1
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Lejeune C, Cornu D, Sago L, Redeker V, Virolle MJ. The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor. Res Microbiol 2024; 175:104177. [PMID: 38159786 DOI: 10.1016/j.resmic.2023.104177] [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: 09/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
S. lividans and S. coelicolor are phylogenetically closely related strains with different abilities to produce the same specialized metabolites. Previous studies revealed that the strong antibiotic producer, S. coelicolor, had a lower ability to assimilate nitrogen and phosphate than the weak producer, Streptomyces lividans, and this resulted into a lower growth rate. A comparative proteomic dataset was used to establish the consequences of these nutritional stresses on the abundance of proteins of the translational apparatus of these strains, grown in low and high phosphate availability. Our study revealed that most proteins of the translational apparatus were less abundant in S. coelicolor than in S. lividans whereas it was the opposite for ET-Tu 3 and a TrmA-like methyltransferase. The expression of the latter being known to be under the positive control of the stringent response whereas that of the other ribosomal proteins is under its negative control, this indicated the occurrence of a strong activation of the stringent response in S. coelicolor. Furthermore, in S. lividans, ribosomal proteins were more abundant in phosphate proficiency than in phosphate limitation suggesting that a limitation in phosphate, that was also shown to trigger RelA expression, contributes to the induction of the stringent response.
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Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France.
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
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2
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Lahry K, Datta M, Varshney U. Genetic analysis of translation initiation in bacteria: An initiator tRNA-centric view. Mol Microbiol 2024. [PMID: 38410838 DOI: 10.1111/mmi.15243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
Translation of messenger RNA (mRNA) in bacteria occurs in the steps of initiation, elongation, termination, and ribosome recycling. The initiation step comprises multiple stages and uses a special transfer RNA (tRNA) called initiator tRNA (i-tRNA), which is first aminoacylated and then formylated using methionine and N10 -formyl-tetrahydrofolate (N10 -fTHF), respectively. Both methionine and N10 -fTHF are produced via one-carbon metabolism, linking translation initiation with active cellular metabolism. The fidelity of i-tRNA binding to the ribosomal peptidyl-site (P-site) is attributed to the structural features in its acceptor stem, and the highly conserved three consecutive G-C base pairs (3GC pairs) in the anticodon stem. The acceptor stem region is important in formylation of the amino acid attached to i-tRNA and in its initial binding to the P-site. And, the 3GC pairs are crucial in transiting the i-tRNA through various stages of initiation. We utilized the feature of 3GC pairs to investigate the nuanced layers of scrutiny that ensure fidelity of translation initiation through i-tRNA abundance and its interactions with the components of the translation apparatus. We discuss the importance of i-tRNA in the final stages of ribosome maturation, as also the roles of the Shine-Dalgarno sequence, ribosome heterogeneity, initiation factors, ribosome recycling factor, and coevolution of the translation apparatus in orchestrating a delicate balance between the fidelity of initiation and/or its leakiness to generate proteome plasticity in cells to confer growth fitness advantages in response to the dynamic nutritional states.
