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Kozome D, Sljoka A, Laurino P. Remote loop evolution reveals a complex biological function for chitinase enzymes beyond the active site. Nat Commun 2024; 15:3227. [PMID: 38622119 PMCID: PMC11018821 DOI: 10.1038/s41467-024-47588-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
Loops are small secondary structural elements that play a crucial role in the emergence of new enzyme functions. However, the evolutionary molecular mechanisms how proteins acquire these loop elements and obtain new function is poorly understood. To address this question, we study glycoside hydrolase family 19 (GH19) chitinase-an essential enzyme family for pathogen degradation in plants. By revealing the evolutionary history and loops appearance of GH19 chitinase, we discover that one loop which is remote from the catalytic site, is necessary to acquire the new antifungal activity. We demonstrate that this remote loop directly accesses the fungal cell wall, and surprisingly, it needs to adopt a defined structure supported by long-range intramolecular interactions to perform its function. Our findings prove that nature applies this strategy at the molecular level to achieve a complex biological function while maintaining the original activity in the catalytic pocket, suggesting an alternative way to design new enzyme function.
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Affiliation(s)
- Dan Kozome
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, 904-0495, Japan
| | - Adnan Sljoka
- Center for Advanced Intelligence Project, RIKEN, Tokyo, 103-0027, Japan
- Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, 904-0495, Japan.
- Institute for Protein Research, Osaka University, Suita, Japan.
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2
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Tran DM, Do TO, Nguyen QV. Whole genome sequence data of Paenibacillus tyrfis YSS-72.2.G2, a chitinolytic bacterium newly isolated from a National Park of Vietnam. Data Brief 2024; 53:110087. [PMID: 38328300 PMCID: PMC10847853 DOI: 10.1016/j.dib.2024.110087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Paenibacillus tyrfis YSS-72.2.G2 is a soil chitinolytic bacterium newly isolated from Yok Don National Park of Vietnam. Our previous results demonstrated that this bacterium was a strong chitinase producer, possessed plant growth promotion, and had high activity against phytopathogenic fungi. However, the genome sequence of this strain is unknown. This work aimed to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system for further assessments regarding biocontrol mechanisms and plant growth promotion. The P. tyrfis YSS-72.2.G2 genome is 7,756,121 bp in size and 53.4 % G+C. It harbors 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays. Genes involved in heavy metal resistance (5 genes), iron acquisition (5 genes), and IAA biosynthesis (5 genes) were predicted in the genome. There were 234 carbohydrate-active enzymes found in this genome; among them, 13 enzymes possibly possess activity against phytopathogens. Chitin-degrading system of YSS-72.2.G2 contains 15 chitinolytic enzymes. In addition, 28 gene clusters coding for antimicrobial metabolites were identified, of these, 14 show no sequence similarities to the known clusters. The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889. The genome sequence of P. tyrfis YSS-72.2.G2 has been deposited in the DDBJ/GenBank/EMBL database under accession number NZ_BSDJ00000000. Data provide insight into the genomic information of strain YSS-72.2.G2. This is the first work reporting data on the genome sequence of P. tyrfis isolated from Vietnam.
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Affiliation(s)
- Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Vietnam
| | - Tu Oanh Do
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Vietnam
| | - Quang Vinh Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Vietnam
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3
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Pentekhina I, Nedashkovskaya O, Seitkalieva A, Gorbach V, Slepchenko L, Kirichuk N, Podvolotskaya A, Son O, Tekutyeva L, Balabanova L. Chitinolytic and Fungicidal Potential of the Marine Bacterial Strains Habituating Pacific Ocean Regions. Microorganisms 2023; 11:2255. [PMID: 37764100 PMCID: PMC10535946 DOI: 10.3390/microorganisms11092255] [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] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Screening for chitinolytic activity in the bacterial strains from different Pacific Ocean regions revealed that the highly active representatives belong to the genera Microbulbifer, Vibrio, Aquimarina, and Pseudoalteromonas. The widely distributed chitinolytic species was Microbulbifer isolated from the sea urchin Strongylocentrotus intermedius. Among seventeen isolates with confirmed chitinolytic activity, only the type strain P. flavipulchra KMM 3630T and the strains of putatively new species Pseudoalteromonas sp. B530 and Vibrio sp. Sgm 5, isolated from sea water (Vietnam mollusc farm) and the sea urchin S. intermedius (Peter the Great Gulf, the Sea of Japan), significantly suppressed the hyphal growth of Aspergillus niger that is perspective for the biocontrol agents' development. The results on chitinolytic activities and whole-genome sequencing of the strains under study, including agarolytic type strain Z. galactanivorans DjiT, found the new functionally active chitinase structures and biotechnological potential.
