1
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Almeida DV, Ciancaglini I, Sandano ALH, Roman EKB, Andrade VB, Nunes AB, Tramontina R, da Silva VM, Gabel F, Corrêa TLR, Damasio A, Muniz JRC, Squina FM, Garcia W. Unveiling the crystal structure of thermostable dienelactone hydrolase exhibiting activity on terephthalate esters. Enzyme Microb Technol 2024; 180:110498. [PMID: 39182429 DOI: 10.1016/j.enzmictec.2024.110498] [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: 05/03/2024] [Revised: 08/06/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Dienelactone hydrolase (DLH) is one of numerous hydrolytic enzymes with an α/β-hydrolase fold, which catalyze the hydrolysis of dienelactone to maleylacetate. The DLHs share remarkably similar tertiary structures and a conserved arrangement of catalytic residues. This study presents the crystal structure and comprehensive functional characterization of a novel thermostable DLH from the bacterium Hydrogenobacter thermophilus (HtDLH). The crystal structure of the HtDLH, solved at a resolution of about 1.67 Å, exhibits a canonical α/β-hydrolase fold formed by eight β-sheet strands in the core, with one buried α-helix and six others exposed to the solvent. The structure also confirmed the conserved catalytic triad of DHLs formed by Cys121, Asp170, and His202 residues. The HtDLH forms stable homodimers in solution. Functional studies showed that HtDLH has the expected esterase activity over esters with short carbon chains, such as p-nitrophenyl acetate, reaching optimal activity at pH 7.5 and 70 °C. Furthermore, HtDLH maintains more than 50 % of its activity even after incubation at 90 °C for 16 h. Interestingly, HtDLH exhibits catalytic activity towards polyethylene terephthalate (PET) monomers, including bis-1,2-hydroxyethyl terephthalate (BHET) and 1-(2-hydroxyethyl) 4-methyl terephthalate, as well as other aliphatic and aromatic esters. These findings associated with the lack of activity on amorphous PET indicate that HtDLH has characteristic of a BHET-degrading enzyme. This work expands our understanding of enzyme families involved in PET degradation, providing novel insights for plastic biorecycling through protein engineering, which could lead to eco-friendly solutions to reduce the accumulation of plastic in landfills and natural environments.
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Affiliation(s)
- Dnane Vieira Almeida
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil
| | - Iara Ciancaglini
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Ellen K B Roman
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Viviane Brito Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil
| | - Ana Bárbara Nunes
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Robson Tramontina
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Viviam Moura da Silva
- Institut de Biologie Structurale (IBS), CEA, CNRS, UGA, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Frank Gabel
- Institut de Biologie Structurale (IBS), CEA, CNRS, UGA, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Thamy L R Corrêa
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Fabio Marcio Squina
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil.
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil.
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2
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Antipov A, Okorokova N, Mordkovich N, Safonova T, Veiko V. Role of phosphate-coordinating arginine residues in the thermal stability of uridine phosphorylase from Shewanella oneidensis MR-1. Biochimie 2024; 225:19-25. [PMID: 38723939 DOI: 10.1016/j.biochi.2024.05.008] [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: 01/23/2024] [Revised: 03/15/2024] [Accepted: 05/06/2024] [Indexed: 05/24/2024]
Abstract
The role of phosphate-coordinating arginine residues in the thermal stability of uridine phosphorylase from Shewanella oneidensis MR-1 was investigated by mutation analysis. Uridine phosphorylase mutant genes were constructed by site-directed mutagenesis. The enzyme mutants were prepared and isolated, and their kinetic parameters were determined. It was shown that all these arginine residues play an important role both in the catalysis and thermal stability. The arginine residues 176 were demonstrated to form a kind of a phosphate pore in the hexameric structure of uridine phosphorylase, and they not only contribute to thermal stabilization of the enzyme but also have a regulatory function. The replacement of arginine 176 with an alanine residue resulted in a significant decrease in the kinetic stability of the enzyme but led to a twofold increase in its specific activity.
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Affiliation(s)
- Alexey Antipov
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia.
| | - Natalya Okorokova
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Nadezhda Mordkovich
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Tatyana Safonova
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Vladimir Veiko
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
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3
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Meshcheryakova OV, Bogdanov MA, Efimov AV. Relationship between thermal stability of collagens and the fraction of hydrophobic residues in their molecules. J Struct Biol 2024; 216:108114. [PMID: 39094716 DOI: 10.1016/j.jsb.2024.108114] [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: 05/23/2024] [Revised: 07/18/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
In this study, a database of the thermal stability of collagens and their synthetic analogues has been compiled taking into account literature sources. In total, our database includes 1200 records. As a result of a comparative theoretical analysis of the collected experimental data, the relationship between the melting temperature (Tm) or denaturation temperature (Td) of collagens and the fraction of hydrophobic residues (f) in their molecules has been established. It is shown that this relationship is linear: the larger the f value, the higher the denaturation or melting temperature of a given collagen.
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Affiliation(s)
- Olga V Meshcheryakova
- Centre for Biomedical Research of the Karelian Research Centre of the Russian Academy of Sciences, Pushkinskaya St., 11, Petrozavodsk 185910 Russia.
| | - Maxim A Bogdanov
- Laboratory of Intellectual Services and Applications, ITMO University, Kronverksky Pr., 49, St.Petersburg 197101, Russia
| | - Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya St., 4, Pushchino, Moscow Region 142290 Russia.
