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Villanueva M, Vostal LE, Cohen DN, Biesbrock D, Kuwaye EP, Driver SG, Hart KM. Differential effects of disulfide bond formation in TEM-1 versus CTX-M-9 β-lactamase. Protein Sci 2024; 33:e4816. [PMID: 37897253 PMCID: PMC10731493 DOI: 10.1002/pro.4816] [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: 06/30/2023] [Revised: 08/18/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
To investigate how disulfide bonds can impact protein energy landscapes, we surveyed the effects of adding or removing a disulfide in two β-lactamase enzymes, TEM-1 and CTX-M-9. The homologs share a structure and 38% sequence identity, but only TEM-1 contains a native disulfide bond. They also differ in thermodynamic stability and in the number of states populated at equilibrium: CTX-M-9 is two-state whereas TEM-1 has an additional intermediate state. We hypothesized that the disulfide bond is the major underlying determinant for these observed differences in their energy landscapes. To test this, we removed the disulfide bridge from TEM-1 and introduced a disulfide bridge at the same location in CTX-M-9. This modest change to sequence modulates the stabilities-and therefore populations-of TEM-1's equilibrium states and, more surprisingly, creates a novel third state in CTX-M-9. Unlike TEM-1's partially folded intermediate, this third state is a higher-order oligomer with reduced cysteines that retains the native fold and is fully active. Sub-denaturing concentrations of urea shifts the equilibrium to the monomeric form, allowing the disulfide bond to form. Interestingly, comparing the stability of the oxidized monomer with a variant lacking cysteines reveals the disulfide is neither stabilizing nor destabilizing in CTX-M-9, in contrast with the observed stabilization in TEM-1. Thus, we can conclude that engineering disulfide bonds is not always an effective stabilization strategy even when analogous disulfides exist in more stable structural homologs. This study also illustrates how homo-oligomerization can result from a small number of mutations, suggesting complex formation might be easily accessed during a protein family's evolution.
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Affiliation(s)
- Miranda Villanueva
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Biological Chemistry DepartmentDavid Geffen School of Medicine, UCLALos AngelesCaliforniaUSA
| | - Lauren E. Vostal
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Chemistry and Cell BiologyThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Drew N. Cohen
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Devin Biesbrock
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Cellular and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Elise P. Kuwaye
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Department of Biological SciencesColumbia UniversityNew YorkNew YorkUSA
| | - Sasha G. Driver
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
| | - Kathryn M. Hart
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
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Liu Z, Zhao F, Huang Z, Hu Q, Meng R, Lin Y, Qi J, Lin G. Revisiting the Asian Buffalo Leech ( Hirudinaria manillensis) Genome: Focus on Antithrombotic Genes and Their Corresponding Proteins. Genes (Basel) 2023; 14:2068. [PMID: 38003011 PMCID: PMC10671345 DOI: 10.3390/genes14112068] [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: 10/04/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Leeches are well-known annelids due to their obligate blood-feeding habits. Some leech species secrete various biologically active substances which have important medical and pharmaceutical value in antithrombotic treatments. In this study, we provided a high-quality genome of the Asian buffalo leech (Hirudinaria manillensis), based on which we performed a systematic identification of potential antithrombotic genes and their corresponding proteins. Combining automatic and manual prediction, we identified 21 antithrombotic gene families including fourteen coagulation inhibitors, three platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. A total of 72 antithrombotic genes, including two pseudogenes, were identified, including most of their corresponding proteins forming three or more disulfide bonds. Three protein families (LDTI, antistasin, and granulin) had internal tandem repeats containing 6, 10, and 12 conserved cysteines, respectively. We also measured the anticoagulant activities of the five identified hirudins (hirudin_Hman1 ~ hirudin_Hman5). The results showed that three (hirudin_Hman1, hirudin_Hman2, and hirudin_Hman5), but not the remaining two, exhibited anticoagulant activities. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from a leech to date. These results will greatly facilitate the research and application of leech derivatives for medical and pharmaceutical purposes in the treatment of thrombotic diseases.
