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Mishra A, Chakraborty S, Jaiswal TP, Bhattacharjee S, Kesarwani S, Mishra AK, Singh SS. Untangling the adaptive strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1 under low temperature. Extremophiles 2024; 28:31. [PMID: 39020126 DOI: 10.1007/s00792-024-01346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
The present study investigates the low temperature tolerance strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1, which grows optimally at 55 °C , by subjecting it to a temperature down-shift of 10 °C (45 °C) for 4 and 6 h followed by studying its growth, morphophysiological, molecular and proteomic responses. Results suggested that although TPH1 experienced increased growth inhibition, ROS production, protein oxidation and membrane disruption after 4 h of incubation at 45 °C yet maintained its DNA integrity and cellular structure through the increased expression of DNA damage repair and cell envelop synthesizing proteins and also progressively alleviated growth inhibition by 20% within two hours i.e., 6 h, by inducing the expression of antioxidative enzymes, production of unsaturated fatty acids, capsular and released exopolysaccharides and forming biofilm along with chemotaxis proteins. Conclusively, the adaptation of Anoxybacillus rupiensis TPH1 to lower temperature is mainly mediated by the synthesis of large numbers of defense proteins and exopolysaccharide rich biofilm formation.
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Affiliation(s)
- Aditi Mishra
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Sindhunath Chakraborty
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Tameshwar Prasad Jaiswal
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Samujjal Bhattacharjee
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Shreya Kesarwani
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Satya Shila Singh
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India.
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Liew KJ, Shahar S, Shamsir MS, Shaharuddin NB, Liang CH, Chan KG, Pointing SB, Sani RK, Goh KM. Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation. ENVIRONMENTAL MICROBIOME 2024; 19:29. [PMID: 38706006 PMCID: PMC11071339 DOI: 10.1186/s40793-024-00572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. RESULTS Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. CONCLUSIONS This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.
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Grants
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- 4J549 UTM QuickWin grant
- 4J549 UTM QuickWin grant
- T2EP30123-0028 Singapore Ministry of Education ARC Tier 2 fund
- 1736255, 1849206, and 1920954 National Science Foundation
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Affiliation(s)
- Kok Jun Liew
- Codon Genomics, 42300 Seri Kembangan, Selangor, Malaysia
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Nawal Binti Shaharuddin
- School of Professional and Continuing Education, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Chee Hung Liang
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Stephen Brian Pointing
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
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Singh MK, Shin Y, Ju S, Han S, Choe W, Yoon KS, Kim SS, Kang I. Heat Shock Response and Heat Shock Proteins: Current Understanding and Future Opportunities in Human Diseases. Int J Mol Sci 2024; 25:4209. [PMID: 38673794 PMCID: PMC11050489 DOI: 10.3390/ijms25084209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The heat shock response is an evolutionarily conserved mechanism that protects cells or organisms from the harmful effects of various stressors such as heat, chemicals toxins, UV radiation, and oxidizing agents. The heat shock response triggers the expression of a specific set of genes and proteins known as heat shock genes/proteins or molecular chaperones, including HSP100, HSP90, HSP70, HSP60, and small HSPs. Heat shock proteins (HSPs) play a crucial role in thermotolerance and aiding in protecting cells from harmful insults of stressors. HSPs are involved in essential cellular functions such as protein folding, eliminating misfolded proteins, apoptosis, and modulating cell signaling. The stress response to various environmental insults has been extensively studied in organisms from prokaryotes to higher organisms. The responses of organisms to various environmental stressors rely on the intensity and threshold of the stress stimuli, which vary among organisms and cellular contexts. Studies on heat shock proteins have primarily focused on HSP70, HSP90, HSP60, small HSPs, and ubiquitin, along with their applications in human biology. The current review highlighted a comprehensive mechanism of heat shock response and explores the function of heat shock proteins in stress management, as well as their potential as therapeutic agents and diagnostic markers for various diseases.
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Affiliation(s)
- Manish Kumar Singh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yoonhwa Shin
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Songhyun Ju
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sunhee Han
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Wonchae Choe
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kyung-Sik Yoon
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Soo Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Insug Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
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Chaudhary S, Selvaraj V, Awasthi P, Bhuria S, Purohit R, Kumar S, Hallan V. Small Heat Shock Protein (sHsp22.98) from Trialeurodes vaporariorum Plays Important Role in Apple Scar Skin Viroid Transmission. Viruses 2023; 15:2069. [PMID: 37896846 PMCID: PMC10611230 DOI: 10.3390/v15102069] [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] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 10/29/2023] Open
Abstract
Trialeurodes vaporariorum, commonly known as the greenhouse whitefly, severely infests important crops and serves as a vector for apple scar skin viroid (ASSVd). This vector-mediated transmission may cause the spread of infection to other herbaceous crops. For effective management of ASSVd, it is important to explore the whitefly's proteins, which interact with ASSVd RNA and are thereby involved in its transmission. In this study, it was found that a small heat shock protein (sHsp) from T. vaporariorum, which is expressed under stress, binds to ASSVd RNA. The sHsp gene is 606 bp in length and encodes for 202 amino acids, with a molecular weight of 22.98 kDa and an isoelectric point of 8.95. Intermolecular interaction was confirmed through in silico analysis, using electrophoretic mobility shift assays (EMSAs) and northwestern assays. The sHsp22.98 protein was found to exist in both monomeric and dimeric forms, and both forms showed strong binding to ASSVd RNA. To investigate the role of sHsp22.98 during ASSVd infection, transient silencing of sHsp22.98 was conducted, using a tobacco rattle virus (TRV)-based virus-induced gene silencing system. The sHsp22.98-silenced whiteflies showed an approximate 50% decrease in ASSVd transmission. These results suggest that sHsp22.98 from T. vaporariorum is associated with viroid RNA and plays a significant role in transmission.
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Affiliation(s)
- Savita Chaudhary
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
| | - Vijayanandraj Selvaraj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Plant Molecular Virology Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Preshika Awasthi
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Swati Bhuria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Plant Molecular Virology Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Rituraj Purohit
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
- Bioinformatics Lab, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Surender Kumar
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vipin Hallan
- Plant Virology Laboratory, Division of Biotechnology, CSIR—Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India (R.P.)
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Hibshman JD, Carra S, Goldstein B. Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation. Commun Biol 2023; 6:121. [PMID: 36717706 PMCID: PMC9887055 DOI: 10.1038/s42003-023-04512-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Small heat shock proteins (sHSPs) are chaperones with well-characterized roles in heat stress, but potential roles for sHSPs in desiccation tolerance have not been as thoroughly explored. We identified nine sHSPs from the tardigrade Hypsibius exemplaris, each containing a conserved alpha-crystallin domain flanked by disordered regions. Many of these sHSPs are highly expressed. Multiple tardigrade and human sHSPs could improve desiccation tolerance of E. coli, suggesting that the capacity to contribute to desicco-protection is a conserved property of some sHSPs. Purification and subsequent analysis of two tardigrade sHSPs, HSP21 and HSP24.6, revealed that these proteins can oligomerize in vitro. These proteins limited heat-induced aggregation of the model enzyme citrate synthase. Heterologous expression of HSP24.6 improved bacterial heat shock survival, and the protein significantly reduced heat-induced aggregation of soluble bacterial protein. Thus, HSP24.6 likely chaperones against protein aggregation to promote heat tolerance. Furthermore, HSP21 and HSP24.6 limited desiccation-induced aggregation and loss of function of citrate synthase. This suggests a mechanism by which tardigrade sHSPs promote desiccation tolerance, by limiting desiccation-induced protein aggregation, thereby maintaining proteostasis and supporting survival. These results suggest that sHSPs provide a mechanism of general stress resistance that can also be deployed to support survival during anhydrobiosis.
