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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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2
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Assefa NG, Hansen H, Altermark B. A unique class I polyhydroxyalkanoate synthase (PhaC) from Brevundimonas sp. KH11J01 exists as a functional trimer: A comparative study with PhaC from Cupriavidus necator H16. N Biotechnol 2022; 70:57-66. [DOI: 10.1016/j.nbt.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/25/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
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3
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Development of a DNA double-strand break-free base editing tool in Corynebacterium glutamicum for genome editing and metabolic engineering. Metab Eng Commun 2020; 11:e00135. [PMID: 32577397 PMCID: PMC7300154 DOI: 10.1016/j.mec.2020.e00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
As a traditional amino acid producing bacterium, Corynebacterium glutamicum is a platform strain for production of various fine chemicals. Based on the CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas9 system, gene editing tools that enable base conversion in the genome of C. glutamicum have been developed. However, some problems such as genomic instability caused by DNA double-strand break (DSB) and off-target effects need to be solved. In this study, a DSB-free single nucleotide genome editing system was developed by construction of a bi-directional base conversion tool TadA-dCas9-AID. This system includes cytosine base editors (CBEs): activation-induced cytidine deaminase (AID) and adenine deaminase (ABEs): tRNA adenosine deaminase (TadA), which can specifically target the gene through a 20-nt single guide RNA (sgRNA) and achieve the base conversion of C-T, C-G and A-G in the 28-bp editing window upstream of protospacer adjacent motif. Finally, as a proof-of-concept demonstration, the system was used to construct a mutant library of zwf gene in C. glutamicum S9114 genome to improve the production of a typical nutraceutical N-acetylglucosamine (GlcNAc). The GlcNAc titer of the mutant strain K293R was increased by 31.9% to 9.1 g/L in shake flask. Here, the developed bases conversion tool TadA-dCas9-AID does not need DNA double-strand break and homologous template, and is effective for genome editing and metabolic engineering in C. glutamicum. A DNA double-strand break-free base editing tool was developed in Corynebacterium glutamicum S9114, which can produce diverse single base mutations. The base editing tool can be used for base mutations on genome and metabolic engineering of C. glutamicum S9114. High efficiency 20N target sequence linking strategy was developed. The base editing tool is used to increase the titer of GlcNAc.
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Sočan J, Purg M, Åqvist J. Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme. Nat Commun 2020; 11:2644. [PMID: 32457471 PMCID: PMC7250929 DOI: 10.1038/s41467-020-16341-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
Cold-adapted enzymes from psychrophilic species show the general characteristics of being more heat labile, and having a different balance between enthalpic and entropic contributions to free energy barrier of the catalyzed reaction compared to mesophilic orthologs. Among cold-adapted enzymes, there are also examples that show an enigmatic inactivation at higher temperatures before unfolding of the protein occurs. Here, we analyze these phenomena by extensive computer simulations of the catalytic reactions of psychrophilic and mesophilic α-amylases. The calculations yield temperature dependent reaction rates in good agreement with experiment, and also elicit the anomalous rate optimum for the cold-adapted enzyme, which occurs about 15 °C below the melting point. This result allows us to examine the structural basis of thermal inactivation, which turns out to be caused by breaking of a specific enzyme-substrate interaction. This type of behaviour is also likely to be relevant for other enzymes displaying such anomalous temperature optima.
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Affiliation(s)
- Jaka Sočan
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden
| | - Miha Purg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.
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Buchinger E, Wiik SÅ, Kusnierczyk A, Rabe R, Aas PA, Kavli B, Slupphaug G, Aachmann FL. Backbone 1H, 13C and 15N chemical shift assignment of full-length human uracil DNA glycosylase UNG2. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:15-22. [PMID: 28879561 DOI: 10.1007/s12104-017-9772-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Human uracil N-glycosylase isoform 2-UNG2 consists of an N-terminal intrinsically disordered regulatory domain (UNG2 residues 1-92, 9.3 kDa) and a C-terminal structured catalytic domain (UNG2 residues 93-313, 25.1 kDa). Here, we report the backbone 1H, 13C, and 15N chemical shift assignment as well as secondary structure analysis of the N-and C-terminal domains of UNG2 representing the full-length UNG2 protein.
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Affiliation(s)
- Edith Buchinger
- NOBIPOL, Department of Biotechnology, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Siv Å Wiik
- NOBIPOL, Department of Biotechnology, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Anna Kusnierczyk
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Renana Rabe
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per A Aas
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Bodil Kavli
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway.
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Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans. J Struct Biol 2015; 191:87-99. [PMID: 26172070 DOI: 10.1016/j.jsb.2015.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 12/14/2022]
Abstract
While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Δ76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all α-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity.
