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Kumar A, Mukhia S, Kumar R. Industrial applications of cold-adapted enzymes: challenges, innovations and future perspective. 3 Biotech 2021; 11:426. [PMID: 34567931 DOI: 10.1007/s13205-021-02929-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Extreme cold environments are potential reservoirs of microorganisms producing unique and novel enzymes in response to environmental stress conditions. Such cold-adapted enzymes prove to be valuable tools in industrial biotechnology to meet the increasing demand for efficient biocatalysts. The inherent properties like high catalytic activity at low temperature, high specific activity and low activation energy make the cold-adapted enzymes well suited for application in various industries. The interest in this group of enzymes is expanding as they are the preferred alternatives to harsh chemical synthesis owing to their biodegradable and non-toxic nature. Irrespective of the multitude of applications, the use of cold-adapted enzymes at the industrial level is still limited. The current review presents the unique adaptive features and the role of cold-adapted enzymes in major industries like food, detergents, molecular biology and bioremediation. The review highlights the significance of omics technology i.e., metagenomics, metatranscriptomics and metaproteomics in enzyme bioprospection from extreme environments. It further points out the challenges in using cold-adapted enzymes at the industrial level and the innovations associated with novel enzyme prospection strategies. Documentations on cold-adapted enzymes and their applications are abundant; however, reports on the role of omics tools in exploring cold-adapted enzymes are still scarce. So, the review covers the aspect concerning the novel techniques for enzyme discovery from nature.
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Affiliation(s)
- Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002 India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
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Yang Z, Huang X, Liao H, Zhang Z, Sun F, Kou S, Bao Z. Structure and functional analysis reveal an important regulated role of arginine kinase in Patinopecten yessoensis under low pH stress. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105452. [PMID: 32092594 DOI: 10.1016/j.aquatox.2020.105452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Arginine kinase (AK), an important member of the phosphokinase family, is involved in temporal and spatial adenosine triphosphate (ATP) buffering systems. AK plays an important role in physiological function and metabolic regulations, in particular tissues with high and fluctuating energy demands. In present study, four AK genes were firstly identified from Yesso scallop (Patinopecten yessoensis) genome, respectively named PyAK1-4. PyAKs have highly conserved structures with a six-exon/five-exon structure, except for PyAK3. PyAK3 contains an unusual two-domain structure and a "bridge intron" between the two domains, which may originate from gene duplication and subsequent fusion. Phylogenetic analysis showed that all PyAKs belonged to an AK supercluster together with other AK proteins from Mollusca, Platyhelminthes, Arthropoda, and Nematode. A transcriptome database demonstrated that PyAK3 and PyAK4 were the main functional executors with high expression level during larval development and in adult tissues, while PyAK1 and PyAK2 were expressed at a low level. Furthermore, both PyAK2 and PyAK3 showed notably high expression in the male gonad, and PyAK4 was broadly expressed in almost all tissues with the highest level in striated muscle, indicating a tissue-specific expression pattern of PyAKs. In addition, quantitative real-time PCR results demonstrated that the expression of PyAK2, PyAK3 and PyAK4 were significantly upregulated in response to pH stress, especially in an extremely acidifying condition (pH 6.5), revealing the possible involvement of PyAKs in energetic homeostasis during environmental changes. Collectively, a comprehensive analysis of PyAKs was conducted in P. yessoensis. The diversity of PyAKs and their specific expression patterns promote a better understanding of energy metabolism in the growth, development and environmental response of P. yessoensis.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Zhengrui Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fanhua Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Sihua Kou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Kong X, Li Y, Zhang H. Adaptation evolution and bioactivity of galectin from the deep sea Vesicomyidae clam Archivesica packardana. FISH & SHELLFISH IMMUNOLOGY 2020; 97:483-492. [PMID: 31870969 DOI: 10.1016/j.fsi.2019.12.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Hydrothermal vents and cold seep zones are two special habitats in the deep sea. These habitats are always dark, and have extreme temperatures (low or high), heavy metals and toxic substances (sulfide, methane). Vesicomyidae clams, which maintain endosymbionts in their gills, are common species in these two special zones and are thought to develop an efficacious immune system against unusual habitats. In the present study, a novel galectin (Apgalectin) was identified from the Vesicomyidae clam Archivesica packardana. The phylogenetic tree indicated that Apgalectin had two CRDs and was closely clustered with galectins from invertebrates, especially mollusks. A branch-site model showed that 9 positively selected sites (ω2 = 6.83950) were identified comparing to galectins from the Order Veneroida, implying a different function of Vesicomyidae galectins. A microbe binding assay showed that rApgalectin could bind to gram-positive bacteria, gram-negative bacteria and fungi. A PAMP binding assay indicated that Apgalectin could bind LPS, PGN, β-1,3-glucan, glucan from yeast and Poly I:C in dose-dependent manner. Apgalectin only agglutinated Micrococcus luteus and agglutination could be inhibited by galactose which demonstrated that Apgalectin might be involved in immune defense by recognizing and binding bacteria in a β-galactoside manner. Further experiments showed that Apgalectin might play an indirect effector role in the immune response because of its limited antibacterial spectrum. All analyses validated that Apgalectin from Archivesica packardana plays a variety of functions in immune responses and provided basal information for the immune study of deep-sea mollusks.