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Affiliation(s)
- Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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3
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Zhang D, Gao Y, Zhu L, Wang Y, Li P. Advances and opportunities in methods to study protein translation - A review. Int J Biol Macromol 2024; 259:129150. [PMID: 38171441 DOI: 10.1016/j.ijbiomac.2023.129150] [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: 08/02/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Abstract
It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, particularly in the field of omics, have revolutionized protein translation research. These studies not only help characterize changes in protein translation during specific biological or pathological processes but also have significant implications in disease prevention and treatment. In this review, we summarize the latest methods in ribosome-based translation omics. We specifically focus on the application of fluorescence imaging technology and omics technology in studying overall protein translation. Additionally, we analyze the advantages, disadvantages, and application of these experimental methods, aiming to provide valuable insights and references to researchers studying translation.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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4
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Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
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5
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Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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6
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Bhattacharya U, Thavathiru E, Neizer-Ashun F, Xu C, Gatalica Z, Dwivedi SKD, Dey A, Mukherjee P, Bhattacharya R. The deubiquitinase USP10 protects pancreatic cancer cells from endoplasmic reticulum stress. NPJ Precis Oncol 2022; 6:93. [PMID: 36543867 PMCID: PMC9772324 DOI: 10.1038/s41698-022-00336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The ubiquitin-specific peptidase 10 (USP10) plays a context-specific, pro or anti-tumorigenic role in different malignancies. However, the role of USP10 in pancreatic cancer remains unclear. Our protein and RNA level analysis from archived specimens and public databases show that USP10 is overexpressed in pancreatic ductal adenocarcinoma (PDAC) and expression correlates with poor overall patient survival. Phenotypically, silencing USP10 decreased viability, clonal growth and invasive properties of pancreatic cancer cells. Mechanistically, silencing USP10 upregulated BiP and induced endoplasmic reticulum (ER) stress that led to an unfolded protein response (UPR) and upregulation of PERK, IRE1α. Decreased cell viability of USP10 silenced cells could be rescued by a chemical chaperone that promotes protein folding. Our studies suggest that USP10 by protecting pancreatic cancer cells from ER stress may support tumor progression.
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Affiliation(s)
- Udayan Bhattacharya
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Elangovan Thavathiru
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Fiifi Neizer-Ashun
- grid.266902.90000 0001 2179 3618Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Chao Xu
- grid.266902.90000 0001 2179 3618Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Zoran Gatalica
- grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Shailendra Kumar Dhar Dwivedi
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Anindya Dey
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Priyabrata Mukherjee
- grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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7
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Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894. Int J Mol Sci 2022; 23:ijms232012705. [PMID: 36293559 PMCID: PMC9603859 DOI: 10.3390/ijms232012705] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific antibiotic resistance in a multidrug-tolerant clinical strain of Acinetobacter baumannii Sequence Type (ST) 1894. Comparative transcriptome analysis was performed in untreated biofilm and biofilm treated with sub-MIC doses of imipenem and colistin. RNA sequencing data showed that 78 and 285 genes were differentially expressed in imipenem and colistin-treated biofilm cells, respectively. Among the differentially expressed genes (DEGs), 48 and 197 genes were upregulated exclusively in imipenem and colistin-treated biofilm cells, respectively. The upregulated genes included those encoding matrix synthesis (pgaB), multidrug efflux pump (novel00738), fimbrial proteins, and homoserine lactone synthase (AbaI). Upregulation of biofilm-associated genes might enhance biofilm formation when treated with sub-MICs of antibiotics. The downregulated genes include those encoding DNA gyrase (novel00171), 30S ribosomal protein S20 (novel00584), and ribosome releasing factor (RRF) were downregulated when the biofilm cells were treated with imipenem and colistin. Downregulation of these genes affects protein synthesis, which in turn slows down cell metabolism and makes biofilm cells more tolerant to antibiotics. In this investigation, we also found that 5 of 138 small RNAs (sRNAs) were differentially expressed in biofilm regardless of antibiotic treatment or not. Of these, sRNA00203 showed the highest expression levels in biofilm. sRNAs regulate gene expression and are associated with biofilm formation, which may in turn affect the expression of biofilm-specific antibiotic resistance. In summary, when biofilm cells were exposed to sub-MIC doses of colistin and imipenem, coordinated gene responses result in increased biofilm production, multidrug efflux pump expression, and the slowdown of metabolism, which leads to drug tolerance in biofilm. Targeting antibiotic-induced or repressed biofilm-specific genes represents a new strategy for the development of innovative and effective treatments for biofilm-associated infections caused by A. baumannii.
