antivirulent indole vinyl isonitriles. We report on conversion of simple derivatives of indoles to their C3-vinyl isonitriles, as the enzymes employed here demonstrated broader substrate tolerance. In toto, eight distinct L-Tryptophan derived α-amino acids (7) were converted to their bioactive vinyl isonitriles (3) by action of an isonitrile synthase (WelI1) and an Fe(II)-α-ketoglutarate-dependent oxygenase (WelI3) yielding structural variants possessing antivirulence against MRSA. These indole vinyl isonitriles at 10 μg/mL are effective as antivirulent compounds against MRSA, as evidenced through analysis of rabbit blood hemolysis assay. Based on a homology modelling exercise, of enzyme-substrate complexes, we deduced potential three dimensional alignments of active sites and glean mechanistic insights into the substrate tolerance of the Fe(II)-α-ketoglutarate-dependent oxygenase.
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Rix G, Watkins-Dulaney EJ, Almhjell PJ, Boville CE, Arnold FH, Liu CC. Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. Nat Commun 2020; 11:5644. [PMID: 33159067 PMCID: PMC7648111 DOI: 10.1038/s41467-020-19539-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 06/24/2020] [Accepted: 10/19/2020] [Indexed: 01/11/2023] Open
Abstract
Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolve the Thermotoga maritima tryptophan synthase β-subunit (TmTrpB) through multi-mutation pathways in many independent replicates, selecting only on TmTrpB's primary activity of synthesizing L-tryptophan from indole and L-serine. We find that the resulting sequence-diverse TmTrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of biomolecular functions.
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Affiliation(s)
- Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Ella J Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christina E Boville
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aralez Bio, Emeryville, CA, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chang C Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
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Smaldone G, Ruggiero A, Balasco N, Vitagliano L. Development of a Protein Scaffold for Arginine Sensing Generated through the Dissection of the Arginine-Binding Protein from Thermotoga maritima. Int J Mol Sci 2020; 21:ijms21207503. [PMID: 33053818 PMCID: PMC7589609 DOI: 10.3390/ijms21207503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Arginine is one of the most important nutrients of living organisms as it plays a major role in important biological pathways. However, the accumulation of arginine as consequence of metabolic defects causes hyperargininemia, an autosomal recessive disorder. Therefore, the efficient detection of the arginine is a field of relevant biomedical/biotechnological interest. Here, we developed protein variants suitable for arginine sensing by mutating and dissecting the multimeric and multidomain structure of Thermotoga maritima arginine-binding protein (TmArgBP). Indeed, previous studies have shown that TmArgBP domain-swapped structure can be manipulated to generate simplified monomeric and single domain scaffolds. On both these stable scaffolds, to measure tryptophan fluorescence variations associated with the arginine binding, a Phe residue of the ligand binding pocket was mutated to Trp. Upon arginine binding, both mutants displayed a clear variation of the Trp fluorescence. Notably, the single domain scaffold variant exhibited a good affinity (~3 µM) for the ligand. Moreover, the arginine binding to this variant could be easily reverted under very mild conditions. Atomic-level data on the recognition process between the scaffold and the arginine were obtained through the determination of the crystal structure of the adduct. Collectively, present data indicate that TmArgBP scaffolds represent promising candidates for developing arginine biosensors.
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Affiliation(s)
- Giovanni Smaldone
- IRCCS SDN, Via Emanuele Gianturco, 113 80143 Naples, Italy
- Correspondence: (G.S.); (A.R.)
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
- Correspondence: (G.S.); (A.R.)
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
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Swinehart W, Deutsch C, Sarachan KL, Luthra A, Bacusmo JM, de Crécy-Lagard V, Swairjo MA, Agris PF, Iwata-Reuyl D. Specificity in the biosynthesis of the universal tRNA nucleoside N6-threonylcarbamoyl adenosine (t 6A)-TsaD is the gatekeeper. RNA 2020; 26:1094-1103. [PMID: 32385138 PMCID: PMC7430679 DOI: 10.1261/rna.075747.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
N6-threonylcarbamoyl adenosine (t6A) is a nucleoside modification found in all kingdoms of life at position 37 of tRNAs decoding ANN codons, which functions in part to restrict translation initiation to AUG and suppress frameshifting at tandem ANN codons. In Bacteria the proteins TsaB, TsaC (or C2), TsaD, and TsaE, comprise the biosynthetic apparatus responsible for t6A formation. TsaC(C2) and TsaD harbor the relevant active sites, with TsaC(C2) catalyzing the formation of the intermediate threonylcarbamoyladenosine monophosphate (TC-AMP) from ATP, threonine, and CO2, and TsaD catalyzing the transfer of the threonylcarbamoyl moiety from TC-AMP to A37 of substrate tRNAs. Several related modified nucleosides, including hydroxynorvalylcarbamoyl adenosine (hn6A), have been identified in select organisms, but nothing is known about their biosynthesis. To better understand the mechanism and structural constraints on t6A formation, and to determine if related modified nucleosides are formed via parallel biosynthetic pathways or the t6A pathway, we carried out biochemical and biophysical investigations of the t6A systems from E. coli and T. maritima to address these questions. Using kinetic assays of TsaC(C2), tRNA modification assays, and NMR, our data demonstrate that TsaC(C2) exhibit relaxed substrate specificity, producing a variety of TC-AMP analogs that can differ in both the identity of the amino acid and nucleotide component, whereas TsaD displays more stringent specificity, but efficiently produces hn6A in E. coli and T. maritima tRNA. Thus, in organisms that contain modifications such as hn6A in their tRNA, we conclude that their origin is due to formation via the t6A pathway.
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Affiliation(s)
- William Swinehart
- Department of Chemistry, Portland State University, Portland, Oregon 97201, USA
| | - Christopher Deutsch
- Department of Chemistry, Portland State University, Portland, Oregon 97201, USA
| | - Kathryn L Sarachan
- The RNA Institute, State University of New York, Albany, New York 12222, USA
| | - Amit Luthra
- Department of Chemistry and Biochemistry, and The Viral Information Institute, San Diego State University, San Diego, California 92182, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainsville, Florida 32611, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainsville, Florida 32611, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, and The Viral Information Institute, San Diego State University, San Diego, California 92182, USA
| | - Paul F Agris
- The RNA Institute, State University of New York, Albany, New York 12222, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, Oregon 97201, USA
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Cho EJ, Nguyen QA, Lee YG, Song Y, Park BJ, Bae HJ. Enhanced Biomass Yield of and Saccharification in Transgenic Tobacco Over-Expressing β-Glucosidase. Biomolecules 2020; 10:E806. [PMID: 32456184 PMCID: PMC7278181 DOI: 10.3390/biom10050806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/04/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022] Open
Abstract
Here, we report an increase in biomass yield and saccharification in transgenic tobacco plants (Nicotiana tabacumL.) overexpressing thermostable β-glucosidase from Thermotoga maritima, BglB, targeted to the chloroplasts and vacuoles. The transgenic tobacco plants showed phenotypic characteristics that were significantly different from those of the wild-type plants. The biomass yield and life cycle (from germination to flowering and harvest) of the transgenic tobacco plants overexpressing BglB were 52% higher and 36% shorter than those of the wild-type tobacco plants, respectively, indicating a change in the genome transcription levels in the transgenic tobacco plants. Saccharification in biomass samples from the transgenic tobacco plants was 92% higher than that in biomass samples from the wild-type tobacco plants. The transgenic tobacco plants required a total investment (US$/year) corresponding to 52.9% of that required for the wild-type tobacco plants, but the total biomass yield (kg/year) of the transgenic tobacco plants was 43% higher than that of the wild-type tobacco plants. This approach could be applied to other plants to increase biomass yields and overproduce β-glucosidase for lignocellulose conversion.
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Affiliation(s)
- Eun Jin Cho
- Bio-Energy Research Center, Chonnam National University, Gwangju 61186, Korea; (E.J.C.); (Q.A.N.); (Y.S.)
| | - Quynh Anh Nguyen
- Bio-Energy Research Center, Chonnam National University, Gwangju 61186, Korea; (E.J.C.); (Q.A.N.); (Y.S.)
| | - Yoon Gyo Lee
- Department of Bioenergy science and Technology, Chonnam National University, Gwangju 61186, Korea;
| | - Younho Song
- Bio-Energy Research Center, Chonnam National University, Gwangju 61186, Korea; (E.J.C.); (Q.A.N.); (Y.S.)
| | - Bok Jae Park
- Division of Business and Commerce, Chonnam National University, Yeosu 500-749, Korea;
| | - Hyeun-Jong Bae
- Bio-Energy Research Center, Chonnam National University, Gwangju 61186, Korea; (E.J.C.); (Q.A.N.); (Y.S.)