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4
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Peña-Montes C, Bermúdez-García E, Castro-Ochoa D, Vega-Pérez F, Esqueda-Domínguez K, Castro-Rodríguez JA, González-Canto A, Segoviano-Reyes L, Navarro-Ocaña A, Farrés A. ANCUT1, a novel thermoalkaline cutinase from Aspergillus nidulans and its application on hydroxycinnamic acids lipophilization. Biotechnol Lett 2024; 46:409-430. [PMID: 38416309 PMCID: PMC11055803 DOI: 10.1007/s10529-024-03467-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/17/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
One of the four cutinases encoded in the Aspergillus nidulans genome, ANCUT1, is described here. Culture conditions were evaluated, and it was found that this enzyme is produced only when cutin is present in the culture medium, unlike the previously described ANCUT2, with which it shares 62% amino acid identity. The differences between them include the fact that ANCUT1 is a smaller enzyme, with experimental molecular weight and pI values of 22 kDa and 6, respectively. It shows maximum activity at pH 9 and 60 °C under assayed conditions and retains more than 60% of activity after incubation for 1 h at 60 °C in a wide range of pH values (6-10) after incubations of 1 or 3 h. It has a higher activity towards medium-chain esters and can modify long-chain length hydroxylated fatty acids constituting cutin. Its substrate specificity properties allow the lipophilization of alkyl coumarates, valuable antioxidants and its thermoalkaline behavior, which competes favorably with other fungal cutinases, suggests it may be useful in many more applications.
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Affiliation(s)
- Carolina Peña-Montes
- Tecnológico Nacional de México/IT Veracruz, Unidad de Investigación y Desarrollo en Alimentos (UNIDA), Calzada Miguel Angel de Quevedo, 2779. Col. Formando Hogar, Veracruz, México, CP 91897
| | - Eva Bermúdez-García
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico
| | - Denise Castro-Ochoa
- Tecnológico Nacional de México/IT Mochis, Juan de Dios Batiz y 20 de Noviembre, CP 81259, Los Mochis, Sinaloa, Mexico
| | - Fernanda Vega-Pérez
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico
| | - Katia Esqueda-Domínguez
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico
| | - José Augusto Castro-Rodríguez
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico
| | - Augusto González-Canto
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Hospital General de México, Dr. Balmis, 148, CP 06726, Ciudad de México, Mexico
| | - Laura Segoviano-Reyes
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico
| | - Arturo Navarro-Ocaña
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico
| | - Amelia Farrés
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, CP 04510, Ciudad de México, Mexico.
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5
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Arisan D, Moya-Beltrán A, Rojas-Villalobos C, Issotta F, Castro M, Ulloa R, Chiacchiarini PA, Díez B, Martín AJM, Ñancucheo I, Giaveno A, Johnson DB, Quatrini R. Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ' Igneacidithiobacillus'. Front Microbiol 2024; 15:1360268. [PMID: 38633703 PMCID: PMC11021618 DOI: 10.3389/fmicb.2024.1360268] [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: 12/22/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Abstract
Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.
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Affiliation(s)
- Dilanaz Arisan
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| | - Ana Moya-Beltrán
- Departamento de Informática y Computación, Facultad de Ingeniería, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Camila Rojas-Villalobos
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Francisco Issotta
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile
| | - Matías Castro
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Ricardo Ulloa
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Patricia A. Chiacchiarini
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Beatriz Díez
- Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile
- Center for Climate and Resilience Research (CR), Santiago, Chile
| | - Alberto J. M. Martín
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Iván Ñancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur, Concepción, Chile
| | - Alejandra Giaveno
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - D. Barrie Johnson
- College of Natural Sciences, Bangor University, Bangor, United Kingdom
- Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
- Natural History Museum, London, United Kingdom
| | - Raquel Quatrini
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
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6
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Hait S, Kundu S. Revisiting structural organization of proteins at high temperature from a network perspective. Comput Biol Chem 2024; 108:107978. [PMID: 37956471 DOI: 10.1016/j.compbiolchem.2023.107978] [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: 08/01/2023] [Revised: 10/08/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023]
Abstract
Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
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7
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Fujii S, Sakaguchi R, Oki H, Kawahara K, Ohkubo T, Fujiyoshi S, Sambongi Y. Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'. J Struct Biol 2023; 215:108031. [PMID: 37758155 DOI: 10.1016/j.jsb.2023.108031] [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: 03/14/2023] [Revised: 09/05/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023]
Abstract
Two homologous cytochromes c', SBCP and SVCP, from deep-sea Shewanella benthica and Shewanella violacea respectively exhibit only nine surface amino acid substitutions, along with one at the N-terminus. Despite the small sequence difference, SBCP is thermally more stable than SVCP. Here, we examined the thermal stability of SBCP variants, each containing one of the nine substituted residues in SVCP, and found that the SBCP K87V variant was the most destabilized. We then determined the X-ray crystal structure of the SBCP K87V variant at a resolution of 2.1 Å. The variant retains a four-helix bundle structure similar to the wild-type, but notable differences are observed in the hydration structure around the mutation site. Instead of forming of the intrahelical salt bridge between Lys-87 and Asp-91 in the wild-type, a clathrate-like hydration around Val-87 through a hydrogen bond network with the nearby amino acid residues is observed. This network potentially enhances the ordering of surrounding water molecules, leading to an entropic destabilization of the protein. These results suggest that the unfavorable hydrophobic hydration environment around Val-87 and the inability to form the Asp-91-mediated salt bridge contribute to the observed difference in stability between SBCP and SVCP. These findings will be useful in future protein engineering for controlling protein stability through the manipulation of surface intrahelical salt bridges.
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Affiliation(s)
- Sotaro Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK.
| | - Riku Sakaguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroya Oki
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan; Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Kazuki Kawahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - So Fujiyoshi
- The IDEC Institute, Hiroshima University, Higashi-Hiroshima, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Higashi-Hiroshima, Japan.
