2
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Joho Y, Vongsouthi V, Spence MA, Ton J, Gomez C, Tan LL, Kaczmarski JA, Caputo AT, Royan S, Jackson CJ, Ardevol A. Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella sakaiensis PETase and Variants with Improved Stability and Activity. Biochemistry 2023; 62:437-450. [PMID: 35951410 DOI: 10.1021/acs.biochem.2c00323] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The improved production, recycling, and removal of plastic waste, such as polyethylene terephthalate (PET), are pressing environmental and economic issues for society. Biocatalytic (enzymatic) PET depolymerization is potentially a sustainable, low-energy solution to PET recycling, especially when compared with current disposal methods such as landfills, incineration, or gasification. IsPETase has been extensively studied for its use in PET depolymerization; however, its evolution from cutinases is not fully understood, and most engineering studies have neglected the majority of the available sequence space remote from the active site. In this study, ancestral protein reconstruction (ASR) has been used to trace the evolutionary trajectory from ancient serine hydrolases to IsPETase, while ASR and the related design approach, protein repair one-stop shop, were used to identify enzyme variants with improved activity and stability. Kinetic and structural characterization of these variants reveals new insights into the evolution of PETase activity and the role of second-shell mutations around the active site. Among the designed and reconstructed variants, we identified several with melting points 20 °C higher than that of IsPETase and two variants with significantly higher catalytic activity.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia.,Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jennifer Ton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Li Lynn Tan
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Joe A Kaczmarski
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Alessandro T Caputo
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia
| | - Santana Royan
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia.,CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
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4
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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5
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Eicholt LA, Aubel M, Berk K, Bornberg‐Bauer E, Lange A. Heterologous expression of naturally evolved putative de novo proteins with chaperones. Protein Sci 2022; 31:e4371. [PMID: 35900020 PMCID: PMC9278007 DOI: 10.1002/pro.4371] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/03/2022] [Accepted: 05/14/2022] [Indexed: 11/23/2022]
Abstract
Over the past decade, evidence has accumulated that new protein-coding genes can emerge de novo from previously non-coding DNA. Most studies have focused on large scale computational predictions of de novo protein-coding genes across a wide range of organisms. In contrast, experimental data concerning the folding and function of de novo proteins are scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are short and predicted to be disordered. Here, we propose a guideline for the effective expression of eukaryotic de novo proteins in Escherichia coli. We used 11 sequences from Drosophila melanogaster and 10 from Homo sapiens, that are predicted de novo proteins from former studies, for heterologous expression. The candidate de novo proteins have varying secondary structure and disorder content. Using multiple combinations of purification tags, E. coli expression strains, and chaperone systems, we were able to increase the number of solubly expressed putative de novo proteins from 30% to 62%. Our findings indicate that the best combination for expressing putative de novo proteins in E. coli is a GST-tag with T7 Express cells and co-expressed chaperones. We found that, overall, proteins with higher predicted disorder were easier to express. STATEMENT: Today, we know that proteins do not only evolve by duplication and divergence of existing proteins but also arise from previously non-coding DNA. These proteins are called de novo proteins. Their properties are still poorly understood and their experimental analysis faces major obstacles. Here, we aim to present a starting point for soluble expression of de novo proteins with the help of chaperones and thereby enable further characterization.
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Affiliation(s)
- Lars A. Eicholt
- Institute for Evolution and BiodiversityUniversity of MuensterMünsterGermany
| | - Margaux Aubel
- Institute for Evolution and BiodiversityUniversity of MuensterMünsterGermany
| | - Katrin Berk
- Institute for Evolution and BiodiversityUniversity of MuensterMünsterGermany
| | - Erich Bornberg‐Bauer
- Institute for Evolution and BiodiversityUniversity of MuensterMünsterGermany
- Max Planck‐Institute for Biology TuebingenTübingenGermany
| | - Andreas Lange
- Institute for Evolution and BiodiversityUniversity of MuensterMünsterGermany
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