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Affiliation(s)
- Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Serena Carra
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Roy M, Bhakta K, Ghosh A. Minimal Yet Powerful: The Role of Archaeal Small Heat Shock Proteins in Maintaining Protein Homeostasis. Front Mol Biosci 2022; 9:832160. [PMID: 35647036 PMCID: PMC9133787 DOI: 10.3389/fmolb.2022.832160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Small heat shock proteins (sHsp) are a ubiquitous group of ATP-independent chaperones found in all three domains of life. Although sHsps in bacteria and eukaryotes have been studied extensively, little information was available on their archaeal homologs until recently. Interestingly, archaeal heat shock machinery is strikingly simplified, offering a minimal repertoire of heat shock proteins to mitigate heat stress. sHsps play a crucial role in preventing protein aggregation and holding unfolded protein substrates in a folding-competent form. Besides protein aggregation protection, archaeal sHsps have been shown recently to stabilize membranes and contribute to transferring captured substrate proteins to chaperonin for refolding. Furthermore, recent studies on archaeal sHsps have shown that environment-induced oligomeric plasticity plays a crucial role in maintaining their functional form. Despite being prokaryotes, the archaeal heat shock protein repository shares several features with its highly sophisticated eukaryotic counterpart. The minimal nature of the archaeal heat shock protein repository offers ample scope to explore the function and regulation of heat shock protein(s) to shed light on their evolution. Moreover, similar structural dynamics of archaeal and human sHsps have made the former an excellent system to study different chaperonopathies since archaeal sHsps are more stable under in vitro experiments.
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7
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Karachitos A, Grabiński W, Baranek M, Kmita H. Redox-Sensitive VDAC: A Possible Function as an Environmental Stress Sensor Revealed by Bioinformatic Analysis. Front Physiol 2021; 12:750627. [PMID: 34966287 PMCID: PMC8710658 DOI: 10.3389/fphys.2021.750627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Voltage-dependent anion-selective channel (VDAC) allows the exchange of small metabolites and inorganic ions across the mitochondrial outer membrane. It is involved in complex interactions that regulate mitochondrial and cellular functioning. Many organisms have several VDAC paralogs that play distinct but poorly understood roles in the life and death of cells. It is assumed that such a large diversity of VDAC-encoding genes might cause physiological plasticity to cope with abiotic and biotic stresses known to impact mitochondrial function. Moreover, cysteine residues in mammalian VDAC paralogs may contribute to the reduction-oxidation (redox) sensor function based on disulfide bond formation and elimination, resulting in redox-sensitive VDAC (rsVDAC). Therefore, we analyzed whether rsVDAC is possible when only one VDAC variant is present in mitochondria and whether all VDAC paralogs present in mitochondria could be rsVDAC, using representatives of currently available VDAC amino acid sequences. The obtained results indicate that rsVDAC can occur when only one VDAC variant is present in mitochondria; however, the possibility of all VDAC paralogs in mitochondria being rsVDAC is very low. Moreover, the presence of rsVDAC may correlate with habitat conditions as rsVDAC appears to be prevalent in parasites. Thus, the channel may mediate detection and adaptation to environmental conditions.
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Affiliation(s)
- Andonis Karachitos
- Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Grabiński
- Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Martyna Baranek
- Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Hanna Kmita
- Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries. Sci Rep 2021; 11:21023. [PMID: 34697325 PMCID: PMC8546028 DOI: 10.1038/s41598-021-00172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022] Open
Abstract
The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.
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Hibshman JD, Clegg JS, Goldstein B. Mechanisms of Desiccation Tolerance: Themes and Variations in Brine Shrimp, Roundworms, and Tardigrades. Front Physiol 2020; 11:592016. [PMID: 33192606 PMCID: PMC7649794 DOI: 10.3389/fphys.2020.592016] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/25/2020] [Indexed: 01/05/2023] Open
Abstract
Water is critical for the survival of most cells and organisms. Remarkably, a small number of multicellular animals are able to survive nearly complete drying. The phenomenon of anhydrobiosis, or life without water, has been of interest to researchers for over 300 years. In this review we discuss advances in our understanding of protectants and mechanisms of desiccation tolerance that have emerged from research in three anhydrobiotic invertebrates: brine shrimp (Artemia), roundworms (nematodes), and tardigrades (water bears). Discovery of molecular protectants that allow each of these three animals to survive drying diversifies our understanding of desiccation tolerance, and convergent themes suggest mechanisms that may offer a general model for engineering desiccation tolerance in other contexts.
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Affiliation(s)
- Jonathan D. Hibshman
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - James S. Clegg
- Bodega Marine Laboratory, University of California, Davis, Davis, CA, United States
| | - Bob Goldstein
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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10
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Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius. Extremophiles 2020; 24:681-692. [DOI: 10.1007/s00792-020-01184-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022]
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Abstract
AbstractExtremophiles are microorganisms that love extreme conditions, such as high temperatures up to the boiling point of water or low temperatures down to below the freezing point. Moreover, some extreme microbes prefer to live in acidic or alkaline environments, under high pressure or high salinity. Three extremophilic species are presented in this article: Lacinutrix algicola, a psychrophilic bacterium that grows at temperatures between 0 and 25 °C, Anaerobranca gottschalkii, a thermophilic and alkaliphilic bacterium growing optimally at 50–55 °C under alkaline conditions, and Pyrococcus furiosus, a famous hyperthermophilic archaeon that prefers 100 °C for growth. These extraordinary microorganisms are examples of extremophiles that possess remarkable adaptation mechanisms and additionally produce unique enzymes called extremozymes. These robust biocatalysts can be applied in various biotechnologic processes to enable substrate conversions under extreme process conditions. Due to their unusual properties, extremophiles and extremozymes will play a pivotal role in the development of modern circular bioeconomy.
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Patel AK, Singhania RR, Sim SJ, Pandey A. Thermostable cellulases: Current status and perspectives. BIORESOURCE TECHNOLOGY 2019; 279:385-392. [PMID: 30685132 DOI: 10.1016/j.biortech.2019.01.049] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 05/18/2023]
Abstract
It is envisaged that the utilization of lignocellulosic biomass for ethanol production for transport sector, would make cellulases the most demanded industrial enzyme. The greatest potential of cellulolytic enzymes lies in ethanol production from biomass by enzymatic hydrolysis of cellulose but low thermostability and low titer of cellulase production resulting into high cost of the enzyme which is the major set-back. A number of research groups are working on cellulase to improve its thermostability so as to be able to perform hydrolysis at elevated temperatures which would eventually increase the efficiency of cellulose hydrolysis. The technologies developed from lignocellulosic biomass via cellulose hydrolysis promise environmental and economical sustainability in the long run along with non-dependence on nonrenewable energy source. This review deals with the important sources of thermostable cellulases, mechanism, its regulation, strategies to enhance the thermostability further with respect to its importance for biofuel applications.
