1
|
Edkins AL, Boshoff A. General Structural and Functional Features of Molecular Chaperones. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1340:11-73. [PMID: 34569020 DOI: 10.1007/978-3-030-78397-6_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular chaperones are a group of structurally diverse and highly conserved ubiquitous proteins. They play crucial roles in facilitating the correct folding of proteins in vivo by preventing protein aggregation or facilitating the appropriate folding and assembly of proteins. Heat shock proteins form the major class of molecular chaperones that are responsible for protein folding events in the cell. This is achieved by ATP-dependent (folding machines) or ATP-independent mechanisms (holders). Heat shock proteins are induced by a variety of stresses, besides heat shock. The large and varied heat shock protein class is categorised into several subfamilies based on their sizes in kDa namely, small Hsps (HSPB), J domain proteins (Hsp40/DNAJ), Hsp60 (HSPD/E; Chaperonins), Hsp70 (HSPA), Hsp90 (HSPC), and Hsp100. Heat shock proteins are localised to different compartments in the cell to carry out tasks specific to their environment. Most heat shock proteins form large oligomeric structures, and their functions are usually regulated by a variety of cochaperones and cofactors. Heat shock proteins do not function in isolation but are rather part of the chaperone network in the cell. The general structural and functional features of the major heat shock protein families are discussed, including their roles in human disease. Their function is particularly important in disease due to increased stress in the cell. Vector-borne parasites affecting human health encounter stress during transmission between invertebrate vectors and mammalian hosts. Members of the main classes of heat shock proteins are all represented in Plasmodium falciparum, the causative agent of cerebral malaria, and they play specific functions in differentiation, cytoprotection, signal transduction, and virulence.
Collapse
Affiliation(s)
- Adrienne Lesley Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, South Africa.
- Rhodes University, Makhanda/Grahamstown, South Africa.
| | - Aileen Boshoff
- Rhodes University, Makhanda/Grahamstown, South Africa.
- Biotechnology Innovation Centre, Rhodes University, Makhanda/Grahamstown, South Africa.
| |
Collapse
|
2
|
Min B, Yoo D, Lee Y, Seo M, Kim H. Complete Genomic Analysis of Enterococcus faecium Heat-Resistant Strain Developed by Two-Step Adaptation Laboratory Evolution Method. Front Bioeng Biotechnol 2020; 8:828. [PMID: 32793575 PMCID: PMC7391244 DOI: 10.3389/fbioe.2020.00828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Stress resistance is an important trait expected of lactic acid bacteria used in food manufacturing. Among the various sources of stress, high temperature is a key factor that interrupts bacterial growth. In this regards, constant efforts are made for the development of heat-resistant strains, but few studies were done accompanying genomic analysis to identify the causal factors of the resistance mechanisms. Furthermore, it is also thought that tolerance to multiple stresses are equally important. Herein, we isolated one Enterococcus faecium strain named BIOPOP-3 and completed a full-length genome sequence. Using this strain, a two-step adaptive laboratory evolution (ALE) method was applied to obtain a heat-resistant strain, BIOPOP-3 ALE. After sequencing the whole genome, we compared the two full-length sequences and identified one non-synonymous variant and four indel variants that could potentially confer heat resistance, which were technically validated by resequencing. We experimentally verified that the evolved strain was significantly enhanced in not only heat resistance but also acid and bile resistance. We demonstrated that the developed heat-resistant strain can be applied in animal feed manufacturing processes. The multi-stress-resistant BIOPOP-3 ALE strain developed in this study and the two-step ALE method are expected to be widely applied in industrial and academic fields. In addition, we expect that the identified variants which occurred specifically in heat-resistant strain will enhance molecular biological understanding and be broadly applied to the biological engineering field.
Collapse
Affiliation(s)
- Bonggyu Min
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - DongAhn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Youngho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Minseok Seo
- Department of Computer Convergence Software, Korea University, Sejong, South Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.,C&K Genomics Inc., Seoul, South Korea
| |
Collapse
|
3
|
Ten-Caten F, Vêncio RZN, Lorenzetti APR, Zaramela LS, Santana AC, Koide T. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA Biol 2018; 15:1119-1132. [PMID: 30175688 PMCID: PMC6161675 DOI: 10.1080/15476286.2018.1509661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.
