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Zhao X, Liu Y, Yan F, Lin Z, Zhao Y, Chen X, Zhang Y. OmpU and OmpC are the key OMPs for Litopenaeus vannamei hemocyanin recognizes Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109409. [PMID: 38325593 DOI: 10.1016/j.fsi.2024.109409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/25/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
Hemocyanin is a multifunctional protein present in arthropods and mollusks, responsible for oxygen transport and participating in multiple roles of immune defense including antibacterial activity. However, the molecular basis of how hemocyanin recognizes pathogens and exerts antibacterial activity remains poorly understood. In the present study, the pull-down assay was used to isolate Vibrio parahaemolyticus outer membrane proteins (OMPs) that bind to Litopenaeus vannamei hemocyanin. Two interacting OMPs bands were determined as OmpC and OmpU, and the heterogeneous interaction between hemocyanin and the two OMPs was further confirmed by far-Western blot. After construction of ompC and ompU deletion mutants, we found that the agglutinating activity and antibacterial activity of hemocyanin significantly decreased compared to the wild-type strain. After hemocyanin treatment, we identified four intracellular proteins of V. parahaemolyticus, including fructose-bisphosphate aldolase and ribosomal proteins could interact with rOmpC and rOmpU, respectively. Furthermore, we found that the mRNA levels of ompC, ompU, fbaA, rpsB and rpsC significantly decreased after hemocyanin treatment. These findings indicated that OmpC and OmpU are the key targets for L. vannamei hemocyanin recognize pathogens and exert its antibacterial activity.
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Affiliation(s)
- Xianliang Zhao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Yao Liu
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Fang Yan
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Zhongyang Lin
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Yongzhen Zhao
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Xiuli Chen
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China.
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2
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Byju S, Hassan A, Whitford PC. The energy landscape of the ribosome. Biopolymers 2024; 115:e23570. [PMID: 38051695 DOI: 10.1002/bip.23570] [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: 08/27/2023] [Revised: 10/17/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023]
Abstract
The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large-scale (10-100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.
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Affiliation(s)
- Sandra Byju
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Asem Hassan
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
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3
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Liu S, Gao Y, Shi R, Huang H, Xu Y, Chen Z. Transcriptomics Provide Insights into the Photoperiodic Regulation of Reproductive Diapause in the Green Lacewing, Chrysoperla nipponensis (Okamoto) (Neuroptera: Chrysopidae). INSECTS 2024; 15:136. [PMID: 38392555 PMCID: PMC10889211 DOI: 10.3390/insects15020136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Chrysoperla nipponensis (Okamoto) displays typical adult reproductive diapause under short photoperiods; however, our understanding of the molecular mechanism underlying photoperiod-sensitive reproduction remains limited. In this study, we performed transcriptome profiling of four treatments (the diapause-sensitive stage and pre-diapause phase under long and short photoperiods) of C. nipponensis using RNA sequencing (RNA-seq). A total of 71,654 unigenes were obtained from the samples. Enrichment analysis showed that fatty acid metabolism-related pathways were altered under a short photoperiod. Moreover, β-oxidation-related gene expression was active during the diapause-sensitive period under a short photoperiod. The knockdown of juvenile hormone acid methyltransferase 1 (Jhamt1) prolonged the pre-oviposition period but did not affect the reproductive ability of female individuals in C. nipponensis. These findings provided us with a more comprehensive understanding of the molecular mechanisms of photoperiod-sensitive diapause and show that groundwork is crucial for bolstering the long-term storage and biocontrol potential of C. nipponensis.
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Affiliation(s)
- Shaoye Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Yuqing Gao
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Rangjun Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haiyi Huang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Yongyu Xu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Zhenzhen Chen
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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Sun Y, Wang Y, Zhang Y, Hasan N, Yang N, Xie Y, Tang C. Identification and characterization of the Bicupin domain family and functional analysis of GhBCD11 in response to verticillium wilt in cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111875. [PMID: 37769874 DOI: 10.1016/j.plantsci.2023.111875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Bicupin domain protein (BCD) family, an important component of Cupin domain superfamily, plays important roles in oxalic acid (OA) degradation and stress responses in high plants. However, no studies have been reported on the Cupin domain family in cotton up till now. In our study, a total 110 proteins including Cupin domain were identified from the upland cotton (Gossypium hirsutum). Among them, 17 proteins contained Bicupin domain. Subsequently, we found that V. dahliae produces OA leading to cotton leaf wilting. RT-qPCR analysis of GhBCDs revealed that OA and V. dahliae Vd080 significantly enhanced the expression of GhBCD11. The Virus-induced gene silencing and overexpression analysis showed that GhBCD11 positively regulates plant resistance to V. dahliae. Subcellular localization showed GhBCD11 located on the plasma membrane. The analysis of expression pattern showed that GhBCD11 can be induced via hormone-mediated signal pathway including salicylic acid (SA), ethephon (ET), methyl jasmonate (JA) and abscisic acid (ABA). In addition, we identified an interaction between 60 S ribosomal protein GhRPL12-3 and GhBCD11 by yeast double hybridization. Overall, this is the first study, where we identified Cupin domain family in cotton, clarified the role of GhBCD11 in cotton for resistance to V. dahliae and found an interaction between GhRPL12-3 and GhBCD11.
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Affiliation(s)
- Ying Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, Henan, China
| | - Nadeem Hasan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Na Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yijing Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Canming Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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Leow BCS, Kok CH, Yeung DT, Hughes TP, White DL, Eadie LN. The acquisition order of leukemic drug resistance mutations is directed by the selective fitness associated with each resistance mechanism. Sci Rep 2023; 13:13110. [PMID: 37567965 PMCID: PMC10421868 DOI: 10.1038/s41598-023-40279-2] [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: 05/17/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
In Chronic Myeloid Leukemia, the transition from drug sensitive to drug resistant disease is poorly understood. Here, we used exploratory sequencing of gene transcripts to determine the mechanisms of drug resistance in a dasatinib resistant cell line model. Importantly, cell samples were collected sequentially during drug exposure and dose escalation, revealing several resistance mechanisms which fluctuated over time. BCR::ABL1 overexpression, BCR::ABL1 kinase domain mutation, and overexpression of the small molecule transporter ABCG2, were identified as dasatinib resistance mechanisms. The acquisition of mutations followed an order corresponding with the increase in selective fitness associated with each resistance mechanism. Additionally, it was demonstrated that ABCG2 overexpression confers partial ponatinib resistance. The results of this study have broad applicability and help direct effective therapeutic drug usage and dosing regimens and may be useful for clinicians to select the most efficacious therapy at the most beneficial time.
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Affiliation(s)
- Benjamin C S Leow
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Chung H Kok
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - David T Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
- Australasian Leukaemia & Lymphoma Group, Richmond, VIC, 3121, Australia
- Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Timothy P Hughes
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
- Australasian Leukaemia & Lymphoma Group, Richmond, VIC, 3121, Australia
- Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Deborah L White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
- Australasian Leukaemia & Lymphoma Group, Richmond, VIC, 3121, Australia
- Australian & New Zealand Children's Haematology/Oncology Group, Clayton, VIC, 3168, Australia
- Australian Genomics Health Alliance, Parkville, VIC, 3052, Australia
| | - Laura N Eadie
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia.
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.
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6
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Yu P, Zhou S, Gao Y, Liang Y, Guo W, Wang DO, Ding S, Lin S, Wang J, Cun Y. Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:834-849. [PMID: 35952936 PMCID: PMC10787195 DOI: 10.1016/j.gpb.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Although the function of tRNAs in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. Moreover, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression at amino acid level. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.
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Affiliation(s)
- Peng Yu
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510080, China
| | - Siting Zhou
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan Gao
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Yu Liang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenbing Guo
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Dan Ohtan Wang
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shuaiwen Ding
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China; RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yixian Cun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China.
