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Kiefl E, Esen OC, Miller SE, Kroll KL, Willis AD, Rappé MS, Pan T, Eren AM. Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. SCIENCE ADVANCES 2023; 9:eabq4632. [PMID: 36812328 DOI: 10.1126/sciadv.abq4632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
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Affiliation(s)
- Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ozcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Samuel E Miller
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Kourtney L Kroll
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96822, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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2
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Kurt F, Filiz E, Yildiz K, Akbudak MA. Genome-Wide Identification, Characterization and Expression Profiling of Potato ( Solanum tuberosum) Frataxin ( FH) Gene. Genes (Basel) 2023; 14:468. [PMID: 36833395 PMCID: PMC9957314 DOI: 10.3390/genes14020468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Frataxin (FH) plays a crucial role in the biogenesis of mitochondria and the regulation of iron in the cells of various organisms. However, there has been very little research on FH in plants. In this study, the potato FH gene (StFH) was identified and characterized using a genome-wide approach, and its sequence was compared to those of FH genes from Arabidopsis, rice, and maize. The FH genes were found to have a lineage-specific distribution and were more conserved in monocots than in dicots. While multiple copies of FH genes have been reported in some species, including plants, only one isoform of FH was found in potato. The expression of StFH in leaves and roots was analyzed under two different abiotic stress conditions, and the results showed that StFH was upregulated more in leaves and that its expression levels increased with the severity of the stress. This is the first study to examine the expression of an FH gene under abiotic stress conditions.
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Affiliation(s)
- Firat Kurt
- Department of Plant Production and Technologies, Faculty of Applied Sciences, Mus Alparslan University, 49250 Mus, Turkey
| | - Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, Cilimli, 81750 Duzce, Turkey
| | - Kubra Yildiz
- Department of Agricultural Biotechnology, Akdeniz University, 07058 Antalya, Turkey
| | - M. Aydın Akbudak
- Department of Agricultural Biotechnology, Akdeniz University, 07058 Antalya, Turkey
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3
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Abeywickrama HLTC, Rabindrakumar MSK, Pathira Kankanamge LS, Thoradeniya T, Galhena GH. TMPRSS6 rs855791 polymorphism is associated with iron deficiency in a cohort of Sri Lankan pregnant women. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Background
Hepcidin is the key regulator of systemic iron homeostasis and is downregulated by matriptase 2 (MT2), a protease encoded by TMPRSS6 gene. In the presence of low iron levels, MT2 cleaves membrane-bound hemojuvelin (HJV), causing a negative regulation of hepcidin at the gene level, and restores iron balance. rs855791T > C, a missense variant in the catalytic domain of MT2, causes valine to alanine change at 736 position. The current study aimed to investigate the association of TMPRSS6 rs855791 on iron status among a cohort of pregnant women in Sri Lanka and to predict the possible molecular mechanisms.
Methods
The study was conducted among 73 pregnant women at ≤ 12 weeks of gestation. Iron deficiency was defined as serum ferritin < 30 μg/L after adjusting for inflammation. rs855791 was genotyped with a PCR–RFLP, and its association with iron deficiency was analyzed using binary logistic regression. Docking of HJV with MT2 protein encoded by the two rs855791 alleles was undertaken in silico to predict the molecular mechanism of the observed associations.
Results
The majority of the study population (70%) were iron deficient. Among the subjects, T allele was prevalent in the iron deficient group with a frequency of 61.8%, with a nearly twofold enhanced risk for iron deficiency (OR = 2.566, 95%CI; P = 0.011). For TT genotype, the risk of iron deficiency was nearly sixfold (OR = 5.867; 95%CI; P = 0.023). According to the in silico analysis, MT2 736A and HJV complex is more stable with an interface energy of − 7.934 kJ/mol compared to the MT2 736 V and HJV complex which generates an interface energy of − 4.689 kJ/mol.
Conclusion
The current study suggests that the iron regulatory effect of rs855791 of TMPRSS6 is brought about by the differences in thermodynamic stability of the two protein complexes made by MT2 and HJV proteins. The prevalence of iron deficiency observed among Sri Lankan pregnant women may be an interplay between the prevalence of rs855791 T allele and the low dietary iron intake.
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4
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Mitra A, Acharya K, Bhattacharya A. Evolutionary analysis of globin domains from kinetoplastids. Arch Microbiol 2022; 204:493. [PMID: 35841431 DOI: 10.1007/s00203-022-03107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Globin (Gb) domains function in sensing gaseous ligands like oxygen and nitric oxide. In recent years, Gb domain containing heme binding adenylate cyclases (OsAC or GbAC) emerged as significant modulator of Leishmania response to hypoxia and oxidative stress. During progression of life cycle stages, kinetoplastids experience altered condition in insect vectors or other hosts. Moreover, marked diversity in life style has been accounted among kinetoplastids. Distribution and abundance of Gb-domains vary between different groups of kinetoplastids. While in bodonoids, Gbs are not combined with any other functional domains, in trypanosomatids it is either fused with adenylate cyclase (AC) or oxidoreductase (OxR) domains. In salivarian trypanosomatids and Leishmania (Viannia) subtypes, no gene product featuring Gbs can be identified. In this context, evolution of Gb-domains in kinetoplastids was explored. GbOxR derived Gbs clustered with bacterial flavohemoglobins (fHb) including one fHb from Advenella, an endosymbiont of monoxeneous trypanosomatids. Codon adaptation and other evolutionary analysis suggested that OsAC (LmjF.28.0090), the solitary Gb-domain featuring gene product in Leishmania, was acquired via possible horizontal gene transfer. Substantial functional divergence was estimated between orthologues of genes encoding GbAC or GbOxR; an observation also reflected in structural alignment and heme-binding residue predictions. Orthologue-paralogue and synteny analysis indicated genomic reduction in GbOxR and GbAC loci for dixeneous trypanosomatids.