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Affiliation(s)
- Anil K Patel
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | | | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, Indian Institute of Toxicological Research, Lucknow 226 001, India
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Ghosh S, Salama F, Dines M, Lahav A, Adir N. Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:442-452. [PMID: 30711645 DOI: 10.1016/j.bbapap.2018.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
Small heat shock proteins (sHSPs) belong to the superfamily of molecular chaperones. They prevent aggregation of partially unfolded or misfolded client proteins, providing protection to organisms under stress conditions. Here, we report the biophysical and structural characterization of a small heat shock protein (HspA) from a thermophilic cyanobacterium Thermosynechococcus vulcanus in the presence of 2 M urea. HspA has been shown to be important for the protection of Photosystem II and the Phycobilisome antenna complex at elevated temperatures. Heterologously expressed HspA requires the presence of 1-2 M urea to maintain its solubility at concentrations required for most characterization methods. Spectroscopic studies reveal the presence of the β-sheet structure and intactness of the tertiary fold in HspA. In vitro assays show that the HspA maintains chaperone-like activity in protecting soluble proteins from thermal aggregation. Chromatography and electron microscopy show that the HspA exists as a mixture of oligomeric forms in the presence of 2 M urea. HspA was successfully crystallized only in the presence of 2 M urea. The crystal structure of HspA shows urea-induced loss of about 30% of the secondary structure without major alteration in the tertiary structure of the protein. The electron density maps reveal changes in the hydrogen bonding network which we attribute to the presence of urea. The crystal structure of HspA demonstrates a mixture of both direct interactions between urea and protein functionalities and interactions between urea and the surrounding solvent that indirectly affect the protein, which are in accordance with previously published studies.
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Affiliation(s)
- Sudeshna Ghosh
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Faris Salama
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Monica Dines
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Avital Lahav
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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14
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Heat shock response in archaea. Emerg Top Life Sci 2018; 2:581-593. [DOI: 10.1042/etls20180024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 11/17/2022]
Abstract
An adequate response to a sudden temperature rise is crucial for cellular fitness and survival. While heat shock response (HSR) is well described in bacteria and eukaryotes, much less information is available for archaea, of which many characterized species are extremophiles thriving in habitats typified by large temperature gradients. Here, we describe known molecular aspects of archaeal heat shock proteins (HSPs) as key components of the protein homeostasis machinery and place this in a phylogenetic perspective with respect to bacterial and eukaryotic HSPs. Particular emphasis is placed on structure–function details of the archaeal thermosome, which is a major element of the HSR and of which subunit composition is altered in response to temperature changes. In contrast with the structural response, it is largely unclear how archaeal cells sense temperature fluctuations and which molecular mechanisms underlie the corresponding regulation. We frame this gap in knowledge by discussing emerging questions related to archaeal HSR and by proposing methodologies to address them. Additionally, as has been shown in bacteria and eukaryotes, HSR is expected to be relevant for the control of physiology and growth in various stress conditions beyond temperature stress. A better understanding of this essential cellular process in archaea will not only provide insights into the evolution of HSR and of its sensing and regulation, but also inspire the development of biotechnological applications, by enabling transfer of archaeal heat shock components to other biological systems and for the engineering of archaea as robust cell factories.
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Ajayi OO, Peters SO, De Donato M, Sowande SO, Mujibi FDN, Morenikeji OB, Thomas BN, Adeleke MA, Imumorin IG. Computational genome-wide identification of heat shock protein genes in the bovine genome. F1000Res 2018; 7:1504. [PMID: 30542619 PMCID: PMC6259560 DOI: 10.12688/f1000research.16058.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber (
ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for
DNAJC22, a member of HSP40 gene family. The uniqueness of
DNAJA3 and
DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass
in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.
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Affiliation(s)
- Oyeyemi O Ajayi
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria.,International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA
| | - Marcos De Donato
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Sunday O Sowande
- Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Olanrewaju B Morenikeji
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Matthew A Adeleke
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Ikhide G Imumorin
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA.,African Institute of Bioscience Research and Training, Ibadan, Nigeria
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16
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An YJ, Rowland SE, Na JH, Spigolon D, Hong SK, Yoon YJ, Lee JH, Robb FT, Cha SS. Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium. Nat Commun 2017; 8:827. [PMID: 29018216 PMCID: PMC5635000 DOI: 10.1038/s41467-017-00980-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
The chaperonins (CPNs) are megadalton sized hollow complexes with two cavities that open and close to encapsulate non-native proteins. CPNs are assigned to two sequence-related groups that have distinct allosteric mechanisms. In Group I CPNs a detachable co-chaperone, GroES, closes the chambers whereas in Group II a built-in lid closes the chambers. Group I CPNs have a bacterial ancestry, whereas Group II CPNs are archaeal in origin. Here we describe open and closed crystal structures representing a new phylogenetic branch of CPNs. These Group III CPNs are divergent in sequence and structure from extant CPNs, but are closed by a built-in lid like Group II CPNs. A nucleotide-sensing loop, present in both Group I and Group II CPNs, is notably absent. We identified inter-ring pivot joints that articulate during ring closure. These Group III CPNs likely represent a relic from the ancestral CPN that formed distinct bacterial and archaeal branches. Chaperonins (CPNs) are ATP-dependent protein-folding machines. Here the authors present the open and closed crystal structures of a Group III CPN from the thermophilic bacterium Carboxydothermus hydrogenoformans, discuss its mechanism and structurally compare it with Group I and II CPNs.
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Affiliation(s)
- Young Jun An
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Sara E Rowland
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA
| | - Jung-Hyun Na
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Dario Spigolon
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA
| | - Seung Kon Hong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Frank T Robb
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA. .,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea.
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17
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Fonseca EMB, Scorsato V, Dos Santos ML, Júnior AT, Tada SFS, Dos Santos CA, de Toledo MAS, de Souza AP, Polikarpov I, Aparicio R. Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure. Acta Crystallogr F Struct Biol Commun 2017; 73:222-227. [PMID: 28368281 PMCID: PMC5379172 DOI: 10.1107/s2053230x17004101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/14/2017] [Indexed: 11/10/2022] Open
Abstract
Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.