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7
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Jia X, Wang P, Huang C, Zhao D, Wu Q, Lu B, Nie W, Huang L, Tian X, Li P, Laster KV, Jiang Y, Li X, Li H, Dong Z, Liu K. Toosendanin targeting eEF2 impedes Topoisomerase I & II protein translation to suppress esophageal squamous cell carcinoma growth. J Exp Clin Cancer Res 2023; 42:97. [PMID: 37088855 PMCID: PMC10124032 DOI: 10.1186/s13046-023-02666-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/08/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Although molecular targets such as HER2, TP53 and PIK3CA have been widely studied in esophageal cancer, few of them were successfully applied for clinical treatment. Therefore, it is urgent to discover novel actionable targets and inhibitors. Eukaryotic translational elongation factor 2 (eEF2) is reported to be highly expressed in various cancers. However, its contribution to the maintenance and progression of cancer has not been fully clarified. METHODS In the present study, we utilized tissue array to evaluate eEF2 protein expression and clinical significance in esophageal squamous cell carcinoma (ESCC). Next, we performed knockdown, overexpression, RNA-binding protein immunoprecipitation (RIP) sequence, and nascent protein synthesis assays to explore the molecular function of eEF2. Furthermore, we utilized compound screening, Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC) assay, cell proliferation and Patient derived xenograft (PDX) mouse model assays to discover an eEF2 inhibitor and assess its effects on ESCC growth. RESULTS We found that eEF2 were highly expressed in ESCC and negatively associated with the prognosis of ESCC patients. Knocking down of eEF2 suppressed the cell proliferation and colony formation of ESCC. eEF2 bond with the mRNA of Topoisomerase II (TOP1) and Topoisomerase II (TOP2) and enhanced the protein biosynthesis of TOP1 and TOP2. We also identified Toosendanin was a novel inhibitor of eEF2 and Toosendanin inhibited the growth of ESCC in vitro and in vivo. CONCLUSIONS Our findings show that Toosendanin treatment suppresses ESCC growth through targeting eEF2 and regulating downstream TOP1 and TOP2 biosynthesis. eEF2 could be supplied as a potential therapeutic target in the further clinical studies.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Penglei Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Traditional Chinese Medicine, Zhengzhou, 450000, Henan, China
| | - Dengyun Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Qiong Wu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Bingbing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Wenna Nie
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Limeng Huang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Xueli Tian
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Pan Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Kyle Vaughn Laster
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Yanan Jiang
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Xiang Li
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China
| | - Honglin Li
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China.
- Basic Medicine Sciences Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, Henan, China.
- Basic Medicine Sciences Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, 450000, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Tianjian Advanced Biomedical Laboratory, Zhengzhou, 450052, Henan, China.
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8
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Ren D, Mo Y, Yang M, Wang D, Wang Y, Yan Q, Guo C, Xiong W, Wang F, Zeng Z. Emerging roles of tRNA in cancer. Cancer Lett 2023; 563:216170. [PMID: 37054943 DOI: 10.1016/j.canlet.2023.216170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Transfer RNAs (tRNAs) play pivotal roles in the transmission of genetic information, and abnormality of tRNAs directly leads to translation disorders and causes diseases, including cancer. The complex modifications enable tRNA to execute its delicate biological function. Alteration of appropriate modifications may affect the stability of tRNA, impair its ability to carry amino acids, and disrupt the pairing between anticodons and codons. Studies confirmed that dysregulation of tRNA modifications plays an important role in carcinogenesis. Furthermore, when the stability of tRNA is impaired, tRNAs are cleaved into small tRNA fragments (tRFs) by specific RNases. Though tRFs have been found to play vital regulatory roles in tumorigenesis, its formation process is far from clear. Understanding improper tRNA modifications and abnormal formation of tRFs in cancer is conducive to uncovering the role of metabolic process of tRNA under pathological conditions, which may open up new avenues for cancer prevention and treatment.
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Affiliation(s)
- Daixi Ren
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Yongzhen Mo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Mei Yang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Fuyan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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9
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Hassan A, Whitford PC. Identifying Strategies to Experimentally Probe Multidimensional Dynamics in the Ribosome. J Phys Chem B 2022; 126:8460-8471. [PMID: 36256879 DOI: 10.1021/acs.jpcb.2c05706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The ribosome is a complex biomolecular machine that utilizes large-scale conformational rearrangements to synthesize proteins. For example, during the elongation cycle, the "head" domain of the ribosomal small subunit (SSU) is known to undergo transient rotation events that allow for movement of tRNA molecules (i.e., translocation). While the head may exhibit rigid-body-like properties, the precise relationship between experimentally accessible probes and multidimensional rotations has yet to be established. To address this gap, we perform molecular dynamics simulations of the translocation step of the elongation cycle in the ribosome, where the SSU head spontaneously undergoes rotation and tilt-like motions. With this data set (1250 simulated events), we used statistical and information-theory-based measures to identify possible single-molecule probes that can isolate SSU head rotation and head tilting. This analysis provides a molecular interpretation for previous single-molecule measurements, while establishing a framework for the design of next-generation experiments that may precisely probe the mechanistic and kinetic aspects of the ribosome.
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Affiliation(s)
- Asem Hassan
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts02115, United States.,Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts02115, United States
| | - Paul C Whitford
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts02115, United States.,Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts02115, United States
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10
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Yuan J, Cheng L, Li H, An C, Wang Y, Zhang F. Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro. BMC PLANT BIOLOGY 2022; 22:481. [PMID: 36210448 PMCID: PMC9549635 DOI: 10.1186/s12870-022-03852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. RESULTS A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. CONCLUSIONS This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.
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Affiliation(s)
- Jianlong Yuan
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lixiang Cheng
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huijun Li
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Congcong An
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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11
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Cheng L, Yuan J, Yu B, Wang X, Wang Y, Zhang F. Leaf proteome reveals the alterations in photosynthesis and defense-related proteins between potato tetraploid cultivars and diploid wild species. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153779. [PMID: 35952453 DOI: 10.1016/j.jplph.2022.153779] [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: 04/26/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Potato (Solanum tuberosum L.) as the important food crop worldwide has abundant morphological and genetic diversity. To understand the underlying molecular mechanisms determining phenotypic differences in wild species and cultivated potato, a comparative proteomics approach was applied to analyze leaf proteome alteration among three tetraploid cultivars and three diploid wild species using two-dimensional gel electrophoresis (2-DE). Quantitative image analysis showed a total of 47 protein spots with significantly altered abundance (>3-fold, P < 0.05), and 45 differentially abundant proteins were identified by MALDI-TOF/TOF MS. These proteins exhibited both the qualitative and quantitative changes. Most of them were involved in photosynthesis, cell defense and rescue, protein biosynthesis, which might exhibit the main differences between tetraploid cultivars and diploid wild species. The photosynthesis and protein biosynthesis-related proteins were up-regulated or only present in tetraploid cultivars, suggesting the higher photosynthetic efficiency and more newly synthesized peptides. It might contribute to some superior traits of tetraploid cultivars, such as larger leaf size, greater growth vigor, better tuber yield and quality. However, some cell defense and rescue-related proteins, especially the pathogenesis-related proteins and antioxidant enzymes, were up-regulated or only present in diploid wild species. It might be responsible for stronger resistance to diseases and pests or tolerance to environmental stresses in diploid wild species. This study would provide valuable information for the underlying molecular mechanisms of potato genetic diversity, and help in developing strategies for the utilization of wild species for potato improvement.
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Affiliation(s)
- Lixiang Cheng
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jianlong Yuan
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Bin Yu
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaoqing Wang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, China.
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12
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Srinivas P, Keiler KC, Dunham CM. Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action. Bioessays 2022; 44:e2200046. [PMID: 35719031 PMCID: PMC9308750 DOI: 10.1002/bies.202200046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/03/2023]
Abstract
Bacteria use trans-translation to rescue stalled ribosomes and target incomplete proteins for proteolysis. Despite similarities between tRNAs and transfer-messenger RNA (tmRNA), the key molecule for trans-translation, new structural and biochemical data show important differences between translation and trans-translation at most steps of the pathways. tmRNA and its binding partner, SmpB, bind in the A site of the ribosome but do not trigger the same movements of nucleotides in the rRNA that are required for codon recognition by tRNA. tmRNA-SmpB moves from the A site to the P site of the ribosome without subunit rotation to generate hybrid states, and moves from the P site to a site outside the ribosome instead of to the E site. During catalysis, transpeptidation to tmRNA appears to require the ribosomal protein bL27, which is dispensable for translation, suggesting that this protein may be conserved in bacteria due to trans-translation. These differences provide insights into the fundamental nature of trans-translation, and provide targets for new antibiotics that may have decrease cross-reactivity with eukaryotic ribosomes.
