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Chakafana G, Middlemiss CJ, Zininga T, Shonhai A. Swapping the linkers of canonical Hsp70 and Hsp110 chaperones compromises both self-association and client selection. Heliyon 2024; 10:e29690. [PMID: 38707424 PMCID: PMC11066147 DOI: 10.1016/j.heliyon.2024.e29690] [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: 12/12/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024] Open
Abstract
Plasmodium falciparum heat shock protein 70-1 (PfHsp70-1) and PfHsp70-z are essential cytosol localised chaperones of the malaria parasite. The two chaperones functionally interact to drive folding of several parasite proteins. While PfHsp70-1 is regarded as a canonical Hsp70 chaperone, PfHsp70-z belongs to the Hsp110 subcluster. One of the distinctive features of PfHsp70-z is its unique linker segment which delineates it from canonical Hsp70. In the current study, we elucidated the role of the linker in regulating Hsp70 self-association and client selection. Using recombinant forms of PfHsp70-1, PfHsp70-z and E. coli Hsp70 (DnaK) and their respective linker switch mutants we investigated self-association of the chaperones using surface plasmon resonance (SPR) analysis. The effect of the changes on client selectivity was investigated on DnaK and its mutant through co-affinity chromatography coupled to LC-MS analysis. Our findings demonstrated that the linker is important for both Hsp70 self-association and client binding.
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Affiliation(s)
- Graham Chakafana
- Department of Biochemistry, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
- Department of Chemistry and Biochemistry, Hampton University, 23668, Virginia, USA
| | - Caitlin J. Middlemiss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Tawanda Zininga
- Department of Biochemistry, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Addmore Shonhai
- Department of Biochemistry, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
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Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
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Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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Azaharuddin M, Pal A, Mitra S, Dasgupta R, Basu T. A review on oligomeric polydispersity and oligomers-dependent holding chaperone activity of the small heat-shock protein IbpB of Escherichia coli. Cell Stress Chaperones 2023; 28:689-696. [PMID: 37910345 PMCID: PMC10746692 DOI: 10.1007/s12192-023-01392-3] [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: 07/27/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
Inclusion body-associated proteins IbpA and IbpB of MW 16 KDa are the two small heat-shock proteins (sHSPs) of Escherichia coli, and they have only holding, but not folding, chaperone activity. In vitro holdase activity of IbpB is more than that of IbpA, and in combination, they synergise. Both IbpA and IbpB monomers first form homodimers, which as building blocks subsequently oligomerize to make heavy oligomers with MW of MDa range; for IbpB, the MW range of heavy oligomers is 2.0-3.0 MDa, whereas for IbpA oligomers, the values in MDa are not so specified/reported. By temperature upshift, such large oligomers of IbpB, but not of IbpA, dissociate to make relatively small oligomeric assemblies of MW around 600-700KDa. The larger oligomers of IbpB are assumed to be inactive storage form, which on facing heat or oxidative stress dissociate into smaller oligomers of ATP-independent holding chaperone activity. These smaller oligomers bind with stress-induced partially denatured/unfolded and thereby going to be aggregated proteins, to give them protection against permanent damage and aggregation. On withdrawal of stress, IbpB transfers the bound substrate protein to the ATP-dependent bi-chaperone system DnaKJE-ClpB, having both holdase and foldase properties, to finally refold the protein. Of the two sHSPs IbpA and IbpB of E. coli, this review covers the recent advances in research on IbpB only.
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Affiliation(s)
- Md Azaharuddin
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Anabadya Pal
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Sangeeta Mitra
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Rakhi Dasgupta
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Tarakdas Basu
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India.
