1
|
Rivera AM, Swanson WJ. The Importance of Gene Duplication and Domain Repeat Expansion for the Function and Evolution of Fertilization Proteins. Front Cell Dev Biol 2022; 10:827454. [PMID: 35155436 PMCID: PMC8830517 DOI: 10.3389/fcell.2022.827454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
The process of gene duplication followed by gene loss or evolution of new functions has been studied extensively, yet the role gene duplication plays in the function and evolution of fertilization proteins is underappreciated. Gene duplication is observed in many fertilization protein families including Izumo, DCST, ZP, and the TFP superfamily. Molecules mediating fertilization are part of larger gene families expressed in a variety of tissues, but gene duplication followed by structural modifications has often facilitated their cooption into a fertilization function. Repeat expansions of functional domains within a gene also provide opportunities for the evolution of novel fertilization protein. ZP proteins with domain repeat expansions are linked to species-specificity in fertilization and TFP proteins that experienced domain duplications were coopted into a novel sperm function. This review outlines the importance of gene duplications and repeat domain expansions in the evolution of fertilization proteins.
Collapse
Affiliation(s)
- Alberto M. Rivera
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | | |
Collapse
|
2
|
Nirthanan S. Snake three-finger α-neurotoxins and nicotinic acetylcholine receptors: molecules, mechanisms and medicine. Biochem Pharmacol 2020; 181:114168. [PMID: 32710970 DOI: 10.1016/j.bcp.2020.114168] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
Abstract
Snake venom three-finger α-neurotoxins (α-3FNTx) act on postsynaptic nicotinic acetylcholine receptors (nAChRs) at the neuromuscular junction (NMJ) to produce skeletal muscle paralysis. The discovery of the archetypal α-bungarotoxin (α-BgTx), almost six decades ago, exponentially expanded our knowledge of membrane receptors and ion channels. This included the localisation, isolation and characterization of the first receptor (nAChR); and by extension, the pathophysiology and pharmacology of neuromuscular transmission and associated pathologies such as myasthenia gravis, as well as our understanding of the role of α-3FNTxs in snakebite envenomation leading to novel concepts of targeted treatment. Subsequent studies on a variety of animal venoms have yielded a plethora of novel toxins that have revolutionized molecular biomedicine and advanced drug discovery from bench to bedside. This review provides an overview of nAChRs and their subtypes, classification of α-3FNTxs and the challenges of typifying an increasing arsenal of structurally and functionally unique toxins, and the three-finger protein (3FP) fold in the context of the uPAR/Ly6/CD59/snake toxin superfamily. The pharmacology of snake α-3FNTxs including their mechanisms of neuromuscular blockade, variations in reversibility of nAChR interactions, specificity for nAChR subtypes or for distinct ligand-binding interfaces within a subtype and the role of α-3FNTxs in neurotoxic envenomation are also detailed. Lastly, a reconciliation of structure-function relationships between α-3FNTx and nAChRs, derived from historical mutational and biochemical studies and emerging atomic level structures of nAChR models in complex with α-3FNTxs is discussed.
Collapse
Affiliation(s)
- Selvanayagam Nirthanan
- School of Medical Science, Griffith Health Group, Griffith University, Gold Coast, Queensland, Australia.
| |
Collapse
|
3
|
Leth JM, Leth-Espensen KZ, Kristensen KK, Kumari A, Lund Winther AM, Young SG, Ploug M. Evolution and Medical Significance of LU Domain-Containing Proteins. Int J Mol Sci 2019; 20:ijms20112760. [PMID: 31195646 PMCID: PMC6600238 DOI: 10.3390/ijms20112760] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
Proteins containing Ly6/uPAR (LU) domains exhibit very diverse biological functions and have broad taxonomic distributions in eukaryotes. In general, they adopt a characteristic three-fingered folding topology with three long loops projecting from a disulfide-rich globular core. The majority of the members of this protein domain family contain only a single LU domain, which can be secreted, glycolipid anchored, or constitute the extracellular ligand binding domain of type-I membrane proteins. Nonetheless, a few proteins contain multiple LU domains, for example, the urokinase receptor uPAR, C4.4A, and Haldisin. In the current review, we will discuss evolutionary aspects of this protein domain family with special emphasis on variations in their consensus disulfide bond patterns. Furthermore, we will present selected cases where missense mutations in LU domain-containing proteins leads to dysfunctional proteins that are causally linked to genesis of human disease.