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Affiliation(s)
- Pooja Srinivas
- Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, USA
| | - Kenneth C. Keiler
- The Pennsylvania State University, Department of Biochemistry & Molecular Biology, University Park, PA, USA,Corresponding authors: Kenneth C. Keiler, , Christine M. Dunham,
| | - Christine M. Dunham
- Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, USA,Corresponding authors: Kenneth C. Keiler, , Christine M. Dunham,
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13
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Gu X, Zhang Y, Qin X, Ma S, Huang Y, Ju S. Transfer RNA-derived small RNA: an emerging small non-coding RNA with key roles in cancer. Exp Hematol Oncol 2022; 11:35. [PMID: 35658952 PMCID: PMC9164556 DOI: 10.1186/s40164-022-00290-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
Transfer RNAs (tRNAs) promote protein translation by binding to the corresponding amino acids and transporting them to the ribosome, which is essential in protein translation. tRNA-derived small RNAs (tsRNAs) are derived fragments of tRNAs that are cleaved explicitly under certain conditions. An increasing amount of research has demonstrated that tsRNAs have biological functions rather than just being degradation products. tsRNAs can exert functions such as regulating gene expression to influence cancer progression. Their dysregulation is closely associated with various cancers and can serve as diagnostic and prognostic biomarkers for cancer. This review summarizes the generation, classification, and biological functions of tsRNAs, and highlights the roles of tsRNAs in different cancers and their applications as tumor markers.
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Affiliation(s)
- Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xinyue Qin
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shuo Ma
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, China. .,Department of Medical Oncology, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.
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14
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Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
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Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
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15
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Fairman CM, Lønbro S, Cardaci TD, VanderVeen BN, Nilsen TS, Murphy AE. Muscle wasting in cancer: opportunities and challenges for exercise in clinical cancer trials. JCSM RAPID COMMUNICATIONS 2022; 5:52-67. [PMID: 36118249 PMCID: PMC9481195 DOI: 10.1002/rco2.56] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND Low muscle in cancer is associated with an increase in treatment-related toxicities and is a predictor of cancer-related and all-cause mortality. The mechanisms of cancer-related muscle loss are multifactorial, including anorexia, hypogonadism, anaemia, inflammation, malnutrition, and aberrations in skeletal muscle protein turnover and metabolism. METHODS In this narrative review, we summarise relevant literature to (i) review the factors influencing skeletal muscle mass regulation, (ii) provide an overview of how cancer/treatments negatively impact these, (iii) review factors beyond muscle signalling that can impact the ability to participate in and respond to an exercise intervention to counteract muscle loss in cancer, and (iv) provide perspectives on critical areas of future research. RESULTS Despite the well-known benefits of exercise, there remains a paucity of clinical evidence supporting the impact of exercise in cancer-related muscle loss. There are numerous challenges to reversing muscle loss with exercise in clinical cancer settings, ranging from the impact of cancer/treatments on the molecular regulation of muscle mass, to clinical challenges in responsiveness to an exercise intervention. For example, tumour-related/treatment-related factors (e.g. nausea, pain, anaemia, and neutropenia), presence of comorbidities (e.g. diabetes, arthritis, and chronic obstructive pulmonary disease), injuries, disease progression and bone metastases, concomitant medications (e.g., metformin), can negatively affect an individual's ability to exercise safely and limit subsequent adaptation. CONCLUSIONS This review identifies numerous gaps and oppportunities in the area of low muscle and muscle loss in cancer. Collaborative efforts between preclinical and clinical researchers are imperative to both understanding the mechanisms of atrophy, and develop appropriate therapeutic interventions.
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Affiliation(s)
- Ciaran M. Fairman
- Department of Exercise Science, University of South Carolina, Columbia, South Carolina 29033, USA
- Correspondence to: Ciaran Fairman, Department of Exercise Science, University of South Carolina, Columbia, SC 29033, USA.
| | - Simon Lønbro
- Department of Public Health, Section for Sports Science, Aarhus University, Aarhus, Denmark
| | - Thomas D. Cardaci
- Department of Exercise Science, University of South Carolina, Columbia, South Carolina 29033, USA
| | - Brandon N. VanderVeen
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina, USA
| | - Tormod S. Nilsen
- Department of Physical Performance, Norwegian School of Sports Sciences, Oslo, Norway
| | - Angela E. Murphy
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina, USA
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16
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Li J, Shen Z, Luo L, Ye D, Deng H, Gu S, Zhou C. tRNA Ini CAT inhibits proliferation and promotes apoptosis of laryngeal squamous cell carcinoma cells. J Clin Lab Anal 2021; 35:e23821. [PMID: 34048096 PMCID: PMC8274982 DOI: 10.1002/jcla.23821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Laryngeal squamous cell carcinoma (LSCC) brings a heavy blow to the patient's voice. Transfer RNA (tRNA) is a common RNA, the roles of tRNAs in LSCC are largely unknown. METHODS The tRNA expression profile in LSCC tissues and adjacent normal tissues was measured by a tRNA qRT-PCR array. The expression level of tRNAIni CAT in LSCC tissues and plasmas was detected by qRT-PCR. The receiver operating characteristic (ROC) curve was established. tRNAIni CAT was upregulated by a lentivirus vector in the LSCC cell line. Moreover, tRNAIni CAT was upregulated in LSCC xenograft nude mouse model and the xenografts were used for pathological analysis and transmission electron microscope (TEM) observation. RESULTS The top 10 upregulated tRNAs were tRNALys CTT -1, tRNALeu TAA , tRNAPhe GAA , tRNALeu CAG , tRNATyr ATA , tRNAMet CAT , tRNATyr GTA -1, tRNAThr CGT , tRNATyr GTA -2, tRNAAla AGC ; and the top 10 downregulated tRNAs were tRNAIni CAT , mt-tRNAGlu TTC , tRNAVal CAC -3, mt-tRNATrp TCA , mt-tRNATyr GTA , mt-tRNALys TTT , mt-tRNAThr TGT , mt-tRNAAsp GTC , mt-tRNAAsn GTT , mt-tRNAPro TGG . tRNAIni CAT was downregulated in LSCC tissues and plasma. The area under the ROC curve (AUC) in LSCC tissues and the plasma of patients with LSCC was 0.717 and 0.808, respectively. tRNAIni CAT inhibited LSCC cell proliferation and promoted apoptosis. The in vivo results showed that tRNAIni CAT inhibited the growth of the xenografts and promoted apoptosis. CONCLUSIONS This is the first study to provide tRNA expression profiles for LSCC tissues. tRNAIni CAT may be used as a new biomarker for the early diagnosis of LSCC. tRNAIni CAT inhibits cell proliferation and promotes apoptosis in vitro and in vivo.
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MESH Headings
- Animals
- Apoptosis/genetics
- Carcinoma, Squamous Cell/blood
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Green Fluorescent Proteins/metabolism
- Humans
- Laryngeal Neoplasms/blood
- Laryngeal Neoplasms/diagnosis
- Laryngeal Neoplasms/genetics
- Laryngeal Neoplasms/pathology
- Mice, Inbred BALB C
- Mice, Nude
- RNA, Transfer/blood
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- ROC Curve
- Up-Regulation/genetics
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Jun Li
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
- Department of Biochemistry and Molecular BiologyZhejiang Key Laboratory of PathophysiologyNingbo University School of MedicalNingboChina
| | - Zhisen Shen
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Lin Luo
- Department of Biochemistry and Molecular BiologyZhejiang Key Laboratory of PathophysiologyNingbo University School of MedicalNingboChina
| | - Dong Ye
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Hongxia Deng
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Shanshan Gu
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Chongchang Zhou
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
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17
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Freitas FC, Fuchs G, de Oliveira RJ, Whitford PC. The dynamics of subunit rotation in a eukaryotic ribosome. BIOPHYSICA 2021; 1:204-221. [PMID: 37484008 PMCID: PMC10361705 DOI: 10.3390/biophysica1020016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ~1MDa) undergoes spontaneous and reversible rotations (~8°). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Gabriele Fuchs
- Department of Biological Sciences, The RNA Institute, University at Albany 1400 Washington Ave, Albany, NY,12222
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Paul Charles Whitford
- Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
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18
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A steric gate controls P/E hybrid-state formation of tRNA on the ribosome. Nat Commun 2020; 11:5706. [PMID: 33177497 PMCID: PMC7658246 DOI: 10.1038/s41467-020-19450-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022] Open
Abstract
The ribosome is a biomolecular machine that undergoes multiple large-scale structural rearrangements during protein elongation. Here, we focus on a conformational rearrangement during translocation, known as P/E hybrid-state formation. Using a model that explicitly represents all non-hydrogen atoms, we simulated more than 120 spontaneous transitions, where the tRNA molecule is displaced between the P and E sites of the large subunit. In addition to predicting a free-energy landscape that is consistent with previous experimental observations, the simulations reveal how a six-residue gate-like region can limit P/E formation, where sub-angstrom structural perturbations lead to an order-of-magnitude change in kinetics. Thus, this precisely defined set of residues represents a novel target that may be used to control functional dynamics in bacterial ribosomes. This theoretical analysis establishes a direct relationship between ribosome structure and large-scale dynamics, and it suggests how next-generation experiments may precisely dissect the energetics of hybrid formation on the ribosome. The ribosome undergoes multiple large-scale structural rearrangements during protein elongation. Here the authors present an all-atom model of the ribosome to study the energetics of P/E hybrid-state formation, an early conformational rearrangement occurring during translocation.