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Affiliation(s)
- Iuliia Pentekhina
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Olga Nedashkovskaya
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Aleksandra Seitkalieva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Vladimir Gorbach
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Lubov Slepchenko
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Natalya Kirichuk
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Anna Podvolotskaya
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Oksana Son
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Liudmila Tekutyeva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Larissa Balabanova
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
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4
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Kawamoto D, Takashima T, Fukamizo T, Numata T, Ohnuma T. A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region. Glycobiology 2021; 32:356-364. [PMID: 34939106 DOI: 10.1093/glycob/cwab117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
Plant GH19 chitinases have several loop structures, which may define their enzymatic properties. Among these loops, the longest loop, Loop-III, is most frequently conserved in GH19 enzymes. A GH19 chitinase from the moss Bryum coronatum (BcChi-A) has only one loop structure, Loop-III, which is connected to the catalytically important β-sheet region. Here, we produced and characterized a Loop-III-deleted mutant of BcChi-A (BcChi-A-ΔIII) and found that its stability and chitinase activity were strongly reduced. The deletion of Loop-III also moderately affected the chitooligosaccharide binding ability as well as the binding mode to the substrate-binding groove. The crystal structure of an inactive mutant of BcChi-A-ΔIII was successfully solved, revealing that the remaining polypeptide chain has an almost identical fold to that of the original protein. Loop-III is not necessarily essential for the folding of the enzyme protein. However, closer examination of the crystal structure revealed that the deletion of Loop-III altered the arrangement of the catalytic triad, Glu61, Glu70 and Ser102, and the orientation of the Trp103 side chain, which is important for sugar residue binding. We concluded that Loop-III is not directly involved in the enzymatic activity but assists the enzyme function by stabilizing the conformation of the β-sheet region and the adjacent substrate-binding platform from behind the core-functional regions.
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Affiliation(s)
- Daiki Kawamoto
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Tomoya Takashima
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan.,Laboratory of Pharmaceutics, Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566 Japan
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan.,Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
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5
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Abady SM, M Ghanem K, Ghanem NB, Embaby AM. Molecular cloning, heterologous expression, and in silico sequence analysis of Enterobacter GH19 class I chitinase (chiRAM gene). Mol Biol Rep 2021; 49:951-969. [PMID: 34773550 DOI: 10.1007/s11033-021-06914-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/30/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Using in silico sequence analyses, the present study aims to clone and express the gene-encoding sequence of a GH19 chitinase from Enterobacter sp. in Escherichia coli. METHODS AND RESULTS The putative open reading frame of a GH19 chitinase from Enterobacter sp. strain EGY1 was cloned and expressed into pGEM®-T and pET-28a (+) vectors, respectively using a degenerate primer. The isolated nucleotide sequence (1821 bp, GenBank accession no.: MK533791.2) was translated to a chiRAM protein (606 amino acids, UniProt accession no.: A0A4D6J2L9). The in silico protein sequence analysis of chiRAM revealed a class I GH19 chitinase: an N-terminus signal peptide (Met1-Ala23), a catalytic domain (Val83-Glu347 and the catalytic triad Glu149, Glu171, and Ser218), a proline-rich hinge region (Pro414 -Pro450), a polycystic kidney disease protein motif (Gly 465-Ser 533), a C-terminus chitin-binding domain (Ala553- Glu593), and conserved class I motifs (NYNY and AQETGG). A three-dimensional model was constructed by LOMETS MODELLER of PDB template: 2dkvA (class I chitinase of Oryza sativa L. japonica). Recombinant chiRAM was overexpressed as inclusion bodies (IBs) (~ 72 kDa; SDS-PAGE) in 1.0 mM IPTG induced E. coli BL21 (DE3) Rosetta strain at room temperature 18 h after induction. Optimized expression yielded active chiRAM with 1.974 ± 0.0002 U/mL, on shrimp colloidal chitin (SCC), in induced E. coli BL21 (DE3) Rosetta cells growing in SB medium. LC-MS/MS identified a band of 72 kDa in the soluble fraction with a 52.3% coverage sequence exclusive to the GH19 chitinase of Enterobacter cloacae (WP_063869339.1). CONCLUSIONS Although chiRAM of Enterobacter sp. was successfully cloned and expressed in E. coli with appreciable chitinase activity, future studies should focus on minimizing IBs to facilitate chiRAM purification and characterization.
