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Kavanaugh LG, Dey D, Shafer WM, Conn GL. Structural and functional diversity of Resistance-Nodulation-Division (RND) efflux pump transporters with implications for antimicrobial resistance. Microbiol Mol Biol Rev 2024; 88:e0008923. [PMID: 39235227 PMCID: PMC11426026 DOI: 10.1128/mmbr.00089-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024] Open
Abstract
SUMMARYThe discovery of bacterial efflux pumps significantly advanced our understanding of how bacteria can resist cytotoxic compounds that they encounter. Within the structurally and functionally distinct families of efflux pumps, those of the Resistance-Nodulation-Division (RND) superfamily are noteworthy for their ability to reduce the intracellular concentration of structurally diverse antimicrobials. RND systems are possessed by many Gram-negative bacteria, including those causing serious human disease, and frequently contribute to resistance to multiple antibiotics. Herein, we review the current literature on the structure-function relationships of representative transporter proteins of tripartite RND efflux pumps of clinically important pathogens. We emphasize their contribution to bacterial resistance to clinically used antibiotics, host defense antimicrobials and other biocides, as well as highlighting structural similarities and differences among efflux transporters that help bacteria survive in the face of antimicrobials. Furthermore, we discuss technical advances that have facilitated and advanced efflux pump research and suggest future areas of investigation that will advance antimicrobial development efforts.
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Affiliation(s)
- Logan G Kavanaugh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Graduate Program in Microbiology and Molecular Genetics, Emory University, Atlanta, Georgia, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William M Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratories of Microbial Pathogenesis, VA Medical Research Service, Veterans Affairs Medical Center, Decatur, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
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2
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Wall RJ, MacGowan SA, Hallyburton I, Syed AJ, Ajay Castro S, Dey G, Milne R, Patterson S, Phelan J, Wiedemar N, Wyllie S. ResMAP-a saturation mutagenesis platform enabling parallel profiling of target-specific resistance-conferring mutations in Plasmodium. mBio 2024:e0170824. [PMID: 39191404 DOI: 10.1128/mbio.01708-24] [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: 06/04/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
New and improved drugs are required for the treatment and ultimate eradication of malaria. The efficacy of front-line therapies is now threatened by emerging drug resistance; thus, new tools to support the development of drugs with a lower propensity for resistance are needed. Here, we describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in Plasmodium drug targets. Proof-of-concept studies focused on interrogating the antimalarial drug target, Plasmodium falciparum lysyl tRNA synthetase (PfKRS). Saturation mutagenesis was used to construct a plasmid library encoding all conceivable mutations within a 20-residue span at the base of the PfKRS ATP-binding pocket. The superior transfection efficiency of Plasmodium knowlesi was exploited to generate a high coverage parasite library expressing PfKRS bearing all possible amino acid changes within this region of the enzyme. The selection of the library with PfKRS inhibitors, cladosporin and DDD01510706, successfully identified multiple resistance-conferring substitutions. Genetic validation of a subset of these mutations confirmed their direct role in resistance, with computational modeling used to dissect the structural basis of resistance. The application of ResMAP to inform the development of resistance-resilient antimalarials of the future is discussed. IMPORTANCE An increase in treatment failures for malaria highlights an urgent need for new tools to understand and minimize the spread of drug resistance. We describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in Plasmodium spp, the causative agent of malaria. Saturation mutagenesis was used to generate a mutation library containing all conceivable mutations for a region of the antimalarial-binding site of a promising drug target, Plasmodium falciparum lysyl tRNA synthetase (PfKRS). Screening of this high-coverage library with characterized PfKRS inhibitors revealed multiple resistance-conferring substitutions including several clinically relevant mutations. Genetic validation of these mutations confirmed resistance of up to 100-fold and computational modeling dissected their role in drug resistance. We discuss potential applications of this data including the potential to design compounds that can bypass the most serious resistance mutations and future resistance surveillance.