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Affiliation(s)
- Akash Mitra
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.,Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Mangalore, 575018, India
| | - Kusumita Acharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India
| | - Arijit Bhattacharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.
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5
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Bzówka M, Mitusińska K, Raczyńska A, Skalski T, Samol A, Bagrowska W, Magdziarz T, Góra A. Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases? PLoS Comput Biol 2022; 18:e1010119. [PMID: 35580137 PMCID: PMC9140254 DOI: 10.1371/journal.pcbi.1010119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 05/27/2022] [Accepted: 04/19/2022] [Indexed: 12/27/2022] Open
Abstract
The evolutionary variability of a protein’s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to α/β-hydrolase fold proteins—one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We selected soluble epoxide hydrolases as representative of this family to conduct the first systematic study on the evolution of tunnels. We hypothesised that tunnels are lined by mostly conserved residues, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. The hypothesis was confirmed, and we suggested a general and detailed way of the tunnels’ evolution analysis based on entropy values calculated for tunnels’ residues. We also found three different cases of entropy distribution among tunnel-lining residues. These observations can be applied for protein reengineering mimicking the natural evolution process. We propose a ‘perforation’ mechanism for new tunnels design via the merging of internal cavities or protein surface perforation. Based on the literature data, such a strategy of new tunnel design could significantly improve the enzyme’s performance and can be applied widely for enzymes with buried active sites. So far very little is known about proteins tunnels evolution. The goal of this study is to evaluate the evolution of tunnels in the family of soluble epoxide hydrolases—representatives of numerous α/β-hydrolase fold enzymes. As a result two types of tunnels evolution analysis were proposed (a general and a detailed approach), as well as a ‘perforation’ mechanism which can mimic native evolution in proteins and can be used as an additional strategy for enzymes redesign.
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Affiliation(s)
- Maria Bzówka
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Skalski
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Aleksandra Samol
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Weronika Bagrowska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Magdziarz
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
- * E-mail:
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6
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Stark TL, Kaufman RS, Maltepes MA, Chi PB, Liberles DA. Detecting Selection on Segregating Gene Duplicates in a Population. J Mol Evol 2021; 89:554-564. [PMID: 34341836 DOI: 10.1007/s00239-021-10024-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/20/2021] [Indexed: 11/26/2022]
Abstract
Gene duplication is a fundamental process that has the potential to drive phenotypic differences between populations and species. While evolutionarily neutral changes have the potential to affect phenotypes, detecting selection acting on gene duplicates can uncover cases of adaptive diversification. Existing methods to detect selection on duplicates work mostly inter-specifically and are based upon selection on coding sequence changes, here we present a method to detect selection directly on a copy number variant segregating in a population. The method relies upon expected relationships between allele (new duplication) age and frequency in the population dependent upon the effective population size. Using both a haploid and a diploid population with a Moran Model under several population sizes, the neutral baseline for copy number variants is established. The ability of the method to reject neutrality for duplicates with known age (measured in pairwise dS value) and frequency in the population is established through mathematical analysis and through simulations. Power is particularly good in the diploid case and with larger effective population sizes, as expected. With extension of this method to larger population sizes, this is a tool to analyze selection on copy number variants in any natural or experimentally evolving population. We have made an R package available at https://github.com/peterbchi/CNVSelectR/ which implements the method introduced here.
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Affiliation(s)
- Tristan L Stark
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
- Discipline of Mathematics, University of Tasmania, Hobart, Tasmania, 7001, Australia.
| | - Rebecca S Kaufman
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Maria A Maltepes
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
- Department of Mathematics and Statistics, Villanova University, Villanova, PA, 19085, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
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7
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Primetis E, Chavlis S, Pavlidis P. Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods. Proteins 2021; 89:1565-1576. [PMID: 34278605 DOI: 10.1002/prot.26178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/27/2021] [Accepted: 07/11/2021] [Indexed: 11/10/2022]
Abstract
Intra-protein residual vicinities depend on the involved amino acids. Energetically favorable vicinities (or interactions) have been preserved during evolution, while unfavorable vicinities have been eliminated. We describe, statistically, the interactions between amino acids using resolved protein structures. Based on the frequency of amino acid interactions, we have devised an amino acid substitution model that implements the following idea: amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors. Using known tertiary structures for α-helical membrane (HM) proteins, we build evolutionary substitution matrices. We constructed maximum likelihood phylogenies using our amino acid substitution matrices and compared them to widely-used methods. Our results suggest that amino acid substitutions are associated with the spatial neighborhoods of amino acid residuals, providing, therefore, insights into the amino acid substitution process.
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Affiliation(s)
- Elias Primetis
- Department of Biology, University of Crete, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Heraklion, Greece
| | - Spyridon Chavlis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Hellas, Heraklion, Greece
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8
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Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs. Int J Mol Sci 2021; 22:ijms22031364. [PMID: 33573010 PMCID: PMC7866422 DOI: 10.3390/ijms22031364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.