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Affiliation(s)
- Shahinaz M Abady
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Khaled M Ghanem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Nevine B Ghanem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, P.O.Box 832, 163 Horreya Avenue, Chatby, Alexandria, 21526, Egypt.
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Orlando M, Buchholz PCF, Lotti M, Pleiss J. The GH19 Engineering Database: Sequence diversity, substrate scope, and evolution in glycoside hydrolase family 19. PLoS One 2021; 16:e0256817. [PMID: 34699529 PMCID: PMC8547705 DOI: 10.1371/journal.pone.0256817] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/16/2021] [Indexed: 01/21/2023] Open
Abstract
The glycoside hydrolase 19 (GH19) is a bifunctional family of chitinases and endolysins, which have been studied for the control of plant fungal pests, the recycle of chitin biomass, and the treatment of multi-drug resistant bacteria. The GH19 domain-containing sequences (22,461) were divided into a chitinase and an endolysin subfamily by analyzing sequence networks, guided by taxonomy and the substrate specificity of characterized enzymes. The chitinase subfamily was split into seventeen groups, thus extending the previous classification. The endolysin subfamily is more diverse and consists of thirty-four groups. Despite their sequence diversity, twenty-six residues are conserved in chitinases and endolysins, which can be distinguished by two specific sequence patterns at six and four positions, respectively. Their location outside the catalytic cleft suggests a possible mechanism for substrate specificity that goes beyond the direct interaction with the substrate. The evolution of the GH19 catalytic domain was investigated by large-scale phylogeny. The inferred evolutionary history and putative horizontal gene transfer events differ from previous works. While no clear patterns were detected in endolysins, chitinases varied in sequence length by up to four loop insertions, causing at least eight distinct presence/absence loop combinations. The annotated GH19 sequences and structures are accessible via the GH19 Engineering Database (GH19ED, https://gh19ed.biocatnet.de). The GH19ED has been developed to support the prediction of substrate specificity and the search for novel GH19 enzymes from neglected taxonomic groups or in regions of the sequence space where few sequences have been described yet.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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7
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Sinelnikov IG, Siedhoff NE, Chulkin AM, Zorov IN, Schwaneberg U, Davari MD, Sinitsyna OA, Shcherbakova LA, Sinitsyn AP, Rozhkova AM. Expression and Refolding of the Plant Chitinase From Drosera capensis for Applications as a Sustainable and Integrated Pest Management. Front Bioeng Biotechnol 2021; 9:728501. [PMID: 34621729 PMCID: PMC8490864 DOI: 10.3389/fbioe.2021.728501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Recently, the study of chitinases has become an important target of numerous research projects due to their potential for applications, such as biocontrol pest agents. Plant chitinases from carnivorous plants of the genus Drosera are most aggressive against a wide range of phytopathogens. However, low solubility or insolubility of the target protein hampered application of chitinases as biofungicides. To obtain plant chitinase from carnivorous plants of the genus Drosera in soluble form in E.coli expression strains, three different approaches including dialysis, rapid dilution, and refolding on Ni-NTA agarose to renaturation were tested. The developed « Rapid dilution » protocol with renaturation buffer supplemented by 10% glycerol and 2M arginine in combination with the redox pair of reduced/oxidized glutathione, increased the yield of active soluble protein to 9.5 mg per 1 g of wet biomass. A structure-based removal of free cysteines in the core domain based on homology modeling of the structure was carried out in order to improve the soluble of chitinase. One improved chitinase variant (C191A/C231S/C286T) was identified which shows improved expression and solubility in E. coli expression systems compared to wild type. Computational analyzes of the wild-type and the improved variant revealed overall higher fluctuations of the structure while maintaining a global protein stability. It was shown that free cysteines on the surface of the protein globule which are not involved in the formation of inner disulfide bonds contribute to the insolubility of chitinase from Drosera capensis. The functional characteristics showed that chitinase exhibits high activity against colloidal chitin (360 units/g) and high fungicidal properties of recombinant chitinases against Parastagonospora nodorum. Latter highlights the application of chitinase from D. capensis as a promising enzyme for the control of fungal pathogens in agriculture.
