1
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Kostelac A, Taborda A, Martins LO, Haltrich D. Evolution and separation of actinobacterial pyranose and C-glycoside-3-oxidases. Appl Environ Microbiol 2024; 90:e0167623. [PMID: 38179968 PMCID: PMC10807413 DOI: 10.1128/aem.01676-23] [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: 09/21/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
FAD-dependent pyranose oxidase (POx) and C-glycoside-3-oxidase (CGOx) are both members of the glucose-methanol-choline superfamily of oxidoreductases and belong to the same sequence space. Pyranose oxidases had been studied for their oxidation of monosaccharides such as D-glucose, but recently, a bacterial C-glycoside-3-oxidase that is phylogenetically related to POx and that reacts with C-glycosides such as carminic acid, mangiferin or puerarin has been described. Since these actinobacterial CGOx enzymes belong to the same sequence space as bacterial POx, they must have evolved from the same ancestor. Here, we performed a phylogenetic analysis of actinobacterial sequences and resurrected seven ancestral enzymes of the POx/CGOx sequence space to study the evolutionary trajectory of substrate preferences for monosaccharides and C-glycosides. Clade I, with its dimeric member POx from Kitasatospora aureofaciens, shows strict preference for monosaccharides (D-glucose and D-xylose) and does not react with any of the glycosides tested. No extant member of clade II has been studied to date. The two extant members of clades III and IV, monomeric POx/CGOx from Pseudoarthrobacter siccitolerans and Streptomyces canus, oxidized both monosaccharides as well as various C-glycosides (homoorientin, isovitexin, mangiferin, and puerarin). Steady-state kinetic parameters of several clades III and IV ancestral enzymes indicate that the generalist ancestor N35 slowly evolved to present-day enzymes with a much higher preference for C-glycosides than monosaccharides. Based on structural predictions of ancestors, we hypothesize that the strict specificity of bacterial clade I POx (and also fungal POx) is the result of oligomerization, which in turn results from the evolution of protein segments that were shown to be important for oligomerization, the arm, and the head domain.IMPORTANCEC-Glycosides often form active compounds in various plants. Breakage of the C-C bond in these glycosides to release the aglycone is challenging and proceeds via a two-step reaction, the oxidation of the sugar and subsequent cleavage of the C-C bond. Recently, an enzyme from a soil bacterium, FAD-dependent C-glycoside-3-oxidase (CGOx), was shown to catalyze the initial oxidation reaction. Here, we show that CGOx belongs to the same sequence space as pyranose oxidase (POx), and that an actinobacterial ancestor of the POx/CGOx family evolved into four clades, two of which show a high preference for C-glycosides.
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Affiliation(s)
- Anja Kostelac
- Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Austria
- Doctoral Programme BioToP—Biomolecular Technology of Proteins, BOKU—University of Natural Resources and Life Sciences, Vienna, Austria
| | - André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dietmar Haltrich
- Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Austria
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2
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Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
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Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
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3
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Mardikoraem M, Wang Z, Pascual N, Woldring D. Generative models for protein sequence modeling: recent advances and future directions. Brief Bioinform 2023; 24:bbad358. [PMID: 37864295 PMCID: PMC10589401 DOI: 10.1093/bib/bbad358] [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: 06/13/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/22/2023] Open
Abstract
The widespread adoption of high-throughput omics technologies has exponentially increased the amount of protein sequence data involved in many salient disease pathways and their respective therapeutics and diagnostics. Despite the availability of large-scale sequence data, the lack of experimental fitness annotations underpins the need for self-supervised and unsupervised machine learning (ML) methods. These techniques leverage the meaningful features encoded in abundant unlabeled sequences to accomplish complex protein engineering tasks. Proficiency in the rapidly evolving fields of protein engineering and generative AI is required to realize the full potential of ML models as a tool for protein fitness landscape navigation. Here, we support this work by (i) providing an overview of the architecture and mathematical details of the most successful ML models applicable to sequence data (e.g. variational autoencoders, autoregressive models, generative adversarial neural networks, and diffusion models), (ii) guiding how to effectively implement these models on protein sequence data to predict fitness or generate high-fitness sequences and (iii) highlighting several successful studies that implement these techniques in protein engineering (from paratope regions and subcellular localization prediction to high-fitness sequences and protein design rules generation). By providing a comprehensive survey of model details, novel architecture developments, comparisons of model applications, and current challenges, this study intends to provide structured guidance and robust framework for delivering a prospective outlook in the ML-driven protein engineering field.
