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Abulfaraj AA, Shami AY, Alotaibi NM, Alomran MM, Aloufi AS, Al-Andal A, AlHamdan NR, Alshehrei FM, Sefrji FO, Alsaadi KH, Abuauf HW, Alshareef SA, Jalal RS. Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum. AMB Express 2024; 14:27. [PMID: 38381255 PMCID: PMC10881953 DOI: 10.1186/s13568-024-01678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/28/2024] [Indexed: 02/22/2024] Open
Abstract
The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes.
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Affiliation(s)
- Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia.
| | - Ashwag Y Shami
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Maryam M Alomran
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Abeer Al-Andal
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Fatimah M Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, Makkah 21955, Saudi Arabia
| | - Fatmah O Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Khloud H Alsaadi
- Department of Biological Science, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Haneen W Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 24381, Saudi Arabia
| | - Sahar A Alshareef
- Department of Biological Science, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21921, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biological Science, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia.
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2
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Banerjee A, Pata J, Chaptal V, Boumendjel A, Falson P, Prasad R. Structure, function, and inhibition of catalytically asymmetric ABC transporters: Lessons from the PDR subfamily. Drug Resist Updat 2023; 71:100992. [PMID: 37567064 DOI: 10.1016/j.drup.2023.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
ATP-binding cassette (ABC) superfamily comprises a large group of ubiquitous transmembrane proteins that play a crucial role in transporting a diverse spectrum of substrates across cellular membranes. They participate in a wide array of physiological and pathological processes including nutrient uptake, antigen presentation, toxin elimination, and drug resistance in cancer and microbial cells. ABC transporters couple ATP binding and hydrolysis to undergo conformational changes allowing substrate translocation. Within this superfamily, a set of ABC transporters has lost the capacity to hydrolyze ATP at one of their nucleotide-binding sites (NBS), called the non-catalytic NBS, whose importance became evident with extensive biochemistry carried out on yeast pleiotropic drug resistance (PDR) transporters. Recent single-particle cryogenic electron microscopy (cryo-EM) advances have further catapulted our understanding of the architecture of these pumps. We provide here a comprehensive overview of the structural and functional aspects of catalytically asymmetric ABC pumps with an emphasis on the PDR subfamily. Furthermore, given the increasing evidence of efflux-mediated antifungal resistance in clinical settings, we also discuss potential grounds to explore PDR transporters as therapeutic targets.
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Affiliation(s)
- Atanu Banerjee
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India.
| | - Jorgaq Pata
- Drug Resistance & Membrane Proteins group, CNRS-Lyon 1 University Laboratory 5086, IBCP, Lyon, France
| | - Vincent Chaptal
- Drug Resistance & Membrane Proteins group, CNRS-Lyon 1 University Laboratory 5086, IBCP, Lyon, France
| | | | - Pierre Falson
- Drug Resistance & Membrane Proteins group, CNRS-Lyon 1 University Laboratory 5086, IBCP, Lyon, France.
| | - Rajendra Prasad
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India.
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Stanchev LD, Marek M, Xian F, Klöhn M, Silvestro D, Dittmar G, López-Marqués RL, Günther Pomorski T. Functional Significance of Conserved Cysteines in the Extracellular Loops of the ATP Binding Cassette Transporter Pdr11p. J Fungi (Basel) 2020; 7:jof7010002. [PMID: 33375075 PMCID: PMC7822014 DOI: 10.3390/jof7010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
The pleiotropic drug resistance (PDR) transporter Pdr11p is expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae, where it facilitates the uptake of exogenous sterols. Members of the fungal PDR family contain six conserved cysteines in their extracellular loops (ECL). For the functional analysis of these cysteine residues in Pdr11p, we generated a series of single cysteine-to-serine mutants. All mutant proteins expressed well and displayed robust ATPase activity upon purification. Mass-spectrometry analysis identified two cysteine residues (C582 and C603) in ECL3 forming a disulfide bond. Further characterization by cell-based assays showed that all mutants are compromised in facilitating sterol uptake, protein stability, and trafficking to the plasma membrane. Our data highlight the fundamental importance of all six extracellular cysteine residues for the functional integrity of Pdr11p and provide new structural insights into the PDR family of transporters.
