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Abstract
B-family DNA polymerases (PolBs) of different groups are widespread in Archaea, and different PolBs often coexist in the same organism. Many of these PolB enzymes remain to be investigated. One of the main groups that is poorly characterized is PolB2, whose members occur in many archaea but are predicted to be inactivated forms of DNA polymerase. Here, Sulfolobus islandicus DNA polymerase 2 (Dpo2), a PolB2 enzyme, was expressed in its native host and purified. Characterization of the purified enzyme revealed that the polymerase possesses a robust nucleotide incorporation activity but is devoid of the 3'-5' exonuclease activity. Enzyme kinetics analyses showed that Dpo2 replicates undamaged DNA templates with high fidelity, which is consistent with its inefficient nucleotide insertion activity opposite different DNA lesions. Strikingly, the polymerase is highly efficient in extending mismatches and mispaired primer termini once a nucleotide is placed opposite a damaged site. This extender polymerase represents a novel type of prokaryotic PolB specialized for DNA damage repair in Archaea. IMPORTANCE In this work, we report that Sulfolobus islandicus Dpo2, a B-family DNA polymerase once predicted to be an inactive form, is a bona fide DNA polymerase functioning in translesion synthesis. S. islandicus Dpo2 is a member of a large group of B-family DNA polymerases (PolB2) that are present in many archaea and some bacteria, and they carry variations in well-conserved amino acids in the functional domains responsible for polymerization and proofreading. However, we found that this prokaryotic B-family DNA polymerase not only replicates undamaged DNA with high fidelity but also extends mismatch and DNA lesion-containing substrates with high efficiencies. With these data, we propose this enzyme functions as an extender polymerase, the first prokaryotic enzyme of this type. Our data also suggest this PolB2 enzyme represents a functional counterpart of the eukaryotic DNA polymerase Pol zeta, an enzyme that is devoted to DNA damage repair.
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2
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Abstract
Since its invention, recombinant protein expression has greatly facilitated our understanding of various cellular processes in different biological systems because theoretically this technique renders any gene to be expressed in a mesophilic host like Escherichia coli, thus allowing functional characterizations of proteins of interest. However, such a practice has only yielded a limited success for proteins encoded in thermophilic archaea since thermophilic proteins are often present in an insoluble form when expressed in E. coli. As a result, it is advantageous to express recombinant proteins of thermophilic archaea in a homologous host, allowing a native form of recombinant protein to be purified and characterized. Here we present a detailed protocol for the homologous expression and purification of proteins in the thermophilic archaeon, Sulfolobus islandicus Rey15A.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China.
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3
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Feng X, Liu X, Xu R, Zhao R, Feng W, Liao J, Han W, She Q. A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota. Front Microbiol 2020; 11:1585. [PMID: 32793138 PMCID: PMC7390963 DOI: 10.3389/fmicb.2020.01585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Sulfolobus islandicus codes for four DNA polymerases: three are of the B-family (Dpo1, Dpo2, and Dpo3), and one is of the Y-family (Dpo4). Western analysis revealed that among the four polymerases, only Dpo2 exhibited DNA damage-inducible expression. To investigate how these DNA polymerases could contribute to DNA damage tolerance in S. islandicus, we conducted genetic analysis of their encoding genes in this archaeon. Plasmid-borne gene expression revealed that Dpo2 increases cell survival upon DNA damage at the expense of mutagenesis. Gene deletion studies showed although dpo1 is essential, the remaining three genes are dispensable. Furthermore, although Dpo4 functions in housekeeping translesion DNA synthesis (TLS), Dpo2, a B-family DNA polymerase once predicted to be inactive, functions as a damage-inducible TLS enzyme solely responsible for targeted mutagenesis, facilitating GC to AT/TA conversions in the process. Together, our data indicate that Dpo2 is the main DNA polymerase responsible for DNA damage tolerance and is the primary source of targeted mutagenesis. Given that crenarchaea encoding a Dpo2 also have a low-GC composition genome, the Dpo2-dependent DNA repair pathway may be conserved in this archaeal lineage.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Liu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianglan Liao
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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4
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Gong P, Lei P, Wang S, Zeng A, Lou H. Post-Translational Modifications Aid Archaeal Survival. Biomolecules 2020; 10:biom10040584. [PMID: 32290118 PMCID: PMC7226565 DOI: 10.3390/biom10040584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high diversity, and ability to grow in special environments. Archaea often thrive in extreme conditions such as high temperature, high/low pH, high salinity, and anoxic ecosystems. All of these are threats to the stability and proper functioning of biological molecules, especially proteins and nucleic acids. Post-translational modifications (PTMs), such as phosphorylation, methylation, acetylation, and glycosylation, are reportedly widespread in Archaea and represent a critical adaptive mechanism to extreme habitats. Here, we summarize our current understanding of the contributions of PTMs to aid in extremophile survival, with a particular focus on the maintenance of genome stability.
