51
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Jin F. Structural insights into the mechanism of a novel protein targeting pathway in Gram-negative bacteria. FEBS Open Bio 2020; 10:561-579. [PMID: 32068344 PMCID: PMC7137807 DOI: 10.1002/2211-5463.12813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/05/2020] [Accepted: 02/16/2020] [Indexed: 12/02/2022] Open
Abstract
Many nascent polypeptides synthesized in the cytoplasm are translocated across membranes via a specific ‘translocon’ composed of protein complexes. Recently, a novel targeting pathway for the outer membrane β‐barrel proteins (OMPs) in Gram‐negative bacteria was discovered. The cell envelope of Gram‐negative bacteria is composed of the inner (plasma) membrane (IM) and the outer membrane (OM). In this new pathway, a SecAN protein, which is mainly present in the IM as a homo‐oligomer, translocates nascent OMPs across the IM; at the same time, SecAN directly interacts with the β‐barrel assembly machinery (BAM) complex embedded within the OM. A supercomplex (containing SecAN, the BAM complex and many other proteins) spans the IM and OM, and is involved in the biogenesis of OMPs. Investigation of the function of SecAN and the supercomplex, as well as the translocation mechanism, will require elucidation of their structures. However, no such structures are available. Therefore, here, I describe the use of protein modeling to build homology models for SecAN and theoretical structures for the core‐complex composed of SecAN and the BAM complex, which is a key part of the supercomplex. The modeling data are consistent with previous experimental observations and demonstrated a conformational change of the core‐complex. I conclude by proposing mechanisms for how SecAN and the supercomplex function in the biogenesis of OMPs.
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Affiliation(s)
- Feng Jin
- School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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52
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Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil. Antonie van Leeuwenhoek 2020; 113:839-850. [PMID: 32114684 DOI: 10.1007/s10482-020-01394-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
Abstract
A Gram-staining-positive and aerobic coccus with the ability to degrade petroleum bacterium, designated Y42T, was isolated from the Lenghu oil field located in the northern margin of the Qaidam Basin. Phylogenetic and signature nucleotides analyses revealed that strain Y42T belongs to the genus Planococcus. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that strain Y42T formed a distinct lineage with the other Planococcus clade. The average nucleotide identity (ANI) and DNA-DNA hybridization values (DDH) between strain Y42T and the reference strains were 69.5-70.1 and 19.4-21.7%, respectively, which values were below the threshold for species delineation. The major fatty acids of strain Y42T were anteiso-C15:0. The respiratory quinone was MK-7 (71.8%) as the predominant menaquinone followed the MK-6 (28.2%) and the cell-wall hydrolysates contained LL-diaminopimelic acid. The polar lipid was composed of diphosphatidyl glycerol, phosphatidyl glycerol, phosphoglycolipid, aminophospholipid and four unidentified lipids. The peptidoglycan type was A4α (L-Lys-D-Glu). The strain Y42T possessed larger genome (approximately 4 MB) and revealed obvious differences for the abundance of the COG categories compared with the other Planococcus bacteria. Also, the strain Y42T also possessed more unique orthologous proteins. The structural characteristics of the strain Y42T genome provided a competitive advantage for better survival in petroleum-polluted environments. Combined with the 16S rRNA gene and genome sequence, phenotypic as well as chemotaxonomic characterisations, strain Y42T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus lenghuensis sp. nov. be proposed. The type strain is Y42T (= CGMCC 1.15921T = JCM 32719T).
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53
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Chaudhuri A, Das S, Das B. Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1591. [PMID: 32101377 DOI: 10.1002/wrna.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Intracellular trafficking and localization of mRNAs provide a mechanism of regulation of expression of genes with excellent spatial control. mRNA localization followed by localized translation appears to be a mechanism of targeted protein sorting to a specific cell-compartment, which is linked to the establishment of cell polarity, cell asymmetry, embryonic axis determination, and neuronal plasticity in metazoans. However, the complexity of the mechanism and the components of mRNA localization in higher organisms prompted the use of the unicellular organism Saccharomyces cerevisiae as a simplified model organism to study this vital process. Current knowledge indicates that a variety of mRNAs are asymmetrically and selectively localized to the tip of the bud of the daughter cells, to the vicinity of endoplasmic reticulum, mitochondria, and nucleus in this organism, which are connected to diverse cellular processes. Interestingly, specific cis-acting RNA localization elements (LEs) or RNA zip codes play a crucial role in the localization and trafficking of these localized mRNAs by providing critical binding sites for the specific RNA-binding proteins (RBPs). In this review, we present a comprehensive account of mRNA localization in S. cerevisiae, various types of localization elements influencing the mRNA localization, and the RBPs, which bind to these LEs to implement a number of vital physiological processes. Finally, we emphasize the significance of this process by highlighting their connection to several neuropathological disorders and cancers. This article is categorized under: RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Anusha Chaudhuri
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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54
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Lee S, Shin Y, Kim K, Song Y, Kim Y, Kang SW. Protein Translocation Acquires Substrate Selectivity Through ER Stress-Induced Reassembly of Translocon Auxiliary Components. Cells 2020; 9:cells9020518. [PMID: 32102453 PMCID: PMC7072789 DOI: 10.3390/cells9020518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 11/16/2022] Open
Abstract
Protein import across the endoplasmic reticulum membrane is physiologically regulated in a substrate-selective manner to ensure the protection of stressed ER from the overload of misfolded proteins. However, it is poorly understood how different types of substrates are accurately distinguished and disqualified during translocational regulation. In this study, we found poorly assembled translocon-associated protein (TRAP) complexes in stressed ER. Immunoaffinity purification identified calnexin in the TRAP complex in which poor assembly inhibited membrane insertion of the prion protein (PrP) in a transmembrane sequence-selective manner, through translocational regulation. This reaction was induced selectively by redox perturbation, rather than calcium depletion, in the ER. The liberation of ERp57 from calnexin appeared to be the reason for the redox sensitivity. Stress-independent disruption of the TRAP complex prevented a pathogenic transmembrane form of PrP (ctmPrP) from accumulating in the ER. This study uncovered a previously unappreciated role for calnexin in assisting the redox-sensitive function of the TRAP complex and provided insights into the ER stress-induced reassembly of translocon auxiliary components as a key mechanism by which protein translocation acquires substrate selectivity.
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Affiliation(s)
- Sohee Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea; (S.L.); (Y.S.); (Y.S.)
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul 05505, Korea
| | - Yejin Shin
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea; (S.L.); (Y.S.); (Y.S.)
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul 05505, Korea
| | - Kyunggon Kim
- Department of Convergence Medicine, Asan Medical Center, Seoul 05505, Korea;
| | - Youngsup Song
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea; (S.L.); (Y.S.); (Y.S.)
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul 05505, Korea
| | - Yongsub Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea; (S.L.); (Y.S.); (Y.S.)
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul 05505, Korea
| | - Sang-Wook Kang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea; (S.L.); (Y.S.); (Y.S.)
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul 05505, Korea
- Correspondence: ; Tel.: +82-2-3010-2205
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55
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Phelps DS, Chinchilli VM, Weisz J, Shearer D, Zhang X, Floros J. Using toponomics to characterize phenotypic diversity in alveolar macrophages from male mice treated with exogenous SP-A1. Biomark Res 2020; 8:5. [PMID: 32082572 PMCID: PMC7020580 DOI: 10.1186/s40364-019-0181-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/30/2019] [Indexed: 01/12/2023] Open
Abstract
Background We used the Toponome Imaging System (TIS) to identify “patterns of marker expression”, referred to here as combinatorial molecular phenotypes (CMPs) in alveolar macrophages (AM) in response to the innate immune molecule, SP-A1. Methods We compared 114 AM from male SP-A deficient mice. One group (n = 3) was treated with exogenous human surfactant protein A1 (hSP-A1) and the other with vehicle (n = 3). AM obtained by bronchoalveolar lavage were plated onto slides and analyzed using TIS to study the AM toponome, the spatial network of proteins within intact cells. With TIS, each slide is sequentially immunostained with multiple FITC-conjugated antibodies. Images are analyzed pixel-by-pixel identifying all of the proteins within each pixel, which are then designated as CMPs. CMPs represent organized protein clusters postulated to contribute to specific functions. Results 1) We compared identical CMPs in KO and SP-A1 cells and found them to differ significantly (p = 0.0007). Similarities between pairs of markers in the two populations also differed significantly (p < 0.0001). 2) Focusing on the 20 most abundant CMPs for each cell, we developed a method to generate CMP “signatures” that characterized various groups of cells. Phenotypes were defined as cells exhibiting similar signatures of CMPs. i) AM were extremely diverse and each group contained cells with multiple phenotypes. ii) Among the 114 AM analyzed, no two cells were identical. iii) However, CMP signatures could distinguish among cell subpopulations within and between groups. iv) Some cell populations were enriched with SP-A1 treatment, some were more common without SP-A1, and some seemed not to be influenced by the presence of SP-A1. v) We also found that AM were more diverse in mice treated with SP-A1 compared to those treated with vehicle. Conclusions AM diversity is far more extensive than originally thought. The increased diversity of SP-A1-treated mice points to the possibility that SP-A1 enhances or activates several pathways in the AM to better prepare it for its innate immune functions and other functions shown previously to be affected by SP-A treatment. Future studies may identify key protein(s) responsible for CMP integrity and consequently for a given function, and target it for therapeutic purposes.