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Affiliation(s)
- Emanuella Maria Barreto Fonseca
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP6154, 13083-970 Campinas-SP, Brazil
| | - Valéria Scorsato
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP6154, 13083-970 Campinas-SP, Brazil
| | - Marcelo Leite Dos Santos
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP6154, 13083-970 Campinas-SP, Brazil
| | - Atilio Tomazini Júnior
- Molecular Biotechnology Group, Department of Physics and Interdisciplinary Science, Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Avenida Trabalhador São-carlense 400, Parque Arnold Schimidt, 13566-590 São Carlos-SP, Brazil
| | - Susely Ferraz Siqueira Tada
- Laboratory of Molecular and Genetic Analysis, Center for Molecular Biology and Genetic Engineering, Institute of Biology, University of Campinas, CP6010, 13083-875 Campinas-SP, Brazil
| | - Clelton Aparecido Dos Santos
- Laboratory of Molecular and Genetic Analysis, Center for Molecular Biology and Genetic Engineering, Institute of Biology, University of Campinas, CP6010, 13083-875 Campinas-SP, Brazil
| | - Marcelo Augusto Szymanski de Toledo
- Laboratory of Molecular and Genetic Analysis, Center for Molecular Biology and Genetic Engineering, Institute of Biology, University of Campinas, CP6010, 13083-875 Campinas-SP, Brazil
| | - Anete Pereira de Souza
- Laboratory of Molecular and Genetic Analysis, Center for Molecular Biology and Genetic Engineering, Institute of Biology, University of Campinas, CP6010, 13083-875 Campinas-SP, Brazil
| | - Igor Polikarpov
- Molecular Biotechnology Group, Department of Physics and Interdisciplinary Science, Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Avenida Trabalhador São-carlense 400, Parque Arnold Schimidt, 13566-590 São Carlos-SP, Brazil
| | - Ricardo Aparicio
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP6154, 13083-970 Campinas-SP, Brazil
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18
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Hong SJ, Park CE, Park GS, Kim MC, Jung BK, Shin JH. Draft genome sequence of sulfur-reducing archaeon Thermococcus thioreducens DSM 14981 T. Braz J Microbiol 2016; 48:3-4. [PMID: 27328615 PMCID: PMC5220636 DOI: 10.1016/j.bjm.2016.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/06/2016] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
Thermococcus thioreducens DSM 14981T, a sulfur-reducing archaeon, was isolated from the rainbow hydrothermal vent site on the Mid-Atlantic Ridge. Herein, we report the draft genome sequence of T. thioreducens DSM 14981T; we obtained 41 contigs with a genome size of 2,052,483 bp and G + C content of 53.5%. This genome sequence will not only help understand how the archaeon adapts to the deep-sea hydrothermal environment but also aid the development of enzymes that are highly stable under extreme conditions for industrial applications.
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Affiliation(s)
- Sung-Jun Hong
- Kyungpook National University, College of Agriculture and Life Sciences, School of Applied Biosciences, Daegu, Republic of Korea
| | - Chang Eon Park
- Kyungpook National University, College of Agriculture and Life Sciences, School of Applied Biosciences, Daegu, Republic of Korea
| | - Gun-Seok Park
- Kyungpook National University, College of Agriculture and Life Sciences, School of Applied Biosciences, Daegu, Republic of Korea
| | - Min-Chul Kim
- Kyungpook National University, College of Agriculture and Life Sciences, School of Applied Biosciences, Daegu, Republic of Korea
| | - Byung Kwon Jung
- Kyungpook National University, College of Agriculture and Life Sciences, School of Applied Biosciences, Daegu, Republic of Korea
| | - Jae-Ho Shin
- Kyungpook National University, College of Agriculture and Life Sciences, School of Applied Biosciences, Daegu, Republic of Korea.
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19
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Hwang HH, Liu YT, Huang SC, Tung CY, Huang FC, Tsai YL, Cheng TF, Lai EM. Overexpression of the HspL Promotes Agrobacterium tumefaciens Virulence in Arabidopsis Under Heat Shock Conditions. PHYTOPATHOLOGY 2015; 105:160-168. [PMID: 25163013 DOI: 10.1094/phyto-05-14-0133-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Agrobacterium tumefaciens transfers a specific DNA fragment from the resident tumor-inducing (Ti) plasmid and effector virulence (Vir) proteins to plant cells during infection. A. tumefaciens VirB1-11 and VirD4 proteins assemble as the type IV secretion system (T4SS), which mediates transfer of the T-DNA and effector Vir protein into plant cells, thus resulting in crown gall disease in plants. Previous studies revealed that an α-crystallin-type, small heat-shock protein (HspL) is a more effective VirB8 chaperone than three other small heat-shock proteins (HspC, HspAT1, and HspAT2). Additionally, HspL contributes to efficient T4SS-mediated DNA transfer and tumorigenesis under room-temperature growth. In this study, we aimed to characterize the impact of HspL on Agrobacterium-mediated transformation efficiency under heat-shock treatment. During heat shock, transient transformation efficiency and VirB8 protein accumulation were lower in the hspL deletion mutant than in the wild type. Overexpression of HspL in A. tumefaciens enhanced the transient transformation efficiency in root explants of both susceptible and recalcitrant Arabidopsis ecotypes. In addition, the reduced transient transformation efficiency during heat stress was recovered by overexpression of HspL in A. tumefaciens. HspL may help maintain VirB8 homeostasis and elevate Agrobacterium-mediated transformation efficiency under both heat-shock and nonheat-shock growth.
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20
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Chang Z. Understanding What Small Heat Shock Proteins Do for Bacterial Cells. HEAT SHOCK PROTEINS 2015. [DOI: 10.1007/978-3-319-16077-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Impact of trehalose transporter knockdown on Anopheles gambiae stress adaptation and susceptibility to Plasmodium falciparum infection. Proc Natl Acad Sci U S A 2013; 110:17504-9. [PMID: 24101462 DOI: 10.1073/pnas.1316709110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Anopheles gambiae is a major vector mosquito for Plasmodium falciparum, the deadly pathogen causing most human malaria in sub-Saharan Africa. Synthesized in the fat body, trehalose is the predominant sugar in mosquito hemolymph. It not only provides energy but also protects the mosquito against desiccation and heat stresses. Trehalose enters the mosquito hemolymph by the trehalose transporter AgTreT1. In adult female A. gambiae, AgTreT1 is predominantly expressed in the fat body. We found that AgTreT1 expression is induced by environmental stresses such as low humidity or elevated temperature. AgTreT1 RNA silencing reduces the hemolymph trehalose concentration by 40%, and the mosquitoes succumb sooner after exposure to desiccation or heat. After an infectious blood meal, AgTreT1 RNA silencing reduces the number of P. falciparum oocysts in the mosquito midgut by over 70% compared with mock-injected mosquitoes. These data reveal important roles for AgTreT1 in stress adaptation and malaria pathogen development in a major vector mosquito. Thus, AgTreT1 may be a potential target for malaria vector control.