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Affiliation(s)
- Mehrsa Mardikoraem
- Michigan State University (MSU)‘s Department of Chemical Engineering and Materials Science
| | - Zirui Wang
- Regeneron Pharmaceuticals, Inc. Having received his B.S. in Chemical Engineering from MSU, he is currently pursuing a M.S. in Computer Science from Syracuse University
| | | | - Daniel Woldring
- MSU’s Department of Chemical Engineering and Materials Science and a member of MSU’s Institute for Quantitative Health Sciences and Engineering
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4
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Hager M, Pöhler MT, Reinhardt F, Wellner K, Hübner J, Betat H, Prohaska S, Mörl M. Substrate Affinity Versus Catalytic Efficiency: Ancestral Sequence Reconstruction of tRNA Nucleotidyltransferases Solves an Enzyme Puzzle. Mol Biol Evol 2022; 39:6835633. [PMID: 36409584 PMCID: PMC9728577 DOI: 10.1093/molbev/msac250] [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] [Indexed: 11/22/2022] Open
Abstract
In tRNA maturation, CCA-addition by tRNA nucleotidyltransferase is a unique and highly accurate reaction. While the mechanism of nucleotide selection and polymerization is well understood, it remains a mystery why bacterial and eukaryotic enzymes exhibit an unexpected and surprisingly low tRNA substrate affinity while they efficiently catalyze the CCA-addition. To get insights into the evolution of this high-fidelity RNA synthesis, the reconstruction and characterization of ancestral enzymes is a versatile tool. Here, we investigate a reconstructed candidate of a 2 billion years old CCA-adding enzyme from Gammaproteobacteria and compare it to the corresponding modern enzyme of Escherichia coli. We show that the ancestral candidate catalyzes an error-free CCA-addition, but has a much higher tRNA affinity compared with the extant enzyme. The consequence of this increased substrate binding is an enhanced reverse reaction, where the enzyme removes the CCA end from the mature tRNA. As a result, the ancestral candidate exhibits a lower catalytic efficiency in vitro as well as in vivo. Furthermore, the efficient tRNA interaction leads to a processive polymerization, while the extant enzyme catalyzes nucleotide addition in a distributive way. Thus, the modern enzymes increased their polymerization efficiency by lowering the binding affinity to tRNA, so that CCA synthesis is efficiently promoted due to a reduced reverse reaction. Hence, the puzzling and at a first glance contradicting and detrimental weak substrate interaction represents a distinct activity enhancement in the evolution of CCA-adding enzymes.