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19
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Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F. The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity. Nucleic Acids Res 2020; 48:6170-6183. [PMID: 32266934 PMCID: PMC7293025 DOI: 10.1093/nar/gkaa221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
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Affiliation(s)
- Ketty Pernod
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Laure Schaeffer
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, CNRS FRC1589, Université de Strasbourg, 2, allée Konrad Roentgen Descartes, F-67084 Strasbourg, France
| | - Eveline Hok
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Christian Rick
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Michael Ryckelynck
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
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20
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Kim HK, Yeom JH, Kay MA. Transfer RNA-Derived Small RNAs: Another Layer of Gene Regulation and Novel Targets for Disease Therapeutics. Mol Ther 2020; 28:2340-2357. [PMID: 32956625 DOI: 10.1016/j.ymthe.2020.09.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/23/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Decades after identification as essential for protein synthesis, transfer RNAs (tRNAs) have been implicated in various cellular processes beyond translation. tRNA-derived small RNAs (tsRNAs), referred to as tRNA-derived fragments (tRFs) or tRNA-derived, stress-induced RNAs (tiRNAs), are produced by cleavage at different sites from mature or pre-tRNAs. They are classified into six major types representing potentially thousands of unique sequences and have been implicated to play a wide variety of regulatory roles in maintaining normal homeostasis, cancer cell viability, tumorigenesis, ribosome biogenesis, chromatin remodeling, translational regulation, intergenerational inheritance, retrotransposon regulation, and viral replication. However, the detailed mechanisms governing these processes remain unknown. Aberrant expression of tsRNAs is found in various human disease conditions, suggesting that a further understanding of the regulatory role of tsRNAs will assist in identifying novel biomarkers, potential therapeutic targets, and gene-regulatory tools. Here, we highlight the classification, biogenesis, and biological role of tsRNAs in regulatory mechanisms of normal and disease states.
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Affiliation(s)
- Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.
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21
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Cui W, Ma A, Huang Z, Wang X, Liu Z, Xia D, Yang S, Zhao T. Comparative transcriptomic analysis reveals mechanisms of divergence in osmotic regulation of the turbot Scophthalmus maximus. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1519-1536. [PMID: 32383147 DOI: 10.1007/s10695-020-00808-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
The turbot Scophthalmus maximus has evolved extensive physiological ability to adapt to multiple environmental salinities. The morphological changes of the kidney indicated the adaptability difference and similarity of turbot to salinity stress. Identify transcriptome-wide differences between low-salinity seawater (LSW, salinity 5)- and high-salinity seawater (HSW, salinity 50)-acclimated kidneys of turbot to decipher the osmotic regulation mechanism. We identified 688 differentially expressed genes (DEGs) in the LSW-acclimated kidneys and 2441 DEGs in the HSW-acclimated kidneys of turbot compared with seawater-acclimated kidneys, respectively. We investigated three patterns of gene regulation to salinity stress that involved in ion channels and transporters, functions of calcium regulation, organic osmolytes, energy demand, cell cycle regulation, and cell protection. Additionally, protein-protein interaction (PPI) analysis of DEGs suggested the presence of a frequent functional interaction pattern and that crucial genes in the PPI network are involved in hyper-osmotic regulation. Based on the analysis of comparative transcriptome data and related literature reports, we conclude that the mechanisms responsible for osmotic regulation and its divergence in turbot are related to various genes that are involved in canonical physiological functions. These findings provide insight into the divergence in osmoregulation of turbot and valuable information about osmoregulation mechanisms that will benefit other studies in this field.
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Affiliation(s)
- Wenxiao Cui
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Aijun Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Zhihui Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xinan Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Zhifeng Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Dandan Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Shuangshuang Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Tingting Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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22
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Rofeal M, El-Malek FA. Ribosomal proteins as a possible tool for blocking SARS-COV 2 virus replication for a potential prospective treatment. Med Hypotheses 2020; 143:109904. [PMID: 32502901 PMCID: PMC7834321 DOI: 10.1016/j.mehy.2020.109904] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/17/2020] [Accepted: 05/28/2020] [Indexed: 01/17/2023]
Abstract
Coronavirus disease (COVID-19) is caused by SARS-COV2 and has resulted in more than four million cases globally and the death cases exceeded 300,000. Normally, a range of surviving and propagating host factors must be employed for the completion of the infectious process including RPs. Viral protein biosynthesis involves the interaction of numerous RPs with viral mRNA, proteins which are necessary for viruses replication regulation and infection inside the host cells. Most of these interactions are crucial for virus activation and accumulation. However, only small percentage of these proteins is specifically responsible for host cells protection by triggering the immune pathway against virus. This research proposes RPs extracted from bacillus sp. and yeast as new forum for the advancement of antiviral therapy. Hitherto, antiviral therapy with RPs-involving viral infection has not been widely investigated as critical targets. Also, exploring antiviral strategy based on RPs could be a promising guide for more potential therapeutics.
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Affiliation(s)
- Marian Rofeal
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Egypt
| | - Fady Abd El-Malek
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Egypt.
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23
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Yu HZ, Li NY, Zeng XD, Song JC, Yu XD, Su HN, Chen CX, Yi L, Lu ZJ. Transcriptome Analyses of Diaphorina citri Midgut Responses to Candidatus Liberibacter Asiaticus Infection. INSECTS 2020; 11:insects11030171. [PMID: 32156093 PMCID: PMC7143376 DOI: 10.3390/insects11030171] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/29/2020] [Accepted: 03/05/2020] [Indexed: 11/13/2022]
Abstract
The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is an important transmission vector of the citrus greening disease Candidatus Liberibacter asiaticus (CLas). The D. citri midgut exhibits an important tissue barrier against CLas infection. However, the molecular mechanism of the midgut response to CLas infection has not been comprehensively elucidated. In this study, we identified 778 differentially expressed genes (DEGs) in the midgut upon CLas infection, by comparative transcriptome analyses, including 499 upregulated DEGs and 279 downregulated DEGs. Functional annotation analysis showed that these DEGs were associated with ubiquitination, the immune response, the ribosome, endocytosis, the cytoskeleton and insecticide resistance. KEGG enrichment analysis revealed that most of the DEGs were primarily involved in endocytosis and the ribosome. A total of fourteen DEG functions were further validated by reverse transcription quantitative PCR (RT-qPCR). This study will contribute to our understanding of the molecular interaction between CLas and D. citri.
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Affiliation(s)
- Hai-Zhong Yu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Ning-Yan Li
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
| | - Xiang-Dong Zeng
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
| | - Jian-Chun Song
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
| | - Xiu-Dao Yu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Hua-Nan Su
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | | | - Long Yi
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Zhan-Jun Lu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
- Correspondence:
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24
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Cheng L, Wang D, Wang Y, Xue H, Zhang F. An integrative overview of physiological and proteomic changes of cytokinin-induced potato (Solanum tuberosum L.) tuber development in vitro. PHYSIOLOGIA PLANTARUM 2020; 168:675-693. [PMID: 31343748 DOI: 10.1111/ppl.13014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Accepted: 07/22/2019] [Indexed: 05/24/2023]
Abstract
Potato tuberization is a complicated biological process regulated by multiple phytohormones, in particular cytokinins (CKs). The information available on the molecular mechanisms regulating tuber development by CKs remains largely unclear. Physiological results initially indicated that low 6-benzylaminopurine (BAP) concentration (3 mg l-1 ) advanced the tuberization beginning time and promoted tuber formation. A comparative proteomics approach was applied to investigate the proteome change of tuber development by two-dimensional gel electrophoresis in vitro, subjected to exogenous BAP treatments (0, 3, 6 and 13 mg l-1 ). Quantitative image analysis showed a total of 83 protein spots with significantly altered abundance (>2.5-fold, P < 0.05), and 55 differentially abundant proteins were identified by MALDI-TOF/TOF MS. Among these proteins, 22 proteins exhibited up-regulation with the increase of exogenous BAP concentration, and 31 proteins were upregulated at 3 mg l-1 BAP whereas being downregulated at higher BAP concentrations. These proteins were involved in metabolism and bioenergy, storage, redox homeostasis, cell defense and rescue, transcription and translation, chaperones, signaling and transport. The favorable effects of low BAP concentrations on tuber development were found in various cellular processes, mainly including the stimulation of starch and storage protein accumulation, the enhancement of the glycolysis pathway and ATP synthesis, the cellular homeostasis maintenance, the activation of pathogen defense, the higher efficiency of transcription and translation, as well as the enhanced metabolite transport. However, higher BAP concentration, especially 13 mg l-1 , showed disadvantageous effects. The proposed hypothetical model would explain the interaction of these proteins associated with CK-induced tuber development in vitro.