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Affiliation(s)
- Xue Kong
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yanan Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Haibin Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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Positive selection adaptation of two-domain arginine kinase (AK) from cold seep Vesicomyidae clams. Mol Biol Rep 2018; 45:1527-1532. [PMID: 29982891 DOI: 10.1007/s11033-018-4227-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Arginine kinase (AK) is an important member of Phosphagen kinases which engage in energy metabolism process, and AKs from cold seep clams may develop an effective mechanism to adapt a special habitat (e.g. low temperature). Three Vesicomyidae clams and seven Veneridae clams (belong to the same Order Veneroida) were chosen to analyze the evolution of two-domain AKs. In the present study, ten two-domain AKs were identified and Neighbor-joining tree showed that AKs were divided into two groups. Branch-site model indicated that two-domain AKs were subjected to strong positive selection (ω2a = 17.5058). 16 positively selective sites were detected and five of them showed posterior probabilities of 0.95 or more. Comparative analysis found that domain 2 might be suffered from more evolutionary selection pressure than domain 1, as most positively sites were located at domain 2. Residue Pro (positively selective site) (587P in ApAK) in domain 2 from all Vesicomyidae AKs might participate in change of the synergism and in the function of its cold-adapted characteristics. In conclusion, our studies provide evidence of positive Darwinian selection in the two-domain AKs family of Vesicomyidae clams, and may contribute to a better understanding of its adaptation mechanisms to cold seep habitats.
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Yang S, Zhang X, Wang J, Wang S, Pan Y, Zhang J, Xi J. Identification and analysis of up-regulated proteins in Lissorhoptrus oryzophilus adults for rapid cold hardening. Gene 2018; 642:9-15. [DOI: 10.1016/j.gene.2017.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/17/2017] [Accepted: 11/01/2017] [Indexed: 11/26/2022]
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Chouno K, Yano D, Uda K, Fujita T, Iwasaki N, Suzuki T. Arginine kinases from the marine feather star Tropiometra afra macrodiscus: The first finding of a prenylation signal sequence in metazoan phosphagen kinases. Comp Biochem Physiol B Biochem Mol Biol 2015; 187:55-61. [PMID: 25964010 DOI: 10.1016/j.cbpb.2015.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023]
Abstract
Two arginine kinase cDNAs (AK1 and AK2) were isolated from the marine feather star Tropiometra afra macrodiscus, and the gene structure (exon/intron organization) of AK1 was determined. The cDNA-derived amino acid sequences and the exon/intron organization of the Tropiometra AK1 gene were homologous to those of a human creatine kinase (CK) as well as the AK of the sea cucumber Stichopus. Phylogenetic analysis also supports the close relationship between human CKs and echinoderm AKs, indicating that the latter AKs evolved from an ancestral CK gene. We observed that the Tropiometra AK1 gene has a novel C-terminal extension (approximately 50 amino acid residues) encoded by a unique exon. Moreover, a typical prenylation signal sequence (CSLL) was found at the C-terminal end of this extension, suggesting that AK1 is anchored to a membrane. AK2 had no such C-terminal extension. This is the first finding of a prenylation signal in metazoan phosphagen kinases. Recombinant Tropiometra AK1 and AK2 enzymes were successfully expressed in Escherichia coli, and their kinetic constants were determined. Both enzymes showed activity comparable to that of typical invertebrate AKs.
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Affiliation(s)
- Kaai Chouno
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Daichi Yano
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Toshihiko Fujita
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Nozomu Iwasaki
- Faculty of Geo-environment Science, Rissho University, Magechi 1700, Kumagaya 360-0194, Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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Suzuki T, Kanou Y. Two distinct arginine kinases in Neocaridina denticulate: Psychrophilic and mesophilic enzymes. Int J Biol Macromol 2014; 67:433-8. [DOI: 10.1016/j.ijbiomac.2014.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 11/25/2022]
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Psychrophily and catalysis. BIOLOGY 2013; 2:719-41. [PMID: 24832805 PMCID: PMC3960892 DOI: 10.3390/biology2020719] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.
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