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Affiliation(s)
- Richard J Wall
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Stuart A MacGowan
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Irene Hallyburton
- Drug Discovery Unit, Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Aisha J Syed
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Gourav Dey
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Rachel Milne
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Stephen Patterson
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Natalie Wiedemar
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Center for Anti-infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
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3
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Jiang Z, van Vlimmeren AE, Karandur D, Semmelman A, Shah NH. Revealing the principles of inter- and intra-domain regulation in a signaling enzyme via scanning mutagenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593907. [PMID: 39091798 PMCID: PMC11291063 DOI: 10.1101/2024.05.13.593907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Multi-domain enzymes can be regulated by both inter-domain interactions and structural features intrinsic to the catalytic domain. The tyrosine phosphatase SHP2 is a quintessential example of a multi-domain protein that is regulated by inter-domain interactions. This enzyme has a protein tyrosine phosphatase (PTP) domain and two phosphotyrosine-recognition domains (N-SH2 and C-SH2) that regulate phosphatase activity through autoinhibitory interactions. SHP2 is canonically activated by phosphoprotein binding to the SH2 domains, which causes large inter-domain rearrangements, but autoinhibition can also be disrupted by disease-associated mutations. Many details of the SHP2 activation mechanism are still unclear, the physiologically-relevant active conformations remain elusive, and hundreds of human variants of SHP2 have not been functionally characterized. Here, we perform deep mutational scanning on both full-length SHP2 and its isolated PTP domain to examine mutational effects on inter-domain regulation and catalytic activity. Our experiments provide a comprehensive map of SHP2 mutational sensitivity, both in the presence and absence of inter-domain regulation. Coupled with molecular dynamics simulations, our investigation reveals novel structural features that govern the stability of the autoinhibited and active states of SHP2. Our analysis also identifies key residues beyond the SHP2 active site that control PTP domain dynamics and intrinsic catalytic activity. This work expands our understanding of SHP2 regulation and provides new insights into SHP2 pathogenicity.
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4
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Gao J, Ververi A, Thompson E, Tryon R, Sotiriadis A, Rouvalis F, Grange DK, Giannios C, Nichols CG. A novel ABCC9 variant in a Greek family with Cantu syndrome affecting multiple generations highlights the functional role of the SUR2B NBD1. Am J Med Genet A 2024:e63815. [PMID: 39031464 DOI: 10.1002/ajmg.a.63815] [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: 06/04/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/22/2024]
Abstract
Cantu syndrome (CS) (OMIM #239850) is an autosomal dominant multiorgan system condition, associated with a characteristic facial phenotype, hypertrichosis, and multiple cardiovascular complications. CS is caused by gain-of-function (GOF) variants in KCNJ8 or ABCC9 that encode pore-forming Kir6.1 and regulatory SUR2 subunits of ATP-sensitive potassium (KATP) channels. A novel heterozygous ABCC9 variant, c.2440G>T; p.Gly814Trp, was identified in three individuals from a four generation Greek family. The membrane potential in cells stably expressing hKir6.1 and hSUR2B with p.Gly814Trp was hyperpolarized compared to cells expressing WT channels, and inside-out patch-clamp assays of KATP channels formed with hSUR2B p.Gly814Trp demonstrated a decreased sensitivity to ATP inhibition, confirming a relatively mild GOF effect of this variant. The specific location of the variant reveals an unrecognized functional role of the first glycine in the signature motif of the nucleotide binding domains in ATP-binding cassette (ABC) protein ion channels.
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Affiliation(s)
- Jian Gao
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Athina Ververi
- Department for Genetics of Rare Diseases, Papageorgiou General Hospital, Thessaloniki, Greece
| | - Ellen Thompson
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Rob Tryon
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alexandros Sotiriadis
- Second Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Ippokrateio Hospital, Thessaloniki, Greece
| | | | - Dorothy K Grange
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Christos Giannios
- Department of Developmental Paediatrics, Naval Hospital of Athens, Athens, Greece
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St. Louis, St. Louis, Missouri, USA
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5
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Karapanagioti F, Atlason ÚÁ, Slotboom DJ, Poolman B, Obermaier S. Fitness landscape of substrate-adaptive mutations in evolved amino acid-polyamine-organocation transporters. eLife 2024; 13:RP93971. [PMID: 38916596 PMCID: PMC11198987 DOI: 10.7554/elife.93971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024] Open
Abstract
The emergence of new protein functions is crucial for the evolution of organisms. This process has been extensively researched for soluble enzymes, but it is largely unexplored for membrane transporters, even though the ability to acquire new nutrients from a changing environment requires evolvability of transport functions. Here, we demonstrate the importance of environmental pressure in obtaining a new activity or altering a promiscuous activity in members of the amino acid-polyamine-organocation (APC)-type yeast amino acid transporters family. We identify APC members that have broader substrate spectra than previously described. Using in vivo experimental evolution, we evolve two of these transporter genes, AGP1 and PUT4, toward new substrate specificities. Single mutations on these transporters are found to be sufficient for expanding the substrate range of the proteins, while retaining the capacity to transport all original substrates. Nonetheless, each adaptive mutation comes with a distinct effect on the fitness for each of the original substrates, illustrating a trade-off between the ancestral and evolved functions. Collectively, our findings reveal how substrate-adaptive mutations in membrane transporters contribute to fitness and provide insights into how organisms can use transporter evolution to explore new ecological niches.