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Affiliation(s)
- Lixiang Cheng
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Dongxia Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Hongwei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
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25
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Jiang B, Xing Y, Li G, Zhang N, Lian L, Sun G, Zhang D. iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources. Front Microbiol 2020; 10:2906. [PMID: 31993023 PMCID: PMC6971185 DOI: 10.3389/fmicb.2019.02906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022] Open
Abstract
DNA damage response allows microorganisms to repair or bypass DNA damage and maintain the genome integrity. It has attracted increasing attention but the underlying influential factors affecting DNA damage response are still unclear. In this work, isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis was used to investigate the influence of carbon sources on the translational response of Acinetobacter baylyi ADP1 to DNA damage. After cultivating in a nutrient-rich medium (LB) and defined media supplemented with four different carbon sources (acetate, citrate, pyruvate, and succinate), a total of 2807 proteins were identified. Among them, 84 proteins involved in stress response were significantly altered, indicating the strong influence of carbon source on the response of A. baylyi ADP1 to DNA damage and other stresses. As the first study on the comparative global proteomic changes in A. baylyi ADP1 under DNA damage across nutritional environments, our findings revealed that DNA damage response in A. baylyi ADP1 at the translational level is significantly altered by carbon source, providing an insight into the complex protein interactions across carbon sources and offering theoretical clues for further study to elucidate their general regulatory mechanism to adapt to different nutrient environments.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Nana Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Luning Lian
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Guangdong Sun
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
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26
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Walter NG. Biological Pathway Specificity in the Cell-Does Molecular Diversity Matter? Bioessays 2019; 41:e1800244. [PMID: 31245864 PMCID: PMC6684156 DOI: 10.1002/bies.201800244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/09/2019] [Indexed: 01/07/2023]
Abstract
Biology arises from the crowded molecular environment of the cell, rendering it a challenge to understand biological pathways based on the reductionist, low-concentration in vitro conditions generally employed for mechanistic studies. Recent evidence suggests that low-affinity interactions between cellular biopolymers abound, with still poorly defined effects on the complex interaction networks that lead to the emergent properties and plasticity of life. Mass-action considerations are used here to underscore that the sheer number of weak interactions expected from the complex mixture of cellular components significantly shapes biological pathway specificity. In particular, on-pathway-i.e., "functional"-become those interactions thermodynamically and kinetically stable enough to survive the incessant onslaught of the many off-pathway ("nonfunctional") interactions. Consequently, to better understand the molecular biology of the cell a further paradigm shift is needed toward mechanistic experimental and computational approaches that probe intracellular diversity and complexity more directly. Also see the video abstract here https://youtu.be/T19X_zYaBzg.
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27
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Cheng L, Zhang S, Yang L, Wang Y, Yu B, Zhang F. Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro. PLANTA 2019; 250:199-217. [PMID: 30976909 DOI: 10.1007/s00425-019-03163-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/05/2019] [Indexed: 05/05/2023]
Abstract
The present study is the first to integrate physiological and proteomic data providing information on Fe, Mn and Zn deficiency-responsive mechanisms of potato plants in vitro. Micronutrient deficiency is an important limiting factor for potato production that causes substantial tuber yield and quality losses. To under the underlying molecular mechanisms of potato in response to Fe, Mn and Zn deficiency, a comparative proteomic approach was applied. Leaf proteome change of in vitro-propagated potato plantlets subjected to a range of Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA), Mn-deficiency treatments (1 and 0 μM MnCl2·4H2O) and Zn-deficiency treatment (0 μM ZnCl2) using two-dimensional gel electrophoresis was analyzed. Quantitative image analysis showed a total of 146, 55 and 42 protein spots under Fe, Mn and Zn deficiency with their abundance significantly altered (P < 0.05) more than twofold, respectively. By MALDI-TOF/TOF MS analyses, the differentially abundant proteins were found mainly involved in bioenergy and metabolism, photosynthesis, defence, redox homeostasis and protein biosynthesis/degradation under the metal deficiencies. Signaling, transport, cellular structure and transcription-related proteins were also identified. The hierarchical clustering results revealed that these proteins were involved in a dynamic network in response to Fe, Mn and Zn deficiency. All these metal deficiencies caused cellular metabolic remodeling to improve metal acquisition and distribution in potato plants. The reduced photosynthetic efficiency occurred under each metal deficiency, yet Fe-deficient plants showed a more severe damage of photosynthesis. More defence mechanisms were induced by Fe deficiency than Mn and Zn deficiency, and the antioxidant systems showed different responses to each metal deficiency. Reprogramming of protein biosynthesis/degradation and assembly was more strongly required for acclimation to Fe deficiency. The signaling cascades involving auxin and NDPKs might also play roles in micronutrient stress signaling and pinpoint interesting candidates for future studies. Our results first provide an insight into the complex functional and regulatory networks in potato plants under Fe, Mn and Zn deficiency.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shaomei Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lili Yang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Bin Yu
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China.
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28
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Adamla F, Rollins J, Newsom M, Snow S, Schosserer M, Heissenberger C, Horrocks J, Rogers AN, Ignatova Z. A Novel Caenorhabditis Elegans Proteinopathy Model Shows Changes in mRNA Translational Frameshifting During Aging. Cell Physiol Biochem 2019; 52:970-983. [PMID: 30977983 DOI: 10.33594/000000067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND/AIMS Regulation of mRNA translation is central to protein homeostasis and is optimized for speed and accuracy. Spontaneous recoding events occur virtually at any codon but at very low frequency and are commonly assumed to increase as the cell ages. METHODS Here, we leveraged the polyglutamine(polyQ)-frameshifting model of huntingtin exon 1 with CAG repeat length in the pathological range (Htt51Q), which undergoes enhanced non-programmed translational -1 frameshifting. RESULTS In body muscle cells of Caenorhabditis elegans, -1 frameshifting occured at the onset of expression of the zero-frame product, correlated with mRNA level of the non-frameshifted expression and formed aggregates correlated with reduced motility in C. elegans. Spontaneous frameshifting was modulated by IFG-1, the homologue of the nutrient-responsive eukaryotic initiation factor 4G (eIF4G), under normal growth conditions and NSUN-5, a conserved ribosomal RNA methyltransferase, under osmotic stress. CONCLUSION Our results suggest that frameshifting and aggregation occur at even early stages of development and, because of their intrinsic stability, may persist and accelerate the onset of age-related proteinopathies.
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Affiliation(s)
- Frauke Adamla
- Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
| | - Jarod Rollins
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Matthew Newsom
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Santina Snow
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Markus Schosserer
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Heissenberger
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jordan Horrocks
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Aric N Rogers
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA,
| | - Zoya Ignatova
- Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany,
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29
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The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways. Int J Mol Sci 2019; 20:ijms20081981. [PMID: 31018531 PMCID: PMC6514570 DOI: 10.3390/ijms20081981] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 01/26/2023] Open
Abstract
The evolution of release factors catalyzing the hydrolysis of the final peptidyl-tRNA bond and the release of the polypeptide from the ribosome has been a longstanding paradox. While the components of the translation apparatus are generally well-conserved across extant life, structurally unrelated release factor peptidyl hydrolases (RF-PHs) emerged in the stems of the bacterial and archaeo-eukaryotic lineages. We analyze the diversification of RF-PH domains within the broader evolutionary framework of the translation apparatus. Thus, we reconstruct the possible state of translation termination in the Last Universal Common Ancestor with possible tRNA-like terminators. Further, evolutionary trajectories of the several auxiliary release factors in ribosome quality control (RQC) and rescue pathways point to multiple independent solutions to this problem and frequent transfers between superkingdoms including the recently characterized ArfT, which is more widely distributed across life than previously appreciated. The eukaryotic RQC system was pieced together from components with disparate provenance, which include the long-sought-after Vms1/ANKZF1 RF-PH of bacterial origin. We also uncover an under-appreciated evolutionary driver of innovation in rescue pathways: effectors deployed in biological conflicts that target the ribosome. At least three rescue pathways (centered on the prfH/RFH, baeRF-1, and C12orf65 RF-PH domains), were likely innovated in response to such conflicts.