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Affiliation(s)
- Ping Gong
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
- Correspondence: (P.G.); (H.L.)
| | - Ping Lei
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Shengping Wang
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Ao Zeng
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No.2 Yuan-Ming-Yuan West Road, Beijing 100193, China
- Correspondence: (P.G.); (H.L.)
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Li J, Pan A, Xie M, Zhang P, Gu X. Characterization of a thermostable κ-carrageenase from a hot spring bacterium and plant protection activity of the oligosaccharide enzymolysis product. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:1812-1819. [PMID: 30255626 DOI: 10.1002/jsfa.9374] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/08/2018] [Accepted: 09/18/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Seaweed oligosaccharides are environmentally-friendly natural products and their use for disease control in sustainable agriculture is extremely promising. Enzymatic digestion to prepare seaweed oligosaccharides has drawn considerable interest. However, the study of enzymatically degraded products of carrageenan is still in its infancy compared with that of other hydrocolloids such as agar and alginate. To prepare degraded carrageenan on a commercial scale, it is necessary to select superior producer bacterial strains to improve the yield and thermostability of carrageenases. RESULTS The carrageenan-degrading bacterium Bacillus sp. HT19 was isolated from sediment of a hot spring in Indonesia, and a κ-carrageenase with high activity was purified from the culture supernatant. The purified enzyme, named Car19, had maximum activity (538 U mg-1 ) at 60 °C and pH 7.0. Notably, the enzyme retained >90% of its initial activity after incubation at 60 °C for 24 h. The Ca2+ obviously improved the thermostability of Car19 at 70 °C. The Km and Vmax values of purified Car19 were 0.061 mg mL-1 and 115.13 U mg-1 , respectively, with κ-carrageenan as substrate. Thin-layer chromatography and electrospray ionization mass-spectrometry analysis of hydrolysates indicated that the enzyme exolytically depolymerized κ-carrageenan to neo-carrabiose. The hydrolysate enhanced the resistance of cucumber to cucumber mosaic virus and increased the activity of antioxidant enzymes in infected plants. CONCLUSION To our knowledge, Car19 is the most thermostable κ-carrageenase reported so far. Its high optimal reaction temperature and thermostability, and unitary hydrolysate constituent, makes Car19 a promising candidate for the preparation of carrageenan oligosaccharides with plant protection activity. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jiang Li
- Key Laboratory of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration, Qingdao, P. R. China
| | - Aihong Pan
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, P. R. China
| | - Maisheng Xie
- Key Laboratory of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration, Qingdao, P. R. China
| | - Pingping Zhang
- College of Biological Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, P. R. China
| | - Xiaoqian Gu
- Key Laboratory of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration, Qingdao, P. R. China
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Stiefler-Jensen D, Schwarz-Linnet T, de Lichtenberg C, Nguyen TTTN, Rand KD, Huang L, She Q, Teilum K. The extraordinary thermal stability of EstA from S. islandicus is independent of post translational modifications. Protein Sci 2017; 26:1819-1827. [PMID: 28681456 DOI: 10.1002/pro.3220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022]
Abstract
Enzymes from thermophilic and hyper-thermophilic organisms have an intrinsic high stability. Understanding the mechanisms behind their high stability will be important knowledge for the engineering of novel enzymes with high stability. Lysine methylation of proteins is prevalent in Sulfolobus, a genus of hyperthermophilic and acidophilic archaea. Both unspecific and temperature dependent lysine methylations are seen, but the significance of this post-translational modification has not been investigated. Here, we test the effect of eliminating in vivo lysine methylation on the stability of an esterase (EstA). The enzyme was purified from the native host S. islandicus as well as expressed as a recombinant protein in E. coli, a mesophilic host that does not code for any machinery for in vivo lysine methylation. We find that lysine mono methylation indeed has a positive effect on the stability of EstA, but the effect is small. The effect of the lysine methylation on protein stability is secondary to that of protein expression in E. coli, as the E. coli recombinant enzyme is compromised both on stability and activity. We conclude that these differences are not attributed to any covalent difference between the protein expressed in hyperthermophilic versus mesophilic hosts.
