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Sailer ZR, Shafik SH, Summers RL, Joule A, Patterson-Robert A, Martin RE, Harms MJ. Inferring a complete genotype-phenotype map from a small number of measured phenotypes. PLoS Comput Biol 2020; 16:e1008243. [PMID: 32991585 PMCID: PMC7546491 DOI: 10.1371/journal.pcbi.1008243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/09/2020] [Accepted: 08/13/2020] [Indexed: 01/02/2023] Open
Abstract
Understanding evolution requires detailed knowledge of genotype-phenotype maps; however, it can be a herculean task to measure every phenotype in a combinatorial map. We have developed a computational strategy to predict the missing phenotypes from an incomplete, combinatorial genotype-phenotype map. As a test case, we used an incomplete genotype-phenotype dataset previously generated for the malaria parasite’s ‘chloroquine resistance transporter’ (PfCRT). Wild-type PfCRT (PfCRT3D7) lacks significant chloroquine (CQ) transport activity, but the introduction of the eight mutations present in the ‘Dd2’ isoform of PfCRT (PfCRTDd2) enables the protein to transport CQ away from its site of antimalarial action. This gain of a transport function imparts CQ resistance to the parasite. A combinatorial map between PfCRT3D7 and PfCRTDd2 consists of 256 genotypes, of which only 52 have had their CQ transport activities measured through expression in the Xenopus laevis oocyte. We trained a statistical model with these 52 measurements to infer the CQ transport activity for the remaining 204 combinatorial genotypes between PfCRT3D7 and PfCRTDd2. Our best-performing model incorporated a binary classifier, a nonlinear scale, and additive effects for each mutation. The addition of specific pairwise- and high-order-epistatic coefficients decreased the predictive power of the model. We evaluated our predictions by experimentally measuring the CQ transport activities of 24 additional PfCRT genotypes. The R2 value between our predicted and newly-measured phenotypes was 0.90. We then used the model to probe the accessibility of evolutionary trajectories through the map. Approximately 1% of the possible trajectories between PfCRT3D7 and PfCRTDd2 are accessible; however, none of the trajectories entailed eight successive increases in CQ transport activity. These results demonstrate that phenotypes can be inferred with known uncertainty from a partial genotype-phenotype dataset. We also validated our approach against a collection of previously published genotype-phenotype maps. The model therefore appears general and should be applicable to a large number of genotype-phenotype maps. Biological macromolecules are built from chains of building blocks. The function of a macromolecule depends on the specific chemical properties of the building blocks that make it up. Macromolecules evolve through mutations that swap one building block for another. Understanding how biomolecules work and evolve therefore requires knowledge of the effects of mutations. The effects of mutations can be measured experimentally; however, because there are a vast number of possible combinations of mutations, it is often difficult to make enough measurements to understand biomolecular function and evolution. In this paper, we describe a simple method to predict the effects of mutations on biomolecules from a small number of measurements. This method works by appropriately averaging the effects of mutations seen in different contexts. We test the method by predicting the effects of mutations on a PfCRT—a macromolecule from the malarial parasite that confers drug resistance. We find that our method is fast and effective. Using a small number of measurements, we were able to gain insight into the evolutionary steps by which this macromolecule conferred drug resistance. To make this method accessible to other researchers, we have released it as an open-source software package: https://gpseer.readthedocs.io.
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Affiliation(s)
- Zachary R. Sailer
- Institute for Molecular Biology, University of Oregon, Eugene, OR, United States of America
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, United States of America
| | - Sarah H. Shafik
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Robert L. Summers
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Alex Joule
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Rowena E. Martin
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- * E-mail: (REM); (MJH)
| | - Michael J. Harms
- Institute for Molecular Biology, University of Oregon, Eugene, OR, United States of America
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, United States of America
- * E-mail: (REM); (MJH)
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Becker HM, Deitmer JW. Transport Metabolons and Acid/Base Balance in Tumor Cells. Cancers (Basel) 2020; 12:cancers12040899. [PMID: 32272695 PMCID: PMC7226098 DOI: 10.3390/cancers12040899] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Solid tumors are metabolically highly active tissues, which produce large amounts of acid. The acid/base balance in tumor cells is regulated by the concerted interplay between a variety of membrane transporters and carbonic anhydrases (CAs), which cooperate to produce an alkaline intracellular, and an acidic extracellular, environment, in which cancer cells can outcompete their adjacent host cells. Many acid/base transporters form a structural and functional complex with CAs, coined "transport metabolon". Transport metabolons with bicarbonate transporters require the binding of CA to the transporter and CA enzymatic activity. In cancer cells, these bicarbonate transport metabolons have been attributed a role in pH regulation and cell migration. Another type of transport metabolon is formed between CAs and monocarboxylate transporters, which mediate proton-coupled lactate transport across the cell membrane. In this complex, CAs function as "proton antenna" for the transporter, which mediate the rapid exchange of protons between the transporter and the surroundings. These transport metabolons do not require CA catalytic activity, and support the rapid efflux of lactate and protons from hypoxic cancer cells to allow sustained glycolytic activity and cell proliferation. Due to their prominent role in tumor acid/base regulation and metabolism, transport metabolons might be promising drug targets for new approaches in cancer therapy.
