MP
Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and respiration in mycobacteria
Justin M. Di Trani, Jiacheng Yu, Gautier M. Courbon, Ana Paula Lobez Rodriguez, Chen-Yi Cheung, Yingke Liang, Claire E. Coupland, Stephanie A. Bueler, Gregory M. Cook, Peter Brzezinski, John L. Rubinstein
bioRxiv 2024.10.09.617439;
doi: https://doi.org/10.1101/2024.10.09.617439
Cryo-EM of Mycobacterium smegmatis inverted membrane vesicles => Krebs cycle enzyme (malate-quinone oxidoreductase) associates directly with respiratory supercomplex (Complex III / IV).
This interaction facilitates rapid electron transfer from malate to the electron transport chain, enabling malate-driven respiration and linking the Krebs cycle with a specific branch of the respiratory chain.
And a membrane to rule them all !
Structure and function of Mycobacterium tuberculosis EfpA as a lipid transporter and its inhibition by BRD-8000.3.
Li D, Zhang X, Yao Y, Sun X, Sun J, Ma X, Yuan K, Bai G, Pang X, Hua R, Guo T, Mi Y, Wu L, Zhang J, Wu Y, Liu Y, Wang P, Wong CCL, Chen XW, Xiao H, Gao GF, Gao F.
Proc Natl Acad Sci U S A. 2024 Oct 29;121(44):e2412653121.
doi: 10.1073/pnas.2412653121. Epub 2024 Oct 23.
PMID: 39441632.
EfpA = first MFS identified in Mycobacterium tuberculosis: implicated in resistance to multiple drugs. The biological function of EfpA has not yet been elucidated.
Here: cryo-EM structures of EfpA complexed with lipids or inhibitor.
=> EfpA forms an antiparallel dimer and functional studies suggest that EfpA is a lipid transporter.
Structural and biochemical analysis of ligand binding in yeast Niemann-Pick type C1-related protein.
Nel L, Thaysen K, Jamecna D, Olesen E, Szomek M, Langer J, Frain KM, Höglinger D, Wüstner D, Pedersen BP.
Life Sci Alliance. 2024 Oct 25;8(1):e202402990.
doi: 10.26508/lsa.202402990.
PMID: 39455279.
In eukaryotes, the NPC system (= NCR1, MP, and NPC2, soluble portein) is essential for incorporating sterols into the vacuolar/lysosomal membrane.
Here: study shows that NCR1’s NTD binds both ergosterol and cholesterol and can also interact with other lipids (including phospholipids, sphingosine, and ceramide).
=> suggests that the yeast NPC system facilitates vacuolar homeostasis for a wide range of lipid types, beyond just sterols.
Fluorescent non-canonical amino acid provides insight into the human serotonin transporter.
Nygaard A, Zachariassen LG, Larsen KS, Kristensen AS, Loland CJ.
Nat Commun. 2024 Oct 27;15(1):9267.
doi: 10.1038/s41467-024-53584-9.
PMID: 39463388.
The serotonin transporter (SERT) which enables serotonin reuptake, is a key target for antidepressants.
Here: use of a fluorescent amino acid (Anap) to track conformational dynamics in SERT, revealing how ions, substrates, and inhibitors competitively bind and affect its structure.
Plant membrane transporters function under abiotic stresses: a review.
Mishra G, Mohapatra SK, Rout GR.
Planta. 2024 Oct 24;260(6):125.
doi: 10.1007/s00425-024-04548-2.
PMID: 39448443.
Review exploring how membrane transporters contribute to plant resilience against abiotic stresses, with potential applications in breeding climate-resilient crops.
The Bor1 elevator transport cycle is subject to autoinhibition and activation.
Jiang Y, Jiang J.
Nat Commun. 2024 Oct 22;15(1):9090.
doi: 10.1038/s41467-024-53411-1.
PMID: 39433547.
Boron, though essential for plant growth, requires precise control to avoid toxicity, managed by borate transporters like AtBor1 in Arabidopsis thaliana.