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30
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Opron K, Burton ZF. Ribosome Structure, Function, and Early Evolution. Int J Mol Sci 2018; 20:ijms20010040. [PMID: 30583477 PMCID: PMC6337491 DOI: 10.3390/ijms20010040] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/03/2018] [Accepted: 12/16/2018] [Indexed: 11/16/2022] Open
Abstract
Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S⁻50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species.
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Affiliation(s)
- Kristopher Opron
- Bioinformatics Core, University of Michigan, Ann Arbor, MI 48109-0674, USA.
| | - Zachary F Burton
- Department of Biochemistry and Molecular Biology, 603 Wilson Rd., Michigan State University, MI 48824-1319, USA.
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31
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Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Bürger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep 2018; 25:2676-2688.e7. [PMID: 30517857 PMCID: PMC6314685 DOI: 10.1016/j.celrep.2018.11.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/14/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023] Open
Abstract
Translocation moves the tRNA2⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA2⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.
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Affiliation(s)
- Julia Flis
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Emily J Rundlet
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Marylena Dabrowski
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Tatyana V Budkevich
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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32
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Deciphering the Role of the Non-Coding Genome in Regulating Gene-Diet Interactions. Nutrients 2018; 10:nu10121831. [PMID: 30486341 PMCID: PMC6316136 DOI: 10.3390/nu10121831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Protein encoding genes constitute a small fraction of mammalian genomes. In addition to the protein coding genes, there are other functional units within the genome that are transcribed, but not translated into protein, the so called non-coding RNAs. There are many types of non-coding RNAs that have been identified and shown to have important roles in regulating gene expression either at the transcriptional or post-transcriptional level. A number of recent studies have highlighted that dietary manipulation in mammals can influence the expression or function of a number of classes of non-coding RNAs that contribute to the protein translation machinery. The identification of protein translation as a common target for nutritional regulation underscores the need to investigate how this may mechanistically contribute to phenotypes and diseases that are modified by nutritional intervention. Finally, we describe the state of the art and the application of emerging ‘-omics’ technologies to address the regulation of protein translation in response to diet.
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33
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Wan J, Gao X, Mao Y, Zhang X, Qian SB. A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity. RESEARCH (WASHINGTON, D.C.) 2018; 2018:7089174. [PMID: 31549036 PMCID: PMC6750092 DOI: 10.1155/2018/7089174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/28/2018] [Indexed: 06/10/2023]
Abstract
Upon initiation at a start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. While some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known about how the ribosome normally prevents spontaneous frameshift errors that can have dire consequences if uncorrected. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3' end of 18S rRNA to scan the AUG-like codons after the decoding process. The postdecoding mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a retrospective mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like "sticky" codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes the codon "stickiness". Further supporting the role of "sticky" sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes. These results suggest an important layer of information embedded within the protein-coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.
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Affiliation(s)
- Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xiangwei Gao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
- Graduate Programs in Genetics Genomics and Development, Biochemistry Molecular and Cellular Biology, Cornell University, Ithaca, NY 14853, USA
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34
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Huang SQ, Sun B, Xiong ZP, Shu Y, Zhou HH, Zhang W, Xiong J, Li Q. The dysregulation of tRNAs and tRNA derivatives in cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:101. [PMID: 29743091 PMCID: PMC5944149 DOI: 10.1186/s13046-018-0745-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/29/2018] [Indexed: 11/14/2022]
Abstract
Transfer RNAs (tRNAs), traditionally considered to participate in protein translation, were interspersed in the entire genome. Recent studies suggested that dysregulation was observed in not only tRNAs, but also tRNA derivatives generated by the specific cleavage of pre- and mature tRNAs in the progression of cancer. Accumulating evidence had identified that certain tRNAs and tRNA derivatives were involved in proliferation, metastasis and invasiveness of cancer cell, as well as tumor growth and angiogenesis in several malignant human tumors. This paper reviews the importance of the dysregulation of tRNAs and tRNA derivatives during the development of cancer, such as breast cancer, lung cancer, and melanoma, aiming at a better understanding of the tumorigenesis and providing new ideas for the treatment of these cancers.
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Affiliation(s)
- Shi-Qiong Huang
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Bao Sun
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Zong-Ping Xiong
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Yan Shu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Wei Zhang
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China
| | - Jing Xiong
- Department of gynaecology and obstetrics, The Second Xiangya Hospital of Central South University, Central South University, Changsha, 410078, People's Republic of China.
| | - Qing Li
- Department of Clinical Pharmacology, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, People's Republic of China.
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35
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Levi M, Nguyen K, Dukaye L, Whitford PC. Quantifying the Relationship between Single-Molecule Probes and Subunit Rotation in the Ribosome. Biophys J 2018; 113:2777-2786. [PMID: 29262370 DOI: 10.1016/j.bpj.2017.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022] Open
Abstract
A major challenge in the study of biomolecular assemblies is to identify reaction coordinates that precisely monitor conformational rearrangements. This is central to the interpretation of single-molecule fluorescence resonance energy transfer measurements, where the observed dynamics depends on the labeling strategy. As an example, different probes of subunit rotation in the ribosome have provided qualitatively distinct descriptions. In one study, changes in fluorescence suggested that the 30S body undergoes a single rotation/back-rotation cycle during the process of mRNA-tRNA translocation. In contrast, an alternate assay implicated the presence of reversible rotation events before completing translocation. For future single-molecule experiments to unambiguously measure the relationship between subunit rotation and translocation, it is necessary to rationalize these conflicting descriptions. To this end, we have simulated hundreds of spontaneous subunit rotation events (≈8°) using a residue-level coarse-grained model of the ribosome. We analyzed nine different reaction coordinates and found that the apparently inconsistent measurements are likely a consequence of ribosomal flexibility. Further, we propose a metric for quantifying the degree of energetic coupling between experimentally measured degrees of freedom and subunit rotation. This analysis provides a physically grounded framework that can guide the development of more precise single-molecule techniques.
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Affiliation(s)
- Mariana Levi
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Kien Nguyen
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Liah Dukaye
- Department of Physics, Northeastern University, Boston, Massachusetts
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36
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Zhang M, Xu JY, Hu H, Ye BC, Tan M. Systematic Proteomic Analysis of Protein Methylation in Prokaryotes and Eukaryotes Revealed Distinct Substrate Specificity. Proteomics 2017; 18. [PMID: 29150981 DOI: 10.1002/pmic.201700300] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/25/2017] [Indexed: 11/07/2022]
Abstract
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, is largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles. In this study, we deeply explored the methylated sites in three species Escherichia coli, Saccharomyces cerevisiae, and HeLa cells by employing MS-based proteomic approach coupled with heavy methyl SILAC method. We identify a total of 234 methylated sites on 187 proteins with high localization confidence, including 94 unreported methylated sites on nine different amino acid residues. KEGG and gene ontology analysis show the pathways enriched with methylated proteins are mainly involved in central metabolism for E. coli and S. cerevisiae, but related to spliceosome for HeLa cells. The analysis of methylation preference on different amino acids is conducted in three species. Protein N-terminal methylation is dominant in E. coli while methylated lysines and arginines are widely identified in S. cerevisiae and HeLa cells, respectively. To study whether some atypical protein methylation has biological relevance in the pathological process in mammalian cells, we focus on histone methylation in diet-induced obese (DIO) mouse. Two glutamate methylation sites showed statistical significance in DIO mice compared with chow-fed mice, suggesting their potential roles in diabetes and obesity. Together, these findings expanded the methylome database from microbes to mammals, which will benefit our further appreciation for the protein methylation as well as its possible functions on disease.