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8
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Sharma N, Agarwal A, Bijoy A, Pandit S, Sharma RK. Lignocellulolytic extremozymes and their biotechnological applications. Extremophiles 2023; 28:2. [PMID: 37950773 DOI: 10.1007/s00792-023-01314-2] [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: 01/02/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent these enzymes from performing as intended. On the other side, extremozymes are enzymes produced by extremophiles that can function in extremely acidic or basic; hot or cold; under high or low salinity conditions. These severe conditions might denature the normal enzymes that are produced by mesophilic microorganisms. The increased stability of these enzymes has been contributed to a number of conformational modifications in their structures. These modifications may result from a few amino acid substitutions, an improved hydrophobic core, the existence of extra ion pairs and salt bridges, an increase in compactness, or an increase in positively charged amino acids. These enzymes are the best option for industrial and bioremediation activities that must be carried out under difficult conditions due to their improved stability. The review, therefore, discusses lignocellulolytic extremozymes, their structure and mechanisms along with industrial and biotechnological applications.
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Affiliation(s)
- Nikita Sharma
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Aditi Agarwal
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Ananya Bijoy
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Sunidhi Pandit
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Rakesh Kumar Sharma
- Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur, India.
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9
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Komp E, Alanzi HN, Francis R, Vuong C, Roberts L, Mosallanejad A, Beck DAC. Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe. Sci Data 2023; 10:682. [PMID: 37805601 PMCID: PMC10560248 DOI: 10.1038/s41597-023-02553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
Stability of proteins at high temperature has been a topic of interest for many years, as this attribute is favourable for applications ranging from therapeutics to industrial chemical manufacturing. Our current understanding and methods for designing high-temperature stability into target proteins are inadequate. To drive innovation in this space, we have curated a large dataset, learn2thermDB, of protein-temperature examples, totalling 24 million instances, and paired proteins across temperatures based on homology, yielding 69 million protein pairs - orders of magnitude larger than the current largest. This important step of pairing allows for study of high-temperature stability in a sequence-dependent manner in the big data era. The data pipeline is parameterized and open, allowing it to be tuned by downstream users. We further show that the data contains signal for deep learning. This data offers a new doorway towards thermal stability design models.
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Affiliation(s)
- Evan Komp
- Department of Chemical Engineering, University of Washington, Seattle, USA.
| | - Humood N Alanzi
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Ryan Francis
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Chau Vuong
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Logan Roberts
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Amin Mosallanejad
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- eScience Institute, University of Washington, Seattle, USA.
- Paul G. Allen School of Computer Science, University of Washington, Seattle, USA.
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10
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Arias PM, Butler J, Randhawa GS, Soltysiak MPM, Hill KA, Kari L. Environment and taxonomy shape the genomic signature of prokaryotic extremophiles. Sci Rep 2023; 13:16105. [PMID: 37752120 PMCID: PMC10522608 DOI: 10.1038/s41598-023-42518-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as the k-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of [Formula: see text] extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, [Formula: see text]. The supervised learning resulted in high accuracies for taxonomic classifications at [Formula: see text], and medium to medium-high accuracies for environment category classifications of the same datasets at [Formula: see text]. For [Formula: see text], our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.
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Affiliation(s)
- Pablo Millán Arias
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada.
| | - Joseph Butler
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Gurjit S Randhawa
- School of Mathematical and Computational Sciences, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Kathleen A Hill
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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11
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Vallina Estrada E, Zhang N, Wennerström H, Danielsson J, Oliveberg M. Diffusive intracellular interactions: On the role of protein net charge and functional adaptation. Curr Opin Struct Biol 2023; 81:102625. [PMID: 37331204 DOI: 10.1016/j.sbi.2023.102625] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
A striking feature of nucleic acids and lipid membranes is that they all carry net negative charge and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal intermolecular repulsion that keeps the cytosolic content suitably 'fluid' for function. We focus in this review on the experimental, theoretical and genetic findings which serve to underpin this idea and the new questions they raise. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the 'random' protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. It is further evident that this dynamic protein-protein interplay is under evolutionary control and finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long-range but also the collective properties of the cellular interior as a whole.
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Affiliation(s)
- Eloy Vallina Estrada
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Nannan Zhang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Håkan Wennerström
- Division of Physical Chemistry, Department of Chemistry, Lund University, Box 124, 22100 Lund, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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12
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Dou Z, Sun Y, Jiang X, Wu X, Li Y, Gong B, Wang L. Data-driven strategies for the computational design of enzyme thermal stability: trends, perspectives, and prospects. Acta Biochim Biophys Sin (Shanghai) 2023; 55:343-355. [PMID: 37143326 PMCID: PMC10160227 DOI: 10.3724/abbs.2023033] [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: 07/06/2022] [Accepted: 11/23/2022] [Indexed: 03/05/2023] Open
Abstract
Thermal stability is one of the most important properties of enzymes, which sustains life and determines the potential for the industrial application of biocatalysts. Although traditional methods such as directed evolution and classical rational design contribute greatly to this field, the enormous sequence space of proteins implies costly and arduous experiments. The development of enzyme engineering focuses on automated and efficient strategies because of the breakthrough of high-throughput DNA sequencing and machine learning models. In this review, we propose a data-driven architecture for enzyme thermostability engineering and summarize some widely adopted datasets, as well as machine learning-driven approaches for designing the thermal stability of enzymes. In addition, we present a series of existing challenges while applying machine learning in enzyme thermostability design, such as the data dilemma, model training, and use of the proposed models. Additionally, a few promising directions for enhancing the performance of the models are discussed. We anticipate that the efficient incorporation of machine learning can provide more insights and solutions for the design of enzyme thermostability in the coming years.