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9
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Gangele K, Gulati K, Joshi N, Kumar D, Poluri KM. Molecular insights into the differential structure-dynamics-stability features of interleukin-8 orthologs: Implications to functional specificity. Int J Biol Macromol 2020; 164:3221-3234. [PMID: 32853623 DOI: 10.1016/j.ijbiomac.2020.08.176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
Chemokines are a sub-group of chemotactic cytokines that regulate the leukocyte migration by binding to G-protein coupled receptors (GPCRs) and cell surface glycosaminoglycans (GAGs). Interleukin-8 (CXCL8/IL8) is one of the most essential CXC chemokine that has been reported to be involved in various pathophysiological conditions. Structure-function relationships of human IL8 have been studied extensively. However, no such detailed information is available on IL8 orthologs, although they exhibit significant functional divergence. In order to unravel the differential structure-dynamics-stability-function relationship of IL8 orthologs, comparative molecular analysis was performed on canine (laurasians) and human (primates) IL8 proteins using in-silico molecular evolutionary analysis and solution NMR spectroscopy methods. The residue level NMR studies suggested that, although the overall structural architecture of canine IL8 is similar to that of human IL8, systematic differences were observed in their backbone dynamics and low-energy excited states due to amino acid substitutions. Further, these substitutions also resulted in attenuation of stability and heparin binding affinity in the canine IL8 as compared to its human counterpart. Indeed, structural and sequence analysis evidenced for specificity of molecular interactions with cognate receptor (CXCR1) and glycosaminoglycan (heparin), thus providing evidence for a noticeable functional specificity and divergence between the two IL8 orthologs.
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Affiliation(s)
- Krishnakant Gangele
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nidhi Joshi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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10
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Hernández L, Vicens A, Eguiarte LE, Souza V, De Anda V, González JM. Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria. PeerJ 2020; 8:e9861. [PMID: 32974097 PMCID: PMC7487153 DOI: 10.7717/peerj.9861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.
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Affiliation(s)
- Laura Hernández
- Departamento de Microbiología, Universidad de La Laguna, La Laguna, Spain
| | - Alberto Vicens
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Mexico
| | - Valerie De Anda
- Department of Marine Sciences, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
| | - José M González
- Departamento de Microbiología, Universidad de La Laguna, La Laguna, Spain
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11
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Filiz E, Kurt F. Antimicrobial peptides Snakin/GASA gene family in sorghum (Sorghum bicolor): Genome-wide identification and bioinformatics analyses. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Behloul N, Baha S, Shi R, Meng J. Role of the GTNGTKR motif in the N-terminal receptor-binding domain of the SARS-CoV-2 spike protein. Virus Res 2020; 286:198058. [PMID: 32531235 PMCID: PMC7282740 DOI: 10.1016/j.virusres.2020.198058] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/18/2020] [Accepted: 06/07/2020] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 S1-NTD presents different receptor binding motifs compared to the SARS-CoV. Functional motifs similar to the S1-NTD GTNGTKR loop were identified in other proteins. The GTNGTKR loop is very likely to allow the SARS-CoV-2 to bind other receptors. The GTNGTKR motif is very likely an evolutionary acquisition under functional constraints.
The 2019 novel coronavirus disease (COVID-19) that emerged in China has been declared as public health emergency of international concern by the World Health Organization and the causative pathogen was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this report, we analyzed the structural characteristics of the N-terminal domain of the S1 subunit (S1-NTD) of the SARS-CoV-2 spike protein in comparison to the SARS-CoV in particular, and to other viruses presenting similar characteristic in general. Given the severity and the wide and rapid spread of the SARS-CoV-2 infection, it is very likely that the virus recognizes other receptors/co-receptors besides the ACE2. The NTD of the SARS-CoV-2 contains a receptor-binding motif different from that of SARS-CoV, with some insertions that could confer to the new coronavirus new receptor binding abilities. In particular, motifs similar to the insertion 72GTNGTKR78 have been found in structural proteins of other viruses; and these motifs were located in putative regions involved in recognizing protein and sugar receptors, suggesting therefore that similar binding abilities could be displayed by the SARS-CoV-2 S1-NTD. Moreover, concerning the origin of these NTD insertions, our findings point towards an evolutionary acquisition rather than the hypothesis of an engineered virus.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Animals
- Betacoronavirus/chemistry
- Betacoronavirus/genetics
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Chiroptera
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Evolution, Molecular
- Gene Expression
- Host-Pathogen Interactions/drug effects
- Host-Pathogen Interactions/genetics
- Humans
- Middle East Respiratory Syndrome Coronavirus/chemistry
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/metabolism
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Severe acute respiratory syndrome-related coronavirus/chemistry
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/metabolism
- SARS-CoV-2
- Sequence Alignment
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Structural Homology, Protein
- Thermodynamics
- Virus Attachment
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Affiliation(s)
- Nouredine Behloul
- College of Basic Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Sarra Baha
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Ruihua Shi
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, Jiangsu Province, China.
| | - Jihong Meng
- College of Basic Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
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13
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Gangele K, Jamsandekar M, Mishra A, Poluri KM. Unraveling the evolutionary origin of ELR motif using fish CXC chemokine CXCL8. FISH & SHELLFISH IMMUNOLOGY 2019; 93:17-27. [PMID: 31310848 DOI: 10.1016/j.fsi.2019.07.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 05/19/2023]
Abstract
Chemokines are chemotactic proteins involved in host defense through the migration of immune-regulatory cells to the site of infection. Interleukin-8 (CXCL8/IL8) is the most studied "ELR-CXC chemokine/neutrophil activating chemokine (NAC) that regulate neutrophil trafficking during infections and inflammation by binding to its cognate G-protein coupled receptors CXCR1/CXCR2. The "ELR" motif of NAC chemokines is essential for the CXCR1/CXCR2 receptor activation. In order to understand the evolutionary origin of "ELR" motif in the CXC chemokines, a thorough evolutionary study of CXCL8 gene from various fishes and primates was performed. Phylogenetic analysis revealed that the CXCL8 gene can be classified into four distinct lineages (CXCL8-L1a, CXCL8-L1b, CXCL8-L2, and CXCL8-L3), where CXCL8-L1a is the fastest evolving lineage and CXCL8-L3 is the slowest. Selection analysis suggested that The "ELR/DLR" motif containing branches (gadoid and coelacanth) are positively selected. The probable evolutionary trend of "ELR" motif suggested that this motif in ancestor CXCL8 is evolved from the GGR of Lamprey (Agnatha), followed by duplication giving rise to two main motifs in CXCL8 "NXH" in L3 lineage and "ELR/DLR" in L1a/L1b lineages. Although, structural analysis suggested that the overall topology of the CXCL8 proteins is similar, differences do exist at the individual structural elements among the members of different lineages. Functional distance analysis suggested that the CXCL8-L3 lineage is more distant compared to the CXCL8-L1a and L1b lineages from the inferred ancestor. Functional divergence analysis between different lineages suggested that most of the selected residues are important for receptor or glycosaminoglycan binding. Such a functional diversification can be attributed to the novel set of functions adopted by CXCL8 in various species.
