DOCSLIB.ORG

A Database for the Analysis of Small Heat Shock Proteins Emmanuel Jaspard, Gilles Hunault

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Database for the Analysis of Small Heat Shock Proteins Emmanuel Jaspard, Gilles Hunault sHSPdb: a database for the analysis of small Heat Shock Proteins Emmanuel Jaspard, Gilles Hunault To cite this version: Emmanuel Jaspard, Gilles Hunault. sHSPdb: a database for the analysis of small Heat Shock Proteins. BMC Plant Biology, BioMed Central, 2016, 16, pp.1-11. 10.1186/s12870-016-0820-6. hal-01602002 HAL Id: hal-01602002 https://hal.archives-ouvertes.fr/hal-01602002 Submitted on 27 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Jaspard and Hunault BMC Plant Biology (2016) 16:135 DOI 10.1186/s12870-016-0820-6 DATABASE Open Access sHSPdb: a database for the analysis of small Heat Shock Proteins Emmanuel Jaspard1,2,3* and Gilles Hunault4 Abstract Background: small Heat Shock Proteins (sHSP) is a wide proteins family. SHSP are found in all kingdoms and they play critical roles in plant stress tolerance mechanisms (as well as in pathogenic microorganisms and are implicated in human diseases). Results: sHSPdb (small Heat Shock Proteins database) is an integrated resource containing non-redundant, full-length and curated sequences of sHSP, classified on the basis of amino acids motifs and physico-chemical properties. sHSPdb gathers data about sHSP defined by various databases (Uniprot, PFAM, CDD, InterPro). It provides a browser interface for retrieving information from the whole database and a search interface using various criteria for retrieving a refined subset of entries. Physicochemical properties, amino acid composition and combinations are calculated for each entry. sHSPdb provides automatic statistical analysis of all sHSP properties. Among various possibilities, sHSPdb allows BLAST searches, alignment of selected sequences and submission of sequences. Conclusions: sHSPdb is a new database containing information about sHSP from all kingdoms. sHSPdb provides a classification of sHSP, as well as tools and data for the analysis of the structure - function relationships of sHSP. Data are mainly related to various physico-chemical properties of the amino acids sequences of sHSP. sHSPdb is accessible at http://forge.info.univ-angers.fr/~gh/Shspdb/index.php. Keywords: Small heat shock proteins, Amino acids sequence, Physico-chemical properties Background dimmers [6–8]. A study of all sHSP merged have shown Heat Shock Proteins (HSP) are proteins whose expres- that the average length of ACD is 90 ± 10 residues [9] sion is increased when cells are exposed to elevated and this length is much more constant than the N- and temperatures or other stress. Among HSP, sHSP belong C-terminal domains. However, we have classified sHSP to the superfamily of protein chaperones. They coun- into 21 classes and this value of average length of ACD teract the irreversible aggregation of misfolded proteins. does not apply anymore when considering sHSP class by sHSP are ubiquitous proteins found in all living organ- class. The N-terminal part of ACD is likely not necessary isms, from bacteria to mammals and especially in for dimerization or chaperone activity, but seems required plants [1–4]. Moreover, sHSP display a variety of sub- for higher order aggregates formation [10]. cellular localization and/or tissue distribution [3, 5]. As members of the chaperone network, sHSP play sHSP contain : (i) a highly variable (in both length important roles in cells exposed to heat and other and in sequence) N-terminal domain; (ii) a very con- stress, but their functional molecular mechanisms are served central domain called the Alpha Crystallin not fully elucidated. sHSP monomers (12–42 kDa) usu- Domain (ACD) involved in dimerization leading to the ally associate into large homo-oligomers of mostly 24 building block of higher order sHSP structure; (iii) a subunits [9, 11]. sHSP quaternary structures have a short C-terminal domain that links monomers inside high degree of plasticity due to changes in their oligo- meric state under different cellular conditions or to * Correspondence: [email protected] exchange of their subunits. Loosening of subunit 1 Université d’Angers, UMR 1345 IRHS, SFR 4207 QUASAV, Angers, France organization leads to more dynamic properties thus en- 2INRA, UMR 1345 IRHS, Beaucouzé, France Full list of author information is available at the end of the article hancing the available chaperone sites for the client © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Jaspard and Hunault BMC Plant Biology (2016) 16:135 Page 2 of 11 proteins. For example, it was shown that the sequence sHSP issue. The pertinence of the files annotation and that RLFDQ (found at the N-terminal part of ACD of of the sequences were checked using: (i) the sHSPdb « HSP27 - class number 12) contributes to the higher Search » option (see below); (ii) BLAST homology analysis order assembly of their subunits as well as their struc- and multiple alignments software; (iii) MOCAR (http:// tural stability [12]. Structural studies of numerous sHSP forge.info.univ-angers.fr/~gh/wstat/Mocar/), a program have brought details in monomer, transition of the