- Department of Bioenergy science and Technology, Chonnam National University, Gwangju 61186, Korea;
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11
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Wang S, Lin R, Ren Y, Zhang T, Lu H, Wang L, Fan D. Non-chromatographic purification of thermostable endoglucanase from Thermotoga maritima by fusion with a hydrophobic elastin-like polypeptide. Protein Expr Purif 2020; 173:105634. [PMID: 32325232 DOI: 10.1016/j.pep.2020.105634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/26/2020] [Accepted: 03/31/2020] [Indexed: 01/08/2023]
Abstract
Endoglucanase EG12B from Thermotoga maritima is a thermophilic cellulase that has great potential for industrial applications. Here, to enable the selective purification of EG12B in a simple and efficient manner, an elastin-like polypeptide (ELP), which acts as a thermally responsive polypeptide, was fused with EG12B to enable its inverse phase transition cycling (ITC). A small gene library comprising ELPs from ELP5 to ELP50 was constructed using recursive directional ligation by plasmid reconstruction. ELP50 was added to the C-terminus of EG12B as a fusion tag to obtain the expression vector pET28-EG12B-ELP50, which was transformed into Escherichia coli BL21 (DE3) to enable the expression of fusion protein via IPTG induction. Gray scanning analysis revealed that the EG12B-ELP50 expression level was up to about 35% of the total cellular proteins. After three rounds of ITC, 8.14 mg of EG12B-ELP50 was obtained from 500-mL lysogeny broth culture medium. The recovery rate and purification fold of EG12B-ELP50 purified by ITC reached 78.1% and 11.8, respectively. The cellulase activity assay showed that EG12B-ELP50 had a better thermostability, higher optimal temperature, and longer half-life than those of free EG12B. Overall, our results suggested that ELP50 could be used as a favorable fusion tag, providing a rapid, simple, and inexpensive strategy for non-chromatographic target-protein purification.
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Affiliation(s)
- Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, China; Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, 710069, China.
| | - Rui Lin
- Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, 300052, China
| | - Yanyan Ren
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, China
| | - Daidi Fan
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, 710069, China.
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12
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Wang L, Peng R, Tian Y, Gao J, Wang B, Yao Q. A thermostable 5-enolpyruvylshikimate-3-phosphate synthase from Thermotoga maritima enhances glyphosate tolerance in Escherichia coli and transgenic Arabidopsis. Extremophiles 2019; 23:659-667. [PMID: 31338597 DOI: 10.1007/s00792-019-01118-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 02/14/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) overexpression, attempting to provide excess EPSPS to combine with glyphosate, is one way to improve glyphosate resistance of plants. The EPSPS in extremophiles which is selected by nature to withstand the evolutionary pressure may possess some potential-specific biological functions. In this study, we reported the cloning, expression and enzymatic characterization of a novel Class II EPSPS AroAT. maritima from Thermotoga maritima MSB8. The enzyme showed low sequence identities with other EPSPSs, and was one of the most thermostable EPSPSs so far, which showed the optimum enzyme activity at 80 °C. The enzyme maintains the activity below 50 °C and in a wide range of pH 4.0-10, which indicated its stability under rough environment, especially in tropical regions and alkaline soil. Excellent Ki/Km value of AroAT. maritima suggested that the enzyme showed powerful competitive binding capacity of PEP over glyphosate and high glyphosate tolerance. Furthermore, aroAT. maritima gene was transformed into Arabidopsis thaliana. The transgenic lines were resistant to 15 mM glyphosate, which proved the application value in the cultivation of glyphosate-tolerant plants.
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Affiliation(s)
- Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Jianjie Gao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
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13
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Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry 2018; 57:5864-5876. [PMID: 30204415 PMCID: PMC6189639 DOI: 10.1021/acs.biochem.8b00783] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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] [Indexed: 01/25/2023]
Abstract
The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-, and tetrasaccharides. Two of these proteins (tmMBP1 and tmMBP2) share significant sequence identity, approximately 90%, while the third (tmMBP3) shares less than 40% identity. MBP from Escherichia coli (ecMBP) shares 35% sequence identity with the tmMBPs. This subset of MBP isoforms offers an interesting opportunity to investigate the mechanisms underlying the evolution of substrate specificity and affinity profiles in a genome where redundant MBP genes are present. In this study, the X-ray crystal structures of tmMBP1, tmMBP2, and tmMBP3 are reported in the absence and presence of oligosaccharides. tmMBP1 and tmMBP2 have binding pockets that are larger than that of tmMBP3, enabling them to bind to larger substrates, while tmMBP1 and tmMBP2 also undergo substrate-induced hinge bending motions (∼52°) that are larger than that of tmMBP3 (∼35°). Small-angle X-ray scattering was used to compare protein behavior in solution, and computer simulations provided insights into dynamics of these proteins. Comparing quantitative protein-substrate interactions and dynamical properties of tmMBPs with those of the promiscuous ecMBP and disaccharide selective Thermococcus litoralis MBP provides insights into the features that enable selective binding. Collectively, the results provide insights into how the structure and dynamics of tmMBP homologues enable them to differentiate between a myriad of chemical entities while maintaining their common fold.
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Affiliation(s)
- Shantanu Shukla
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
| | - Caeley Gullett
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dean A. A. Myles
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Deparment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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14
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Luthra A, Swinehart W, Bayooz S, Phan P, Stec B, Iwata-Reuyl D, Swairjo MA. Structure and mechanism of a bacterial t6A biosynthesis system. Nucleic Acids Res 2018; 46:1395-1411. [PMID: 29309633 PMCID: PMC5814804 DOI: 10.1093/nar/gkx1300] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 11/12/2022] Open
Abstract
The universal N(6)-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs is central to translational fidelity. In bacteria, t6A biosynthesis is catalyzed by the proteins TsaB, TsaC/TsaC2, TsaD and TsaE. Despite intense research, the molecular mechanisms underlying t6A biosynthesis are poorly understood. Here, we report biochemical and biophysical studies of the t6A biosynthesis system from Thermotoga maritima. Small angle X-ray scattering analysis reveals a symmetric 2:2 stoichiometric complex of TsaB and TsaD (TsaB2D2), as well as 2:2:2 complex (TsaB2D2E2), in which TsaB acts as a dimerization module, similar to the role of Pcc1 in the archaeal system. The TsaB2D2 complex is the minimal platform for the binding of one tRNA molecule, which can then accommodate a single TsaE subunit. Kinetic data demonstrate that TsaB2D2 alone, and a TsaB2D2E1 complex with TsaE mutants deficient in adenosine triphosphatase (ATPase) activity, can catalyze only a single cycle of t6A synthesis, while gel shift experiments provide evidence that the role of TsaE-catalyzed ATP hydrolysis occurs after the release of product tRNA. Based on these results, we propose a model for t6A biosynthesis in bacteria.
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Affiliation(s)
- Amit Luthra
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - William Swinehart
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Susan Bayooz
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Phuc Phan
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Boguslaw Stec
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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15
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Brzezinski K, Czyrko J, Sliwiak J, Nalewajko-Sieliwoniuk E, Jaskolski M, Nocek B, Dauter Z. S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. Int J Biol Macromol 2017; 104:584-596. [PMID: 28629859 PMCID: PMC7888557 DOI: 10.1016/j.ijbiomac.2017.06.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 03/30/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022]
Abstract
Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity. To explain the mechanism of thermal activation, two crystal structures of the inactive form of T. maritima SAHase (iTmSAHase) were determined for an incomplete binary complex with the reduced cofactor (NADH), and in a mixture of binary complexes with NADH and with adenosine. In contrast to active SAHases, in iTmSAHase only two of the four subunits contain a bound cofactor, predominantly in its non-reactive, reduced state. Moreover, the closed-like conformation of the cofactor-containing subunits precludes substrate delivery to the active site. The two other subunits cannot be involved in the enzymatic reaction either; although they have an open-like conformation, they do not contain the cofactor, whose binding site may be occupied by an adenosine molecule. The results suggest that this enzyme, when expressed in mesophilic cells, is arrested in the activity-incompatible conformation revealed by its crystal structures.