Here: structural and functional analyses => AtBor1 operates through two regulatory mechanisms: an autoinhibitory domain blocking the transport pathway and phosphorylation of Thr410, which activates borate transport.
Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene
Kookjoo Kim, Huan Li, Qi Yuan, Zephan Melville, Ran Zalk, Amédée des Georges, Joachim Frank, Wayne A. Hendrickson, Andrew R. Marks, Oliver B. Clarke
bioRxiv 2024.10.21.619409;
doi: https://doi.org/10.1101/2024.10.21.619409
Malignant hyperthermia (MH) is a life-threatening pharmacogenetic condition triggered by volatile anesthetics, which activate pathogenic RyR1 mutants.
Dantrolene has long been used to treat MH.
Here: cryo-EM structures of RyR1 bound to dantrolene and to the MH trigger agent.
A Comprehensive Review of Membrane Transporters and MicroRNA Regulation in Alzheimer’s Disease.
Mishra S, Stany B, Das A, Kanagavel D, Vijayan M.
Mol Neurobiol. 2024 Nov;61(11):8739-8758.
doi: 10.1007/s12035-024-04135-2. Epub 2024 Apr 1.
PMID: 38558361.
There is growing interest in how membrane transporters (SLCs) and microRNAs (miRNAs) contribute to Alzheimer’s disease (AD).
Here: review examining SLC transporters critical for brain function, their interaction with miRNAs, and their relevance in AD.
Substrate dependence of transport coupling and phenotype of a small multidrug resistance transporter in Pseudomonas aeruginosa.
Wegrzynowicz AK, Heelan WJ, Demas SP, McLean MS, Peters JM, Henzler-Wildman KA.
J Bacteriol. 2024 Oct 24;206(10):e0015124.
doi: 10.1128/jb.00151-24. Epub 2024 Sep 11.
PMID: 39258918.
Small multidrug resistance (SMR) transporters, while typically defending pathogens against toxins, can paradoxically increase susceptibility to certain compounds through drug-gated proton leak, which disrupts the pmf in bacteria.
Here: studies on EmrE in E. coli and its homolog PAsmr in P. aeruginosa.
=> both can perform antiport and proton uniport, leading to substrate-dependent resistance or susceptibility.
=> novel antibiotic target by depleting bacterial energy without requiring the transporter to be the primary resistance mechanism ?
Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling.
Zhang R, Jagessar KL, Brownd M, Polasa A, Stein RA, Moradi M, Karakas E, Mchaourab HS.
Nat Commun. 2024 Oct 20;15(1):9055.
doi: 10.1038/s41467-024-53420-0.
PMID: 39428489.
Protease-containing ABC transporters (PCATs) couple the energy of ATP hydrolysis to the processing and export of diverse cargo proteins across cell membranes.
Here: cryoEM, DEER in lipid bilayers and computational analysis.
=> competitive interplay between nucleotides and cargo protein binding.
Membrane-Dependent Dynamics and Dual Translocation Mechanisms of ABCB4: Insights from Molecular Dynamics Simulations
Veronica Crespi, Ágota Tóth, Angelika Janaszkiewicz, Thomas Falguières, Florent Di Meo
bioRxiv 2024.10.20.618436;
doi: https://doi.org/10.1101/2024.10.20.618436
ABCB4 = ABC transporter that moves PC into bile, essential for liver function.
MD => membrane composition affects ABCB4’s conformational dynamics (distinct lipid-binding patterns and influence of cholesterol).
=>Results support a canonical ATP-driven transport model + suggests an additional “credit-card swipe” mechanism.
The molecular structure of an axle-less F1-ATPase.
Furlong EJ, Reininger-Chatzigiannakis IP, Zeng YC, Brown SHJ, Sobti M, Stewart AG.
Biochim Biophys Acta Bioenerg. 2024 Oct 18:149521.
doi: 10.1016/j.bbabio.2024.149521. Epub ahead of print.
