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Kumar S, Chakraborty S, Chakraborty N. Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108359. [PMID: 38237420 DOI: 10.1016/j.plaphy.2024.108359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.
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Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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2
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Tsaplina O, Khaitlina S, Chukhontseva K, Karaseva M, Demidyuk I, Bakhlanova I, Baitin D, Artamonova T, Vedyaykin A, Khodorkovskii M, Vishnyakov I. Protealysin Targets the Bacterial Housekeeping Proteins FtsZ and RecA. Int J Mol Sci 2022; 23:ijms231810787. [PMID: 36142700 PMCID: PMC9505478 DOI: 10.3390/ijms231810787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/04/2022] Open
Abstract
Serratia proteamaculans synthesizes the intracellular metalloprotease protealysin. This work was aimed at searching for bacterial substrates of protealysin among the proteins responsible for replication and cell division. We have shown that protealysin unlimitedly cleaves the SOS response protein RecA. Even 20% of the cleaved RecA in solution appears to be incorporated into the polymer of uncleaved monomers, preventing further polymerization and inhibiting RecA ATPase activity. Transformation of Escherichia coli with a plasmid carrying the protealysin gene reduces the bacterial UV survival up to 10 times. In addition, the protealysin substrate is the FtsZ division protein, found in both E. coli and Acholeplasma laidlawii, which is only 51% identical to E. coli FtsZ. Protealysin cleaves FtsZ at the linker between the globular filament-forming domain and the C-terminal peptide that binds proteins on the bacterial membrane. Thus, cleavage of the C-terminal segment by protealysin can lead to the disruption of FtsZ’s attachment to the membrane, and thereby inhibit bacterial division. Since the protealysin operon encodes not only the protease, but also its inhibitor, which is typical for the system of interbacterial competition, we assume that in the case of penetration of protealysin into neighboring bacteria that do not synthesize a protealysin inhibitor, cleavage of FtsZ and RecA by protealysin may give S. proteamaculans an advantage in interbacterial competition.
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Affiliation(s)
- Olga Tsaplina
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-297-42-96
| | - Sofia Khaitlina
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Ksenia Chukhontseva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Maria Karaseva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Ilya Demidyuk
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Irina Bakhlanova
- Kurchatov Genome Center—PNPI, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre ‘‘Kurchatov Institute”, 188300 Gatchina, Russia
| | - Dmitry Baitin
- Kurchatov Genome Center—PNPI, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre ‘‘Kurchatov Institute”, 188300 Gatchina, Russia
| | - Tatiana Artamonova
- Department of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Alexey Vedyaykin
- Department of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Mikhail Khodorkovskii
- Department of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
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3
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The division protein FtsZ interacts with the small heat shock protein IbpA in Acholeplasma laidlawii. Biochim Biophys Acta Gen Subj 2022; 1866:130220. [DOI: 10.1016/j.bbagen.2022.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
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4
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Lazenby JJ, Li ES, Whitchurch CB. Cell wall deficiency - an alternate bacterial lifestyle? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925044 DOI: 10.1099/mic.0.001218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Historically, many species of bacteria have been reported to produce viable, cell wall deficient (CWD) variants. A variety of terms have been used to refer to CWD bacteria and a plethora of methods described in which to induce, cultivate and propagate them. In this review, we will examine the long history of scientific research on CWD bacteria examining the methods by which CWD bacteria are generated; the requirements for survival in a CWD state; the replicative processes within a CWD state; and the reversion of CWD bacteria into a walled state, or lack thereof. In doing so, we will present evidence that not all CWD variants are alike and that, at least in some cases, CWD variants arise through an adaptive lifestyle switch that enables them to live and thrive without a cell wall, often to avoid antimicrobial activity. Finally, the implications of CWD bacteria in recurring infections, tolerance to antibiotic therapy and antimicrobial resistance will be examined to illustrate the importance of greater understanding of the CWD bacteria in human health and disease.
