Prokaryotic cell membrane‑based protein technologies (Review)
- Authors:
- Mohammed Suhaib Al Huq
- Kalpana Raja
- Iyappan Ramalakshmi Oviya
-
Affiliations: Department of Electronics and Communication Engineering, Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Chennai, Tamil Nadu 601103, India, Section for Biomedical Informatics and Data Science, School of Medicine, Yale University, New Haven, CT 06511, USA, Department of Computer Science and Engineering, Amrita School of Computing, Amrita Vishwa Vidyapeetham, Chennai, Tamil Nadu 601103, India - Published online on: January 29, 2024 https://doi.org/10.3892/wasj.2024.227
- Article Number: 12
-
Copyright : © Suhaib Al Huq et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY 4.0].
This article is mentioned in:
Abstract
 |
|
Watson H: Biological membranes. Essays Biochem. 59:43–69. 2015.PubMed/NCBI View Article : Google Scholar | |
|
Gopalakrishnan G, Awasthi A, Belkaid W, De Faria O Jr, Liazoghli D, Colman DR and Dhaunchak AS: Lipidome and proteome map of myelin membranes. J Neurosci Res. 91:321–334. 2013.PubMed/NCBI View Article : Google Scholar | |
|
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A and Tajkhorshid E: Characterization of lipid-protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation. Chem Rev. 119:6086–6161. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Wardhan R and Mudgal P: Membrane Proteins in Textbook of Membrane Biology. Springer, Singapore, pp49-80, 2017. | |
|
Bai L and Li H: Structural insights into the membrane chaperones for multi-pass membrane protein biogenesis. Curr Opin Struct Biol. 79(102563)2023.PubMed/NCBI View Article : Google Scholar | |
|
Hegde RS and Keenan RJ: The mechanisms of integral membrane protein biogenesis. Nat Rev Mol Cell Biol. 23:107–124. 2022.PubMed/NCBI View Article : Google Scholar | |
|
Tzen JTC: Integral proteins in plant oil bodies. ISRN Botany. 2012:1–16. 2012. | |
|
Che T: Advances in the treatment of chronic pain by targeting GPCRs. Biochemistry. 60:1401–1412. 2021.PubMed/NCBI View Article : Google Scholar | |
|
Li Y, Zhang H, Kosturakis AK, Cassidy RM, Zhang H, Kennamer-Chapman RM, Jawad AB, Colomand CM, Harrison DS and Dougherty PM: MAPK signaling downstream to TLR4 contributes to paclitaxel-induced peripheral neuropathy. Brain Behav Immun. 49:255–266. 2015.PubMed/NCBI View Article : Google Scholar | |
|
Müller GA and Müller TD: (Patho)Physiology of glycosylphosphatidylinositol-anchored proteins I: Localization at plasma membranes and extracellular compartments. Biomolecules. 13(855)2023.PubMed/NCBI View Article : Google Scholar | |
|
Lee IH, Imanaka M, Modahl EH and Torres-Ocampo AP: Lipid raft phase modulation by membrane-anchored proteins with inherent phase separation properties. ACS Omega. 4:6551–6559. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Henderson JC, Zimmerman SM, Crofts AA, Boll JM, Kuhns LG, Herrera CM and Trent MS: The power of asymmetry: Architecture and assembly of the gram-negative outer membrane lipid bilayer. Ann Rev Microbiol. 70:255–278. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Lorent JH, Levental KR, Ganesan L, Rivera-Longsworth G, Sezgin E, Doktorova M, Lyman E and levental I: Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape. Nat Chem Biol. 16:642–652. 2020.PubMed/NCBI View Article : Google Scholar | |
|
Coskun O: Separation techniques: Chromatography. North Clin Istanb. 3:156–160. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Jorrin-Novo JV, Komatsu S, Sanchez-Lucas R and de Francisco LE: Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics! J Proteomics. 198:1–10. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Orwick-Rydmark M, Arnold T and Linke D: The use of detergents to purify membrane proteins. Curr Protoc Protein Sci. 84:4.8.1–4.8.35. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Zhou D, Zhong S, Han X, Liu D, Fang H and Wang Y: Protocol for mitochondrial isolation and sub-cellular localization assay for mitochondrial proteins. STAR Protoc. 4(102088)2023.PubMed/NCBI View Article : Google Scholar | |