olig- developed specifically for our sHSP classification based on omeric state [13–15] and sHSP chaperone mechanism pattern motif recognition in any Fasta sequences dataset; [12, 16]. (iv) the « Analyze »andthe«Statistical analysis »tools However, such approaches do not allow the compari- implemented in sHSPdb; (v) Finally, the motifs deter- sonofmorethanafewsHSPatatime.Onthecon- mined for each class of sHSP were further used to per- trary, sHSPdb offers access to large-scale analysis of form PHI-Blast allowing to get additional sequences. sHSP. Moreover, since sHSP is a very large protein fam- Sequence conflict (in particular in the case of AGI ily there is a wide discrepancy in annotation, definition entries for Arabidopsis thaliana) was checked using an- and terminology: sHSPdb provides a classification of notations from the Uniprot files. Identical sequences sHSP based on selective motifs, physicochemical prop- were removed using a program developed for sHSPdb erties and previous classification [17–19]. sHSPdb has feeding. This allowed detecting truncated, ambiguous been conceived with multiple functions to search and (e.g., annotated « unnamed protein », « hypothetical », describe the different sHSP. sHSPdb provides a global « unknown product »…, although some few populated vision of sHSP physicochemical properties, amino acid sHSP classes may contain such annotated files) or false usage, literature as well as statistical analysis on any sHSP sHSP sequences. Sequences containing the undefined dataset built by the user. Such a resource will be invalu- amino acid symbol (X) were removed. All files are able for computational analyses of sHSP structure - func- stored in sHSPdb but only non-redundant, full-length tion relationships, especially regarding the specific roles of and annotated ones are accessible. each of the three domains. sHSPdb is useful to gather The two holding chaperones (holdases) families, i.e., information about sHSPs from all kingdom. sHSPdb HSP31 and HSP33, cannot be considered formally as provides the largest set of sHSP sequences, a new clas- sHSP since they do not harbor the ACD domain, and sification and a precise description of each class of sHSP. interact with client proteins through Cys and disulfide Physico-chemical properties and statistical analysis pro- bonds formation [22]. However, these redox regulated vided by sHSPdb represent an actual plus-value. molecular chaperones have physico-chemical properties close to those of sHSP and also contribute to protein Construction and content homeostasis under stress conditions. Moreover, they are Data sources and characteristics of the dataset redox regulated molecular chaperones: they protect both To fill sHSPdb, we used a two-stage process. The first thermally unfolded and oxidatively damaged proteins step filled automatically the fields of the tables of the from irreversible aggregation and play an important role database using PHP and perl scripts, getting the infor- in the bacterial defense system toward oxidative stress. mation from text and XML files from the following da- Therefore, the two classes HSP31 and HSP33 were in- tabases: NCBI/Proteins, NCBI/CDD, NCBI/Taxonomy, corporated into sHSPdb. EBI/Picr, UNIPROT, Interpro, SANGER/Pfam, AMIGO. The main goal of sHSPdb is the analysis of the Starting with the NCBI accession number, we retrieved structure-function relationships of sHSP. This is why the « GenPept » file to derive the GI number, the even- only amino acids sequences
Load more

Recommended publications
  • Computational Genome-Wide Identification of Heat Shock Protein Genes in the Bovine Genome [Version 1; Peer Review: 2 Approved, 1 Approved with Reservations]
    F1000Research 2018, 7:1504 Last updated: 08 AUG 2021 RESEARCH ARTICLE Computational genome-wide identification of heat shock protein genes in the bovine genome [version 1; peer review: 2 approved, 1 approved with reservations] Oyeyemi O. Ajayi1,2, Sunday O. Peters3, Marcos De Donato2,4, Sunday O. Sowande5, Fidalis D.N. Mujibi6, Olanrewaju B. Morenikeji2,7, Bolaji N. Thomas 8, Matthew A. Adeleke 9, Ikhide G. Imumorin2,10,11 1Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria 2International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA 3Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA 4Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico 5Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria 6Usomi Limited, Nairobi, Kenya 7Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria 8Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA 9School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa 10School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA 11African Institute of Bioscience Research and Training, Ibadan, Nigeria v1 First published: 20 Sep 2018, 7:1504 Open Peer Review https://doi.org/10.12688/f1000research.16058.1 Latest published: 20 Sep 2018, 7:1504 https://doi.org/10.12688/f1000research.16058.1 Reviewer Status Invited Reviewers Abstract Background: Heat shock proteins (HSPs) are molecular chaperones 1 2 3 known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, version 1 we carried out a computational genome-wide survey of the bovine 20 Sep 2018 report report report genome.