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Affiliation(s)
| | - Troels Schwarz-Linnet
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Casper de Lichtenberg
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacology, University of Copenhagen, København, Denmark
| | - Kasper D Rand
- Department of Pharmacology, University of Copenhagen, København, Denmark
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, København, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
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Identification and Characterization of a Novel Thermophilic, Organic Solvent Stable Lipase of Bacillus from a Hot Spring. Lipids 2017; 52:619-627. [DOI: 10.1007/s11745-017-4265-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 05/09/2017] [Indexed: 12/20/2022]
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8
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Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea. SCIENCE CHINA-LIFE SCIENCES 2017; 60:370-385. [DOI: 10.1007/s11427-016-0355-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/18/2016] [Indexed: 12/26/2022]
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9
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Characterization of a novel cold active and salt tolerant esterase from Zunongwangia profunda. Enzyme Microb Technol 2016; 85:1-11. [DOI: 10.1016/j.enzmictec.2015.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 12/18/2015] [Accepted: 12/29/2015] [Indexed: 01/13/2023]
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Maester TC, Pereira MR, Machado Sierra EG, Balan A, de Macedo Lemos EG. Characterization of EST3: a metagenome-derived esterase with suitable properties for biotechnological applications. Appl Microbiol Biotechnol 2016; 100:5815-27. [DOI: 10.1007/s00253-016-7385-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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11
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Cloning and characterization of a novel thermostable esterase from Bacillus gelatini KACC 12197. Protein Expr Purif 2015; 116:90-7. [DOI: 10.1016/j.pep.2015.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/07/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022]
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12
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A cold-adapted, solvent and salt tolerant esterase from marine bacterium Psychrobacter pacificensis. Int J Biol Macromol 2015; 81:180-7. [DOI: 10.1016/j.ijbiomac.2015.07.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/20/2022]
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13
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Expression and Characterization of a New Thermostable Esterase from Clostridium thermocellum. Appl Biochem Biotechnol 2015; 177:1437-46. [DOI: 10.1007/s12010-015-1824-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/21/2015] [Indexed: 11/25/2022]
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14
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Zhang X, Zhang Y, Yang G, Xie Y, Xu L, An J, Cui L, Feng Y. Modulation of the thermostability and substrate specificity of Candida rugosa lipase1 by altering the acyl-binding residue Gly414 at the α-helix-connecting bend. Enzyme Microb Technol 2015; 82:34-41. [PMID: 26672446 DOI: 10.1016/j.enzmictec.2015.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/13/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Candida rugosa Lipase1 (LIP1) is widely used in industrial applications. Optimizing its catalytic performance is still a challenging goal for protein engineers. Mutagenesis of key residues in the active site of the enzyme may provide an effective strategy for enhancing stability and altering substrate specificity. In this study, multiple sequence alignment and structural analysis revealed that the acyl-binding residue, Gly414, of LIP1, which is located at a bend connecting α-helixes, was the non-conserved residue in five other isoenzymes. Using saturation mutagenesis, four mutants with improved stability (G414A, G414M, G414H and G414W) were obtained. Compared to the wild type, the best mutant (G414W) exhibited a remarkable 6.5-fold enhancement in half-life at 60 °C and a 14 °C higher T50(15). Its optimum temperature was increased by 15 °C. Simultaneously, G414W displayed a shift in substrate preference from medium-chain to short-chain pNP-ester. Modeling analysis showed that the multiple interactions formed by hydrophobic clusters and hydrogen bonds in the acyl-binding tunnel might lead to the observed thermostability improvement. Additionally, the bulky tryptophan substitution formed a strong steric hindrance to the accommodation of long-chain substrates in the tunnel. These results indicate that the key acyl-binding residues at the α-helix-connecting bend could mediate enzyme stability and catalytic substrate spectra.