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Affiliation(s)
- Krishnakant Gangele
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Minal Jamsandekar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, 342011, Rajasthan, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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14
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Abstract
A Monte Carlo simulation based sequence design method is proposed to explore the effect of correlated pair mutations in proteins. In the designed sequences, the most correlated residue pairs are identified and mutated with all possible amino acid pairs except those already present. The cumulative correlated pair mutations generated an array of mutated sequences. Results show a significant increase in the probability of misfolding for correlated pair mutations as compared to that of the random pair mutations. The pair mutations of correlated residues that are in contact record a higher probability of misfolding as compared to the correlated residues that are not in contact. The probability of misfolding increases on pair mutation of nonlocally correlated residue pairs as compared to that of the locally correlated residue pairs. The choice of a compact or expanded conformation does not depend on the type of correlated pair mutations. Pair mutation of the most correlated residue pairs at the surface with hydrophobic amino acids results in higher misfolding probability as compared to that in the core. An exactly opposite behavior is observed on pair mutation with hydrophilic and charged amino acid pairs. The neutral amino acid pairs do not differentiate between core and surface sites. This study may be used for targeted mutation experiments to predict complex mutation patterns, reengineer the existing proteins, and design new proteins with reduced misfolding propensity.
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Affiliation(s)
- Adesh Kumar
- Department of Chemistry , University of Delhi , Delhi 110007 , India
| | - Parbati Biswas
- Department of Chemistry , University of Delhi , Delhi 110007 , India
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15
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Abstract
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype-phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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16
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Upadhyay A. Structure of proteins: Evolution with unsolved mysteries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:160-172. [PMID: 31014967 DOI: 10.1016/j.pbiomolbio.2019.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
Abstract
Evolution of macromolecules could be considered as a milestone in the history of life. Nucleic acids are the long stretches of nucleotides that contain all the possible codes and information of life. On the other hand, proteins are their actual translated outcomes, or reflections of modifications in their structure that have occurred at a slow, but steady rate over a very long period of evolution. Over the years of research, biophysicists, biochemists, molecular and structural biologists have unfurled several layers of the structural convolutions in these chemical molecules; however evolutionists look over their structures through a different prism, which may or may not coincide with others. There remains a need to outline several well-known, but less discussed features of protein structures, like intrinsically disordered states, degron signals and different types of ubiquitin chains providing degradation signals, which help the cellular proteolytic machinery to identify and target the proteins towards degradation pathways. There are several important factors, which are critical for folding of proteins into their native three-dimensional conformations by the cytoplasmic chaperones; but in real time how the chaperones fold the newly synthesized polypeptide sequences into a particular three-dimensional shape within a fraction of second is still a mystery for biologists as well as mathematicians. Multiple similar unsolved or unaddressed questions need to be addressed in detail so that future line of research can dig deeper into the finer details of these structures of the proteins.
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Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India.
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17
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Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution. J Mol Biol 2019; 431:1298-1307. [DOI: 10.1016/j.jmb.2019.01.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/08/2023]
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18
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Structural modules of the stress-induced protein HflX: an outlook on its evolution and biological role. Curr Genet 2018; 65:363-370. [PMID: 30448945 DOI: 10.1007/s00294-018-0905-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 12/23/2022]
Abstract
Multifunctional proteins often show modular structures. A functional domain and the structural modules within the domain show evolutionary conservation of their spatial arrangement since that gives the protein its functionality. However, the question remains as to how members of different domains of life (Archaea, Bacteria, Eukarya), polish and perfect these modules within conserved multidomain proteins, to tailor functional proteins according to their specific requirements. In the quest for plausible answers to this question, we studied the bacterial protein HflX. HflX is a universally conserved member of the Obg-GTPase superfamily but its functional role in Archaea and Eukarya is barely known. It is a multidomain protein and possesses, in addition to its conserved GTPase domain, an ATP-binding N-terminal domain. It is involved in heat stress response in Escherichia coli and our laboratory recently identified an ATP-dependent RNA helicase activity of E. coli HflX, which is likely instrumental in rescuing ribosomes during heat stress. Because perception and response to stress is expected to be different in different life forms, the question is whether this activity is preserved in higher organisms or not. Thus, we explored the evolution pattern of different structural modules of HflX, with particular emphasis on the ATP-binding domain, to understand plausible biological role of HflX in other forms of life. Our analyses indicate that, while the evolutionary pattern of the GTPase domain follows a conserved phylogeny, conservation of the ATP-binding domain shows a complicated pattern. The limited analysis described here hints towards possible evolutionary adaptations and modifications of the domain, something which needs to be investigated in more depth in homologs from other life forms. Deciphering how nature 'tweaks' such modules, both structurally and functionally, may help in understanding the evolution of such proteins, and, on a large-scale, of stress-related proteins in general as well.
