1
|
Mustafa A, Shabbir M, Badshah Y, Khan K, Abid F, Trembley JH, Afsar T, Almajwal A, Razak S. Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites. BMC Cancer 2024; 24:1147. [PMID: 39272077 PMCID: PMC11401371 DOI: 10.1186/s12885-024-12900-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Variations in untranslated regions (UTR) alter regulatory pathways impacting phenotype, disease onset, and course of disease. Protein kinase C Zeta (PRKCZ), a serine-threonine kinase, is implicated in cardiovascular, neurological and oncological disorders. Due to limited research on PRKCZ, this study aimed to investigate the impact of UTR genetic variants' on binding sites for transcription factors and miRNA. RNA secondary structure, eQTLs, and variation tolerance analysis were also part of the study. METHODS The data related to PRKCZ gene variants was downloaded from the Ensembl genome browser, COSMIC and gnomAD. The RegulomeDB database was used to assess the functional impact of 5' UTR and 3'UTR variants. The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. To predict the effect of variants on microRNA binding sites, PolymiRTS was utilized for 3' UTR variants, and the SNPinfo tool was used for 5' UTR variants. RESULTS The results obtained indicated that a total of 24 variants present in the 3' UTR and 25 variants present in the 5' UTR were most detrimental. TFBS analysis revealed that 5' UTR variants added YY1, repressor, and Oct1, whereas 3' UTR variants added AP-2alpha, AhR, Da, GR, and USF binding sites. The study predicted TFs that influenced PRKCZ expression. RNA secondary structure analysis showed that eight 5' UTR and six 3' UTR altered the RNA structure by either removal or addition of the stem-loop. The microRNA binding site analysis highlighted that seven 3' UTR and one 5' UTR variant altered the conserved site and also created new binding sites. eQTLs analysis showed that one variant was associated with PRKCZ expression in the lung and thyroid. The variation tolerance analysis revealed that PRKCZ was an intolerant gene. CONCLUSION This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target.
Collapse
Affiliation(s)
- Aneela Mustafa
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Maria Shabbir
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan.
| | - Yasmin Badshah
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | | | - Fizzah Abid
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Janeen H Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
| |
Collapse
|
2
|
Kerkhofs K, Guydosh NR, Bayfield MA. Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606199. [PMID: 39131278 PMCID: PMC11312563 DOI: 10.1101/2024.08.02.606199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Viral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5'-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5'-cap structures of host mRNAs and thus inhibition of cap-dependent translation initiation would likely also reduce viral translation. We confirmed that RSV limits widespread translation initiation inhibition and unexpectedly found that the fraction of ribosomes within polysomes increases during infection, indicating higher ribosome loading on mRNAs during infection. We found that AU-rich host transcripts that are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar to RSV transcripts. Viral transcripts are transcribed in cytoplasmic inclusion bodies, where the viral AU-rich binding protein M2-1 has been shown to bind viral transcripts and shuttle them into the cytoplasm. We further demonstrated that M2-1 is found on polysomes, and that M2-1 might deliver host AU-rich transcripts for translation.
Collapse
Affiliation(s)
- Kyra Kerkhofs
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
| | - Nicholas R. Guydosh
- Section on mRNA Regulation and Translation, Laboratory of Biochemistry & Genetics. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A. Bayfield
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
| |
Collapse
|
3
|
Idowu M, Taiwo G, Sidney T, Adewoye A, Ogunade IM. Plasma proteomic analysis reveals key pathways associated with divergent residual body weight gain phenotype in beef steers. Front Vet Sci 2024; 11:1415594. [PMID: 39104547 PMCID: PMC11298483 DOI: 10.3389/fvets.2024.1415594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/17/2024] [Indexed: 08/07/2024] Open
Abstract
We utilized plasma proteomics profiling to explore metabolic pathways and key proteins associated with divergent residual body weight gain (RADG) phenotype in crossbred (Angus × Hereford) beef steers. A group of 108 crossbred growing beef steers (average BW = 282.87 ± 30 kg; age = 253 ± 28 days) were fed a high-forage total mixed ration for 49 days in five dry lot pens (20-22 beef steers per pen), each equipped with two GrowSafe8000 intake nodes to determine their RADG phenotype. After RADG identification, blood samples were collected from the beef steers with the highest RADG (most efficient; n = 15; 0.76 kg/d) and lowest RADG (least efficient; n = 15; -0.65 kg/d). Plasma proteomics analysis was conducted on all plasma samples using a nano LC-MS/MS platform. Proteins with FC ≥ 1.2 and false-discovery rate-adjusted p-values (FDR) ≤ 0.05 were considered significantly differentially abundant. The analysis identified 435 proteins, with 59 differentially abundant proteins (DAPs) between positive and negative-RADG beef steers. Plasma abundance of 38 proteins, such as macrophage stimulating 1 and peptidase D was upregulated (FC ≥ 1.2, FDR ≤ 0.05) in positive-RADG beef steers, while 21 proteins, including fibronectin and ALB protein were greater (FC < 1.2, FDR ≤ 0.05) in negative-RADG beef steers. The results of the Gene Ontology (GO) analysis of all the DAPs showed enrichment of pathways such as metabolic processes, biological regulation, and catalytic activity in positive-RADG beef steers. Results of the EuKaryotic Orthologous Groups (KOG) analysis revealed increased abundance of DAPs involved in energy production and conversion, amino acid transport and metabolism, and lipid transport and metabolism in positive-RADG beef steers. The results of this study revealed key metabolic pathways and proteins associated with divergent RADG phenotype in beef cattle which give more insight into the biological basis of feed efficiency in crossbred beef cattle.