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Affiliation(s)
- David S Phelps
- 1Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and Departments of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Vernon M Chinchilli
- 2Public Health Sciences; and Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Judith Weisz
- 3Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Debra Shearer
- 3Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Xuesheng Zhang
- 1Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and Departments of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Joanna Floros
- 1Penn State Center for Host defense, Inflammation, and Lung Disease (CHILD) Research and Departments of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA.,3Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
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56
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Hardenbrook NJ, Liu S, Zhou K, Ghosal K, Zhou ZH, Krantz BA. Atomic structures of anthrax toxin protective antigen channels bound to partially unfolded lethal and edema factors. Nat Commun 2020; 11:840. [PMID: 32047164 PMCID: PMC7012834 DOI: 10.1038/s41467-020-14658-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/15/2020] [Indexed: 11/09/2022] Open
Abstract
Following assembly, the anthrax protective antigen (PA) forms an oligomeric translocon that unfolds and translocates either its lethal factor (LF) or edema factor (EF) into the host cell. Here, we report the cryo-EM structures of heptameric PA channels with partially unfolded LF and EF at 4.6 and 3.1-Å resolution, respectively. The first α helix and β strand of LF and EF unfold and dock into a deep amphipathic cleft, called the α clamp, which resides at the interface of two PA monomers. The α-clamp-helix interactions exhibit structural plasticity when comparing the structures of lethal and edema toxins. EF undergoes a largescale conformational rearrangement when forming the complex with the channel. A critical loop in the PA binding interface is displaced for about 4 Å, leading to the weakening of the binding interface prior to translocation. These structures provide key insights into the molecular mechanisms of translocation-coupled protein unfolding and translocation.
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Affiliation(s)
- Nathan J Hardenbrook
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, 21201, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Kang Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Koyel Ghosal
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, 21201, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
| | - Bryan A Krantz
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, 21201, USA.
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57
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Kapuy O, Márton M, Bánhegyi G, Vinod PK. Multiple system-level feedback loops control life-and-death decisions in endoplasmic reticulum stress. FEBS Lett 2019; 594:1112-1123. [PMID: 31769869 DOI: 10.1002/1873-3468.13689] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/14/2019] [Indexed: 12/25/2022]
Abstract
Scientific results have revealed that autophagy is able to promote cell survival in response to endoplasmic reticulum (ER) stress, while drastic events result in apoptotic cell death. Here, we analyse the important crosstalk of life-and-death decisions from a systems biological perspective by studying the regulatory modules of the unfolded protein response (UPR). While a double-negative loop between autophagy and apoptosis inducers is crucial for the switch-like characteristic of the stress response mechanism, a positive feedback loop between ER stress sensors is also essential. Corresponding to experimental data, here, we show the dynamical significance of Gadd34-CHOP connections inside the PERK branch of the UPR. The multiple system-level feedback loops seem to be crucial for managing a robust life-and-death decision depending on the level and durability of cellular stress.
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Affiliation(s)
- Orsolya Kapuy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Margita Márton
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Gábor Bánhegyi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.,Pathobiochemistry Research Group of the Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - P K Vinod
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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58
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Van Puyenbroeck V, Pauwels E, Provinciael B, Bell TW, Schols D, Kalies KU, Hartmann E, Vermeire K. Preprotein signature for full susceptibility to the co-translational translocation inhibitor cyclotriazadisulfonamide. Traffic 2019; 21:250-264. [PMID: 31675144 DOI: 10.1111/tra.12713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 01/13/2023]
Abstract
Cyclotriazadisulfonamide (CADA) inhibits the co-translational translocation of human CD4 (huCD4) into the endoplasmic reticulum lumen in a signal peptide (SP)-dependent way. We propose that CADA binds the nascent huCD4 SP in a folded conformation within the translocon resembling a normally transitory state during translocation. Here, we used alanine scanning on the huCD4 SP to identify the signature for full susceptibility to CADA. In accordance with our previous work, we demonstrate that residues in the vicinity of the hydrophobic h-region are critical for sensitivity to CADA. In particular, exchanging Gln-15, Val-17 or Pro-20 in the huCD4 SP for Ala resulted in a resistant phenotype. Together with positively charged residues at the N-terminal portion of the mature protein, these residues mediate full susceptibility to the co-translational translocation inhibitory activity of CADA towards huCD4. In addition, sensitivity to CADA is inversely related to hydrophobicity in the huCD4 SP. In vitro translocation experiments confirmed that the general hydrophobicity of the h-domain and positive charges in the mature protein are key elements that affect both the translocation efficiency of huCD4 and the sensitivity towards CADA. Besides these two general SP parameters that determine the functionality of the signal sequence, unique amino acid pairs (L14/Q15 and L19/P20) in the SP hydrophobic core add specificity to the sensitivity signature for a co-translational translocation inhibitor.
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Affiliation(s)
- Victor Van Puyenbroeck
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Eva Pauwels
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Becky Provinciael
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Thomas W Bell
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Dominique Schols
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai-Uwe Kalies
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Kurt Vermeire
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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59
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Hegde RS, Zavodszky E. Recognition and Degradation of Mislocalized Proteins in Health and Disease. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033902. [PMID: 30833453 DOI: 10.1101/cshperspect.a033902] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A defining feature of eukaryotic cells is the segregation of complex biochemical processes among different intracellular compartments. The protein targeting, translocation, and trafficking pathways that sustain compartmentalization must recognize a diverse range of clients via degenerate signals. This recognition is imperfect, resulting in polypeptides at incorrect cellular locations. Cells have evolved mechanisms to selectively recognize mislocalized proteins and triage them for degradation or rescue. These spatial quality control pathways maintain cellular protein homeostasis, become especially important during organelle stress, and might contribute to disease when they are impaired or overwhelmed.
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Affiliation(s)
- Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Eszter Zavodszky
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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A Mechanistic Perspective on PEX1 and PEX6, Two AAA+ Proteins of the Peroxisomal Protein Import Machinery. Int J Mol Sci 2019; 20:ijms20215246. [PMID: 31652724 PMCID: PMC6862443 DOI: 10.3390/ijms20215246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
In contrast to many protein translocases that use ATP or GTP hydrolysis as the driving force to transport proteins across biological membranes, the peroxisomal matrix protein import machinery relies on a regulated self-assembly mechanism for this purpose and uses ATP hydrolysis only to reset its components. The ATP-dependent protein complex in charge of resetting this machinery—the Receptor Export Module (REM)—comprises two members of the “ATPases Associated with diverse cellular Activities” (AAA+) family, PEX1 and PEX6, and a membrane protein that anchors the ATPases to the organelle membrane. In recent years, a large amount of data on the structure/function of the REM complex has become available. Here, we discuss the main findings and their mechanistic implications.
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61
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Shcherbakov D, Teo Y, Boukari H, Cortes-Sanchon A, Mantovani M, Osinnii I, Moore J, Juskeviciene R, Brilkova M, Duscha S, Kumar HS, Laczko E, Rehrauer H, Westhof E, Akbergenov R, Böttger EC. Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis. Commun Biol 2019; 2:381. [PMID: 31637312 PMCID: PMC6797716 DOI: 10.1038/s42003-019-0626-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Translation fidelity is the limiting factor in the accuracy of gene expression. With an estimated frequency of 10-4, errors in mRNA decoding occur in a mostly stochastic manner. Little is known about the response of higher eukaryotes to chronic loss of ribosomal accuracy as per an increase in the random error rate of mRNA decoding. Here, we present a global and comprehensive picture of the cellular changes in response to translational accuracy in mammalian ribosomes impaired by genetic manipulation. In addition to affecting established protein quality control pathways, such as elevated transcript levels for cytosolic chaperones, activation of the ubiquitin-proteasome system, and translational slowdown, ribosomal mistranslation led to unexpected responses. In particular, we observed increased mitochondrial biogenesis associated with import of misfolded proteins into the mitochondria and silencing of the unfolded protein response in the endoplasmic reticulum.