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Affiliation(s)
- Zichao Liu
- Engineering Research Center for Exploitation and Utilization of Leech Resources in Universities of Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming 650214, China; (Z.L.); (Q.H.); (R.M.)
| | - Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji’an 343009, China; (F.Z.); (Z.H.); (Y.L.)
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji’an 343009, China; (F.Z.); (Z.H.); (Y.L.)
| | - Qingmei Hu
- Engineering Research Center for Exploitation and Utilization of Leech Resources in Universities of Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming 650214, China; (Z.L.); (Q.H.); (R.M.)
| | - Renyuan Meng
- Engineering Research Center for Exploitation and Utilization of Leech Resources in Universities of Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming 650214, China; (Z.L.); (Q.H.); (R.M.)
| | - Yiquan Lin
- School of Life Sciences, Jinggangshan University, Ji’an 343009, China; (F.Z.); (Z.H.); (Y.L.)
| | - Jianxia Qi
- Nujiang Management Bureau of Gaoligongshan National Nature Reserve, Nujiang 673199, China;
| | - Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji’an 343009, China; (F.Z.); (Z.H.); (Y.L.)
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3
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Willems P, Huang J, Messens J, Van Breusegem F. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures. Free Radic Biol Med 2023; 194:220-229. [PMID: 36493985 DOI: 10.1016/j.freeradbiomed.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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Hao J, Liang Y, Ping J, Li J, Shi W, Su Y, Wang T. Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L. BMC PLANT BIOLOGY 2022; 22:580. [PMID: 36510137 PMCID: PMC9746204 DOI: 10.1186/s12870-022-03960-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/24/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Characterization of the key factors determining gene expression level has been of significant interest. Previous studies on the relationship among evolutionary rates, codon usage bias, and expression level mostly focused on either nuclear genes or unicellular/multicellular organisms but few in chloroplast (cp) genes. Ophioglossum vulgatum is a unique fern and has important scientific and medicinal values. In this study, we sequenced its cp genome and transcriptome to estimate the evolutionary rates (dN and dS), selective pressure (dN/dS), gene expression level, codon usage bias, and their correlations. RESULTS The correlation coefficients between dN, dS, and dN/dS, and Transcripts Per Million (TPM) average values were -0.278 (P = 0.027 < 0.05), -0.331 (P = 0.008 < 0.05), and -0.311 (P = 0.013 < 0.05), respectively. The codon adaptation index (CAI) and tRNA adaptation index (tAI) were significantly positively correlated with TPM average values (P < 0.05). CONCLUSIONS Our results indicated that when the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was stronger. We provided evidence from cp gene data which supported the E-R (E stands for gene expression level and R stands for evolutionary rate) anti-correlation.
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Affiliation(s)
- Jing Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingyi Liang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jingyao Ping
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinye Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanxin Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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5
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Critical roles of protein disulfide isomerases in balancing proteostasis in the nervous system. J Biol Chem 2022; 298:102087. [PMID: 35654139 PMCID: PMC9253707 DOI: 10.1016/j.jbc.2022.102087] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 02/08/2023] Open
Abstract
Protein disulfide isomerases (PDIs) constitute a family of oxidoreductases promoting redox protein folding and quality control in the endoplasmic reticulum. PDIs catalyze disulfide bond formation, isomerization, and reduction, operating in concert with molecular chaperones to fold secretory cargoes in addition to directing misfolded proteins to be refolded or degraded. Importantly, PDIs are emerging as key components of the proteostasis network, integrating protein folding status with central surveillance mechanisms to balance proteome stability according to cellular needs. Recent advances in the field driven by the generation of new mouse models, human genetic studies, and omics methodologies, in addition to interventions using small molecules and gene therapy, have revealed the significance of PDIs to the physiology of the nervous system. PDIs are also implicated in diverse pathologies, ranging from neurodevelopmental conditions to neurodegenerative diseases and traumatic injuries. Here, we review the principles of redox protein folding in the ER with a focus on current evidence linking genetic mutations and biochemical alterations to PDIs in the etiology of neurological conditions.