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Affiliation(s)
- James J Lazenby
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Erica S Li
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Cynthia B Whitchurch
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TK, UK
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5
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Vishnyakov IE. Cell-in-Cell Phenomena in Wall-Less Bacteria: Is It Possible? Int J Mol Sci 2022; 23:ijms23084345. [PMID: 35457161 PMCID: PMC9030286 DOI: 10.3390/ijms23084345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
This work describes curious structures formed by the mainly phytopathogenic mycoplasma Acholeplasma laidlawii, as well as the human pathogen Ureaplasma parvum cells which resemble cell-in-cell structures of higher eukaryotes and protists. The probable significance of such structures for the mycoplasma cell is discussed. The possibility of their formation in nature and their potential role in the transformation of genetic material, for example, by maintaining (on the one hand) the stability of the genome in the line of generations during asexual reproduction or (on the other hand) the genome plasticity, are substantiated. It should be especially noted that all the arguments presented are based only on morphological data. However, closer attention to unusual structures, the existence of which was shown by electron microscopy images in this case, may prompt researchers to analyze their data more carefully and find something rare and non-trivial among seemingly trivial things. If it is proven by additional methods that cell-in-cell structures can indeed be formed by prokaryotes without a cell wall, this phenomenon may acquire general biological significance.
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6
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Wang Y, Wei Y, Shang N, Li P. Synergistic Inhibition of Plantaricin E/F and Lactic Acid Against Aeromonas hydrophila LPL-1 Reveals the Novel Potential of Class IIb Bacteriocin. Front Microbiol 2022; 13:774184. [PMID: 35242114 PMCID: PMC8886044 DOI: 10.3389/fmicb.2022.774184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/04/2022] [Indexed: 01/15/2023] Open
Abstract
Plantaricin E/F (PlnEF) is a pair of two-component class IIb bacteriocin produced by lactic acid bacteria. PlnEF commonly displays potent antimicrobial activity against certain Gram-positive organisms. In this study, we investigated the synergistic activity of PlnEF combined with lactic acid against Gram-negative food and aquaculture potential pathogen Aeromonas hydrophila LPL-1, which is naturally resistant to PlnEF. We applied SDS-PAGE, wavelength-scanning, laser confocal microscopy, flow cytometer, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and two-dimensional electrophoresis to investigate their synergistic inhibitory activities. The results showed that L-lactic acid drove the release of LPS from A. hydrophila, making it possible for PlnEF to contact the inner cell membrane of A. hydrophila. Besides, co-treatment of lactic acid and PlnEF caused severe morphological and intracellular changes of A. hydrophila, including blebs on the cell surface, abnormal cell elongation, inner membrane disruption, pore-forming through the outer and inner membrane, coagulation of the cytoplasm, and structural transformation of DNA. Protein profile analysis revealed that combined treatment of lactic acid and PlnEF inhibited the energy metabolism, protein synthesis, protein folding, and DNA replication in A. hydrophila. These findings proved that PlnEF combined with lactic acid was efficient against A. hydrophila and shed light on bacteriocin’s potential and a new inhibition mechanism against A. hydrophila.
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Affiliation(s)
- Yang Wang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Tianjin Key Laboratory of Aqua-Ecology and Aquaculture College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Yunlu Wei
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Nan Shang
- College of Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Pinglan Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
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7
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Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochem Biophys Res Commun 2021; 583:43-48. [PMID: 34735878 DOI: 10.1016/j.bbrc.2021.10.051] [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: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022]
Abstract
The coding gene for peptidoglycan editing factor (pdeF) is located in the division and cell wall (dcw) cluster, and encodes a protein that has an editing function for misplaced amino acids in peptidoglycan in E. coli. In this study, we determined the crystal structure of PdeF from Bacillus cereus (BcPdeF) at a 1.60 Å resolution. BcPdeF exists as a monomer in solution and consists of two domains: a core domain containing a Pfam motif DUF152 and a smaller subdomain. The X-ray fluorescence spectrum of BcPdeF crystal elucidated that the protein has a Zn2+ ion in its active site and the metal ion was coordinated by two histidine and one cysteine residue. We also performed docking calculations of the N-acetylmuramate (MurNAc)-L-Ser-D-iGlu ligand in the BcPdeF structure and revealed the substrate binding mode of the enzyme. Furthermore, structural comparisons between BcPdeF and human fatty acid metabolism-immunity nexus (FAMIN), which also contains the DUF152 motif in its core domain, provided a structural basis how the two structurally similar proteins have completely different physiological functions.