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Affiliation(s)
- Krzysztof Brzezinski
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland.
| | - Justyna Czyrko
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | | | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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16
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Ullah J, Chen H, Vastermark A, Jia J, Wu B, Ni Z, Le Y, Wang H. Impact of orientation and flexibility of peptide linkers on T. maritima lipase Tm1350 displayed on Bacillus subtilis spores surface using CotB as fusion partner. World J Microbiol Biotechnol 2017; 33:166. [PMID: 28822027 DOI: 10.1007/s11274-017-2327-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/26/2017] [Indexed: 11/27/2022]
Abstract
Fusion protein construction often requires peptide linkers for prolonged conformation, extended stability and enzyme activity. In this study a series of fusion between Thermotoga maritima lipase Tm1350 and Bacillus subtillis coat protein CotB, comprising of several peptide linkers, with different length, flexibility and orientations were constructed. Effects of temperature, pH and chemicals were examined, on the activity of displayed enzyme. The fusion protein with longer flexible linkers L9 [(GGGGS)4] and L7 (GGGGS-GGGGS-EAAAK-EAAAK-GGGGS-GGGGS) possess 1.29 and 1.16-fold higher activity than the original, under optimum temperature and pH respectively. Moreover, spore surface displaying Tm1350 with L3 (EAAAK-GGGGS) and L9 ((GGGGS)4) showed extended thermostably, maintaining 1.40 and 1.35-fold higher activity than the original respectively, at 80 °C after 5 h of incubation. The enzyme activity of linkers with different orientation, including L5, L6 and L7 was determined, where L7 maintained 1.05 and 1.27-fold higher activity than L5 and L6. Effect of 0.1% proteinase K, bromelain, 20% ethanol and 30% methanol was investigated. Linkers with appropriate Glycine residues (flexible) showed higher activity than Alanine residues (rigid). The activity of the displayed enzyme can be improved by maintaining orientation and flexibility of peptide linkers, to evaluate high activity and stability in industrial processes.
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Affiliation(s)
- Jawad Ullah
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China
| | - Huayou Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China.
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.
| | - Ake Vastermark
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093‑0116, USA
- Nitech, Showa-ku, Nagoya, 466-8555, Japan
| | - Jinru Jia
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China
| | - Bangguo Wu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China
| | - Zhong Ni
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China
| | - Yilin Le
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China
| | - Hongcheng Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, People's Republic of China
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17
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Wang Z, Zhou S, Zhang S, Zhang S, Zhu F, Jin X, Chen Z, Xu X. Semi-rational engineering of a thermostable aldo-keto reductase from Thermotoga maritima for synthesis of enantiopure ethyl-2-hydroxy-4-phenylbutyrate (EHPB). Sci Rep 2017; 7:4007. [PMID: 28638047 PMCID: PMC5479831 DOI: 10.1038/s41598-017-03947-8] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/05/2017] [Indexed: 11/29/2022] Open
Abstract
A novel aldo-keto reductase Tm1743 characterized from Thermotoga maritima was explored as an effective biocatalyst in chiral alcohol production. Natural Tm1743 catalyzes asymmetric reduction of ethyl 2-oxo-4-phenylbutyrate (EOPB) at high efficiency, but the production of, ethyl (S)-2-hydroxy-4-phenylbutyrate ((S)-EHPB), which is less desirable, is preferred with an enantiomeric excess (ee) value of 76.5%. Thus, altering the enantioselectivity of Tm1743 to obtain the more valuable product (R)-EHPB for angiotensin drug synthesis is highly desired. In this work, we determined the crystal structure of Tm1743 in complex with its cofactor NADP+ at 2.0 Å resolution, and investigated the enantioselectivity of Tm1743 through semi-rational enzyme design. Molecular simulations based on the crystal structure obtained two binding models representing the pro-S and pro-R conformations of EOPB. Saturation mutagenesis studies revealed that Trp21 and Trp86 play important roles in determining the enantioselectivity of Tm1743. The best (R)- and (S)-EHPB preferring Tm1743 mutants, denoted as W21S/W86E and W21L/W118H, were identified; their ee values are 99.4% and 99.6% and the catalytic efficiencies are 0.81 and 0.12 mM-1s-1, respectively. Our work presents an efficient strategy to improve the enantioselectivity of a natural biocatalyst, which will serve as a guide for further exploration of new green catalysts for asymmetric reactions.
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Affiliation(s)
- Zhiguo Wang
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Shuo Zhou
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | | | - Sa Zhang
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Fangmeng Zhu
- Apeloa Pharmaceutical Co., Ltd., Dongyang, Zhejiang, 322118, China
| | - Xiaolu Jin
- Yosemade Pharmaceutical Co., Ltd., Jinhua, Zhejiang, 321025, China
| | - Zhenming Chen
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Xiaoling Xu
- Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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18
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Boucher N, Noll KM. Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories. Extremophiles 2016; 20:771-83. [PMID: 27457081 DOI: 10.1007/s00792-016-0866-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/12/2016] [Indexed: 12/30/2022]
Abstract
The Thermotogae possess a large number of ATP-binding cassette (ABC) transporters, including two mannan binding proteins, ManD and CelE (previously called ManE). We show that a gene encoding an ancestor of these was acquired by the Thermotogae from the archaea followed by gene duplication. To address the functional evolution of these proteins as a consequence of their evolutionary histories, we measured the binding affinities of ManD and CelE orthologs from representative Thermotogae. Both proteins bind cellobiose, cellotriose, cellotetraose, β-1,4-mannotriose, and β-1,4-mannotetraose. The CelE orthologs additionally bind β-1,4-mannobiose, laminaribiose, laminaritriose and sophorose while the ManD orthologs additionally only weakly bind β-1,4-mannobiose. The CelE orthologs have higher unfolding temperatures than the ManD orthologs. An examination of codon sites under positive selection revealed that many of these encode residues located near or in the binding site, suggesting that the proteins experienced selective pressures in regions that might have changed their functions. The gene arrangement, phylogeny, binding properties, and putative regulatory networks suggest that the ancestral mannan binding protein was a CelE ortholog which gave rise to the ManD orthologs. This study provides a window on how one class of proteins adapted to new functions and temperatures to fit the physiologies of their new hosts.
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Affiliation(s)
- Nathalie Boucher
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA
- New York State Department of Health, Wadsworth Center, Albany, NY, 12201, USA
| | - Kenneth M Noll
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA.
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Yu T, Anbarasan S, Wang Y, Telli K, Aslan AS, Su Z, Zhou Y, Zhang L, Iivonen P, Havukainen S, Mentunen T, Hummel M, Sixta H, Binay B, Turunen O, Xiong H. Hyperthermostable Thermotoga maritima xylanase XYN10B shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids. Extremophiles 2016; 20:515-24. [PMID: 27240671 PMCID: PMC4921120 DOI: 10.1007/s00792-016-0841-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 01/29/2016] [Accepted: 05/15/2016] [Indexed: 01/16/2023]
Abstract
The gene of Thermotoga maritima GH10 xylanase (TmXYN10B) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ILs). TmXYN10B expressed from Pichia pastoris showed maximal activity at 100 °C and retained 92 % of maximal activity at 105 °C in a 30-min assay. Although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), TmXYN10B retained partial activity in 15-35 % hydrophilic ILs, even at 75-90 °C. TmXYN10B retained over 80 % of its activity at 90 °C in 15 % [EMIM]OAc and 15-25 % 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) during 22-h reactions. [EMIM]OAc may rigidify the enzyme and lower V max. However, only minor changes in kinetic parameter K m showed that competitive inhibition by [EMIM]OAc of TmXYN10B is minimal. In conclusion, when extended enzymatic reactions under extreme conditions are required, TmXYN10B shows extraordinary potential.
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Affiliation(s)
- Tianyi Yu
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Sasikala Anbarasan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Yawei Wang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Kübra Telli
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Aşkın Sevinç Aslan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Zhengding Su
- Hubei University of Technology, Wuhan, 430068, China
| | - Yin Zhou
- Wuhan Sunhy Biology Co., Ltd, Wuhan, 430074, China
| | - Li Zhang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Piia Iivonen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Sami Havukainen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Tero Mentunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Michael Hummel
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Herbert Sixta
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze Kocaeli, Turkey
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland.
| | - Hairong Xiong
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China.
