351
|
Marshall CM, Tartaglio V, Duarte M, Harmon FG. The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing. THE PLANT CELL 2016; 28:2560-2575. [PMID: 27624757 PMCID: PMC5134976 DOI: 10.1105/tpc.16.00223] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/29/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
The circadian clock allows plants to anticipate and respond to daily changes in ambient temperature. Mechanisms establishing the timing of circadian rhythms in Arabidopsis thaliana through temperature entrainment remain unclear. Also incompletely understood is the temperature compensation mechanism that maintains consistent period length within a range of ambient temperatures. A genetic screen for Arabidopsis mutants affecting temperature regulation of the PSEUDO-RESPONSE REGULATOR7 promoter yielded a novel allele of the SICKLE (SIC) gene. This mutant, sic-3, and the existing sic-1 mutant both exhibit low-amplitude or arrhythmic expression of core circadian clock genes under cool ambient temperature cycles, but not under light-dark entrainment. sic mutants also lengthen free running period in a manner consistent with impaired temperature compensation. sic mutant alleles accumulate LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) splice variants, among other alternatively spliced transcripts, which is exacerbated by cool temperatures. The cca1-1 lhy-20 double mutant is epistatic to sic-3, indicating the LHY and CCA1 splice variants are needed for sic-3 circadian clock phenotypes. It is not expected that SIC is directly involved in the circadian clock mechanism; instead, SIC likely contributes to pre-mRNA metabolism, and the splice variants that accumulate in sic mutants likely affect the circadian clock response to cool ambient temperature.
Collapse
Affiliation(s)
- Carine M Marshall
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Virginia Tartaglio
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Maritza Duarte
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Frank G Harmon
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| |
Collapse
|
352
|
Zhao Y, Li L, Ma D, Luo J, Ma Z, Wang X, Pan Y, Chen J, Xi J, Yang J, Qiu L, Bai C, Jiang L, Shan X, Sun Q. Molecular Characterization and Viral Origin of the 2015 Dengue Outbreak in Xishuangbanna, Yunnan, China. Sci Rep 2016; 6:34444. [PMID: 27681163 PMCID: PMC5041078 DOI: 10.1038/srep34444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/13/2016] [Indexed: 11/17/2022] Open
Abstract
A total of 1067 serum samples were collected from febrile patients in Xishuangbanna, Yunnan, 2015. Of these, 852 cases were confirmed to be dengue NS1-positive. 76 structural protein genes were sequenced through RT-PCR based on the viral RNAs extracted from serum samples. Phylogenetic analysis revealed that all strains were classified as cosmopolitan genotype of DENV-2. After comparing with the DENV-2SS, 173 base substitutions were found in 76 sequences, resulting in 43 nonsynonymous mutations, of which 22 mutations existed among all samples. According to secondary structure prediction, 8 new possible nucelotide/protein binding sites were found and another 4 sites were lost among the 775 amino acids of DENV structural proteins as compared with DENV-2SS. Meanwhile, 6 distinct amino acid changes were found in the helix and strand regions, and the distribution of the exposed and buried regions was slightly altered. The results indicated that the epidemic dengue strains of Xishuangbanna in 2015 are most similar to the Indian strain in 2001 and the Sri Lankan strain in 2004. Moreover, it also show a very strong similarity to the epidemic strains of Fujian province in 1999 and 2010, which show that there is an internal recycling epidemic trend of DENV in China.
Collapse
Affiliation(s)
- Yujiao Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Lihua Li
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Dehong Ma
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Jia Luo
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
- Kunming Medical University, Kunming 650500, PR China
| | - Zhiqiang Ma
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Xiaodan Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Junying Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Juemin Xi
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Jiajia Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Lijuan Qiu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Chunhai Bai
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Liming Jiang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Xiyun Shan
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| |
Collapse
|
353
|
Bernhofer M, Kloppmann E, Reeb J, Rost B. TMSEG: Novel prediction of transmembrane helices. Proteins 2016; 84:1706-1716. [PMID: 27566436 DOI: 10.1002/prot.25155] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/18/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022]
Abstract
Transmembrane proteins (TMPs) are important drug targets because they are essential for signaling, regulation, and transport. Despite important breakthroughs, experimental structure determination remains challenging for TMPs. Various methods have bridged the gap by predicting transmembrane helices (TMHs), but room for improvement remains. Here, we present TMSEG, a novel method identifying TMPs and accurately predicting their TMHs and their topology. The method combines machine learning with empirical filters. Testing it on a non-redundant dataset of 41 TMPs and 285 soluble proteins, and applying strict performance measures, TMSEG outperformed the state-of-the-art in our hands. TMSEG correctly distinguished helical TMPs from other proteins with a sensitivity of 98 ± 2% and a false positive rate as low as 3 ± 1%. Individual TMHs were predicted with a precision of 87 ± 3% and recall of 84 ± 3%. Furthermore, in 63 ± 6% of helical TMPs the placement of all TMHs and their inside/outside topology was correctly predicted. There are two main features that distinguish TMSEG from other methods. First, the errors in finding all helical TMPs in an organism are significantly reduced. For example, in human this leads to 200 and 1600 fewer misclassifications compared to the second and third best method available, and 4400 fewer mistakes than by a simple hydrophobicity-based method. Second, TMSEG provides an add-on improvement for any existing method to benefit from. Proteins 2016; 84:1706-1716. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Michael Bernhofer
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany.
| | - Edda Kloppmann
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York, 10027
| | - Jonas Reeb
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany
| | - Burkhard Rost
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York, 10027.,Institute of Advanced Study (TUM-IAS), Lichtenbergstr. 2a, Garching/Munich, 85748, Germany.,Institute for Food and Plant Sciences WZW - Weihenstephan, Alte Akademie 8, Freising, Germany
| |
Collapse
|
354
|
Zhou T, Fleming JR, Franke B, Bogomolovas J, Barsukov I, Rigden DJ, Labeit S, Mayans O. CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex. FEBS Lett 2016; 590:3098-110. [PMID: 27531639 DOI: 10.1002/1873-3468.12362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 11/07/2022]
Abstract
The cardiac ankyrin repeat protein (CARP) is up-regulated in the myocardium during cardiovascular disease and in response to mechanical or toxic stress. Stress-induced CARP interacts with the N2A spring region of the titin filament to modulate muscle compliance. We characterize the interaction between CARP and titin-N2A and show that the binding site in titin spans the dual domain UN2A-Ig81. We find that the unique sequence UN2A is not structurally disordered, but that it has a stable, elongated α-helical fold that possibly acts as a constant force spring. Our findings portray CARP/titin-N2A as a structured node and help to rationalize the molecular basis of CARP mechanosensing in the sarcomeric I-band.
Collapse
Affiliation(s)
- Tiankun Zhou
- Department of Biology, University of Konstanz, Germany.,Institute of Integrative Biology, University of Liverpool, UK
| | - Jennifer R Fleming
- Department of Biology, University of Konstanz, Germany.,Institute of Integrative Biology, University of Liverpool, UK
| | | | - Julius Bogomolovas
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Igor Barsukov
- Institute of Integrative Biology, University of Liverpool, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, UK
| | - Siegfried Labeit
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Germany. .,Institute of Integrative Biology, University of Liverpool, UK.
| |
Collapse
|
355
|
Tian S, Chen H, Sun T, Wang H, Zhang X, Liu Y, Xia J, Guo C, Lin D. Expression, purification and characterization of Esx-1 secretion-associated protein EspL from Mycobacterium tuberculosis. Protein Expr Purif 2016; 128:42-51. [PMID: 27496726 DOI: 10.1016/j.pep.2016.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 01/13/2023]
Abstract
The Esx-1 cluster encodes a special secretion system that is important for granuloma formation and virulence when Mycobacterium tuberculosis infects the host. As one of the 'core' genes in the cluster, Rv3880c gene codes an Esx-1 secretion-associated protein EspL from Mycobacterium tuberculosis (MtEspL). It has been reported that EspL had a strong influence on the secretion of other two virulence factors, EsxA and EspE. However, so far little is known about the tertiary structure and specific function of MtEspL due to the difficulty in preparing the high-quality protein. In this study, we tried several fusion tags and various expression conditions to recombinantly express MtEspL. Through a four-step purification procedure, ultimately, we successfully prepared the full-length MtEspL in Escherichia coli BL21 (DE3) with a purity of 98%. The yields of the purified MtEspL protein were 14 mg/L in Luria Bertani medium and 5.6 mg/L in M9 minimal medium, respectively. Biophysical experiments showed that MtEspL existed in a dimeric form. Moreover, the (1)H-(15)N HSQC spectrum recorded on MtEspL illustrates a favorable dispersion of the resonance peaks, indicating that the symmetric dimeric MtEspL adopted a well-folded structure and might be feasible to determine its solution structure by NMR spectroscopy. Moreover, we identified a strong DNA-binding ability of MtEspL with fluorescence quenching experiments. Our work lays the basis for further structural determination and functional exploration of MtEspL.
Collapse
Affiliation(s)
- Shuangliang Tian
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Hanyu Chen
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Tao Sun
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Huilin Wang
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xuelian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Liu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jinmei Xia
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China
| | - Chenyun Guo
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Donghai Lin
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| |
Collapse
|
356
|
Xkr8 phospholipid scrambling complex in apoptotic phosphatidylserine exposure. Proc Natl Acad Sci U S A 2016; 113:9509-14. [PMID: 27503893 DOI: 10.1073/pnas.1610403113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Xk-related protein (Xkr) 8, a protein carrying 10 transmembrane regions, is essential for scrambling phospholipids during apoptosis. Here, we found Xkr8 as a complex with basigin (BSG) or neuroplastin (NPTN), type I membrane proteins in the Ig superfamily. In BSG(-/-)NPTN(-/-) cells, Xkr8 localized intracellularly, and the apoptosis stimuli failed to expose phosphatidylserine, indicating that BSG and NPTN chaperone Xkr8 to the plasma membrane to execute its scrambling activity. Mutational analyses of BSG showed that the atypical glutamic acid in the transmembrane region is required for BSG's association with Xkr8. In cells exposed to apoptotic signals, Xkr8 was cleaved at the C terminus and the Xkr8/BSG complex formed a higher-order complex, likely to be a heterotetramer consisting of two molecules of Xkr8 and two molecules of BSG or NPTN, suggesting that this cleavage causes the formation of a larger complex of Xkr8-BSG/NPTN for phospholipid scrambling.