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Affiliation(s)
- Holger M. Becker
- Institute of Physiological Chemistry, University of Veterinary Medicine Hannover, D-30559 Hannover, Germany
- Correspondence:
| | - Joachim W. Deitmer
- Department of Biology, University of Kaiserslautern, D-67653 Kaiserslautern, Germany;
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Richards SN, Nash MN, Baker ES, Webster MW, Lehane AM, Shafik SH, Martin RE. Molecular Mechanisms for Drug Hypersensitivity Induced by the Malaria Parasite's Chloroquine Resistance Transporter. PLoS Pathog 2016; 12:e1005725. [PMID: 27441371 PMCID: PMC4956231 DOI: 10.1371/journal.ppat.1005725] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/03/2016] [Indexed: 01/23/2023] Open
Abstract
Mutations in the Plasmodium falciparum ‘chloroquine resistance transporter’ (PfCRT) confer resistance to chloroquine (CQ) and related antimalarials by enabling the protein to transport these drugs away from their targets within the parasite’s digestive vacuole (DV). However, CQ resistance-conferring isoforms of PfCRT (PfCRTCQR) also render the parasite hypersensitive to a subset of structurally-diverse pharmacons. Moreover, mutations in PfCRTCQR that suppress the parasite’s hypersensitivity to these molecules simultaneously reinstate its sensitivity to CQ and related drugs. We sought to understand these phenomena by characterizing the functions of PfCRTCQR isoforms that cause the parasite to become hypersensitive to the antimalarial quinine or the antiviral amantadine. We achieved this by measuring the abilities of these proteins to transport CQ, quinine, and amantadine when expressed in Xenopus oocytes and complemented this work with assays that detect the drug transport activity of PfCRT in its native environment within the parasite. Here we describe two mechanistic explanations for PfCRT-induced drug hypersensitivity. First, we show that quinine, which normally accumulates inside the DV and therewithin exerts its antimalarial effect, binds extremely tightly to the substrate-binding site of certain isoforms of PfCRTCQR. By doing so it likely blocks the normal physiological function of the protein, which is essential for the parasite’s survival, and the drug thereby gains an additional killing effect. In the second scenario, we show that although amantadine also sequesters within the DV, the parasite’s hypersensitivity to this drug arises from the PfCRTCQR-mediated transport of amantadine from the DV into the cytosol, where it can better access its antimalarial target. In both cases, the mutations that suppress hypersensitivity also abrogate the ability of PfCRTCQR to transport CQ, thus explaining why rescue from hypersensitivity restores the parasite’s sensitivity to this antimalarial. These insights provide a foundation for understanding clinically-relevant observations of inverse drug susceptibilities in the malaria parasite. In acquiring resistance to one drug, many pathogens and cancer cells become hypersensitive to other drugs. This phenomenon could be exploited to combat existing drug resistance and to delay the emergence of resistance to new drugs. However, much remains to be understood about the mechanisms that underlie drug hypersensitivity in otherwise drug-resistant microbes. Here, we describe two mechanisms by which the Plasmodium falciparum ‘chloroquine resistance transporter’ (PfCRT) causes the malaria parasite to become hypersensitive to structurally-diverse drugs. First, we show that an antimalarial drug that normally exerts its killing effect within the parasite’s digestive vacuole is also able to bind extremely tightly to certain forms of PfCRT. This activity will block the natural, essential function of the protein and thereby provide the drug with an additional killing effect. The second mechanism arises when a cytosolic-acting drug that normally sequesters within the digestive vacuole is leaked back into the cytosol via PfCRT. In both cases, mutations that suppress hypersensitivity also abrogate the ability of PfCRT to transport chloroquine, thus explaining why rescue from hypersensitivity restores the parasite’s sensitivity to this antimalarial. These insights provide a foundation for understanding and exploiting the hypersensitivity of chloroquine-resistant parasites to several of the current antimalarials.