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20
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Talens-Perales D, Polaina J, Marín-Navarro J. Structural Dissection of the Active Site of Thermotoga maritima β-Galactosidase Identifies Key Residues for Transglycosylating Activity. J Agric Food Chem 2016; 64:2917-2924. [PMID: 26998654 DOI: 10.1021/acs.jafc.6b00222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Glycoside hydrolases, specifically β-galactosidases, can be used to synthesize galacto-oligosaccharides (GOS) due to the transglycosylating (secondary) activity of these enzymes. Site-directed mutagenesis of a thermoresistant β-galactosidase from Thermotoga maritima has been carried out to study the structural basis of transgalactosylation and to obtain enzymatic variants with better performance for GOS biosynthesis. Rational design of mutations was based on homologous sequence analysis and structural modeling. Analysis of mutant enzymes indicated that residue W959, or an alternative aromatic residue at this position, is critical for the synthesis of β-3'-galactosyl-lactose, the major GOS obtained with the wild-type enzyme. Mutants W959A and W959C, but not W959F, showed an 80% reduced synthesis of this GOS. Other substitutions, N574S, N574A, and F571L, increased the synthesis of β-3'-galactosyl-lactose about 40%. Double mutants F571L/N574S and F571L/N574A showed an increase of about 2-fold.
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Affiliation(s)
- David Talens-Perales
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Paterna, Valencia, Spain
| | - Julio Polaina
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Paterna, Valencia, Spain
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Paci E, Brockwell DJ, Dougan L. Tuning protein mechanics through an ionic cluster graft from an extremophilic protein. Soft Matter 2016; 12:2688-2699. [PMID: 26809452 DOI: 10.1039/c5sm02938d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
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22
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Brunk E, Mih N, Monk J, Zhang Z, O’Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. BMC Syst Biol 2016; 10:26. [PMID: 26969117 PMCID: PMC4787049 DOI: 10.1186/s12918-016-0271-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology. RESULTS Here, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/). CONCLUSIONS Translating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM-PRO offers insight into the physical embodiment of an organism's genotype, and its use in this comparative framework enables exploration of adaptive strategies for these organisms, opening the door to many new lines of research. With these provided tools, tutorials, and background, the reader will be in a position to run GEM-PRO for their own purposes.
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Affiliation(s)
- Elizabeth Brunk
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| | - Nathan Mih
- />Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA 92093 USA
| | - Jonathan Monk
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Zhen Zhang
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Edward J. O’Brien
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Spencer E. Bliven
- />Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA 92093 USA
- />National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Ke Chen
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Roger L. Chang
- />Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA
| | - Philip E. Bourne
- />Office of the Director, National Institutes of Health, Bethesda, MD 20894 USA
| | - Bernhard O. Palsson
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
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Popova B, Schubert S, Bulla I, Buchwald D, Kramer W. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules. PLoS One 2015; 10:e0136778. [PMID: 26355961 PMCID: PMC4565649 DOI: 10.1371/journal.pone.0136778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/08/2015] [Indexed: 11/19/2022] Open
Abstract
A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.
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Affiliation(s)
- Blagovesta Popova
- Department Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
| | - Steffen Schubert
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Dermatology, Venereology and Allergology, University Medical Center, Göttingen, Germany
- Information Network of Departments of Dermatology (IVDK), Göttingen, Germany
| | - Ingo Bulla
- Theoretical Biology and Biophysics, Group T-6, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Institute for Mathematics and Informatics, Universität Greifswald, Greifswald, Germany
- Department Bioinformatics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Daniela Buchwald
- Department Bioinformatics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Neurobiology Laboratory, German Primate Center GmbH, Göttingen, Germany
| | - Wilfried Kramer
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Molecular Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
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Abstract
To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg(-1)·min(-1) of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg(-1)·min(-1) of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes.
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Affiliation(s)
- Jinfeng Zhang
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Hao Shi
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Linyu Xu
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
| | - Xiaoyan Zhu
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, Jiangsu 223300, P. R. China
| | - Xiangqian Li
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- School of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, P. R. China
- * E-mail:
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25
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Del Toro Duany Y, Ganguly A, Klostermeier D. Differential contributions of the latch in Thermotoga maritima reverse gyrase to the binding of single-stranded DNA before and after ATP hydrolysis. Biol Chem 2014; 395:83-93. [PMID: 23959663 DOI: 10.1515/hsz-2013-0177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/14/2013] [Indexed: 11/15/2022]
Abstract
Reverse gyrase catalyzes the ATP-dependent introduction of positive supercoils into DNA. Supercoiling requires the functional cooperation of its N-terminal helicase domain with the C-terminal topoisomerase domain. The helicase domain contains a superfamily 2 helicase core formed by two RecA domains, H1 and H2. We show here that a helicase domain lacking the latch, an insertion in H2, fails to close the cleft in the helicase core in response to nucleotide and DNA binding at the beginning of the catalytic cycle. In the presence of the pre-hydrolysis ATP analog ADP·BeFx, however, the closed conformer can still be formed in the absence of the latch. The helicase domain lacking the latch exhibits reduced DNA affinities. The energetic difference between the two nucleotide states involved in duplex separation is diminished, rationalizing the unwinding deficiency of reverse gyrase lacking the latch. The latch most strongly contributes to binding of single-stranded DNA in the post-hydrolysis state, before phosphate release. Our results are in line with contributions of the latch in determining the direction of strand passage, and in orienting the cleaved single-stranded DNA for re-ligation. At the same time, the latch may coordinate the re-ligation reaction with strand passage and with the nucleotide cycle.
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26
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Sugimura M, Nishimoto M, Kitaoka M. Characterization of Glycosynthase Mutants Derived from Glycoside Hydrolase Family 10 Xylanases. Biosci Biotechnol Biochem 2014; 70:1210-7. [PMID: 16717424 DOI: 10.1271/bbb.70.1210] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [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: 11/08/2022]
Abstract
Four xylanases belonging to glycoside hydrolase family 10-Thermotoga maritima XylB (TM), Clostridium stercorarium XynB (CS), Bacillus halodurans XynA (BH), and Cellulomonas fimi Cex (CF)-were converted to glycosynthases by substituting the nucleophilic glutamic acid residues with glycine, alanine, and serine. The glycine mutants exhibited the highest levels of glycosynthase activity with all four enzymes. All the glycine mutants formed polymeric beta-1,4-linked xylopyranose as a precipitate during reaction with alpha-xylobiosyl fluoride. Two glycine mutants (TM and CF) recognized X(2) as an effective acceptor molecule to prohibit the formation of the polymer, while the other two (CS and BH) did not. The difference in acceptor specificity is considered to reflect the difference in substrate affinity at their +2 subsites. The results agreed with the structural predictions of the subsite, where TM and CF exhibit high affinity at subsite 2, suggesting that the glycosynthase technique is useful for investigating the affinity of +subsites.
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27
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Mehmood MA, Shahid I, Hussain K, Latif F, Rajoka MI. Thermodynamic properties of the β-glucosidase from Thermotoga maritima extend the upper limit of thermophilicity. Protein Pept Lett 2014; 21:1282-1288. [PMID: 24939659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/05/2014] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
Enzymes from thermophilic organisms are believed to be strong candidates for industrial applications due to their ability to withstand temperature-induced enzyme inactivation. The present study demonstrated molecular cloning, over-expression, purification and characterization of β-glucosidase from Thermotoga maritima. The bglA gene with a capacity to encode a 51 kDa enzyme was heterologously expressed in E. coli M15. The enzyme was produced @130 mgL(-1) in LB media and @440 mgL(-1) in Dubos salt medium accounting 40-47 % of total cellular soluble proteins when lactose was used as an inducer. The enzyme showed a peak activity between pH and temperature range of 5.0-7.0 and 80-100 °C, respectively. The activity was fairly stable up to 140 °C. The turnover rate (kcat) of the enzyme was 187.1±20 s(-1), whereas the Km and Vmax values were 0.56 mM and 238±2.4 IU mg(-1) protein, respectively. The enzyme was shown to have half-life of 136, 71 and 12.6 h at 80, 90 and 100 °C, respectively. Thermodynamics parameters including melting temperature (130 °C), activation energy for inactivation (36.92 kJmole(-1)), enthalpy (33.73 kJmole(-1)), Gibb's free energy (127.96 kJmole(-1)) and entropy (-246.46 Jmole(-1)K(-1)) have shown that the enzyme have enhanced hydrophobic interactions to prevent its thermal unfolding. These features endorse the industrial applications of the enzyme.