Collapse
|
357
|
Gill HK, Cohen JD, Ayala-Figueroa J, Forman-Rubinsky R, Poggioli C, Bickard K, Parry JM, Pu P, Hall DH, Sundaram MV. Integrity of Narrow Epithelial Tubes in the C. elegans Excretory System Requires a Transient Luminal Matrix. PLoS Genet 2016; 12:e1006205. [PMID: 27482894 PMCID: PMC4970718 DOI: 10.1371/journal.pgen.1006205] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/28/2016] [Indexed: 02/07/2023] Open
Abstract
Most epithelial cells secrete a glycoprotein-rich apical extracellular matrix that can have diverse but still poorly understood roles in development and physiology. Zona Pellucida (ZP) domain glycoproteins are common constituents of these matrices, and their loss in humans is associated with a number of diseases. Understanding of the functions, organization and regulation of apical matrices has been hampered by difficulties in imaging them both in vivo and ex vivo. We identified the PAN-Apple, mucin and ZP domain glycoprotein LET-653 as an early and transient apical matrix component that shapes developing epithelia in C. elegans. LET-653 has modest effects on shaping of the vulva and epidermis, but is essential to prevent lumen fragmentation in the very narrow, unicellular excretory duct tube. We were able to image the transient LET-653 matrix by both live confocal imaging and transmission electron microscopy. Structure/function and fluorescence recovery after photobleaching studies revealed that LET-653 exists in two separate luminal matrix pools, a loose fibrillar matrix in the central core of the lumen, to which it binds dynamically via its PAN domains, and an apical-membrane-associated matrix, to which it binds stably via its ZP domain. The PAN domains are both necessary and sufficient to confer a cyclic pattern of duct lumen localization that precedes each molt, while the ZP domain is required for lumen integrity. Ectopic expression of full-length LET-653, but not the PAN domains alone, could expand lumen diameter in the developing gut tube, where LET-653 is not normally expressed. Together, these data support a model in which the PAN domains regulate the ability of the LET-653 ZP domain to interact with other factors at the apical membrane, and this ZP domain interaction promotes expansion and maintenance of lumen diameter. These data identify a transient apical matrix component present prior to cuticle secretion in C. elegans, demonstrate critical roles for this matrix component in supporting lumen integrity within narrow bore tubes such as those found in the mammalian microvasculature, and reveal functional importance of the evolutionarily conserved ZP domain in this tube protecting activity. Most organs in the body are made up of networks of tubes that transport fluids or gases. These tubes come in many different sizes and shapes, with some narrow capillaries being only one cell in diameter. As tubes develop and take their final shapes, they secrete various glycoproteins into their hollow interior or lumen. The functions of these luminal proteins are not well understood, but there is increasing evidence that they are important for lumen shaping and that their loss can contribute to diseases such as cardiovascular disease and chronic kidney disease. Through studies of the nematode C. elegans, we identified a luminal glycoprotein, LET-653, that is transiently expressed in multiple developing tube types but is particularly critical to maintain integrity of the narrowest, unicellular tubes. We identified protein domains that direct LET-653 to specific apical matrix compartments and mediate its oscillatory pattern of lumen localization. Furthermore, we showed that the LET-653 tube-protecting activity depends on a Zona Pellucida (ZP) domain similar to that found in the mammalian egg-coat and in many other luminal or sensory matrix proteins involved in human disease.
Collapse
Affiliation(s)
- Hasreet K. Gill
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jennifer D. Cohen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jesus Ayala-Figueroa
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rachel Forman-Rubinsky
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Corey Poggioli
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin Bickard
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jean M. Parry
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Georgian Court University, Lakewood, New Jersey, United States of America
| | - Pu Pu
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David H. Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Meera V. Sundaram
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
358
|
Mathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C. The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 2016; 283:3134-54. [PMID: 27390177 DOI: 10.1111/febs.13801] [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: 01/28/2016] [Revised: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED Transcription factors are known to modify the DNA that they bind. However, DNA can also serve as an allosteric ligand whose binding modifies the conformation of transcriptional regulators. Here, we describe how heterodimer PBX1:PREP1, formed by proteins playing major roles in embryonic development and tumorigenesis, undergoes an allosteric transition upon DNA binding. We demonstrate through a number of biochemical and biophysical methods that PBX1:PREP1 exhibits a structural change upon DNA binding. Small-angle X-ray scattering (SAXS), circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis demonstrate a different shape, α-helical content, thermodynamic behavior, and solution environment of the holo-complex (with DNA) compared to the apo-complex (without DNA). Given that PBX1 as such does not have a defined DNA selectivity, structural changes upon DNA binding become major factors in the function of the PBX1:PREP1 complex. The observed changes are mapped at both the amino- and carboxy-terminal regions of the two proteins thereby providing important insights to determine how PBX1:PREP1 dimer functions. DATABASE Small-angle scattering data are available in SASBDB under accession numbers SASDAP7, SASDAQ7, and SASDAR7.
Collapse
Affiliation(s)
- Lisa Mathiasen
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | | | - Angela Cattaneo
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Francesco Blasi
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | - Chiara Bruckmann
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| |
Collapse
|
359
|
Banushi B, Forneris F, Straatman-Iwanowska A, Strange A, Lyne AM, Rogerson C, Burden JJ, Heywood WE, Hanley J, Doykov I, Straatman KR, Smith H, Bem D, Kriston-Vizi J, Ariceta G, Risteli M, Wang C, Ardill RE, Zaniew M, Latka-Grot J, Waddington SN, Howe SJ, Ferraro F, Gjinovci A, Lawrence S, Marsh M, Girolami M, Bozec L, Mills K, Gissen P. Regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis. Nat Commun 2016; 7:12111. [PMID: 27435297 PMCID: PMC4961739 DOI: 10.1038/ncomms12111] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 06/01/2016] [Indexed: 01/12/2023] Open
Abstract
Post-translational modifications are necessary for collagen precursor molecules (procollagens) to acquire final shape and function. However, the mechanism and contribution of collagen modifications that occur outside the endoplasmic reticulum and Golgi are not understood. We discovered that VIPAR, with its partner proteins, regulate sorting of lysyl hydroxylase 3 (LH3, also known as PLOD3) into newly identified post-Golgi collagen IV carriers and that VIPAR-dependent sorting is essential for modification of lysines in multiple collagen types. Identification of structural and functional collagen abnormalities in cells and tissues from patients and murine models of the autosomal recessive multisystem disorder Arthrogryposis, Renal dysfunction and Cholestasis syndrome caused by VIPAR and VPS33B deficiencies confirmed our findings. Thus, regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis and for the development and function of multiple organs and tissues.
Collapse
Affiliation(s)
- Blerida Banushi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Federico Forneris
- Department of Biology and Biotechnology, The Armenise-Harvard Laboratory of Structural Biology, University of Pavia, Via Ferrata 9/A – 27100, Pavia, Italy
- Division of Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Adam Strange
- Eastman Dental Institute, University College London, London WC1X 8LD, UK
| | - Anne-Marie Lyne
- Department of Statistical Science, University College London, London WC1E 6BT, UK
| | - Clare Rogerson
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Jemima J. Burden
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Wendy E. Heywood
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Joanna Hanley
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ivan Doykov
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Kornelis R. Straatman
- Centre for Core Biotechnology Services, University of Leicester, Leicester LE1 9HN, UK
| | - Holly Smith
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Danai Bem
- Centre for Cardiovascular Sciences, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Janos Kriston-Vizi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Gema Ariceta
- Department of Pediatric Nephrology, University Hospital Vall d'Hebron, Universitat Autonoma Barcelona, 119-129-08035 Barcelona, Spain
| | - Maija Risteli
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, 90220 Oulu, Finland
- Unit of Cancer Research and Translational Medicine, Faculty of Medicine, University of Oulu, Oulu 90014, Finland
- Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu 90029, Finland
| | - Chunguang Wang
- Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu 90029, Finland
- Medical Microbiology and Immunology, Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu 90014, Finland
| | | | | | - Julita Latka-Grot
- Children's Memorial Health Institute, 04-730 Warsaw, 20 Dzieci Polskich Avenue, Poland
| | - Simon N. Waddington
- Institute for Women's Health, University College London, London WC1E 6AU, UK
| | - S. J. Howe
- Institute for Women's Health, University College London, London WC1E 6AU, UK
| | - Francesco Ferraro
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Asllan Gjinovci
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Scott Lawrence
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Mark Girolami
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Laurent Bozec
- Eastman Dental Institute, University College London, London WC1X 8LD, UK
| | - Kevin Mills
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Institute of Child Health, University College London, London WC1N 1EH, UK
- Inherited Metabolic Diseases Unit, Great Ormond Street Hospital, London WC1N 3JH, UK
| |
Collapse
|
360
|
Import of a major mitochondrial enzyme depends on synergy between two distinct helices of its presequence. Biochem J 2016; 473:2813-29. [PMID: 27422783 PMCID: PMC5095901 DOI: 10.1042/bcj20160535] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Abstract
Mammalian glutamate dehydrogenase (GDH), a nuclear-encoded enzyme central to cellular metabolism, is among the most abundant mitochondrial proteins (constituting up to 10% of matrix proteins). To attain such high levels, GDH depends on very efficient mitochondrial targeting that, for human isoenzymes hGDH1 and hGDH2, is mediated by an unusually long cleavable presequence (N53). Here, we studied the mitochondrial transport of these proteins using isolated yeast mitochondria and human cell lines. We found that both hGDHs were very rapidly imported and processed in isolated mitochondria, with their presequences (N53) alone being capable of directing non-mitochondrial proteins into mitochondria. These presequences were predicted to form two α helices (α1: N 1–10; α2: N 16–32) separated by loops. Selective deletion of the α1 helix abolished the mitochondrial import of hGDHs. While the α1 helix alone had a very weak hGDH mitochondrial import capacity, it could direct efficiently non-mitochondrial proteins into mitochondria. In contrast, the α2 helix had no autonomous mitochondrial-targeting capacity. A peptide consisting of α1 and α2 helices without intervening sequences had GDH transport efficiency comparable with that of N53. Mutagenesis of the cleavage site blocked the intra-mitochondrial processing of hGDHs, but did not affect their mitochondrial import. Replacement of all three positively charged N-terminal residues (Arg3, Lys7 and Arg13) by Ala abolished import. We conclude that the synergistic interaction of helices α1 and α2 is crucial for the highly efficient import of hGDHs into mitochondria.