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Affiliation(s)
- Sashika N. Richards
- Research School of Biology, Australian National University, Canberra, Australia
| | - Megan N. Nash
- Research School of Biology, Australian National University, Canberra, Australia
| | - Eileen S. Baker
- Research School of Biology, Australian National University, Canberra, Australia
| | - Michael W. Webster
- Research School of Biology, Australian National University, Canberra, Australia
| | - Adele M. Lehane
- Research School of Biology, Australian National University, Canberra, Australia
| | - Sarah H. Shafik
- Research School of Biology, Australian National University, Canberra, Australia
| | - Rowena E. Martin
- Research School of Biology, Australian National University, Canberra, Australia
- * E-mail:
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Marchetti RV, Lehane AM, Shafik SH, Winterberg M, Martin RE, Kirk K. A lactate and formate transporter in the intraerythrocytic malaria parasite, Plasmodium falciparum. Nat Commun 2015; 6:6721. [PMID: 25823844 DOI: 10.1038/ncomms7721] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/23/2015] [Indexed: 12/24/2022] Open
Abstract
The intraerythrocytic malaria parasite relies primarily on glycolysis to fuel its rapid growth and reproduction. The major byproduct of this metabolism, lactic acid, is extruded into the external medium. In this study, we show that the human malaria parasite Plasmodium falciparum expresses at its surface a member of the microbial formate-nitrite transporter family (PfFNT), which, when expressed in Xenopus laevis oocytes, transports both formate and lactate. The transport characteristics of PfFNT in oocytes (pH-dependence, inhibitor-sensitivity and kinetics) are similar to those of the transport of lactate and formate across the plasma membrane of mature asexual-stage P. falciparum trophozoites, consistent with PfFNT playing a major role in the efflux of lactate and hence in the energy metabolism of the intraerythrocytic parasite.
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Abstract
Carbonic anhydrases (CAs) have not only been identified as ubiquitous enzymes catalyzing the fast reversible hydration of carbon dioxide to generate or consume protons and bicarbonate, but also as intra- and extracellular proteins, which facilitate transport function of many acid/base transporting membrane proteins, coined 'transport metabolon'. Functional interaction between CAs and acid/base transporters, such as chloride/bicarbonate exchanger (AE), sodium-bicarbonate cotransporter (NBC) and sodium/hydrogen exchanger (NHE) has been shown to require both catalytic CA activity as well as direct binding of the enzyme to specific sites on the transporter. In contrast, functional interaction between different CA isoforms and lactate-proton-cotransporting monocarboxylate transporters (MCT) has been found to be isoform-specific and independent of CA catalytic activity, but seems to require an intramolecular proton shuttle within the enzyme. In this chapter, we review the various types of interactions between acid/base-coupled membrane carriers and different CA isoforms, as studied in vitro, in intact Xenopus oocytes, and in various mammalian cell types. Furthermore, we discuss recent findings that indicate the significance of these 'transport metabolons' for normal cell functions.
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Becker HM. Transport of Lactate: Characterization of the Transporters Involved in Transport at the Plasma Membrane by Heterologous Protein Expression in Xenopus Oocytes. Brain Energy Metabolism 2014. [DOI: 10.1007/978-1-4939-1059-5_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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Schueler C, Becker HM, McKenna R, Deitmer JW. Transport activity of the sodium bicarbonate cotransporter NBCe1 is enhanced by different isoforms of carbonic anhydrase. PLoS One 2011; 6:e27167. [PMID: 22076132 PMCID: PMC3208603 DOI: 10.1371/journal.pone.0027167] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 10/11/2011] [Indexed: 12/31/2022] Open
Abstract
Transport metabolons have been discussed between carbonic anhydrase II (CAII) and several membrane transporters. We have now studied different CA isoforms, expressed in Xenopus oocytes alone and together with the electrogenic sodium bicarbonate cotransporter 1 (NBCe1), to determine their catalytic activity and their ability to enhance NBCe1 transport activity. pH measurements in intact oocytes indicated similar activity of CAI, CAII and CAIII, while in vitro CAIII had no measurable activity and CAI only 30% of the activity of CAII. All three CA isoforms increased transport activity of NBCe1, as measured by the transport current and the rate of intracellular sodium rise in oocytes. Two CAII mutants, altered in their intramolecular proton pathway, CAII-H64A and CAII-Y7F, showed significant catalytic activity and also enhanced NBCe1 transport activity. The effect of CAI, CAII, and CAII mutants on NBCe1 activity could be reversed by blocking CA activity with ethoxyzolamide (EZA, 10 µM), while the effect of the less EZA-sensitive CAIII was not reversed. Our results indicate that different CA isoforms and mutants, even if they show little enzymatic activity in vitro, may display significant catalytic activity in intact cells, and that the ability of CA to enhance NBCe1 transport appears to depend primarily on its catalytic activity.
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Affiliation(s)
- Christina Schueler
- Abteilung für Allgemeine Zoologie, FB Biologie, TU Kaiserslautern, Kaiserslautern, Germany.
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Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 555] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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Weise A, Becker HM, Deitmer JW. Enzymatic Suppression of the Membrane Conductance Associated with the Glutamine Transporter SNAT3 Expressed in XenopusOocytes by Carbonic Anhydrase II. J Biophys Biochem Cytol 2007. [DOI: 10.1083/jcb1784oia7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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