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8
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Heinz J, Doellinger J, Maus D, Schneider A, Lasch P, Grossart HP, Schulze-Makuch D. Perchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines. Environ Microbiol 2022; 24:5051-5065. [PMID: 35920032 DOI: 10.1111/1462-2920.16152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO4 -induced stresses share many common metabolic features, e.g., signaling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for life on Mars, which - given the environmental conditions - likely developed chaotropic defense strategies such as stabilized confirmations of biomacromolecules and the formation of cell clusters. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jacob Heinz
- Center for Astronomy and Astrophysics, RG Astrobiology, Technische Universität Berlin, Berlin, Germany
| | - Joerg Doellinger
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Deborah Maus
- Robert Koch-Institute, Metabolism of Microbial Pathogens (NG2), Berlin, Germany
| | - Andy Schneider
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Peter Lasch
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775 Stechlin, Germany.,Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics, RG Astrobiology, Technische Universität Berlin, Berlin, Germany.,Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775 Stechlin, Germany.,GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany.,School of the Environment, Washington State University, Pullman, Washington, USA
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9
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Avendaño-Herrera R, Saldivia P, Bethke J, Vargas C, Hernández M. Proteomic analysis reveals Renibacterium salmoninarum grown under iron-limited conditions induces iron uptake mechanisms and overproduction of the 57-kDa protein. JOURNAL OF FISH DISEASES 2022; 45:289-300. [PMID: 34791674 DOI: 10.1111/jfd.13554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Renibacterium salmoninarum, a slow-growing facultative intracellular pathogen, is the causative agent of bacterial kidney disease, a chronic, progressive and granulomatous infection that threatens farmed and wild salmonids worldwide. Pathogenic R. salmoninarum colonizes tissues and invades the host through cell surface-associated and secreted proteins. While correlations between iron acquisition genes and virulence have been demonstrated in vitro, these mechanisms have not undergone proteomic characterization. The present study applied a proteomic approach to elucidate the differences between the virulent Chilean R. salmoninarum H-2 strain and the type strain ATCC 33209T . Analyses were conducted under normal (control) and iron-limited conditions (DIP) emulating the host environment. Interestingly, strain H-2 apparently responded better to the iron-limited condition-for example, only this strain presented a significantly enriched iron ion homeostasis pathway. Furthermore, key virulence factors related to an iron-limited environment were more abundant in strain H-2. Importantly, the lack of iron favoured the expression of the 57-kDa protein in strain H-2, the principal virulence factor for R. salmoninarum. Our findings can be employed in the design and development of treatments targeted to iron uptake mechanisms (e.g. siderophore synthesis or haem uptake), which represents a promising therapeutic approach for treating this persistent fastidious bacterium.
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Affiliation(s)
- Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Pablo Saldivia
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Concepción, Chile
| | - Jorn Bethke
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Cristian Vargas
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Concepción, Chile
| | - Mauricio Hernández
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Concepción, Chile
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10
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Bange G, Brodersen DE, Liuzzi A, Steinchen W. Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp. Annu Rev Microbiol 2021; 75:383-406. [PMID: 34343020 DOI: 10.1146/annurev-micro-042621-122343] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Under stressful growth conditions and nutrient starvation, bacteria adapt by synthesizing signaling molecules that profoundly reprogram cellular physiology. At the onset of this process, called the stringent response, members of the RelA/SpoT homolog (RSH) protein superfamily are activated by specific stress stimuli to produce several hyperphosphorylated forms of guanine nucleotides, commonly referred to as (p)ppGpp. Some bifunctional RSH enzymes also harbor domains that allow for degradation of (p)ppGpp by hydrolysis. (p)ppGpp synthesis or hydrolysis may further be executed by single-domain alarmone synthetases or hydrolases, respectively. The downstream effects of (p)ppGpp rely mainly on direct interaction with specific intracellular effectors, which are widely used throughout most cellular processes. The growing number of identified (p)ppGpp targets allows us to deduce both common features of and differences between gram-negative and gram-positive bacteria. In this review, we give an overview of (p)ppGpp metabolism with a focus on the functional and structural aspects of the enzymes involved and discuss recent findings on alarmone-regulated cellular effectors. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Anastasia Liuzzi
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Wieland Steinchen
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
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11
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Abstract
Inhibiting eukaryotic protein translation with small molecules is emerging as a powerful therapeutic strategy. The advantage of targeting cellular translational machinery is that it is required for the highly proliferative state of many neoplastic cells, replication of certain viruses, and ultimately the expression of a wide variety of protein targets. Although, this approach has been exploited to develop clinical agents, such as homoharringtonine (HHT, 1), used to treat chronic myeloid leukemia (CML), inhibiting components of the translational machinery is often associated with cytotoxic phenotypes. However, recent studies have demonstrated that certain small molecules can inhibit the translation of specific subsets of proteins, leading to lower cytotoxicity, and opening-up therapeutic opportunities for translation inhibitors to be deployed in indications beyond oncology and infectious disease. This review summarizes efforts to develop inhibitors of the eukaryotic translational machinery as therapeutic agents and highlights emerging opportunities for translation inhibitors in the future.