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Affiliation(s)
- Zhixin Dou
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237China
| | - Yuqing Sun
- School of SoftwareShandong UniversityJinan250101China
| | - Xukai Jiang
- National Glycoengineering Research CenterShandong UniversityQingdao266237China
| | - Xiuyun Wu
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237China
| | - Yingjie Li
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237China
| | - Bin Gong
- School of SoftwareShandong UniversityJinan250101China
| | - Lushan Wang
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237China
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13
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Jasilionis A, Plotka M, Wang L, Dorawa S, Lange J, Watzlawick H, van den Bergh T, Vroling B, Altenbuchner J, Kaczorowska A, Pohl E, Kaczorowski T, Nordberg Karlsson E, Freitag‐Pohl S. AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase. Protein Sci 2023; 32:e4585. [PMID: 36721347 PMCID: PMC9929850 DOI: 10.1002/pro.4585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
Bacteriophages encode a wide variety of cell wall disrupting enzymes that aid the viral escape in the final stages of infection. These lytic enzymes have accumulated notable interest due to their potential as novel antibacterials for infection treatment caused by multiple-drug resistant bacteria. Here, the detailed functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, a globular Amidase_3 type lytic enzyme adapted to high temperatures is presented. The sequence and structure comparison with homologous lytic amidases reveals the key adaptation traits that ensure the activity and stability of AmiP at high temperatures. The crystal structure determined at a resolution of 1.8 Å displays a compact α/β-fold with multiple secondary structure elements omitted or shortened compared with protein structures of similar proteins. The functional characterization of AmiP demonstrates high efficiency of catalytic activity and broad substrate specificity toward thermophilic and mesophilic bacteria strains containing Orn-type or DAP-type peptidoglycan. The here presented AmiP constitutes the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme biochemically characterized with a temperature optimum at 85°C. The extraordinary high melting temperature Tm 102.6°C confirms fold stability up to approximately 100°C. Furthermore, AmiP is shown to be more active over the alkaline pH range with pH optimum at pH 8.5 and tolerates NaCl up to 300 mM with the activity optimum at 25 mM NaCl. This set of beneficial characteristics suggests that AmiP can be further exploited in biotechnology.
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Affiliation(s)
- Andrius Jasilionis
- Division of Biotechnology, Department of ChemistryLund UniversityLundSweden
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of BiologyUniversity of GdanskGdanskPoland
| | - Lei Wang
- Institute of Biomedical GeneticsUniversity of StuttgartStuttgartGermany
| | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of BiologyUniversity of GdanskGdanskPoland
| | | | | | | | | | | | - Anna‐Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of BiologyUniversity of GdanskGdanskPoland
| | - Ehmke Pohl
- Department of BiosciencesDurham UniversityDurhamUK
- Department of ChemistryDurham UniversityDurhamUK
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of BiologyUniversity of GdanskGdanskPoland
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14
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Hait S, Basu S, Kundu S. Charge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy. J Biomol Struct Dyn 2023; 41:1745-1752. [PMID: 34996344 DOI: 10.1080/07391102.2021.2024258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins from thermophilic organisms are a matter of immense interest for decades because of its application in fields like de-novo protein design, thermostable variants of biocatalysts etc. Previous studies have found several sequence and structural adaptations related to thermal stability, while charge reversal study remains ignored. Here we address whether charge reversal mutations naturally occur in mesophilic-thermophilic/hyperthermophilic orthologous proteins. Do they contribute to thermal stability? Our systematic study on 1550 mesophilic-thermophilic/hyperthermophilic orthologous protein pairs with remarkable structural and topological similarity, shows gain in coulombic interaction energy in thermophilic/hyperthermophilic proteins at short range associated with partially exposed and buried charge reversal mutations, which may enhance thermostability. Our findings call forth its application in future protein engineering studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
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15
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Kumar S, Duggineni VK, Singhania V, Misra SP, Deshpande PA. Unravelling and Quantifying the Biophysical– Biochemical Descriptors Governing Protein Thermostability by Machine Learning. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Vinay Kumar Duggineni
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Vibhuti Singhania
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Swayam Prabha Misra
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Parag A. Deshpande
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
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16
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Peng Z, Miao Z, Ji X, Zhang G, Zhang J. Engineering flexible loops to enhance thermal stability of keratinase for efficient keratin degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157161. [PMID: 35817113 DOI: 10.1016/j.scitotenv.2022.157161] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Keratinase-catalyzed degradation of keratin waste has been shown to be a promising recycling method. Although the recombinant KerZ1 derived from Bacillus subtilis has shown the highest activity among the keratinases reported so far, the low thermal stability caused by the unstable flexible loops limited its keratin-degrading ability. To this end, the flexible loops of KerZ1 were engineered to be more hydrophobic and rigid through B-factor calculations, molecular dynamics simulations, and β-turn redesign. We developed several highly thermostable keratinase variants and showed enhanced keratin degradation activity. In particular, the loop regions of the variants KerZ1A128D/L240N, KerZ1T77E/L240N and KerZ1T77C/A128D were designed to be more stable, with Tm values increased by 8 °C, 6 °C and 5 °C, and corresponding t1/2 increased by 2.3, 3.3 and 5.0 times. The keratin degradation activity of the variant KerZ1T77C/A128D at 60 °C was enhanced by 46 % compared with KerZ1WT. The strategy of this research and the obtained keratinase variants will be a significant improvement in the complete degradation of keratin.