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Weadick CJ. Molecular Evolutionary Analysis of Nematode Zona Pellucida (ZP) Modules Reveals Disulfide-Bond Reshuffling and Standalone ZP-C Domains. Genome Biol Evol 2021; 12:1240-1255. [PMID: 32426804 PMCID: PMC7456536 DOI: 10.1093/gbe/evaa095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Zona pellucida (ZP) modules mediate extracellular protein-protein interactions and contribute to important biological processes including syngamy and cellular morphogenesis. Although some biomedically relevant ZP modules are well studied, little is known about the protein family's broad-scale diversity and evolution. The increasing availability of sequenced genomes from "nonmodel" systems provides a valuable opportunity to address this issue and to use comparative approaches to gain new insights into ZP module biology. Here, through phylogenetic and structural exploration of ZP module diversity across the nematode phylum, I report evidence that speaks to two important aspects of ZP module biology. First, I show that ZP-C domains-which in some modules act as regulators of ZP-N domain-mediated polymerization activity, and which have never before been found in isolation-can indeed be found as standalone domains. These standalone ZP-C domain proteins originated in independent (paralogous) lineages prior to the diversification of extant nematodes, after which they evolved under strong stabilizing selection, suggesting the presence of ZP-N domain-independent functionality. Second, I provide a much-needed phylogenetic perspective on disulfide bond variability, uncovering evidence for both convergent evolution and disulfide-bond reshuffling. This result has implications for our evolutionary understanding and classification of ZP module structural diversity and highlights the usefulness of phylogenetics and diverse sampling for protein structural biology. All told, these findings set the stage for broad-scale (cross-phyla) evolutionary analysis of ZP modules and position Caenorhabditis elegans and other nematodes as important experimental systems for exploring the evolution of ZP modules and their constituent domains.
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7
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Medinas DB, Hazari Y, Hetz C. Disruption of Endoplasmic Reticulum Proteostasis in Age-Related Nervous System Disorders. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 59:239-278. [PMID: 34050870 DOI: 10.1007/978-3-030-67696-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Endoplasmic reticulum (ER) stress is a prominent cellular alteration of diseases impacting the nervous system that are associated to the accumulation of misfolded and aggregated protein species during aging. The unfolded protein response (UPR) is the main pathway mediating adaptation to ER stress, but it can also trigger deleterious cascades of inflammation and cell death leading to cell dysfunction and neurodegeneration. Genetic and pharmacological studies in experimental models shed light into molecular pathways possibly contributing to ER stress and the UPR activation in human neuropathies. Most of experimental models are, however, based on the overexpression of mutant proteins causing familial forms of these diseases or the administration of neurotoxins that induce pathology in young animals. Whether the mechanisms uncovered in these models are relevant for the etiology of the vast majority of age-related sporadic forms of neurodegenerative diseases is an open question. Here, we provide a systematic analysis of the current evidence linking ER stress to human pathology and the main mechanisms elucidated in experimental models. Furthermore, we highlight the recent association of metabolic syndrome to increased risk to undergo neurodegeneration, where ER stress arises as a common denominator in the pathogenic crosstalk between peripheral organs and the nervous system.
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Affiliation(s)
- Danilo B Medinas
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile. .,Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile. .,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile.
| | - Younis Hazari
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile.,Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile. .,Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile. .,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile. .,Buck Institute for Research on Aging, Novato, CA, USA.
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8
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Alvarez-Ponce D. Richard Dickerson, Molecular Clocks, and Rates of Protein Evolution. J Mol Evol 2020; 89:122-126. [PMID: 33205299 DOI: 10.1007/s00239-020-09973-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/07/2020] [Indexed: 12/29/2022]
Abstract
Proteins approximately behave as molecular clocks, accumulating amino acid replacements at a more or less constant rate. Nonetheless, each protein displays a characteristic rate of evolution: whereas some proteins remain largely unaltered over large periods of time, others can rapidly accumulate amino acid replacements. An article by Richard Dickerson, published in the first issue of the Journal of Molecular Evolution (J Mol Evol 1:26-45, 1971), described the first analysis in which the rates of evolution of many proteins were compared, and the differences were interpreted in the light of their function. When comparing the sequences of fibrinopeptides, hemoglobin, and cytochrome c of different species, he observed a linear relationship between the number of amino acid replacements and divergence time. Remarkably, fibrinopeptides had evolved fast, cytochrome c had evolved slowly, and hemoglobin exhibited an intermediate rate of evolution. As the Journal of Molecular Evolution celebrates its 50th anniversary, I highlight this landmark article and reflect on its impact on the field of Molecular Evolution.