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Affiliation(s)
- Xiaofei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lishi Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao An
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130021, China
| | - Li Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Huang Q, Li Y, Zeng C, Song T, Yan Z, Ni J, She Q, Shen Y. Genetic analysis of the Holliday junction resolvases Hje and Hjc in Sulfolobus islandicus. Extremophiles 2015; 19:505-14. [PMID: 25644236 DOI: 10.1007/s00792-015-0734-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/20/2015] [Indexed: 11/26/2022]
Abstract
The in vivo functions of Hje and Hjc, two Holliday junction resolvases in Sulfolobus islandicus were investigated. We found that deletion of either hje or hjc had no effect on normal cell growth, while deletion of both hje and hjc is lethal. Although Hjc is the conserved resolvase in all archaea, the hje deletion rather than hjc deletion rendered cells more sensitive to DNA-damaging agents such as hydroxyurea, cisplatin, and methyl methanesulfonate than the wild type (WT). Intriguingly, the sensitivity of Δhje could not be rescued by ectopic expression of Hje from a plasmid and Hje overexpression slowed growth and large cells appeared with more than two genome equivalents. We showed that Hje was maintained at a low level in WT cells. Furthermore, transcriptomic microarray analysis revealed that the abundance of transcripts of many genes including those involved in DNA replication, repair, transcription regulation, and cell division changed drastically in the Hje-overexpressed strain. However, only limited genes were up- or downregulated in the hje deletion strain. Our findings collectively suggest that Hje is the primary resolvase involved in DNA repair and its expression must be tightly controlled in cells.
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Affiliation(s)
- Qihong Huang
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, People's Republic of China
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Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szymański W, Feringa BL, Marrink SJ, Janssen DB. Computational library design for increasing haloalkane dehalogenase stability. Chembiochem 2014; 15:1660-72. [PMID: 24976371 DOI: 10.1002/cbic.201402128] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 11/05/2022]
Abstract
We explored the use of a computational design framework for the stabilization of the haloalkane dehalogenase LinB. Energy calculations, disulfide bond design, molecular dynamics simulations, and rational inspection of mutant structures predicted many stabilizing mutations. Screening of these in small mutant libraries led to the discovery of seventeen point mutations and one disulfide bond that enhanced thermostability. Mutations located in or contacting flexible regions of the protein had a larger stabilizing effect than mutations outside such regions. The combined introduction of twelve stabilizing mutations resulted in a LinB mutant with a 23 °C increase in apparent melting temperature (Tm,app , 72.5 °C) and an over 200-fold longer half-life at 60 °C. The most stable LinB variants also displayed increased compatibility with co-solvents, thus allowing substrate conversion and kinetic resolution at much higher concentrations than with the wild-type enzyme.