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Affiliation(s)
- Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Adrian Cortes-Sanchon
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Matilde Mantovani
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Ivan Osinnii
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - James Moore
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Reda Juskeviciene
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Margarita Brilkova
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | | | - Endre Laczko
- Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, 8057 Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, 8057 Zurich, Switzerland
| | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
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Ito K, Mori H, Chiba S. Monitoring substrate enables real-time regulation of a protein localization pathway. FEMS Microbiol Lett 2019; 365:4983124. [PMID: 29790986 DOI: 10.1093/femsle/fny109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein localization machinery supports cell survival and physiology, suggesting the potential importance of its expression regulation. Here, we summarize a remarkable scheme of regulation, which allows real-time feedback regulation of the machinery expression. A class of regulatory nascent polypeptides, called monitoring substrates, undergoes force-sensitive translation arrest. The resulting ribosome stalling on the mRNA then affects mRNA folding to expose the ribosome-binding site of the downstream target gene and upregulate its translation. The target gene encodes a component of the localization machinery, whose physical action against the monitoring substrate leads to arrest cancellation. Thus, this scheme of feedback loop allows the cell to adjust the amount of the machinery to correlate inversely with the effectiveness of the process at a given moment. The system appears to have emerged late in evolution, in which a narrow range of organisms selected a distinct monitoring substrate-machinery combination. Currently, regulatory systems of SecM-SecA, VemP-SecDF2 and MifM-YidC2 are known to occur in different bacterial species.
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Affiliation(s)
- Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
| | - Hiroyuki Mori
- Japan and Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
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Abstract
In 1989, Normark and coworkers reported on fibrous surface structures called curli on strains of Escherichia coli that were suspected of causing bovine mastitis. Subsequent work by many groups has revealed an elegant and highly regulated curli biogenesis pathway also referred to as the type VIII secretion system. Curli biogenesis is governed by two divergently transcribed operons, csgBAC and csgDEFG. The csgBAC operon encodes the structural subunits of curli, CsgA and CsgB, along with a chaperone-like protein, CsgC. The csgDEFG operon encodes the accessory proteins required for efficient transcription, secretion, and assembly of the curli fiber. CsgA and CsgB are secreted as largely unstructured proteins and transition to β-rich structures that aggregate into regular fibers at the cell surface. Since both of these proteins have been shown to be amyloidogenic in nature, the correct spatiotemporal synthesis of the curli fiber is of paramount importance for proper functioning and viability. Gram-negative bacteria have evolved an elegant machinery for the safe handling, secretion, and extracellular assembly of these amyloidogenic proteins.
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Becker T, Song J, Pfanner N. Versatility of Preprotein Transfer from the Cytosol to Mitochondria. Trends Cell Biol 2019; 29:534-548. [PMID: 31030976 DOI: 10.1016/j.tcb.2019.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 11/16/2022]
Abstract
Mitochondrial biogenesis requires the import of a large number of precursor proteins from the cytosol. Although specific membrane-bound preprotein translocases have been characterized in detail, it was assumed that protein transfer from the cytosol to mitochondria mainly involved unselective binding to molecular chaperones. Recent findings suggest an unexpected versatility of protein transfer to mitochondria. Cytosolic factors have been identified that bind to selected subsets of preproteins and guide them to mitochondrial receptors in a post-translational manner. Cotranslational import processes are emerging. Mechanisms for crosstalk between protein targeting to mitochondria and other cell organelles, in particular the endoplasmic reticulum (ER) and peroxisomes, have been uncovered. We discuss how a network of cytosolic machineries and targeting pathways promote and regulate preprotein transfer into mitochondria.
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Affiliation(s)
- Thomas Becker
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany.
| | - Jiyao Song
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany.
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65
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Lee YW, Luther DC, Kretzmann JA, Burden A, Jeon T, Zhai S, Rotello VM. Protein Delivery into the Cell Cytosol using Non-Viral Nanocarriers. Theranostics 2019; 9:3280-3292. [PMID: 31244954 PMCID: PMC6567963 DOI: 10.7150/thno.34412] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/02/2019] [Indexed: 12/19/2022] Open
Abstract
Protein delivery into cells is a potentially transformative tool for treating "undruggable" targets in diseases associated with protein deficiencies or mutations. The vast majority of these targets are accessed via the cytosol, a challenging prospect for proteins with therapeutic and diagnostic relevance. In this review we will present promising non-viral approaches for intracellular and ultimately cytosolic delivery of proteins using nanocarriers. We will also discuss the mechanistic properties that govern the efficacy of nanocarrier-mediated protein delivery, applications of nanomaterials, and key challenges and opportunities in the use of nanocarriers for intracellular protein delivery.
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Affiliation(s)
- Yi-Wei Lee
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
| | - David C. Luther
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
| | - Jessica A. Kretzmann
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Andrew Burden
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
| | - Taewon Jeon
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
| | - Shumei Zhai
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
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Comparative Genome Characterization of a Petroleum-Degrading Bacillus subtilis Strain DM2. Int J Genomics 2019; 2019:7410823. [PMID: 31205931 PMCID: PMC6530121 DOI: 10.1155/2019/7410823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/19/2019] [Accepted: 03/24/2019] [Indexed: 12/12/2022] Open
Abstract
The complete genome sequence of Bacillus subtilis strain DM2 isolated from petroleum-contaminated soil on the Tibetan Plateau was determined. The genome of strain DM2 consists of a circular chromosome of 4,238,631 bp for 4458 protein-coding genes and a plasmid of 84,240 bp coding for 103 genes. Thirty-four genomic islands coding for 330 proteins and 5 prophages are found in the genome. The DDH value shows that strain DM2 belongs to B. subtilis subsp. subtilis subspecies, but significant variations of the genome are also present. Comparative analysis showed that the genome of strain DM2 encodes some strain-specific proteins in comparison with B. subtilis subsp. subtilis str. 168, such as carboxymuconolactone decarboxylase family protein, gfo/Idh/MocA family oxidoreductases, GlsB/YeaQ/YmgE family stress response membrane protein, HlyC/CorC family transporters, LLM class flavin-dependent oxidoreductase, and LPXTG cell wall anchor domain-containing protein. Most of the common strain-specific proteins in DM2 and MJ01 strains, or proteins unique to DM2 strain, are involved in the pathways related to stress response, signaling, and hydrocarbon degradation. Furthermore, the strain DM2 genome contains 122 genes coding for developed two-component systems and 138 genes coding for ABC transporter systems. The prominent features of the strain DM2 genome reflect the evolutionary fitness of this strain to harsh conditions and hydrocarbon utilization.
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Hsu YH, Chuang HC, Lee YH, Lin YF, Chen YJ, Hsiao TC, Wu MY, Chiu HW. Traffic-related particulate matter exposure induces nephrotoxicity in vitro and in vivo. Free Radic Biol Med 2019; 135:235-244. [PMID: 30878646 DOI: 10.1016/j.freeradbiomed.2019.03.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/03/2019] [Accepted: 03/09/2019] [Indexed: 12/14/2022]
Abstract
Traffic emission is responsible for most small-sized particulate matter (PM) air pollution in urban areas. Several recent studies have indicated that traffic-related PM may aggravate kidney disease. Furthermore, exposure to particulate air pollution may be related to the risk of chronic kidney disease (CKD). However, the underlying molecular mechanisms have not been adequately addressed. In the present study, we studied the mechanisms of renal damage that might be associated with exposure to PM. In a real world of whole-body exposure to traffic-related PM model for 3-6 months, PM in urban ambient air can affect kidney function and induce autophagy, endoplasmic reticulum (ER) stress and apoptosis in kidney tissues. Exposure to traffic-related diesel particulate matter (DPM) led to a reduction in cell viability in human kidney tubular epithelial cells HK-2. DPM increased mitochondrial reactive oxygen species (ROS) and decreased the mitochondrial membrane potential. Furthermore, DPM induced ER stress and activated the unfolded protein response (UPR) pathway. Eventually, DPM exposure induced caspase pathways and triggered apoptosis. In addition, DPM induced autophagy through the inhibition of the Akt/mTOR pathway. Autophagy inhibition resulted in significantly increased cytotoxicity and apoptosis. These findings suggest that air pollution in urban areas may cause nephrotoxicity and autophagy as a protective role in PM-induced cytotoxicity.
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Affiliation(s)
- Yung-Ho Hsu
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Yu-Hsuan Lee
- Department of Food Safety/Hygiene &Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuh-Feng Lin
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Jie Chen
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ta-Chih Hsiao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Taiwan
| | - Mei-Yi Wu
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Graduate of Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Hui-Wen Chiu
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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Boos F, Mühlhaus T, Herrmann JM. Detection of Internal Matrix Targeting Signal-like Sequences (iMTS-Ls) in Mitochondrial Precursor Proteins Using the TargetP Prediction Tool. Bio Protoc 2018; 8:e2474. [PMID: 34395785 DOI: 10.21769/bioprotoc.2474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/06/2017] [Accepted: 12/15/2017] [Indexed: 11/02/2022] Open
Abstract
Mitochondria contain hundreds of proteins which are encoded by the nuclear genome and synthesized in the cytosol from where they are imported into the organelle. Sorting signals encoded in the primary and secondary sequence of these proteins mediate the recognition of newly synthesized precursor proteins and their subsequent translocation through the mitochondrial TOM and TIM translocases. Proteins of the mitochondrial matrix employ aminoterminal matrix targeting signals (MTSs), also called presequences, that are necessary and sufficient for their import into mitochondria. In most cases, these MTSs are proteolytically removed from the mature part of precursor proteins subsequent to their translocation into the matrix. Recently, internal MTS-like sequences (iMTS-Ls) were discovered in the mature region of many precursor proteins. Although these sequences are not sufficient for matrix targeting, they strongly increase the import competence of precursors by supporting their interaction with mitochondrial surface receptors. Due to their similarity to N-terminal MTSs, these iMTS-Ls can be identified using mitochondrial targeting prediction tools such as TargetP which was initially trained to recognize MTSs. In this protocol we describe how TargetP can be used to identify iMTS-Ls in protein sequences.