Collapse
Affiliation(s)
- Modoluwamu Idowu
- Division of Animal Science, West Virginia University, Morgantown, WV, United States
| | - Godstime Taiwo
- Division of Animal Science, West Virginia University, Morgantown, WV, United States
| | - Taylor Sidney
- Division of Animal Science, West Virginia University, Morgantown, WV, United States
| | - Anjola Adewoye
- Department of Chemistry, West Virginia University, Morgantown, WV, United States
| | - Ibukun M. Ogunade
- Division of Animal Science, West Virginia University, Morgantown, WV, United States
| |
Collapse
|
4
|
Ghafoor D, Zeb A, Ali SS, Ali M, Akbar F, Ud Din Z, Ur Rehman S, Suleman M, Khan W. Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses. J Biomol Struct Dyn 2024; 42:3641-3658. [PMID: 37222664 DOI: 10.1080/07391102.2023.2214228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Dawood Ghafoor
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Wuhan, Hubei, China
| | - Adnan Zeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ud Din
- Center for Advanced Studies in Vaccinology and Biotechnology, University of Balochistan Quetta, Quetta, Pakistan
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| |
Collapse
|
5
|
Wang J, Zhu H, Gan J, Liang G, Li L, Zhao Y. Engineered mRNA Delivery Systems for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308029. [PMID: 37805865 DOI: 10.1002/adma.202308029] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/05/2023] [Indexed: 10/09/2023]
Abstract
Messenger RNA (mRNA)-based therapeutic strategies have shown remarkable promise in preventing and treating a staggering range of diseases. Optimizing the structure and delivery system of engineered mRNA has greatly improved its stability, immunogenicity, and protein expression levels, which has led to a wider range of uses for mRNA therapeutics. Herein, a thorough analysis of the optimization strategies used in the structure of mRNA is first provided and delivery systems are described in great detail. Furthermore, the latest advancements in biomedical engineering for mRNA technology, including its applications in combatting infectious diseases, treating cancer, providing protein replacement therapy, conducting gene editing, and more, are summarized. Lastly, a perspective on forthcoming challenges and prospects concerning the advancement of mRNA therapeutics is offered. Despite these challenges, mRNA-based therapeutics remain promising, with the potential to revolutionize disease treatment and contribute to significant advancements in the biomedical field.
Collapse
Affiliation(s)
- Ji Wang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Haofang Zhu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jingjing Gan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Gaofeng Liang
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
| | - Ling Li
- Department of Endocrinology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
| |
Collapse
|
6
|
Dong H. Application of genome editing techniques to regulate gene expression in crops. BMC PLANT BIOLOGY 2024; 24:100. [PMID: 38331711 PMCID: PMC10854132 DOI: 10.1186/s12870-024-04786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Enhanced agricultural production is urgently required to meet the food demands of the increasing global population. Abundant genetic diversity is expected to accelerate crop development. In particular, the development of the CRISPR/Cas genome editing technology has greatly enhanced our ability to improve crop's genetic diversity through direct artificial gene modification. However, recent studies have shown that most crop improvement efforts using CRISPR/Cas techniques have mainly focused on the coding regions, and there is a relatively lack of studies on the regulatory regions of gene expression. RESULTS This review briefly summarizes the development of CRISPR/Cas system in the beginning. Subsequently, the importance of gene regulatory regions in plants is discussed. The review focuses on recent developments and applications of mutations in regulatory regions via CRISPR/Cas techniques in crop breeding. CONCLUSION Finally, an outline of perspectives for future crop breeding using genome editing technologies is provided. This review provides new research insights for crop improvement using genome editing techniques.