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Affiliation(s)
| | | | - Franziska Reinhardt
- Computational EvoDevo Group, Institute for Computer Science, Leipzig University, Härtelstr. 16-18, 04109 Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04109 Leipzig, Germany
| | - Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Jessica Hübner
- Computational EvoDevo Group, Institute for Computer Science, Leipzig University, Härtelstr. 16-18, 04109 Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Sonja Prohaska
- Computational EvoDevo Group, Institute for Computer Science, Leipzig University, Härtelstr. 16-18, 04109 Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04109 Leipzig, Germany,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA,Complexity Science Hub Vienna, Josefstädter Str. 39, 1080 Wien, Austria
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5
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Blazeck J, Karamitros CS, Ford K, Somody C, Qerqez A, Murray K, Burkholder NT, Marshall N, Sivakumar A, Lu WC, Tan B, Lamb C, Tanno Y, Siddiqui MY, Ashoura N, Coma S, Zhang XM, McGovern K, Kumada Y, Zhang YJ, Manfredi M, Johnson KA, D’Arcy S, Stone E, Georgiou G. Bypassing evolutionary dead ends and switching the rate-limiting step of a human immunotherapeutic enzyme. Nat Catal 2022; 5:952-967. [PMID: 36465553 PMCID: PMC9717613 DOI: 10.1038/s41929-022-00856-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
The Trp metabolite kynurenine (KYN) accumulates in numerous solid tumours and mediates potent immunosuppression. Bacterial kynureninases (KYNases), which preferentially degrade kynurenine, can relieve immunosuppression in multiple cancer models, but immunogenicity concerns preclude their clinical use, while the human enzyme (HsKYNase) has very low activity for kynurenine and shows no therapeutic effect. Using fitness selections, we evolved a HsKYNase variant with 27-fold higher activity, beyond which exploration of >30 evolutionary trajectories involving the interrogation of >109 variants led to no further improvements. Introduction of two amino acid substitutions conserved in bacterial KYNases reduced enzyme fitness but potentiated rapid evolution of variants with ~500-fold improved activity and reversed substrate specificity, resulting in an enzyme capable of mediating strong anti-tumour effects in mice. Pre-steady-state kinetics revealed a switch in rate-determining step attributable to changes in both enzyme structure and conformational dynamics. Apart from its clinical significance, our work highlights how rationally designed substitutions can potentiate trajectories that overcome barriers in protein evolution.
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Affiliation(s)
- John Blazeck
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Christos S. Karamitros
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Ford
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Catrina Somody
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Ahlam Qerqez
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Nathaniel T. Burkholder
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Nicholas Marshall
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Anirudh Sivakumar
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Wei-Cheng Lu
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Bing Tan
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Menna Y. Siddiqui
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Norah Ashoura
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Silvia Coma
- Ikena Oncology, Cambridge, Massachusetts, USA
| | | | | | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
| | | | - Kenneth A. Johnson
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Sheena D’Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Everett Stone
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA
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6
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Hueting DA, Vanga SR, Syrén PO. Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability. J Phys Chem B 2022; 126:3809-3821. [PMID: 35583961 PMCID: PMC9169049 DOI: 10.1021/acs.jpcb.1c10605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Thermostability is
the key to maintain the structural integrity
and catalytic activity of enzymes in industrial biotechnological processes,
such as terpene cyclase-mediated generation of medicines, chiral synthons,
and fine chemicals. However, affording a large increase in the thermostability
of enzymes through site-directed protein engineering techniques can
constitute a challenge. In this paper, we used ancestral sequence
reconstruction to create a hyperstable variant of the ent-copalyl diphosphate synthase PtmT2, a terpene cyclase involved in
the assembly of antibiotics. Molecular dynamics simulations on the
μs timescale were performed to shed light on possible molecular
mechanisms contributing to activity at an elevated temperature and
the large 40 °C increase in melting temperature observed for
an ancestral variant of PtmT2. In silico analysis
revealed key differences in the flexibility of a loop capping the
active site, between extant and ancestral proteins. For the modern
enzyme, the loop collapses into the active site at elevated temperatures,
thus preventing biocatalysis, whereas the loop remains in a productive
conformation both at ambient and high temperatures in the ancestral
variant. Restoring a Pro loop residue introduced in the ancestral
variant to the corresponding Gly observed in the extant protein led
to reduced catalytic activity at high temperatures, with only moderate
effects on the melting temperature, supporting the importance of the
flexibility of the capping loop in thermoadaptation. Conversely, the
inverse Gly to Pro loop mutation in the modern enzyme resulted in
a 3-fold increase in the catalytic rate. Despite an overall decrease
in maximal activity of ancestor compared to wild type, its increased
thermostability provides a robust backbone amenable for further enzyme
engineering. Our work cements the importance of loops in enzyme catalysis
and provides a molecular mechanism contributing to thermoadaptation
in an ancestral enzyme.