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Affiliation(s)
- Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern, Germany
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69
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Abstract
The billions of proteins inside a eukaryotic cell are organized among dozens of sub-cellular compartments, within which they are further organized into protein complexes. The maintenance of both levels of organization is crucial for normal cellular function. Newly made proteins that fail to be segregated to the correct compartment or assembled into the appropriate complex are defined as orphans. In this review, we discuss the challenges faced by a cell of minimizing orphaned proteins, the quality control systems that recognize orphans, and the consequences of excess orphans for protein homeostasis and disease.
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70
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Quintana JF, Pino RCD, Yamada K, Zhang N. Adaptation and Therapeutic Exploitation of the Plasma Membrane of African Trypanosomes. Genes (Basel) 2018; 9:E368. [PMID: 30037058 PMCID: PMC6071061 DOI: 10.3390/genes9070368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 12/19/2022] Open
Abstract
African trypanosomes are highly divergent from their metazoan hosts, and as part of adaptation to a parasitic life style have developed a unique endomembrane system. The key virulence mechanism of many pathogens is successful immune evasion, to enable survival within a host, a feature that requires both genetic events and membrane transport mechanisms in African trypanosomes. Intracellular trafficking not only plays a role in immune evasion, but also in homeostasis of intracellular and extracellular compartments and interactions with the environment. Significantly, historical and recent work has unraveled some of the connections between these processes and highlighted how immune evasion mechanisms that are associated with adaptations to membrane trafficking may have, paradoxically, provided specific sensitivity to drugs. Here, we explore these advances in understanding the membrane composition of the trypanosome plasma membrane and organelles and provide a perspective for how transport could be exploited for therapeutic purposes.
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Affiliation(s)
- Juan F Quintana
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | | | - Kayo Yamada
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | - Ning Zhang
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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71
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Measurement of Internal pH in Helicobacter pylori by Using Green Fluorescent Protein Fluorimetry. J Bacteriol 2018; 200:JB.00178-18. [PMID: 29735759 DOI: 10.1128/jb.00178-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/01/2018] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori is an organism known to colonize the normal human stomach. Previous studies have shown that the bacterium does this by elevating its periplasmic pH via the hydrolysis of urea. However, the value of the periplasmic pH was calculated indirectly from the proton motive force equation. To measure the periplasmic pH directly in H. pylori, we fused enhanced green fluorescent protein (EGFP) to the predicted twin-arginine signal peptides of HydA and KapA from H. pylori and TorA from Escherichia coli The fusion proteins were expressed in the H. pylori genome under the control of the cagA promoter. Confocal microscopic and cell fractionation/immunoblotting analyses detected TorA-EGFP in the periplasm and KapA-EGFP in both the periplasm and cytoplasm, while the mature form of HydA-EGFP was seen at low levels in the periplasm, with major cytoplasmic retention of the precursor form. With H. pylori expressing TorA-EGFP, we established a system to directly measure periplasmic pH based on the pH-sensitive fluorimetry of EGFP. These measurements demonstrated that the addition of 5 mM urea has little effect on the periplasmic pH at a medium pH higher than pH 6.5 but rapidly increases the periplasmic pH to pH 6.1 at an acidic medium pH (pH 5.0), corresponding to the opening of the proton-gated channel, UreI, and confirming the basis of gastric colonization. Measurements of the periplasmic pH in an HP0244 (FlgS)-deficient mutant of H. pylori expressing TorA-EGFP revealed a significant loss of the urea-dependent increase in the periplasmic pH at an acidic medium pH, providing additional evidence that FlgS is responsible for recruitment of urease to the inner membrane in association with UreI.IMPORTANCEHelicobacter pylori has been identified as the major cause of chronic superficial gastritis and peptic ulcer disease. In addition, persistent infection with H. pylori, which, if untreated, lasts for the lifetime of an infected individual, predisposes one to gastric malignancies, such as adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. A unique feature of the neutralophilic bacterium H. pylori is its ability to survive in the extremely acidic environment of the stomach through its acid acclimation mechanism. The presented results on measurements of periplasmic pH in H. pylori based on fluorimetry of fully active green fluorescent protein fusion proteins exported with the twin-arginine translocase system provide a reliable and rapid tool for the investigation of acid acclimation in H. pylori.
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De Miccolis Angelini RM, Abate D, Rotolo C, Gerin D, Pollastro S, Faretra F. De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits. BMC Genomics 2018; 19:436. [PMID: 29866047 PMCID: PMC5987419 DOI: 10.1186/s12864-018-4817-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/22/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses. RESULTS Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola, 31,103 for M. laxa and 28,890 for M. fructigena. Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea, Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola, 30 in M. laxa and 31 in M. fructigena. Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements. CONCLUSIONS This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola, M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.
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Affiliation(s)
- Rita M. De Miccolis Angelini
- Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy
| | - Domenico Abate
- Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy
| | - Caterina Rotolo
- Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy
| | - Donato Gerin
- Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy
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Xu C, Zhang BZ, Lin Q, Deng J, Yu B, Arya S, Yuen KY, Huang JD. Live attenuated Salmonella typhimurium vaccines delivering SaEsxA and SaEsxB via type III secretion system confer protection against Staphylococcus aureus infection. BMC Infect Dis 2018; 18:195. [PMID: 29699491 PMCID: PMC5921394 DOI: 10.1186/s12879-018-3104-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 04/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Staphylococcus aureus (S. aureus) causes a wide range of infectious diseases in human and animals. The emergence of antibiotic-resistant strains demands novel strategies for prophylactic vaccine development. In this study, live attenuated S. enterica subsp. enterica serotype Typhimurium (S. Typhimurium) vaccine against S. aureus infection was developed, in which Salmonella Pathogenesis Island-1 Type 3 Secretion System (SPI-1 T3SS) was employed to deliver SaEsxA and SaEsxB, two of ESAT-6-like (Early Secreted Antigenic Target-6) virulence factors of S. aureus. METHODS Antigens SaEsxA and SaEsxB were fused with the N-terminal secretion and translocation domain of SPI-1 effector SipA. And cytosolic delivery of Staphylococcal antigens into macrophages was examined by western blot. BALB/c mice were orally immunized with S. Typhimurium-SaEsxA and S. Typhimurium-SaEsxB vaccines. Antigen-specific humoral and Th1/Th17 immune responses were examined by ELISA and ELISPOT assays 7-9 days after the 2nd booster. For ELISPOT assays, the statistical significance was determined by Student's t test. The vaccine efficacy was evaluated by lethal challenge with two S. aureus clinical isolates Newman strain and USA 300 strain. Statistical significance was determined by Log rank (Mantel-Cox) analysis. And a P value of < 0.05 was considered statistically significant. RESULTS Oral administration of S. Typhimurium-SaEsxA and S. Typhimurium-SaEsxB vaccines induced antigen-specific humoral and Th1/Th17 immune responses, which increased the survival rate for vaccinated mice when challenged with S. aureus strains. CONCLUSIONS The newly developed S. Typhimurium-based vaccines delivering SaEsxA and SaEsxB by SPI-1 T3SS could confer protection against S. aureus infection. This study provides evidence that translocation of foreign antigens via Salmonella SPI-1 T3SS into the cytosol of antigen presenting cells (APCs) could induce potent immune responses against pathogens.
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Affiliation(s)
- Chen Xu
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Bao-Zhong Zhang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Qiubin Lin
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Jian Deng
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Bin Yu
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Smriti Arya
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China. .,HKU-Shenzhen Institute of Research and Innovation, Shenzhen, China. .,Shenzhen Institute of Advanced Technologies, Shenzhen, China.
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74
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Energy Requirements for Protein Secretion via the Flagellar Type III Secretion System. Methods Mol Biol 2018; 1615:449-457. [PMID: 28667628 DOI: 10.1007/978-1-4939-7033-9_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Protein transport across the cytoplasmic membrane is coupled to energy derived from adenosine triphosphate hydrolysis or the protein motive force (pmf). A sophisticated, multi-component type III secretion system exports substrate proteins of both the bacterial flagellum and virulence-associated injectisome system of many Gram-negative pathogens. The type-III secretion system is primarily a pmf-driven protein exporter. Here, I describe methods to investigate the export of substrate proteins into the culture supernatant under conditions that manipulate the pmf.
