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Umarao P, Rath PP, Gourinath S. Cdc42/Rac Interactive Binding Containing Effector Proteins in Unicellular Protozoans With Reference to Human Host: Locks of the Rho Signaling. Front Genet 2022; 13:781885. [PMID: 35186026 PMCID: PMC8847673 DOI: 10.3389/fgene.2022.781885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
Small GTPases are the key to actin cytoskeleton signaling, which opens the lock of effector proteins to forward the signal downstream in several cellular pathways. Actin cytoskeleton assembly is associated with cell polarity, adhesion, movement and other functions in eukaryotic cells. Rho proteins, specifically Cdc42 and Rac, are the primary regulators of actin cytoskeleton dynamics in higher and lower eukaryotes. Effector proteins, present in an inactive state gets activated after binding to the GTP bound Cdc42/Rac to relay a signal downstream. Cdc42/Rac interactive binding (CRIB) motif is an essential conserved sequence found in effector proteins to interact with Cdc42 or Rac. A diverse range of Cdc42/Rac and their effector proteins have evolved from lower to higher eukaryotes. The present study has identified and further classified CRIB containing effector proteins in lower eukaryotes, focusing on parasitic protozoans causing neglected tropical diseases and taking human proteins as a reference point to the highest evolved organism in the evolutionary trait. Lower eukaryotes’ CRIB containing proteins fall into conventional effector molecules, PAKs (p21 activated kinase), Wiskoit-Aldrich Syndrome proteins family, and some have unique domain combinations unlike any known proteins. We also highlight the correlation between the effector protein isoforms and their selective specificity for Cdc42 or Rac proteins during evolution. Here, we report CRIB containing effector proteins; ten in Dictyostelium and Entamoeba, fourteen in Acanthamoeba, one in Trypanosoma and Giardia. CRIB containing effector proteins that have been studied so far in humans are potential candidates for drug targets in cancer, neurological disorders, and others. Conventional CRIB containing proteins from protozoan parasites remain largely elusive and our data provides their identification and classification for further in-depth functional validations. The tropical diseases caused by protozoan parasites lack combinatorial drug targets as effective paradigms. Targeting signaling mechanisms operative in these pathogens can provide greater molecules in combatting their infections.
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Affiliation(s)
- Preeti Umarao
- Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pragyan Parimita Rath
- Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Samudrala Gourinath
- Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Rani P, Gautam G, Anwar T, Gourinath S, Datta A. Crystal structure of Gig2 protein from Candida albicans provides a structural insight into DUF1479 family oxygenases. Int J Biol Macromol 2020; 150:1272-1280. [PMID: 31743702 DOI: 10.1016/j.ijbiomac.2019.10.138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 11/15/2022]
Affiliation(s)
- Priya Rani
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Gunjan Gautam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tamanna Anwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Asis Datta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India; National Institute of Plant Genome Research, New Delhi, India.
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Alex JM, Rennie ML, Engilberge S, Lehoczki G, Dorottya H, Fizil Á, Batta G, Crowley PB. Calixarene-mediated assembly of a small antifungal protein. IUCRJ 2019; 6:238-247. [PMID: 30867921 PMCID: PMC6400181 DOI: 10.1107/s2052252519000411] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/08/2019] [Indexed: 05/24/2023]
Abstract
Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Martin L. Rennie
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Gábor Lehoczki
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Hajdu Dorottya
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Ádám Fizil
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Gyula Batta
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
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EhFP10: A FYVE family GEF interacts with myosin IB to regulate cytoskeletal dynamics during endocytosis in Entamoeba histolytica. PLoS Pathog 2019; 15:e1007573. [PMID: 30779788 PMCID: PMC6396940 DOI: 10.1371/journal.ppat.1007573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/01/2019] [Accepted: 01/08/2019] [Indexed: 01/07/2023] Open
Abstract
Motility and phagocytosis are key processes that are involved in invasive amoebiasis disease caused by intestinal parasite Entamoeba histolytica. Previous studies have reported unconventional myosins to play significant role in membrane based motility as well as endocytic processes. EhMyosin IB is the only unconventional myosin present in E. histolytica, is thought to be involved in both of these processes. Here, we report an interaction between the SH3 domain of EhMyosin IB and c-terminal domain of EhFP10, a Rho guanine nucleotide exchange factor. EhFP10 was found to be confined to Entamoeba species only, and to contain a c-terminal domain that binds and bundles actin filaments. EhFP10 was observed to localize in the membrane ruffles, phagocytic and macropinocytic cups of E. histolytica trophozoites. It was also found in early pinosomes but not early phagosomes. A crystal structure of the c-terminal SH3 domain of EhMyosin IB (EhMySH3) in complex with an EhFP10 peptide and co-localization studies established the interaction of EhMySH3 with EhFP10. This interaction was shown to lead to inhibition of actin bundling activity and to thereby regulate actin dynamics during endocytosis. We hypothesize that unique domain architecture of EhFP10 might be compensating the absence of Wasp and related proteins in Entamoeba, which are known partners of myosin SH3 domains in other eukaryotes. Our findings also highlights the role of actin bundling during endocytosis.
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Ghedira K, Harigua-Souiai E, Ben Hamda C, Fournier P, Pujic P, Guesmi S, Guizani I, Miotello G, Armengaud J, Normand P, Sghaier H. The PEG-responding desiccome of the alder microsymbiont Frankia alni. Sci Rep 2018; 8:759. [PMID: 29335550 PMCID: PMC5768760 DOI: 10.1038/s41598-017-18839-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
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Affiliation(s)
- Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
- Université de Carthage, Faculté des Sciences de Bizerte, Tunis, 7021, Tunisia
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Sihem Guesmi
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- National Agronomy Institute (INAT), Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- Associated with Laboratory "Biotechnology and Nuclear Technology" (LR16CNSTN01) & Laboratory "Biotechnology and Bio-Geo Resources Valorization" (LR11ES31), Sidi Thabet Technopark, 2020, Tunisia
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