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Affiliation(s)
- Robert J Floor
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
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17
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Zhang S, Wu G, Liu Z, Shao Z, Liu Z. Characterization of EstB, a novel cold-active and organic solvent-tolerant esterase from marine microorganism Alcanivorax dieselolei B-5(T). Extremophiles 2013; 18:251-9. [PMID: 24318107 DOI: 10.1007/s00792-013-0612-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/21/2013] [Indexed: 10/25/2022]
Abstract
A novel esterase gene, estB, was cloned from the marine microorganism Alcanivorax dieselolei B-5(T) and overexpressed in E. coli DE3 (BL21). The expressed protein EstB with a predicted molecular weight of 45.1 kDa had a distinct catalytic triad (Ser(211)-Trp(353)-Gln(385)) and the classical consensus motif conserved in most lipases and esterases Gly(209)-X-Ser(211)-X-Gly(213). EstB showed very low similarity to any known proteins and displayed the highest similarity to the hypothetical protein (46%) from Rhodococcus jostii RHA1. EstB showed the optimal activity around pH 8.5 and 20 °C and was identified to be extremely cold-adaptative retaining more than 95% activity between 0 and 10 °C. The values of kinetic parameters on p-NP caproate (K m, K cat and K cat/K m) were 0.15 mM, 0.54 × 10(3) s(-1) and 3.6 × 10(3) s(-1) mM(-1), respectively. In addition, EstB showed remarkable stability in several studied organic solvents and detergents of high concentrations with the retention of more than 70% activity after treatment for 30 min. The cold activity and its tolerance towards organic solvents made it a promising biocatalyst for industrial applications under extreme conditions.
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Affiliation(s)
- Shanshan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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18
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Shao H, Xu L, Yan Y. Thermostable lipases from extremely radioresistant bacteriumDeinococcus radiodurans: Cloning, expression, and biochemical characterization. J Basic Microbiol 2013; 54:984-95. [DOI: 10.1002/jobm.201300434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/21/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Hua Shao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology; Huazhong University of Science and Technology; Wuhan P. R. China
| | - Li Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology; Huazhong University of Science and Technology; Wuhan P. R. China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology; Huazhong University of Science and Technology; Wuhan P. R. China
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19
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Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes. Biochem Soc Trans 2013; 41:405-10. [PMID: 23356319 DOI: 10.1042/bst20120285] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recently, a novel gene-deletion method was developed for the crenarchaeal model Sulfolobus islandicus, which is a suitable tool for addressing gene essentiality in depth. Using this technique, we have investigated functions of putative DNA repair genes by constructing deletion mutants and studying their phenotype. We found that this archaeon may not encode a eukarya-type of NER (nucleotide excision repair) pathway because depleting each of the eukaryal NER homologues XPD, XPB and XPF did not impair the DNA repair capacity in their mutants. However, among seven homologous recombination proteins, including RadA, Hel308/Hjm, Rad50, Mre11, HerA, NurA and Hjc, only the Hjc nuclease is dispensable for cell viability. Sulfolobus encodes redundant BER (base excision repair) enzymes such as two uracil DNA glycosylases and two putative apurinic/apyrimidinic lyases, but inactivation of one of the redundant enzymes already impaired cell growth, highlighting their important roles in archaeal DNA repair. Systematically characterizing these mutants and generating mutants lacking two or more DNA repair genes will yield further insights into the genetic mechanisms of DNA repair in this model organism.
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20
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An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease. Biosci Rep 2013; 32:609-18. [PMID: 22950735 PMCID: PMC3497727 DOI: 10.1042/bsr20120074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A putative protease gene (tldD) was previously identified from studying tolerance of letD encoding the CcdB toxin of a toxin–antidote system of the F plasmid in Escherichia coli. While this gene is evolutionarily conserved in archaea and bacteria, the proteolytic activity of encoded proteins remained to be demonstrated experimentally. Here we studied Sso0660, an archaeal TldD homologue encoded in Sulfolobus solfataricus by overexpression of the recombinant protein and characterization of the purified enzyme. We found that the enzyme is active in degrading azocasein and FITC–BSA substrates. Protease inhibitor studies showed that EDTA and o-phenanthroline, two well-known metalloprotease inhibitors, either abolished completely or strongly inhibited the enzyme activity, and flame spectrometric analysis showed that a zinc ion is a cofactor of the protease. Furthermore, the protein forms disulfide bond via the Cys416 residue, yielding protein dimer that is the active form of the enzyme. These results establish for the first time that tidD genes encode zinc-containing proteases, classifying them as a family in the metalloprotease class.