Collapse
Affiliation(s)
- Felipe Ten-Caten
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ricardo Z N Vêncio
- b Department of Computation and Mathematics, Faculdade de Filosofia , Ciências e Letras de Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
| | - Alan Péricles R Lorenzetti
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Livia Soares Zaramela
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ana Carolina Santana
- c Department of Cell and Molecular Biology and Pathogenic Bioagents , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Tie Koide
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| |
Collapse
|
4
|
Hess K, Oliverio R, Nguyen P, Le D, Ellis J, Kdeiss B, Ord S, Chalkia D, Nikolaidis N. Concurrent action of purifying selection and gene conversion results in extreme conservation of the major stress-inducible Hsp70 genes in mammals. Sci Rep 2018; 8:5082. [PMID: 29572464 PMCID: PMC5865164 DOI: 10.1038/s41598-018-23508-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/14/2018] [Indexed: 12/28/2022] Open
Abstract
Several evolutionary mechanisms alter the fate of mutations and genes within populations based on their exhibited functional effects. To understand the underlying mechanisms involved in the evolution of the cellular stress response, a very conserved mechanism in the course of organismal evolution, we studied the patterns of natural genetic variation and functional consequences of polymorphisms of two stress-inducible Hsp70 genes. These genes, HSPA1A and HSPA1B, are major orchestrators of the cellular stress response and are associated with several human diseases. Our phylogenetic analyses revealed that the duplication of HSPA1A and HSPA1B originated in a lineage proceeding to placental mammals, and henceforth they remained in conserved synteny. Additionally, analyses of synonymous and non-synonymous changes suggest that purifying selection shaped the HSPA1 gene diversification, while gene conversion resulted in high sequence conservation within species. In the human HSPA1-cluster, the vast majority of mutations are synonymous and specific genic regions are devoid of mutations. Furthermore, functional characterization of several human polymorphisms revealed subtle differences in HSPA1A stability and intracellular localization. Collectively, the observable patterns of HSPA1A-1B variation describe an evolutionary pattern, in which purifying selection and gene conversion act simultaneously and conserve a major orchestrator of the cellular stress response.
Collapse
Affiliation(s)
- Kyle Hess
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ryan Oliverio
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA
| | - Peter Nguyen
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA
| | - Dat Le
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA
| | - Jacqueline Ellis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA
| | - Brianna Kdeiss
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA
| | - Sara Ord
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA
| | - Dimitra Chalkia
- UCLA Center for Systems Biomedicine, Division of Digestive Diseases, School of Medicine, Los Angeles, CA, USA
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, California State University, Fullerton, Fullerton, CA, 92834, USA.
| |
Collapse
|
5
|
Jia H, Fan Y, Feng X, Li C. Enhancing stress-resistance for efficient microbial biotransformations by synthetic biology. Front Bioeng Biotechnol 2014; 2:44. [PMID: 25368869 PMCID: PMC4202804 DOI: 10.3389/fbioe.2014.00044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/04/2014] [Indexed: 12/23/2022] Open
Abstract
Chemical conversions mediated by microorganisms, otherwise known as microbial biotransformations, are playing an increasingly important role within the biotechnology industry. Unfortunately, the growth and production of microorganisms are often hampered by a number of stressful conditions emanating from environment fluctuations and/or metabolic imbalances such as high temperature, high salt condition, strongly acidic solution, and presence of toxic metabolites. Therefore, exploring methods to improve the stress tolerance of host organisms could significantly improve the biotransformation process. With the help of synthetic biology, it is now becoming feasible to implement strategies to improve the stress-resistance of the existing hosts. This review summarizes synthetic biology efforts to enhance the efficiency of biotransformations by improving the robustness of microbes. Particular attention will be given to strategies at the cellular and the microbial community levels.