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Affiliation(s)
- David Alvarez-Ponce
- Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA.
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9
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Friedman DA, York RA, Hilliard AT, Gordon DM. Gene expression variation in the brains of harvester ant foragers is associated with collective behavior. Commun Biol 2020; 3:100. [PMID: 32139795 PMCID: PMC7057964 DOI: 10.1038/s42003-020-0813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/10/2020] [Indexed: 01/10/2023] Open
Abstract
Natural selection on collective behavior acts on variation among colonies in behavior that is associated with reproductive success. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success. We used RNA-seq to examine gene expression in the brains of foragers in a natural setting. We find that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with two colony traits: sensitivity of foraging activity to humidity, and forager brain dopamine to serotonin ratio. Loci that were correlated with colony behavioral differences were enriched in neurotransmitter receptor signaling & metabolic functions, tended to be more central to coexpression networks, and are evolving under higher protein-coding sequence constraint. Natural selection may shape colony foraging behavior through variation in gene expression.
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Affiliation(s)
| | | | | | - Deborah M Gordon
- Stanford University, Department of Biology, Stanford, CA, 94305, USA.
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10
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Orts F, Ten Have A. Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi. BMC Bioinformatics 2018; 19:464. [PMID: 30514213 PMCID: PMC6278154 DOI: 10.1186/s12859-018-2404-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Sedolisins are acid proteases that are related to the basic subtilisins. They have been identified in all three superkingdoms but are not ubiquitous, although fungi that secrete acids as part of their lifestyle can have up to six paralogs. Both TriPeptidyl Peptidase (TPP) and endopeptidase activity have been identified and it has been suggested that these correspond to separate subfamilies. Results We studied eukaryotic sedolisins by computational analysis. A maximum likelihood tree shows one major clade containing non-fungal sequences only and two major as well as two minor clades containing only fungal sequences. One of the major fungal clades contains all known TPPs whereas the other contains characterized endosedolisins. We identified four Cluster Specific Inserts (CSIs) in endosedolisins, of which CSIs 1, 3 and 4 appear as solvent exposed according to structure modeling. Part of CSI2 is exposed but a short stretch forms a novel and partially buried α-helix that induces a conformational change near the binding pocket. We also identified a total of 15 specificity determining positions (SDPs) of which five, identified in two independent analyses, form highly connected SDP sub-networks. Modeling of virtual mutants suggests a key role for the W307A or F307A substitution. The remaining four key SDPs physically interact at the interface of the catalytic domain and the enzyme’s prosegment. Modeling of virtual mutants suggests these SDPs are indeed required to compensate the conformational change induced by CSI2 and the A307. One of the two small fungal clades concerns a subfamily that contains 213 sequences, is mostly similar to the major TPP subfamily but differs, interestingly, in position 307, showing mostly isoleucine and threonine. Conclusions Analysis confirms there are at least two sedolisin subfamilies in fungi: TPPs and endopeptidases, and suggests a third subfamily with unknown characteristics. Sequence and functional diversification was centered around buried SDP307 and resulted in a conformational change of the pocket. Mutual Information network analysis forms a useful instrument in the corroboration of predicted SDPs. Electronic supplementary material The online version of this article (10.1186/s12859-018-2404-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Facundo Orts
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina.