    [Show full text]
  • Identification of the Binding Partners for Hspb2 and Cryab Reveals
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity.
    [Show full text]
  • Gene Transfer of Heat-Shock Protein 20 Protects Against Ischemia/ Reperfusion Injury in Rat Hearts1
    Acta Pharmacologica Sinica 2005 Oct; 26 (10): 1193–1200 Full-length article Gene transfer of heat-shock protein 20 protects against ischemia/ reperfusion injury in rat hearts1 Yan-hui ZHU, Tie-min MA, Xian WANG2 Department of Physiology and Pathophysiology, Basic Medical College, Key Laboratory of Molecular Cardiovascular Biology, Ministry of Education, Peking University, Beijing 100083, China Key words Abstract reperfusion injury; adenovirus; apoptosis; Aim: To explore whether overexpression of HSP20 in the myocardium could pro- myocardial infarction; heat-shock proteins tect against ischemia/reperfusion injury in rats. Methods: Rat hearts were in- jected with vector, recombinant adenovirus encoding green fluorescent protein 1 Project supported by the National Basic Res- (Ad.GFP) or recombinant adenovirus encoding wild-type HSP20 (Ad.HSP20) in earch Program of China (No G2000056908) the left ventricle. Four days later, hearts were removed and expression of HSP20 awarded to Xian WANG. 2 Correspondence to Prof Xian WANG. was measured in the left ventricle. Subsets of animals in the vector-, Ad.GFP- , and Phn/Fax 86-10-8280-1443. Ad.HSP20-treated groups were subjected to 20-min ischemia and 120-min E-mail [email protected] reperfusion. Myocardial injury was evaluated by infarct size and level of serum Received 2004-12-08 cardiac troponin T and creatine phosphokinase. Apoptosis of cardiomyocytes Accepted 2005-03-30 was determined by TUNEL staining. Cardiac function was evaluated by hemody- namic indexes. Results: Infarct size and serum cardiac troponin T and creatine doi: 10.1111/j.1745-7254.2005.00139.x phosphokinase levels were significantly reduced in Ad.HSP20-treated hearts com- pared with vector- and Ad.GFP-treated hearts.
    [Show full text]
  • Small Heat Shock Proteins in Cellular Adhesion and Migration Evidence from Plasmodium Genetics
    COMMENTARY Cell Adhesion & Migration 6:2, 1–7; March/April 2012; G 2012 Landes Bioscience Small heat shock proteins in cellular adhesion and migration Evidence from Plasmodium genetics Georgina N. Montagna,1 Kai Matuschewski1,2,* and Carlos A. Buscaglia3 1Max Planck Institute for Infection Biology; Berlin, Germany; 2Institute of Biology; Humboldt University; Berlin, Germany; 3Instituto de Investigaciones Biotecnológicas (IIB-INTECH); Universidad Nacional de San Martín; San Martín, Buenos Aires, Argentina ellular locomotion and adhesion domain of ~90 amino acid residues C critically depend on regulated (PFAM: PF00011).1-4 Variable N- and turnover of filamentous actin. C- termini flank this central domain, Biochemical data from diverse model resulting in an overall small molecular systems support a role for the family of mass, ranging from 12 to 43 kDa. HSPB small heat shock proteins (HSPBs) in molecules (1) have the tendency to form microfilament regulation. The small cha- large oligomers,2-5 (2) display classical © 2012 Landesperones could either act directly, Bioscience. through chaperone activity and suppress protein competition with the motor myosin, or aggregation6,7 and (3) associate with lipid indirectly, through modulation of actin bilayers, potentially preserving membrane depolymerizing factor/cofilin activity. integrity.8,9 The physiological importance However, a direct link between HSPBs of HSPBs is underscored by their ubi- and actin-based cellular motility remained quitous presence in all three domains of Do notto be established. distribute. In a recent experimental life, i.e., archaea, bacteria and eukarya,10,11 genetics study, we provided evidence for and by their association with a variety of regulation of Plasmodium motility by severe diseases, e.g., cataracts, myopathies, HSPB6/Hsp20.