|
Webster J and Oxley D: Protein identification by MALDI-TOF mass spectrometry. Methods Mol Biol. 2012:227–240. 2012.PubMed/NCBI View Article : Google Scholar | |
|
Santos IC, Hildenbrand ZL and Schug KA: Applications of MALDI-TOF MS in environmental microbiology. Analyst. 141:2827–2837. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Crook AA and Powers R: Quantitative NMR-based biomedical metabolomics: Current status and applications. Molecules. 25(5128)2020.PubMed/NCBI View Article : Google Scholar | |
|
Hatzakis E: Nuclear magnetic resonance (NMR) spectroscopy in food science: A comprehensive review. Compr Rev Food Sci Food Saf. 18:189–220. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Li M, Xu W and Su Y: Solid-state NMR spectroscopy in pharmaceutical sciences. Trends Anal Chem. 135(116152)2021. | |
|
D'cruz D, Babu A and Joshy E: Bioanalytical method development and validation of ticagrelor by rp-Hplc. Int J App Pharm. 9(51)2017. | |
|
Aneesh TP, Radhakrishnan R, Sasidharan APM and Choyal M: RP-HPLC method for simultaneous determination of losartan and chlorthalidone in pharmaceutical dosage form. Int Res J Pharm. 6:453–457. 2015. | |
|
Sobsey CA, Ibrahim S, Richard VR, Gaspar V, Mitsa G, Lacasse V, Zahedi RP, Batist G and Borchers CH: Targeted and untargeted proteomics approaches in biomarker development. Proteomics. 20(1900029)2020.PubMed/NCBI View Article : Google Scholar | |
|
Gallagher RI, Wulfkuhle J, Wolf DM, Brown-Swigart L, Yau C, O'Grady N, Basu A, Lu R, Campbell MJ, Magbanua MJ, et al: Protein signaling and drug target activation signatures to guide therapy prioritization: Therapeutic resistance and sensitivity in the I-SPY 2 trial. Cell Rep Med. 4(101312)2023.PubMed/NCBI View Article : Google Scholar | |
|
Mann M: The rise of mass spectrometry and the fall of edman degradation. Clin Chem. 62:293–294. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Matsudaira P: A Practical Guide to Protein and Peptide Purification for Microsequencing. Matsudaira P (ed). 2nd edition. Academic Press, San Diego, CA, pp1-13, 1993. | |
|
Pomerantz SC and McCloskey JA: Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol. 193:796–824. 1990.PubMed/NCBI View Article : Google Scholar | |
|
Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ and Dedon PC: Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nat Protoc. 9:828–841. 2014.PubMed/NCBI View Article : Google Scholar | |
|
Cupp-Sutton KA and Wu S: High-throughput quantitative top-down proteomics. Mol Omics. 16:91–99. 2020.PubMed/NCBI View Article : Google Scholar | |
|
Gao Y and Yates JR III: Protein analysis by shotgun proteomics. In: Mass Spectrometry-Based Chemical Proteomics. John Wiley & Sons, Ltd., Hoboken NJ, pp1-38, 2019. | |
|
Rozario LT, Sharker T and Nila TA: In silico analysis of deleterious SNPs of human MTUS1 gene and their impacts on subsequent protein structure and function. PLoS One. 16(e0252932)2021.PubMed/NCBI View Article : Google Scholar | |
|
Huang C, Hou C, Ijaz M, Yan T, Li X, Li Y and Zhang D: Proteomics discovery of protein biomarkers linked to meat quality traits in post-mortem muscles: Current trends and future prospects: A review. Trends Food Sci Technol. 105:416–432. 2020. | |
|
Yokota H: Applications of proteomics in pharmaceutical research and development. Biochim Biophys Acta Proteins Proteom. 1867:17–21. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Zhao Y, Sun Q and Huo B: Focal adhesion regulates osteogenic differentiation of mesenchymal stem cells and osteoblasts. Biomater Transl. 2:312–322. 2021.PubMed/NCBI View Article : Google Scholar | |
|
de Oliveira Garcia FA, de Andrade ES and Palmero EI: Insights on variant analysis in silico tools for pathogenicity prediction. Front Genet. 13(1010327)2022.PubMed/NCBI View Article : Google Scholar | |
|
Deshpande RR, Tiwari AP, Nyayanit N and Modak M: In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2. Eur J Pharmacol. 886(173430)2020.PubMed/NCBI View Article : Google Scholar | |