Collapse
|
361
|
Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics 2016; 32:3501-3503. [PMID: 27412096 PMCID: PMC5181560 DOI: 10.1093/bioinformatics/btw474] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/03/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022] Open
Abstract
Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information:Supplementary data are available at Bioinformatics online. Contact:msa@bio.sh
Collapse
Affiliation(s)
- Guy Yachdav
- Bioinformatik - I12, TUM, Garching, 85748, Germany.,Biosof LLC, New York, NY 10001, USA
| | | | | | - Robert Sheridan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ian Sillitoe
- Institute of Structure and Molecular Biology, University College London, London, UK
| | - James Procter
- Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | | | - Burkhard Rost
- Bioinformatik - I12, TUM, Garching, 85748, Germany.,Biosof LLC, New York, NY 10001, USA
| | | |
Collapse
|
362
|
Vasudevan K, Vera Cruz CM, Gruissem W, Bhullar NK. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib. FRONTIERS IN PLANT SCIENCE 2016; 7:915. [PMID: 27446145 PMCID: PMC4917536 DOI: 10.3389/fpls.2016.00915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level.
Collapse
Affiliation(s)
- Kumar Vasudevan
- Plant Biotechnology, Department of Biology ETH Zurich, Switzerland
| | | | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology ETH Zurich, Switzerland
| | | |
Collapse
|
363
|
Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2. Extremophiles 2016; 20:631-9. [PMID: 27315164 DOI: 10.1007/s00792-016-0852-8] [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: 02/11/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
Abstract
Na(+)/H(+) antiporters play important roles in ion and pH homeostasis. In this study, two NhaD homologues that effectively catalyze Na(+)/H(+) antiporter were identified from Halomonas sp. Y2, a halotolerant and alkaliphilic strain isolated from sodium enriched black liquor. They exhibited high sequence identity of 72 % and similar binding affinities for Na(+) and Li(+) translocation, while having different pH profiles. Ha-NhaD1 was active at pH 6.0 and most active at pH 8.0-8.5, whereas Ha-NhaD2 lacked activity at pH 6.0 but exhibited maximum activity at pH 9.5 or higher. Based on multiple alignments, 11 partially conserved residues were selected and corresponding mutants were generated for Ha-NhaD1. As expected, replacement of most of the hydrophobic residues abolished the cation exchange activities. Three serine residues at positions 200, 282 and 353 in Ha-NhaD1 were replaceable by alanines with partial retention of activity. The S353A mutant exhibited significantly reduced binding affinity for Na(+) and Li(+), while S282 mutant exhibited an alkaline shift of about 1.5 pH units, as compared to the wild type Ha-NhaD1. Serine at position 282 was predicted to be located in transmembrane segment VIII and was found to be important in regulating pH sensitivity in concert with flanking residues.
Collapse
|
364
|
De Petrocellis L, Arroyo FJ, Orlando P, Schiano Moriello A, Vitale RM, Amodeo P, Sánchez A, Roncero C, Bianchini G, Martín MA, López-Alvarado P, Menéndez JC. Tetrahydroisoquinoline-Derived Urea and 2,5-Diketopiperazine Derivatives as Selective Antagonists of the Transient Receptor Potential Melastatin 8 (TRPM8) Channel Receptor and Antiprostate Cancer Agents. J Med Chem 2016; 59:5661-83. [PMID: 27232526 DOI: 10.1021/acs.jmedchem.5b01448] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tetrahydroisoquinoline derivatives containing embedded urea functions were identified as selective TRPM8 channel receptor antagonists. Structure-activity relationships were investigated, with the following conclusions: (a) The urea function and the tetrahydroisoquinoline system are necessary for activity. (b) Bis(1-aryl-6,7dimethoxy-1,2,3,4-tetrahydroisoquinolyl)ureas are more active than compounds containing one tetrahydroisoquinoline ring and than an open phenetylamine ureide. (c) Trans compounds are more active than their cis isomers. (d) Aryl substituents are better than alkyls at the isoquinoline C-1 position. (e) Electron-withdrawing substituents lead to higher activities. The most potent compound is the 4-F derivative, with IC50 in the 10(-8) M range and selectivities around 1000:1 for most other TRP receptors. Selected compounds were found to be active in reducing the growth of LNCaP prostate cancer cells. TRPM8 inhibition reduces proliferation in the tumor cells tested but not in nontumor prostate cells, suggesting that the activity against prostate cancer is linked to TRPM8 inhibition.
Collapse
Affiliation(s)
- Luciano De Petrocellis
- Endocannabinoid Research Group, Institute of Protein Biochemistry and Institute of Applied Sciences & Intelligent Systems, National Research Council , Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Naples, Italy
| | - Francisco J Arroyo
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| | - Pierangelo Orlando
- Endocannabinoid Research Group, Institute of Protein Biochemistry, National Research Council , Via P. Castellino 111, 80131 Naples, Italy
| | - Aniello Schiano Moriello
- Endocannabinoid Research Group, Institute of Protein Biochemistry and Institute of Applied Sciences & Intelligent Systems, National Research Council , Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Naples, Italy
| | - Rosa Maria Vitale
- Endocannabinoid Research Group, Institute of Protein Biochemistry and Institute of Applied Sciences & Intelligent Systems, National Research Council , Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Naples, Italy
| | - Pietro Amodeo
- Endocannabinoid Research Group, Institute of Protein Biochemistry and Institute of Applied Sciences & Intelligent Systems, National Research Council , Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Naples, Italy
| | - Aránzazu Sánchez
- Departamento de Bioquímica y Biología Molecular II, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| | - Cesáreo Roncero
- Departamento de Bioquímica y Biología Molecular II, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| | - Giulia Bianchini
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| | - M Antonia Martín
- S.D. Química Analítica, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| | - Pilar López-Alvarado
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| | - J Carlos Menéndez
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense , 28040 Madrid, Spain
| |
Collapse
|
365
|
Mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase. Sci Rep 2016; 6:27638. [PMID: 27279452 PMCID: PMC4899746 DOI: 10.1038/srep27638] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 01/14/2023] Open
Abstract
The Japanese firefly squid Hotaru-ika (Watasenia scintillans) produces intense blue light from photophores at the tips of two arms. These photophores are densely packed with protein microcrystals that catalyse the bioluminescent reaction using ATP and the substrate coelenterazine disulfate. The squid is the only organism known to produce light using protein crystals. We extracted microcrystals from arm tip photophores and identified the constituent proteins using mass spectrometry and transcriptome libraries prepared from arm tip tissue. The crystals contain three proteins, wsluc1–3, all members of the ANL superfamily of adenylating enzymes. They share 19 to 21% sequence identity with firefly luciferases, which produce light using ATP and the unrelated firefly luciferin substrate. We propose that wsluc1–3 form a complex that crystallises inside the squid photophores, and that in the crystal one or more of the proteins catalyses the production of light using coelenterazine disulfate and ATP. These results suggest that ANL superfamily enzymes have independently evolved in distant species to produce light using unrelated substrates.
Collapse
|
366
|
Nosenko T, Böndel KB, Kumpfmüller G, Stephan W. Adaptation to low temperatures in the wild tomato species Solanum chilense. Mol Ecol 2016; 25:2853-69. [PMID: 27037798 DOI: 10.1111/mec.13637] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022]
Abstract
Molecular adaptation to abiotic stresses in plants is a complex process based mainly on the modifications of gene transcriptional activity and the alteration of protein-protein interactions. We used a combination of population genetic, comparative transcriptomic and plant physiology approaches to investigate the mechanisms of adaptation to low temperatures in Solanum chilense populations distributed along Andean altitudinal gradients. We found that plants from all populations have high chilling tolerance, which does not correlate with temperatures in their native habitats. In contrast, tolerance to freezing shows a significant association with altitude and temperature variables. We also observed the differences in expression patterns of cold-response genes between plants from high- and low-altitude populations. These results suggest that genetic adaptations to low temperatures evolved in high-altitude populations of S. chilense. At the transcriptional level, these adaptations may include high levels of constitutive expression of the genes encoding ICE1, the key transcription factor of the cold signalling pathway, and chloroplast ω-3 fatty acid desaturase FAD7. At the sequence level, a signature of selection associated with the adaptation to high altitudes was detected at the C-terminal part of ICE1 encoding the ACT regulatory domain.
Collapse
Affiliation(s)
- Tetyana Nosenko
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany
| | - Katharina B Böndel
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany.,Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9, 3FL, UK
| | - Gabriele Kumpfmüller
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany.,Museum für Naturkunde Berlin, Invalidenstr. 4, Berlin, 10115, Germany
| |
Collapse
|
367
|
Conserved Tryptophan Motifs in the Large Tegument Protein pUL36 Are Required for Efficient Secondary Envelopment of Herpes Simplex Virus Capsids. J Virol 2016; 90:5368-5383. [PMID: 27009950 DOI: 10.1128/jvi.03167-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/15/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Herpes simplex virus (HSV) replicates in the skin and mucous membranes, and initiates lytic or latent infections in sensory neurons. Assembly of progeny virions depends on the essential large tegument protein pUL36 of 3,164 amino acid residues that links the capsids to the tegument proteins pUL37 and VP16. Of the 32 tryptophans of HSV-1-pUL36, the tryptophan-acidic motifs (1766)WD(1767) and (1862)WE(1863) are conserved in all HSV-1 and HSV-2 isolates. Here, we characterized the role of these motifs in the HSV life cycle since the rare tryptophans often have unique roles in protein function due to their large hydrophobic surface. The infectivity of the mutants HSV-1(17(+))Lox-pUL36-WD/AA-WE/AA and HSV-1(17(+))Lox-CheVP26-pUL36-WD/AA-WE/AA, in which the capsid has been tagged with the fluorescent protein Cherry, was significantly reduced. Quantitative electron microscopy shows that there were a larger number of cytosolic capsids and fewer enveloped virions compared to their respective parental strains, indicating a severe impairment in secondary capsid envelopment. The capsids of the mutant viruses accumulated in the perinuclear region around the microtubule-organizing center and were not dispersed to the cell periphery but still acquired the inner tegument proteins pUL36 and pUL37. Furthermore, cytoplasmic capsids colocalized with tegument protein VP16 and, to some extent, with tegument protein VP22 but not with the envelope glycoprotein gD. These results indicate that the unique conserved tryptophan-acidic motifs in the central region of pUL36 are required for efficient targeting of progeny capsids to the membranes of secondary capsid envelopment and for efficient virion assembly. IMPORTANCE Herpesvirus infections give rise to severe animal and human diseases, especially in young, immunocompromised, and elderly individuals. The structural hallmark of herpesvirus virions is the tegument, which contains evolutionarily conserved proteins that are essential for several stages of the herpesvirus life cycle. Here we characterized two conserved tryptophan-acidic motifs in the central region of the large tegument protein pUL36 of herpes simplex virus. When we mutated these motifs, secondary envelopment of cytosolic capsids and the production of infectious particles were severely impaired. Our data suggest that pUL36 and its homologs in other herpesviruses, and in particular such tryptophan-acidic motifs, could provide attractive targets for the development of novel drugs to prevent herpesvirus assembly and spread.