Collapse
Affiliation(s)
- Huirong Dong
- College of Agronomy and Biotechnology, Yunnan Agriculture University, Kunming, 650201, Yunnan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572024, China.
| |
Collapse
|
7
|
Kong Y, Fu W, Wang L, Li F, Li W, Yue X. Molecular characterization of SPATA6 and association of its SNPs with testicular size in sheep. Theriogenology 2024; 215:205-213. [PMID: 38096624 DOI: 10.1016/j.theriogenology.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024]
Abstract
The testis is an important organ for maintaining fertility in males, and testis size is positively correlated with ejaculate volume, sperm motility, thus fertility. Spermatogenesis-associated 6 (SPATA6) is an evolutionarily conserved testis-specific gene reported in many species. However, the effect of SPATA6 expression levels on testicular development and the effect of single nucleotide polymorphisms (SNPs) on testis and epididymis phenotype in sheep have not been studied. The purpose of the research was to investigate the expression profile of SPATA6 and its effect on testicular development and to confirm the effect of SNPs on the testis and epididymis phenotype. In this study, we detected a 1245bp coding sequence (CDS) of SPATA6 and encoded 414 amino acids. The expression levels of SPATA6 were significantly higher in the testis than in other tissues and gradually increased with testis development. Moreover, the expression level in the large testis was significantly higher than that in the small testis at six months. A total of 11 SNPs were detected in the coding region of SPATA6 by cDNA-pooling sequencing and improved multiplex ligation detection reaction (iMLDR) methods. Correlation analysis showed that SNP2 (c. 3631C > G) significantly affected left epididymis weight (LEW) and right epididymis weight (REW), and SNP10 (c. 937 A > G) significantly affected REW. And the combined genotype of SNP1 (c. 4245 G > A) and SNP2 significantly affected REW. The current study concluded that SPATA6 plays an important role in testicular development and the SNPs significantly associated with the epididymis phenotype can provide molecular markers for the early selection of high-fertility Hu sheep.
Collapse
Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Weiwei Fu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Li Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wanhong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| |
Collapse
|
8
|
Huang H, Wang S, Guan Y, Ren J, Liu X. Molecular basis and current insights of atypical Rho small GTPase in cancer. Mol Biol Rep 2024; 51:141. [PMID: 38236467 DOI: 10.1007/s11033-023-09140-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Atypical Rho GTPases are a subtype of the Rho GTPase family that are involved in diverse cellular processes. The typical Rho GTPases, led by RhoA, Rac1 and Cdc42, have been well studied, while relative studies on atypical Rho GTPases are relatively still limited and have great exploration potential. With the increase in studies, current evidence suggests that atypical Rho GTPases regulate multiple biological processes and play important roles in the occurrence and development of human cancers. Therefore, this review mainly discusses the molecular basis of atypical Rho GTPases and their roles in cancer. We summarize the sequence characteristics, subcellular localization and biological functions of each atypical Rho GTPase. Moreover, we review the recent advances and potential mechanisms of atypical Rho GTPases in the development of multiple cancers. A comprehensive understanding and extensive exploration of the biological functions of atypical Rho GTPases and their molecular mechanisms in tumors will provide important insights into the pathophysiology of tumors and the development of cancer therapeutic strategies.
Collapse
Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Yifei Guan
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100853, China.
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China.
- Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China.
| |
Collapse
|
9
|
Lu Y, Luo F, Zhou A, Yi C, Chen H, Li J, Guo Y, Xie Y, Zhang W, Lin D, Yang Y, Wu Z, Zhang Y, Xu S, Hu W. Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution. Gigascience 2024; 13:giae064. [PMID: 39311763 PMCID: PMC11417965 DOI: 10.1093/gigascience/giae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/08/2024] [Accepted: 08/07/2024] [Indexed: 09/26/2024] Open
Abstract
Pomacea canaliculata, an invasive species native to South America, is recognized for its broad geographic distribution and adaptability to a variety of ecological conditions. The details concerning the evolution and adaptation of P. canaliculate remain unclear due to a lack of whole-genome resequencing data. We examined 173 P. canaliculata genomes representing 17 geographic populations in East and Southeast Asia. Interestingly, P. canaliculata showed a higher level of genetic diversity than other mollusks, and our analysis suggested that the dispersal of P. canaliculata could have been driven by climate changes and human activities. Notably, we identified a set of genes associated with low temperature adaptation, including Csde1, a cold shock protein coding gene. Further RNA sequencing analysis and reverse transcription quantitative polymerase chain reaction experiments demonstrated the gene's dynamic pattern and biological functions during cold exposure. Moreover, both positive selection and balancing selection are likely to have contributed to the rapid environmental adaptation of P. canaliculata populations. In particular, genes associated with energy metabolism and stress response were undergoing positive selection, while a large number of immune-related genes showed strong signatures of balancing selection. Our study has advanced our understanding of the evolution of P. canaliculata and has provided a valuable resource concerning an invasive species.