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22
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Xia H, Zhao C, Hou L, Li A, Zhao S, Bi Y, An J, Zhao Y, Wan S, Wang X. Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness. BMC Genomics 2013; 14:517. [PMID: 23895441 PMCID: PMC3765196 DOI: 10.1186/1471-2164-14-517] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/23/2013] [Indexed: 12/12/2022] Open
Abstract
Background After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried in soil. It is interesting to study the mechanisms of gynophore development and pod formation in peanut. Results In this study, transcriptome analysis of peanut gynophore was performed using Illumina HiSeq™ 2000 to understand the mechanisms of geocarpy. More than 13 million short sequences were assembled into 72527 unigenes with average size of 394 bp. A large number of genes that were not identified previously in peanut EST projects were identified in this study, including most genes involved in plant circadian rhythm, intra-cellular transportation, plant spliceosome, eukaryotes basal transcription factors, genes encoding ribosomal proteins, brassinosteriod biosynthesis, light-harvesting chlorophyll protein complex, phenylpropanoid biosynthesis and TCA cycle. RNA-seq based gene expression profiling results showed that before and after gynophore soil penetration, the transcriptional level of a large number of genes changed significantly. Genes encoding key enzymes for hormone metabolism, signaling, photosynthesis, light signaling, cell division and growth, carbon and nitrogen metabolism as well as genes involved in stress responses were high lighted. Conclusions Transcriptome analysis of peanut gynophore generated a large number of unigenes which provide useful information for gene cloning and expression study. Digital gene expression study suggested that gynophores experience global changes and reprogram from light to dark grown condition to resume embryo and fruit development.
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23
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The limits for life under multiple extremes. Trends Microbiol 2013; 21:204-12. [DOI: 10.1016/j.tim.2013.01.006] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
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Kocabıyık S, Aygar S. Improvement of protein stability and enzyme recovery under stress conditions by using a small HSP (tpv-HSP 14.3) from Thermoplasma volcanium. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Wang J, Zhao B, Yi Y, Zhang W, Wu X, Zhang L, Shen Y. Mycoepoxydiene, a fungal polyketide inhibits MCF-7 cells through simultaneously targeting p53 and NF-κB pathways. Biochem Pharmacol 2012; 84:891-9. [PMID: 22796259 DOI: 10.1016/j.bcp.2012.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/04/2012] [Accepted: 07/06/2012] [Indexed: 12/28/2022]
Abstract
Mycoepoxydiene (MED) is a cytotoxic polyketide that is isolated from the marine fungal strain Diaporthe sp. HLY-1, which is associated with mangroves; however, the mechanism of action of MED remains unknown. Here, we report the molecular mechanisms of apoptosis activation and growth inhibition induced by MED in MCF-7 cells. The present results show that MED induces DNA damage through the production of reactive oxygen species (ROS), which resulted in the phosphorylation of H2AX and the activation of the Ataxia telangiectasia mutated kinase (ATM) and p53 signaling pathways. In addition, MED increases the accumulation of IκBα and enhances the association between IKKγ and Hsp27 via the activation of Hsp27, which eventually resulted in the inhibition of TNF-α-induced NF-κB transactivation. Therefore, we conclude that MED inhibits MCF-7 cells by simultaneously activating p53 to induce apoptosis and suppressing NF-κB to disrupt cell proliferation. Because small molecules having both of these effects are rare, further exploration of MED as an antitumor lead compound is needed.
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Affiliation(s)
- Jifeng Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, PR China
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Biologic activities of molecular chaperones and pharmacologic chaperone imidazole-containing dipeptide-based compounds: natural skin care help and the ultimate challenge: implication for adaptive responses in the skin. Am J Ther 2012; 19:e69-89. [PMID: 20861720 DOI: 10.1097/mjt.0b013e3181e71fb7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Accumulation of molecular damage and increased molecular heterogeneity are hallmarks of photoaged skin and pathogenesis of human cutaneous disease. Growing evidence demonstrates the ability of molecular chaperone proteins and of pharmacologic chaperones to decrease the environmental stress and ameliorate the oxidation stress-related and glycation disease phenotypes, suggesting that the field of chaperone therapy might hold novel treatments for skin diseases and aging. In this review, we examine the evidence suggesting a role for molecular chaperone proteins in the skin and their inducer and protecting agents: pharmacologic chaperone imidazole dipeptide-based agents (carcinine and related compounds) in cosmetics and dermatology. Furthermore, we discuss the use of chaperone therapy for the treatment of skin photoaging diseases and other skin pathologies that have a component of increased glycation and/or free radical-induced oxidation in their genesis. We examine biologic activities of molecular and pharmacologic chaperones, including strategies for identifying potential chaperone compounds and for experimentally demonstrating chaperone activity in in vitro and in vivo models of human skin disease. This allows the protein to function and traffic to the appropriate location in the skin, thereby increasing protein activity and cellular function and reducing stress on skin cells. The benefits of imidazole dipeptide antioxidants with transglycating activity (such as carcinine) in skin care are that they help protect and repair cell membrane damage and help retain youthful, younger-looking skin. All skin types will benefit from daily, topical application of pharmacologic chaperone antioxidants, anti-irritants, in combination with water-binding protein agents that work to mimic the structure and function of healthy skin. General strategies are presented addressing ground techniques to improve absorption of usually active chaperone proteins and dipeptide compounds, include encapsulation into hydrophobic carriers, a combination with penetration enhancers, active electrical transport, or chemical modification to increase hydrophobicity.
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Acharya S, Chaudhary A. Bioprospecting thermophiles for cellulase production: a review. Braz J Microbiol 2012; 43:844-56. [PMID: 24031898 PMCID: PMC3768857 DOI: 10.1590/s1517-83822012000300001] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 11/25/2011] [Accepted: 06/07/2012] [Indexed: 11/22/2022] Open
Abstract
Most of the potential bioprospecting is currently related to the study of the extremophiles and their potential use in industrial processes. Recently microbial cellulases find applications in various industries and constitute a major group of industrial enzymes. Considerable amount of work has been done on microbial cellulases, especially with resurgence of interest in biomass ethanol production employing cellulases and use of cellulases in textile and paper industry. Most efficient method of lignocellulosic biomass hydrolysis is through enzymatic saccharification using cellulases. Significant information has also been gained about the physiology of thermophilic cellulases producers and process development for enzyme production and biomass saccharification. The review discusses the current knowledge on cellulase producing thermophilic microorganisms, their physiological adaptations and control of cellulase gene expression. It discusses the industrial applications of thermophilic cellulases, their cost of production and challenges in cellulase research especially in the area of improving process economics of enzyme production.