Collapse
Affiliation(s)
- Haiyang Jia
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| | - Yanshuang Fan
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| | - Xudong Feng
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| | - Chun Li
- Department of Biological Engineering, School of Life Science, Beijing Institute of Technology , Beijing , China
| |
Collapse
|
6
|
Shekhawat SD, Jain RK, Gaherwar HM, Purohit HJ, Taori GM, Daginawala HF, Kashyap RS. Heat shock proteins: possible biomarkers in pulmonary and extrapulmonary tuberculosis. Hum Immunol 2013; 75:151-8. [PMID: 24269695 DOI: 10.1016/j.humimm.2013.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 11/17/2022]
Abstract
Tuberculosis (TB) and Tuberculous meningitis (TBM) caused by Mycobacterium tuberculosis (MTB) continue to be a major cause of morbidity and mortality. Therefore there is a need to explore potential biomarkers and heat shock proteins [Hsp(s)] could be one such candidate. We found that host (Hsp 25, Hsp 60, Hsp 70 and Hsp 90) and MTB Hsp(s) (Hsp 16, Hsp 65 and Hsp 71) to be an important feature of the immune response in human clinical samples of pulmonary and extrapulmonary TB patients and in MTB infected monocytes. Notably, the host (Hsp 25, Hsp 70 and Hsp 90) and MTB (Hsp 16, Hsp 65 and Hsp 71) Hsp(s) increases significantly in the clinical samples as well as in cell line model after TB infection. Collectively, results revealed that alteration in immune response leads to a change in the both host and MTB Hsp profile, highlighting them as possible biomarkers for the disease.
Collapse
Affiliation(s)
- Seema D Shekhawat
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Ruchika K Jain
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Hari M Gaherwar
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Hemant J Purohit
- Environmental Genomics Unit, National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440 020, India
| | - Girdhar M Taori
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Hatim F Daginawala
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Rajpal S Kashyap
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India.
| |
Collapse
|
7
|
Diversity in the origins of proteostasis networks--a driver for protein function in evolution. Nat Rev Mol Cell Biol 2013; 14:237-48. [PMID: 23463216 DOI: 10.1038/nrm3542] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the sequence of a protein largely determines its function, proteins can adopt different folding states in response to changes in the environment, some of which may be deleterious to the organism. All organisms--Bacteria, Archaea and Eukarya--have evolved a protein homeostasis, or proteostasis, network comprising chaperones and folding factors, degradation components, signalling pathways and specialized compartmentalized modules that manage protein folding in response to environmental stimuli and variation. Surveying the origins of proteostasis networks reveals that they have co-evolved with the proteome to regulate the physiological state of the cell, reflecting the unique stresses that different cells or organisms experience, and that they have a key role in driving evolution by closely managing the link between the phenotype and the genotype.
Collapse
|
8
|
Petitjean C, Moreira D, López-García P, Brochier-Armanet C. Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea. BMC Evol Biol 2012. [PMID: 23181628 PMCID: PMC3564930 DOI: 10.1186/1471-2148-12-226] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer) domain. Surprisingly, the same protein was also found in Viridiplantae (green algae and land plants). Because J domain-containing proteins are known to interact with the major chaperone DnaK/Hsp70, this suggested that a DnaK protein was present in Thaumarchaeota. DnaK/Hsp70, its co-chaperone DnaJ and the nucleotide exchange factor GrpE are involved, among others, in heat shocks and heavy metal cellular stress responses. Results Using phylogenomic approaches we have investigated the evolutionary history of the DnaJ-Fer protein and of interacting proteins DnaK, DnaJ and GrpE in Thaumarchaeota. These proteins have very complex histories, involving several inter-domain horizontal gene transfers (HGTs) to explain the contemporary distribution of these proteins in archaea. These transfers include one from Cyanobacteria to Viridiplantae and one from Viridiplantae to Thaumarchaeota for the DnaJ-Fer protein, as well as independent HGTs from Bacteria to mesophilic archaea for the DnaK/DnaJ/GrpE system, followed by HGTs among mesophilic and thermophilic archaea. Conclusions We highlight the chimerical origin of the set of proteins DnaK, DnaJ, GrpE and DnaJ-Fer in Thaumarchaeota and suggest that the HGT of these proteins has played an important role in the adaptation of several archaeal groups to mesophilic and thermophilic environments from hyperthermophilic ancestors. Finally, the evolutionary history of DnaJ-Fer provides information useful for the relative dating of the diversification of Archaeplastida and Thaumarchaeota.