Collapse
|
368
|
Glaubman J, Hofmann J, Bonney ME, Park S, Thomas JM, Kokona B, Ramos Falcón LI, Chung YK, Fairman R, Okeke IN. Self-association motifs in the enteroaggregative Escherichia coli heat-resistant agglutinin 1. MICROBIOLOGY-SGM 2016; 162:1091-1102. [PMID: 27166217 DOI: 10.1099/mic.0.000303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The heat-resistant agglutinin 1 (Hra1) is an integral outer membrane protein found in strains of Escherichia coli that are exceptional colonizers. Hra1 from enteroaggregative E. coli strain 042 is sufficient to confer adherence to human epithelial cells and to cause bacterial autoaggregation. Hra1 is closely related to the Tia invasin, which also confers adherence, but not autoaggregation. Here, we have demonstrated that Hra1 mediates autoaggregation by self-association and we hypothesize that at least some surface-exposed amino acid sequences that are present in Hra1, but absent in Tia, represent autoaggregation motifs. We inserted FLAG tags along the length of Hra1 and used immune-dot blots to verify that four in silico-predicted outer loops were indeed surface exposed. In Hra1 we swapped nine candidate motifs in three of these loops, ranging from one to ten amino acids in length, to the corresponding sequences in Tia. Three of the motifs were required for Hra1-mediated autoaggregation. The database was searched for other surface proteins containing these motifs; the GGXWRDDXK motif was also present in a surface-exposed region of Rck, a Salmonella enterica serotype Typhimurium complement resistance protein. Cloning and site-specific mutagenesis demonstrated that Rck can confer weak, GGXWRDDXK-dependent autoaggregation by self-association. Hra1 and Rck appear to form heterologous associations and GGXWRDDXK is required on both molecules for Hra1-Rck association. However, a GGYWRDDLKE peptide was not sufficient to interfere with Hra1-mediated autoaggregation. In the present study, three autoaggregation motifs in an integral outer membrane protein have been identified and it was demonstrated that at least one of them works in the context of a different cell surface.
Collapse
Affiliation(s)
| | | | - Megan E Bonney
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Sumin Park
- Department of Biology, Haverford College, Haverford, PA, USA
| | | | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, PA, USA
| | | | - Yoonjie K Chung
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Iruka N Okeke
- Department of Biology, Haverford College, Haverford, PA, USA
| |
Collapse
|
369
|
Pickles JC, Pant K, Mcginty LA, Yasaei H, Roberts T, Scott AD, Newbold RF. A mechanistic evaluation of the Syrian hamster embryo cell transformation assay (pH 6.7) and molecular events leading to senescence bypass in SHE cells. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 802:50-8. [PMID: 27169376 PMCID: PMC4877681 DOI: 10.1016/j.mrgentox.2016.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022]
Abstract
The implementation of the Syrian hamster embryo cell transformation assay (SHE CTA) into test batteries and its relevance in predicting carcinogenicity has been long debated. Despite prevalidation studies to ensure reproducibility and minimise the subjective nature of the assay's endpoint, an underlying mechanistic and molecular basis supporting morphological transformation (MT) as an indicator of carcinogenesis is still missing. We found that only 20% of benzo(a)pyrene-induced MT clones immortalised suggesting that, alone, the MT phenotype is insufficient for senescence bypass. From a total of 12 B(a)P- immortalised MT lines, inactivating p53 mutations were identified in 30% of clones, and the majority of these were consistent with the potent carcinogen's mode of action. Expression of p16 was commonly silenced or markedly reduced with extensive promoter methylation observed in 45% of MT clones, while Bmi1 was strongly upregulated in 25% of clones. In instances where secondary events to MT appeared necessary for senescence bypass, as evidenced by a transient cellular crisis, clonal growth correlated with monoallelic deletion of the CDKN2A/B locus. The findings further implicate the importance of p16 and p53 pathways in regulating senescence while providing a molecular evaluation of SHE CTA -derived variant MT clones induced by benzo(a)pyrene.
Collapse
Affiliation(s)
- Jessica C Pickles
- Institute of Cancer Genetics and Pharmacogenomics, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, United Kingdom.
| | - Kamala Pant
- BioReliance Corporation, 14920 Broschart Road, Rockville, MD 20850-3349, USA
| | - Lisa A Mcginty
- Institute of Cancer Genetics and Pharmacogenomics, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, United Kingdom
| | - Hemad Yasaei
- Institute of Cancer Genetics and Pharmacogenomics, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, United Kingdom
| | - Terry Roberts
- Institute of Cancer Genetics and Pharmacogenomics, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, United Kingdom
| | - Andrew D Scott
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedford MK44 1LQ, United Kingdom
| | - Robert F Newbold
- Institute of Cancer Genetics and Pharmacogenomics, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, United Kingdom.
| |
Collapse
|
370
|
Alva V, Nam SZ, Söding J, Lupas AN. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res 2016; 44:W410-5. [PMID: 27131380 PMCID: PMC4987908 DOI: 10.1093/nar/gkw348] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/19/2016] [Indexed: 12/21/2022] Open
Abstract
The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g. HHpred, HHblits, PCOILS). While a beta version of the Toolkit was released 10 years ago, the current production-level release has been available since 2008 and has serviced more than 1.6 million external user queries. The usage of the Toolkit has continued to increase linearly over the years, reaching more than 400 000 queries in 2015. In fact, through the breadth of its tools and their tight interconnection, the Toolkit has become an excellent platform for experimental scientists as well as a useful resource for teaching bioinformatic inquiry to students in the life sciences. In this article, we report on the evolution of the Toolkit over the last ten years, focusing on the expansion of the tool repertoire (e.g. CS-BLAST, HHblits) and on infrastructural work needed to remain operative in a changing web environment.
Collapse
Affiliation(s)
- Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Seung-Zin Nam
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Johannes Söding
- Group for Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen D-37077, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| |
Collapse
|
371
|
Kwon YC, Kim S, Lee YS, Lee JC, Cho MJ, Lee WK, Kang HL, Song JY, Baik SC, Ro HS. Novel nuclear targeting coiled-coil protein of Helicobacter pylori showing Ca2+-independent, Mg2+-dependent DNase I activity. J Microbiol 2016; 54:387-95. [DOI: 10.1007/s12275-016-5631-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 01/02/2023]
|
372
|
Chen H, Wang H, Sun T, Tian S, Lin D, Guo C. Recombinant preparation and functional studies of EspI ATP binding domain from Mycobacterium tuberculosis. Protein Expr Purif 2016; 123:51-9. [PMID: 27017992 DOI: 10.1016/j.pep.2016.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 10/22/2022]
Abstract
The ESX-1 secretion system of Mycobacterium tuberculosis is required for the virulence of tubercle bacillus. EspI, the ESX-1 secretion-associated protein in Mycobacterium tuberculosis (MtEspI), is involved in repressing the activity of ESX-1-mediated secretion when the cellular ATP level is low. The ATP binding domain of MtEspI plays a crucial role in this regulatory process. However, further structural and functional studies of MtEspI are hindered due to the bottleneck of obtaining stable and pure recombinant protein. In this study, we systematically analyzed the structure and function of MtEspI using bioinformatics tools and tried various expression constructs to recombinantly express full-length and truncated MtEspI ATP binding domain. Finally, we prepared pure and stable MtEspI ATP binding domain, MtEspI415-493, in Escherichia coli by fusion expression and purification with dual tag, Glutathione S-transferase (GST) tag and (His)6 tag. (31)P NMR titration assay indicated that MtEspI415-493 possessed a moderate affinity (∼μM) for ATP and the residue K425 was located at the binding site. The protocol described here may provide a train of thought for recombinant preparation of other ESX-1 secretion-associated proteins.
Collapse
Affiliation(s)
- Hanyu Chen
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China
| | - Huilin Wang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China
| | - Tao Sun
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China
| | - Shuangliang Tian
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China.
| |
Collapse
|
373
|
Lear S, Cobb SL. Pep-Calc.com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment. J Comput Aided Mol Des 2016; 30:271-7. [PMID: 26909892 PMCID: PMC4801989 DOI: 10.1007/s10822-016-9902-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023]
Abstract
The ability to calculate molecular properties such as molecular weights, isoelectric points, and extinction coefficients is vital for scientists using and/or synthesizing peptides and peptoids for research. A suite of two web utilities: Peptide Calculator and Peptoid Calculator, available free at http://www.pep-calc.com, are presented. Both tools allow the calculation of peptide/peptoid chemical formulae and molecular weight, ChemDraw structure file export and automatic assignment of mass spectral peaks to deletion sequences and metal/protecting group adducts. Peptide Calculator also provides a calculated isoelectric point, molar extinction coefficient, graphical peptide charge summary and β-strand contiguity profile (for aggregation-prone sequences), indicating potential regions of synthesis difficulty. In addition to the unique automatic spectral assignment features offered across both utilities, Peptoid Calculator represents a first-of-a-kind resource for researchers in the field of peptoid science. With a constantly expanding database of over 120 amino acids, non-natural peptide building blocks and peptoid building blocks, it is anticipated that Pep-Calc.com will act as a valuable asset to those working on the synthesis and/or application of peptides and peptoids in the biophysical and life sciences fields.