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Affiliation(s)
- Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Zhoudi Miao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xiaomei Ji
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Guoqiang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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17
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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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18
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Rahban M, Zolghadri S, Salehi N, Ahmad F, Haertlé T, Rezaei-Ghaleh N, Sawyer L, Saboury AA. Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure. Int J Biol Macromol 2022; 214:642-654. [DOI: 10.1016/j.ijbiomac.2022.06.154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 01/28/2023]
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19
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Yang MJ, Kim J, Lee Y, Lee W, Park CJ. NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus. Int J Mol Sci 2022; 23:ijms23063099. [PMID: 35328522 PMCID: PMC8954794 DOI: 10.3390/ijms23063099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.
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Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
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20
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Development of thermostable sucrose phosphorylase by semi-rational design for efficient biosynthesis of alpha-D-glucosylglycerol. Appl Microbiol Biotechnol 2021; 105:7309-7319. [PMID: 34542685 PMCID: PMC8494705 DOI: 10.1007/s00253-021-11551-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/03/2021] [Accepted: 08/24/2021] [Indexed: 12/03/2022]
Abstract
Abstract Sucrose phosphorylase (SPase) can specifically catalyze transglycosylation reactions and can be used to enzymatically synthesize α-D-glycosides. However, the low thermostability of SPase has been a bottleneck for its industrial application. In this study, a SPase gene from Leuconostoc mesenteroides ATCC 12,291 (LmSPase) was synthesized with optimized codons and overexpressed successfully in Escherichia coli. A semi-rational design strategy that combined the FireProt (a web server designing thermostable proteins), structure–function analysis, and molecular dynamic simulations was used to improve the thermostability of LmSPase. Finally, one single-point mutation T219L and a combination mutation I31F/T219L/T263L/S360A (Mut4) with improved thermostability were obtained. The half-lives at 50 °C of T219L and Mut4 both increased approximately two-fold compared to that of wild-type LmSPase (WT). Furthermore, the two variants T219L and Mut4 were used to produce α-D-glucosylglycerol (αGG) from sucrose and glycerol by incubating with 40 U/mL crude extracts at 37 °C for 60 h and achieved the product concentration of 193.2 ± 12.9 g/L and 195.8 ± 13.1 g/L, respectively, which were approximately 1.3-fold higher than that of WT (150.4 ± 10.0 g/L). This study provides an effective strategy for improving the thermostability of an industrial enzyme. Key points • Predicted potential hotspot residues directing the thermostability of LmSPase by semi-rational design • Screened two positive variants with higher thermostability and higher activity • Synthesized α-D-glucosylglycerol to a high level by two screened positive variants Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11551-0.
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21
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Jin R, Grasso M, Zhou M, Marmorstein R, Baumgart T. Unfolding Mechanisms and Conformational Stability of the Dimeric Endophilin N-BAR Domain. ACS OMEGA 2021; 6:20790-20803. [PMID: 34423187 PMCID: PMC8374900 DOI: 10.1021/acsomega.1c01905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Endophilin, which is a member of the Bin-amphiphysin-Rvs (BAR) domain protein superfamily, contains a homodimeric N-BAR domain of a characteristic crescent shape. The N-BAR domain comprises a six-helix bundle and is known to sense and generate membrane curvature. Here, we characterize aspects of the unfolding mechanism of the endophilin A1 N-BAR domain during thermal denaturation and examine factors that influence the thermal stability of this domain. Far-UV circular dichroism (CD) spectroscopy was applied to monitor changes in the secondary structure above room temperature. The protein's conformational changes were further characterized through Foerster resonance energy transfer and cross-linking experiments at varying temperatures. Our results indicate that thermal unfolding of the endophilin N-BAR is (minimally) a two-step process, with a dimeric intermediate that displays partial helicity loss. Furthermore, a thermal shift assay and temperature-dependent CD were applied to compare the unfolding processes of several truncated versions of endophilin. The melting temperature of the N-BAR domain decreased when we deleted either the N-terminal H0 helix or the unstructured linker of endophilin. This result suggests that these intrinsically disordered domains may play a role in structurally stabilizing the functional N-BAR domain in vivo. Finally, we show that single-site mutations can also compromise endophilin's thermal stability.
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Affiliation(s)
- Rui Jin
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael Grasso
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mingyang Zhou
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson
Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson
Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Tobias Baumgart
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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22
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Phospholipid N-methyltransferases produce various methylated phosphatidylethanolamine derivatives in thermophilic bacteria. Appl Environ Microbiol 2021; 87:e0110521. [PMID: 34288711 DOI: 10.1128/aem.01105-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the most common pathways for the biosynthesis of the phospholipid phosphatidylcholine (PC) in bacteria is the successive three-fold N-methylation of phosphatidylethanolamine (PE) catalyzed by phospholipid N-methyltransferases (Pmts). Pmts with different activities have been described in a number of mesophilic bacteria. In the present study, we identified and characterized the substrate and product spectrum of four Pmts from thermophilic bacteria. Three of these enzymes were purified in an active form. The Pmts from Melghirimyces thermohalophilus, Thermochromogena staphylospora and Thermobifida fusca produce monomethyl-PE (MMPE) and dimethyl-PE (DMPE). T. fusca encodes two Pmt candidates, one is mutationally inactivated and the other is responsible for the accumulation of large amounts of MMPE. The Pmt enzyme from Rubellimicrobium thermophilum catalyzes all three methylation reactions to synthesize PC. Moreover, we show that PE, previously reported to be absent in R. thermophilum, is in fact produced and serves as precursor for the methylation pathway. In an alternative route, the strain is able to produce PC by the PC synthase pathway when choline is available. The activity of all purified thermophilic Pmt enzymes was stimulated by anionic lipids suggesting membrane recruitment of these cytoplasmic proteins via electrostatic interactions. Our study provides novel insights into the functional characteristics of phospholipid N-methyltransferases in a previously unexplored set of thermophilic environmental bacteria. Importance In recent years, the presence of phosphatidylcholine (PC) in bacterial membranes has gained increasing attention, partly due to its critical role in the interaction with eukaryotic hosts. PC biosynthesis via a three-step methylation of phosphatidylethanolamine, catalyzed by phospholipid N-methyltransferases (Pmts), has been described in a range of mesophilic bacteria. Here, we expand our knowledge on bacterial PC formation by the identification, purification and characterization of Pmts from phylogenetically diverse thermophilic bacteria, and thereby provide insights into the functional characteristics of Pmt enzymes in thermophilic actinomycetes and proteobacteria.