Collapse
Affiliation(s)
- Céline Petitjean
- UPR CNRS 9043, Laboratoire de Chimie Bactérienne, Université d’Aix-Marseille (AMU), 13402 Marseille, Cedex 20, France
| | | | | | | |
Collapse
|
9
|
Tomasello G, Sciumé C, Rappa F, Rodolico V, Zerilli M, Martorana A, Cicero G, De Luca R, Damiani P, Accardo FM, Romeo M, Farina F, Bonaventura G, Modica G, Zummo G, Conway de Macario E, Macario AJL, Cappello F. Hsp10, Hsp70, and Hsp90 immunohistochemical levels change in ulcerative colitis after therapy. Eur J Histochem 2011; 55:e38. [PMID: 22297444 PMCID: PMC3284240 DOI: 10.4081/ejh.2011.e38] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 10/17/2011] [Accepted: 10/17/2011] [Indexed: 01/11/2023] Open
Abstract
Ulcerative colitis (UC) is a form of inflammatory bowel disease (IBD) characterized by damage of large bowel mucosa and frequent extra-intestinal autoimmune comorbidities. The role played in IBD pathogenesis by molecular chaperones known to interact with components of the immune system involved in inflammation is unclear. We previously demonstrated that mucosal Hsp60 decreases in UC patients treated with conventional therapies (mesalazine, probiotics), suggesting that this chaperonin could be a reliable biomarker useful for monitoring response to treatment, and that it might play a role in pathogenesis. In the present work we investigated three other heat shock protein/molecular chaperones: Hsp10, Hsp70, and Hsp90. We found that the levels of these proteins are increased in UC patients at the time of diagnosis and decrease after therapy, supporting the notion that these proteins deserve attention in the study of the mechanisms that promote the development and maintenance of IBD, and as biomarkers of this disease (e.g., to monitor response to treatment at the histological level).
Collapse
Affiliation(s)
- G Tomasello
- Dipartimento di Discipline Chirurgiche ed Oncologiche, Università di Palermo, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Richter K, Haslbeck M, Buchner J. The heat shock response: life on the verge of death. Mol Cell 2010; 40:253-66. [PMID: 20965420 DOI: 10.1016/j.molcel.2010.10.006] [Citation(s) in RCA: 1263] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/03/2010] [Accepted: 10/05/2010] [Indexed: 12/16/2022]
Abstract
Organisms must survive a variety of stressful conditions, including sudden temperature increases that damage important cellular structures and interfere with essential functions. In response to heat stress, cells activate an ancient signaling pathway leading to the transient expression of heat shock or heat stress proteins (Hsps). Hsps exhibit sophisticated protection mechanisms, and the most conserved Hsps are molecular chaperones that prevent the formation of nonspecific protein aggregates and assist proteins in the acquisition of their native structures. In this Review, we summarize the concepts of the protective Hsp network.
Collapse
Affiliation(s)
- Klaus Richter
- Munich Center for Integrated Protein Science, Department Chemie Technische Universität München, 85747 Garching, Germany
| | | | | |
Collapse
|
11
|
Abstract
Chaperonins (CPN) are ubiquitous oligomeric protein machines that mediate the ATP-dependent folding of polypeptide chains. These chaperones have not only been assigned stress response and normal housekeeping functions but also have a role in certain human disease states. A longstanding convention divides CPNs into two groups that share many conserved sequence motifs but differ in both structure and distribution. Group I complexes are the well known GroEL/ES heat-shock proteins in bacteria, that also occur in some species of mesophilic archaea and in the endosymbiotic organelles of eukaryotes. Group II CPNs are found only in the cytosol of archaea and eukaryotes. Here we report a third, divergent group of CPNs found in several species of bacteria. We propose to name these Group III CPNs because of their distant relatedness to both Group I and II CPNs as well as their unique genomic context, within the hsp70 operon. The prototype Group III CPN, Carboxydothermus hydrogenoformans chaperonin (Ch-CPN), is able to refold denatured proteins in an ATP-dependent manner and is structurally similar to the Group II CPNs, forming a 16-mer with each subunit contributing to a flexible lid domain. The Group III CPN represent a divergent group of bacterial CPNs distinct from the GroEL/ES CPN found in all bacteria. The Group III lineage may represent an ancient horizontal gene transfer from an archaeon into an early Firmicute lineage. An analysis of their functional and structural characteristics may provide important insights into the early history of this ubiquitous family of proteins.