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Affiliation(s)
- Angela Fan
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Phillip P Sharp
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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12
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Bhattacharya U, Neizer-Ashun F, Mukherjee P, Bhattacharya R. When the chains do not break: the role of USP10 in physiology and pathology. Cell Death Dis 2020; 11:1033. [PMID: 33277473 PMCID: PMC7718870 DOI: 10.1038/s41419-020-03246-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/24/2022]
Abstract
Deubiquitination is now understood to be as important as its partner ubiquitination for the maintenance of protein half-life, activity, and localization under both normal and pathological conditions. The enzymes that remove ubiquitin from target proteins are called deubiquitinases (DUBs) and they regulate a plethora of cellular processes. DUBs are essential enzymes that maintain intracellular protein homeostasis by recycling ubiquitin. Ubiquitination is a post-translational modification where ubiquitin molecules are added to proteins thus influencing activation, localization, and complex formation. Ubiquitin also acts as a tag for protein degradation, especially by proteasomal or lysosomal degradation systems. With ~100 members, DUBs are a large enzyme family; the ubiquitin-specific peptidases (USPs) being the largest group. USP10, an important member of this family, has enormous significance in diverse cellular processes and many human diseases. In this review, we discuss recent studies that define the roles of USP10 in maintaining cellular function, its involvement in human pathologies, and the molecular mechanisms underlying its association with cancer and neurodegenerative diseases. We also discuss efforts to modulate USPs as therapy in these diseases.
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Affiliation(s)
- Udayan Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Fiifi Neizer-Ashun
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Priyabrata Mukherjee
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA. .,Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA. .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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Ferdosh S, Banerjee S, Pathak BK, Sengupta J, Barat C. Hibernating ribosomes exhibit chaperoning activity but can resist unfolded protein-mediated subunit dissociation. FEBS J 2020; 288:1305-1324. [PMID: 32649051 DOI: 10.1111/febs.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/24/2020] [Accepted: 07/07/2020] [Indexed: 02/03/2023]
Abstract
Ribosome hibernation is a prominent cellular strategy to modulate protein synthesis during starvation and the stationary phase of bacterial cell growth. Translational suppression involves the formation of either factor-bound inactive 70S monomers or dimeric 100S hibernating ribosomal complexes, the biological significance of which is poorly understood. Here, we demonstrate that the Escherichia coli 70S ribosome associated with stationary phase factors hibernation promoting factor or protein Y or ribosome-associated inhibitor A and the 100S ribosome isolated from both Gram-negative and Gram-positive bacteria are resistant to unfolded protein-mediated subunit dissociation and subsequent degradation by cellular ribonucleases. Considering that the increase in cellular stress is accompanied by accumulation of unfolded proteins, such resistance of hibernating ribosomes towards dissociation might contribute to their maintenance during the stationary phase. Analysis of existing structures provided clues on the mechanism of inhibition of the unfolded protein-mediated disassembly in case of hibernating factor-bound ribosome. Further, the factor-bound 70S and 100S ribosomes can suppress protein aggregation and assist in protein folding. The chaperoning activity of these ribosomes is the first evidence of a potential biological activity of the hibernating ribosome that might be crucial for cell survival under stress conditions.