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Affiliation(s)
- Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Feng Xian
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Rue Thomas Edison 1A-B, L-1445 Strassen, Luxembourg; (F.X.); (G.D.)
| | - Mara Klöhn
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
| | - Daniele Silvestro
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Rue Thomas Edison 1A-B, L-1445 Strassen, Luxembourg; (F.X.); (G.D.)
| | - Rosa Laura López-Marqués
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
- Correspondence: ; Tel.: +49-234-322-4430
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Ye Z, Lu Y, Wu T. The impact of ATP-binding cassette transporters on metabolic diseases. Nutr Metab (Lond) 2020; 17:61. [PMID: 32774439 PMCID: PMC7398066 DOI: 10.1186/s12986-020-00478-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
Currently, many people worldwide suffer from metabolic diseases caused by heredity and external factors, such as diet. One of the symptoms of metabolic diseases is abnormal lipid metabolism. ATP binding cassette (ABC) transporters are one of the largest transport protein superfamilies that exist in nearly all living organisms and are mainly located on lipid-processing cells. ABC transporters have been confirmed to be closely related to the pathogenesis of diseases such as metabolic diseases, cancer and Alzheimer's disease based on their transport abilities. Notably, the capability to transport lipids makes ABC transporters critical in metabolic diseases. In addition, gene polymorphism in ABC transporters has been reported to be a risk factor for metabolic diseases, and it has been reported that relevant miRNAs have significant roles in regulating ABC transporters. In this review, we integrate recent studies to examine the roles of ABC transporters in metabolic diseases and aim to build a network with ABC transporters as the core, linking their transport abilities with metabolic and other diseases.
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Affiliation(s)
- Zixiang Ye
- Center of Chinese Medical Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Shanghai, 201203 China
| | - Yifei Lu
- Center of Chinese Medical Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Shanghai, 201203 China
| | - Tao Wu
- Center of Chinese Medical Therapy and Systems Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Shanghai, 201203 China
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van 't Klooster JS, Cheng TY, Sikkema HR, Jeucken A, Moody DB, Poolman B. Membrane Lipid Requirements of the Lysine Transporter Lyp1 from Saccharomyces cerevisiae. J Mol Biol 2020; 432:4023-4031. [PMID: 32413406 PMCID: PMC8005870 DOI: 10.1016/j.jmb.2020.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/25/2022]
Abstract
Membrane lipids act as solvents and functional cofactors for integral membrane proteins. The yeast plasma membrane is unusual in that it may have a high lipid order, which coincides with low passive permeability for small molecules and a slow lateral diffusion of proteins. Yet, membrane proteins whose functions require altered conformation must have flexibility within membranes. We have determined the molecular composition of yeast plasma membrane lipids located within a defined diameter of model proteins, including the APC-superfamily lysine transporter Lyp1. We now use the composition of lipids that naturally surround Lyp1 to guide testing of lipids that support the normal functioning of the transporter, when reconstituted in vesicles of defined lipid composition. We find that phosphatidylserine and ergosterol are essential for Lyp1 function, and the transport activity displays a sigmoidal relationship with the concentration of these lipids. Non-bilayer lipids stimulate transport activity, but different types are interchangeable. Remarkably, Lyp1 requires a relatively high fraction of lipids with one or more unsaturated acyl chains. The transport data and predictions of the periprotein lipidome of Lyp1 support a new model in which a narrow band of lipids immediately surrounding the transmembrane stalk of a model protein allows conformational changes in the protein.