Collapse
Affiliation(s)
- Stephen M. Techtmann
- Institute of Marine and Environmental Technology, Program in the Biology of Model Systems, 701 East Pratt Street, Baltimore, MD 21202 and Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201
| | - Frank T. Robb
- Institute of Marine and Environmental Technology, Program in the Biology of Model Systems, 701 East Pratt Street, Baltimore, MD 21202 and Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201
| |
Collapse
|
12
|
Tian S, Haney RA, Feder ME. Phylogeny disambiguates the evolution of heat-shock cis-regulatory elements in Drosophila. PLoS One 2010; 5:e10669. [PMID: 20498853 PMCID: PMC2871787 DOI: 10.1371/journal.pone.0010669] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 04/23/2010] [Indexed: 11/19/2022] Open
Abstract
Heat-shock genes have a well-studied control mechanism for their expression that is mediated through cis-regulatory motifs known as heat-shock elements (HSEs). The evolution of important features of this control mechanism has not been investigated in detail, however. Here we exploit the genome sequencing of multiple Drosophila species, combined with a wealth of available information on the structure and function of HSEs in D. melanogaster, to undertake this investigation. We find that in single-copy heat shock genes, entire HSEs have evolved or disappeared 14 times, and the phylogenetic approach bounds the timing and direction of these evolutionary events in relation to speciation. In contrast, in the multi-copy gene Hsp70, the number of HSEs is nearly constant across species. HSEs evolve in size, position, and sequence within heat-shock promoters. In turn, functional significance of certain features is implicated by preservation despite this evolutionary change; these features include tail-to-tail arrangements of HSEs, gapped HSEs, and the presence or absence of entire HSEs. The variation among Drosophila species indicates that the cis-regulatory encoding of responsiveness to heat and other stresses is diverse. The broad dimensions of variation uncovered are particularly important as they suggest a substantial challenge for functional studies.
Collapse
Affiliation(s)
- Sibo Tian
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Robert A. Haney
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Martin E. Feder
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
13
|
Zhang H, Cui P, Lin L, Shen P, Tang B, Huang YP. Transcriptional analysis of the hsp70 gene in a haloarchaeon Natrinema sp. J7 under heat and cold stress. Extremophiles 2009; 13:669-78. [PMID: 19448969 DOI: 10.1007/s00792-009-0251-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 04/28/2009] [Indexed: 01/17/2023]
Abstract
Although ubiquitous in all haloarchaea, little is known about the transcription and regulation of the haloarchaeal hsp70. The purpose of this study is to investigate the transcription of the haloarchaeal hsp70 gene in Natrinema sp. J7 under the temperature and osmotic stress. The hsp70 gene was found to be both temperature- and osmotic-induced, while the response of hsp70 to cold shock was stronger than that to heat shock. Western blot analysis corroborated the similar results at the level of Hsp70 protein. Northern blot and primer extension analyses indicated that the hsp70 was transcribed into a monocistronic transcript and the thermal stress had no effect on the transcription initiation sites choice. The deletion analyses showed that two putative elements, TATA-box (TTTAAAA) and BRE (AGTAAC) located -27 bp upstream of the transcription initiation site played an essential role for the basal transcription of P( hsp70 ). The results suggested that there are some special regulators of hsp70 gene in Natrinema sp. J7.