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23
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Nour I, Hanif A, Alanazi IO, Al-Ashkar I, Alhetheel A, Eifan S. Novel insights of waterborne human rotavirus A in Riyadh (Saudi Arabia) involving G2 predominance and emergence of a thermotolerant sequence. Sci Rep 2021; 11:12132. [PMID: 34108565 PMCID: PMC8190275 DOI: 10.1038/s41598-021-91607-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
The routine evaluation of water environments is necessary to manage enteric virus-mediated fecal contamination and the possible emergence of novel variants. Here, we detected human rotavirus A (HRVA) circulating in two wastewater treatment plants, two lakes, irrigation water and a wastewater landfill located in Riyadh. VP7-derived surface protein sequences were assessed by phylogenetic analyses and inspection of thermotolerance-mediated secondary structure and seasonal variation. HRVA was most prevalent at An-Nazim wastewater landfill (AN-WWLF; 63.89%). Phylogenetic analyzes revealed the predominance of HRVA G2 lineage for the first time in Saudi Arabia. Moreover, a single HRVA sequence (2B64I-ANLF3/2018) was recovered at 45 °C from AN-WWLF; secondary structure prediction indicated that this sequence was thermotolerant with a high hydrophobicity, an absence of Ramachandran outliers, and a higher content of proline patches on the protein surface. Varied relationships were significantly observed between sampling areas influenced by temperature ranges (p < 0.05). HRVA prevalence was influenced by seasonal variations, favoring moderate temperatures in late autumn and early winter in all locations. However, a significant temperature impact was detected in Wadi-Hanifah Lake (p = 0.01). Our study extends the knowledge of currently circulating HRVA genotypes, and indicates the probable emergence of thermotolerant strains and seasonally mediated HRVA prevalence.
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Affiliation(s)
- Islam Nour
- grid.56302.320000 0004 1773 5396Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Atif Hanif
- grid.56302.320000 0004 1773 5396Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim O. Alanazi
- grid.452562.20000 0000 8808 6435National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ibrahim Al-Ashkar
- grid.56302.320000 0004 1773 5396Biotechnology Laboratory, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia ,grid.411303.40000 0001 2155 6022Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Abdulkarim Alhetheel
- grid.56302.320000 0004 1773 5396Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Eifan
- grid.56302.320000 0004 1773 5396Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
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Gao J, Li Q, Li D. Novel Proteome and N-Glycoproteome of the Thermophilic Fungus Chaetomium thermophilum in Response to High Temperature. Front Microbiol 2021; 12:644984. [PMID: 34163440 PMCID: PMC8216556 DOI: 10.3389/fmicb.2021.644984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
Thermophilic fungi are eukaryotic species that grow at high temperatures, but little is known about the underlying basis of thermophily at cell and molecular levels. Here the proteome and N-glycoproteome of Chaetomium thermophilum at varying culture temperatures (30, 50, and 55°C) were studied using hydrophilic interaction liquid chromatography enrichment and high-resolution liquid chromatography–tandem mass spectroscopy analysis. With respect to the proteome, the numbers of differentially expressed proteins were 1,274, 1,374, and 1,063 in T50/T30, T55/T30, and T55/T50, respectively. The upregulated proteins were involved in biological processes, such as protein folding and carbohydrate metabolism. Most downregulated proteins were involved in molecular functions, including structural constituents of the ribosome and other protein complexes. For the N-glycoproteome, the numbers of differentially expressed N-glycoproteins were 160, 176, and 128 in T50/T30, T55/T30, and T55/T50, respectively. The differential glycoproteins were mainly involved in various types of N-glycan biosynthesis, mRNA surveillance pathway, and protein processing in the endoplasmic reticulum. These results indicated that an efficient protein homeostasis pathway plays an essential role in the thermophily of C. thermophilum, and N-glycosylation is involved by affecting related proteins. This is the novel study to reveal thermophilic fungi’s physiological response to high-temperature adaptation using omics analysis, facilitating the exploration of the thermophily mechanism of thermophilic fungi.
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Affiliation(s)
- Jinpeng Gao
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Qingchao Li
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Duochuan Li
- Department of Mycology, Shandong Agricultural University, Taian, China
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25
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Sunny JS, Nisha K, Natarajan A, Saleena LM. IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage. Extremophiles 2021; 25:319-325. [PMID: 33961119 DOI: 10.1007/s00792-021-01231-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/22/2021] [Indexed: 10/21/2022]
Abstract
Biocatalysts provide many advantages over the traditional chemically assisted processes prevalent in industries. Consequently, the search for novel enzymes has increased over the years with a renewed interest in thermophilic and psychrophilic bacterial species. Enzymes or extremozymes extracted from such species have exhibited an affinity to extreme temperatures which is a prerequisite for many industrial applications. However, utilisation of these enzymes faces a major bottleneck. The distribution of sequence data associated with thermophiles and psychrophiles is overwhelming, spanning various databases and scientific literature. Based on more than 100 publications and genomes from over 300 thermophilic and psychrophilic bacterial species, we have constructed the database IND-Enzymes (indenzymes.srmist.edu.in). This database consists of over 20,120 nucleotide and protein sequences belonging to the hydrolytic enzyme class lipase, protease, esterase and amylase. Users can access over 100 published enzymes, 200 PDB structural data. Enzymes derived from genomes can be directly downloaded and users can also access the entire annotation data derived from species individually. Along with an alignment tool and python based pipelines, IND-Enzymes serves as the largest sequence repository for hydrolytic enzymes from thermophilic and psychrophilic bacterial species. This database showcases resources that are essential for protein engineering of hot-cold stable enzymes.