Collapse
Affiliation(s)
- Sam Lear
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| |
Collapse
|
374
|
Jimenez-Lopez JC, Zafra A, Palanco L, Florido JF, Alché JDD. Identification and Assessment of the Potential Allergenicity of 7S Vicilins in Olive (Olea europaea L.) Seeds. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4946872. [PMID: 27034939 PMCID: PMC4789380 DOI: 10.1155/2016/4946872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/25/2016] [Accepted: 02/03/2016] [Indexed: 12/23/2022]
Abstract
Olive seeds, which are a raw material of interest, have been reported to contain 11S seed storage proteins (SSPs). However, the presence of SSPs such as 7S vicilins has not been studied. In this study, following a search in the olive seed transcriptome, 58 sequences corresponding to 7S vicilins were retrieved. A partial sequence was amplified by PCR from olive seed cDNA and subjected to phylogenetic analysis with other sequences. Structural analysis showed that olive 7S vicilin contains 9 α-helixes and 22 β-sheets. Additionally, 3D structural analysis displayed good superimposition with vicilin models generated from Pistacia and Sesamum. In order to assess potential allergenicity, T and B epitopes present in these proteins were identified by bioinformatic approaches. Different motifs were observed among the species, as well as some species-specific motifs. Finally, expression analysis of vicilins was carried out in protein extracts obtained from seeds of different species, including the olive. Noticeable bands were observed for all species in the 15-75 kDa MW interval, which were compatible with vicilins. The reactivity of the extracts to sera from patients allergic to nuts was also analysed. The findings with regard to the potential use of olive seed as food are discussed.
Collapse
Affiliation(s)
- Jose C. Jimenez-Lopez
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Adoración Zafra
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
- Elayo Group, Castillo de Locubín, 23670 Jaén, Spain
| | - Lucía Palanco
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | | | - Juan de Dios Alché
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| |
Collapse
|
375
|
Yeon JH, Heinkel F, Sung M, Na D, Gsponer J. Systems-wide Identification of cis-Regulatory Elements in Proteins. Cell Syst 2016; 2:89-100. [PMID: 27135163 DOI: 10.1016/j.cels.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/15/2015] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
Abstract
Protein interactions in cis that can activate or autoinhibit protein function play an important role in the fine-tuning of regulatory and signaling processes in the cell, but thus far cis-regulatory elements (CREs) in proteins have not been systematically identified and studied. Here, we introduce a computational tool that identifies intrinsically disordered protein segments that contribute to protein function regulation via interactions in cis. We apply this tool to estimate the prevalence of CREs in the human proteome and reveal that cis regulation is enriched in several signaling pathways, including the MAP kinase pathway, for which we provide a detailed map of its "cis regulome." We also show that disease-causing mutations are highly enriched in CREs, but not in motifs that classically mediate protein-protein interactions of disordered protein segments. Our approach should facilitate the discovery and characterization of CREs in proteins and the identification of disease-causing mutations that disrupt protein regulation in cis.
Collapse
Affiliation(s)
- Ju Hun Yeon
- Department of Integrative Bioscience, University of Brain Education, 284-31 Gyocheonjisan-gil, Mokcheon-eup, Dongnam-gu, Cheonan, Chungcheongnam-do 31228, Republic of Korea
| | - Florian Heinkel
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Minhui Sung
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada.
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada; Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
376
|
Sreedharan S, Kothandan G, Sankaranarayanan K. Structural insights into the Aedes aegypti aquaporins and aquaglyceroporins – an in silico study. J Recept Signal Transduct Res 2016; 36:543-557. [DOI: 10.3109/10799893.2016.1141954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sandhya Sreedharan
- AU-KBC Research Centre, Madras Institute of Technology, Anna University, Chennai, India and
| | - Gugan Kothandan
- Centre for Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | | |
Collapse
|
377
|
Neuhaus K, Landstorfer R, Fellner L, Simon S, Schafferhans A, Goldberg T, Marx H, Ozoline ON, Rost B, Kuster B, Keim DA, Scherer S. Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics 2016; 17:133. [PMID: 26911138 PMCID: PMC4765031 DOI: 10.1186/s12864-016-2456-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 02/09/2016] [Indexed: 12/30/2022] Open
Abstract
Background Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome). Results Using the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. Seven were verified by mass spectrometry. Fifty-seven genes are annotated in other enterobacteriaceae, mainly as hypothetical genes; the remaining 15 genes constitute novel discoveries. In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. Many of the novel genes show differential transcription when grown under eleven diverse growth conditions suggesting environmental regulation. Three genes were found to confer a phenotype in previous studies, e.g., decreased cattle colonization. Conclusions These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. All 72 genes are taxonomically restricted and, therefore, appear to have evolved relatively recently de novo. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2456-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Klaus Neuhaus
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
| | - Richard Landstorfer
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
| | - Lea Fellner
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
| | - Svenja Simon
- Lehrstuhl für Datenanalyse und Visualisierung, Fachbereich Informatik und Informationswissenschaft, Universität Konstanz, Box 78, 78457, Konstanz, Germany.
| | - Andrea Schafferhans
- Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität München, Boltzmannstraße 3, 85748, Garching, Germany.
| | - Tatyana Goldberg
- Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität München, Boltzmannstraße 3, 85748, Garching, Germany.
| | - Harald Marx
- Chair of Proteomics and Bioanalytics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany.
| | - Olga N Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, Moscow Region, 142290, Pushchino, Russia.
| | - Burkhard Rost
- Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität München, Boltzmannstraße 3, 85748, Garching, Germany.
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany. .,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany.
| | - Daniel A Keim
- Lehrstuhl für Datenanalyse und Visualisierung, Fachbereich Informatik und Informationswissenschaft, Universität Konstanz, Box 78, 78457, Konstanz, Germany.
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
| |
Collapse
|
378
|
PPIP5K1 interacts with the exocyst complex through a C-terminal intrinsically disordered domain and regulates cell motility. Cell Signal 2016; 28:401-411. [PMID: 26854614 DOI: 10.1016/j.cellsig.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/24/2022]
Abstract
Cellular signaling involves coordinated regulation of many events. Scaffolding proteins are crucial regulators of cellular signaling, because they are able to affect numerous events by coordinating specific interactions among multiple protein partners in the same pathway. Scaffolding proteins often contain intrinsically disordered regions (IDR) that facilitate the formation and function of distinct protein complexes. We show that PPIP5K1 contains an unusually long and evolutionarily conserved IDR. To investigate the biological role(s) of this domain, we identified interacting proteins using affinity purification coupled with mass spectrometry. Here, we report that PPIP5K1 is associated with a network of proteins that regulate vesicle-mediated transport. We further identified exocyst complex component 1 as a direct interactor with the IDR of PPIP5K1. Additionally, we report that knockdown of PPIP5K1 decreases motility of HeLa cells in a wound-healing assay. These results suggest that PPIP5K1 might play an important role in regulating function of exocyst complex in establishing cellular polarity and directional migration of cells.
Collapse
|
379
|
Savini F, Gallina L, Alberti A, Müller M, Scagliarini A. Bovine papillomavirus type 7 in Italy: complete genomes and sequence variants. Virus Genes 2016; 52:253-60. [PMID: 26837892 DOI: 10.1007/s11262-016-1298-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/19/2016] [Indexed: 01/09/2023]
Abstract
Two novel bovine papillomavirus type 7 (BPV-7) variants have been identified in teat cutaneous papillomas affecting dairy cows in northern Italy. The entire genome sequences of two BPV-7 Italian variants showed major sequence differences in the long control region (LCR) and in the L2 gene compared to the Japanese reference strain. In order to define the stability of these genetic variants, the L2 and LCR sequences of seven further BPV-7 positive isolates were characterized. An insertion of six amino acids in the L2 structural protein has been detected in all samples while different genetic variants have been identified for the LCR. These findings provide new insights on intra-type variability of BPVs and represent a starting point for future studies aimed at establishing the biological role of the different BPV genomic regions and investigating the pathogenic potential of papillomavirus variants.
Collapse
Affiliation(s)
- Federica Savini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Laura Gallina
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Alberto Alberti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Martin Müller
- Infections and Cancer Program, German Cancer Research Center (DKFZ), F035, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Alessandra Scagliarini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| |
Collapse
|
380
|
González Bardeci N, Caramelo JJ, Blumenthal DK, Rinaldi J, Rossi S, Moreno S. The PKA regulatory subunit from yeast forms a homotetramer: Low-resolution structure of the N-terminal oligomerization domain. J Struct Biol 2016; 193:141-54. [DOI: 10.1016/j.jsb.2015.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/13/2015] [Accepted: 12/06/2015] [Indexed: 01/23/2023]
|
381
|
In-Silico Computing of the Most Deleterious nsSNPs in HBA1 Gene. PLoS One 2016; 11:e0147702. [PMID: 26824843 PMCID: PMC4733110 DOI: 10.1371/journal.pone.0147702] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/07/2016] [Indexed: 01/30/2023] Open
Abstract
Background α-Thalassemia (α-thal) is a genetic disorder caused by the substitution of single amino acid or large deletions in the HBA1 and/or HBA2 genes. Method Using modern bioinformatics tools as a systematic in-silico approach to predict the deleterious SNPs in the HBA1 gene and its significant pathogenic impact on the functions and structure of HBA1 protein was predicted. Results and Discussion A total of 389 SNPs in HBA1 were retrieved from dbSNP database, which includes: 201 non-coding synonymous (nsSNPs), 43 human active SNPs, 16 intronic SNPs, 11 mRNA 3′ UTR SNPs, 9 coding synonymous SNPs, 9 5′ UTR SNPs and other types. Structural homology-based method (PolyPhen) and sequence homology-based tool (SIFT), SNPs&Go, PROVEAN and PANTHER revealed that 2.4% of the nsSNPs are pathogenic. Conclusions A total of 5 nsSNPs (G60V, K17M, K17T, L92F and W15R) were predicted to be responsible for the structural and functional modifications of HBA1 protein. It is evident from the deep comprehensive in-silico analysis that, two nsSNPs such as G60Vand W15R in HBA1 are highly deleterious. These “2 pathogenic nsSNPs” can be considered for wet-lab confirmatory analysis.
Collapse
|
382
|
The non-structural protein μNS of piscine orthoreovirus (PRV) forms viral factory-like structures. Vet Res 2016; 47:5. [PMID: 26743679 PMCID: PMC4705589 DOI: 10.1186/s13567-015-0302-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 09/04/2015] [Indexed: 01/15/2023] Open
Abstract
Piscine orthoreovirus (PRV) is associated with heart- and skeletal muscle inflammation in farmed Atlantic salmon. The virus is ubiquitous and found in both farmed and wild salmonid fish. It belongs to the family Reoviridae, closely related to the genus Orthoreovirus. The PRV genome comprises ten double-stranded RNA segments encoding at least eight structural and two non-structural proteins. Erythrocytes are the major target cells for PRV. Infected erythrocytes contain globular inclusions resembling viral factories; the putative site of viral replication. For the mammalian reovirus (MRV), the non-structural protein μNS is the primary organizer in factory formation. The analogous PRV protein was the focus of the present study. The subcellular location of PRV μNS and its co-localization with the PRV σNS, µ2 and λ1 proteins was investigated. We demonstrated that PRV μNS forms dense globular cytoplasmic inclusions in transfected fish cells, resembling the viral factories of MRV. In co-transfection experiments with μNS, the σNS, μ2 and λ1 proteins were recruited to the globular structures. The ability of μNS to recruit other PRV proteins into globular inclusions indicates that it is the main viral protein involved in viral factory formation and pivotal in early steps of viral assembly.