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Xu J, Zhuang Y, Wu B, Su L, He B. Calcium-ion-induced stabilization of the protease from Bacillus cereus WQ9-2 in aqueous hydrophilic solvents: effect of calcium ion binding on the hydration shell and intramolecular interactions. J Biol Inorg Chem 2013; 18:211-221. [PMID: 23322168 DOI: 10.1007/s00775-012-0966-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/24/2012] [Indexed: 01/12/2023]
Abstract
The neutral protease WQ from Bacillus cereus is stable in various aqueous organic mixtures, with the exception of those containing acetonitrile (ACN) and dimethylformamide (DMF). The stability of the enzyme in aqueous hydrophilic solvents was dramatically enhanced with the addition of calcium ions, with the degree of improvement in the half-life relative to different solutions ranging from fourfold to more than 70-fold. Studies of the kinetic constants showed that calcium ions induced slight conformational changes in the active site of the enzyme in aqueous ACN. We investigated the molecular mechanisms underlying this stabilizing effect by employing a combination of biophysical techniques and molecular dynamics simulation. In aqueous ACN, the intrinsic fluorescence and circular dichroism analysis demonstrated that the addition of calcium ions induced a relatively compact conformation and maintained both the native-like microenvironment near the tryptophan residues and the secondary structure. Alternatively, homology modeling confirmed the location of four calcium-ion-binding sites in the enzyme, and molecular dynamics simulation revealed that three other calcium ions were bound to the surface of the enzyme. Calcium ions, known as a type of kosmotrope, can strongly bond with water molecules, thus aiding in the formation of the regional hydration shell required for the maintenance of enzyme activity. In addition, the introduction of calcium ions resulted in the formation of additional ionic interactions, providing propitious means for protein stabilization. Thus, the stronger intramolecular interactions were also expected to contribute partially to the enhanced stability of the enzyme in an aqueous organic solvent.
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Affiliation(s)
- Jiaxing Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Yu Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Long Su
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China.
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A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon Sulfolobus islandicus. Appl Environ Microbiol 2012; 78:5630-7. [PMID: 22660711 DOI: 10.1128/aem.00855-12] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite major progresses in genetic studies of hyperthermophilic archaea, recombinant protein production in these organisms always suffers from low yields and a robust expression system is still in great demand. Here we report a versatile vector that confers high levels of protein expression in Sulfolobus islandicus, a hyperthermophilic crenarchaeon. Two expression vectors, pSeSD and pEXA, harboring 11 unique restriction sites were constructed. They contain coding sequences of two hexahistidine (6×His) peptide tags and those coding for two protease sites, the latter of which make it possible to remove the peptide tags from expressed recombinant proteins. While pEXA employed an araS promoter for protein expression, pSeSD utilized P(araS-SD), an araS derivative promoter carrying an engineered ribosome-binding site (RBS; a Shine-Dalgarno [SD] sequence). We found that P(araS-SD) directed high levels of target gene expression. More strikingly, N-terminal amino acid sequencing of recombinant proteins unraveled that the protein synthesized from pEXA-N-lacS lacked the designed 6×His tag and that translation initiation did not start at the ATG codon of the fusion gene. Instead, it started at multiple sites downstream of the 6×His codons. Intriguingly, inserting an RBS site upstream of the ATG codon regained the expression of the 6×His tag, as shown with pSeSD-N-lacS. These results have yielded novel insight into the archaeal translation mechanism. The crenarchaeon Sulfolobus can utilize N-terminal coding sequences of proteins to specify translation initiation in the absence of an RBS site.
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