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Affiliation(s)
- Sehnaz Ferdosh
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Senjuti Banerjee
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Bani K Pathak
- Structural Biology and Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific and Industrial Research), Kolkata, India
| | - Jayati Sengupta
- Structural Biology and Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific and Industrial Research), Kolkata, India
| | - Chandana Barat
- Department of Biotechnology, St. Xavier's College, Kolkata, India
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Noronha Souza PF, Abreu Oliveira JT, Vasconcelos IM, Magalhães VG, Albuquerque Silva FD, Guedes Silva RG, Oliveira KS, Franco OL, Gomes Silveira JA, Leite Carvalho FE. H 2O 2Accumulation, Host Cell Death and Differential Levels of Proteins Related to Photosynthesis, Redox Homeostasis, and Required for Viral Replication Explain the Resistance of EMS-mutagenized Cowpea to Cowpea Severe Mosaic Virus. JOURNAL OF PLANT PHYSIOLOGY 2020; 245:153110. [PMID: 31918353 DOI: 10.1016/j.jplph.2019.153110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Infection with Cowpea severe mosaic virus (CPSMV) represents one of the main limitations for cowpea (Vigna unguiculata L. Walp.) productivity due to the severity of the disease symptoms, frequency of incidence, and difficulties in dissemination control. This study aimed to identify the proteins and metabolic pathways associated with the susceptibility and resistance of cowpea plants to CPSMV. Therefore, we treated the seeds of a naturally susceptible cowpea genotype (CE-31) with the mutagenic agent ethyl methane sulfonate (EMS) and compared the secondary leaf proteomic profile of the mutagenized resistant plants inoculated with CPSMV (MCPI plant group) to those of the naturally susceptible cowpea genotype CE-31 inoculated (CPI) and noninoculated (CPU) with CPSMV. MCPI responded to CPSMV by accumulating proteins involved in the oxidative burst, increasing H2O2 generation, promoting leaf cell death (LCD), increasing the synthesis of defense proteins, and decreasing host factors important for the establishment of CPSMV infection. In contrast, CPI accumulated several host factors that favor CPSMV infection and did not accumulate H2O2 or present LCD, which allowed CPSMV replication and systemic dissemination. Based on these results, we propose that the differential abundance of defense proteins and proteins involved in the oxidative burst, LCD, and the decrease in cowpea protein factors required for CPSMV replication are associated with the resistance trait acquired by the MCPI plant group.
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Affiliation(s)
| | | | | | | | | | | | - Kleber Sousa Oliveira
- Proteomics Analysis and Biochemical Center, Catholic University of Brasilia, Brasilia, Brazil
| | - Octavio Luis Franco
- Proteomics Analysis and Biochemical Center, Catholic University of Brasilia, Brasilia, Brazil; S-Inova Biotech, Catholic University Dom Bosco, Campo Grande, MS, Brazil.
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15
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Ousalem F, Singh S, Chesneau O, Hunt JF, Boël G. ABC-F proteins in mRNA translation and antibiotic resistance. Res Microbiol 2019; 170:435-447. [PMID: 31563533 DOI: 10.1016/j.resmic.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/01/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022]
Abstract
The ATP binding cassette protein superfamily comprises ATPase enzymes which are, for the most part, involved in transmembrane transport. Within this superfamily however, some protein families have other functions unrelated to transport. One example is the ABC-F family, which comprises an extremely diverse set of cytoplasmic proteins. All of the proteins in the ABC-F family characterized to date act on the ribosome and are translation factors. Their common function is ATP-dependent modulation of the stereochemistry of the peptidyl transferase center (PTC) in the ribosome coupled to changes in its global conformation and P-site tRNA binding geometry. In this review, we give an overview of the function, structure, and theories for the mechanisms-of-action of microbial proteins in the ABC-F family, including those involved in mediating resistance to ribosome-binding antibiotics.
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Affiliation(s)
- Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Shikha Singh
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 75724, Paris Cedex 15, France.
| | - John F Hunt
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States.
