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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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Wu B, Qiao J, Wang X, Liu M, Xu S, Sun D. Factors affecting the rapid changes of protein under short-term heat stress. BMC Genomics 2021; 22:263. [PMID: 33849452 PMCID: PMC8042900 DOI: 10.1186/s12864-021-07560-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Protein content determines the state of cells. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. RESULTS We quantified 47,535 mRNAs and 3742 proteins in the filling grains of wheat in two different thermal environments. The impact of mRNA abundance and sequence features involved in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency were the main drivers of changes in protein expression under heat stress, and their combined contribution explains 58.2 and 66.4% of the protein variation at 30 and 40 °C (20 °C as control), respectively. Transcription contributes more to alterations in protein content at 40 °C (31%) than at 30 °C (6%). Furthermore, the usage of codon AAG may be closely related to the rapid alteration of proteins under heat stress. The contributions of AAG were 24 and 13% at 30 and 40 °C, respectively. CONCLUSION In this study, we analyzed the factors affecting the changes in protein expression in the early stage of heat stress and evaluated their influence.
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Affiliation(s)
- Bingjin Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jianwen Qiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Manshuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Daojie Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Heavy metal sensitivities of gene deletion strains for ITT1 and RPS1A connect their activities to the expression of URE2, a key gene involved in metal detoxification in yeast. PLoS One 2018; 13:e0198704. [PMID: 30231023 PMCID: PMC6145592 DOI: 10.1371/journal.pone.0198704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 11/19/2022] Open
Abstract
Heavy metal and metalloid contaminations are among the most concerning types of pollutant in the environment. Consequently, it is important to investigate the molecular mechanisms of cellular responses and detoxification pathways for these compounds in living organisms. To date, a number of genes have been linked to the detoxification process. The expression of these genes can be controlled at both transcriptional and translational levels. In baker’s yeast, Saccharomyces cerevisiae, resistance to a wide range of toxic metals is regulated by glutathione S-transferases. Yeast URE2 encodes for a protein that has glutathione peroxidase activity and is homologous to mammalian glutathione S-transferases. The URE2 expression is critical to cell survival under heavy metal stress. Here, we report on the finding of two genes, ITT1, an inhibitor of translation termination, and RPS1A, a small ribosomal protein, that when deleted yeast cells exhibit similar metal sensitivity phenotypes to gene deletion strain for URE2. Neither of these genes were previously linked to metal toxicity. Our gene expression analysis illustrates that these two genes affect URE2 mRNA expression at the level of translation.
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Samanfar B, Shostak K, Moteshareie H, Hajikarimlou M, Shaikho S, Omidi K, Hooshyar M, Burnside D, Márquez IG, Kazmirchuk T, Naing T, Ludovico P, York-Lyon A, Szereszewski K, Leung C, Jin JY, Megarbane R, Smith ML, Babu M, Holcik M, Golshani A. The sensitivity of the yeast, Saccharomyces cerevisiae, to acetic acid is influenced by DOM34 and RPL36A. PeerJ 2017; 5:e4037. [PMID: 29158977 PMCID: PMC5691786 DOI: 10.7717/peerj.4037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
The presence of acetic acid during industrial alcohol fermentation reduces the yield of fermentation by imposing additional stress on the yeast cells. The biology of cellular responses to stress has been a subject of vigorous investigations. Although much has been learned, details of some of these responses remain poorly understood. Members of heat shock chaperone HSP proteins have been linked to acetic acid and heat shock stress responses in yeast. Both acetic acid and heat shock have been identified to trigger different cellular responses including reduction of global protein synthesis and induction of programmed cell death. Yeast HSC82 and HSP82 code for two important heat shock proteins that together account for 1–2% of total cellular proteins. Both proteins have been linked to responses to acetic acid and heat shock. In contrast to the overall rate of protein synthesis which is reduced, the expression of HSC82 and HSP82 is induced in response to acetic acid stress. In the current study we identified two yeast genes DOM34 and RPL36A that are linked to acetic acid and heat shock sensitivity. We investigated the influence of these genes on the expression of HSP proteins. Our observations suggest that Dom34 and RPL36A influence translation in a CAP-independent manner.
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Affiliation(s)
- Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Ari-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Kristina Shostak
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Ari-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Maryam Hajikarimlou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sarah Shaikho
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada
| | - Katayoun Omidi
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohsen Hooshyar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Center for Cancer Therapeutics, Ottawa, Ontario, Canada
| | - Daniel Burnside
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Imelda Galván Márquez
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Tom Kazmirchuk
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Thet Naing
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Portugal
| | - Anna York-Lyon
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kama Szereszewski
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Cindy Leung
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jennifer Yixin Jin
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rami Megarbane
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Myron L Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Martin Holcik
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada.,Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
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