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Affiliation(s)
- Min Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Yu Xu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao Hu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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37
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Frank J. The translation elongation cycle-capturing multiple states by cryo-electron microscopy. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0180. [PMID: 28138066 DOI: 10.1098/rstb.2016.0180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
During the work cycle of elongation, the ribosome, a molecular machine of vast complexity, exists in a large number of states distinguished by constellation of its subunits, its subunit domains and binding partners. Single-particle cryogenic electron microscopy (cryo-EM), developed over the past 40 years, is uniquely suited to determine the structure of molecular machines in their native states. With the emergence, 10 years ago, of unsupervised clustering techniques in the analysis of single-particle data, it has been possible to determine multiple structures from a sample containing ribosomes equilibrating in different thermally accessible states. In addition, recent advances in detector technology have made it possible to reach near-atomic resolution for some of these states. With these capabilities, single-particle cryo-EM has been at the forefront of exploring ribosome dynamics during its functional cycle, along with single-molecule fluorescence resonance energy transfer and molecular dynamics computations, offering insights into molecular architecture uniquely honed by evolution to capitalize on thermal energy in the ambient environment.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA .,Howard Hughes Medical Institute, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA
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38
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Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Q Rev Biophys 2017; 50:e12. [DOI: 10.1017/s0033583517000117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractRibosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself. Detailed structural analysis has shown that ribosome dynamics, like aminoacyl-tRNA selection and catalysis of peptide bond formation, is made possible by the properties of ribosomal RNA.
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39
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Gulay SP, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu KY, Dinman JD. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Res 2017; 45:4958-4971. [PMID: 28334755 PMCID: PMC5416885 DOI: 10.1093/nar/gkx112] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/06/2017] [Indexed: 11/15/2022] Open
Abstract
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.
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Affiliation(s)
- Suna P Gulay
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sujal Bista
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Amitabh Varshney
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Serdal Kirmizialtin
- Chemistry Program, New York University Abu Dhabi, Abu Dhabi, UAE.,The New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Karissa Y Sanbonmatsu
- The New Mexico Consortium, Los Alamos, NM 87544, USA.,Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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40
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Ghalei H, Trepreau J, Collins JC, Bhaskaran H, Strunk BS, Karbstein K. The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation. Mol Cell 2017; 67:990-1000.e3. [PMID: 28890337 PMCID: PMC6192259 DOI: 10.1016/j.molcel.2017.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 07/08/2017] [Accepted: 08/11/2017] [Indexed: 01/18/2023]
Abstract
Late in their maturation, nascent small (40S) ribosomal subunits bind 60S subunits to produce 80S-like ribosomes. Because of the analogy of this translation-like cycle to actual translation, and because 80S-like ribosomes do not produce any protein, it has been suggested that this represents a quality control mechanism for subunit functionality. Here we use genetic and biochemical experiments to show that the essential ATPase Fap7 promotes formation of the rotated state, a key intermediate in translocation, thereby releasing the essential assembly factor Dim1 from pre-40S subunits. Bypassing this quality control step produces defects in reading frame maintenance. These results show how progress in the maturation cascade is linked to a test for a key functionality of 40S ribosomes: their ability to translocate the mRNA⋅tRNA pair. Furthermore, our data demonstrate for the first time that the translation-like cycle is a quality control mechanism that ensures the fidelity of the cellular ribosome pool.
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Affiliation(s)
- Homa Ghalei
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Juliette Trepreau
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jason C Collins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hari Bhaskaran
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Bethany S Strunk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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41
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Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position. Molecules 2017; 22:molecules22091427. [PMID: 28850078 PMCID: PMC5753802 DOI: 10.3390/molecules22091427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/15/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023] Open
Abstract
Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5′- and 3′-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.
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42
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Kim HK, Tinoco I. EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals. Nucleic Acids Res 2017; 45:2865-2874. [PMID: 27799473 PMCID: PMC5389563 DOI: 10.1093/nar/gkw1020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 12/05/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1PRF) is tightly regulated by messenger RNA (mRNA) sequences and structures in expressing two or more proteins with precise ratios from a single mRNA. Using single-molecule fluorescence resonance energy transfer (smFRET) between (Cy5)EF-G and (Cy3)tRNALys, we studied the translational elongation dynamics of -1PRF in the Escherichia coli dnaX gene, which contains three frameshifting signals: a slippery sequence (A AAA AAG), a Shine-Dalgarno (SD) sequence and a downstream hairpin. The frameshift promoting signals mostly impair the EF-G-catalyzed translocation step of the two tRNALys and the slippery codons from the A- and P- sites. The hairpin acts as a road block slowing the translocation rate. The upstream SD sequence together with the hairpin promotes dissociation of futile EF-G and thus causes multiple EF-G driven translocation attempts. A slippery sequence also helps dissociation of the EF-G by providing alternative base-pairing options. These results indicate that frameshifting takes place during the repetitive ribosomal conformational changes associated with EF-G dissociation upon unsuccessful translocation attempts of the second slippage codon from the A- to the P- sites.
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Affiliation(s)
- Hee-Kyung Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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43
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iTRAQ-based quantitative proteomics analysis of molecular mechanisms associated with Bombyx mori (Lepidoptera) larval midgut response to BmNPV in susceptible and near-isogenic strains. J Proteomics 2017. [PMID: 28624519 DOI: 10.1016/j.jprot.2017.06.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) has been identified as a major pathogen responsible for severe economic loss. Most silkworm strains are susceptible to BmNPV, with only a few highly resistant strains thus far identified. Here we investigated the molecular basis of silkworm resistance to BmNPV using susceptible (the recurrent parent P50) and resistant (near-isogenic line BC9) strains and a combination of iTRAQ-based quantitative proteomics, reverse-transcription quantitative PCR and Western blotting. By comparing the proteomes of infected and non-infected P50 and BC9 silkworms, we identified 793 differentially expressed proteins (DEPs). By gene ontology and KEGG enrichment analyses, we found that these DEPs are preferentially involved in metabolism, catalytic activity, amino sugar and nucleotide sugar metabolism and carbon metabolism. 114 (14.38%) DEPs were associated with the cytoskeleton, immune response, apoptosis, ubiquitination, translation, ion transport, endocytosis and endopeptidase activity. After removing the genetic background and individual immune stress response proteins, we identified 84 DEPs were found that are potentially involved in resistance to BmNPV. Further studies showed that a serine protease was down-regulated in P50 and up-regulated in BC9 after BmNPV infection. Taken together, these results provide insights into the molecular mechanism of silkworm response to BmNPV. BIOLOGICAL SIGNIFICANCE Bombyx mori nucleopolyhedrovirus (BmNPV) is highly pathogenic, causing serious losses in sericulture every year. However, the molecular mechanisms of BmNPV infection and host defence remain unclear. Here we combined quantitative proteomic, bioinformatics, RT-qPCR and Western blotting analyses and found that BmNPV invasion causes complex protein alterations in the larval midgut, and that these changes are related to cytoskeleton, immune response, apoptosis, ubiquitination, translation, ion transport, endocytosis and endopeptidase activity. Five important differentially expression proteins were validation by independent approaches. These finding will help address the molecular mechanisms of silkworm resistance to BmNPV and provide a molecular target for resisting BmNPV.
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Nguyen K, Yang H, Whitford PC. How the Ribosomal A-Site Finger Can Lead to tRNA Species-Dependent Dynamics. J Phys Chem B 2017; 121:2767-2775. [PMID: 28276690 DOI: 10.1021/acs.jpcb.7b01072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proteins are synthesized by the joint action of the ribosome and tRNA molecules, where the rate of synthesis can be affected by numerous factors, such as the concentration of tRNA, the binding affinity of tRNA for the ribosome, or post-transcriptional modifications. Here, we expand this range of contributors by demonstrating how differences in tRNA structure can give rise to tRNA species-specific dynamics in the ribosome. To show this, we perform simulations of A/P hybrid-state formation for two tRNA species (tRNAPhe and tRNALeu), which differ in the size of their variable loops (VLs). These calculations reveal that steric interactions between the VL and the ribosomal A-site finger (ASF, i.e., H38 of 23S rRNA) can directly modulate the free-energy landscape for each tRNA species. We also find that tRNA and ASF motions are highly correlated, where fluctuations of the ASF are predictive of tRNA transition events. Finally, by introducing perturbations to the model, we demonstrate that ASF flexibility is a determinant of the rate of A/P hybrid-state formation.