Collapse
|
383
|
Fleckenstein JM, Rasko DA. Overcoming Enterotoxigenic Escherichia coli Pathogen Diversity: Translational Molecular Approaches to Inform Vaccine Design. Methods Mol Biol 2016; 1403:363-83. [PMID: 27076141 DOI: 10.1007/978-1-4939-3387-7_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Enterotoxigenic Escherichia coli (ETEC) are a genetically diverse E. coli pathovar that share in the ability to produce heat-labile toxin and/or heat-stable toxins. While these pathogens contribute substantially to the burden of diarrheal illness in developing countries, at present, there is no suitable broadly protective vaccine to prevent these common infections. Most vaccine development attempts to date have followed a classical approach involving a relatively small group of antigens. The extraordinary underlying genetic plasticity of E. coli has confounded the antigen valency requirements based on this approach. The recent discovery of additional virulence proteins within this group of pathogens, as well as the availability of whole-genome sequences from hundreds of ETEC strains to facilitate identification of conserved molecules, now permits a reconsideration of the classical approaches, and the exploration of novel antigenic targets to complement existing strategies overcoming antigenic diversity that has impeded progress toward a broadly protective vaccine. Progress to date in antigen discovery and methods currently available to explore novel immunogens are outlined here.
Collapse
Affiliation(s)
- James M Fleckenstein
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Campus Box 8051, 660 South Euclid Avenue, St. Louis, MO, USA.
- Molecular Microbiology and Molecular Pathogenesis Program, Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA.
- Medicine Service, Veterans Affairs Medical Center, St. Louis, MO, USA.
| | - David A Rasko
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
384
|
Scarpati M, Heavner ME, Wiech E, Singh S. Proteomic Tools for the Analysis of Cytoskeleton Proteins. Methods Mol Biol 2016; 1365:385-413. [PMID: 26498799 DOI: 10.1007/978-1-4939-3124-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteomic analyses have become an essential part of the toolkit of the molecular biologist, given the widespread availability of genomic data and open source or freely accessible bioinformatics software. Tools are available for detecting homologous sequences, recognizing functional domains, and modeling the three-dimensional structure for any given protein sequence. Although a wealth of structural and functional information is available for a large number of cytoskeletal proteins, with representatives spanning all of the major subfamilies, the majority of cytoskeletal proteins remain partially or totally uncharacterized. Moreover, bioinformatics tools provide a means for studying the effects of synthetic mutations or naturally occurring variants of these cytoskeletal proteins. This chapter discusses various freely available proteomic analysis tools, with a focus on in silico prediction of protein structure and function. The selected tools are notable for providing an easily accessible interface for the novice, while retaining advanced functionality for more experienced computational biologists.
Collapse
Affiliation(s)
- Michael Scarpati
- Biology Program, The Graduate Center, City University of New York, New York, NY, USA
| | - Mary Ellen Heavner
- Biochemistry Program, The Graduate Center, City University of New York, New York, NY, USA
| | - Eliza Wiech
- Biology Program, The Graduate Center, City University of New York, New York, NY, USA
| | - Shaneen Singh
- Biochemistry Program, The Graduate Center, City University of New York, New York, NY, USA.
- Department of Biology, Brooklyn College, City University of New York, 209 Ingersoll Hall Extension, 2900 Bedford Ave., Brooklyn, NY, 11210, USA.
- Biology Program, The Graduate Center, City University of New York, New York, NY, USA.
| |
Collapse
|
385
|
TECPR2 mutations cause a new subtype of familial dysautonomia like hereditary sensory autonomic neuropathy with intellectual disability. Eur J Paediatr Neurol 2016; 20:69-79. [PMID: 26542466 DOI: 10.1016/j.ejpn.2015.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/24/2015] [Accepted: 10/04/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND TECPR2 was first described as a disease causing gene when the c.3416delT frameshift mutation was found in five Jewish Bukharian patients with similar features. It was suggested to constitute a new subtype of complex hereditary spastic paraparesis (SPG49). RESULTS We report here 3 additional patients from unrelated non-Bukharian families, harboring two novel mutations (c.1319delT, c.C566T) in this gene. Accumulating clinical data clarifies that in addition to intellectual disability and evolving spasticity the main disabling feature of this unique disorder is autonomic-sensory neuropathy accompanied by chronic respiratory disease and paroxysmal autonomic events. CONCLUSION We suggest that the disease should therefore be classified as a new subtype of hereditary sensory-autonomic neuropathy. The discovery of additional mutations in non-Bukharian patients implies that this disease might be more common than previously appreciated and should therefore be considered in undiagnosed cases of intellectual disability with autonomic features and respiratory symptoms regardless of demographic origin.
Collapse
|
386
|
Lemas D, Lekkas P, Ballif BA, Vigoreaux JO. Intrinsic disorder and multiple phosphorylations constrain the evolution of the flightin N-terminal region. J Proteomics 2015; 135:191-200. [PMID: 26691840 DOI: 10.1016/j.jprot.2015.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/23/2015] [Accepted: 12/04/2015] [Indexed: 01/05/2023]
Abstract
Flightin is a myosin binding phosphoprotein that originated in the ancestor to Pancrustacea ~500 MYA. In Drosophila melanogaster, flightin is essential for length determination and flexural rigidity of thick filaments. Here, we show that among 12 Drosophila species, the N-terminal region is characterized by low sequence conservation, low pI, a cluster of phosphorylation sites, and a high propensity to intrinsic disorder (ID) that is augmented by phosphorylation. Using mass spectrometry, we identified eight phosphorylation sites within a 29 amino acid segment in the N-terminal region of D. melanogaster flightin. We show that phosphorylation of D. melanogaster flightin is modulated during flight and, through a comparative analysis to orthologs from other Drosophila species, we found phosphorylation sites that remain invariant, sites that retain the charge character, and sites that are clade-specific. While the number of predicted phosphorylation sites differs across species, we uncovered a conserved pattern that relates the number of phosphorylation sites to pI and ID. Extending the analysis to orthologs of other insects, we found additional conserved features in flightin despite the near absence of sequence identity. Collectively, our results demonstrate that structural constraints demarcate the evolution of the highly variable N-terminal region.
Collapse
Affiliation(s)
- Dominick Lemas
- Department of Biology, University of Vermont, Burlington, VT 05405, United States
| | - Panagiotis Lekkas
- Department of Biology, University of Vermont, Burlington, VT 05405, United States
| | - Bryan A Ballif
- Department of Biology, University of Vermont, Burlington, VT 05405, United States
| | - Jim O Vigoreaux
- Department of Biology, University of Vermont, Burlington, VT 05405, United States.
| |
Collapse
|
387
|
da Palma JR, Cendron L, Seidah NG, Pasquato A, Kunz S. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P). J Biol Chem 2015; 291:2055-66. [PMID: 26645686 DOI: 10.1074/jbc.m115.677757] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/06/2022] Open
Abstract
The proprotein convertase subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in lipid homeostasis, the unfolded protein response, and lysosome biogenesis. The protease is further hijacked by highly pathogenic emerging viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P requires removal of an N-terminal prodomain, by a multistep process, generating the mature enzyme. Here, we uncover a modular structure of the human SKI-1/S1P prodomain and define its function in folding and activation. We provide evidence that the N-terminal AB fragment of the prodomain represents an autonomous structural and functional unit that is necessary and sufficient for folding and partial activation. In contrast, the C-terminal BC fragment lacks a defined structure but is crucial for autoprocessing and full catalytic activity. Phylogenetic analysis revealed that the sequence of the AB domain is highly conserved, whereas the BC fragment shows considerable variation and seems even absent in some species. Notably, SKI-1/S1P of arthropods, like the fruit fly Drosophila melanogaster, contains a shorter prodomain comprised of full-length AB and truncated BC regions. Swapping the prodomain fragments between fly and human resulted in a fully mature and active SKI-1/S1P chimera. Our study suggests that primordial SKI-1/S1P likely contained a simpler prodomain consisting of the highly conserved AB fragment that represents an independent folding unit. The BC region appears as a later evolutionary acquisition, possibly allowing more subtle fine-tuning of the maturation process.
Collapse
Affiliation(s)
- Joel Ramos da Palma
- From the Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne CH-1011, Switzerland
| | - Laura Cendron
- the Department of Biology, University of Padua, 35122 Padua, Italy, and
| | - Nabil Georges Seidah
- the Laboratory of Biochemical Neuroendocrinology, Clinical Research Institute of Montreal, University of Montreal, Montreal, Quebec H2W 1R7, Canada
| | - Antonella Pasquato
- From the Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne CH-1011, Switzerland,
| | - Stefan Kunz
- From the Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne CH-1011, Switzerland,
| |
Collapse
|
388
|
Farrow P, Khodosevich K, Sapir Y, Schulmann A, Aslam M, Stern-Bach Y, Monyer H, von Engelhardt J. Auxiliary subunits of the CKAMP family differentially modulate AMPA receptor properties. eLife 2015; 4:e09693. [PMID: 26623514 PMCID: PMC4733035 DOI: 10.7554/elife.09693] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/30/2015] [Indexed: 01/01/2023] Open
Abstract
AMPA receptor (AMPAR) function is modulated by auxiliary subunits. Here, we report on three AMPAR interacting proteins—namely CKAMP39, CKAMP52 and CKAMP59—that, together with the previously characterized CKAMP44, constitute a novel family of auxiliary subunits distinct from other families of AMPAR interacting proteins. The new members of the CKAMP family display distinct regional and developmental expression profiles in the mouse brain. Notably, despite their structural similarities they exert diverse modulation on AMPAR gating by influencing deactivation, desensitization and recovery from desensitization, as well as glutamate and cyclothiazide potency to AMPARs. This study indicates that AMPAR function is very precisely controlled by the cell-type specific expression of the CKAMP family members. The brain processes and transmits information through large networks of cells called neurons. A neuron can pass the information it receives to other neurons by releasing chemicals called neurotransmitters across junctions known as synapses. These chemicals bind to receptor proteins on the surface of the neighboring neuron, which triggers changes that affect the activity of this neuron. Glutamate is the most commonly used neurotransmitter in the brain and binds to receptor proteins called AMPA receptors. If a neuron frequently sends glutamate across a particular synapse, the number of AMPA receptors in the second neuron will increase in response. This makes signaling across the synapse easier – a process known as synaptic strengthening. The ability to change the strength of synapses is important for learning and memory. Proteins called auxiliary subunits also bind to AMPA receptors and regulate their properties, and hence also affect the strength of the synapse. For instance, some auxiliary subunits increase the number of AMPA receptors at the synapse, while others have an effect on how the receptor protein works. In 2010, researchers identified a new auxiliary protein called CKAMP44 that modifies AMPA receptor activity. Now, Farrow, Khodosevich, Sapir, Schulmann et al. – including some of the researchers involved in the 2010 study – have identified three other auxiliary proteins that are similar to CKAMP44. Collectively, these four proteins are termed the CKAMP family. The sequences of all four proteins were found to share many common features, especially in the regions that bind to the AMPA receptors. Like CKAMP44, the new members of the CKAMP family are only present in the brain, although each protein is produced in different brain regions. Further investigation revealed that each member of the CKAMP family affects the AMPA receptor channels in a different way. Taken together, Farrow et al.’s results suggest that the different CKAMP family members allow the activity of the AMPA receptors to be precisely controlled. The next challenge is to understand in more detail how each CKAMP family member influences how AMPA receptors work.