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75
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Bridges RJ, Bradbury NA. Cystic Fibrosis, Cystic Fibrosis Transmembrane Conductance Regulator and Drugs: Insights from Cellular Trafficking. Handb Exp Pharmacol 2018; 245:385-425. [PMID: 29460152 DOI: 10.1007/164_2018_103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The eukaryotic cell is organized into membrane-delineated compartments that are characterized by specific cadres of proteins sustaining biochemically distinct cellular processes. The appropriate subcellular localization of proteins is key to proper organelle function and provides a physiological context for cellular processes. Disruption of normal trafficking pathways for proteins is seen in several genetic diseases, where a protein's absence for a specific subcellular compartment leads to organelle disruption, and in the context of an individual, a disruption of normal physiology. Importantly, several drug therapies can also alter protein trafficking, causing unwanted side effects. Thus, a deeper understanding of trafficking pathways needs to be appreciated as novel therapeutic modalities are proposed. Despite the promising efficacy of novel therapeutic agents, the intracellular bioavailability of these compounds has proved to be a potential barrier, leading to failures in treatments for various diseases and disorders. While endocytosis of drug moieties provides an efficient means of getting material into cells, the subsequent release and endosomal escape of materials into the cytosol where they need to act has been a barrier. An understanding of cellular protein/lipid trafficking pathways has opened up strategies for increasing drug bioavailability. Approaches to enhance endosomal exit have greatly increased the cytosolic bioavailability of drugs and will provide a means of investigating previous drugs that may have been shelved due to their low cytosolic concentration.
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Affiliation(s)
- Robert J Bridges
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, USA
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, USA.
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Caraglio M, Orlandini E, Whittington SG. Driven Translocation of Linked Ring Polymers through a Pore. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b02023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Caraglio
- Dipartimento di Fisica e Astronomia, Sezione CNISM, and Università di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - E. Orlandini
- Dipartimento di Fisica e Astronomia, Sezione INFN, and Università di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - S. G. Whittington
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
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Kim SK, Lee DH, Kim OC, Kim JF, Yoon SH. Tunable Control of an Escherichia coli Expression System for the Overproduction of Membrane Proteins by Titrated Expression of a Mutant lac Repressor. ACS Synth Biol 2017; 6:1766-1773. [PMID: 28524655 DOI: 10.1021/acssynbio.7b00102] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Most inducible expression systems suffer from growth defects, leaky basal induction, and inhomogeneous expression levels within a host cell population. These difficulties are most prominent with the overproduction of membrane proteins that are toxic to host cells. Here, we developed an Escherichia coli inducible expression system for membrane protein production based on titrated expression of a mutant lac repressor (mLacI). Performance of the mLacI inducible system was evaluated in conjunction with commonly used lac operator-based expression vectors using a T7 or tac promoter. Remarkably, expression of a target gene can be titrated by the dose-dependent addition of l-rhamnose, and the expression levels were homogeneous in the cell population. The developed system was successfully applied to overexpress three membrane proteins that were otherwise difficult to produce in E. coli. This gene expression control system can be easily applied to a broad range of existing protein expression systems and should be useful in constructing genetic circuits that require precise output signals.
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Affiliation(s)
- Seong Keun Kim
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Biosystems
and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Dae-Hee Lee
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Biosystems
and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Oh Cheol Kim
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jihyun F. Kim
- Department
of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
| | - Sung Ho Yoon
- Department
of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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78
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Straub SP, Stiller SB, Wiedemann N, Pfanner N. Dynamic organization of the mitochondrial protein import machinery. Biol Chem 2017; 397:1097-1114. [PMID: 27289000 DOI: 10.1515/hsz-2016-0145] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 05/17/2016] [Indexed: 01/12/2023]
Abstract
Mitochondria contain elaborate machineries for the import of precursor proteins from the cytosol. The translocase of the outer mitochondrial membrane (TOM) performs the initial import of precursor proteins and transfers the precursors to downstream translocases, including the presequence translocase and the carrier translocase of the inner membrane, the mitochondrial import and assembly machinery of the intermembrane space, and the sorting and assembly machinery of the outer membrane. Although the protein translocases can function as separate entities in vitro, recent studies revealed a close and dynamic cooperation of the protein import machineries to facilitate efficient transfer of precursor proteins in vivo. In addition, protein translocases were found to transiently interact with distinct machineries that function in the respiratory chain or in the maintenance of mitochondrial membrane architecture. Mitochondrial protein import is embedded in a regulatory network that ensures protein biogenesis, membrane dynamics, bioenergetic activity and quality control.
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79
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Abstract
Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, consequently genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily. RNA localization is commonly driven by trans-regulatory factors, including RNA binding proteins at the core, which recognize specific cis-acting zipcode elements within the RNA transcripts. Here, we first review the functions and biological benefits of intracellular RNA trafficking, from the perspective of both coding and non-coding RNAs. Next, we discuss the molecular mechanisms that modulate this localization, emphasizing the diverse features of the cis- and trans-regulators involved, while also highlighting emerging technologies and resources that will prove instrumental in deciphering RNA targeting pathways. We then discuss recent findings that reveal how co-transcriptional regulatory mechanisms operating in the nucleus can dictate the downstream cytoplasmic localization of RNAs. Finally, we survey the growing number of human diseases in which RNA trafficking pathways are impacted, including spinal muscular atrophy, Alzheimer's disease, fragile X syndrome and myotonic dystrophy. Such examples highlight the need to further dissect RNA localization mechanisms, which could ultimately pave the way for the development of RNA-oriented diagnostic and therapeutic strategies. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Ashley Chin
- Institut de recherches cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, Canada
| | - Eric Lécuyer
- Institut de recherches cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, 2900 Boulevard Edouard-Montpetit, Montreal, Quebec, Canada.
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80
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Cuevas EP, Eraso P, Mazón MJ, Santos V, Moreno-Bueno G, Cano A, Portillo F. LOXL2 drives epithelial-mesenchymal transition via activation of IRE1-XBP1 signalling pathway. Sci Rep 2017; 7:44988. [PMID: 28332555 PMCID: PMC5362953 DOI: 10.1038/srep44988] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 02/17/2017] [Indexed: 12/14/2022] Open
Abstract
Epithelial-to-Mesenchymal Transition (EMT) is a key process contributing to the aggressiveness of cancer cells. EMT is triggered by activation of different transcription factors collectively known as EMT-TFs. Different cellular cues and cell signalling networks activate EMT at transcriptional and posttranscriptional level in different biological and pathological situations. Among them, overexpression of LOXL2 (lysyl oxidase-like 2) induces EMT independent of its catalytic activity. Remarkably, perinuclear/cytoplasmic accumulation of LOXL2 is a poor prognosis marker of squamous cell carcinomas and is associated to basal breast cancer metastasis by mechanisms no yet fully understood. Here, we report that overexpression of LOXL2 promotes its accumulation in the Endoplasmic Reticulum where it interacts with HSPA5 leading to activation of the IRE1-XBP1 signalling pathway of the ER-stress response. LOXL2-dependent IRE1-XBP1 activation induces the expression of several EMT-TFs: SNAI1, SNAI2, ZEB2 and TCF3 that are direct transcriptional targets of XBP1. Remarkably, inhibition of IRE1 blocks LOXL2-dependent upregulation of EMT-TFs thus hindering EMT induction.
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Affiliation(s)
- Eva P Cuevas
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain
| | - Pilar Eraso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain
| | - María J Mazón
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain
| | - Vanesa Santos
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain
| | - Gema Moreno-Bueno
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain.,Fundación MD Anderson International, Madrid, Spain
| | - Amparo Cano
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain
| | - Francisco Portillo
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, CIBERONC, Madrid, Spain
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81
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Navarro-Tapia E, Pérez-Torrado R, Querol A. Ethanol Effects Involve Non-canonical Unfolded Protein Response Activation in Yeast Cells. Front Microbiol 2017; 8:383. [PMID: 28326077 PMCID: PMC5339281 DOI: 10.3389/fmicb.2017.00383] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/23/2017] [Indexed: 12/25/2022] Open
Abstract
The unfolded protein response (UPR) is a conserved intracellular signaling pathway that controls transcription of endoplasmic reticulum (ER) homeostasis related genes. Ethanol stress has been recently described as an activator of the UPR response in yeast Saccharomyces cerevisiae, but very little is known about the causes of this activation. Although some authors ensure that the UPR is triggered by the unfolded proteins generated by ethanol in the cell, there are studies which demonstrate that protein denaturation occurs at higher ethanol concentrations than those used to trigger the UPR. Here, we studied UPR after ethanol stress by three different approaches and we concluded that unfolded proteins do not accumulate in the ER under. We also ruled out inositol depletion as an alternative mechanism to activate the UPR under ethanol stress discarding that ethanol effects on the cell decreased inositol levels by different methods. All these data suggest that ethanol, at relatively low concentrations, does not cause unfolded proteins in the yeasts and UPR activation is likely due to other unknown mechanism related with a restructuring of ER membrane due to the effect of ethanol.