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Affiliation(s)
- Somen Acharya
- Division of Environmental Sciences, Indian Agricultural Research Institute , New Delhi-110012 , India
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28
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Rapid degradation kinetics of amyloid fibrils under mild conditions by an archaeal chaperonin. Biochem Biophys Res Commun 2012; 422:97-102. [DOI: 10.1016/j.bbrc.2012.04.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 04/21/2012] [Indexed: 11/24/2022]
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29
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Ribeiro DA, Bem LEVD, Vicentini R, Ferraz LFC, Murakami MT, Ottoboni LMM. The small heat shock proteins from Acidithiobacillus ferrooxidans: gene expression, phylogenetic analysis, and structural modeling. BMC Microbiol 2011; 11:259. [PMID: 22151959 PMCID: PMC3252397 DOI: 10.1186/1471-2180-11-259] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/07/2011] [Indexed: 01/24/2023] Open
Abstract
Background Acidithiobacillus ferrooxidans is an acidophilic, chemolithoautotrophic bacterium that has been successfully used in metal bioleaching. In this study, an analysis of the A. ferrooxidans ATCC 23270 genome revealed the presence of three sHSP genes, Afe_1009, Afe_1437 and Afe_2172, that encode proteins from the HSP20 family, a class of intracellular multimers that is especially important in extremophile microorganisms. Results The expression of the sHSP genes was investigated in A. ferrooxidans cells submitted to a heat shock at 40°C for 15, 30 and 60 minutes. After 60 minutes, the gene on locus Afe_1437 was about 20-fold more highly expressed than the gene on locus Afe_2172. Bioinformatic and phylogenetic analyses showed that the sHSPs from A. ferrooxidans are possible non-paralogous proteins, and are regulated by the σ32 factor, a common transcription factor of heat shock proteins. Structural studies using homology molecular modeling indicated that the proteins encoded by Afe_1009 and Afe_1437 have a conserved α-crystallin domain and share similar structural features with the sHSP from Methanococcus jannaschii, suggesting that their biological assembly involves 24 molecules and resembles a hollow spherical shell. Conclusion We conclude that the sHSPs encoded by the Afe_1437 and Afe_1009 genes are more likely to act as molecular chaperones in the A. ferrooxidans heat shock response. In addition, the three sHSPs from A. ferrooxidans are not recent paralogs, and the Afe_1437 and Afe_1009 genes could be inherited horizontally by A. ferrooxidans.
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Affiliation(s)
- Daniela A Ribeiro
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas - UNICAMP, Candido Rondon Avenue 400, 13083-875-Campinas, SP, Brazil
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 324] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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Heat and phosphate starvation effects on the proteome, morphology and chemical composition of the biomining bacteria Acidithiobacillus ferrooxidans. World J Microbiol Biotechnol 2011; 27:1469-79. [PMID: 25187146 DOI: 10.1007/s11274-010-0599-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 10/19/2010] [Indexed: 12/17/2022]
Abstract
Acidithiobacillus ferrooxidans is a Gram negative, acidophilic, chemolithoautotrophic bacterium that plays an important role in metal bioleaching. During bioleaching, the cells are subjected to changes in the growth temperature and nutrients starvation. The aim of this study was to gather information about the response of the A.ferrooxidans Brazilian strain LR to K2HPO4 starvation and heat stress through investigation of cellular morphology, chemical composition and differential proteome. The scanning electron microscopic results showed that under the tested stress conditions, A. ferrooxidans cells became elongated while the Fourier transform infrared spectroscopy (FT-IR) analysis showed alterations in the wavenumbers between 850 and 1,275 cm(-1), which are related to carbohydrates, phospholipids and phosphoproteins. These findings indicate that the bacterial cell surface is affected by the tested stress conditions. A proteomic analysis, using 2-DE and tandem mass spectrometry, enabled the identification of 44 differentially expressed protein spots, being 30 due to heat stress (40°C) and 14 due to K2HPO4 starvation. The identified proteins belonged to 11 different functional categories, including protein fate, energy metabolism and cellular processes. The upregulated proteins were mainly from protein fate and energy metabolism categories. The obtained results provide evidences that A. ferrooxidans LR responds to heat stress and K2HPO4 starvation by inducing alterations in cellular morphology and chemical composition of the cell surface. Also, the identification of several proteins involved in protein fate suggests that the bacteria cellular homesostasis was affected. In addition, the identification of proteins from different functional categories indicates that the A. ferrooxidans response to higher than optimal temperatures and phosphate starvation involves global changes in its physiology.
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Yang FL, Yang YL, Wu SH. Structure and function of glycolipids in thermophilic bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 705:367-80. [PMID: 21618118 DOI: 10.1007/978-1-4419-7877-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
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Schokraie E, Hotz‐Wagenblatt A, Warnken U, Frohme M, Dandekar T, Schill RO, Schnölzer M. Investigating heat shock proteins of tardigrades in active versus anhydrobiotic state using shotgun proteomics. J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2010.00608.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elham Schokraie
- Functional Proteome Analysis, German Cancer Research Center, Heidelberg
| | | | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center, Heidelberg
| | - Marcus Frohme
- Department of Molecular Biology and Functional Genomics, University of Applied Sciences Wildau, Wildau
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg
| | - Ralph O. Schill
- Department of Zoology, University of Stuttgart, Stuttgart, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center, Heidelberg
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Leigh JA, Albers SV, Atomi H, Allers T. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol Rev 2011; 35:577-608. [PMID: 21265868 DOI: 10.1111/j.1574-6976.2011.00265.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.
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Affiliation(s)
- John A Leigh
- Department of Microbiology, University of Washington, Seattle, WA, USA
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García-Descalzo L, Alcazar A, Baquero F, Cid C. Identification of in vivo HSP90-interacting proteins reveals modularity of HSP90 complexes is dependent on the environment in psychrophilic bacteria. Cell Stress Chaperones 2011; 16:203-18. [PMID: 20890740 PMCID: PMC3059794 DOI: 10.1007/s12192-010-0233-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 12/29/2022] Open
Abstract
Heat shock protein 90 (HSP90) is a conserved molecular chaperone that functions as part of complexes in which different client proteins target it to diverse sets of substrates. In this paper, HSP90 complexes were investigated in γ-proteobacteria from mild (Shewanella oneidensis) and cold environments (Shewanella frigidimarina and Psychrobacter frigidicola), to determine changes in HSP90 interactions with client proteins in response to the adaptation to cold environments. HSP90 participation in cold adaptation was determined using the specific inhibitor 17-allylamino-geldanamycin. Then, HSP90 was immunoprecipitated from bacterial cultures, and the proteins in HSP90 complexes were analyzed by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. According to HSP90-associated protein analysis, only 15 common proteins were found in both species from the same genus, S. oneidensis and S. frigidimarina, whereas a significant higher number of common proteins were found in both psychrophilic species S. frigidimarina and P. frigidicola 21 (p < 0.001). Only two HSP90-interacting proteins, the chaperone proteins DnaK and GroEL, were common to the three species. Interestingly, some proteins related to energy metabolism (isocitrate lyase, succinyl-CoA synthetase, alcohol dehydrogenase, NAD(+) synthase, and malate dehydrogenase) and some translation factors only interacted with HSP90 in psychrophilic bacteria. We can conclude that HSP90 and HSP90-associated proteins might take part in the mechanism of adaptation to cold environments, and interestingly, organisms living in similar environments conserve similar potential HSP90 interactors in opposition to phylogenetically closely related organisms of the same genus but from different environments.