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Affiliation(s)
| | | | | | | | - Muhammad I Rajoka
- National Institute for Biotechnology & Genetic Engineering, Faisalabad-38000, Pakistan.
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28
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Chen Z, Pereira JH, Liu H, Tran HM, Hsu NSY, Dibble D, Singh S, Adams PD, Sapra R, Hadi MZ, Simmons BA, Sale KL. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass. PLoS One 2013; 8:e79725. [PMID: 24244549 PMCID: PMC3828181 DOI: 10.1371/journal.pone.0079725] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and ultimately fuels from lignocellulosic biomass. Much of the high cost of enzymes is due to the low catalytic efficiency and stability of lignocellulolytic enzymes, especially cellulases, under conditions that include high temperatures and the presence of residual pretreatment chemicals, such as acids, organic solvents, bases, or ionic liquids. Improving the efficiency of the saccharification process on ionic liquid pretreated biomass will facilitate reduced enzyme loading and cost. Thermophilic cellulases have been shown to be stable and active in ionic liquids but their activity is typically at lower levels. Cel5A_Tma, a thermophilic endoglucanase from Thermotoga maritima, is highly active on cellulosic substrates and is stable in ionic liquid environments. Here, our motivation was to engineer mutants of Cel5A_Tma with higher activity on 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) pretreated biomass. We developed a robotic platform to screen a random mutagenesis library of Cel5A_Tma. Twelve mutants with 25–42% improvement in specific activity on carboxymethyl cellulose and up to 30% improvement on ionic-liquid pretreated switchgrass were successfully isolated and characterized from a library of twenty thousand variants. Interestingly, most of the mutations in the improved variants are located distally to the active site on the protein surface and are not directly involved with substrate binding.
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Affiliation(s)
- Zhiwei Chen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Jose H. Pereira
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hanbin Liu
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Huu M. Tran
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Nathan S. Y. Hsu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dean Dibble
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Paul D. Adams
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Rajat Sapra
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Masood Z. Hadi
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Blake A. Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Kenneth L. Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
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29
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Jung S, Lee DS, Kim YO, Joshi CP, Bae HJ. Improved recombinant cellulase expression in chloroplast of tobacco through promoter engineering and 5' amplification promoting sequence. Plant Mol Biol 2013; 83:317-28. [PMID: 23771581 DOI: 10.1007/s11103-013-0088-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 06/03/2013] [Indexed: 05/07/2023]
Abstract
Economical production of bioethanol from lignocellulosic biomass still faces many technical limitations. Cost-effective production of fermentable sugars is still not practical for large-scale production of bioethanol due to high costs of lignocellulolytic enzymes. Therefore, plant molecular farming, where plants are used as bioreactors, was developed for the mass production of cell wall degrading enzymes that will help reduce costs. Subcellular targeting is also potentially more suitable for the accumulation of recombinant cellulases. Herein, we generated transgenic tobacco plants (Nicotiana tabacum cv. SR1) that accumulated Thermotoga maritima BglB cellulase, which was driven by the alfalfa RbcsK-1A promoter and contained a small subunit of the rubisco complex transit peptide. The generated transformants possessed high specific BglB activity and did not show any abnormal phenotypes. Furthermore, we genetically engineered the RbcsK-1A promoter (MRbcsK-1A) and fused the amplification promoting sequence (aps) to MRbcsK-1A promoter to obtain high expression of BglB in transgenic plants. AMRsB plant lines with aps-MRbcsK-1A promoter showed the highest specific activity of BglB, and the accumulated BglB protein represented up to 9.3 % of total soluble protein. When BglB was expressed in Arabidopsis and tobacco plants, the maximal production capacity of recombinant BglB was 0.59 and 1.42 mg/g wet weight, respectively. These results suggests that suitable recombinant expression of cellulases in subcellular compartments such as chloroplasts will contribute to the cost-effective production of enzymes, and will serve as the solid foundation for the future commercialization of bioethanol production via plant molecular farming.
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Affiliation(s)
- Sera Jung
- Department of Forest Products and Technology, Chonnam National University, Kwangju, 500-757, Republic of Korea
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30
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Xue Y, Song X, Sun H, Cao Z. [Residues affecting hydrolysis of soy isoflavone glycosides, stability and catalytic properties of Thermotoga maritime β-glucosidase]. Prikl Biokhim Mikrobiol 2013; 49:457-66. [PMID: 25474868 DOI: 10.7868/s0555109913050152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The thermostable β-glucosidase A (TmBglA) from Thermotoga maritime is a promising biocatalyst for production of isoflavone aglycones. Use of enzymes with high specificity for soy isoflavone conjugates is however essential for efficient hydrolysis. The effect of the amino acids located in the aglycone binding pocket with non-conserved residues between specificity groups in family 1 glycoside hydrolase (GH1) was studied using wild-type TmBglA and 3 exchange mutants (MI-TmBglA, M2-TmBglA, M1M2-TmBglA). Three mutants were expressed in Escherichia coli, purified and characterized. They had shifts in both optimum tem- perature and thermal stability, and their narrowing pH-activity curve caused by removing the ionized side chain in mutation. All mutants demonstrated the decreased catalytic efficiency more effectively revealed with natural glycoside, salicin, than with artificial substrate, p-nitrophenyl-β-D-glucopyranoside, suggesting that' these amino acids are the key residues to determine aglycone specificity. A lower hydrolysis of genistin and daidzin for M2-TmBglA than M1-TmBglA indicated that L400, A407 and E408 being preferable to V170, A171, V173, G 174 and H180 residues of Tm-BglA could be essential for soy isoflavone glycoside binding and catalysis.
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31
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Cashman DJ, Ortega DR, Zhulin IB, Baudry J. Homology modeling of the CheW coupling protein of the chemotaxis signaling complex. PLoS One 2013; 8:e70705. [PMID: 23950985 PMCID: PMC3737408 DOI: 10.1371/journal.pone.0070705] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/21/2013] [Indexed: 11/23/2022] Open
Abstract
Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model of T. maritima CheW was constructed using the E. coli CheW NMR structure as a template. The conformational space accessible to the homology models and to the NMR structures was investigated using molecular dynamics and Monte Carlo simulations. The results show that even though static homology models of CheW may be partially structurally different from their corresponding experimentally determined structures, the conformational space they can access through their dynamic variations can be similar, for specific regions of the protein, to that of the experimental NMR structures. When CheW homology models are allowed to explore their local accessible conformational space, modeling can provide a rational path to predicting CheW interactions with the MCP and CheA proteins of the chemotaxis complex. Homology models of CheW (and potentially, of other chemotaxis proteins) should be seen as snapshots of an otherwise larger ensemble of accessible conformational space.
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Affiliation(s)
- Derek J. Cashman
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- UT/ORNL Center for Molecular Biophysics, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Davi R. Ortega
- Department of Physics, University of Tennessee, Knoxville, Tennessee, United States of America
- Joint Institute for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Igor B. Zhulin
- Joint Institute for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- UT/ORNL Center for Molecular Biophysics, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Du L, Pang H, Wang Z, Lu J, Wei Y, Huang R. Characterization of an invertase with pH tolerance and truncation of its N-terminal to shift optimum activity toward neutral pH. PLoS One 2013; 8:e62306. [PMID: 23638032 PMCID: PMC3631178 DOI: 10.1371/journal.pone.0062306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 03/19/2013] [Indexed: 11/19/2022] Open
Abstract
Most invertases identified to date have optimal activity at acidic pH, and are intolerant to neutral or alkaline environments. Here, an acid invertase named uninv2 is described. Uninv2 contained 586 amino acids, with a 100 amino acids N-terminal domain, a catalytic domain and a C-terminal domain. With sucrose as the substrate, uninv2 activity was optimal at pH 4.5 and at 45°C. Removal of N-terminal domain of uninv2 has shifted the optimum pH to 6.0 while retaining its optimum temperaure at 45°C. Both uninv2 and the truncated enzyme retained highly stable at neutral pH at 37°C, and they were stable at their optimum pH at 4°C for as long as 30 days. These characteristics make them far superior to invertase from Saccharomyces cerevisiae, which is mostly used as industrial enzyme.