    [Show full text]
  • Mechanisms of Small Heat Shock Proteins
    Downloaded from http://cshperspectives.cshlp.org/ on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Mechanisms of Small Heat Shock Proteins Maria K. Janowska, Hannah E.R. Baughman, Christopher N. Woods, and Rachel E. Klevit Department of Biochemistry, University of Washington, Seattle, Washington 98195 Correspondence: [email protected] Small heat shock proteins (sHSPs) are ATP-independent chaperones that delay formation of harmful protein aggregates. sHSPs’ role in protein homeostasis has been appreciated for decades, but their mechanisms of action remain poorly understood. This gap in understand- ing is largely a consequence of sHSP properties that make them recalcitrant to detailed study. Multiple stress-associated conditions including pH acidosis, oxidation, and unusual avail- ability of metal ions, as well as reversible stress-induced phosphorylation can modulate sHSP chaperone activity. Investigations of sHSPs reveal that sHSPs can engage in transient or long- lived interactions with client proteins depending on solution conditions and sHSP or client identity. Recent advances in the field highlight both the diversity of function within the sHSP family and the exquisite sensitivity of individual sHSPs to cellular and experimental condi- tions. Here, we will present and highlight current understanding, recent progress, and future challenges. lthough small heat shock proteins (sHSPs) et al. 2012). sHSPs are implicated in muscle pro- Awere recognized as protein chaperones a tection, their expression is associated with poor quarter century ago (Horwitz 1992; Jakob et al. prognosis and treatment resistance in cancer, 1993), understanding how they work at a molec- and they play ameliorative roles in Parkinson’s ular level has been slow to emerge.
    [Show full text]
  • Structure and Function of Mitochondrial Small Heat Shock Protein 22 in Drosophila Melanogaster
    Structure and function of mitochondrial small heat shock protein 22 in Drosophila melanogaster Thèse Afrooz Dabbaghizadeh Doctorat en biologie cellulaire et moléculaire Philosophiae Doctor (Ph. D.) Québec, Canada © Afrooz Dabbaghizadeh, 2018 Structure and function of mitochondrial small heat shock protein 22 in Drosophila melanogaster Thèse Afrooz Dabbaghizadeh Sous la direction de : Robert M. Tanguay, directeur de recherche Résumé Les petites protéines de choc thermique (sHsps) ont été découvertes initialement chez Drosophila. Les membres de cette famille sont des chaperons moléculaires sont présents dans la plupart des organismes eucaryotes et procaryotes et certains virus. En plus d’être induites en réponse à la plupart des stresseurs dont un choc thermique, elles sont également exprimés en absence de stress. Les sHsps forment des structures dynamiques s'assemblant en oligomères et elles sont essentielles durant les conditions de stress en empêchant l'agrégation des protéines dénaturées et en favorisant leur repliement par des chaperons moléculaires dépendants de l'ATP. Le génome de Drosophila melanogaster code pour 12 sHsp, qui ont des profils d'expression développementaux, des localisations intracellulaires diverses et des spécificités de substrats distincts. DmHsp22 est jusqu'à présent la seule sHsp localisée dans les mitochondries avant et après un choc thermique. Elle est préférentiellement régulée lors du vieillissement et en réponse à la chaleur et aux stress oxydants. La surexpression de DmHsp22 augmente la durée de vie et la résistance au stress et sa régulation négative est préjudiciable. C'est un chaperon efficace, qui pourrait être impliqué dans la réponse mitochondriale au dépliement protéique (UPRMT). Cependant, le mécanisme exact de son action est mal compris.
    [Show full text]
  • Genome-Wide Identification and Expression Profiling of Tomato Hsp20 Gene Family in Response to Biotic and Abiotic Stresses
    ORIGINAL RESEARCH published: 17 August 2016 doi: 10.3389/fpls.2016.01215 Genome-Wide Identification and Expression Profiling of Tomato Hsp20 Gene Family in Response to Biotic and Abiotic Stresses Jiahong Yu 1, 2 †, Yuan Cheng 1 †, Kun Feng 1, Meiying Ruan 1, Qingjing Ye 1, Rongqing Wang 1, Zhimiao Li 1, Guozhi Zhou 1, Zhuping Yao 1, Yuejian Yang 1 and Hongjian Wan 1* 1 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China, 2 College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China Edited by: The Hsp20 genes are involved in the response of plants to environment stresses Jie Zhou, including heat shock and also play a vital role in plant growth and development. They Zhejiang University, China represent the most abundant small heat shock proteins (sHsps) in plants, but little Reviewed by: is known about this family in tomato (Solanum lycopersicum), an important vegetable Chu-Yu Ye, Zhejiang University, China crop in the world. Here, we characterized heat shock protein 20 (SlHsp20) gene family Jianfei Kuang, in tomato through integration of gene structure, chromosome location, phylogenetic South China Agricultural University, China relationship, and expression profile. Using bioinformatics-based methods, we identified *Correspondence: at least 42 putative SlHsp20 genes in tomato. Sequence analysis revealed that most of Hongjian Wan SlHsp20 genes possessed no intron or a relatively short intron in length. Chromosome [email protected] mapping indicated that inter-arm and intra-chromosome duplication events contributed † These authors have contributed remarkably to the expansion of SlHsp20 genes.