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Affiliation(s)
- Laura García-Descalzo
- Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Alberto Alcazar
- Department of Investigation, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Fernando Baquero
- Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
- Department of Microbiology, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
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Hilario E, Martin FJM, Bertolini MC, Fan L. Crystal structures of Xanthomonas small heat shock protein provide a structural basis for an active molecular chaperone oligomer. J Mol Biol 2011; 408:74-86. [PMID: 21315085 DOI: 10.1016/j.jmb.2011.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 01/27/2011] [Accepted: 02/02/2011] [Indexed: 10/18/2022]
Abstract
Small heat shock proteins (sHsps) are ubiquitous low-molecular-weight chaperones that prevent protein aggregation under cellular stresses. sHsps contain a structurally conserved α-crystallin domain (ACD) of about 100 amino acid residues flanked by varied N- and C-terminal extensions and usually exist as oligomers. Oligomerization is important for the biological functions of most sHsps. However, the active oligomeric states of sHsps are not defined yet. We present here crystal structures (up to 1.65 Å resolution) of the sHspA from the plant pathogen Xanthomonas (XaHspA). XaHspA forms closed or open trimers of dimers (hexamers) in crystals but exists predominantly as 36mers in solution as estimated by size-exclusion chromatography. The XaHspA monomer structures mainly consist of α-crystallin domain with disordered N- and C-terminal extensions, indicating that the extensions are flexible and not essential for the formation of dimers and 36mers. Under reducing conditions where α-lactalbumin (LA) unfolds and aggregates, XaHspA 36mers formed complexes with one LA per XaHspA dimer. Based on XaHspA dimer-dimer interactions observed in crystals, we propose that XaHspA 36mers have four possible conformations, but only XaHspA 36merB, which is formed by open hexamers in 12mer-6mer-6mer-12mer with protruding dimers accessible for substrate (unfolding protein) binding, can bind to 18 reduced LA molecules. Together, our results unravel the structural basis of an active sHsp oligomer.
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Affiliation(s)
- Eduardo Hilario
- Department of Biochemistry, University of California, Riverside, 2482B Boyce Hall, Riverside, CA 92521-0123, USA
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37
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Babizhayev MA, Nikolayev GM, Nikolayeva JG, Yegorov YE. A survey and analysis of the role of molecular chaperone proteins and imidazole-containing dipeptide-based compounds as molecular escorts into the skin during stress, injury, water structuring and other types of cutaneous pathophysiology. Int J Cosmet Sci 2011; 33:1-16. [DOI: 10.1111/j.1468-2494.2010.00601.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ambily Nath IV, Loka Bharathi PA. Diversity in transcripts and translational pattern of stress proteins in marine extremophiles. Extremophiles 2011; 15:129-53. [DOI: 10.1007/s00792-010-0348-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 12/09/2010] [Indexed: 11/28/2022]
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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.
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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
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MacRae TH. Gene expression, metabolic regulation and stress tolerance during diapause. Cell Mol Life Sci 2010; 67:2405-24. [PMID: 20213274 PMCID: PMC11115916 DOI: 10.1007/s00018-010-0311-0] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 01/31/2010] [Accepted: 02/10/2010] [Indexed: 12/31/2022]
Abstract
Diapause entails molecular, physiological and morphological remodeling of living animals, culminating in a dormant state characterized by enhanced stress tolerance. Molecular mechanisms driving diapause resemble those responsible for biochemical processes in proliferating cells and include transcriptional, post-transcriptional and post-translational processes. The results are directed gene expression, differential mRNA and protein accumulation and protein modifications, including those that occur in response to changes in cellular redox potential. Biochemical pathways switch, metabolic products change and energy production is adjusted. Changes to biosynthetic activities result for example in the synthesis of molecular chaperones, late embryogenesis abundant (LEA) proteins and protective coverings, all contributing to stress tolerance. The purpose of this review is to consider regulatory and mechanistic strategies that are potentially key to metabolic control and stress tolerance during diapause, while remembering that organisms undergoing diapause are as diverse as the processes itself. Some of the parameters described have well-established roles in diapause, whereas the evidence for others is cursory.
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Affiliation(s)
- Thomas H MacRae
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
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41
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Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. Biochem Biophys Res Commun 2010; 396:736-41. [PMID: 20451495 DOI: 10.1016/j.bbrc.2010.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 05/02/2010] [Indexed: 11/22/2022]
Abstract
Identification of the characteristic structural patterns responsible for protein thermostability is theoretically important and practically useful but largely remains an open problem. These patterns may be revealed through comparative study on thermophilic and mesophilic proteins that have distinct thermostability. In this study, we constructed several distance-dependant potentials from thermophilic and mesophilic proteins. These potentials were then used to evaluate the structural difference between thermophilic and mesophilic proteins. We found that using the subtraction or division of the potentials derived from thermophilic and mesophilic proteins can dramatically increase the discriminatory ability. This approach revealed that the ability to distinct the subtle structural features responsible for protein thermostability may be effectively enhanced through rationally designed comparative study.
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Zhu Y, Zhu J, Wan X, Zhu Y, Zhang T. Gene expression of sHsps, Hsp40 and Hsp60 families in normal and abnormal embryonic development of mouse forelimbs. Toxicol Lett 2010; 193:242-51. [DOI: 10.1016/j.toxlet.2010.01.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 01/20/2010] [Accepted: 01/21/2010] [Indexed: 11/25/2022]
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43
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Morozkina EV, Slutskaya ES, Fedorova TV, Tugay TI, Golubeva LI, Koroleva OV. Extremophilic microorganisms: Biochemical adaptation and biotechnological application (review). APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810010011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Laksanalamai P, Narayan S, Luo H, Robb FT. Chaperone action of a versatile small heat shock protein fromMethanococcoides burtonii, a cold adapted archaeon. Proteins 2009; 75:275-81. [DOI: 10.1002/prot.22261] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Han MJ, Yun H, Lee SY. Microbial small heat shock proteins and their use in biotechnology. Biotechnol Adv 2008; 26:591-609. [PMID: 18789382 DOI: 10.1016/j.biotechadv.2008.08.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2008] [Revised: 08/01/2008] [Accepted: 08/03/2008] [Indexed: 11/29/2022]
Abstract
Small heat shock proteins (sHsps) exist in almost all organisms. Most organisms have more than one sHsp, but their number can be as high as 65, as found in the eukaryote, Vitis vinifera. The function of sHsps is well-known; they confer thermotolerance to cellular cultures and proteins in cellular extracts during prolonged incubations at elevated temperatures. This demonstrates the ability of sHsps to protect cellular proteins, and to maintain cellular viability under conditions of intensive stress, such as heat shock or chemical treatments. sHsps have several properties that distinguish them from heat shock proteins (Hsps): they function as ATP-independent chaperones, require the flexible assembly and reassembly of oligomeric complex structures for their activation, and exhibit a wide range of substrate-binding capacities. Recent studies indicate that sHsps have important biological functions in thermostability, disaggregation, and proteolysis inhibition. These functions can be harnessed for various applications, including nanobiotechnology, proteomics, bioproduction, and bioseparation. In this review, we discuss the properties and diversity of microbial sHsps, as well as their potential uses in the biotechnology industry.