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Arif SM, Geethanandan K, Mishra P, Surolia A, Varshney U, Vijayan M. Structural plasticity inMycobacterium tuberculosisuracil-DNA glycosylase (MtUng) and its functional implications. ACTA ACUST UNITED AC 2015; 71:1514-27. [DOI: 10.1107/s1399004715009311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/15/2015] [Indexed: 12/29/2022]
Abstract
17 independent crystal structures of family I uracil-DNA glycosylase fromMycobacterium tuberculosis(MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5′ position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.
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Wollenberg Valero KC, Pathak R, Prajapati I, Bankston S, Thompson A, Usher J, Isokpehi RD. A candidate multimodal functional genetic network for thermal adaptation. PeerJ 2014; 2:e578. [PMID: 25289178 PMCID: PMC4183952 DOI: 10.7717/peerj.578] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/24/2014] [Indexed: 01/20/2023] Open
Abstract
Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken. We first established a framework of candidate functions for such markers, and then compiled the literature on genes known to adapt to the thermal environment in different lineages of vertebrates. We then identified them in the genomes of human, chicken, and the lizard Anolis carolinensis, and established a functional genetic interaction network in the chicken. Surprisingly, markers initially identified from diverse lineages of vertebrates such as human and fish were all in close functional relationship with each other and more associated than expected by chance. This indicates that the general genetic functional network for thermoregulation and/or thermal adaptation to the environment might be regulated via similar evolutionarily conserved pathways in different vertebrate lineages. We were able to identify seven functions that were statistically overrepresented in this network, corresponding to four of our originally predicted functions plus three unpredicted functions. We describe this network as multimodal: central regulator genes with the function of relaying thermal signal (1), affect genes with different cellular functions, namely (2) lipoprotein metabolism, (3) membrane channels, (4) stress response, (5) response to oxidative stress, (6) muscle contraction and relaxation, and (7) vasodilation, vasoconstriction and regulation of blood pressure. This network constitutes a novel resource for the study of thermal adaptation in the closely related nonavian reptiles and other vertebrate ectotherms.
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Affiliation(s)
| | - Rachana Pathak
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Indira Prajapati
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Shannon Bankston
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Aprylle Thompson
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Jaytriece Usher
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Raphael D Isokpehi
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
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Assefa NG, Niiranen L, Johnson KA, Leiros HKS, Smalås AO, Willassen NP, Moe E. Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2093-100. [PMID: 25084329 PMCID: PMC4118823 DOI: 10.1107/s1399004714011699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/20/2014] [Indexed: 12/01/2022]
Abstract
Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme-substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG-Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG-Ugi complex with previously determined structures of UNG-Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (Kb) which is one order of magnitude larger than that for hUNG-Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein-Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.
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Affiliation(s)
- Netsanet Gizaw Assefa
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Laila Niiranen
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Kenneth A. Johnson
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | - Arne Oskar Smalås
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Nils Peder Willassen
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Elin Moe
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Avenida da Republica (EAN), 2780-157 Oeiras, Portugal
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Roman EA, Faraj SE, Cousido-Siah A, Mitschler A, Podjarny A, Santos J. Frataxin from Psychromonas ingrahamii as a model to study stability modulation within the CyaY protein family. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1168-80. [PMID: 23429177 DOI: 10.1016/j.bbapap.2013.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/26/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
Adaptation of life to low temperatures influences both protein stability and flexibility. Thus, proteins from psychrophilic organisms are excellent models to study relations between these properties. Here we focused on frataxin from Psychromonas ingrahamii (pFXN), an extreme psychrophilic sea ice bacterium that can grow at temperatures as low as -12°C. This α/β protein is highly conserved and plays a key role in iron homeostasis as an iron chaperone. In contrast to other frataxin homologs, chemical and temperature unfolding experiments showed that the thermodynamic stability of pFXN is strongly modulated by pHs: ranging from 5.5±0.9 (pH6.0) to 0.9±0.3kcalmol(-1) (pH8.0). This protein was crystallized and its X-ray structure solved at 1.45Å. Comparison of B-factor profiles between Escherichia coli and P. ingrahamii frataxin variants (51% of identity) suggests that, although both proteins share the same structural features, their flexibility distribution is different. Molecular dynamics simulations showed that protonation of His44 or His67 in pFXN lowers the mobility of regions encompassing residues 20-30 and the C-terminal end, probably through favorable electrostatic interactions with residues Asp27, Glu42 and Glu99. Since the C-terminal end of the protein is critical for the stabilization of the frataxin fold, the predictions presented may be reporting on the microscopic origin of the decrease in global stability produced near neutral pH in the psychrophilic variant. We propose that suboptimal electrostatic interactions may have been an evolutionary strategy for the adaptation of frataxin flexibility and function to cold environments.
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Affiliation(s)
- Ernesto A Roman
- Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
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