PMID: 39428050.
Cryo-EM to analyze an ”axle-less” F1-ATPase => ATP hydrolysis and partial rotation still occur but efficiency is reduced because of a lack of coordination provided by the γ subunit.
Membranes
Conformational changes of the ABC Transporter BmrA Depend on Membrane Curvature
Alicia Damm, Su-Jin Paik, Raj Kumar Sadhu, Aurelie Di Cicco, John Manzi, Michele Castellana, Emmanuel Margeat, Maxime Dahan, Pierre Sens, Daniel Levy, and Patricia Bassereau
bioRxiv posted 26 October 2024
doi:10.1101/2024.01.24.577054
Study of the influence of membrane mechanics (particularly curvature), on BmrA transporter function.
=> ATPase activity significantly decreases in liposomes with smaller diameters (from 125 to 29 nm).
=> single-molecule FRET analysis shows that the proportion of closed conformations diminishes in highly curved vesicles, indicating that the functional cycle of conical transporters is sensitive to membrane curvature.
Membrane structure-responsive lipid scrambling by TMEM63B to control plasma membrane lipid distribution.
Miyata Y, Takahashi K, Lee Y, Sultan CS, Kuribayashi R, Takahashi M, Hata K, Bamba T, Izumi Y, Liu K, Uemura T, Nomura N, Iwata S, Nagata S, Nishizawa T, Segawa K.
Nat Struct Mol Biol. 2024 Oct 18.
doi: 10.1038/s41594-024-01411-6. Epub ahead of print.
PMID: 39424995.
TMEM63B = lipid scramblase that responds to changes in membrane curvature and thickness, facilitating bidirectional lipid translocation.
=> scrambling function relies on specific palmitoylated cysteine residues in its intracellular loops.
=> Mutations lead to constitutive scramblase activity that disrupts membrane phospholipid asymmetry.
The Biosynthesis and Applications of Protein Lipidation.
Ding W, Gu J, Xu W, Wu J, Huang Y, Zhang S, Lin S.
Chem Rev. 2024 Oct 23. doi: 10.1021/acs.chemrev.4c00419. Epub ahead of print. PMID: 39441663.
Review outlining the enzymatic pathways for lipidation in mammalian cells: enzymes involved and the resulting chemical linkages + strategies for engineering these pathways to enhance lipidation.
Also, discussion on site-specific lipidation methods (in vitro and in vivo) and explores small molecules that can modulate lipidation processes.
Alanine Scanning to Define Membrane Protein-Lipid Interaction Sites Using Native Mass Spectrometry
Hiruni S. Jayasekera, Farhana Afrin Mohona, Madison J. De Jesus, Katherine M. Miller, Michael T. Marty
bioRxiv 2024.10.24.620105;
doi: https://doi.org/10.1101/2024.10.24.620105
Screen of a wide array of AqpZ mutants, identifying specific lipid binding sites and measuring the selectivity of different lipids.
=> AqpZ selectively interacts with CL at specific sites, with CL positioning its headgroup towards the cytoplasmic side and its acyl chains engaging a hydrophobic pocket.
Programmable Lipid Bilayer Tension-Control Apparatus for Quantitative Mechanobiology.
Matsuki Y, Iwamoto M, Maki T, Takashima M, Yoshida T, Oiki S.
ACS Nano. 2024 Oct 22.
doi: 10.1021/acsnano.4c09017. Epub ahead of print.
PMID: 39437160.
Study introducing a programmable membrane tension-control apparatus using a contact bubble bilayer (CBB) system => allows for real-time monitoring and precise control of bilayer tension through image analysis.
=> validated by investigating the tension-dependent behavior of KcsA and TREK-1.
Optimization of Cell Membrane Purification for the Preparation and Characterization of Cell Membrane Liposomes.
de Weerd S, Ruiter EA, Calicchia E, Portale G, Schuringa JJ, Roos WH, Salvati A.