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Affiliation(s)
- Kien Nguyen
- Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Huan Yang
- Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Paul C Whitford
- Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Cheng L, Wang Y, He Q, Li H, Zhang X, Zhang F. Comparative proteomics illustrates the complexity of drought resistance mechanisms in two wheat (Triticum aestivum L.) cultivars under dehydration and rehydration. BMC PLANT BIOLOGY 2016; 16:188. [PMID: 27576435 PMCID: PMC5006382 DOI: 10.1186/s12870-016-0871-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/10/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Drought stress is one of the most adverse environmental constraints to plant growth and productivity. Comparative proteomics of drought-tolerant and sensitive wheat genotypes is a strategy to understand the complexity of molecular mechanism of wheat in response to drought. This study attempted to extend findings regarding the potential proteomic dynamics in wheat under drought stress and to enrich the research content of drought tolerance mechanism. RESULTS A comparative proteomics approach was applied to analyze proteome change of Xihan No. 2 (a drought-tolerant cultivar) and Longchun 23 (a drought-sensitive cultivar) subjected to a range of dehydration treatments (18 h, 24 h and 48 h) and rehydration treatment (R24 h) using 2-DE, respectively. Quantitative image analysis showed a total of 172 protein spots in Xihan No. 2 and 215 spots from Longchun 23 with their abundance significantly altered (p < 0.05) more than 2.5-fold. Out of these spots, a total of 84 and 64 differentially abundant proteins were identified by MALDI-TOF/TOF MS in Xihan No. 2 and Longchun 23, respectively. Most of these identified proteins were involved in metabolism, photosynthesis, defence and protein translation/processing/degradation in both two cultivars. In addition, the proteins involved in redox homeostasis, energy, transcription, cellular structure, signalling and transport were also identified. Furthermore, the comparative analysis of drought-responsive proteome allowed for the general elucidation of the major mechanisms associated with differential responses to drought of both two cultivars. These cellular processes work more cooperatively to re-establish homeostasis in Xihan No. 2 than Longchun 23. The resistance mechanisms of Xihan No. 2 mainly included changes in the metabolism of carbohydrates and amino acids as well as in the activation of more antioxidation and defense systems and in the levels of proteins involved in ATP synthesis and protein degradation/refolding. CONCLUSIONS This study revealed that the levels of a number of proteins involved in various cellular processes were affected by drought stress in two wheat cultivars with different drought tolerance. The results showed that there exist specific responses to drought in Xihan No. 2 and Longchun 23. The proposed hypothetical model would explain the interaction of these identified proteins that are associated with drought-responses in two cultivars, and help in developing strategies to improve drought tolerance in wheat.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Qiang He
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Huijun Li
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Wuwei Agricultural and Animal Husbandry Bureau, Wuwei, China
| | - Xiaojing Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Gansu Dingxi Academy of Agricultural Science, Dingxi, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
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Nguyen K, Whitford PC. Capturing Transition States for tRNA Hybrid-State Formation in the Ribosome. J Phys Chem B 2016; 120:8768-75. [PMID: 27479146 DOI: 10.1021/acs.jpcb.6b04476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to quantitatively describe the energetics of biomolecular rearrangements, it is necessary to identify reaction coordinates that accurately capture the relevant transition events. Here, we perform simulations of A-site tRNA movement (∼20 Å) during hybrid-state formation in the ribosome and quantify the ability of interatomic distances to capture the transition state ensemble. Numerous coordinates are found to be accurate indicators of the transition state, allowing tRNA rearrangements to be described as diffusion across a one-dimensional free-energy surface. In addition to providing insights into the physical-chemical relationship between biomolecular structure and dynamics, these results can help enable single-molecule techniques to probe the free-energy landscape of the ribosome.
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Affiliation(s)
- Kien Nguyen
- Department of Physics, Northeastern University , Dana Research Center 123, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Paul C Whitford
- Department of Physics, Northeastern University , Dana Research Center 123, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Integrative analyses shed new light on human ribosomal protein gene regulation. Sci Rep 2016; 6:28619. [PMID: 27346035 PMCID: PMC4921865 DOI: 10.1038/srep28619] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/06/2016] [Indexed: 12/05/2022] Open
Abstract
Ribosomal protein genes (RPGs) are important house-keeping genes that are well-known for their coordinated expression. Previous studies on RPGs are largely limited to their promoter regions. Recent high-throughput studies provide an unprecedented opportunity to study how human RPGs are transcriptionally modulated and how such transcriptional regulation may contribute to the coordinate gene expression in various tissues and cell types. By analyzing the DNase I hypersensitive sites under 349 experimental conditions, we predicted 217 RPG regulatory regions in the human genome. More than 86.6% of these computationally predicted regulatory regions were partially corroborated by independent experimental measurements. Motif analyses on these predicted regulatory regions identified 31 DNA motifs, including 57.1% of experimentally validated motifs in literature that regulate RPGs. Interestingly, we observed that the majority of the predicted motifs were shared by the predicted distal and proximal regulatory regions of the same RPGs, a likely general mechanism for enhancer-promoter interactions. We also found that RPGs may be differently regulated in different cells, indicating that condition-specific RPG regulatory regions still need to be discovered and investigated. Our study advances the understanding of how RPGs are coordinately modulated, which sheds light to the general principles of gene transcriptional regulation in mammals.
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Ero R, Kumar V, Chen Y, Gao YG. Similarity and diversity of translational GTPase factors EF-G, EF4, and BipA: From structure to function. RNA Biol 2016; 13:1258-1273. [PMID: 27325008 PMCID: PMC5207388 DOI: 10.1080/15476286.2016.1201627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
EF-G, EF4, and BipA are members of the translation factor family of GTPases with a common ribosome binding mode and GTPase activation mechanism. However, topological variations of shared as well as unique domains ensure different roles played by these proteins during translation. Recent X-ray crystallography and cryo-electron microscopy studies have revealed the structural basis for the involvement of EF-G domain IV in securing the movement of tRNAs and mRNA during translocation as well as revealing how the unique C-terminal domains of EF4 and BipA interact with the ribosome and tRNAs contributing to the regulation of translation under certain conditions. EF-G, EF-4, and BipA are intriguing examples of structural variations on a common theme that results in diverse behavior and function. Structural studies of translational GTPase factors have been greatly facilitated by the use of antibiotics, which have revealed their mechanism of action.
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Affiliation(s)
- Rya Ero
- a School of Biological Sciences , Nanyang Technological University , Singapore
| | - Veerendra Kumar
- a School of Biological Sciences , Nanyang Technological University , Singapore.,b Institute of Molecular and Cell Biology, A*STAR , Singapore
| | - Yun Chen
- a School of Biological Sciences , Nanyang Technological University , Singapore
| | - Yong-Gui Gao
- a School of Biological Sciences , Nanyang Technological University , Singapore.,b Institute of Molecular and Cell Biology, A*STAR , Singapore
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Simms CL, Thomas EN, Zaher HS. Ribosome-based quality control of mRNA and nascent peptides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27193249 DOI: 10.1002/wrna.1366] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 11/06/2022]
Abstract
Quality control processes are widespread and play essential roles in detecting defective molecules and removing them in order to maintain organismal fitness. Aberrant messenger RNA (mRNA) molecules, unless properly managed, pose a significant hurdle to cellular proteostasis. Often mRNAs harbor premature stop codons, possess structures that present a block to the translational machinery, or lack stop codons entirely. In eukaryotes, the three cytoplasmic mRNA-surveillance processes, nonsense-mediated decay (NMD), no-go decay (NGD), and nonstop decay (NSD), evolved to cope with these aberrant mRNAs, respectively. Nonstop mRNAs and mRNAs that inhibit translation elongation are especially problematic as they sequester valuable ribosomes from the translating ribosome pool. As a result, in addition to RNA degradation, NSD and NGD are intimately coupled to ribosome rescue in all domains of life. Furthermore, protein products produced from all three classes of defective mRNAs are more likely to malfunction. It is not surprising then that these truncated nascent protein products are subject to degradation. Over the past few years, many studies have begun to document a central role for the ribosome in initiating the RNA and protein quality control processes. The ribosome appears to be responsible for recognizing the target mRNAs as well as for recruiting the factors required to carry out the processes of ribosome rescue and nascent protein decay. WIREs RNA 2017, 8:e1366. doi: 10.1002/wrna.1366 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Erica N Thomas
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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