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19
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Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains. Genes (Basel) 2018; 9:genes9110553. [PMID: 30441862 PMCID: PMC6265720 DOI: 10.3390/genes9110553] [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: 10/01/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
Various structural and functional constraints govern the evolution of protein sequences. As a result, the relative rates of amino acid replacement among sites within a protein can vary significantly. Previous large-scale work on Metazoan (Animal) protein sequence alignments indicated that amino acid replacement rates are partially driven by a complex interaction among three factors: intrinsic disorder propensity; secondary structure; and functional domain involvement. Here, we use sequence-based predictors to evaluate the effects of these factors on site-specific sequence evolutionary rates within four eukaryotic lineages: Metazoans; Plants; Saccharomycete Fungi; and Alveolate Protists. Our results show broad, consistent trends across all four Eukaryote groups. In all four lineages, there is a significant increase in amino acid replacement rates when comparing: (i) disordered vs. ordered sites; (ii) random coil sites vs. sites in secondary structures; and (iii) inter-domain linker sites vs. sites in functional domains. Additionally, within Metazoans, Plants, and Saccharomycetes, there is a strong confounding interaction between intrinsic disorder and secondary structure-alignment sites exhibiting both high disorder propensity and involvement in secondary structures have very low average rates of sequence evolution. Analysis of gene ontology (GO) terms revealed that in all four lineages, a high fraction of sequences containing these conserved, disordered-structured sites are involved in nucleic acid binding. We also observe notable differences in the statistical trends of Alveolates, where intrinsically disordered sites are more variable than in other Eukaryotes and the statistical interactions between disorder and other factors are less pronounced.
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20
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Andreou A, Giastas P, Christoforides E, Eliopoulos EE. Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. Genes (Basel) 2018; 9:E386. [PMID: 30065210 PMCID: PMC6115787 DOI: 10.3390/genes9080386] [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: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O- or N-acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain. Genomes of Bacillus anthracis and its relative Bacillus cereus contain multiple genes of putative or known PDAs. A comparison of the functional domains of the recently determined PDAs from B. anthracis and B. cereus and multiple amino acid and nucleotide sequence alignments and phylogenetic analysis performed on these closely related species showed that there were distinct differences in binding site formation, despite the high conservation on the protein sequence, the folding level and the active site assembly. This may indicate that, subject to biochemical verification, the binding site-forming sequence fragments are under functionally driven evolutionary pressure to accommodate and recognize distinct polysaccharide residues according to cell location, use, or environment. Finally, we discuss the suggestion of the paralogous nature of at least two genes of B. anthracis, ba0330 and ba0331, via specific differences in gene sequence, protein structure, selection pressure and available localization patterns. This study may contribute to understanding the mechanisms under which sequences evolve in their structures and how evolutionary processes enable structural variations.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece.
| | - Elias Christoforides
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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21
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Shang J, Zheng Y, Yang Y, Liu C, Geng Q, Luo C, Zhang W, Li F. Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins. PLoS Pathog 2018; 14:e1007009. [PMID: 29684066 PMCID: PMC5933801 DOI: 10.1371/journal.ppat.1007009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/03/2018] [Accepted: 04/03/2018] [Indexed: 01/08/2023] Open
Abstract
As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious bronchitis coronavirus (IBV) spike protein from the γ-genus. The trimeric IBV spike ectodomain contains three receptor-binding S1 heads and a trimeric membrane-fusion S2 stalk. While IBV S2 is structurally similar to those from the other genera, IBV S1 possesses structural features that are unique to different other genera, thereby bridging these diverse spikes into an evolutionary spectrum. Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. Based on the above structural and functional comparisons, we propose that the evolutionary spectrum of coronavirus spikes follows the order of α-, δ-, γ-, and β-genus. This study has provided insight into the evolutionary relationships among coronavirus spikes and deepened our understanding of their structural and functional diversity.
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Affiliation(s)
- Jian Shang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Yuan Zheng
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Yang Yang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Chang Liu
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Qibin Geng
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Chuming Luo
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Wei Zhang
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, United States of America
- Characterization Facility, College of Science and Engineering, University of Minnesota, Minneapolis, MN, United States of America
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
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22
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Tindall SM, Vallières C, Lakhani DH, Islahudin F, Ting KN, Avery SV. Heterologous Expression of a Novel Drug Transporter from the Malaria Parasite Alters Resistance to Quinoline Antimalarials. Sci Rep 2018; 8:2464. [PMID: 29410428 PMCID: PMC5802821 DOI: 10.1038/s41598-018-20816-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/22/2018] [Indexed: 12/15/2022] Open
Abstract
Antimalarial drug resistance hampers effective malaria treatment. Critical SNPs in a particular, putative amino acid transporter were recently linked to chloroquine (CQ) resistance in malaria parasites. Here, we show that this conserved protein (PF3D7_0629500 in Plasmodium falciparum; AAT1 in P. chabaudi) is a structural homologue of the yeast amino acid transporter Tat2p, which is known to mediate quinine uptake and toxicity. Heterologous expression of PF3D7_0629500 in yeast produced CQ hypersensitivity, coincident with increased CQ uptake. PF3D7_0629500-expressing cultures were also sensitized to related antimalarials; amodiaquine, mefloquine and particularly quinine. Drug sensitivity was reversed by introducing a SNP linked to CQ resistance in the parasite. Like Tat2p, PF3D7_0629500-dependent quinine hypersensitivity was suppressible with tryptophan, consistent with a common transport mechanism. A four-fold increase in quinine uptake by PF3D7_0629500 expressing cells was abolished by the resistance SNP. The parasite protein localised primarily to the yeast plasma membrane. Its expression varied between cells and this heterogeneity was used to show that high-expressing cell subpopulations were the most drug sensitive. The results reveal that the PF3D7_0629500 protein can determine the level of sensitivity to several major quinine-related antimalarials through an amino acid-inhibitable drug transport function. The potential clinical relevance is discussed.