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Phan UT, Jeon BW, Kim YH. Microbial engineering of Methylorubrum extorquens AM1 to enhance CO 2 conversion into formate. Enzyme Microb Technol 2023; 168:110264. [PMID: 37244213 DOI: 10.1016/j.enzmictec.2023.110264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Methylorubrum extorquens AM1 has the potential to consume C1 feedstock to produce a wide range of biomaterials, from bioplastic to pharmaceutical. However, the synthetic biology tools for engineering M. extorquens AM1 need to be employed for precise control of recombinant enzyme expression. In this study, we presented an approach to improve the expression level of formate dehydrogenase 1 from M. extorquens AM1 (MeFDH1) using an efficient terminator and 5'-untranslated region (5'-UTR) design for enhanced carbon dioxide (CO2) conversion activity of whole-cell biocatalyst. The rrnB terminator significantly increased mRNA levels of MeFDH1 alpha and beta subunits by 8.2-fold and 11-fold, respectively, compared to the T7 terminator. Moreover, enzyme production was 1.6-fold higher with 2.1 mg/wet cell weight (WCW) using rrnB terminator. Homologous 5'-untranslated regions (5'-UTR) determined based on proteomics data and UTR designer also influenced the expression level of MeFDH1. The 5'-UTR of the formaldehyde activating enzyme (fae) was the strongest, with 2.5-fold higher expression than that of the control sequence (T7g-10L). Furthermore, the electrochemical reaction of recombinant strains as whole-cell biocatalysts was investigated for their applicability to CO2 conversion, showing enhanced formate productivity. The recombinant strain containing the 5'-UTR sequence of fae exhibited formate productivity of 5.0 mM/h, 2.3-fold higher than that of the control strain (T7). Overall, this study suggested practical applications for CO2 conversion into bioavailable formate and provided valuable insights for recombinant expression systems in methylotrophic strains.
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Affiliation(s)
- Uyen Thu Phan
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea.
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Dong K, Li Y, Luo S, Zhang F, Pan H, Zhao L, Wang Y, Liao X. Hydrostatic pressure boost rate and mode to enhance sterilization mediated by GroEL-interacting proteins. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Cardoza E, Singh H. Involvement of CspC in response to diverse environmental stressors in Escherichia coli. J Appl Microbiol 2021; 132:785-801. [PMID: 34260797 DOI: 10.1111/jam.15219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/23/2022]
Abstract
The ability of Escherichia coli surviving a cold shock lies mainly with the induction of a few Csps termed as 'Major cold shock proteins'. Regardless of high sequence similarity among the nine homologous members, CspC appears to be functionally diverse in conferring the cell adaptability to various stresses based on fundamental properties of the protein including nucleic acid binding, nucleic acid melting and regulatory activity. Spanning three different stress regulons of acid, oxidative and heat, CspC regulates gene expression and transcript stability of stress proteins and bestows upon the cell tolerance to lethal-inducing agents ultimately helping it adapt to severe environmental assaults. While its exact role in cellular physiology is still to be detailed, understanding the transcriptional and translational control will likely provide insights into the mechanistic role of CspC under stress conditions. To this end, we review the knowledge on stress protein regulation by CspC and highlight its activity in response to stressors thereby elucidating its role as a major Csp player in response to one too many environmental triggers. The knowledge presented here could see various downstream applications in engineering microbes for industrial, agricultural and research applications in order to achieve high product efficiency and to aid bacteria cope with environmentally harsh conditions.
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Affiliation(s)
- Evieann Cardoza
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
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Morán Luengo T, Mayer MP, Rüdiger SGD. The Hsp70-Hsp90 Chaperone Cascade in Protein Folding. Trends Cell Biol 2018; 29:164-177. [PMID: 30502916 DOI: 10.1016/j.tcb.2018.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/19/2018] [Accepted: 10/24/2018] [Indexed: 12/12/2022]
Abstract
Conserved families of molecular chaperones assist protein folding in the cell. Here we review the conceptual advances on three major folding routes: (i) spontaneous, chaperone-independent folding; (ii) folding assisted by repetitive Hsp70 cycles; and (iii) folding by the Hsp70-Hsp90 cascades. These chaperones prepare their protein clients for folding on their own, without altering their folding path. A particularly interesting role is reserved for Hsp90. The function of Hsp90 in folding is its ancient function downstream of Hsp70, free of cochaperone regulation and present in all kingdoms of life. Eukaryotic signalling networks, however, embrace Hsp90 by a plethora of cochaperones, transforming the profolding machinery to a folding-on-demand factor. We discuss implications for biology and molecular medicine.