Collapse
Affiliation(s)
- Yan Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Center for Evolutionary Biology, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Fang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - An Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Center for Evolutionary Biology, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Cun Yi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Li
- China Basic Medical College, Guangxi Traditional Chinese Medical University, Nanning 530005, China
| | - Yunhai Guo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Yuxiang Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
| | - Wei Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
| | - Datao Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yaming Yang
- Yunnan Institute of Parasitic Diseases, Yunnan 665000, China
| | - Zhongdao Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Center for Evolutionary Biology, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Wei Hu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| |
Collapse
|
10
|
Zhao C, Ding Y, Zhang Y, Chu M, Ning X, Ji J, Wang T, Zhang G, Yin S, Zhang K. Integrated analysis of transcriptome, translatome and proteome reveals insights into yellow catfish (Pelteobagrus fulvidraco) brain in response to hypoxia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 266:106801. [PMID: 38096642 DOI: 10.1016/j.aquatox.2023.106801] [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: 08/26/2023] [Revised: 11/11/2023] [Accepted: 12/10/2023] [Indexed: 01/02/2024]
Abstract
Brain plays a central role in adapting to environmental changes and is highly sensitive to the oxygen level. Although previous studies investigated the molecular response of brain exposure to acute hypoxia in fish, the lack of studies at the translational level hinders further understanding of the regulatory mechanism response to hypoxia from multi-omics levels. Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater aquaculture species; however, hypoxia severely restricts the sustainable development of its breeding industry. In the present study, the transcriptome, translatome, and proteome were integrated to study the global landscapes of yellow catfish brain response to hypoxia. The evidently increased amount of cerebral cortical cells with oedema and pyknotic nuclei has been observed in hypoxia group of yellow catfish. A total of 2750 genes were significantly changed at the translational level. Comparative transcriptional and translational analysis suggested the HIF-1 signaling pathway, autophagy and glycolysis/gluconeogenesis were up-regulated after hypoxia exposure. KEGG enrichment of translational efficiency (TE) differential genes suggested that the lysosome and autophagy were highly enriched. Our result showed that yellow catfish tends to inhibit the TE of genes by increasing the translation of uORFs to adapt to hypoxia. Correlation analysis showed that transcriptome and translatome exhibit higher correlation. In summary, this study demonstrated that hypoxia dysregulated the cerebral function of yellow catfish at the transcriptome, translatome, and proteome, which provides a better understanding of hypoxia adaptation in teleost.
Collapse
Affiliation(s)
- Cheng Zhao
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Yubing Ding
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Yufei Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Mingxu Chu
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze 274015, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang 222005, Jiangsu, China.
| |
Collapse
|
11
|
Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
Collapse
Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| |
Collapse
|
12
|
Ray M, Conard AM, Urban J, Mahableshwarkar P, Aguilera J, Huang A, Vaidyanathan S, Larschan E. Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis. eLife 2023; 12:e87865. [PMID: 37466240 PMCID: PMC10400075 DOI: 10.7554/elife.87865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Sex-specific splicing is an essential process that regulates sex determination and drives sexual dimorphism. Yet, how early in development widespread sex-specific transcript diversity occurs was unknown because it had yet to be studied at the genome-wide level. We use the powerful Drosophila model to show that widespread sex-specific transcript diversity occurs early in development, concurrent with zygotic genome activation. We also present a new pipeline called time2Splice to quantify changes in alternative splicing over time. Furthermore, we determine that one of the consequences of losing an essential maternally deposited pioneer factor called CLAMP (chromatin-linked adapter for MSL proteins) is altered sex-specific splicing of genes involved in diverse biological processes that drive development. Overall, we show that sex-specific differences in transcript diversity exist even at the earliest stages of development..