    [Show full text]
  • Small Heat Shock Proteins, Big Impact on Protein Aggregation in Neurodegenerative Disease
    REVIEW published: 18 September 2019 doi: 10.3389/fphar.2019.01047 Small Heat Shock Proteins, Big Impact on Protein Aggregation in Neurodegenerative Disease Jack M. Webster, April L. Darling, Vladimir N. Uversky and Laura J. Blair* Department of Molecular Medicine, USF Byrd Institute, University of South Florida, Tampa, FL, United States Misfolding, aggregation, and aberrant accumulation of proteins are central components in the progression of neurodegenerative disease. Cellular molecular chaperone systems modulate proteostasis, and, therefore, are primed to influence aberrant protein- induced neurotoxicity and disease progression. Molecular chaperones have a wide range of functions from facilitating proper nascent folding and refolding to degradation or sequestration of misfolded substrates. In disease states, molecular chaperones can display protective or aberrant effects, including the promotion and stabilization of toxic protein aggregates. This seems to be dependent on the aggregating protein and discrete chaperone interaction. Small heat shock proteins (sHsps) are a class of molecular Edited by: chaperones that typically associate early with misfolded proteins. These interactions Chrisostomos Prodromou, hold proteins in a reversible state that helps facilitate refolding or degradation by other University of Sussex, United Kingdom chaperones and co-factors. These sHsp interactions require dynamic oligomerization Reviewed by: state changes in response to diverse cellular triggers and, unlike later steps in the Axel Mogk, chaperone cascade of events, are ATP-independent. Here, we review evidence for Heidelberg University, Germany modulation of neurodegenerative disease-relevant protein aggregation by sHsps. This John Adrian Carver, includes data supporting direct physical interactions and potential roles of sHsps in the Australian National University, stewardship of pathological protein aggregates in brain.
    [Show full text]
  • Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction
    foods Article Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction , Mohammed Gagaoua * y , Muriel Bonnet and Brigitte Picard * National Research Institute for Agriculture, Food and Environment, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, F-63122 Saint Genès Champanelle, France; [email protected] * Correspondence: [email protected] (M.G.); [email protected] (B.P.) Present Address: Food Quality and Sensory Science Department, Teagasc Ashtown Food Research Centre, y Ashtown, Dublin 15, Ireland. Received: 1 August 2020; Accepted: 21 August 2020; Published: 26 August 2020 Abstract: This study evaluated the potential of a panel of 20 protein biomarkers, quantified by Reverse Phase Protein Array (RPPA), to explain and predict two important meat quality traits, these being beef tenderness assessed by Warner–Bratzler shear force (WBSF) and the intramuscular fat (IMF) content (also termed marbling), in a large database of 188 Protected Designation of Origin (PDO) Maine-Anjou cows. Thus, the main objective was to move forward in the progression of biomarker-discovery for beef qualities by evaluating, at the same time for the two quality traits, a list of candidate proteins so far identified by proteomics and belonging to five interconnected biological pathways: (i) energy metabolic enzymes, (ii) heat shock proteins (HSPs), (iii) oxidative stress, (iv) structural proteins and (v) cell death and protein binding. Therefore, three statistical approaches were applied, these being Pearson correlations, unsupervised learning for the clustering of WBSF and IMF into quality classes, and Partial Least Squares regressions (PLS-R) to relate the phenotypes with the 20 biomarkers.