Small Methods. 2024 Oct 21:e2400498.
doi: 10.1002/smtd.202400498. Epub ahead of print.
PMID: 39431332.
Cell membrane nanoparticles = popularity +++ in nanomedicine.
Here: optimized method combining nitrogen cavitation in isotonic buffer and sucrose gradient fractionation to isolate high-purity cell membrane fractions from both suspension and adherent cells.
The resulting cell membrane liposomes (CMLs) demonstrate varied cellular uptake based on their composition.
Lipid bilayer permeabilities and antibiotic effects of tetramethylguanidinium and choline fatty acid ionic liquids.
Dutta A, Burrell B, Prajapati E, Cottle S, Maurer HY, Urban MJ, Pennock SR, Muhamed AM, Harris J, Flores Y, Staman L, Carone BR, Caputo GA, Vaden TD.
Biochim Biophys Acta Biomembr. 2024 Oct 22;1867(1):184393.
doi: 10.1016/j.bbamem.2024.184393. Epub ahead of print.
PMID: 39442605.
Ionic liquids (ILs) can permeabilize lipid membranes and enhance antibacterial activity with minimal human cell toxicity. Here, focus on fatty acid-based ILs (FAILs).
=> decanoate-based FAILs, unlike octanoate-based, effectively permeabilize lipid bilayers and show antibacterial activity at concentrations below their CMC.
=> suggest that FAILs act independently of micelle formation, with specific combinations of cation and fatty-acid anion achieving the strongest permeabilizing and antibacterial effects.
Molecules
Solubilisation & purification of membrane proteins using benzylamine-modified SMA polymers.
Akram A, Hadasha W, Kuyler GC, Smith MP, Bailey-Dallaway S, Preedy A, Browne C, Broadbent L, Hill A, Javaid T, Nazar H, Samra N, Naveed A, Tregunna H, Joshi H, Akhtar N, Javed A, Bowater J, Ravenhill J, Hajdu P, Ali Y, Tailor Y, Mumtaz S, Hamza M, Gill K, Gillett J, Patton F, Arshid H, Zaheer M, Qureshi H, Edwards I, Patel S, Azadi A, Pollock N, Kitchen P, Klumperman B, Rothnie AJ.
Biophys Chem. 2024 Oct 18;316:107343.
doi: 10.1016/j.bpc.2024.107343. Epub ahead of print.
PMID: 39447535.
SMA2000’s polydispersity poses challenges due to its variable lengths and sequences.
Here: RAFT polymerization to create a more controlled 1:1 styrene:maleic anhydride polymer, modified with benzylamine to mimic the hydrophobic-hydrophilic balance of SMA2000.
Methods
Non-canonical amino acids for site-directed spin labeling of membrane proteins.
Ledwitch K, Künze G, Okwei E, Sala D, Meiler J.
Curr Opin Struct Biol. 2024 Oct 24;89:102936.
doi: 10.1016/j.sbi.2024.102936. Epub ahead of print.
PMID: 39454307.
Magnetic resonance combined with site-directed spin labeling = alternative method for obtaining atomic-level structural and dynamic information about MPs.
Here: review of the recent advancements in bioorthogonal click chemistries and genetically engineered non-canonical amino acids for linking spin probes to membrane proteins.
A data portal for providing standardized annotations for cryo-electron tomography.
Ermel U, Cheng A, Ni JX, Gadling J, Venkatakrishnan M, Evans K, Asuncion J, Sweet A, Pourroy J, Wang ZS, Khandwala K, Nelson B, McCarthy D, Wang EM, Agarwal R, Carragher B.
Nat Methods. 2024 Oct 21.
doi: 10.1038/s41592-024-02477-2. Epub ahead of print.
PMID: 39433879.
cryoET Data Portal (https://cryoetdataportal.czscience.com/), containing annotated cryoET datasets in standardized formats, as a resource for the cryoET community.
Microbio
Inosine reverses multidrug resistance in Gram-negative bacteria carrying mobilized RND-type efflux pump gene cluster tmexCD-toprJ.