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Affiliation(s)
- Joury S van 't Klooster
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Tan-Yun Cheng
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA
| | - Hendrik R Sikkema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - Aike Jeucken
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
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Papay M, Klein C, Hapala I, Petriskova L, Kuchler K, Valachovic M. Mutations in the nucleotide‐binding domain of putative sterol importers Aus1 and Pdr11 selectively affect utilization of exogenous sterol species in yeast. Yeast 2019; 37:5-14. [DOI: 10.1002/yea.3456] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 11/07/2022] Open
Affiliation(s)
- Marek Papay
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics Centre of Biosciences of the Slovak Academy of Sciences Bratislava Slovakia
| | - Cornelia Klein
- Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter Medical University of Vienna Vienna Austria
| | - Ivan Hapala
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics Centre of Biosciences of the Slovak Academy of Sciences Bratislava Slovakia
| | - Livia Petriskova
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics Centre of Biosciences of the Slovak Academy of Sciences Bratislava Slovakia
| | - Karl Kuchler
- Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter Medical University of Vienna Vienna Austria
| | - Martin Valachovic
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics Centre of Biosciences of the Slovak Academy of Sciences Bratislava Slovakia
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7
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Rizzo J, Stanchev LD, da Silva VK, Nimrichter L, Pomorski TG, Rodrigues ML. Role of lipid transporters in fungal physiology and pathogenicity. Comput Struct Biotechnol J 2019; 17:1278-1289. [PMID: 31921394 PMCID: PMC6944739 DOI: 10.1016/j.csbj.2019.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/20/2019] [Accepted: 09/02/2019] [Indexed: 02/08/2023] Open
Abstract
The fungal cell wall and membrane are the most common targets of antifungal agents, but the potential of membrane lipid organization in regulating drug-target interactions has yet to be investigated. Energy-dependent lipid transporters have been recently associated with virulence and drug resistance in many pathogenic fungi. To illustrate this view, we discuss (i) the structural and biological aspects of ATP-driven lipid transporters, comprising P-type ATPases and ATP-binding cassette transporters, (ii) the role of these transporters in fungal physiology and virulence, and (iii) the potential of lipid transporters as targets for the development of novel antifungals. These recent observations indicate that the lipid-trafficking machinery in fungi is a promising target for studies on physiology, pathogenesis and drug development.
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Affiliation(s)
- Juliana Rizzo
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Vanessa K.A. da Silva
- Programa de Pós-Graduação em Biologia Parasitária do Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
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Steady state analysis of influx and transbilayer distribution of ergosterol in the yeast plasma membrane. Theor Biol Med Model 2019; 16:13. [PMID: 31412941 PMCID: PMC6694696 DOI: 10.1186/s12976-019-0108-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/15/2019] [Indexed: 01/05/2023] Open
Abstract
Background The transbilayer sterol distribution between both plasma membrane (PM) leaflets has long been debated. Recent studies in mammalian cells and in yeast show that the majority of sterol resides in the inner PM leaflet. Since sterol flip-flop in model membranes is rapid and energy-independent, a mechanistic understanding for net enrichment of sterol in one leaflet is lacking. Import of ergosterol in yeast can take place via the ABC transporters Aus1/Pdr11 under anaerobic growth conditions, eventually followed by rapid non-vesicular sterol transport to the endoplasmic reticulum (ER). Little is known about how these transport steps are dynamically coordinated. Methods Here, a kinetic steady state model is presented which considers sterol import via Aus1/Pdr11, sterol flip-flop across the PM, bi-molecular complex formation and intracellular sterol release followed by eventual transport to and esterification of sterol in the ER. The steady state flux is calculated, and a thermodynamic analysis of feasibility is presented. Results It is shown that the steady state sterol flux across the PM can be entirely controlled by irreversible sterol import via Aus1/Pdr11. The transbilayer sterol flux at steady state is a non-linear function of the chemical potential difference of sterol between both leaflets. Non-vesicular release of sterol on the cytoplasmic side of the PM lowers the attainable sterol enrichment in the inner leaflet. Including complex formation of sterol with phospholipids or proteins can explain several puzzling experimental observations; 1) rapid sterol flip-flop across the PM despite net sterol enrichment in one leaflet, 2) a pronounced steady state sterol gradient between PM and ER despite fast non-vesicular sterol exchange between both compartments and 3) a non-linear dependence of ER sterol on ergosterol abundance in the PM. Conclusions A steady state model is presented that can account for the observed sterol asymmetry in the yeast PM, the strong sterol gradient between PM and ER and threshold-like expansion of ER sterol for increasing sterol influx into the PM. The model also provides new insight into selective uptake of cholesterol and its homeostasis in mammalian cells, and it provides testable predictions for future experiments.
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