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Affiliation(s)
| | | | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos-CSIC Valencia, Spain
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82
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Caballano-Infantes E, Terron-Bautista J, Beltrán-Povea A, Cahuana GM, Soria B, Nabil H, Bedoya FJ, Tejedo JR. Regulation of mitochondrial function and endoplasmic reticulum stress by nitric oxide in pluripotent stem cells. World J Stem Cells 2017; 9:26-36. [PMID: 28289506 PMCID: PMC5329687 DOI: 10.4252/wjsc.v9.i2.26] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/09/2016] [Accepted: 01/14/2017] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial dysfunction and endoplasmic reticulum stress (ERS) are global processes that are interrelated and regulated by several stress factors. Nitric oxide (NO) is a multifunctional biomolecule with many varieties of physiological and pathological functions, such as the regulation of cytochrome c inhibition and activation of the immune response, ERS and DNA damage; these actions are dose-dependent. It has been reported that in embryonic stem cells, NO has a dual role, controlling differentiation, survival and pluripotency, but the molecular mechanisms by which it modulates these functions are not yet known. Low levels of NO maintain pluripotency and induce mitochondrial biogenesis. It is well established that NO disrupts the mitochondrial respiratory chain and causes changes in mitochondrial Ca2+ flux that induce ERS. Thus, at high concentrations, NO becomes a potential differentiation agent due to the relationship between ERS and the unfolded protein response in many differentiated cell lines. Nevertheless, many studies have demonstrated the need for physiological levels of NO for a proper ERS response. In this review, we stress the importance of the relationships between NO levels, ERS and mitochondrial dysfunction that control stem cell fate as a new approach to possible cell therapy strategies.
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83
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Kim EJ, Jeon CS, Hwang I, Chung TD. Translocation Pathway-Dependent Assembly of Streptavidin- and Antibody-Binding Filamentous Virus-Like Particles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1601693. [PMID: 27762503 DOI: 10.1002/smll.201601693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/13/2016] [Indexed: 06/06/2023]
Abstract
Compared to well-tolerated p3 fusion, the display of fast-folding proteins fused to the minor capsid p7 and the major capsid p8, as well as in vivo biotinylation of biotin acceptor peptide (AP) fused to p7, are found to be markedly inefficient using the filamentous phage. Here, to overcome such limitations, the effect of translocation pathways, amber mutation, and phage and phagemid display systems on p7 and p8 display of antibody-binding domains are examined, while comparing the level of in vivo biotinylation of AP fused to p7 or p3. Interestingly, the in vivo biotinylation of AP occurs only in p3 fusion and the fast-folding antibody-binding scaffolds fused to p7 and p8 are best displayed via a twin-arginine translocation pathway in TG1 cells. The lower the expression level of the wild-type p8 and the smaller the size of the guest protein, the better the display of Z-domain fused to the recombinant p8. The in vivo biotinylated multifunctional filamentous virus-like particles can be vertically immobilized on streptavidin (SAV)-coated microspheres to resemble cellular microvilli-like structures, which reportedly enhance protein-protein interactions due to dramatically expanded flexible surface area.
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Affiliation(s)
- Eun Joong Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Chang Su Jeon
- Samsung Electronics Co., Ltd, Samsungjeonja-ro 1, Hwaseong-si, Gyeonggi-do, 18448, Korea
| | - Inseong Hwang
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Taek Dong Chung
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Advanced Institutes of Convergence Technology, Suwon-si, Gyeonggi-do, 16229, Korea
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84
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Lian X, Fang Y, Joseph E, Wang Q, Li J, Banerjee S, Lollar C, Wang X, Zhou HC. Enzyme–MOF (metal–organic framework) composites. Chem Soc Rev 2017; 46:3386-3401. [DOI: 10.1039/c7cs00058h] [Citation(s) in RCA: 791] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the syntheses and applications of metal–organic framework (MOF)–enzyme composites with specific emphasis on the merits MOFs bring to the immobilized enzymes.
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Affiliation(s)
- Xizhen Lian
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Yu Fang
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | | | - Qi Wang
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Jialuo Li
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Sayan Banerjee
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | | | - Xuan Wang
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Hong-Cai Zhou
- Department of Chemistry
- Texas A&M University
- College Station
- USA
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85
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Musich PR, Li Z, Zou Y. Xeroderma Pigmentosa Group A (XPA), Nucleotide Excision Repair and Regulation by ATR in Response to Ultraviolet Irradiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 996:41-54. [PMID: 29124689 DOI: 10.1007/978-3-319-56017-5_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The sensitivity of Xeroderma pigmentosa (XP) patients to sunlight has spurred the discovery and genetic and biochemical analysis of the eight XP gene products (XPA-XPG plus XPV) responsible for this disorder. These studies also have served to elucidate the nucleotide excision repair (NER) process, especially the critical role played by the XPA protein. More recent studies have shown that NER also involves numerous other proteins normally employed in DNA metabolism and cell cycle regulation. Central among these is ataxia telangiectasia and Rad3-related (ATR), a protein kinase involved in intracellular signaling in response to DNA damage, especially DNA damage-induced replicative stresses. This review summarizes recent findings on the interplay between ATR as a DNA damage signaling kinase and as a novel ligand for intrinsic cell death proteins to delay damage-induced apoptosis, and on ATR's regulation of XPA and the NER process for repair of UV-induced DNA adducts. ATR's regulatory role in the cytosolic-to-nuclear translocation of XPA will be discussed. In addition, recent findings elucidating a non-NER role for XPA in DNA metabolism and genome stabilization at ds-ssDNA junctions, as exemplified in prematurely aging progeroid cells, also will be reviewed.
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Affiliation(s)
- Phillip R Musich
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Zhengke Li
- Department of Cancer Genetics and Epigenetics, City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA, 91007, USA
| | - Yue Zou
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
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86
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Pankow S, Bamberger C, Calzolari D, Bamberger A, Yates JR. Deep interactome profiling of membrane proteins by co-interacting protein identification technology. Nat Protoc 2016; 11:2515-2528. [PMID: 27854364 PMCID: PMC5444904 DOI: 10.1038/nprot.2016.140] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Affinity purification coupled to mass spectrometry (AP-MS) is the method of choice for analyzing protein-protein interactions, but common protocols frequently recover only the most stable interactions and tend to result in low bait yield for membrane proteins. Here, we present a novel, deep interactome sequencing approach called CoPIT (co-interacting protein identification technology), which allows comprehensive identification and analysis of membrane protein interactomes and their dynamics. CoPIT integrates experimental and computational methods for a coimmunoprecipitation (Co-IP)-based workflow from sample preparation for mass spectrometric analysis to visualization of protein-protein interaction networks. The approach particularly improves the results for membrane protein interactomes, which have proven to be difficult to identify and analyze. CoPIT was used successfully to identify the interactome of the cystic fibrosis transmembrane conductance regulator (CFTR), demonstrating its validity and performance. The experimental step in this case achieved up to 100-fold-higher bait yield than previous methods by optimizing lysis, elution, sample clean-up and detection of interacting proteins by multidimensional protein identification technology (MudPIT). Here, we further provide evidence that CoPIT is applicable to other types of proteins as well, and that it can be successfully used as a general Co-IP method. The protocol describes all steps, ranging from considerations for experimental design, Co-IP, preparation of the sample for mass spectrometric analysis, and data analysis steps, to the final visualization of interaction networks. Although the experimental part can be performed in <3 d, data analysis may take up to a few weeks.
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Affiliation(s)
- Sandra Pankow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Casimir Bamberger
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Diego Calzolari
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Andreas Bamberger
- Department of Physics, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
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87
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Uppulury K, Kolomeisky AB. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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88
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Chakraborty J, Nath I, Verpoort F. Snapshots of encapsulated porphyrins and heme enzymes in metal-organic materials: A prevailing paradigm of heme mimicry. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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89
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Meng Z, Wang BY, Xiang JF, Shi Q, Chen CF. Self-Assembly of a [2]Pseudorotaxane by an Inchworm-Motion Mechanism. Chemistry 2016; 22:15075-15084. [PMID: 27601275 DOI: 10.1002/chem.201602785] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Indexed: 01/22/2023]
Abstract
The threading of biomolecules through pores or channels in membranes is important to validate the physiological activities of cells. To aid understanding of the controlling factors required for the translocation in space with confined size and distorted conformation, it is desirable to identify experimental systems with minimized complexity. We demonstrate the mechanism of a linear guest L1 threading into a tris(crown ether) host TC with a combinational distorted cavity to form a triply interlocked [2]pseudorotaxane 3in-[L1⊂TC]. An inchworm-motion mechanism is proposed for the process. For the forward-threading steps that lead to the formation of higher-order interlocked species, guest L1 must adopt a bent conformation to find the next crown ether cavity. Two simplified models are applied to investigate the self-assembly dynamic of 3in-[L1⊂TC]. Kinetic NMR spectroscopic and molecular dynamics (MD) studies show that formation of the singly penetrated species is fast, whereas formation of the doubly and triply threaded species is several orders of magnitude slower. During threading the freedom of both the guest L1 and host TC gradually decrease due to their interactions. This results in a significant entropy effect for the threading dynamic, which is also observed for the threading of a biomolecular chain through a channel.
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Affiliation(s)
- Zheng Meng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo-Yang Wang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun-Feng Xiang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Qiang Shi
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Chuan-Feng Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
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90
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Nötzel C, Lingner T, Klingenberg H, Thoms S. Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus. Traffic 2016; 17:1110-24. [PMID: 27392156 DOI: 10.1111/tra.12426] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022]
Abstract
The peroxisomal targeting signal type 1 (PTS1) is a seemingly simple peptide sequence at the C-terminal end of most peroxisomal matrix proteins. PTS1 can be described as a tripeptide with the consensus motif [S/A/C] [K/R/H] L. However, this description is neither necessary nor sufficient. It does not cover all cases of PTS1 proteins, and some proteins in accordance with this consensus do not target to the peroxisome. In order to find new PTS proteins in yeast and to arrive at a more complete description of the PTS1 consensus motif, we developed a machine learning approach that involves orthologue expansion of the set of known peroxisomal proteins. We performed a genome-wide in silico screen, characterised several PTS1-containing peptides and identified two new peroxisomal matrix proteins, which we named Pxp1 (Yel020c) and Pxp2 (Yjr111c). Based on these in silico and in vivo analyses, we revised the yeast PTS1 consensus which now includes all known PTS1 proteins.
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Affiliation(s)
- Christopher Nötzel
- Department of Child and Adolescent Health, University Medical Center, University of Göttingen, Göttingen, Germany.,Current address: Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Thomas Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.,Current address: Microarray and Deep Sequencing Core Facility, University Medical Center, University of Göttingen, Göttingen, Germany
| | - Heiner Klingenberg
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, University of Göttingen, Göttingen, Germany.
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91
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Cruys-Bagger N, Alasepp K, Andersen M, Ottesen J, Borch K, Westh P. Rate of Threading a Cellulose Chain into the Binding Tunnel of a Cellulase. J Phys Chem B 2016; 120:5591-600. [DOI: 10.1021/acs.jpcb.6b01877] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolaj Cruys-Bagger
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
- Novozymes A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Kadri Alasepp
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | - Morten Andersen
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | - Johnny Ottesen
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
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92
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Baldridge RD, Rapoport TA. Autoubiquitination of the Hrd1 Ligase Triggers Protein Retrotranslocation in ERAD. Cell 2016; 166:394-407. [PMID: 27321670 DOI: 10.1016/j.cell.2016.05.048] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/19/2016] [Accepted: 05/13/2016] [Indexed: 12/16/2022]
Abstract
Misfolded proteins of the ER are retrotranslocated to the cytosol, where they are polyubiquitinated, extracted from the membrane, and degraded by the proteasome. To investigate how the ER-associated Degradation (ERAD) machinery can accomplish retrotranslocation of a misfolded luminal protein domain across a lipid bilayer, we have reconstituted retrotranslocation with purified S. cerevisiae proteins, using proteoliposomes containing the multi-spanning ubiquitin ligase Hrd1. Retrotranslocation of the luminal domain of a membrane-spanning substrate is triggered by autoubiquitination of Hrd1. Substrate ubiquitination is a subsequent event, and the Cdc48 ATPase that completes substrate extraction from the membrane is not required for retrotranslocation. Ubiquitination of lysines in Hrd1's RING-finger domain is required for substrate retrotranslocation in vitro and for ERAD in vivo. Our results suggest that Hrd1 forms a ubiquitin-gated protein-conducting channel.
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Affiliation(s)
- Ryan D Baldridge
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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93
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Paul P, Röth S, Schleiff E. Importance of organellar proteins, protein translocation and vesicle transport routes for pollen development and function. PLANT REPRODUCTION 2016; 29:53-65. [PMID: 26874709 DOI: 10.1007/s00497-016-0274-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/18/2016] [Indexed: 05/27/2023]
Abstract
Protein translocation. Cellular homeostasis strongly depends on proper distribution of proteins within cells and insertion of membrane proteins into the destined membranes. The latter is mediated by organellar protein translocation and the complex vesicle transport system. Considering the importance of protein transport machineries in general it is foreseen that these processes are essential for pollen function and development. However, the information available in this context is very scarce because of the current focus on deciphering the fundamental principles of protein transport at the molecular level. Here we review the significance of protein transport machineries for pollen development on the basis of pollen-specific organellar proteins as well as of genetic studies utilizing mutants of known organellar proteins. In many cases these mutants exhibit morphological alterations highlighting the requirement of efficient protein transport and translocation in pollen. Furthermore, expression patterns of genes coding for translocon subunits and vesicle transport factors in Arabidopsis thaliana are summarized. We conclude that with the exception of the translocation systems in plastids-the composition and significance of the individual transport systems are equally important in pollen as in other cell types. Apparently for plastids only a minimal translocon, composed of only few subunits, exists in the envelope membranes during maturation of pollen. However, only one of the various transport systems known from thylakoids seems to be required for the function of the "simple thylakoid system" existing in pollen plastids. In turn, the vesicle transport system is as complex as seen for other cell types as it is essential, e.g., for pollen tube formation.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany
| | - Sascha Röth
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany.
- Cluster of Excellence Frankfurt, Goethe University, 60438, Frankfurt Am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, 60438, Frankfurt Am Main, Germany.
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Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M. An inter-species protein-protein interaction network across vast evolutionary distance. Mol Syst Biol 2016; 12:865. [PMID: 27107014 PMCID: PMC4848758 DOI: 10.15252/msb.20156484] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 02/22/2016] [Accepted: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an "inter-interactome" approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter-interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra-species networks. Although substantially reduced relative to intra-species networks, the levels of functional overlap in the yeast-human inter-interactome network uncover significant remnants of co-functionality widely preserved in the two proteomes beyond human-yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co-functionality. Such non-functional interactions, however, represent a reservoir from which nascent functional interactions may arise.
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Affiliation(s)
- Quan Zhong
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Samuel J Pevzner
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Biomedical Engineering, Boston University, Boston, MA, USA Boston University School of Medicine, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roberto Mosca
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona Catalonia, Spain
| | - Jörg Menche
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA, USA
| | - Mikko Taipale
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Murat Taşan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Changyu Fan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Xinping Yang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Patrick Haley
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan R Murray
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Flora Mer
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fana Gebreab
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Stanley Tam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrew MacWilliams
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Amélie Dricot
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Patrick Reichert
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Balaji Santhanam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas Rolland
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Benoit Charloteaux
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Albert-László Barabási
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA, USA Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona Catalonia, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Michael E Cusick
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yu Xia
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Frederick P Roth
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
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95
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Self-Optimized Biological Channels in Facilitating the Transmembrane Movement of Charged Molecules. JOURNAL OF BIOPHYSICS 2016; 2016:1657679. [PMID: 27022394 PMCID: PMC4789060 DOI: 10.1155/2016/1657679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/13/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022]
Abstract
We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and surface density of negative charges located at the channel interior-lining. These charges induce inside the channel a potential that plays a key role in controlling the particle current through the channel. It was shown that to facilitate the transmembrane particle movement the channel should be reasonably self-optimized so that its potential coincides with the resonant one, resulting in a large particle current across the channel. Observed facilitation appears to be an intrinsic property of biological channels, regardless of the external voltage or the particle concentration gradient. This facilitation is very selective in the sense that a channel of definite structure parameters can facilitate the transmembrane movement of only particles of proper valence at corresponding temperatures. Calculations also show that the modeled channel is nonohmic with the ion conductance which exhibits a resonance at the same channel potential as that identified in the current.
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96
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Peng Y, Kim MJ, Hullinger R, O'Riordan KJ, Burger C, Pehar M, Puglielli L. Improved proteostasis in the secretory pathway rescues Alzheimer's disease in the mouse. Brain 2016; 139:937-52. [PMID: 26787453 PMCID: PMC4805081 DOI: 10.1093/brain/awv385] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/29/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022] Open
Abstract
The aberrant accumulation of toxic protein aggregates is a key feature of many neurodegenerative diseases, including Huntington's disease, amyotrophic lateral sclerosis and Alzheimer's disease. As such, improving normal proteostatic mechanisms is an active target for biomedical research. Although they share common pathological features, protein aggregates form in different subcellular locations. Nε-lysine acetylation in the lumen of the endoplasmic reticulum has recently emerged as a new mechanism to regulate the induction of autophagy. The endoplasmic reticulum acetylation machinery includes AT-1/SLC33A1, a membrane transporter that translocates acetyl-CoA from the cytosol into the endoplasmic reticulum lumen, and ATase1 and ATase2, two acetyltransferases that acetylate endoplasmic reticulum cargo proteins. Here, we used a mutant form of α-synuclein to show that inhibition of the endoplasmic reticulum acetylation machinery specifically improves autophagy-mediated disposal of toxic protein aggregates that form within the secretory pathway, but not those that form in the cytosol. Consequently, haploinsufficiency of AT-1/SLC33A1 in the mouse rescued Alzheimer's disease, but not Huntington's disease or amyotrophic lateral sclerosis. In fact, intracellular toxic protein aggregates in Alzheimer's disease form within the secretory pathway while in Huntington's disease and amyotrophic lateral sclerosis they form in different cellular compartments. Furthermore, biochemical inhibition of ATase1 and ATase2 was also able to rescue the Alzheimer's disease phenotype in a mouse model of the disease. Specifically, we observed reduced levels of soluble amyloid-β aggregates, reduced amyloid-β pathology, reduced phosphorylation of tau, improved synaptic plasticity, and increased lifespan of the animals. In conclusion, our results indicate that Nε-lysine acetylation in the endoplasmic reticulum lumen regulates normal proteostasis of the secretory pathway; they also support therapies targeting endoplasmic reticulum acetyltransferases, ATase1 and ATase2, for a subset of chronic degenerative diseases.
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Affiliation(s)
- Yajing Peng
- 1 Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Mi Jin Kim
- 2 Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Rikki Hullinger
- 1 Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA 3 Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Kenneth J O'Riordan
- 4 Department of Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | - Corinna Burger
- 3 Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA 4 Department of Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mariana Pehar
- 2 Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Luigi Puglielli
- 1 Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA 3 Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA 5 Geriatric Research Education Clinical Center, VA Medical Center, Madison, WI, USA 6 Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA 7 Wisconsin Alzheimer's Disease Research Center, University of Wisconsin-Madison, Madison, WI, USA
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97
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Bionda T, Gross LE, Becker T, Papasotiriou DG, Leisegang MS, Karas M, Schleiff E. Eukaryotic Hsp70 chaperones in the intermembrane space of chloroplasts. PLANTA 2016; 243:733-47. [PMID: 26669598 DOI: 10.1007/s00425-015-2440-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/27/2015] [Indexed: 06/05/2023]
Abstract
MAIN CONCLUSION Multiple eukaryotic Hsp70 typically localized in the cytoplasm are also distributed to the intermembrane space of chloroplasts and might thereby represent the missing link in energizing protein translocation. Protein translocation into organelles is a central cellular process that is tightly regulated. It depends on signals within the preprotein and on molecular machines catalyzing the process. Molecular chaperones participate in transport and translocation of preproteins into organelles to control folding and to provide energy for the individual steps. While most of the processes are explored and the components are identified, the transfer of preproteins into and across the intermembrane space of chloroplasts is not yet understood. The existence of an energy source in this compartment is discussed, because the required transit peptide length for successful translocation into chloroplasts is shorter than that found for mitochondria where energy is provided exclusively by matrix chaperones. Furthermore, a cytosolic-type Hsp70 homologue was proposed as component of the chloroplast translocon in the intermembrane space energizing the initial translocation. The molecular identity of such intermembrane space localized Hsp70 remained unknown, which led to a controversy concerning its existence. We identified multiple cytosolic Hsp70s by mass spectrometry on isolated, thermolysin-treated Medicago sativa chloroplasts. The localization of these Hsp70s of M. sativa or Arabidopsis thaliana in the intermembrane space was confirmed by a self-assembly GFP-based in vivo system. The localization of cytosolic Hsp70s in the stroma of chloroplasts or different mitochondrial compartments could not be observed. Similarly, we could not identify any cytosolic Hsp90 in the intermembrane space of chloroplast. With respect to our results we discuss the possible targeting and function of the Hsp70 found in the intermembrane space.
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Affiliation(s)
- Tihana Bionda
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Institute of Biochemistry II, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Lucia E Gross
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Thomas Becker
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Biochemistry and Molecular Biology, ZBMZ, and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Dimitrios G Papasotiriou
- Pharmaceutical Chemistry, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Syngenta Ltd., Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Matthias S Leisegang
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Michael Karas
- Pharmaceutical Chemistry, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Molecular Cell Biology of Plants, Cluster of Excellence Frankfurt, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Buchmann Institut for Molecular Life Sciences, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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98
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Chen T, Xiao J, Xu J, Wan W, Qin B, Cao A, Chen W, Xing L, Du C, Gao X, Zhang S, Zhang R, Shen W, Wang H, Wang X. Two members of TaRLK family confer powdery mildew resistance in common wheat. BMC PLANT BIOLOGY 2016; 16:27. [PMID: 26810982 PMCID: PMC4727334 DOI: 10.1186/s12870-016-0713-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/11/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Powdery mildew, caused by Blumeria graminearum f.sp. tritici (Bgt), is one of the most severe fungal diseases of wheat. The exploration and utilization of new gene resources is the most effective approach for the powdery mildew control. RESULTS We report the cloning and functional analysis of two wheat LRR-RLKs from T. aestivum c.v. Prins- T. timopheevii introgression line IGV1-465, named TaRLK1 and TaRLK2, which play positive roles in regulating powdery mildew resistance in wheat. The two LRR-RLKs contain an ORF of 3,045 nucleotides, encoding a peptide of 1014 amino acids, with seven amino acids difference. Their predicted proteins possess a signal peptide, several LRRs, a trans-membrane domain, and a Ser/Thr protein kinase domain. In response to Bgt infection, the TaRLK1/2 expression is up-regulated in a developmental-stage-dependent manner. Single-cell transient over-expression and gene-silencing assays indicate that both genes positively regulate the resistance to mixed Bgt inoculums. Transgenic lines over-expressing TaRLK1 or TaRLK2 in a moderate powdery mildew susceptible wheat variety Yangmai 158 led to significantly enhanced powdery mildew resistance. Exogenous applied salicylic acid (SA) or hydrogen peroxide (H2O2) induced the expression of both genes, and H2O2 had a higher accumulation at the Bgt penetration sites in RLK over-expression transgenic plants, suggesting a possible involvement of SA and altered ROS homeostasis in the defense response to Bgt infection. The two LRR-RLKs are located in the long arm of wheat chromosome 2B, in which the powdery mildew resistance gene Pm6 is located, but in different regions. CONCLUSIONS Two members of TaRLK family were cloned from IGV1-465. TaRLK1 and TaRLK2 contribute to powdery mildew resistance of wheat, providing new resistance gene resources for wheat breeding.
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Affiliation(s)
- Tingting Chen
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
| | - Jin Xiao
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Jun Xu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Wentao Wan
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Bi Qin
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.
| | - Aizhong Cao
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Wei Chen
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Liping Xing
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Chen Du
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Xiquan Gao
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Shouzhong Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Ruiqi Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Wenbiao Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Haiyan Wang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Xiue Wang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
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99
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FUJIKI Y. Peroxisome biogenesis and human peroxisome-deficiency disorders. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:463-477. [PMID: 27941306 PMCID: PMC5328784 DOI: 10.2183/pjab.92.463] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Peroxisome is a single-membrane-bounded ubiquitous organelle containing a hundred different enzymes that catalyze various metabolic pathways such as β-oxidation of very long-chain fatty acids and synthesis of plasmalogens. To investigate peroxisome biogenesis and human peroxisome biogenesis disorders (PBDs) including Zellweger syndrome, more than a dozen different complementation groups of Chinese hamster ovary (CHO) cell mutants impaired in peroxisome biogenesis are isolated as a model experimental system. By taking advantage of rapid functional complementation assay of the CHO cell mutants, successful cloning of PEX genes encoding peroxins required for peroxisome assembly invaluably contributed to the accomplishment of cloning of pathogenic genes responsible for PBDs. Peroxins are divided into three groups: 1) peroxins including Pex3p, Pex16p and Pex19p, are responsible for peroxisome membrane biogenesis via Pex19p- and Pex3p-dependent class I and Pex19p- and Pex16p-dependent class II pathways; 2) peroxins that function in matrix protein import; 3) those such as Pex11pβ are involved in peroxisome division where DLP1, Mff, and Fis1 coordinately function.
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Affiliation(s)
- Yukio FUJIKI
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Correspondence should be addressed: Y. Fujiki, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan (e-mail: )
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100
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Nosanchuk JD, Stark RE, Casadevall A. Fungal Melanin: What do We Know About Structure? Front Microbiol 2015; 6:1463. [PMID: 26733993 PMCID: PMC4687393 DOI: 10.3389/fmicb.2015.01463] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/07/2015] [Indexed: 12/22/2022] Open
Abstract
The production of melanin significantly enhances the virulence of many important human pathogenic fungi. Despite fungal melanin’s importance in human disease, as well as melanin’s contribution to the ability of fungi to survive in diverse hostile environments, the structure of melanin remains unsolved. Nevertheless, ongoing research efforts have progressively revealed several notable structural characteristics of this enigmatic pigment, which will be the focus of this review. These compositional and organizational insights could further our ability to develop novel therapeutic approaches to combat fungal disease and enhance our understanding of how melanin is inserted into the cell wall.
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Affiliation(s)
- Joshua D Nosanchuk
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of MedicineBronx, NY, USA; Microbiology and Immunology, Albert Einstein College of MedicineBronx, NY, USA
| | - Ruth E Stark
- Department of Chemistry and Biochemistry, The Graduate Center, The City College of New York, The City University of New YorkNew York, NY, USA; Institute for Macromolecular Assemblies, The City University of New YorkNew York, NY, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
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