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11
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Santibáñez-López CE, Kriebel R, Ballesteros JA, Rush N, Witter Z, Williams J, Janies DA, Sharma PP. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 2018; 6:e5902. [PMID: 30479892 PMCID: PMC6240337 DOI: 10.7717/peerj.5902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
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Affiliation(s)
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel Rush
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - John Williams
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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12
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Mainieri D, Marrano CA, Prinsi B, Maffi D, Tschofen M, Espen L, Stöger E, Faoro F, Pedrazzini E, Vitale A. Maize 16-kD γ-zein forms very unusual disulfide-bonded polymers in the endoplasmic reticulum: implications for prolamin evolution. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5013-5027. [PMID: 30085182 PMCID: PMC6184761 DOI: 10.1093/jxb/ery287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/25/2018] [Indexed: 05/22/2023]
Abstract
In the lumen of the endoplasmic reticulum (ER), prolamin storage proteins of cereal seeds form very large, ordered heteropolymers termed protein bodies (PBs), which are insoluble unless treated with alcohol or reducing agents. In maize PBs, 16-kD γ-zein locates at the interface between a core of alcohol-soluble α-zeins and the outermost layer mainly composed of the reduced-soluble 27-kD γ-zein. 16-kD γ-zein originates from 27-kD γ-zein upon whole-genome duplication and is mainly characterized by deletions in the N-terminal domain that eliminate most Pro-rich repeats and part of the Cys residues involved in inter-chain bonds. 27-kD γ-zein also forms insoluble PBs when expressed in transgenic vegetative tissues. We show that in Arabidopsis leaves, 16-kD γ-zein assembles into disulfide-linked polymers that fail to efficiently become insoluble. Instead of forming PBs, these polymers accumulate as very unusual threads that markedly enlarge the ER lumen, resembling amyloid-like fibers. Domain-swapping between the two γ-zeins indicates that the N-terminal region of 16-kD γ-zein has a dominant effect in preventing full insolubilization. Therefore, a newly evolved prolamin has lost the ability to form homotypic PBs, and has acquired a new function in the assembly of natural, heteropolymeric PBs.
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Affiliation(s)
- Davide Mainieri
- Istituto di Biologia e Biotecnologia Agraria, CNR, Milano, Italy
| | | | - Bhakti Prinsi
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Dario Maffi
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Marc Tschofen
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Luca Espen
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Eva Stöger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Franco Faoro
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Emanuela Pedrazzini
- Istituto di Biologia e Biotecnologia Agraria, CNR, Milano, Italy
- Correspondence: or
| | - Alessandro Vitale
- Istituto di Biologia e Biotecnologia Agraria, CNR, Milano, Italy
- Correspondence: or
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Schumacher J, Herlyn H. Correlates of evolutionary rates in the murine sperm proteome. BMC Evol Biol 2018; 18:35. [PMID: 29580206 PMCID: PMC5870804 DOI: 10.1186/s12862-018-1157-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/19/2018] [Indexed: 01/20/2023] Open
Abstract
Background Protein-coding genes expressed in sperm evolve at different rates. To gain deeper insight into the factors underlying this heterogeneity we examined the relative importance of a diverse set of previously described rate correlates in determining the evolution of murine sperm proteins. Results Using partial rank correlations we detected several major rate indicators: Phyletic gene age, numbers of protein-protein interactions, and survival essentiality emerged as particularly important rate correlates in murine sperm proteins. Tissue specificity, numbers of paralogs, and untranslated region lengths also correlate significantly with sperm genes’ evolutionary rates, albeit to a lesser extent. Multifunctionality, coding sequence or average intron lengths, and mean expression level have insignificant or virtually no independent effects on evolutionary rates in murine sperm genes. Gene ontology enrichment analyses of three equally sized murine sperm protein groups classified based on their evolutionary rates indicate strongest sperm-specific functional specialization in the most quickly evolving gene class. Conclusions We propose a model according to which slowly evolving murine sperm proteins tend to be constrained by factors such as survival essentiality, network connectivity, and/or broad expression. In contrast, evolutionary change may arise especially in less constrained sperm proteins, which might, moreover, be prone to specialize to reproduction-related functions. Our results should be taken into account in future studies on rate variations of reproductive genes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1157-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia Schumacher
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany.
| | - Holger Herlyn
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany.
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