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Affiliation(s)
- David A Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Sudarsana R Vanga
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
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7
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Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes. J Struct Biol 2022; 214:107835. [DOI: 10.1016/j.jsb.2022.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/26/2021] [Accepted: 01/23/2022] [Indexed: 11/21/2022]
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8
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Lichman BR. Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution. Methods Mol Biol 2022; 2505:165-179. [PMID: 35732944 DOI: 10.1007/978-1-0716-2349-7_12] [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] [Indexed: 06/15/2023]
Abstract
The complex and bioactive monoterpene indole alkaloids (MIAs) found in Catharanthus roseus and related species are the products of many millions of years of evolution through mutation and natural selection. Ancestral sequence reconstruction (ASR) is a method that combines phylogenetic analysis and experimental biochemistry to infer details about past events in protein evolution. Here, I propose that ASR could be leveraged to understand how enzymes catalyzing the formation of complex alkaloids arose over evolutionary time. I discuss the steps of ASR, including sequence selection, multiple sequence alignment, tree inference, and the generation and characterization of inferred ancestral enzymes.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK.
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9
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Abstract
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this inference is the ancestral sequence reconstruction (ASR), which can be performed with diverse methodologies implemented in computer frameworks. However, most of these methodologies ignore evolutionary properties frequently observed in microbes, such as genetic recombination and complex selection processes, that can bias the traditional ASR. From a practical perspective, here I review methodologies for the reconstruction of ancestral DNA and protein sequences, with particular focus on microbes, and including biases, recommendations, and software implementations. I conclude that microbial ASR is a complex analysis that should be carefully performed and that there is a need for methods to infer more realistic ancestral microbial sequences.
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Affiliation(s)
- Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain.
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10
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Farihan Afnan Mohd Rozi M, Noor Zaliha Raja Abd Rahman R, Thean Chor Leow A, Shukuri Mohamad Ali M. Ancestral Sequence Reconstruction of Ancient Lipase from Family I.3 Bacterial Lipolytic Enzymes. Mol Phylogenet Evol 2021; 168:107381. [PMID: 34968679 DOI: 10.1016/j.ympev.2021.107381] [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: 08/23/2020] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/14/2023]
Abstract
Family I.3 lipase is distinguished from other families by the amino acid sequence and secretion mechanism. Little is known about the evolutionary process driving these differences. This study attempt to understand how the diverse temperature stabilities of bacterial lipases from family I.3 evolved. To achieve that, eighty-three protein sequences sharing a minimum 30% sequence identity with Antarctic Pseudomonas sp. AMS8 lipase were used to infer phylogenetic tree. Using ancestral sequence reconstruction (ASR) technique, the last universal common ancestor (LUCA) sequence of family I.3 was reconstructed. A gene encoding LUCA was synthesized, cloned and expressed as inclusion bodies in E. coli system. Insoluble form of LUCA was refolded using urea dilution method and then purified using affinity chromatography. The purified LUCA exhibited an optimum temperature and pH at 70℃ and 10 respectively. Various metal ions increased or retained the activity of LUCA. LUCA also demonstrated tolerance towards various organic solvents in 25% v/v concentration. The finding from this study could support the understanding on temperature and environment during ancient time. In overall, reconstructed ancestral enzymes have improved physicochemical properties that make them suitable for industrial applications and ASR technique can be employed as a general technique for enzyme engineering.
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Affiliation(s)
- Mohamad Farihan Afnan Mohd Rozi
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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11
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Shrestha S, Clark AC. Evolution of the folding landscape of effector caspases. J Biol Chem 2021; 297:101249. [PMID: 34592312 PMCID: PMC8628267 DOI: 10.1016/j.jbc.2021.101249] [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: 08/05/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/07/2022] Open
Abstract
Caspases are a family of cysteinyl proteases that control programmed cell death and maintain homeostasis in multicellular organisms. The caspase family is an excellent model to study protein evolution because all caspases are produced as zymogens (procaspases [PCPs]) that must be activated to gain full activity; the protein structures are conserved through hundreds of millions of years of evolution; and some allosteric features arose with the early ancestor, whereas others are more recent evolutionary events. The apoptotic caspases evolved from a common ancestor (CA) into two distinct subfamilies: monomers (initiator caspases) or dimers (effector caspases). Differences in activation mechanisms of the two subfamilies, and their oligomeric forms, play a central role in the regulation of apoptosis. Here, we examine changes in the folding landscape by characterizing human effector caspases and their CA. The results show that the effector caspases unfold by a minimum three-state equilibrium model at pH 7.5, where the native dimer is in equilibrium with a partially folded monomeric (PCP-7, CA) or dimeric (PCP-6) intermediate. In comparison, the unfolding pathway of PCP-3 contains both oligomeric forms of the intermediate. Overall, the data show that the folding landscape was first established with the CA and was retained for >650 million years. Partially folded monomeric or dimeric intermediates in the ancestral ensemble provide mechanisms for evolutionary changes that affect stability of extant caspases. The conserved folding landscape allows for the fine-tuning of enzyme stability in a species-dependent manner while retaining the overall caspase–hemoglobinase fold.