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Affiliation(s)
- Jihye Seok
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jiyoung Park
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea.
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8
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Gene knockout revealed the role of gene feoA in cell growth and division of Lactobacillus delbrueckii subsp. bulgaricus. Arch Microbiol 2021; 203:3541-3549. [PMID: 33942158 DOI: 10.1007/s00203-021-02345-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/17/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Gene feoA plays an important role in cell growth because of its function of transport Fe2+ which is a necessary element for cells. In this study, the recombinant plasmid pUC19-feoA-Tet was successfully constructed using the inserted gene inactivation method. Using the homologous recombination technique, the tet gene was used as a resistance screening marker to knock out the feoA gene of Lactobacillus delbrueckii subsp. bulgaricus 34.5 (strain 34.5). Comparative analysis of growth curves revealed the growth changes in the absence of feoA gene in strain 34.5. The results showed that the growth of the bacteria was prolonged by 2 h and could be restored in the stationary phase. To further study whether feoA is related to the cell division of strain 34.5, the qPCR experiment was carried out. The results showed that, compared with the wild-type strain, the expression of genes related to cell division in the mutant strain was up-regulated in the pre-log phase, down-regulated in the late-log phase, and returned to the original level in the stationary phase. These findings provide ideas for Lactobacillus delbrueckii subsp. bulgaricus to control division and cell cycle.
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9
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Pelletier JF, Sun L, Wise KS, Assad-Garcia N, Karas BJ, Deerinck TJ, Ellisman MH, Mershin A, Gershenfeld N, Chuang RY, Glass JI, Strychalski EA. Genetic requirements for cell division in a genomically minimal cell. Cell 2021; 184:2430-2440.e16. [PMID: 33784496 DOI: 10.1016/j.cell.2021.03.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 01/27/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. Although this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics that result in irregular morphologies. A genome with 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents morphology similar to that of JCVI-syn1.0. We further identified seven of these 19 genes, including two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, which are required together to restore a phenotype similar to that of JCVI-syn1.0. This result emphasizes the polygenic nature of cell division and morphology in a genomically minimal cell.
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Affiliation(s)
- James F Pelletier
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lijie Sun
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Kim S Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Andreas Mershin
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil Gershenfeld
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA.
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10
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Chaudhary R, Mishra S, Kota S, Misra H. Molecular interactions and their predictive roles in cell pole determination in bacteria. Crit Rev Microbiol 2021; 47:141-161. [PMID: 33423591 DOI: 10.1080/1040841x.2020.1857686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacterial cell cycle is divided into well-coordinated phases; chromosome duplication and segregation, cell elongation, septum formation, and cytokinesis. The temporal separation of these phases depends upon the growth rates and doubling time in different bacteria. The entire process of cell division starts with the assembly of divisome complex at mid-cell position followed by constriction of the cell wall and septum formation. In the mapping of mid-cell position for septum formation, the gradient of oscillating Min proteins across the poles plays a pivotal role in several bacteria genus. The cues in the cell that defines the poles and plane of cell division are not fully characterized in cocci. Recent studies have shed some lights on molecular interactions at the poles and the underlying mechanisms involved in pole determination in non-cocci. In this review, we have brought forth recent findings on these aspects together, which would suggest a model to explain the mechanisms of pole determination in rod shaped bacteria and could be extrapolated as a working model in cocci.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
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11
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Singhi D, Srivastava P. How similar or dissimilar cells are produced by bacterial cell division? Biochimie 2020; 176:71-84. [DOI: 10.1016/j.biochi.2020.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
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12
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Boguszewska K, Szewczuk M, Kaźmierczak-Barańska J, Karwowski BT. The Similarities between Human Mitochondria and Bacteria in the Context of Structure, Genome, and Base Excision Repair System. Molecules 2020; 25:E2857. [PMID: 32575813 PMCID: PMC7356350 DOI: 10.3390/molecules25122857] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria emerged from bacterial ancestors during endosymbiosis and are crucial for cellular processes such as energy production and homeostasis, stress responses, cell survival, and more. They are the site of aerobic respiration and adenosine triphosphate (ATP) production in eukaryotes. However, oxidative phosphorylation (OXPHOS) is also the source of reactive oxygen species (ROS), which are both important and dangerous for the cell. Human mitochondria contain mitochondrial DNA (mtDNA), and its integrity may be endangered by the action of ROS. Fortunately, human mitochondria have repair mechanisms that allow protecting mtDNA and repairing lesions that may contribute to the occurrence of mutations. Mutagenesis of the mitochondrial genome may manifest in the form of pathological states such as mitochondrial, neurodegenerative, and/or cardiovascular diseases, premature aging, and cancer. The review describes the mitochondrial structure, genome, and the main mitochondrial repair mechanism (base excision repair (BER)) of oxidative lesions in the context of common features between human mitochondria and bacteria. The authors present a holistic view of the similarities of mitochondria and bacteria to show that bacteria may be an interesting experimental model for studying mitochondrial diseases, especially those where the mechanism of DNA repair is impaired.