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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Uchenunu O, Pollak M, Topisirovic I, Hulea L. Oncogenic kinases and perturbations in protein synthesis machinery and energetics in neoplasia. J Mol Endocrinol 2019; 62:R83-R103. [PMID: 30072418 PMCID: PMC6347283 DOI: 10.1530/jme-18-0058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/01/2018] [Indexed: 12/17/2022]
Abstract
Notwithstanding that metabolic perturbations and dysregulated protein synthesis are salient features of cancer, the mechanism underlying coordination of cellular energy balance with mRNA translation (which is the most energy consuming process in the cell) is poorly understood. In this review, we focus on recently emerging insights in the molecular underpinnings of the cross-talk between oncogenic kinases, translational apparatus and cellular energy metabolism. In particular, we focus on the central signaling nodes that regulate these processes (e.g. the mechanistic/mammalian target of rapamycin MTOR) and the potential implications of these findings on improving the anti-neoplastic efficacy of oncogenic kinase inhibitors.
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Affiliation(s)
- Oro Uchenunu
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada
- Department of Experimental Medicine, Montreal, Quebec, Canada
| | - Michael Pollak
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada
- Department of Experimental Medicine, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, Montreal, Quebec, Canada
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada
- Department of Experimental Medicine, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, Montreal, Quebec, Canada
- Biochemistry Department, McGill University, Montreal, Quebec, Canada
| | - Laura Hulea
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, Montreal, Quebec, Canada
- Correspondence should be addressed to L Hulea:
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Pathak BK, Banerjee S, Mondal S, Chakraborty B, Sengupta J, Barat C. Unfolded protein exhibits antiassociation activity toward the 50S subunit facilitating 70S ribosome dissociation. FEBS J 2017; 284:3915-3930. [DOI: 10.1111/febs.14282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 09/05/2017] [Accepted: 09/26/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Bani K. Pathak
- Department of Biotechnology St Xavier's College KolkataIndia
- Structural Biology and Bio‐Informatics Division Indian Institute of Chemical Biology (Council of Scientific and Industrial Research) Kolkata India
| | | | - Surojit Mondal
- Department of Biotechnology St Xavier's College KolkataIndia
| | - Biprashekhar Chakraborty
- Structural Biology and Bio‐Informatics Division Indian Institute of Chemical Biology (Council of Scientific and Industrial Research) Kolkata India
| | - Jayati Sengupta
- Structural Biology and Bio‐Informatics Division Indian Institute of Chemical Biology (Council of Scientific and Industrial Research) Kolkata India
| | - Chandana Barat
- Department of Biotechnology St Xavier's College KolkataIndia
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Wang H, Ling MH, Chua TK, Poh CL. Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits. ENGINEERING BIOLOGY 2017. [DOI: 10.1049/enb.2017.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Huijuan Wang
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Maurice H.T. Ling
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Tze Kwang Chua
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
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Wong TY, Schwartzbach SD. Protein Mis-Termination Initiates Genetic Diseases, Cancers, and Restricts Bacterial Genome Expansion. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2015; 33:255-285. [PMID: 26087060 DOI: 10.1080/10590501.2015.1053461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein termination is an important cellular process. Protein termination relies on the stop-codons in the mRNA interacting properly with the releasing factors on the ribosome. One third of inherited diseases, including cancers, are associated with the mutation of the stop-codons. Many pathogens and viruses are able to manipulate their stop-codons to express their virulence. The influence of stop-codons is not limited to the primary reading frame of the genes. Stop-codons in the second and third reading frames are referred as premature stop signals (PSC). Stop-codons and PSCs together are collectively referred as stop-signals. The ratios of the stop-signals (referred as translation stop-signals ratio or TSSR) of genetically related bacteria, despite their great differences in gene contents, are much alike. This nearly identical Genomic-TSSR value of genetically related bacteria may suggest that bacterial genome expansion is limited by their unique stop-signals bias. We review the protein termination process and the different types of stop-codon mutation in plants, animals, microbes, and viruses, with special emphasis on the role of PSCs in directing bacterial evolution in their natural environments. Knowing the limit of genomic boundary could facilitate the formulation of new strategies in controlling the spread of diseases and combat antibiotic-resistant bacteria.
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Affiliation(s)
- Tit-Yee Wong
- a Department of Biological Sciences , University of Memphis , Memphis , Tennessee , USA
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