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Affiliation(s)
- Suman Shrestha
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.
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Timr S, Madern D, Sterpone F. Protein thermal stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:239-272. [PMID: 32145947 DOI: 10.1016/bs.pmbts.2019.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins, in general, fold to a well-organized three-dimensional structure in order to function. The stability of this functional shape can be perturbed by external environmental conditions, such as temperature. Understanding the molecular factors underlying the resistance of proteins to the thermal stress has important consequences. First of all, it can aid the design of thermostable enzymes able to perform efficient catalysis in the high-temperature regime. Second, it is an essential brick of knowledge required to decipher the evolutionary pathways of life adaptation on Earth. Thanks to the development of atomistic simulations and ad hoc enhanced sampling techniques, it is now possible to investigate this problem in silico, and therefore provide support to experiments. After having described the methodological aspects, the chapter proposes an extended discussion on two problems. First, we focus on thermophilic proteins, a perfect model to address the issue of thermal stability and molecular evolution. Second, we discuss the issue of how protein thermal stability is affected by crowded in vivo-like conditions.
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Affiliation(s)
- Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | | | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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13
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Viola RE. The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction. Crit Rev Biochem Mol Biol 2020; 54:467-483. [PMID: 31906712 DOI: 10.1080/10409238.2019.1708261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?
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Affiliation(s)
- Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, USA
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Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Phys Chem Chem Phys 2020; 22:18361-18373. [DOI: 10.1039/d0cp02738c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
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Affiliation(s)
- Irene Maffucci
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Damien Laage
- PASTEUR
- Département de chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
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15
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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16
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Hernández K, Szekrenyi A, Clapés P. Nucleophile Promiscuity of Natural and Engineered Aldolases. Chembiochem 2018; 19:1353-1358. [DOI: 10.1002/cbic.201800135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Karel Hernández
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Anna Szekrenyi
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Pere Clapés
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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17
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Okafor CD, Pathak MC, Fagan CE, Bauer NC, Cole MF, Gaucher EA, Ortlund EA. Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus. Structure 2018; 26:118-129.e3. [PMID: 29276038 PMCID: PMC5785943 DOI: 10.1016/j.str.2017.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023]
Abstract
Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into the mechanisms by which proteins become more stable, we use structural and dynamic analyses to compare two popular approaches, ancestral sequence reconstruction (ASR) and the consensus method, used to generate thermostable variants of Elongation Factor Thermo-unstable (EF-Tu). We present crystal structures of ancestral and consensus EF-Tus, accompanied by molecular dynamics simulations aimed at probing the strategies employed to enhance thermostability. All proteins adopt crystal structures similar to extant EF-Tus, revealing no difference in average structure between the methods. Molecular dynamics reveals that ASR-generated sequences retain dynamic properties similar to extant, thermostable EF-Tu from Thermus aquaticus, while consensus EF-Tu dynamics differ from evolution-based sequences. This work highlights the advantage of ASR for engineering thermostability while preserving natural motions in multidomain proteins.
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Affiliation(s)
- C. Denise Okafor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Manish C. Pathak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Crystal E. Fagan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Nicholas C. Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Megan F. Cole
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332 USA
| | - Eric A. Gaucher
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332 USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA,Correspondence:
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