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Affiliation(s)
- Jithin S Sunny
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Room no. 508, SRM Nagar, Kattankulathur, 603203, Kanchipuram, TN, India
| | - Khairun Nisha
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Room no. 508, SRM Nagar, Kattankulathur, 603203, Kanchipuram, TN, India
| | - Anuradha Natarajan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Room no. 508, SRM Nagar, Kattankulathur, 603203, Kanchipuram, TN, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Room no. 508, SRM Nagar, Kattankulathur, 603203, Kanchipuram, TN, India.
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26
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Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
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Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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27
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Mohsin I, Zhang LQ, Li DC, Papageorgiou AC. Crystal structure of a Cu,Zn superoxide dismutase from the thermophilic fungus Chaetomium thermophilum. Protein Pept Lett 2021; 28:1043-1053. [PMID: 33726638 DOI: 10.2174/0929866528666210316104919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Thermophilic fungi have recently emerged as a promising source of thermostable enzymes. Superoxide dismutases are key antioxidant metalloenzymes with promising therapeutic effects in various diseases, both acute and chronic. However, structural heterogeneity and low thermostability limit their therapeutic efficacy. OBJECTIVE Although several studies from hypethermophilic superoxide dismutases (SODs) have been reported, information about Cu,Zn-SODs from thermophilic fungi is scarce. Chaetomium thermophilum is a thermophilic fungus that could provide proteins with thermophilic properties. METHOD The enzyme was expressed in Pichia pastoris cells and crystallized using the vapor-diffusion method. X-ray data were collected, and the structure was determined and refined to 1.56 Å resolution. Structural analysis and comparisons were carried out. RESULTS The presence of 8 molecules (A through H) in the asymmetric unit resulted in four different interfaces. Molecules A and F form the typical homodimer which is also found in other Cu,Zn-SODs. Zinc was present in all subunits of the structure while copper was found in only four subunits with reduced occupancy (C, D, E and F). CONCLUSION The ability of the enzyme to form oligomers and the elevated Thr:Ser ratio may be contributing factors to its thermal stability. Two hydrophobic residues that participate in interface formation and are not present in other CuZn-SODs may play a role in the formation of new interfaces and the oligomerization process. The CtSOD crystal structure reported here is the first Cu,Zn-SOD structure from a thermophilic fungus.
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Affiliation(s)
- Imran Mohsin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20521. Finland
| | - Li-Qing Zhang
- Department of Mycology, Shandong Agricultural University, Taian, Shandong 271018. China
| | - Duo-Chuan Li
- Department of Mycology, Shandong Agricultural University, Taian, Shandong 271018. China
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28
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Jaafar NR, Mahadi NM, Mackeen MM, Illias RM, Murad AMA, Abu Bakar FD. Structural and functional characterisation of a cold-active yet heat-tolerant dehydroquinase from Glaciozyma antarctica PI12. J Biotechnol 2021; 329:118-127. [PMID: 33539893 DOI: 10.1016/j.jbiotec.2021.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/25/2022]
Abstract
Dehydroquinase or 3-dehydroquinate dehydratase (DHQD) reversibly cleaves 3-dehydroquinate to form 3-dehydroshikimate. Here, we describe the functional and structural features of a cold active type II 3-dehydroquinate dehydratase from the psychrophilic yeast, Glaciozyma antarctica PI12 (GaDHQD). Functional studies showed that the enzyme was active at low temperatures (10-30 °C), but displayed maximal activity at 40 °C. Yet the enzyme was stable over a wide range of temperatures (10-70 °C) and between pH 6.0-10.0 with an optimum pH of 8.0. Interestingly, the enzyme was highly thermo-tolerant, denaturing only at approximately 84 °C. Three-dimensional structure analyses showed that the G. antarctica dehydroquinase (GaDHQD) possesses psychrophilic features in comparison with its mesophilic and thermophilic counterparts such as higher numbers of non-polar residues on the surface, lower numbers of arginine and higher numbers of glycine-residues with lower numbers of hydrophobic interactions. On the other hand, GaDHQD shares some traits (i.e. total number of hydrogen bonds, number of proline residues and overall folding) with its mesophilic and thermophilic counterparts. Combined, these features contribute synergistically towards the enzyme's ability to function at both low and high temperatures.
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Affiliation(s)
- Nardiah Rizwana Jaafar
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81210, Skudai, Johor Darul Takzim, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nor Muhammad Mahadi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Mukram Mohamed Mackeen
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia; Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Rosli Md Illias
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81210, Skudai, Johor Darul Takzim, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.
