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Draghi JA, Ogbunugafor CB. Exploring the expanse between theoretical questions and experimental approaches in the modern study of evolvability. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:8-17. [PMID: 35451559 PMCID: PMC10083935 DOI: 10.1002/jez.b.23134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
Abstract
Despite several decades of computational and experimental work across many systems, evolvability remains on the periphery with regards to its status as a widely accepted and regularly applied theoretical concept. Here we propose that its marginal status is partly a result of large gaps between the diverse but disconnected theoretical treatments of evolvability and the relatively narrower range of studies that have tested it empirically. To make this case, we draw on a range of examples-from experimental evolution in microbes, to molecular evolution in proteins-where attempts have been made to mend this disconnect. We highlight some examples of progress that has been made and point to areas where synthesis and translation of existing theory can lead to further progress in the still-new field of empirical measurements of evolvability.
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Affiliation(s)
- Jeremy A Draghi
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - C Brandon Ogbunugafor
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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Prakashrao AS, Beuerle T, Simões ARG, Hopf C, Çiçek SS, Stegemann T, Ober D, Kaltenegger E. The long road of functional recruitment-The evolution of a gene duplicate to pyrrolizidine alkaloid biosynthesis in the morning glories (Convolvulaceae). PLANT DIRECT 2022; 6:e420. [PMID: 35865076 PMCID: PMC9295680 DOI: 10.1002/pld3.420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
In plants, homospermidine synthase (HSS) is a pathway-specific enzyme initiating the biosynthesis of pyrrolizidine alkaloids (PAs), which function as a chemical defense against herbivores. In PA-producing Convolvulaceae ("morning glories"), HSS originated from deoxyhypusine synthase at least >50 to 75 million years ago via a gene duplication event and subsequent functional diversification. To study the recruitment of this ancient gene duplicate to PA biosynthesis, the presence of putative hss gene copies in 11 Convolvulaceae species was analyzed. Additionally, various plant parts from seven of these species were screened for the presence of PAs. Although all of these species possess a putative hss copy, PAs could only be detected in roots of Ipomoea neei (Spreng.) O'Donell and Distimake quinquefolius (L.) A.R.Simões & Staples in this study. A precursor of PAs was detected in roots of Ipomoea alba L. Thus, despite sharing high sequence identities, the presence of an hss gene copy does not correlate with PA accumulation in particular species of Convolvulaceae. In vitro activity assays of the encoded enzymes revealed a broad spectrum of enzyme activity, further emphasizing a functional diversity of the hss gene copies. A recently identified HSS specific amino acid motif seems to be important for the loss of the ancestral protein function-the activation of the eukaryotic initiation factor 5A (eIF5A). Thus, the motif might be indicative for a change of function but allows not to predict the new function. This emphasizes the challenges in annotating functions for duplicates, even for duplicates from closely related species.
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Affiliation(s)
- Arunraj Saranya Prakashrao
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
- Present address:
Heart Research Center GöttingenUniversity Medical Center GöttingenGöttingenGermany.
| | - Till Beuerle
- Institute of Pharmaceutical BiologyTechnische Universität BraunschweigBraunschweigGermany
| | - Ana Rita G. Simões
- Royal Botanic Gardens, KewRichmondUK
- Systematic and Evolutionary Botany LabGhent UniversityGhentBelgium
| | - Christina Hopf
- Department of Structural Biology, Zoological InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Serhat Sezai Çiçek
- Department of Pharmaceutical Biology, Pharmaceutical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Thomas Stegemann
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Dietrich Ober
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Elisabeth Kaltenegger
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
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Bisiak F, Chrenková A, Zhang SD, Pedersen JN, Otzen DE, Zhang YE, Brodersen DE. Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response. J Biol Chem 2022; 298:102142. [PMID: 35714769 PMCID: PMC9293644 DOI: 10.1016/j.jbc.2022.102142] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 11/04/2022] Open
Abstract
The bacterial stringent response involves wide-ranging metabolic reprogramming aimed at increasing long-term survivability during stress conditions. One of the hallmarks of the stringent response is the production of a set of modified nucleotides, known as alarmones, which affect a multitude of cellular pathways in diverse ways. Production and degradation of these molecules depend on the activity of enzymes from the RelA/SpoT homologous family, which come in both bifunctional (containing domains to both synthesize and hydrolyze alarmones) and monofunctional (consisting of only synthetase or hydrolase domain) variants, of which the structure, activity, and regulation of the bifunctional RelA/SpoT homologs have been studied most intensely. Despite playing an important role in guanosine nucleotide homeostasis in particular, mechanisms of regulation of the small alarmone hydrolases (SAHs) are still rather unclear. Here, we present crystal structures of SAH enzymes from Corynebacterium glutamicum (RelHCg) and Leptospira levettii (RelHLl) and show that while being highly similar, structural differences in substrate access and dimer conformations might be important for regulating their activity. We propose that a varied dimer form is a general property of the SAH family, based on current structural information as well as prediction models for this class of enzymes. Finally, subtle structural variations between monofunctional and bifunctional enzymes point to how these different classes of enzymes are regulated.