Collapse
Affiliation(s)
- Hao Zhang
- Wuhan University, People's Republic of China
| | | | | | | | | | | |
Collapse
|
14
|
Abstract
A survey of archaeal genomes for the presence of homologues of bacterial and eukaryotic chaperones reveals several interesting features. All archaea contain chaperonins, also known as Hsp60s (where Hsp is heat-shock protein). These are more similar to the type II chaperonins found in the eukaryotic cytosol than to the type I chaperonins found in bacteria, mitochondria and chloroplasts, although some archaea also contain type I chaperonin homologues, presumably acquired by horizontal gene transfer. Most archaea contain several genes for these proteins. Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea also possess genes for prefoldin proteins and for small heat-shock proteins, but they generally lack genes for Hsp90 and Hsp100 homologues. Genes for Hsp70 (DnaK) and Hsp40 (DnaJ) homologues are only found in a subset of archaea. Thus chaperone-assisted protein folding in archaea is likely to display some unique features when compared with that in eukaryotes and bacteria, and there may be important differences in the process between euryarchaea and crenarchaea.
Collapse
|
15
|
Bellavista E, Mishto M, Santoro A, Bertoni-Freddari C, Sessions RB, Franceschi C. Immunoproteasome in Macaca fascicularis: No Age-Dependent Modification of Abundance and Activity in the Brain and Insight into an in silico Structural Model. Rejuvenation Res 2008; 11:73-82. [DOI: 10.1089/rej.2007.0559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Elena Bellavista
- Interdepartmental Center for Studies on Biophysics, Bioinformatics and Biocomplexity L. Galvani (CIG), University of Bologna, Bologna, Italy
| | - Michele Mishto
- Interdepartmental Center for Studies on Biophysics, Bioinformatics and Biocomplexity L. Galvani (CIG), University of Bologna, Bologna, Italy
| | - Aurelia Santoro
- Interdepartmental Center for Studies on Biophysics, Bioinformatics and Biocomplexity L. Galvani (CIG), University of Bologna, Bologna, Italy
| | | | - Richard B. Sessions
- Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol, United Kingdom
| | - Claudio Franceschi
- Interdepartmental Center for Studies on Biophysics, Bioinformatics and Biocomplexity L. Galvani (CIG), University of Bologna, Bologna, Italy
- Italian National Research Center for Aging, Ancona, Italy
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
| |
Collapse
|
16
|
Shih CJ, Lai MC. Analysis of the AAA+ chaperone clpB gene and stress-response expression in the halophilic methanogenic archaeon Methanohalophilus portucalensis. MICROBIOLOGY-SGM 2007; 153:2572-2583. [PMID: 17660421 DOI: 10.1099/mic.0.2007/007633-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ClpB is a member of the protein-disaggregating chaperone machinery belonging to the AAA+ superfamily. This paper describes a new clpB gene from the halophilic methanoarchaeon Methanohalophilus portucalensis, which has not been reported previously in Archaea. The partial sequence of clpB was identified from the investigation of the salt-stress response of Meh. portucalensis by differential-display RT-PCR (DDRT-PCR). Furthermore, the complete clpB sequence (2610 nt) and its upstream genes encoding the type I chaperonin GroEL/ES were obtained through inverse PCR, Southern hybridization and sequencing. The G+C ratio of clpB is 49.6 mol%. The predicted ClpB polypeptide contains 869 aa and possesses a long central domain and a predicted distinctly discontinuous coiled-coil motif separating two nucleotide-binding domains (NBD1 and NBD2). NBD1 has a single Walker A and two Walker B motifs and NBD2 has only one of each Walker motif, a characteristic of HSP100 proteins. Two repeated Clp amino-terminal domain motifs (ClpN) were identified in ClpB. The putative amino acid sequence shared 75.6 % identity with the predicted clpB homologue annotated as ATPase AAA-2 of Methanococcoides burtonii DSM 6242. Preliminary phylogenetic analysis clustered Meh. portucalensis ClpB (MpClpB) with the low G+C Gram-positive bacteria. Stress response analysis of clpB by Northern blotting showed up to 1.5-fold increased transcription levels in response to both salt up-shock (from 2.1 to 3.1 M NaCl) and down-shock (from 2.1 to 0.9 M NaCl). Both clpB and groEL/ES transcript levels increased when the temperature was shifted from 37 degrees C to 55 degrees C. Under heat stress clpB transcription was repressed by the addition of the osmolyte betaine (1 mM). In conclusion, a novel AAA+ chaperone clpB gene from a halophilic methanogen that responded to the fluctuations in temperature, salt concentration and betaine has been identified and analysed for the first time.