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29
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Tu T, Wang Z, Luo Y, Li Y, Su X, Wang Y, Zhang J, Rouvinen J, Yao B, Hakulinen N, Luo H. Structural Insights into the Mechanisms Underlying the Kinetic Stability of GH28 Endo-Polygalacturonase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:815-823. [PMID: 33404235 DOI: 10.1021/acs.jafc.0c06941] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thermostability is a key property of industrial enzymes. Endo-polygalacturonases of the glycoside hydrolase family 28 have many practical applications, but only few of their structures have been determined, and the reasons for their stability remain unclear. We identified and characterized the Talaromyces leycettanus JCM12802 endo-polygalacturonase TlPGA, which differs from other GH28 family members because of its high catalytic activity, with an optimum temperature of 70 °C. Distinctive features were revealed by comparison of thermophilic TlPGA and all known structures of fungal endo-polygalacturonases, including a relatively large exposed polar accessible surface area in thermophilic TlPGA. By mutating potentially important residues in thermophilic TlPGA, we identified Thr284 as a critical residue. Mutant T284A was comparable to thermophilic TlPGA in melting temperature but exhibited a significantly lower half-life and half-inactivation temperature, implicating residue Thr284 in the kinetic stability of thermophilic TlPGA. Structure analysis of thermophilic TlPGA and mutant T284A revealed that a carbon-oxygen hydrogen bond between the hydroxyl group of Thr284 and the Cα atom of Gln255, and the stable conformation adopted by Gln255, contribute to its kinetic stability. Our results clarify the mechanism underlying the kinetic stability of GH28 endo-polygalacturonases and may guide the engineering of thermostable enzymes for industrial applications.
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Affiliation(s)
- Tao Tu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Zhiyun Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yan Luo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yeqing Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiaoyun Su
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yuan Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jie Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, Joensuu 80130, Finland
| | - Bin Yao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu 80130, Finland
| | - Huiying Luo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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30
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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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31
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The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins. Int J Mol Sci 2020; 21:ijms21228776. [PMID: 33233627 PMCID: PMC7699789 DOI: 10.3390/ijms21228776] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Tryptophan (Trp) holds a unique place in biology for a multitude of reasons. It is the largest of all twenty amino acids in the translational toolbox. Its side chain is indole, which is aromatic with a binuclear ring structure, whereas those of Phe, Tyr, and His are single-ring aromatics. In part due to these elaborate structural features, the biosynthetic pathway of Trp is the most complex and the most energy-consuming among all amino acids. Essential in the animal diet, Trp is also the least abundant amino acid in the cell, and one of the rarest in the proteome. In most eukaryotes, Trp is the only amino acid besides Met, which is coded for by a single codon, namely UGG. Due to the large and hydrophobic π-electron surface area, its aromatic side chain interacts with multiple other side chains in the protein, befitting its strategic locations in the protein structure. Finally, several Trp derivatives, namely tryptophylquinone, oxitriptan, serotonin, melatonin, and tryptophol, have specialized functions. Overall, Trp is a scarce and precious amino acid in the cell, such that nature uses it parsimoniously, for multiple but selective functions. Here, the various aspects of the uniqueness of Trp are presented in molecular terms.
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Biocatalysis at Extreme Temperatures: Enantioselective Synthesis of both Enantiomers of Mandelic Acid by Transesterification Catalyzed by a Thermophilic Lipase in Ionic Liquids at 120 °C. Catalysts 2020. [DOI: 10.3390/catal10091055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The use of biocatalysts in organic chemistry for catalyzing chemo-, regio- and stereoselective transformations has become an usual tool in the last years, both at lab and industrial scale. This is not only because of their exquisite precision, but also due to the inherent increase in the process sustainability. Nevertheless, most of the interesting industrial reactions involve water-insoluble substrates, so the use of (generally not green) organic solvents is generally required. Although lipases are capable of maintaining their catalytic precision working in those solvents, reactions are usually very slow and consequently not very appropriate for industrial purposes. Increasing reaction temperature would accelerate the reaction rate, but this should require the use of lipases from thermophiles, which tend to be more enantioselective at lower temperatures, as they are more rigid than those from mesophiles. Therefore, the ideal scenario would require a thermophilic lipase capable of retaining high enantioselectivity at high temperatures. In this paper, we describe the use of lipase from Geobacillus thermocatenolatus as catalyst in the ethanolysis of racemic 2-(butyryloxy)-2-phenylacetic to furnish both enantiomers of mandelic acid, an useful intermediate in the synthesis of many drugs and active products. The catalytic performance at high temperature in a conventional organic solvent (isooctane) and four imidazolium-based ionic liquids was assessed. The best results were obtained using 1-ethyl-3-methyl imidazolium tetrafluoroborate (EMIMBF4) and 1-ethyl-3-methyl imidazolium hexafluorophosphate (EMIMPF6) at temperatures as high as 120 °C, observing in both cases very fast and enantioselective kinetic resolutions, respectively leading exclusively to the (S) or to the (R)-enantiomer of mandelic acid, depending on the anion component of the ionic liquid.
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33
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Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation. Int J Mol Sci 2020; 21:ijms21072600. [PMID: 32283632 PMCID: PMC7178038 DOI: 10.3390/ijms21072600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/30/2022] Open
Abstract
Thermotoga maritima, a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein (Tm-ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm-ACP, we investigated the structure and dynamics of Tm-ACP by nuclear magnetic resonance (NMR) spectroscopy. The melting temperature of Tm-ACP (101.4 °C) far exceeds that of other ACPs, owing to extensive ionic interactions and tight hydrophobic packing. The D59 residue, which replaces Pro/Ser of other ACPs, mediates ionic clustering between helices III and IV. This creates a wide pocket entrance to facilitate the accommodation of long acyl chains required for hyperthermal adaptation of the T. maritima cell membrane. Tm-ACP is revealed to be the first ACP that harbor an amide proton hyperprotected against hydrogen/deuterium exchange for I15. The hydrophobic interactions mediated by I15 appear to be the key driving forces of the global folding process of Tm-ACP. Our findings provide insights into the structural basis of the hyperthermal adaptation of ACP, which might have allowed T. maritima to survive in hot ancient oceans.
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