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Affiliation(s)
| | | | | | - Bolesław T. Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland; (K.B.); (M.S.); (J.K.-B.)
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13
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Zhukovsky MA, Filograna A, Luini A, Corda D, Valente C. Protein Amphipathic Helix Insertion: A Mechanism to Induce Membrane Fission. Front Cell Dev Biol 2019; 7:291. [PMID: 31921835 PMCID: PMC6914677 DOI: 10.3389/fcell.2019.00291] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022] Open
Abstract
One of the fundamental features of biomembranes is the ability to fuse or to separate. These processes called respectively membrane fusion and fission are central in the homeostasis of events such as those related to intracellular membrane traffic. Proteins that contain amphipathic helices (AHs) were suggested to mediate membrane fission via shallow insertion of these helices into the lipid bilayer. Here we analyze the AH-containing proteins that have been identified as essential for membrane fission and categorize them in few subfamilies, including small GTPases, Atg proteins, and proteins containing either the ENTH/ANTH- or the BAR-domain. AH-containing fission-inducing proteins may require cofactors such as additional proteins (e.g., lipid-modifying enzymes), or lipids (e.g., phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2], phosphatidic acid [PA], or cardiolipin). Both PA and cardiolipin possess a cone shape and a negative charge (-2) that favor the recruitment of the AHs of fission-inducing proteins. Instead, PtdIns(4,5)P2 is characterized by an high negative charge able to recruit basic residues of the AHs of fission-inducing proteins. Here we propose that the AHs of fission-inducing proteins contain sequence motifs that bind lipid cofactors; accordingly (K/R/H)(K/R/H)xx(K/R/H) is a PtdIns(4,5)P2-binding motif, (K/R)x6(F/Y) is a cardiolipin-binding motif, whereas KxK is a PA-binding motif. Following our analysis, we show that the AHs of many fission-inducing proteins possess five properties: (a) at least three basic residues on the hydrophilic side, (b) ability to oligomerize, (c) optimal (shallow) depth of insertion into the membrane, (d) positive cooperativity in membrane curvature generation, and (e) specific interaction with one of the lipids mentioned above. These lipid cofactors favor correct conformation, oligomeric state and optimal insertion depth. The most abundant lipid in a given organelle possessing high negative charge (more negative than -1) is usually the lipid cofactor in the fission event. Interestingly, naturally occurring mutations have been reported in AH-containing fission-inducing proteins and related to diseases such as centronuclear myopathy (amphiphysin 2), Charcot-Marie-Tooth disease (GDAP1), Parkinson's disease (α-synuclein). These findings add to the interest of the membrane fission process whose complete understanding will be instrumental for the elucidation of the pathogenesis of diseases involving mutations in the protein AHs.
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Affiliation(s)
- Mikhail A. Zhukovsky
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
| | | | | | - Daniela Corda
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
| | - Carmen Valente
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
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