Collapse
MESH Headings
- Adaptation, Physiological/genetics
- Adenosine Triphosphatases/genetics
- Amino Acid Motifs
- Archaeal Proteins/biosynthesis
- Archaeal Proteins/genetics
- Base Composition
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Chaperonin 10/genetics
- Chaperonin 60/genetics
- Chaperonins/biosynthesis
- Chaperonins/genetics
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Archaeal
- Heat-Shock Proteins/biosynthesis
- Heat-Shock Proteins/genetics
- Hot Temperature
- Methanosarcinaceae/genetics
- Methanosarcinaceae/metabolism
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Tertiary
- RNA, Messenger/biosynthesis
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sodium Chloride/metabolism
Collapse
Affiliation(s)
- Chao-Jen Shih
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
17
|
Zhang H, Lin L, Zeng C, Shen P, Huang YP. Cloning and characterization of a haloarchaeal heat shock protein 70 functionally expressed in Escherichia coli. FEMS Microbiol Lett 2007; 275:168-74. [PMID: 17711453 DOI: 10.1111/j.1574-6968.2007.00881.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Hsp70 molecular chaperone machine is constituted by the 70-kDa heat shock protein Hsp70 (DnaK), cochaperone protein Hsp40 (DnaJ) and a nucleotide-exchange factor GrpE. Although it is one of the best-characterized molecular chaperone machines, little is known about it in archaea. A 5.2-kb region containing the hsp70 (dnaK) gene was cloned from Natrinema sp. J7 strain and sequenced. It contained the Hsp70 chaperone machine gene locus arranged unidirectionally in the order of grpE, hsp70 and hsp40 (dnaJ). The hsp70 gene from Natrinema sp. J7 was overexpressed in Escherichia coli BL21 (DE3). The recombinant Hsp70 protein was in a soluble and active form, and its ATPase activity was optimally active in 2.0 M KCl, whereas NaCl had less effect. In vivo, the haloarchaeal hsp70 gene allowed an E. coli dnak-null mutant to propagate lambda phages and grow at 42 degrees C. The results suggested that haloarchaeal Hsp70 should be beneficial for extreme halophiles survival in low-salt environments.
Collapse
Affiliation(s)
- Hao Zhang
- Laboratory of Microbial Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | | | | | | | | |
Collapse
|
18
|
Brocchieri L, Conway de Macario E, Macario AJL. Chaperonomics, a new tool to study ageing and associated diseases. Mech Ageing Dev 2006; 128:125-36. [PMID: 17123587 DOI: 10.1016/j.mad.2006.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The participation of molecular chaperones in the process of senescence and in the mechanisms of age-related diseases is currently under investigation in many laboratories. However, accurate, complete information about the number and diversity of chaperone genes in any given genome is scarce. Consequently, the results of efforts aimed at elucidating the role of chaperones in ageing and disease are often confusing and contradictory. To remedy this situation, we have developed chaperonomics, including means to identify and characterize chaperone genes and their families applicable to humans and model organisms. The problem is difficult because in eukaryotic organisms chaperones have evolved into complex multi-gene families. For instance, the occurrence of multiple paralogs in a single genome makes it difficult to interpret results if consideration is not given to the fact that similar but distinct chaperone genes can be differentially expressed in separate cellular compartments, tissues, and developmental stages. The availability of complete genome sequences allows implementation of chaperonomics with the purpose of understanding the composition of chaperone families in all cell compartments, their evolutionary and functional relations and, ultimately, their role in pathogenesis. Here, we present a series of concatenated, complementary procedures for identifying, characterizing, and classifying chaperone genes in genomes and for elucidating evolutionary relations and structural features useful in predicting functional properties. We illustrate the procedures with applications to the complex family of hsp70 genes and show that the kind of data obtained can provide a solid basis for future research.
Collapse
Affiliation(s)
- Luciano Brocchieri
- University of Florida, College of Medicine, Department of Molecular Genetics and Microbiology, UF Genetics Institute, P.O. Box 103610, Gainesville, FL 32610-3610, USA
| | | | | |
Collapse
|