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Affiliation(s)
- Mee-Jung Han
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 305-701, Republic of Korea
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Hess M. Thermoacidophilic proteins for biofuel production. Trends Microbiol 2008; 16:414-9. [PMID: 18691890 DOI: 10.1016/j.tim.2008.06.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 06/17/2008] [Accepted: 06/27/2008] [Indexed: 11/18/2022]
Abstract
Growing concerns about global climate change and energy dependence have led to an increased effort to reduce carbon emissions. A considerable reduction could be achieved by using biofuels from lignocellulosic biomass instead of fossil fuels. One major bottleneck of biofuel production from lignocellulose is the availability of efficient and inexpensive biocatalysts (i.e. alcohol dehydrogenases, cellulases and esterases) that are active and stable at high temperatures and low pH values. Although heterologous gene expression is used effectively to obtain recombinant proteins derived from mesophiles, the production of thermoacidophilic proteins is often unsuccessful. Some of the reasons for this failure and potential solutions for an increased production of novel extremophilic biocatalysts are discussed here.
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Affiliation(s)
- Matthias Hess
- Department of Energy Joint Genome Institute, Genomics Division, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
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Lu Q, Han J, Zhou L, Coker JA, DasSarma P, DasSarma S, Xiang H. Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation. Nucleic Acids Res 2008; 36:3031-42. [PMID: 18390887 PMCID: PMC2396416 DOI: 10.1093/nar/gkn152] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Multiple general transcription factors (GTFs), TBP and TFB, are present in many haloarchaea, and are deemed to accomplish global gene regulation. However, details and the role of GTF-directed transcriptional regulation in stress response are still not clear. Here, we report a comprehensive investigation of the regulatory mechanism of a heat-induced gene (hsp5) from Halobacterium salinarum. We demonstrated by mutation analysis that the sequences 5′ and 3′ to the core elements (TATA box and BRE) of the hsp5 promoter (Phsp5) did not significantly affect the basal and heat-induced gene expression, as long as the transcription initiation site was not altered. Moreover, the BRE and TATA box of Phsp5 were sufficient to render a nonheat-responsive promoter heat-inducible, in both Haloferax volcanii and Halobacterium sp. NRC-1. DNA–protein interactions revealed that two heat-inducible GTFs, TFB2 from H. volcanii and TFBb from Halobacterium sp. NRC-1, could specifically bind to Phsp5 likely in a temperature-dependent manner. Taken together, the heat-responsiveness of Phsp5 was mainly ascribed to the core promoter elements that were efficiently recognized by specific heat-induced GTFs at elevated temperature, thus providing a new paradigm for GTF-directed gene regulation in the domain of Archaea.
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Affiliation(s)
- Qiuhe Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
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Sun Y, Makarava N, Lee CI, Laksanalamai P, Robb FT, Baskakov IV. Conformational stability of PrP amyloid fibrils controls their smallest possible fragment size. J Mol Biol 2008; 376:1155-67. [PMID: 18206163 DOI: 10.1016/j.jmb.2007.12.053] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 12/20/2007] [Accepted: 12/20/2007] [Indexed: 12/28/2022]
Abstract
Fibril fragmentation is considered to be an essential step in prion replication. Recent studies have revealed a strong correlation between the incubation period to prion disease and conformational stability of synthetic prions. To gain insight into the molecular mechanism that accounts for this correlation, we proposed that the conformational stability of prion fibrils controls their intrinsic fragility or the size of the smallest possible fibrillar fragments. Using amyloid fibrils produced from full-length mammalian prion protein under three growth conditions, we found a correlation between conformational stability and the smallest possible fragment sizes. Specifically, the fibrils that were conformationally less stable were found to produce shorter pieces upon fragmentation. Site-specific denaturation experiments revealed that the fibril conformational stability was controlled by the region that acquires a cross-beta-sheet structure. Using atomic force microscopy imaging, we found that fibril fragmentation occurred in both directions--perpendicular to and along the fibrillar axis. Two mechanisms of fibril fragmentation were identified: (i) fragmentation caused by small heat shock proteins, including alpha B-crystallin, and (ii) fragmentation due to mechanical stress arising from adhesion of the fibril to a surface. This study provides new mechanistic insight into the prion replication mechanism and offers a plausible explanation for the correlation between conformational stability of synthetic prions and incubation time to prion disease.
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Affiliation(s)
- Ying Sun
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, 725 West Lombard Street, Baltimore, MD 21201, USA
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Luque-Almagro VM, Huertas MJ, Roldán MD, Moreno-Vivián C, Martínez-Luque M, Blasco R, Castillo F. The cyanotrophic bacterium Pseudomonas pseudoalcaligenes CECT5344 responds to cyanide by defence mechanisms against iron deprivation, oxidative damage and nitrogen stress. Environ Microbiol 2007; 9:1541-9. [PMID: 17504491 DOI: 10.1111/j.1462-2920.2007.01274.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional (2-D) electrophoresis approach has been used to test protein expression changes in response to cyanide in the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344. This is a cyanide-assimilating strain which also grows in media containing cyanide-enriched effluent from the jewellery industry. The bacterium efficiently uses this residue as the sole nitrogen source for aerobic growth under alkaline pH with negligible nitrogen losses as HCN. Cell-free extracts isolated from P. pseudoalcaligenes grown with a jewellery residue, free cyanide or ammonium chloride as nitrogen source were subjected to 2-D electrophoresis and the spot patterns were examined to determine differential protein expression. Electrophoretic plates exhibiting an average of 1000 spots showed significant differences in the expression of about 44 proteins depending on the nitrogen source. Some of these protein spots were analysed by Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Characterization of five of these proteins reveals that cyanide shock induces proteins related to iron acquisition, regulation of nitrogen assimilation pathways and oxidative stress repairing and protection.
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Affiliation(s)
- Victor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
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Spijkerman E, Barua D, Gerloff-Elias A, Kern J, Gaedke U, Heckathorn SA. Stress responses and metal tolerance of Chlamydomonas acidophila in metal-enriched lake water and artificial medium. Extremophiles 2007; 11:551-62. [PMID: 17429574 DOI: 10.1007/s00792-007-0067-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 02/15/2007] [Indexed: 10/23/2022]
Abstract
Chlamydomonas acidophila faces high heavy-metal concentrations in acidic mining lakes, where it is a dominant phytoplankton species. To investigate the importance of metals to C. acidophila in these lakes, we examined the response of growth, photosynthesis, cell structure, heat-shock protein (Hsp) accumulation, and metal adsorption after incubation in metal-rich lake water and artificial growth medium enriched with metals (Fe, Zn). Incubation in both metal-rich lake water and medium caused large decreases in photosystem II function (though no differences among lakes), but no decrease in growth rate (except for medium + Fe). Concentrations of small Hsps were higher in algae incubated in metal-rich lake-water than in metal-enriched medium, whereas Hsp60 and Hsp70A were either less or equally expressed. Cellular Zn and Fe contents were lower, and metals adsorbed to the cell surface were higher, in lake-water-incubated algae than in medium-grown cells. The results indicate that high Zn or Fe levels are likely not the main or only contributor to the low primary production in mining lakes, and multiple adaptations of C. acidophila (e.g., high Hsp levels, decreased metal accumulation) increase its tolerance to metals and permit survival under such adverse environmental conditions. Supposedly, the main stress factor present in the lake water is an interaction between low P and high Fe concentrations.
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Affiliation(s)
- Elly Spijkerman
- Department of Ecology and Ecosystem Modelling, University of Potsdam, Am Neuen Palais 10, Potsdam, Germany.
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