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Affiliation(s)
- Igor G Sinelnikov
- Federal Research Centre Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey M Chulkin
- Federal Research Centre Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan N Zorov
- Federal Research Centre Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.,DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Olga A Sinitsyna
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Arkady P Sinitsyn
- Federal Research Centre Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Aleksandra M Rozhkova
- Federal Research Centre Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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8
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Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases. Sci Rep 2021; 11:2494. [PMID: 33510258 PMCID: PMC7844276 DOI: 10.1038/s41598-021-81903-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/30/2020] [Indexed: 11/08/2022] Open
Abstract
GH19 and GH22 glycoside hydrolases belonging to the lysozyme superfamily have a related structure/function. A highly conserved tryptophan residue, Trp103, located in the binding groove of a GH19 chitinase from moss Bryum coronatum (BcChi-A) appears to have a function similar to that of well-known Trp62 in GH22 lysozymes. Here, we found that mutation of Trp103 to phenylalanine (W103F) or alanine (W103A) strongly reduced the enzymatic activity of BcChi-A. NMR experiments and the X-ray crystal structure suggested a hydrogen bond between the Trp103 side chain and the -2 sugar. Chitooligosaccharide binding experiments using NMR indicated that the W103F mutation reduced the sugar-binding abilities of nearby amino acid residues (Tyr105/Asn106) in addition to Trp103. This appeared to be derived from enhanced aromatic stacking of Phe103 with Tyr105 induced by disruption of the Trp103 hydrogen bond with the -2 sugar. Since the stacking with Tyr105 was unlikely in W103A, Tyr105/Asn106 of W103A was not so affected as in W103F. However, the W103A mutation appeared to reduce the catalytic potency, resulting in the lowest enzymatic activity in W103A. We concluded that Trp103 does not only interact with the sugar, but also controls other amino acids responsible for substrate binding and catalysis. Trp103 (GH19) and Trp62 (GH22) with such a multi-functionality may be advantageous for enzyme action and conserved in the divergent evolution in the lysozyme superfamily.
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9
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Rajninec M, Jopcik M, Danchenko M, Libantova J. Biochemical and antifungal characteristics of recombinant class I chitinase from Drosera rotundifolia. Int J Biol Macromol 2020; 161:854-863. [DOI: 10.1016/j.ijbiomac.2020.06.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
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10
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Pentekhina I, Hattori T, Tran DM, Shima M, Watanabe T, Sugimoto H, Suzuki K. Chitinase system of Aeromonas salmonicida, and characterization of enzymes involved in chitin degradation. Biosci Biotechnol Biochem 2020; 84:1936-1947. [PMID: 32471324 DOI: 10.1080/09168451.2020.1771539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The genes encoding chitin-degrading enzymes in Aeromonas salmonicida SWSY-1.411 were identified and cloned in Escherichia coli. The strain contained two glycoside hydrolase (GH) families 18 chitinases: AsChiA and AsChiB, two GH19 chitinases: AsChiC and AsChiD, and an auxiliary activities family 10 protein, lytic polysaccharide monooxygenase: AsLPMO10A. These enzymes were successfully expressed in E. coli and purified. AsChiB had the highest hydrolytic activity against insoluble chitin. AsChiD had the highest activity against water-soluble chitin. The peroxygenase activity of AsLPMO10A was lower compared to SmLPMO10A from Serratia marcescens. Synergism on powdered chitin degradation was observed when AsChiA and AsLPMO10A were combined with other chitinases of this strain. More than twice the increase of the synergistic effect was observed when powdered chitin was treated by a combination of AsLPMO10A with all chitinases. GH19 chitinases suppressed the hyphal growth of Trichoderma reesei.
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Affiliation(s)
- Iuliia Pentekhina
- Graduate School of Science and Technology, Niigata University , Niigata, Japan.,School of Economics and Management, Far Eastern Federal University , Vladivostok, Russia
| | - Tatsuyuki Hattori
- Graduate School of Science and Technology, Niigata University , Niigata, Japan
| | - Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University , Buon Ma Thuot, Vietnam
| | - Mizuki Shima
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University , Niigata, Japan
| | - Takeshi Watanabe
- Graduate School of Science and Technology, Niigata University , Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University , Niigata, Japan
| | - Hayuki Sugimoto
- Graduate School of Science and Technology, Niigata University , Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University , Niigata, Japan
| | - Kazushi Suzuki
- Graduate School of Science and Technology, Niigata University , Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University , Niigata, Japan.,Sakeology Center, Niigata University , Niigata, Japan
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