Collapse
Affiliation(s)
- Julie Maja Leth
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Katrine Zinck Leth-Espensen
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Kristian Kølby Kristensen
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Anni Kumari
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Anne-Marie Lund Winther
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Michael Ploug
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| |
Collapse
|
4
|
Compression of Large Sets of Sequence Data Reveals Fine Diversification of Functional Profiles in Multigene Families of Proteins: A Study for Peptidyl-Prolyl cis/trans Isomerases (PPIase). Biomolecules 2019; 9:biom9020059. [PMID: 30754725 PMCID: PMC6406343 DOI: 10.3390/biom9020059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/21/2022] Open
Abstract
In this technical note, we describe analyses of more than 15,000 sequences of FK506-binding proteins (FKBP) and cyclophilins, also known as peptidyl-prolyl cis/trans isomerases (PPIases). We have developed a novel way of displaying relative changes of amino acid (AA)-residues at a given sequence position by using heat-maps. This type of representation allows simultaneous estimation of conservation level in a given sequence position in the entire group of functionally-related paralogues (multigene family of proteins). We have also proposed that at least two FKBPs, namely FKBP36, encoded by the Fkbp6 gene and FKBP51, encoded by the Fkbp5 gene, can form dimers bound via a disulfide bridge in the nucleus. This type of dimer may have some crucial function in the regulation of some nuclear complexes at different stages of the cell cycle.
Collapse
|
5
|
Galat A. Peptidylprolyl Isomerases as In Vivo Carriers for Drugs That Target Various Intracellular Entities. Biomolecules 2017; 7:biom7040072. [PMID: 28961224 PMCID: PMC5745455 DOI: 10.3390/biom7040072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/15/2023] Open
Abstract
Analyses of sequences and structures of the cyclosporine A (CsA)-binding proteins (cyclophilins) and the immunosuppressive macrolide FK506-binding proteins (FKBPs) have revealed that they exhibit peculiar spatial distributions of charges, their overall hydrophobicity indexes vary within a considerable level whereas their points isoelectric (pIs) are contained from 4 to 11. These two families of peptidylprolyl cis/trans isomerases (PPIases) have several distinct functional attributes such as: (1) high affinity binding to some pharmacologically-useful hydrophobic macrocyclic drugs; (2) diversified binding epitopes to proteins that may induce transient manifolds with altered flexibility and functional fitness; and (3) electrostatic interactions between positively charged segments of PPIases and negatively charged intracellular entities that support their spatial integration. These three attributes enhance binding of PPIase/pharmacophore complexes to diverse intracellular entities, some of which perturb signalization pathways causing immunosuppression and other system-altering phenomena in humans.
Collapse
Affiliation(s)
- Andrzej Galat
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay, F-91191 Gif/Yvette, France.
| |
Collapse
|
6
|
Kessler P, Marchot P, Silva M, Servent D. The three-finger toxin fold: a multifunctional structural scaffold able to modulate cholinergic functions. J Neurochem 2017; 142 Suppl 2:7-18. [PMID: 28326549 DOI: 10.1111/jnc.13975] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/12/2017] [Accepted: 01/30/2017] [Indexed: 12/26/2022]
Abstract
Three-finger fold toxins are miniproteins frequently found in Elapidae snake venoms. This fold is characterized by three distinct loops rich in β-strands and emerging from a dense, globular core reticulated by four highly conserved disulfide bridges. The number and diversity of receptors, channels, and enzymes identified as targets of three-finger fold toxins is increasing continuously. Such manifold diversity highlights the specific adaptability of this fold for generating pleiotropic functions. Although this toxin superfamily disturbs many biological functions by interacting with a large diversity of molecular targets, the most significant target is the cholinergic system. By blocking the activity of the nicotinic and muscarinic acetylcholine receptors or by inhibiting the enzyme acetylcholinesterase, three-finger fold toxins interfere most drastically with neuromuscular junction functioning. Several of these toxins have become powerful pharmacological tools for studying the function and structure of their molecular targets. Most importantly, since dysfunction of these receptors/enzyme is involved in many diseases, exploiting the three-finger scaffold to create novel, highly specific therapeutic agents may represent a major future endeavor. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms.
Collapse
Affiliation(s)
- Pascal Kessler
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pascale Marchot
- Aix-Marseille Université/Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques laboratory, Faculté des Sciences Campus Luminy, Marseille, France
| | - Marcela Silva
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France.,Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Denis Servent
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| |
Collapse
|