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Affiliation(s)
- Francesco Bisiak
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Adriana Chrenková
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jannik N Pedersen
- Interdisciplinary Nanoscience Centre (iNano), Aarhus University, Aarhus C, Denmark
| | - Daniel E Otzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark; Interdisciplinary Nanoscience Centre (iNano), Aarhus University, Aarhus C, Denmark
| | - Yong E Zhang
- Department of Biology, University of Copenhagen, København N, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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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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Arantes PR, Polêto MD, Pedebos C, Ligabue-Braun R. Making it Rain: Cloud-Based Molecular Simulations for Everyone. J Chem Inf Model 2021; 61:4852-4856. [PMID: 34595915 DOI: 10.1021/acs.jcim.1c00998] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and (2) to exemplify how low-income research groups can perform MD simulations in the microsecond time scale. We hope this work facilitates teaching and learning of molecular simulation throughout the community.
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Affiliation(s)
- Pablo R Arantes
- Department of Bioengineering, University of California, Riverside, California 92521, United States
| | - Marcelo D Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Conrado Pedebos
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, Federal University of Health Sciences of Proto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil
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Lin L, Zou H, Li W, Xu LY, Li EM, Dong G. Redox Potentials of Disulfide Bonds in LOXL2 Studied by Nonequilibrium Alchemical Simulation. Front Chem 2021; 9:797036. [PMID: 34970534 PMCID: PMC8713139 DOI: 10.3389/fchem.2021.797036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) is a metalloenzyme that catalyzes the oxidative deamination ε-amino group of lysine. It is found that LOXL2 is a promotor for the metastasis and invasion of cancer cells. Disulfide bonds are important components in LOXL2, and they play a stabilizing role for protein structure or a functional role for regulating protein bioactivity. The redox potential of disulfide bond is one important property to determine the functional role of disulfide bond. In this study, we have calculated the reduction potential of all the disulfide bonds in LOXL2 by non-equilibrium alchemical simulations. Our results show that seven of seventeen disulfide bonds have high redox potentials between -182 and -298 mV and could have a functional role, viz., Cys573-Cys625, Cys579-Cys695, Cys657-Cys673, and Cys663-Cys685 in the catalytic domain, Cys351-Cys414, Cys464-Cys530, and Cys477-Cys543 in the scavenger receptor cysteine-rich (SRCR) domains. The disulfide bond of Cys351-Cys414 is predicted to play an allosteric function role, which could affect the metastasis and invasion of cancer cells. Other functional bonds have a catalytic role related to enzyme activity. The rest of disulfide bonds are predicted to play a structural role. Our study provides an important insight for the classification of disulfide bonds in LOXL2 and can be utilized for the drug design that targets the cysteine residues in LOXL2.
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Affiliation(s)
- Lirui Lin
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
| | - Haiying Zou
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Cancer Research Center, Shantou University Medical College, Shantou, China
- *Correspondence: Li-Yan Xu, ; En-Min Li, ; Geng Dong,
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- *Correspondence: Li-Yan Xu, ; En-Min Li, ; Geng Dong,
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
- *Correspondence: Li-Yan Xu, ; En-Min Li, ; Geng Dong,
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