Li F, Xu T, Fang D, Wang Z, Liu Y.
mSystems. 2024 Oct 22;9(10):e0079724.
doi: 10.1128/msystems.00797-24. Epub 2024 Sep 10.
PMID: 39254032.
Tigecycline efficacy is undermined due to the emergence of a recently discovered mobilized efflux pump gene cluster tmexCD1-toprJ1.
Here: untargeted metabolomic approaches => expression of tmexCD1-toprJ1 disrupts bacterial purine metabolism, with inosine being a crucial biomarker.
Supplementation of inosine => tigecycline resistance in tmexCD1-toprJ1-positive bacteria is reversed !
Two explanations:
- exogenous inosine enhance the pmf => uptake of tigecycline
- Exogenous inosine enhances succinate biosynthesis by stimulating the Krebs cycle => succinate interacts with the EnvZ/OmpR TCS => upregulation of OmpK 36 => influx of tigecycline.
Determination of Pseudomonas aeruginosa MexXY-OprM specificity in a major efflux knockout system reveals distinct antibiotic substrate classes
Logan G. Kavanaugh, Shraddha M. Hariharan, Graeme L. Conn
bioRxiv 2024.10.18.619101;
doi: https://doi.org/10.1101/2024.10.18.619101
Major efflux KO strain => P. aeruginosa system that enables controlled expression of MexXY-OprM in the absence of background efflux complexes with overlapping substrate profiles.
=> identification of 3 groups of potential substrates: true, partial, and nonsubstrates, and definition of trimethoprim as a new substrate for MexXY-OprM.
Phenotypic heterogeneity in bacteria: the rise of antibiotic persistence, clinical implications, and therapeutic opportunities.
Pani S, Mohapatra SS.
Arch Microbiol. 2024 Oct 26;206(11):446.
doi: 10.1007/s00203-024-04173-3.
PMID: 39460765.
In isogenic population of bacteria, not all cells behave or respond the same way to an antibiotic because of inherent heterogeneity.
3 types of phenotypic heterogeneity: tolerance, persistence, and heteroresistance.
Here: highlight on bacterial persistence with focus on their emergence and the underlying molecular mechanisms.
They propose a possible role of epigenetic mechanisms (methylation) in the development of persistence.
Miscellaneous
Functionalized DNA secondary structures and nanostructures for specific protein modifications.
Albada B.
Trends Biochem Sci. 2024 Oct 22:S0968-0004(24)00208-1.
doi: 10.1016/j.tibs.2024.09.003. Epub ahead of print.
PMID: 39443210.
DNA-based nano-objects can undergo complex functions but also novel catalytic applications.
Most challenging tasks = multifunctional catalytically active DNA-based nanostructures for controlled and precise modification of a WT protein in its natural environment !
It is now possible to chemically modify a specific protein in cell lysates under the influence of an externally added trigger.
Demonstration of Membrane Transport of Histidine using Goat Intestinal Inverted Sacs: An Experiential Pedagogical Tool for Undergraduates.
Haris H, Kumar P, Bhardwaj V, Taritla S, Malhotra V, Narayanasamy N.
J Vis Exp. 2024 Oct 4;(212).
doi: 10.3791/66882.
PMID: 39431781.
Histidine is absorbed in the intestine primarily through sodium-coupled transport.
Here: active absorption of histidine using goat jejunal inverted sacs = effective educational tool for undergraduate students to understand membrane transport concepts by visualizing the intestinal absorption of amino acids and metabolites.
Architectural styles of curiosity in global Wikipedia mobile app readership.
Zhou D, Patankar S, Lydon-Staley DM, Zurn P, Gerlach M, Bassett DS.
Sci Adv. 2024 Oct 25;10(43):eadn3268.
doi: 10.1126/sciadv.adn3268. Epub 2024 Oct 25.
PMID: 39454011.
3 unique styles of curiosity: