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Cea PA, Pérez M, Herrera SM, Muñoz SM, Fuentes-Ugarte N, Coche-Miranda J, Maturana P, Guixé V, Castro-Fernandez V. Deciphering Structural Traits for Thermal and Kinetic Stability across Protein Family Evolution through Ancestral Sequence Reconstruction. Mol Biol Evol 2024; 41:msae127. [PMID: 38913681 PMCID: PMC11229819 DOI: 10.1093/molbev/msae127] [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: 01/30/2024] [Revised: 05/17/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
Natural proteins are frequently marginally stable, and an increase in environmental temperature can easily lead to unfolding. As a result, protein engineering to improve protein stability is an area of intensive research. Nonetheless, since there is usually a high degree of structural homology between proteins from thermophilic organisms and their mesophilic counterparts, the identification of structural determinants for thermoadaptation is challenging. Moreover, in many cases, it has become clear that the success of stabilization strategies is often dependent on the evolutionary history of a protein family. In the last few years, the use of ancestral sequence reconstruction (ASR) as a tool for elucidation of the evolutionary history of functional traits of a protein family has gained strength. Here, we used ASR to trace the evolutionary pathways between mesophilic and thermophilic kinases that participate in the biosynthetic pathway of vitamin B1 in bacteria. By combining biophysics approaches, X-ray crystallography, and molecular dynamics simulations, we found that the thermal stability of these enzymes correlates with their kinetic stability, where the highest thermal/kinetic stability is given by an increase in small hydrophobic amino acids that allow a higher number of interatomic hydrophobic contacts, making this type of interaction the main support for stability in this protein architecture. The results highlight the potential benefits of using ASR to explore the evolutionary history of protein sequence and structure to identify traits responsible for the kinetic and thermal stability of any protein architecture.
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Affiliation(s)
- Pablo A Cea
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Myriam Pérez
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Sixto M Herrera
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Sebastián M Muñoz
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Nicolás Fuentes-Ugarte
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - José Coche-Miranda
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Pablo Maturana
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Victor Castro-Fernandez
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
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Zeng B, Zhao S, Zhou R, Zhou Y, Jin W, Yi Z, Zhang G. Engineering and screening of novel β-1,3-xylanases with desired hydrolysate type by optimized ancestor sequence reconstruction and data mining. Comput Struct Biotechnol J 2022; 20:3313-3321. [PMID: 35832630 PMCID: PMC9251504 DOI: 10.1016/j.csbj.2022.06.050] [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] [Received: 04/21/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/03/2022] Open
Abstract
A novel integrative strategy for engineering β-1,3-xylanases with desired products. AncXyl10 is the first successful example of ASR to shift the hydrolysate types. The hydrolysates of AncXyl10 was only β-1,3-xylobiose and β-1,3-xylotriose. The underlying mechanism laid a new groundwork towards hydrolase engineering.
Engineering of hydrolases to shift their hydrolysate types has not been attempted so far, though computer-assisted enzyme design has been successful. A novel integrative strategy for engineering and screening the β-1,3-xylanase with desired hydrolysate types was proposed, with the purpose to solve problems that the separation and preparation of β-1,3-xylo-oligosaccharides was in high cost yet in low yield as monosaccharides existed in the hydrolysates. By classifying the hydrolysate types and coding them into numerical values, two robust mathematical models with five selected attributes from molecular docking were established based on LogitBoost and partial least squares regression with overall accuracy of 83.3% and 100%, respectively. Then, they were adopted for efficient screening the potential mutagenesis library of β-1,3-xylanases that only product oligosaccharides. The virtually designed AncXyl10 was selected and experimentally verified to produce only β-1,3-xylobiose (60.38%) and β-1,3-xylotriose (39.62%), which facilitated the preparation of oligosaccharides with high purity. The underlying mechanism of AncXyl10 may associated with the gap processing and ancestral amino acid substitution in the process of ancestral sequence reconstruction. Since many carbohydrate-active enzymes have highly conserved active sites, the strategy and their biomolecular basis will shield a new light for engineering carbohydrates hydrolase to produce specific oligosaccharides.
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Gamiz-Arco G, Risso VA, Gaucher EA, Gavira JA, Naganathan AN, Ibarra-Molero B, Sanchez-Ruiz JM. Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression. J Mol Biol 2021; 433:167321. [PMID: 34687715 DOI: 10.1016/j.jmb.2021.167321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022]
Abstract
Obligate symbionts typically exhibit high evolutionary rates. Consequently, their proteins may differ considerably from their modern and ancestral homologs in terms of both sequence and properties, thus providing excellent models to study protein evolution. Also, obligate symbionts are challenging to culture in the lab and proteins from uncultured organisms must be produced in heterologous hosts using recombinant DNA technology. Obligate symbionts thus replicate a fundamental scenario of metagenomics studies aimed at the functional characterization and biotechnological exploitation of proteins from the bacteria in soil. Here, we use the thioredoxin from Candidatus Photodesmus katoptron, an uncultured symbiont of flashlight fish, to explore evolutionary and engineering aspects of protein folding in heterologous hosts. The symbiont protein is a standard thioredoxin in terms of 3D-structure, stability and redox activity. However, its folding outside the original host is severely impaired, as shown by a very slow refolding in vitro and an inefficient expression in E. coli that leads mostly to insoluble protein. By contrast, resurrected Precambrian thioredoxins express efficiently in E. coli, plausibly reflecting an ancient adaptation to unassisted folding. We have used a statistical-mechanical model of the folding landscape to guide back-to-ancestor engineering of the symbiont protein. Remarkably, we find that the efficiency of heterologous expression correlates with the in vitro (i.e., unassisted) folding rate and that the ancestral expression efficiency can be achieved with only 1-2 back-to-ancestor replacements. These results demonstrate a minimal-perturbation, sequence-engineering approach to rescue inefficient heterologous expression which may potentially be useful in metagenomics efforts targeting recent adaptations.
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Affiliation(s)
- Gloria Gamiz-Arco
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jose A Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Avenida de las Palmeras 4, Armilla, Granada 18100, Spain. https://twitter.com/Gavirius
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain.
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain.
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Romero-Romero S, Kordes S, Michel F, Höcker B. Evolution, folding, and design of TIM barrels and related proteins. Curr Opin Struct Biol 2021; 68:94-104. [PMID: 33453500 PMCID: PMC8250049 DOI: 10.1016/j.sbi.2020.12.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
Proteins are chief actors in life that perform a myriad of exquisite functions. This diversity has been enabled through the evolution and diversification of protein folds. Analysis of sequences and structures strongly suggest that numerous protein pieces have been reused as building blocks and propagated to many modern folds. This information can be traced to understand how the protein world has diversified. In this review, we discuss the latest advances in the analysis of protein evolutionary units, and we use as a model system one of the most abundant and versatile topologies, the TIM-barrel fold, to highlight the existing common principles that interconnect protein evolution, structure, folding, function, and design.
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Affiliation(s)
| | - Sina Kordes
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Florian Michel
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
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Non-conservation of folding rates in the thioredoxin family reveals degradation of ancestral unassisted-folding. Biochem J 2020; 476:3631-3647. [PMID: 31750876 PMCID: PMC6906118 DOI: 10.1042/bcj20190739] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 01/04/2023]
Abstract
Evolution involves not only adaptation, but also the degradation of superfluous features. Many examples of degradation at the morphological level are known (vestigial organs, for instance). However, the impact of degradation on molecular evolution has been rarely addressed. Thioredoxins serve as general oxidoreductases in all cells. Here, we report extensive mutational analyses on the folding of modern and resurrected ancestral bacterial thioredoxins. Contrary to claims from recent literature, in vitro folding rates in the thioredoxin family are not evolutionarily conserved, but span at least a ∼100-fold range. Furthermore, modern thioredoxin folding is often substantially slower than ancestral thioredoxin folding. Unassisted folding, as probed in vitro, thus emerges as an ancestral vestigial feature that underwent degradation, plausibly upon the evolutionary emergence of efficient cellular folding assistance. More generally, our results provide evidence that degradation of ancestral features shapes, not only morphological evolution, but also the evolution of individual proteins.
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Isolated domains of recombinant human apo-metallothionein 1A are folded at neutral pH: a denaturant and heat-induced unfolding study using ESI-MS. Biosci Rep 2018; 38:BSR20180592. [PMID: 29858425 PMCID: PMC6050192 DOI: 10.1042/bsr20180592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 12/25/2022] Open
Abstract
Metallothioneins (MTs) are characterized by their high metal loading capacity, small molecular weight, and abundant cysteine residues. It has long been thought that metal-free, or apo-MT peptides were unstructured and only adopted as a distinct conformation upon forming the metal clusters, described as metal-induced folding. More recent studies have suggested that the presence of a globular, yet loosely defined structure actually exists that can be disrupted or unfolded. Residue modification and ion-mobility ESI (IM-ESI)-MS have been used to examine this unusual unfolding process. The structure of apo-MT plays a critical role as the starting point in the flexible metalation pathways that can accommodate numerous soft metals. ESI-MS measurements of the product species formed following the cysteine alkylation of the isolated domain fragments of recombinant human apo-MT 1A with n-ethylmaleimide (NEM) were used in the present study to monitor the denaturant- and heat-induced unfolding at physiological pH. The results indicate that these apo-MT fragments adopt distinct structures at neutral pH that react co-operatively with NEM when folded and non-cooperatively when heated or exposed to high concentrations of the denaturant guanidinium chloride (GdmCl). From these studies, we can conclude that at neutral pH, the domain fragments are folded into globular structures where some of the free cysteine residues are buried within the core and are stabilized by hydrogen bonds. Metalation therefore, must take place from the folded conformation.
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Risso VA, Sanchez-Ruiz JM, Ozkan SB. Biotechnological and protein-engineering implications of ancestral protein resurrection. Curr Opin Struct Biol 2018; 51:106-115. [PMID: 29660672 DOI: 10.1016/j.sbi.2018.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Approximations to the sequences of ancestral proteins can be derived from the sequences of their modern descendants. Proteins encoded by such reconstructed sequences can be prepared in the laboratory and subjected to experimental scrutiny. These 'resurrected' ancestral proteins often display remarkable properties, reflecting ancestral adaptations to intra-cellular and extra-cellular environments that differed from the environments hosting modern/extant proteins. Recent experimental and computational work has specifically discussed high stability, substrate and catalytic promiscuity, conformational flexibility/diversity and altered patterns of interaction with other sub-cellular components. In this review, we discuss these remarkable properties as well as recent attempts to explore their biotechnological and protein-engineering potential.
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Affiliation(s)
- Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain.
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, United States.
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Reply to Candel et al.: Evidence for evolutionary conservation of folding kinetics in the thioredoxin protein family. Proc Natl Acad Sci U S A 2017; 114:E4124. [PMID: 28512227 DOI: 10.1073/pnas.1704669114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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