    [Show full text]
  • A First Line of Stress Defense: Small Heat Shock Proteins and Their Function in Protein Homeostasis
    Article A First Line of Stress Defense: Small Heat Shock Proteins and Their Function in Protein Homeostasis Martin Haslbeck 1 and Elizabeth Vierling 2 1 - Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85 748 Garching, Germany 2 - Department of Biochemistry and Molecular Biology, University of Massachusetts, Life Science Laboratories, N329 240 Thatcher Road, Amherst, MA 01003-9364, USA Correspondence to Martin Haslbeck and Elizabeth Vierling: [email protected]; [email protected] http://dx.doi.org/10.1016/j.jmb.2015.02.002 Edited by J. Buchner Abstract Small heat shock proteins (sHsps) are virtually ubiquitous molecular chaperones that can prevent the irreversible aggregation of denaturing proteins. sHsps complex with a variety of non-native proteins in an ATP-independent manner and, in the context of the stress response, form a first line of defense against protein aggregation in order to maintain protein homeostasis. In vertebrates, they act to maintain the clarity of the eye lens, and in humans, sHsp mutations are linked to myopathies and neuropathies. Although found in all domains of life, sHsps are quite diverse and have evolved independently in metazoans, plants and fungi. sHsp monomers range in size from approximately 12 to 42 kDa and are defined by a conserved β-sandwich α-crystallin domain, flanked by variable N- and C-terminal sequences. Most sHsps form large oligomeric ensembles with a broad distribution of different, sphere- or barrel-like oligomers, with the size and structure of the oligomers dictated by features of the N- and C-termini. The activity of sHsps is regulated by mechanisms that change the equilibrium distribution in tertiary features and/or quaternary structure of the sHsp ensembles.
    [Show full text]
  • Identification and Annotation of Abiotic Stress Responsive Candidate Genes in Peanut Ests
    open access www.bioinformation.net Hypothesis Volume 8(24) Identification and annotation of abiotic stress responsive candidate genes in peanut ESTs Archana Kumari, Ashutosh Kumar, Aakanksha Wany, Gopal Kumar Prajapati & Dev Mani Pandey* Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India; Dev Mani Pandey – Email: [email protected]; Phone: +91 651 2276223; Fax: +91 651 2276052; *Corresponding author Received October 30, 2012; Accepted November 11, 2012; Published December 08, 2012 Abstract: Peanut (Arachis hypogaea L.) ranks fifth among the world oil crops and is widely grown in India and neighbouring countries. Due to its large and unknown genome size, studies on genomics and genetic modification of peanut are still scanty as compared to other model crops like Arabidopsis, rice, cotton and soybean. Because of its favourable cultivation in semi-arid regions, study on abiotic stress responsive genes and its regulation in peanut is very much important. Therefore, we aim to identify and annotate the abiotic stress responsive candidate genes in peanut ESTs. Expression data of drought stress responsive corresponding genes and EST sequences were screened from dot blot experiments shown as heat maps and supplementary tables, respectively as reported by Govind et al. (2009). Some of the screened genes having no information about their ESTs in above mentioned supplementary tables were retrieved from NCBI. A phylogenetic analysis was performed to find a group of utmost similar ESTs for each selected gene. Individual EST of the said group were further searched in peanut ESTs (1,78,490 whole EST sequences) using stand alone BLAST. For the prediction as well as annotation of abiotic stress responsive selected genes, various tools (like Vec-Screen, Repeat Masker, EST-Trimmer, DNA Baser, WISE2 and I-TASSER) were used.
    [Show full text]
  • Sin, Yuan Yan (Angie) (2012) the Roles of HSP20 in Cardiac Hypertrophy
    Sin, Yuan Yan (Angie) (2012) The roles of HSP20 in cardiac hypertrophy. PhD thesis http://theses.gla.ac.uk/3581/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] The roles of HSP20 in cardiac hypertrophy A thesis submitted in fulfillment of the requirements for the Degree of Doctor of Philosophy in Molecular Functions in Disease College of Medicine, Veterinary and Life Sciences, University of Glasgow, United Kingdom Yuan Yan (Angie) Sin 2012 THIS THESIS IS DEDICATED TO MY MOST LOVING PARENTS,, HUSBAND AND ONE VERY SPECIAL LITTLE GIRL,, MY DAUGHTER,, EILIDH HONG.. TABLE OF CONTENTS Abstract ………………………………………………………………………………...….i Author’s declaration ……………………………………………………………………..iii Acknowledgements ………………………………………………………………………iv List of figures …………………………………………………………………………..…v List of tables …………………………………………………………………………….vii Abbreviations ………………………………………………...…………………………viii Publications/Conferences ………………………………………………………………..ix Chapter 1: Introduction 1.1. Heat
    [Show full text]