Collapse
Affiliation(s)
- Paul Farrow
- Synaptic Signalling and Neurodegeneration, German Cancer Research Center, Heidelberg, Germany.,Synaptic Signalling and Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Konstantin Khodosevich
- Department of Clinical Neurobiology, Medical Faculty of Heidelberg University, Heidelberg, Germany.,German Cancer Research Center, Heidelberg, Germany
| | - Yechiam Sapir
- Department of Biochemistry and Molecular Biology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Anton Schulmann
- Department of Clinical Neurobiology, Medical Faculty of Heidelberg University, Heidelberg, Germany.,German Cancer Research Center, Heidelberg, Germany
| | - Muhammad Aslam
- Synaptic Signalling and Neurodegeneration, German Cancer Research Center, Heidelberg, Germany.,Synaptic Signalling and Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Yael Stern-Bach
- Department of Biochemistry and Molecular Biology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Hannah Monyer
- Department of Clinical Neurobiology, Medical Faculty of Heidelberg University, Heidelberg, Germany
| | - Jakob von Engelhardt
- Synaptic Signalling and Neurodegeneration, German Cancer Research Center, Heidelberg, Germany.,Synaptic Signalling and Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany
| |
Collapse
|
389
|
Gnanadhas DP, Elango M, Datey A, Chakravortty D. Chronic lung infection by Pseudomonas aeruginosa biofilm is cured by L-Methionine in combination with antibiotic therapy. Sci Rep 2015; 5:16043. [PMID: 26521707 PMCID: PMC4629202 DOI: 10.1038/srep16043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/07/2015] [Indexed: 01/29/2023] Open
Abstract
Bacterial biofilms are associated with 80-90% of infections. Within the biofilm, bacteria are refractile to antibiotics, requiring concentrations >1,000 times the minimum inhibitory concentration. Proteins, carbohydrates and DNA are the major components of biofilm matrix. Pseudomonas aeruginosa (PA) biofilms, which are majorly associated with chronic lung infection, contain extracellular DNA (eDNA) as a major component. Herein, we report for the first time that L-Methionine (L-Met) at 0.5 μM inhibits Pseudomonas aeruginosa (PA) biofilm formation and disassembles established PA biofilm by inducing DNase expression. Four DNase genes (sbcB, endA, eddB and recJ) were highly up-regulated upon L-Met treatment along with increased DNase activity in the culture supernatant. Since eDNA plays a major role in establishing and maintaining the PA biofilm, DNase activity is effective in disrupting the biofilm. Upon treatment with L-Met, the otherwise recalcitrant PA biofilm now shows susceptibility to ciprofloxacin. This was reflected in vivo, in the murine chronic PA lung infection model. Mice treated with L-Met responded better to antibiotic treatment, leading to enhanced survival as compared to mice treated with ciprofloxacin alone. These results clearly demonstrate that L-Met can be used along with antibiotic as an effective therapeutic against chronic PA biofilm infection.
Collapse
Affiliation(s)
- Divya Prakash Gnanadhas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore, India
| | - Monalisha Elango
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Akshay Datey
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore, India
- The Bioengineering Program, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| |
Collapse
|
390
|
Identification of novel alleles of the rice blast resistance gene Pi54. Sci Rep 2015; 5:15678. [PMID: 26498172 PMCID: PMC4620502 DOI: 10.1038/srep15678] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 10/01/2015] [Indexed: 12/13/2022] Open
Abstract
Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.
Collapse
|
391
|
Vasudevan K, Gruissem W, Bhullar NK. Identification of novel alleles of the rice blast resistance gene Pi54. Sci Rep 2015. [PMID: 26498172 DOI: 10.1038/srep15678.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.
Collapse
Affiliation(s)
- Kumar Vasudevan
- Plant Biotechnology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland
| | - Navreet K Bhullar
- Plant Biotechnology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland
| |
Collapse
|
392
|
Characterization of Cercospora nicotianae Hypothetical Proteins in Cercosporin Resistance. PLoS One 2015; 10:e0140676. [PMID: 26474162 DOI: 10.1371/journal.pone.0140676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/29/2015] [Indexed: 11/19/2022] Open
Abstract
The photoactivated toxin, cercosporin, produced by Cercospora species, plays an important role in pathogenesis of this fungus to host plants. Cercosporin has almost universal toxicity to cells due to its production of reactive oxygen species including singlet oxygen. For that reason, Cercospora species, which are highly resistant to their own toxin, are good candidates to identify genes for resistance to cercosporin and to the reactive oxygen species it produces. In previous research, the zinc cluster transcription factor CRG1 (cercosporin resistance gene 1) was found to be crucial for Cercospora species' resistance against cercosporin, and subtractive hybridization analysis identified 185 genes differentially expressed between Cercospora nicotianae wild type (wt) and a crg1 mutant. The focus of this work was to identify and characterize the hypothetical proteins that were identified in the Cercospora nicotianae subtractive library as potential resistance factors. Quantitative RT-PCR analysis of the 20 genes encoding hypothetical proteins showed that two, 24cF and 71cR, were induced under conditions of cercosporin toxicity, suggesting a role in resistance. Transformation and expression of 24cF and 71cR in the cercosporin-sensitive fungus, Neurospora crassa, showed that 71cR provided increased resistance to cercosporin toxicity, whereas no significant increase was observed in 24cF transformants. Gene disruption was used to generate C. nicotianae 71cR mutants; these mutants did not differ from wt C. nicotianae in cercosporin resistance or production. Quantitative RT-PCR analysis showed induction of other resistance genes in the 71cR mutant that may compensate for the loss of 71cR. Analysis of 71cR conserved domains and secondary and tertiary structure identify the protein as having an NTF2-like superfamily DUF1348 domain with unknown function, to be intracellular and localized in the cytosol, and to have similarities to proteins in the steroid delta-isomerase family.
Collapse
|
393
|
Specific binding of eukaryotic ORC to DNA replication origins depends on highly conserved basic residues. Sci Rep 2015; 5:14929. [PMID: 26456755 PMCID: PMC4601075 DOI: 10.1038/srep14929] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/09/2015] [Indexed: 12/16/2022] Open
Abstract
In eukaryotes, the origin recognition complex (ORC) heterohexamer preferentially binds replication origins to trigger initiation of DNA replication. Crystallographic studies using eubacterial and archaeal ORC orthologs suggested that eukaryotic ORC may bind to origin DNA via putative winged-helix DNA-binding domains and AAA+ ATPase domains. However, the mechanisms how eukaryotic ORC recognizes origin DNA remain elusive. Here, we show in budding yeast that Lys-362 and Arg-367 residues of the largest subunit (Orc1), both outside the aforementioned domains, are crucial for specific binding of ORC to origin DNA. These basic residues, which reside in a putative disordered domain, were dispensable for interaction with ATP and non-specific DNA sequences, suggesting a specific role in recognition. Consistent with this, both residues were required for origin binding of Orc1 in vivo. A truncated Orc1 polypeptide containing these residues solely recognizes ARS sequence with low affinity and Arg-367 residue stimulates sequence specific binding mode of the polypeptide. Lys-362 and Arg-367 residues of Orc1 are highly conserved among eukaryotic ORCs, but not in eubacterial and archaeal orthologs, suggesting a eukaryote-specific mechanism underlying recognition of replication origins by ORC.
Collapse
|
394
|
Filteau M, Hamel V, Pouliot MC, Gagnon-Arsenault I, Dubé AK, Landry CR. Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. Mol Syst Biol 2015; 11:832. [PMID: 26459777 PMCID: PMC4631203 DOI: 10.15252/msb.20156444] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Since deleterious mutations may be rescued by secondary mutations during evolution, compensatory evolution could identify genetic solutions leading to therapeutic targets. Here, we tested this hypothesis and examined whether these solutions would be universal or would need to be adapted to one's genetic and environmental makeups. We performed experimental evolutionary rescue in a yeast disease model for the Wiskott–Aldrich syndrome in two genetic backgrounds and carbon sources. We found that multiple aspects of the evolutionary rescue outcome depend on the genotype, the environment, or a combination thereof. Specifically, the compensatory mutation rate and type, the molecular rescue mechanism, the genetic target, and the associated fitness cost varied across contexts. The course of compensatory evolution is therefore highly contingent on the initial conditions in which the deleterious mutation occurs. In addition, these results reveal biologically favored therapeutic targets for the Wiskott–Aldrich syndrome, including the target of an unrelated clinically approved drug. Our results experimentally illustrate the importance of epistasis and environmental evolutionary constraints that shape the adaptive landscape and evolutionary rate of molecular networks.