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Affiliation(s)
| | | | - Dirk J Slotboom
- Department of Biochemistry, University of GroningenGroningenNetherlands
| | - Bert Poolman
- Department of Biochemistry, University of GroningenGroningenNetherlands
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6
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Burata OE, O'Donnell E, Hyun J, Lucero RM, Thomas JE, Gibbs EM, Reacher I, Carney NA, Stockbridge RB. Peripheral positions encode transport specificity in the small multidrug resistance exporters. Proc Natl Acad Sci U S A 2024; 121:e2403273121. [PMID: 38865266 PMCID: PMC11194549 DOI: 10.1073/pnas.2403273121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/02/2024] [Indexed: 06/14/2024] Open
Abstract
In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ever O'Donnell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Jeonghoon Hyun
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Rachael M Lucero
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Junius E Thomas
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ethan M Gibbs
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Isabella Reacher
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Nolan A Carney
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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7
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Nazarov PA, Maximov VS, Firsov AM, Karakozova MV, Panfilova V, Kotova EA, Skulachev MV, Antonenko YN. Rhodamine 19 Alkyl Esters as Effective Antibacterial Agents. Int J Mol Sci 2024; 25:6137. [PMID: 38892325 PMCID: PMC11173286 DOI: 10.3390/ijms25116137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Mitochondria-targeted antioxidants (MTAs) have been studied quite intensively in recent years as potential therapeutic agents and vectors for the delivery of other active substances to mitochondria and bacteria. Their most studied representatives are MitoQ and SkQ1, with its fluorescent rhodamine analog SkQR1, a decyl ester of rhodamine 19 carrying plastoquinone. In the present work, we observed a pronounced antibacterial action of SkQR1 against Gram-positive bacteria, but virtually no effect on Gram-negative bacteria. The MDR pump AcrAB-TolC, known to expel SkQ1, did not recognize and did not pump out SkQR1 and dodecyl ester of rhodamine 19 (C12R1). Rhodamine 19 butyl (C4R1) and ethyl (C2R1) esters more effectively suppressed the growth of ΔtolC Escherichia coli, but lost their potency with the wild-type E. coli pumping them out. The mechanism of the antibacterial action of SkQR1 may differ from that of SkQ1. The rhodamine derivatives also proved to be effective antibacterial agents against various Gram-positive species, including Staphylococcus aureus and Mycobacterium smegmatis. By using fluorescence correlation spectroscopy and fluorescence microscopy, SkQR1 was shown to accumulate in the bacterial membrane. Thus, the presentation of SkQR1 as a fluorescent analogue of SkQ1 and its use for visualization should be performed with caution.
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Affiliation(s)
- Pavel A. Nazarov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
| | - Vladislav S. Maximov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexander M. Firsov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
| | - Marina V. Karakozova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
| | - Veronika Panfilova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
| | - Elena A. Kotova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
| | - Maxim V. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
- Mitotech LLC, 119991 Moscow, Russia
| | - Yuri N. Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (M.V.K.)
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8
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Nijland M, Lefebvre SN, Thangaratnarajah C, Slotboom DJ. Bidirectional ATP-driven transport of cobalamin by the mycobacterial ABC transporter BacA. Nat Commun 2024; 15:2626. [PMID: 38521790 PMCID: PMC10960864 DOI: 10.1038/s41467-024-46917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
BacA is a mycobacterial ATP-binding cassette (ABC) transporter involved in the translocation of water-soluble compounds across the lipid bilayer. Whole-cell-based assays have shown that BacA imports cobalamin as well as unrelated hydrophilic compounds such as the antibiotic bleomycin and the antimicrobial peptide Bac7 into the cytoplasm. Surprisingly, there are indications that BacA also mediates the export of different antibacterial compounds, which is difficult to reconcile with the notion that ABC transporters generally operate in a strictly unidirectional manner. Here we resolve this conundrum by developing a fluorescence-based transport assay to monitor the transport of cobalamin across liposomal membranes. We find that BacA transports cobalamin in both the import and export direction. This highly unusual bidirectionality suggests that BacA is mechanistically distinct from other ABC transporters and facilitates ATP-driven diffusion, a function that may be important for the evolvability of specific transporters, and may bring competitive advantages to microbial communities.
