The direction of protein evolution is destined by the stability

Ota, Natsuko; Kurahashi, Ryo; Сано, С.; Takano, Kazufumi

doi:10.1016/j.biochi.2018.05.006

Cited by 20 publications

(10 citation statements)

References 62 publications

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“…In general, organismal fitness drops after environmental changes, but largely recovers through subsequent evolution and delayed adaptation at the genetic level (104; 105). For example, changes to the fitness landscape of Hsp90 in Saccharomyces cerevisiae were observed in elevated salinity with previously adaptive mutations becoming deleterious in the new environment (106), and the accessible evolutionary pathways in an esterase were shown to change at different growth temperatures (107).…”

Section: Environment and The Fitness Landscapementioning

confidence: 99%

Molecular Fitness Landscapes from High-Coverage Sequence Profiling

Blanco

Janzen

Pressman

et al. 2019

Annu. Rev. Biophys.

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The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The accessibility of high-throughput sequencing (HTS) has transformed this study, enabling large-scale enumeration of fitness for many mutants and even complete sequence spaces in some cases. We review the progress of high-throughput studies in mapping molecular fitness landscapes, both in vitro and in vivo, as well as opportunities for future research. Such studies are rapidly growing in number. HTS is expected to have a profound effect on the understanding of real molecular fitness landscapes.

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Section: Environment and The Fitness Landscapementioning

confidence: 99%

Molecular Fitness Landscapes from High-Coverage Sequence Profiling

Blanco

Janzen

Pressman

et al. 2019

Annu. Rev. Biophys.

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“…A number of studies over the past decade have demonstrated that the enhanced stability of thermophilic and hyperthermophilic proteins is characterized by their ability to resist irreversible unfolding when subjected to denaturing conditions. For example, a thermophilic protein unfolded when subjected to heat and chemical denaturants but then refolded into a structure nearly identical to its native state after the denaturing agent was removed [13,14,15]. Many studies have been performed to tease out the factors contributing to enhanced stability of thermophilic proteins.…”

Section: Thermophilic Proteins and Their High Thermostabilitymentioning

confidence: 99%

Thermophilic Proteins as Versatile Scaffolds for Protein Engineering

Finch

Kim

2018

Microorganisms

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Literature from the past two decades has outlined the existence of a trade-off between protein stability and function. This trade-off creates a unique challenge for protein engineers who seek to introduce new functionality to proteins. These engineers must carefully balance the mutation-mediated creation and/or optimization of function with the destabilizing effect of those mutations. Subsequent research has shown that protein stability is positively correlated with “evolvability” or the ability to support mutations which bestow new functionality on the protein. Since the ultimate goal of protein engineering is to create and/or optimize a protein’s function, highly stable proteins are preferred as potential scaffolds for protein engineering. This review focuses on the application potential for thermophilic proteins as scaffolds for protein engineering. The relatively high inherent thermostability of these proteins grants them a great deal of mutational robustness, making them promising scaffolds for various protein engineering applications. Comparative studies on the evolvability of thermophilic and mesophilic proteins have strongly supported the argument that thermophilic proteins are more evolvable than mesophilic proteins. These findings indicate that thermophilic proteins may represent the scaffold of choice for protein engineering in the future.

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“…Improved thermal stability of the enzyme components in an in vitro biosystem-based industrial process is important for increasing robustness, and moreover protein stability in general is important in allowing toleration of destabilizing mutations that can result as a protein structure is optimized for other properties or functions [40,41]. The amino acid sequence of the UDH from Agrobacterium tumefaciens (AtUDH) is 55 % identical and 67 % identical or similar to that of CsUDH (Fig.…”

Section: Resultsmentioning

confidence: 99%

Chromohalobacter salixigens uronate dehydrogenase: Directed evolution for improved thermal stability and mutant CsUDH-inc X-ray crystal structure

Wagschal

Chan

Pereira

et al. 2022

Process Biochemistry

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Chromohalobacter salixigens contains a uronate dehydrogenase termed CsUDH that can convert uronic acids to their corresponding C1,C6-dicarboxy aldaric acids, an important enzyme reaction applicable for biotechnological use of sugar acids. To increase the thermal stability of this enzyme for biotechnological processes, directed evolution using gene family shuffling was applied, and the hits selected from 2-tier screening of a shuffled gene family library contained in total 16 mutations, only some of which when examined individually appreciably increased thermal stability. Most mutations, while having minimal or no effect on thermal stability when tested in isolation, were found to exhibit synergy when combined; CsUDH-inc containing all 16 mutations had ΔK t 0.5 +18°C, such that k cat was unaffected by incubation for 1 h at ∼70°C. X-ray crystal structure of CsUDH-inc showed tight packing of the mutated residue side-chains, and comparison of rescaled B-values showed no obvious differences between wild type and mutant structures. Activity of CsUDH-inc was severely depressed on glucuronic and galacturonic acids. Combining select combinations of only three mutations resulted in good or comparable activity on these uronic acids, while maintaining some improved thermostability with ΔK t 0.5 ∼+ 10°C, indicating potential to further thermally optimize CsUDH for hyperthermophilic reaction environments.

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The direction of protein evolution is destined by the stability

Cited by 20 publications

References 62 publications

Molecular Fitness Landscapes from High-Coverage Sequence Profiling

Molecular Fitness Landscapes from High-Coverage Sequence Profiling

Thermophilic Proteins as Versatile Scaffolds for Protein Engineering

Chromohalobacter salixigens uronate dehydrogenase: Directed evolution for improved thermal stability and mutant CsUDH-inc X-ray crystal structure

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