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Affiliation(s)
- Tania Morán Luengo
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Zhuo L, Zhang Z, Pan Z, Sheng DH, Hu W, Li YZ. CIRCE element evolved for the coordinated transcriptional regulation of bacterial duplicate groELs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:928-937. [PMID: 30496038 DOI: 10.1016/j.bbagrm.2018.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 01/16/2023]
Abstract
Chaperonin groEL genes are duplicated in approximately 20% of bacteria, and the duplicates are differentially transcribed due to their divergent functions. The coordinated regulation of this differential transcription is as yet undetermined. In this study, we reported that the controlling inverted repeat of chaperone expression (CIRCE) element (the HrcA-binding site located upstream of the promoter) evolved for the transcriptional regulation of duplicate groELs. CIRCE composition and locations were found to be phylogenetically conserved in bacterial taxa. Myxococcus xanthus DK1622 has two CIRCE elements (CIRCE1groESL1 and CIRCE2groESL1) in the promoter region of groESL1 and one CIRCE element (CIRCEgroEL2) before groEL2. We also found that negative HrcA and positive ?32 regulators coordinated the transcription of duplicate groELs, and that the double deletion in DK1622 eliminated transcriptional differences and reduced the heat-shock responses of groELs. In vitro binding assays showed that HrcA protein binding was biased towards CIRCE1groESL1, followed by CIRCEgroEL2, but that HrcA proteins failed to bind with CIRCE2groESL1. Mutation experiments revealed that single-nucleotide mutations in the inverted repeat regions changed the HrcA-binding abilities of CIRCEs. We constructed an in vivo transcription-regulation system in Escherichia coli to pair each of the regulators with a groEL promoter. The results indicated that the transcriptional regulation performed by HrcA and ?32 was biased towards the groEL2 and groEL1 promoters, respectively. Based on promoter-sequence characteristics, we proposed a model of the coordinated regulation of the transcription of duplicate groELs in M. xanthus DK1622.
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Affiliation(s)
- Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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Roncarati D, Scarlato V. Regulation of heat-shock genes in bacteria: from signal sensing to gene expression output. FEMS Microbiol Rev 2017; 41:549-574. [PMID: 28402413 DOI: 10.1093/femsre/fux015] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/14/2017] [Indexed: 02/07/2023] Open
Abstract
The heat-shock response is a mechanism of cellular protection against sudden adverse environmental growth conditions and results in the prompt production of various heat-shock proteins. In bacteria, specific sensory biomolecules sense temperature fluctuations and transduce intercellular signals that coordinate gene expression outputs. Sensory biomolecules, also known as thermosensors, include nucleic acids (DNA or RNA) and proteins. Once a stress signal is perceived, it is transduced to invoke specific molecular mechanisms controlling transcription of genes coding for heat-shock proteins. Transcriptional regulation of heat-shock genes can be under either positive or negative control mediated by dedicated regulatory proteins. Positive regulation exploits specific alternative sigma factors to redirect the RNA polymerase enzyme to a subset of selected promoters, while negative regulation is mediated by transcriptional repressors. Interestingly, while various bacteria adopt either exclusively positive or negative mechanisms, in some microorganisms these two opposite strategies coexist, establishing complex networks regulating heat-shock genes. Here, we comprehensively summarize molecular mechanisms that microorganisms have adopted to finely control transcription of heat-shock genes.
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Affiliation(s)
- Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
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Chakraborty R, Basu T. Metallic copper nanoparticles induce apoptosis in a human skin melanoma A-375 cell line. NANOTECHNOLOGY 2017; 28:105101. [PMID: 28067213 DOI: 10.1088/1361-6528/aa57b0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In two earlier communications (Chatterjee et al 2012 Nanotechnology 23 085103, Chatterjee et al 2014 Nanotechnology 25 135101), we reported the development of a simple and unique method of synthesizing highly stable metallic copper nanoparticles (Cu NPs) with high antibacterial activity. Here we report on the cytotoxic potency of the NPs against cancer cells. The value of the IC50 dose of the Cu NPs against human skin cancer cell A-375 was found to be 1.71 μg ml-1 only, which was much less than values reported so far, and this concentration had no cytotoxic effect on normal white blood cells. The NPs caused (i) lowering of cell membrane rigidity, (ii) DNA degradation, (iii) chromosomal condensation, (iv) cell cycle arrest in the G2/M phase, (v) depolarization of the mitochondrial membrane and (vi) apoptosis of cells. Cellular apoptosis occurred in the caspase-9-mediated intrinsic pathway. This study revealed that our Cu NPs had high anticancer properties by killing tumor cells through the apoptotic pathway. Since this particle has high antibacterial activity, our Cu NPs might be developed in future as a dual action drug-anticancer as well as antibacterial.
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Affiliation(s)
- Ruchira Chakraborty
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani-741235, West Bengal, India
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