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Affiliation(s)
- Sarah M Tindall
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Cindy Vallières
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Dev H Lakhani
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Farida Islahudin
- Faculty of Pharmacy, Universiti Kebangsaan, Kuala Lumpur, 50300, Malaysia
| | - Kang-Nee Ting
- Department of Biomedical Sciences, University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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23
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Ahrens JB, Nunez-Castilla J, Siltberg-Liberles J. Evolution of intrinsic disorder in eukaryotic proteins. Cell Mol Life Sci 2017; 74:3163-3174. [PMID: 28597295 PMCID: PMC11107722 DOI: 10.1007/s00018-017-2559-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022]
Abstract
Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.
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Affiliation(s)
- Joseph B Ahrens
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Janelle Nunez-Castilla
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA.
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24
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Swint-Kruse L. Using Evolution to Guide Protein Engineering: The Devil IS in the Details. Biophys J 2017; 111:10-8. [PMID: 27410729 DOI: 10.1016/j.bpj.2016.05.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/18/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022] Open
Abstract
For decades, protein engineers have endeavored to reengineer existing proteins for novel applications. Overall, protein folds and gross functions can be readily transferred from one protein to another by transplanting large blocks of sequence (i.e., domain recombination). However, predictably fine-tuning function (e.g., by adjusting ligand affinity, specificity, catalysis, and/or allosteric regulation) remains a challenge. One approach has been to use the sequences of protein families to identify amino acid positions that change during the evolution of functional variation. The rationale is that these nonconserved positions could be mutated to predictably fine-tune function. Evolutionary approaches to protein design have had some success, but the engineered proteins seldom replicate the functional performances of natural proteins. This Biophysical Perspective reviews several complexities that have been revealed by evolutionary and experimental studies of protein function. These include 1) challenges in defining computational and biological thresholds that define important amino acids; 2) the co-occurrence of many different patterns of amino acid changes in evolutionary data; 3) difficulties in mapping the patterns of amino acid changes to discrete functional parameters; 4) the nonconventional mutational outcomes that occur for a particular group of functionally important, nonconserved positions; 5) epistasis (nonadditivity) among multiple mutations; and 6) the fact that a large fraction of a protein's amino acids contribute to its overall function. To overcome these challenges, new goals are identified for future studies.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.
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25
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Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network. Sci Rep 2017; 7:44948. [PMID: 28337996 PMCID: PMC5364480 DOI: 10.1038/srep44948] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/16/2017] [Indexed: 12/27/2022] Open
Abstract
A key question regarding protein evolution is how proteins adapt to the dynamic environment in which they function and how in turn their evolution shapes the protein interaction network. We used extant and resurrected ancestral plant MADS-domain transcription factors to understand how SEPALLATA3, a protein with hub and glue properties, evolved and takes part in network organization. Although the density of dimeric interactions was saturated in the network, many new interactions became mediated by SEPALLATA3 after a whole genome triplication event. By swapping SEPALLATA3 and its ancestors between dimeric networks of different ages, we found that the protein lost the capacity of promiscuous interaction and acquired specificity in evolution. This was accompanied with constraints on conformations through proline residue accumulation, which made the protein less flexible. SHORT VEGETATIVE PHASE on the other hand (non-hub) was able to gain protein-protein interactions due to a C-terminal domain insertion, allowing for a larger interaction interface. These findings illustrate that protein interaction evolution occurs at the level of conformational dynamics, when the binding mechanism concerns an induced fit or conformational selection. Proteins can evolve towards increased specificity with reduced flexibility when the complexity of the protein interaction network requires specificity.
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26
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Rahaman J, Siltberg-Liberles J. Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses. Genome Biol Evol 2016; 8:3471-3484. [PMID: 27797946 PMCID: PMC5203785 DOI: 10.1093/gbe/evw246] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.
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Affiliation(s)
- Jordon Rahaman
- Department of Biological Sciences, Florida International University, Miami, FL
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Florida International University, Miami, FL .,Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL
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27
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Głąb B, Beganovic M, Anaokar S, Hao MS, Rasmusson AG, Patton-Vogt J, Banaś A, Stymne S, Lager I. Cloning of Glycerophosphocholine Acyltransferase (GPCAT) from Fungi and Plants: A NOVEL ENZYME IN PHOSPHATIDYLCHOLINE SYNTHESIS. J Biol Chem 2016; 291:25066-25076. [PMID: 27758859 PMCID: PMC5122774 DOI: 10.1074/jbc.m116.743062] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/06/2016] [Indexed: 12/22/2022] Open
Abstract
Glycero-3-phosphocholine (GPC), the product of the complete deacylation of phosphatidylcholine (PC), was long thought to not be a substrate for reacylation. However, it was recently shown that cell-free extracts from yeast and plants could acylate GPC with acyl groups from acyl-CoA. By screening enzyme activities of extracts derived from a yeast knock-out collection, we were able to identify and clone the yeast gene (GPC1) encoding the enzyme, named glycerophosphocholine acyltransferase (GPCAT). By homology search, we also identified and cloned GPCAT genes from three plant species. All enzymes utilize acyl-CoA to acylate GPC, forming lyso-PC, and they show broad acyl specificities in both yeast and plants. In addition to acyl-CoA, GPCAT efficiently utilizes LPC and lysophosphatidylethanolamine as acyl donors in the acylation of GPC. GPCAT homologues were found in the major eukaryotic organism groups but not in prokaryotes or chordates. The enzyme forms its own protein family and does not contain any of the acyl binding or lipase motifs that are present in other studied acyltransferases and transacylases. In vivo labeling studies confirm a role for Gpc1p in PC biosynthesis in yeast. It is postulated that GPCATs contribute to the maintenance of PC homeostasis and also have specific functions in acyl editing of PC (e.g. in transferring acyl groups modified at the sn-2 position of PC to the sn-1 position of this molecule in plant cells).
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Affiliation(s)
- Bartosz Głąb
- From the Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-822 Gdańsk, Poland
| | - Mirela Beganovic
- the Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden
| | - Sanket Anaokar
- the Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, and
| | - Meng-Shu Hao
- the Department of Biology, Lund University, Biology Building A, Sölvegatan 35, 223 62 Lund, Sweden
| | - Allan G Rasmusson
- the Department of Biology, Lund University, Biology Building A, Sölvegatan 35, 223 62 Lund, Sweden
| | - Jana Patton-Vogt
- the Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, and
| | - Antoni Banaś
- From the Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-822 Gdańsk, Poland
| | - Sten Stymne
- the Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden
| | - Ida Lager
- the Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden,
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28
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Chi PB, Liberles DA. Selection on protein structure, interaction, and sequence. Protein Sci 2016; 25:1168-78. [PMID: 26808055 PMCID: PMC4918422 DOI: 10.1002/pro.2886] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
Abstract
Characterizing the probabilities of observing amino acid substitutions at specific sites in a protein over evolutionary time is a major goal in the field of molecular evolution. While purely statistical approaches at different levels of complexity exist, approaches rooted in underlying biological processes are necessary to characterize both the context-dependence of sequence changes (epistasis) and to extrapolate to sequences not observed in biological databases. To develop such approaches, an understanding of the different selective forces that act on amino acid substitution is necessary. Here, an overview of selection on and corresponding modeling of folding stability, folding specificity, binding affinity and specificity for ligands, the evolution of new binding sites on protein surfaces, protein dynamics, intrinsic disorder, and protein aggregation as well as the interplay with protein expression level (concentration) and biased mutational processes are presented.
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Affiliation(s)
- Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
- Department of Mathematics and Computer Science, Ursinus College, Collegeville, Pennsylvania, 19426
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
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29
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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30
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dos Santos HG, Nunez-Castilla J, Siltberg-Liberles J. Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One 2016; 11:e0151961. [PMID: 27003913 PMCID: PMC4803236 DOI: 10.1371/journal.pone.0151961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Conformational and functional flexibility promote protein evolvability. High evolvability allows related proteins to functionally diverge and perhaps to neostructuralize. p53 is a multifunctional protein frequently referred to as the Guardian of the Genome–a hub for e.g. incoming and outgoing signals in apoptosis and DNA repair. p53 has been found to be structurally disordered, an extreme form of conformational flexibility. Here, p53, and its paralogs p63 and p73, were studied for further insights into the evolutionary dynamics of structural disorder, secondary structure, and phosphorylation. This study is focused on the post gene duplication phase for the p53 family in vertebrates, but also visits the origin of the protein family and the early domain loss and gain events. Functional divergence, measured by rapid evolutionary dynamics of protein domains, structural properties, and phosphorylation propensity, is inferred across vertebrate p53 proteins, in p63 and p73 from fish, and between the three paralogs. In particular, structurally disordered regions are redistributed among paralogs, but within clades redistribution of structural disorder also appears to be an ongoing process. Despite its deemed importance as the Guardian of the Genome, p53 is indeed a protein with high evolvability as seen not only in rearranged structural disorder, but also in fluctuating domain sequence signatures among lineages.
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Affiliation(s)
- Helena G. dos Santos
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
| | - Janelle Nunez-Castilla
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
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31
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Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Genetically modified proteins: functional improvement and chimeragenesis. Bioengineered 2015. [PMID: 26211369 DOI: 10.1080/21655979.2015.1075674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis for the functional improvement of proteins in areas where traditional protein engineering methods have been extensively used and practically exhausted. The novel path for the creation of the novel proteins has been created on the farther development of the new structure and sequence optimization algorithms for generating and designing the accurate structure models in result of x-ray crystallography studies of a lot of proteins and their mutant forms. Artificial genetic modifications aim to expand nature's repertoire of biomolecules. One of the most exciting potential results of mutagenesis or chimeragenesis finding could be design of effective diagnostics, bio-therapeutics and biocatalysts. A sampling of recent examples is listed below for the in vivo and in vitro genetically improvement of various binding protein and enzyme functions, with references for more in-depth study provided for the reader's benefit.
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Affiliation(s)
- Larissa Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | - Vasily Golotin
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | | | - Valery Rasskazov
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia
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32
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Liberles DA, Teufel AI, Liu L, Stadler T. On the need for mechanistic models in computational genomics and metagenomics. Genome Biol Evol 2014; 5:2008-18. [PMID: 24115604 PMCID: PMC3814209 DOI: 10.1093/gbe/evt151] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Computational genomics is now generating very large volumes of data that have the potential to be used to address important questions in both basic biology and biomedicine. Addressing these important biological questions becomes possible when mechanistic models rooted in biochemistry and evolutionary/population genetic processes are developed, instead of fitting data to off-the-shelf statistical distributions that do not enable mechanistic inference. Three examples are presented, the first involving ecological processes inferred from metagenomic data, the second involving mechanisms of gene regulation rooted in protein–DNA interactions with consideration of DNA structure, and the third involving existing models for the retention of duplicate genes that enables prediction of evolutionary mechanisms. This description of mechanistic models is generalized toward future developments in computational genomics and the need for biological mechanisms and processes in biological models.