|
Cramer P: AlphaFold2 and the future of structural biology. Nat Struct Mol Biol. 28:704–705. 2021.PubMed/NCBI View Article : Google Scholar | |
|
Cavasotto CN and Phatak SS: Homology modeling in drug discovery: Current trends and applications. Drug Discov Today. 14:676–683. 2009.PubMed/NCBI View Article : Google Scholar | |
|
Taha MO, Atallah N, Al-Bakri AG, Paradis-Bleau C, Zalloum H, Younis KS and Levesque RC: Discovery of new MurF inhibitors via pharmacophore modeling and QSAR analysis followed by in-silico screening. Bioorg Med Chem. 16:1218–1235. 2008.PubMed/NCBI View Article : Google Scholar | |
|
Huang YZ, Chen SY and Deng F: Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction. Comput Struct Biotechnol J. 14:298–303. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Dereeper A, Audic S, Claverie JM and Blanc G: BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 10(8)2010.PubMed/NCBI View Article : Google Scholar | |
|
Meglécz E, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Grenier R and Martin J: QDD version 3.1: A user-friendly computer program for microsatellite selection and primer design revisited: Experimental validation of variables determining genotyping success rate. Mol Ecol Resour. 14:1302–1313. 2014.PubMed/NCBI View Article : Google Scholar | |
|
Jess R, Ling T, Xiong Y, Wright CJ and Zhao F: Mechanical environment for in vitro cartilage tissue engineering assisted by in silico models. Biomater Transl. 4:18–26. 2023.PubMed/NCBI View Article : Google Scholar | |
|
Wu YW, Simmons BA and Singer SW: MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 32:605–607. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Xiao J and Goley ED: Redefining the roles of the FtsZ-ring in bacterial cytokinesis. Curr Opin Microbiol. 34:90–96. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Paulin S, Jamshad M, Dafforn TR, Garcia-Lara J, Foster SJ, Galley NF, Roper DI, Rosado H and Taylor PW: Surfactant-free purification of membrane protein complexes from bacteria: Application to the staphylococcal penicillin-binding protein complex PBP2/PBP2a. Nanotechnology. 25(285101)2014.PubMed/NCBI View Article : Google Scholar | |
|
Meeske AJ, Riley EP, Robins WP, Uehara T, Mekalanos JJ, Kahne D, Walker S, Kruse AC, Bernhardt TG and Rudner DZ: SEDS proteins are a widespread family of bacterial cell wall polymerases. Nature. 537:634–638. 2016.PubMed/NCBI View Article : Google Scholar | |
|
Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T and Buchanan SK: Structural insight into the biogenesis of β-barrel membrane proteins. Nature. 501:385–390. 2013.PubMed/NCBI View Article : Google Scholar | |
|
Rassam P, Copeland NA, Birkholz O, Tóth C, Chavent M, Duncan AL, Cross SJ, Housden NG, Kaminska R, Seger U, et al: Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria. Nature. 523:333–336. 2015.PubMed/NCBI View Article : Google Scholar | |
|
Foster TJ: The MSCRAMM family of cell-wall-anchored surface proteins of gram-positive cocci. Trends Microbiol. 27:927–941. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Lecointe K, Cornu M, Leroy J, Coulon P and Sendid B: Polysaccharides cell wall architecture of mucorales. Front Microbiol. 10(469)2019.PubMed/NCBI View Article : Google Scholar | |
|
Heinisch JJ and Rodicio R: Protein kinase C in fungi-more than just cell wall integrity. FEMS Microbiol Rev 42: 10.1093/femsre/fux051, 2018. | |
|
Kermani AA: A guide to membrane protein X-ray crystallography. FEBS J. 288:5788–5804. 2021.PubMed/NCBI View Article : Google Scholar | |
|
Alexandrov AI, Mileni M, Chien EYT, Hanson MA and Stevens RC: Microscale fluorescent thermal stability assay for membrane proteins. Structure. 16:351–359. 2008.PubMed/NCBI View Article : Google Scholar | |
|
Kwan TOC, Reis R, Siligardi G, Hussain R, Cheruvara H and Moraes I: Selection of biophysical methods for characterisation of membrane proteins. Int J Mol Sci. 20(2605)2019.PubMed/NCBI View Article : Google Scholar | |
|
Kermani AA, Aggarwal S and Ghanbarpour A: Chapter 11 - Advances in X-ray crystallography methods to study structural dynamics of macromolecules. Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics. 2023:309–355. 2023. | |
|
Chen D, McCool EN, Yang Z, Shen X, Lubeckyj RA, Xu T, Wang Q and Sun L: Recent advances (2019-2021) of capillary electrophoresis-mass spectrometry for multilevel proteomics. Mass Spectrom Rev. 42:617–642. 2023.PubMed/NCBI View Article : Google Scholar | |
|
Wu G, Yu C, Wang W, Du J, Xu G, Fu Z and Wang L: Charge variants analysis of a bispecific antibody using a fully automated one-step capillary isoelectric focusing-mass spectrometry method. Curr Pharm Anal. 18:860–870. 2022. | |
|
Giraudeau P: NMR-based metabolomics and fluxomics: Developments and future prospects. Analyst. 145:2457–2472. 2020.PubMed/NCBI View Article : Google Scholar | |
|
Hiroaki H: Molecular mechanisms of amyloid-β peptide fibril and oligomer formation: NMR-based challenges. Biophys Physicobiol. 20(e200007)2023.PubMed/NCBI View Article : Google Scholar | |
|
Sobolev AP, Thomas F, Donarskic J, Ingallinad C, Circid S, Marincolae FC, Capitania D and Mannina L: Use of NMR applications to tackle future food fraud issues. Trends Food Sci Technol. 91:347–353. 2019. | |
|
Alexandrov T: Spatial metabolomics and imaging mass spectrometry in the age of artificial intelligence. Ann Rev Biomed Data Sci. 3:61–87. 2020.PubMed/NCBI View Article : Google Scholar | |
|
Silantyev AS, Falzone L, Libra M, Gurina OI, Kardashova KS, Nikolouzakis TK, Nosyrev AE, Sutton CW, Mitsias PD and Tsatsakis A: Current and future trends on diagnosis and prognosis of glioblastoma: From molecular biology to proteomics. Cells. 8(863)2019.PubMed/NCBI View Article : Google Scholar | |
|
Kuo TH, Dutkiewicz EP, Pei J and Hsu CC: Ambient ionization mass spectrometry today and tomorrow: Embracing challenges and opportunities. Anal Chem. 92:2353–2363. 2020.PubMed/NCBI View Article : Google Scholar | |
|
Kroll AV, Fang RH and Zhang L: Biointerfacing and applications of cell membrane-coated nanoparticles. Bioconjug Chem. 28:23–32. 2017.PubMed/NCBI View Article : Google Scholar | |
|
Ahmad R and Budnik B: A review of the current state of single-cell proteomics and future perspective. Anal Bioanal Chem. 415:6889–6899. 2023.PubMed/NCBI View Article : Google Scholar | |
|
Khan WA: Chapter 3-Whole-exome and whole-genome sequencing in the molecular diagnostic laboratory. In: Diagnostic Molecular Pathology. Coleman WB and Tsongalis GJ (eds). 2nd edition. Academic Press, San Diego, CA pp27-38, 2024. | |
|
Wang F, Guo J, Wang S, Wang Y, Chen J, Hu Y, Zhang H, Xu K, Wei Y, Cao L, et al: B-cell lymphoma-3 controls mesenchymal stem cell commitment and senescence during skeletal aging. Clin Transl Med. 12(e955)2022.PubMed/NCBI View Article : Google Scholar | |
|
Al Huq Mohammed S and Rajamani K: Role of chaperones and endoplasmic reticulum stress in protein complexity associated with dyslipidemia: A future perspective to novel therapeutics (Review). World Acad Sci J. 6:1–9. 2024. | |
|
Kingsak M, Maturavongsadit P, Jiang H and Wang Q: Cellular responses to nanoscale substrate topography of TiO2 nanotube arrays: Cell morphology and adhesion. Biomater Transl. 3:221–233. 2022.PubMed/NCBI View Article : Google Scholar | |
|
Xue X, Liu H, Wang S, Hu Y, Huang B, Li M, Gao J, Wang X and Su J: Neutrophil-erythrocyte hybrid membrane-coated hollow copper sulfide nanoparticles for targeted and photothermal/ anti-inflammatory therapy of osteoarthritis. Composites Part B: Engineering. 237(109855)2022. | |
|
Nie D, Hu Y, Chen Z, Li M, Hou Z, Luo X, Mao X and Xue X: Outer membrane protein A (OmpA) as a potential therapeutic target for Acinetobacter baumannii infection. J Biomed Sci. 27(26)2020.PubMed/NCBI View Article : Google Scholar | |
|
Chen Z, Wang Y, Cheng Y, Wang X, Tong S, Yang H and Wang Z: Efficient biodegradation of highly crystallized polyethylene terephthalate through cell surface display of bacterial PETase. Sci Total Environ. 709(136138)2020.PubMed/NCBI View Article : Google Scholar | |
|
Ding JL, Hou J, Feng MG and Ying SH: Transcriptomic analyses reveal comprehensive responses of insect hemocytes to mycopathogen Beauveria bassiana, and fungal virulence-related cell wall protein assists pathogen to evade host cellular defense. Virulence. 11:1352–1365. 2020.PubMed/NCBI View Article : Google Scholar | |
|
Wang J, Xu W, Wang R, Cheng R, Tang Z and Zhang M: The outer membrane protein Amuc_1100 of Akkermansia muciniphila promotes intestinal 5-HT biosynthesis and extracellular availability through TLR2 signalling. Food Funct. 12:3597–3610. 2021.PubMed/NCBI View Article : Google Scholar | |
|
Devi SM, Raj N and Sashidhar RB: Efficacy of short-synthetic antifungal peptides on pathogenic Aspergillus flavus. Pestic Biochem Physiol. 174(104810)2021.PubMed/NCBI View Article : Google Scholar | |
|
Peng J, Wu L, Zhang W, Zhang Q, Xing Q, Wang X, Li X and Yan J: Systemic identification and functional characterization of common in fungal extracellular membrane proteins in lasiodiplodia theobromae. Front Plant Sci. 12(804696)2021.PubMed/NCBI View Article : Google Scholar | |
|
Doyle MT and Bernstein HD: Bacterial outer membrane proteins assemble via asymmetric interactions with the BamA β-barrel. Nat Commun. 10(3358)2019.PubMed/NCBI View Article : Google Scholar | |
|
Oluwole A, Shutin D and Bolla JR: Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem. 67:201–213. 2023.PubMed/NCBI View Article : Google Scholar | |
|
Peterson JH, Doyle MT and Bernstein HD: Small molecule antibiotics inhibit distinct stages of bacterial outer membrane protein assembly. mBio. 13(e0228622)2022.PubMed/NCBI View Article : Google Scholar | |
|
Sun J, Rutherford ST, Silhavy TJ and Huang KC: Physical properties of the bacterial outer membrane. Nat Rev Microbiol. 20:236–248. 2022.PubMed/NCBI View Article : Google Scholar | |
|
Tomasek D and Kahne D: The assembly of β-barrel outer membrane proteins. Curr Opin Microbiol. 60:16–23. 2021.PubMed/NCBI View Article : Google Scholar | |
|
Muras V, Toulouse C, Fritz G and Steuber J: Respiratory membrane protein complexes convert chemical energy. Bacterial Cell Walls and Membranes. 2019:301–335. 2019.PubMed/NCBI View Article : Google Scholar | |
|
den Blaauwen T and Luirink J: Checks and balances in bacterial cell division. MBio. 10:e00149–e00119. 2019.PubMed/NCBI View Article : Google Scholar | |
|
Nguyen HTV, Chen X, Parada C, Luo AC, Shih O, Jeng US, Huang CY, Shih YL and Ma C: Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome. Nat Commun. 14(1903)2023.PubMed/NCBI View Article : Google Scholar | |
|
Grabowski L, Łepek K, Stasiłojć M, Kosznik-Kwaśnicka K, Zdrojewska K, Maciąg-Dorszyńska M, Węgrzyn G and Węgrzyn A: Bacteriophage-encoded enzymes destroying bacterial cell membranes and walls, and their potential use as antimicrobial agents. Microbiol Res. 248(126746)2021.PubMed/NCBI View Article : Google Scholar | |
|
Sharma U, Vipra A and Channabasappa S: Phage-derived lysins as potential agents for eradicating biofilms and persisters. Drug Discovery Today. 23:848–856. 2018.PubMed/NCBI View Article : Google Scholar | |
|
Avila-Calderón ED, Ruiz-Palma MDS, Aguilera-Arreola MG, Velázquez-Guadarrama N, Ruiz EA, Gomez-Lunar Z, Witonsky S and Contreras-Rodríguez A: Outer membrane vesicles of gram-negative bacteria: An outlook on biogenesis. Front Microbiol. 12(557902)2021.PubMed/NCBI View Article : Google Scholar | |
|
McDowell MA, Heimes M and Sinning I: Structural and molecular mechanisms for membrane protein biogenesis by the Oxa1 superfamily. Nat Struct Mol Biol. 28:234–239. 2021.PubMed/NCBI View Article : Google Scholar | |
|
Diederichs KA, Pitt AS, Varughese JT, Hackel TN, Buchanan SK and Shaw PL: Mechanistic insights into fungal mitochondrial outer membrane protein biogenesis. Curr Opin Struct Biol. 74(102383)2022.PubMed/NCBI View Article : Google Scholar | |
|
Lübeck M and Lübeck PS: Fungal cell factories for efficient and sustainable production of proteins and peptides. Microorganisms. 10(753)2022.PubMed/NCBI View Article : Google Scholar |