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Affiliation(s)
- Mark Nijland
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Solène N Lefebvre
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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9
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Zhang X, Zhang M, Cui H, Zhang T, Wu L, Xu C, Yin C, Gao J. Autophagy-modulating biomembrane nanostructures: A robust anticancer weapon by modulating the inner and outer cancer environment. J Control Release 2024; 366:85-103. [PMID: 38142964 DOI: 10.1016/j.jconrel.2023.12.032] [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: 08/21/2023] [Revised: 11/09/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Recently, biomembrane nanostructures, such as liposomes, cell membrane-coated nanostructures, and exosomes, have demonstrated promising anticancer therapeutic effects. These nanostructures possess remarkable biocompatibility, multifunctionality, and low toxicity. However, their therapeutic efficacy is impeded by chemoresistance and radiotherapy resistance, which are closely associated with autophagy. Modulating autophagy could enhance the therapeutic sensitivity and effectiveness of these biomembrane nanostructures by influencing the immune system and the cancer microenvironment. For instance, autophagy can regulate the immunogenic cell death of cancer cells, antigen presentation of dendritic cells, and macrophage polarization, thereby activating the inflammatory response in the cancer microenvironment. Furthermore, combining autophagy-regulating drugs or genes with biomembrane nanostructures can exploit the targeting and long-term circulation properties of these nanostructures, leading to increased drug accumulation in cancer cells. This review explores the role of autophagy in carcinogenesis, cancer progression, metastasis, cancer immune responses, and resistance to treatment. Additionally, it highlights recent research advancements in the synergistic anticancer effects achieved through autophagy regulation by biomembrane nanostructures. The review also discusses the prospects and challenges associated with the future clinical translation of these innovative treatment strategies. In summary, these findings provide valuable insights into autophagy, autophagy-modulating biomembrane-based nanostructures, and the underlying molecular mechanisms, thereby facilitating the development of promising cancer therapeutics.
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Affiliation(s)
- Xinyi Zhang
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China; Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Mengya Zhang
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Hengqing Cui
- Department of Burns and Plastic Surgery, Shanghai Changzheng Hospital, Shanghai 200003, China; Tongji Hospital,School of Medicine, Tongji University, Shanghai 200092, China
| | - Tinglin Zhang
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Lili Wu
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Can Xu
- Department of Gastroenterology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China.
| | - Chuan Yin
- Department of Gastroenterology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China.
| | - Jie Gao
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China.
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10
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Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. J Am Chem Soc 2024; 146:2757-2768. [PMID: 38231868 PMCID: PMC10843641 DOI: 10.1021/jacs.3c12494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Modulating allosteric coupling offers unique opportunities for biomedical applications. Such efforts can benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of cooperativity between distant sites. We demonstrate that effects of allostery hotspot mutations can be evaluated qualitatively and semiquantitatively by molecular dynamics simulations in a bacterial tetracycline repressor (TetR). The simulations recapitulate the effects of these mutations on abolishing the induction function of TetR and provide a rationale for the different rescuabilities observed to restore allosteric coupling of the hotspot mutations. We demonstrate that the same noninducible phenotype could be the result of perturbations in distinct structural and energetic properties of TetR. Our work underscores the value of explicitly computing the functional free energy landscapes to effectively evaluate and rank hotspot mutations despite the prevalence of compensatory interactions and therefore provides quantitative guidance to allostery modulation for therapeutic and engineering applications.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuchen Yuan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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11
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Di Cesare M, Kaplan E, Rendon J, Gerbaud G, Valimehr S, Gobet A, Ngo TAT, Chaptal V, Falson P, Martinho M, Dorlet P, Hanssen E, Jault JM, Orelle C. The transport activity of the multidrug ABC transporter BmrA does not require a wide separation of the nucleotide-binding domains. J Biol Chem 2024; 300:105546. [PMID: 38072053 PMCID: PMC10821409 DOI: 10.1016/j.jbc.2023.105546] [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: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and pathogenic microorganisms, respectively. Despite a wealth of structural data gained in the last two decades, the molecular mechanism of these multidrug efflux pumps remains elusive, including the extent of separation between the two nucleotide-binding domains (NBDs) during the transport cycle. Based on recent outward-facing structures of BmrA, a homodimeric multidrug ABC transporter from Bacillus subtilis, we introduced a cysteine mutation near the C-terminal end of the NBDs to analyze the impact of disulfide-bond formation on BmrA function. Interestingly, the presence of the disulfide bond between the NBDs did not prevent the ATPase, nor did it affect the transport of Hoechst 33342 and doxorubicin. Yet, the 7-amino-actinomycin D was less efficiently transported, suggesting that a further opening of the transporter might improve its ability to translocate this larger compound. We solved by cryo-EM the apo structures of the cross-linked mutant and the WT protein. Both structures are highly similar, showing an intermediate opening between their NBDs while their C-terminal extremities remain in close proximity. Distance measurements obtained by electron paramagnetic resonance spectroscopy support the intermediate opening found in these 3D structures. Overall, our data suggest that the NBDs of BmrA function with a tweezers-like mechanism distinct from the related lipid A exporter MsbA.