Collapse
Affiliation(s)
- Marie Filteau
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, Québec, Qc, Canada
| | - Véronique Hamel
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, Québec, Qc, Canada
| | - Marie-Christine Pouliot
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, Québec, Qc, Canada
| | - Isabelle Gagnon-Arsenault
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, Québec, Qc, Canada
| | - Alexandre K Dubé
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, Québec, Qc, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, Québec, Qc, Canada
| |
Collapse
|
395
|
The Ty1 Retrotransposon Restriction Factor p22 Targets Gag. PLoS Genet 2015; 11:e1005571. [PMID: 26451601 PMCID: PMC4599808 DOI: 10.1371/journal.pgen.1005571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/15/2015] [Indexed: 01/09/2023] Open
Abstract
A novel form of copy number control (CNC) helps maintain a low number of Ty1 retrovirus-like transposons in the Saccharomyces genome. Ty1 produces an alternative transcript that encodes p22, a trans-dominant negative inhibitor of Ty1 retrotransposition whose sequence is identical to the C-terminal half of Gag. The level of p22 increases with copy number and inhibits normal Ty1 virus-like particle (VLP) assembly and maturation through interactions with full length Gag. A forward genetic screen for CNC-resistant (CNCR) mutations in Ty1 identified missense mutations in GAG that restore retrotransposition in the presence of p22. Some of these mutations map within a predicted UBN2 domain found throughout the Ty1/copia family of long terminal repeat retrotransposons, and others cluster within a central region of Gag that is referred to as the CNCR domain. We generated multiple alignments of yeast Ty1-like Gag proteins and found that some Gag proteins, including those of the related Ty2 elements, contain non-Ty1 residues at multiple CNCR sites. Interestingly, the Ty2-917 element is resistant to p22 and does not undergo a Ty1-like form of CNC. Substitutions conferring CNCR map within predicted helices in Ty1 Gag that overlap with conserved sequence in Ty1/copia, suggesting that p22 disturbs a central function of the capsid during VLP assembly. When hydrophobic residues within predicted helices in Gag are mutated, Gag level remains unaffected in most cases yet VLP assembly and maturation is abnormal. Gag CNCR mutations do not alter binding to p22 as determined by co-immunoprecipitation analyses, but instead, exclude p22 from Ty1 VLPs. These findings suggest that the CNCR alleles enhance retrotransposition in the presence of p22 by allowing productive Gag-Gag interactions during VLP assembly. Our work also expands the strategies used by retroviruses for developing resistance to Gag-like restriction factors to now include retrotransposons. The presence of transposable elements in the eukaryotic genome threatens genomic stability and normal gene function, thus various defense mechanisms exist to silence element expression and target integration to benign locations in the genome. Even though the budding yeast Saccharomyces lacks many of the defense systems present in other eukaryotes, including RNAi, DNA methylation, and APOBEC3 proteins, they maintain low numbers of mobile elements in their genome. In the case of the Saccharomyces retrotransposon Ty1, a system called copy number control (CNC) helps determine the number of elements in the genome. Recently, we demonstrated that the mechanism of CNC relies on a trans-acting protein inhibitor of Ty1 expressed from the element itself. This protein inhibitor, called p22, impacts the replication of Ty1 as its copy number increases. To identify a molecular target of p22, mutagenized Ty1 was subjected to a forward genetic screen for CNC-resistance. Mutations in specific domains of Gag, including the UBN2 Gag motif and a novel region we have named the CNCR domain, confer CNCR by preventing the incorporation of p22 into assembling virus-like particles (VLPs), which restores maturation and completion of the Ty1 life cycle. The mechanism of Ty1 inhibition by p22 is conceptually similar to Gag-like restriction factors in mammals since they inhibit normal particle function. In particular, resistance to p22 and the enJS56A1 restriction factor of sheep involves exclusion of the restriction factor during particle assembly, although Ty1 CNCR achieves this in a way that is distinct from the Jaagsiekte retrovirus escape mutants. Our work introduces an intriguing variation on resistance mechanisms to retroviral restriction factors.
Collapse
|
396
|
Martín-Folgar R, de la Fuente M, Morcillo G, Martínez-Guitarte JL. Characterization of six small HSP genes from Chironomus riparius (Diptera, Chironomidae): Differential expression under conditions of normal growth and heat-induced stress. Comp Biochem Physiol A Mol Integr Physiol 2015; 188:76-86. [DOI: 10.1016/j.cbpa.2015.06.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/17/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
|
397
|
Calvete O, Martinez P, Garcia-Pavia P, Benitez-Buelga C, Paumard-Hernández B, Fernandez V, Dominguez F, Salas C, Romero-Laorden N, Garcia-Donas J, Carrillo J, Perona R, Triviño JC, Andrés R, Cano JM, Rivera B, Alonso-Pulpon L, Setien F, Esteller M, Rodriguez-Perales S, Bougeard G, Frebourg T, Urioste M, Blasco MA, Benítez J. A mutation in the POT1 gene is responsible for cardiac angiosarcoma in TP53-negative Li-Fraumeni-like families. Nat Commun 2015; 6:8383. [PMID: 26403419 DOI: 10.1038/ncomms9383] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 08/14/2015] [Indexed: 12/30/2022] Open
Abstract
Cardiac angiosarcoma (CAS) is a rare malignant tumour whose genetic basis is unknown. Here we show, by whole-exome sequencing of a TP53-negative Li-Fraumeni-like (LFL) family including CAS cases, that a missense variant (p.R117C) in POT1 (protection of telomeres 1) gene is responsible for CAS. The same gene alteration is found in two other LFL families with CAS, supporting the causal effect of the identified mutation. We extend the analysis to TP53-negative LFL families with no CAS and find the same mutation in a breast AS family. The mutation is recently found once in 121,324 studied alleles in ExAC server but it is not described in any other database or found in 1,520 Spanish controls. In silico structural analysis suggests how the mutation disrupts POT1 structure. Functional and in vitro studies demonstrate that carriers of the mutation show reduced telomere-bound POT1 levels, abnormally long telomeres and increased telomere fragility.
Collapse
Affiliation(s)
- Oriol Calvete
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Paula Martinez
- Telomeres and Telomerase Group, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Pablo Garcia-Pavia
- Department of Cardiology. Hospital Universitario Puerta de Hierro, Mahadahonda, Madrid 28222, Spain.,Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Carlos Benitez-Buelga
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain
| | - Beatriz Paumard-Hernández
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain
| | - Victoria Fernandez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain
| | - Fernando Dominguez
- Department of Cardiology. Hospital Universitario Puerta de Hierro, Mahadahonda, Madrid 28222, Spain
| | - Clara Salas
- Department of Pathology. Hospital Universitario Puerta de Hierro Majadahonda, Madrid 28222, Spain
| | - Nuria Romero-Laorden
- Oncology Department, Clara Campal Comprehensive Cancer Center, Sanchinarro, Madrid 28050, Spain
| | - Jesus Garcia-Donas
- Oncology Department, Clara Campal Comprehensive Cancer Center, Sanchinarro, Madrid 28050, Spain
| | - Jaime Carrillo
- Department of Experimental Models of Human Disease. Instituto Investigaciones Biomédicas (CSIC/UAM), Madrid 28029, Spain
| | - Rosario Perona
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Department of Experimental Models of Human Disease. Instituto Investigaciones Biomédicas (CSIC/UAM), Madrid 28029, Spain
| | | | - Raquel Andrés
- Medical Oncology Service, Hospital Universitario Lozano Blesa, Zaragoza 50009, Spain
| | - Juana María Cano
- Medical Oncology Service, Hospital General de Ciudad Real, Ciudad Real 13005, Spain
| | - Bárbara Rivera
- Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Luis Alonso-Pulpon
- Department of Cardiology. Hospital Universitario Puerta de Hierro, Mahadahonda, Madrid 28222, Spain
| | - Fernando Setien
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona 08007, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | | | - Gaelle Bougeard
- Genetics Department, Rouen University Hospital, Rouen 76000, France
| | - Tierry Frebourg
- Genetics Department, Rouen University Hospital, Rouen 76000, France
| | - Miguel Urioste
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain
| |
Collapse
|
398
|
Architecture of the mammalian mechanosensitive Piezo1 channel. Nature 2015; 527:64-9. [PMID: 26390154 DOI: 10.1038/nature15247] [Citation(s) in RCA: 294] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/24/2015] [Indexed: 12/12/2022]
Abstract
Piezo proteins are evolutionarily conserved and functionally diverse mechanosensitive cation channels. However, the overall structural architecture and gating mechanisms of Piezo channels have remained unknown. Here we determine the cryo-electron microscopy structure of the full-length (2,547 amino acids) mouse Piezo1 (Piezo1) at a resolution of 4.8 Å. Piezo1 forms a trimeric propeller-like structure (about 900 kilodalton), with the extracellular domains resembling three distal blades and a central cap. The transmembrane region has 14 apparently resolved segments per subunit. These segments form three peripheral wings and a central pore module that encloses a potential ion-conducting pore. The rather flexible extracellular blade domains are connected to the central intracellular domain by three long beam-like structures. This trimeric architecture suggests that Piezo1 may use its peripheral regions as force sensors to gate the central ion-conducting pore.
Collapse
|
399
|
Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol 2015; 35:49-59. [PMID: 26402567 DOI: 10.1016/j.sbi.2015.08.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.
Collapse
Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium; Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
400
|
Gee JA, Frausto RF, Chung DWD, Tangmonkongvoragul C, Le DJ, Wang C, Han J, Aldave AJ. Identification of novel PIKFYVE gene mutations associated with Fleck corneal dystrophy. Mol Vis 2015; 21:1093-100. [PMID: 26396486 PMCID: PMC4575904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/15/2015] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To report the identification of a novel frameshift mutation and copy number variation (CNV) in PIKFYVE in two probands with fleck corneal dystrophy (FCD). METHODS Slit-lamp examination was performed to identify characteristic features of FCD. After genomic DNA was collected, PCR amplification and automated sequencing of all 41 exons of PIKFYVE was performed. Using genomic DNA, quantitative PCR (qPCR) was performed to detect CNVs within PIKFYVE. RESULTS In the first FCD proband, numerous panstromal punctate opacities were observed in each of the proband's corneas, consistent with the diagnosis of FCD. Screening of PIKFYVE demonstrated a novel heterozygous frameshift mutation in exon 19, c.3151dupA, which is predicted to encode for a truncated PIKFYVE protein, p.(Asp1052Argfs*18). This variant was identified in an affected sister but not in the proband's unaffected mother or brother or 200 control chromosomes. The second FCD proband presented with bilateral, discrete, punctate, grayish-white stromal opacities. Exonic screening of PIKFYVE revealed no causative variant. However, CNV analysis demonstrated the hemizygous deletion of exons 15 and 16. CONCLUSIONS We report a novel heterozygous frameshift mutation (c.3151dupA) and a CNV in PIKFYVE, representing the first CNV and the fifth frameshift mutation associated with FCD.
Collapse
|