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Affiliation(s)
- Liqin Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
| | - Hao Pang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Zilong Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
| | - Jian Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
| | - Yutuo Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
| | - Ribo Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
- * E-mail:
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Martín del Campo JS, Chun Y, Kim JE, Patiño R, Zhang YHP. Discovery and characterization of a novel ATP/polyphosphate xylulokinase from a hyperthermophilic bacterium Thermotoga maritima. J Ind Microbiol Biotechnol 2013; 40:661-9. [PMID: 23584458 DOI: 10.1007/s10295-013-1265-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/30/2013] [Indexed: 01/11/2023]
Abstract
Xylulokinase (XK, E.C. 2.7.1.17) is one of the key enzymes in xylose metabolism and it is essential for the activation of pentoses for the sustainable production of biocommodities from biomass sugars. The open reading frame (TM0116) from the hyperthermophilic bacterium Thermotoga maritima MSB8 encoding a putative xylulokinase were cloned and expressed in Escherichia coli BL21 Star (DE3) in the Luria-Bertani and auto-inducing high-cell-density media. The basic biochemical properties of this thermophilic XK were characterized. This XK has the optimal temperature of 85 °C. Under a suboptimal condition of 60 °C, the k cat was 83 s⁻¹, and the K(m) values for xylulose and ATP were 1.24 and 0.71 mM, respectively. We hypothesized that this XK could work on polyphosphate possibly because this ancestral thermophilic microorganism utilizes polyphosphate to regulate the Embden-Meyerhof pathway and its substrate-binding residues are somewhat similar to those of other ATP/polyphosphate-dependent kinases. This XK was found to work on low-cost polyphosphate, exhibiting 41 % of its specific activity on ATP. This first ATP/polyphosphate XK could have a great potential for xylose utilization in thermophilic ethanol-producing microorganisms and cell-free biosystems for low-cost biomanufacturing without the use of ATP.
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Affiliation(s)
- Julia S Martín del Campo
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
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Awwad K, Desai A, Smith C, Sommerhalter M. Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr 2013; 69:184-93. [PMID: 23385455 PMCID: PMC3565439 DOI: 10.1107/s0907444912044630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/29/2012] [Indexed: 11/11/2022]
Abstract
The hyperthermophilic bacterium Thermotoga maritima has a noncanonical nucleoside triphosphatase that catalyzes the conversion of inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) into inosine monophosphate (IMP), deoxyinosine monophosphate (IMP) and xanthosine monophosphate (XMP), respectively. The k(cat)/K(m) values determined at 323 and 353 K fall between 1.31 × 10(4) and 7.80 × 10(4) M(-1) s(-1). ITP and dITP are slightly preferred over XTP. Activity towards canonical nucleoside triphosphates (ATP and GTP) was not detected. The enzyme has an absolute requirement for Mg(2+) as a cofactor and has a preference for alkaline conditions. A protein X-ray structure of the enzyme with bound IMP was obtained at 2.15 Å resolution. The active site houses a well conserved network of residues that are critical for substrate recognition and catalysis. The crystal structure shows a tetramer with two possible dimer interfaces. One of these interfaces strongly resembles the dimer interface that is found in the structures of other noncanonical nucleoside pyrophosphatases from human (human ITPase) and archaea (Mj0226 and PhNTPase).
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Affiliation(s)
- Khaldeyah Awwad
- Chemistry and Biochemistry, California State University East Bay, 25800 Carlos Bee Boulevard, Hayward, CA 94542, USA
| | - Anna Desai
- Chemistry and Biochemistry, California State University East Bay, 25800 Carlos Bee Boulevard, Hayward, CA 94542, USA
| | - Clyde Smith
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Monika Sommerhalter
- Chemistry and Biochemistry, California State University East Bay, 25800 Carlos Bee Boulevard, Hayward, CA 94542, USA
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Willett JW, Kirby JR. Genetic and biochemical dissection of a HisKA domain identifies residues required exclusively for kinase and phosphatase activities. PLoS Genet 2012; 8:e1003084. [PMID: 23226719 PMCID: PMC3510030 DOI: 10.1371/journal.pgen.1003084] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 09/25/2012] [Indexed: 02/04/2023] Open
Abstract
Two-component signal transduction systems, composed of histidine kinases (HK) and response regulators (RR), allow bacteria to respond to diverse environmental stimuli. The HK can control both phosphorylation and subsequent dephosphorylation of its cognate RR. The majority of HKs utilize the HisKA subfamily of dimerization and histidine phosphotransfer (DHp) domains, which contain the phospho-accepting histidine and directly contact the RR. Extensive genetics, biochemistry, and structural biology on several prototypical TCS systems including NtrB-NtrC and EnvZ-OmpR have provided a solid basis for understanding the function of HK–RR signaling. Recently, work on NarX, a HisKA_3 subfamily protein, indicated that two residues in the highly conserved region of the DHp domain are responsible for phosphatase activity. In this study we have carried out both genetic and biochemical analyses on Myxococcus xanthus CrdS, a member of the HisKA subfamily of bacterial HKs. CrdS is required for the regulation of spore formation in response to environmental stress. Following alanine-scanning mutagenesis of the α1 helix of the DHp domain of CrdS, we determined the role for each mutant protein for both kinase and phosphatase activity. Our results indicate that the conserved acidic residue (E372) immediately adjacent to the site of autophosphorylation (H371) is specifically required for kinase activity but not for phosphatase activity. Conversely, we found that the conserved Thr/Asn residue (N375) was required for phosphatase activity but not for kinase activity. We extended our biochemical analyses to two CrdS homologs from M. xanthus, HK1190 and HK4262, as well as Thermotoga maritima HK853. The results were similar for each HisKA family protein where the conserved acidic residue is required for kinase activity while the conserved Thr/Asn residue is required for phosphatase activity. These data are consistent with conserved mechanisms for kinase and phosphatase activities in the broadly occurring HisKA family of sensor kinases in bacteria. Bacterial histidine kinases (HK) serve as bifunctional enzymes capable of both phosphorylation and dephosphorylation of their cognate response regulators (RR). The majority of HKs (77%) belong to the HisKA subfamily. While both kinase and phosphatase functions have been assayed for HisKA proteins, relatively few examples have been studied to determine which residues are required for kinase and phosphatase activity. Recent studies on NarX, a HisKA_3 family protein, and the dedicated phosphatases CheZ and CheX illustrate requirements for two amino acids for phosphatase function. In this study, we undertook saturating mutagenesis of the proposed interaction surface between the HK and its cognate RR and conclude that only one residue (T/N) is required exclusively for phosphatase activity for HisKA family proteins in evolutionarily distant organisms Myxococcus xanthus and Thermotoga maritima. In addition, we identified only one residue (E/D), adjacent to the conserved site of phosphorylation, required exclusively for kinase activity within the highly conserved motif H-E/D-x-x-T/N. Because similar sequences are found in nearly all HisKA kinases, these residues provide excellent targets for dissection of kinase and phosphatase activities within this broadly occurring family of bacterial kinases.
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Affiliation(s)
| | - John R. Kirby
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM. Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs. PLoS One 2012; 7:e40236. [PMID: 22768259 PMCID: PMC3387000 DOI: 10.1371/journal.pone.0040236] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/03/2012] [Indexed: 11/20/2022] Open
Abstract
The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompα) and the porin OmpB (or Ompβ). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant β-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had β-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.
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Affiliation(s)
- Amanda K. Petrus
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Kristen S. Swithers
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Chaman Ranjit
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richmond, Washington, United States of America
| | - Heather M. Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richmond, Washington, United States of America
| | - J. Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richmond, Washington, United States of America
| | - Kenneth M. Noll
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
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Abstract
The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states.
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Affiliation(s)
| | - Ben Powell
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Martin R. Webb
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- * E-mail: .
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Jeong E, Jo H, Kim TG, Ban C. Characterization of multi-functional properties and conformational analysis of MutS2 from Thermotoga maritima MSB8. PLoS One 2012; 7:e34529. [PMID: 22545085 PMCID: PMC3335848 DOI: 10.1371/journal.pone.0034529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/01/2012] [Indexed: 11/18/2022] Open
Abstract
The MutS2 homologues have received attention because of their unusual activities that differ from those of MutS. In this work, we report on the functional characteristics and conformational diversities of Thermotoga maritima MutS2 (TmMutS2). Various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (SPM), ATPase assays, analytical ultracentrifugation, DNA binding assays, size chromatography, and limited proteolytic analysis. Dimeric TmMutS2 showed the temperature-dependent ATPase activity. The non-specific nicking endonuclease activities of TmMutS2 were inactivated in the presence of nonhydrolytic ATP (ADPnP) and enhanced by the addition of TmMutL. In addition, TmMutS2 suppressed the TmRecA-mediated DNA strand exchange reaction in a TmMutL-dependent manner. We also demonstrated that small-angle X-ray scattering (SAXS) analysis of dimeric TmMutS2 exhibited nucleotide- and DNA-dependent conformational transitions. Particularly, TmMutS2-ADPnP showed the most compressed form rather than apo-TmMutS2 and the TmMutS2-ADP complex, in accordance with the results of biochemical assays. In the case of the DNA-binding complexes, the stretched conformation appeared in the TmMutS2-four-way junction (FWJ)-DNA complex. Convergences of biochemical- and SAXS analysis provided abundant information for TmMutS2 and clarified ambiguous experimental results.
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Affiliation(s)
- Euiyoung Jeong
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
- * E-mail:
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Singh N, Kuppili RR, Bose K. The structural basis of mode of activation and functional diversity: a case study with HtrA family of serine proteases. Arch Biochem Biophys 2011; 516:85-96. [PMID: 22027029 DOI: 10.1016/j.abb.2011.10.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [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: 09/14/2011] [Accepted: 10/03/2011] [Indexed: 12/15/2022]
Abstract
HtrA (High temperature requirement protease A) proteins that are primarily involved in protein quality control belong to a family of serine proteases conserved from bacteria to humans. HtrAs are oligomeric proteins that share a common trimeric pyramidal architecture where each monomer comprises a serine protease domain and one or two PDZ domains. Although the overall structural integrity is well maintained and they exhibit similar mechanism of activation, subtle conformational changes and structural plasticity especially in the flexible loop regions and domain interfaces lead to differences in their active site conformation and hence in their specificity and functions.
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Affiliation(s)
- Nitu Singh
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
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40
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Abstract
Apart from the ribosome, the crystal structure of the bacterial RNase P in complex with a tRNA, reported by Reiter and colleagues recently, constitutes the first example of a multiple turnover RNA enzyme. Except in rare exceptions, RNase P is ubiquitous and, like the ribosome, is older than the initial branch point of the phylogenetic tree. Importantly, the structure shows how the RNA and the protein moieties cooperate to process the pre-tRNA substrates. The catalytic site comprises some critical RNA residues spread over the secondary structure but gathered in a compact volume next to the protein, which helps recognize and orient the substrate. The discussion here outlines some important aspects of that crystal structure, some of which could apply to RNA molecules in general.
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MESH Headings
- Amino Acid Sequence
- Bacillus subtilis/enzymology
- Bacillus subtilis/genetics
- Base Pairing
- Catalytic Domain
- Crystallography
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Evolution, Molecular
- Holoenzymes
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Quaternary
- RNA Precursors/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribonuclease P/chemistry
- Ribonuclease P/genetics
- Ribonuclease P/metabolism
- Substrate Specificity
- Thermotoga maritima/enzymology
- Thermotoga maritima/genetics
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Affiliation(s)
- Benoît Masquida
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire du CNRS, Université de Strasbourg, 67084 Strasbourg Cedex, France.
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41
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Mahadevan SA, Wi SG, Kim YO, Lee KH, Bae HJ. In planta differential targeting analysis of Thermotoga maritima Cel5A and CBM6-engineered Cel5A for autohydrolysis. Transgenic Res 2011; 20:877-86. [PMID: 21152978 DOI: 10.1007/s11248-010-9464-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [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: 05/18/2010] [Accepted: 11/08/2010] [Indexed: 11/24/2022]
Abstract
The heterologous expression of glycosyl hydrolases in bioenergy crops can improve the lignocellulosic conversion process for ethanol production. We attempted to obtain high-level expression of an intact Thermotoga maritima endoglucanase, Cel5A, and CBM6-engineered Cel5A in transgenic tobacco plants for the mass production and autohydrolysis of endoglucanase. Cel5A expression was targeted to different subcellular compartments, namely, the cytosol, apoplast, and chloroplast, using the native form of the pathogenesis-related protein 1a (PR1a) and Rubisco activase (RA) transit peptides. Cel5A transgenic tobacco plants with the chloroplast transit peptide showed the highest average endoglucanase activity and protein accumulation up to 4.5% total soluble protein. Cel5A-CBM6 was targeted to the chloroplast and accumulated up to 5.2% total soluble protein. In terms of the direct conversion of plant tissue into free sugar, the Cel5A-CBM6 transgenic plant was 33% more efficient than the Cel5A transgenic plant. The protein stability of Cel5A and Cel5A-CBM6 in lyophilized leaf material is an additional advantage in the bioconversion process.
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Affiliation(s)
- Shobana Arumugam Mahadevan
- Department of Forest Products and Technology (BK21 Program), Chonnam National University, Gwangju, 500-757, Republic of Korea
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42
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Liu Y, Reeves D, Kropachev K, Cai Y, Ding S, Kolbanovskiy M, Kolbanovskiy A, Bolton JL, Broyde S, Van Houten B, Geacintov NE. Probing for DNA damage with β-hairpins: similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro. DNA Repair (Amst) 2011; 10:684-96. [PMID: 21741328 DOI: 10.1016/j.dnarep.2011.04.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nucleotide excision repair (NER) is an important prokaryotic and eukaryotic defense mechanism that removes a large variety of structurally distinct lesions in cellular DNA. While the proteins involved are completely different, the mode of action of these two repair systems is similar, involving a cut-and-patch mechanism in which an oligonucleotide sequence containing the lesion is excised. The prokaryotic and eukaryotic NER damage-recognition factors have common structural features of β-hairpin intrusion between the two DNA strands at the site of the lesion. In the present study, we explored the hypothesis that this common β-hairpin intrusion motif is mirrored in parallel NER incision efficiencies in the two systems. We have utilized human HeLa cell extracts and the prokaryotic UvrABC proteins to determine their relative NER incision efficiencies. We report here comparisons of relative NER efficiencies with a set of stereoisomeric DNA lesions derived from metabolites of benzo[a]pyrene and equine estrogens in different sequence contexts, utilizing 21 samples. We found a general qualitative trend toward similar relative NER incision efficiencies for ∼65% of these substrates; the other cases deviate mostly by ∼30% or less from a perfect correlation, although several more distant outliers are also evident. This resemblance is consistent with the hypothesis that lesion recognition through β-hairpin insertion, a common feature of the two systems, is facilitated by local thermodynamic destabilization induced by the lesions in both cases. In the case of the UvrABC system, varying the nature of the UvrC endonuclease, while maintaining the same UvrA/B proteins, can markedly affect the relative incision efficiencies. These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER.
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Affiliation(s)
- Yang Liu
- Chemistry Department, New York University, New York, NY 10003, USA
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Kim JY, Kavas M, Fouad WM, Nong G, Preston JF, Altpeter F. Production of hyperthermostable GH10 xylanase Xyl10B from Thermotoga maritima in transplastomic plants enables complete hydrolysis of methylglucuronoxylan to fermentable sugars for biofuel production. Plant Mol Biol 2011; 76:357-69. [PMID: 21080212 DOI: 10.1007/s11103-010-9712-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 10/27/2010] [Indexed: 05/10/2023]
Abstract
Overcoming the recalcitrance in lignocellulosic biomass for efficient hydrolysis of the polysaccharides cellulose and hemicellulose to fermentable sugars is a research priority for the transition from a fossilfuel-based economy to a renewable carbohydrate economy. Methylglucuronoxylans (MeGXn) are the major components of hemicellulose in woody biofuel crops. Here, we describe efficient production of the GH10 xylanase Xyl10B from Thermotoga maritima in transplastomic plants and demonstrate exceptional stability and catalytic activities of the in planta produced enzyme. Fully expanded leaves from homotransplastomic plants contained enzymatically active Xyl10B at a level of 11-15% of their total soluble protein. Transplastomic plants and their seed progeny were morphologically indistinguishable from non-transgenic plants. Catalytic activity of in planta produced Xyl10B was detected with poplar, sweetgum and birchwood xylan substrates following incubation between 40 and 90 °C and was also stable in dry and stored leaves. Optimal yields of Xyl10B were obtained from dry leaves if crude protein extraction was performed at 85 °C. The transplastomic plant derived Xyl10B showed exceptional catalytic activity and enabled the complete hydrolysis of MeGXn to fermentable sugars with the help of a single accessory enzyme (α-glucuronidase) as revealed by the sugar release assay. Even without this accessory enzyme, the majority of MeGXn was hydrolyzed by the transplastomic plant-derived Xyl10B to fermentable xylose and xylobiose.
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Affiliation(s)
- Jae Yoon Kim
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida-IFAS, Gainesville, FL, USA
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Xia Y, Lundbäck AK, Sahaf N, Nordlund G, Brzezinski P, Eshaghi S. Co2+ selectivity of Thermotoga maritima CorA and its inability to regulate Mg2+ homeostasis present a new class of CorA proteins. J Biol Chem 2011; 286:16525-32. [PMID: 21454699 PMCID: PMC3091257 DOI: 10.1074/jbc.m111.222166] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/19/2011] [Indexed: 01/12/2023] Open
Abstract
CorA is a family of divalent cation transporters ubiquitously present in bacteria and archaea. Although CorA can transport both Mg(2+) and Co(2+) almost equally well, its main role has been suggested to be that of primary Mg(2+) transporter of prokaryotes and hence the regulator of Mg(2+) homeostasis. The reason is that the affinity of CorA for Co(2+) is relatively low and thus considered non-physiological. Here, we show that Thermotoga maritima CorA (TmCorA) is incapable of regulating the Mg(2+) homeostasis and therefore cannot be the primary Mg(2+) transporter of T. maritima. Further, our in vivo experiments confirm that TmCorA is a highly selective Co(2+) transporter, as it selects Co(2+) over Mg(2+) at >100 times lower concentrations. In addition, we present data that show TmCorA to be extremely thermostable in the presence of Co(2+). Mg(2+) could not stabilize the protein to the same extent, even at high concentrations. We also show that addition of Co(2+), but not Mg(2+), specifically induces structural changes to the protein. Altogether, these data show that TmCorA has the role of being the transporter of Co(2+) but not Mg(2+). The physiological relevance and requirements of Co(2+) in T. maritima is discussed and highlighted. We suggest that CorA may have different roles in different organisms. Such functional diversity is presumably a reflection of minor, but important structural differences within the CorA family that regulate the gating, substrate selection, and transport.
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Affiliation(s)
- Yu Xia
- From the Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore 138673, Singapore and
| | - Anna-Karin Lundbäck
- From the Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore 138673, Singapore and
| | - Newsha Sahaf
- From the Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore 138673, Singapore and
| | - Gustav Nordlund
- the Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Peter Brzezinski
- the Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Said Eshaghi
- From the Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore 138673, Singapore and
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Abstract
The genus Thermotoga comprises extremely thermophilic (Topt > or = 70 degrees C) and hyperthermophilic (Topt > or = 80 degrees C) bacteria, which have been extensively studied for insights into the basis for life at elevated temperatures and for biotechnological opportunities (e.g. biohydrogen production, biocatalysis). Over the past decade, genome sequences have become available for a number of Thermotoga species, leading to functional genomics efforts to understand growth physiology as well as genomics-based identification and characterization of novel high-temperature biocatalysts. Discussed here are recent developments along these lines for this group of microorganisms.
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Affiliation(s)
- Andrew D Frock
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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Santa-Maria MC, Chou CJ, Yencho GC, Haigler CH, Thompson WF, Kelly RM, Sosinski B. Plant cell calcium-rich environment enhances thermostability of recombinantly produced alpha-amylase from the hyperthermophilic bacterium Thermotoga maritime. Biotechnol Bioeng 2009; 104:947-56. [PMID: 19585523 DOI: 10.1002/bit.22468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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: 11/09/2022]
Abstract
In the industrial processing of starch for sugar syrup and ethanol production, a liquefaction step is involved where starch is initially solubilized at high temperature and partially hydrolyzed with a thermostable and thermoactive alpha-amylase. Most amylases require calcium as a cofactor for their activity and stability, therefore calcium, along with the thermostable enzyme, are typically added to the starch mixture during enzymatic liquefaction, thereby increasing process costs. An attractive alternative would be to produce the enzyme directly in the tissue to be treated. In a proof of concept study, tobacco cell cultures were used as model system to test in planta production of a hyperthermophilic alpha-amylase from Thermotoga maritima. While comparable biochemical properties to recombinant production in Escherichia coli were observed, thermostability of the plant-produced alpha-amylase benefited significantly from high intrinsic calcium levels in the tobacco cells. The plant-made enzyme retained 85% of its initial activity after 3 h incubation at 100 degrees C, whereas the E. coli-produced enzyme was completely inactivated after 30 min under the same conditions. The addition of Ca(2+) or plant cell extracts from tobacco and sweetpotato to the E. coli-produced enzyme resulted in a similar stabilization, demonstrating the importance of a calcium-rich environment for thermostability, as well as the advantage of producing this enzyme directly in plant cells where calcium is readily available.
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Affiliation(s)
- Monica C Santa-Maria
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695, USA
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Strange RW, Antonyuk SV, Ellis MJ, Bessho Y, Kuramitsu S, Shinkai A, Yokoyama S, Hasnain SS. Structure of a putative beta-phosphoglucomutase (TM1254) from Thermotoga maritima. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1218-21. [PMID: 20054115 PMCID: PMC2802867 DOI: 10.1107/s1744309109046302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 06/25/2009] [Accepted: 11/03/2009] [Indexed: 11/10/2022]
Abstract
The structure of TM1254, a putative beta-phosphoglucomutase from T. maritima, was determined to 1.74 A resolution in a high-throughput structural genomics programme. Diffraction data were obtained from crystals belonging to space group P22(1)2(1), with unit-cell parameters a = 48.16, b = 66.70, c = 83.80 A, and were refined to an R factor of 19.2%. The asymmetric unit contained one protein molecule which is comprised of two domains. Structural homologues were found from protein databases that confirmed a strong resemblance between TM1254 and members of the haloacid dehalogenase (HAD) hydrolase family.
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Affiliation(s)
- Richard W. Strange
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Mark J. Ellis
- STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, England
| | - Yoshitaka Bessho
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Seiki Kuramitsu
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Shigeyuki Yokoyama
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
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Cuneo MJ, Beese LS, Hellinga HW. Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold. J Biol Chem 2009; 284:33217-23. [PMID: 19801540 PMCID: PMC2785164 DOI: 10.1074/jbc.m109.041624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 09/10/2009] [Indexed: 11/06/2022] Open
Abstract
Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of beta(1-->4)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures.
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Affiliation(s)
- Matthew J. Cuneo
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Lorena S. Beese
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Homme W. Hellinga
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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Xue Y, Yu J, Song X. Hydrolysis of soy isoflavone glycosides by recombinant beta-glucosidase from hyperthermophile Thermotoga maritima. J Ind Microbiol Biotechnol 2009; 36:1401-8. [PMID: 19693552 DOI: 10.1007/s10295-009-0626-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Accepted: 07/24/2009] [Indexed: 11/30/2022]
Abstract
A recombinant Thermotoga maritima beta-glucosidase A (BglA) was purified to homogeneity for performing enzymatic hydrolysis of isoflavone glycosides from soy flour. The kinetic properties K(m), k(cat), and k(cat)/K(m) of BglA towards isoflavone glycosides, determined using high-performance liquid chromatography, confirmed the higher efficiency of BglA in hydrolyzing malonylglycosides than non-conjugated glycosides (daidzin and genistin). During hydrolysis of soy flour by BglA at 80 degrees C, the isoflavone glycosides (soluble form) were extracted from soy flour (solid state) into the solution (liquid state) in thermal condition and converted to their aglycones (insoluble form), which mostly existed in the pellet to be separated from BglA in the reaction solution. The enzymatic hydrolysis in one-step and two-step approaches yielded 0.38 and 0.35 mg genistein and daidzein per gram of soy flour, respectively. The optimum conditions for conversion of isoflavone aglycones were 100 U per gram of soy flour, substrate concentration 25% (w/v), and incubation time 3 h for 80 degrees C.
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Affiliation(s)
- Yemin Xue
- Nanjing Engineering and Technology Research Center for Microbiology, Jiangsu Key Laboratory for Biodiversity and Biotechnology, Nanjing Normal University, Nanjing, People's Republic of China.
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50
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Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 2009; 325:1544-9. [PMID: 19762644 PMCID: PMC2833182 DOI: 10.1126/science.1174671] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.
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Affiliation(s)
- Ying Zhang
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
| | - Ines Thiele
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Zhanwen Li
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Krzysztof Ginalski
- Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, Structure Determination Core, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - John Wooley
- Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, Crystallomics Core, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bernhard Palsson
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412, USA
| | - Andrei Osterman
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Adam Godzik
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093, USA
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