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Affiliation(s)
- Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Elise Kaplan
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Julia Rendon
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | | | - Sepideh Valimehr
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Thu-Anh Thi Ngo
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | | | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
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Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555381. [PMID: 37905112 PMCID: PMC10614727 DOI: 10.1101/2023.08.29.555381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Modulating allosteric coupling offers unique opportunities for biomedical applications. Such efforts can benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of co-operativity between distant sites. We demonstrate that effects of allostery hotspot mutations can be evaluated qualitatively and semi-quantitatively by molecular dynamics simulations in a bacterial tetracycline repressor (TetR). The simulations recapitulate the effects of these mutations on abolishing the induction function of TetR and provide a rationale for the different degrees of rescuability observed to restore allosteric coupling of the hotspot mutations. We demonstrate that the same non-inducible phenotype could be the result of perturbations in distinct structural and energetic properties of TetR. Our work underscore the value of explicitly computing the functional free energy landscapes to effectively evaluate and rank hotspot mutations despite the prevalence of compensatory interactions, and therefore provide quantitative guidance to allostery modulation for therapeutic and engineering applications.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuchen Yuan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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13
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Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS. ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570727. [PMID: 38106144 PMCID: PMC10723403 DOI: 10.1101/2023.12.07.570727] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.
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Affiliation(s)
| | | | | | | | | | | | | | - Ada Shaw
- Applied Mathematics, Harvard University
| | | | | | - Mafalda Dias
- Centre for Genomic Regulation, Universitat Pompeu Fabra
| | | | | | - Yarin Gal
- Computer Science, University of Oxford
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14
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Schramm T, Lubrano P, Pahl V, Stadelmann A, Verhülsdonk A, Link H. Mapping temperature-sensitive mutations at a genome scale to engineer growth switches in Escherichia coli. Mol Syst Biol 2023; 19:e11596. [PMID: 37642940 PMCID: PMC10568205 DOI: 10.15252/msb.202311596] [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: 02/14/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Temperature-sensitive (TS) mutants are a unique tool to perturb and engineer cellular systems. Here, we constructed a CRISPR library with 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. 1,269 of these mutants showed temperature-sensitive growth in a time-resolved competition assay. We reconstructed 94 TS mutants and measured their metabolism under growth arrest at 42°C using metabolomics. Metabolome changes were strong and mutant-specific, showing that metabolism of nongrowing E. coli is perturbation-dependent. For example, 24 TS mutants of metabolic enzymes overproduced the direct substrate metabolite due to a bottleneck in their associated pathway. A strain with TS homoserine kinase (ThrBF267D ) produced homoserine for 24 h, and production was tunable by temperature. Finally, we used a TS subunit of DNA polymerase III (DnaXL289Q ) to decouple growth from arginine overproduction in engineered E. coli. These results provide a strategy to identify TS mutants en masse and demonstrate their large potential to produce bacterial metabolites with nongrowing cells.
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Affiliation(s)
- Thorben Schramm
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
- Present address:
Department of Biology, Institute of Molecular Systems BiologyETH ZurichZürichSwitzerland
| | - Paul Lubrano
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Vanessa Pahl
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Amelie Stadelmann
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Andreas Verhülsdonk
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
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15
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