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33
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Rao R, Xu D, Thelen JJ, Miernyk JA. Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation. BMC Bioinformatics 2013; 14 Suppl 14:S14. [PMID: 24267725 PMCID: PMC3851202 DOI: 10.1186/1471-2105-14-s14-s14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are typically studied individually, herein we describe the potential for cross-talk and hierarchical regulation. RESULTS The proximity of Met to Ser/Thr/Tyr within the proteome has not previously been addressed. In order to consider the possibility of a generalized interaction, we performed a trans-kingdom sequence analysis of known phosphorylation sites in proteins from bacteria, fungi, plants, and animals. The proportion of phosphorylation sites that include a Met within a 13-residue window centered upon Ser/Thr/Tyr is significantly less than the occurrence of Met in proximity to all Ser/Thr/Tyr residues. Met residues are present at all positions (-6 to +6, inclusive) within the 13-residue window that we have considered. Detailed analysis of sequences from eight disparate plant taxa revealed that many conserved phosphorylation sites have a Met residue in the proximity. Results from GO enrichment analysis indicated that the potential for phosphorylation and Met oxidation crosstalk is most prevalent in kinases and proteins involved in signalling. CONCLUSION The large proportion of known phosphorylation sites with Met in the proximity fulfils the necessary condition for cross-talk. Kinases/signalling proteins are enriched for Met around phosphorylation sites. These proteins/sites are likely candidates for cross-talk between oxidative signalling and reversible phosphorylation.
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34
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Ortiz JF, MacDonald ML, Masterson P, Uversky VN, Siltberg-Liberles J. Rapid evolutionary dynamics of structural disorder as a potential driving force for biological divergence in flaviviruses. Genome Biol Evol 2013; 5:504-13. [PMID: 23418179 PMCID: PMC3622304 DOI: 10.1093/gbe/evt026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein structure is commonly regarded to be conserved and to dictate function. Most proteins rely on conformational flexibility to some degree. Are regions that convey conformational flexibility conserved over evolutionary time? Can changes in conformational flexibility alter protein function? Here, the evolutionary dynamics of structurally ordered and disordered (flexible) regions are investigated genome-wide in flaviviruses, revealing that the amount and location of structural disorder fluctuates highly among related proteins. Some regions are prone to shift between structured and flexible states. Increased evolutionary dynamics of structural disorder is observed for some lineages but not in others. Lineage-specific transitions of this kind could alter the conformational ensemble accessible to the same protein in different species, causing a functional change, even if the predominant function remains conserved. Thus, rapid evolutionary dynamics of structural disorder is a potential driving force for phenotypic divergence among flaviviruses.
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Affiliation(s)
- Juan F Ortiz
- Department of Molecular Biology, University of Wyoming, USA
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35
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Du D, Lee CF, Li XQ. Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome. PLoS One 2012; 7:e44872. [PMID: 23028653 PMCID: PMC3446998 DOI: 10.1371/journal.pone.0044872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/08/2012] [Indexed: 11/18/2022] Open
Abstract
Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in directional ranking? C) Are high ranked proteins more evolutionarily conserved than low ranked ones? D) Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.
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Affiliation(s)
- Donglei Du
- Quantiative Study Group, Faculty of Business Administration, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Connie F. Lee
- Quantiative Study Group, Faculty of Business Administration, University of New Brunswick, Fredericton, New Brunswick, Canada
- The Fu Foundation School of Engineering and Applied Science, Columbia University, New York, New York, United States of America
| | - Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
- * E-mail:
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36
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Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012; 21:769-85. [PMID: 22528593 PMCID: PMC3403413 DOI: 10.1002/pro.2071] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 12/20/2022]
Abstract
Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
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Affiliation(s)
- David A Liberles
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Sarah A Teichmann
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of PittsburghPittsburgh, Pennsylvania 15213
| | - Ugo Bastolla
- Bioinformatics Unit. Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid28049 Cantoblanco Madrid, Spain
| | - Jesse Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington 98109
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of MuensterGermany
| | - Lucy J Colwell
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - A P Jason de Koning
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of ColoradoAurora, Colorado
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillNorth Carolina 27599
| | - Julian Echave
- Escuela de Ciencia y Tecnología, Universidad Nacional de San MartínMartín de Irigoyen 3100, 1650 San Martín, Buenos Aires, Argentina
| | - Arne Elofsson
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University106 91 Stockholm, Sweden
| | - Dietlind L Gerloff
- Biomolecular Engineering Department, University of CaliforniaSanta Cruz, California 95064
| | - Richard A Goldstein
- Division of Mathematical Biology, National Institute for Medical Research (MRC)Mill Hill, London NW7 1AA, United Kingdom
| | - Johan A Grahnen
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Mark T Holder
- Department of Ecology and Evolutionary Biology, University of KansasLawrence, Kansas 66045
| | - Clemens Lakner
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, North Carolina 27695
| | - Nicholas Lartillot
- Département de Biochimie, Faculté de Médecine, Université de MontréalMontréal, QC H3T1J4, Canada
| | - Simon C Lovell
- Faculty of Life Sciences, University of ManchesterManchester M13 9PT, United Kingdom
| | - Gavin Naylor
- Department of Biology, College of CharlestonCharleston, South Carolina 29424
| | - Tina Perica
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of ColoradoAurora, Colorado
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven 06511
| | - Andrew Roger
- Department of Biochemistry and Molecular Biology, Dalhousie UniversityHalifax, NS, Canada
| | - Nimrod Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridge, Massachusetts 02138
| | - Kimmen Sjölander
- Department of Bioengineering, University of CaliforniaBerkeley, Berkeley, California 94720
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School77 Avenue Louis Pasteur, Boston, Massachusetts 02115
| | - Ashley I Teufel
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, North Carolina 27695
| | - Joseph W Thornton
- Howard Hughes Medical Institute and Institute for Ecology and Evolution, University of OregonEugene, Oregon 97403
- Department of Human Genetics, University of ChicagoChicago, Illinois 60637
- Department of Ecology and Evolution, University of ChicagoChicago, Illinois 60637
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, and Center for Computational Molecular Biology, Brown UniversityProvidence, Rhode Island 02912
| | - Simon Whelan
- Faculty of Life Sciences, University of ManchesterManchester M13 9PT, United Kingdom
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