Collapse
Affiliation(s)
- Mukulika Ray
- MCB department, Brown UniversityProvidenceUnited States
| | | | - Jennifer Urban
- Biology department, Johns Hopkins UniversityBaltimoreUnited States
| | - Pranav Mahableshwarkar
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
| | | | - Annie Huang
- MCB department, Brown UniversityProvidenceUnited States
| | - Smriti Vaidyanathan
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
| | | |
Collapse
|
13
|
Muthmann N, Albers M, Rentmeister A. CAPturAM, a Chemo-Enzymatic Strategy for Selective Enrichment and Detection of Physiological CAPAM-Targets. Angew Chem Int Ed Engl 2023; 62:e202211957. [PMID: 36282111 PMCID: PMC10107118 DOI: 10.1002/anie.202211957] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Modified nucleotides impact all aspects of eukaryotic mRNAs and contribute to regulation of gene expression at the transcriptional and translational level. At the 5' cap, adenosine as first transcribed nucleotide is often N6 -methyl-2'-O-methyl adenosine (m6 Am ). This modification is tissue dependent and reversible, pointing to a regulatory function. CAPAM was recently identified as methyltransferase responsible for m6 Am formation, however, the direct assignment of its target transcripts proves difficult. Antibodies do not discriminate between internal N6 -methyl adenosine (m6 A) and m6 Am . Here we present CAPturAM, an antibody-free chemical biology approach for direct enrichment and probing of physiological CAPAM-targets. We harness CAPAM's cosubstrate promiscuity to install propargyl groups on its targets. Subsequent functionalization with an affinity handle allows for their enrichment. Using wildtype and CAPAM-/- cells, we successfully applied CAPturAM to confirm or disprove CAPAM-targets, facilitating the verification and identification of CAPAM targets.
Collapse
Affiliation(s)
- Nils Muthmann
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| | - Marvin Albers
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| |
Collapse
|
14
|
Investigation of UTR Variants by Computational Approaches Reveal Their Functional Significance in PRKCI Gene Regulation. Genes (Basel) 2023; 14:genes14020247. [PMID: 36833174 PMCID: PMC9956319 DOI: 10.3390/genes14020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/02/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are associated with many diseases including neurological disorders, heart diseases, diabetes, and different types of cancers. In the context of cancer, the variations within non-coding regions, including UTRs, have gained utmost importance. In gene expression, translational regulation is as important as transcriptional regulation for the normal functioning of cells; modification in normal functions can be associated with the pathophysiology of many diseases. UTR-localized SNPs in the PRKCI gene were evaluated using the PolymiRTS, miRNASNP, and MicroSNIper for association with miRNAs. Furthermore, the SNPs were subjected to analysis using GTEx, RNAfold, and PROMO. The genetic intolerance to functional variation was checked through GeneCards. Out of 713 SNPs, a total of thirty-one UTR SNPs (three in 3' UTR region and twenty-nine in 5' UTR region) were marked as ≤2b by RegulomeDB. The associations of 23 SNPs with miRNAs were found. Two SNPs, rs140672226 and rs2650220, were significantly linked with expression in the stomach and esophagus mucosa. The 3' UTR SNPs rs1447651774 and rs115170199 and the 5' UTR region variants rs778557075, rs968409340, and 750297755 were predicted to destabilize the mRNA structure with substantial change in free energy (∆G). Seventeen variants were predicted to have linkage disequilibrium with various diseases. The SNP rs542458816 in 5' UTR was predicted to put maximum influence on transcription factor binding sites. Gene damage index(GDI) and loss of function (o:e) ratio values for PRKCI suggested that the gene is not tolerant to loss of function variants. Our results highlight the effects of 3' and 5' UTR SNP on miRNA, transcription and translation of PRKCI. These analyses suggest that these SNPs can have substantial functional importance in the PRKCI gene. Future experimental validation could provide further basis for the diagnosis and therapeutics of various diseases.
Collapse
|
15
|
Bahari Khasraghi L, Nouri M, Vazirzadeh M, Hashemipour N, Talebi M, Aghaei Zarch F, Majidpoor J, Kalhor K, Farnia P, Najafi S, Aghaei Zarch SM. MicroRNA-206 in human cancer: Mechanistic and clinical perspectives. Cell Signal 2023; 101:110525. [PMID: 36400383 DOI: 10.1016/j.cellsig.2022.110525] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs), small non-coding RNAs approximately 20-25 nt in length, play important roles via directly binding to the corresponding 3' UTR of target mRNAs. Recent research has shown that miRNAs cover a wide range of diseases, including several types of cancer. It is interesting to note that miR-206 operates as a tumor suppressor and is downregulated in abundant cancer types, such as breast cancer, lung cancer, colorectal cancer, and so forth. Interestingly, a growing number of studies have also reported that miR-206 could function as an oncogene and promote tumor cell proliferation. Thereby, miR-206 may act as either oncogenes or tumor suppressors under certain conditions. In addition, it was widely acknowledged that restoring tumor-suppressor miR-206 has emerged as an unconventional cancer therapy strategy. Therefore, miR-206 might be a newfangled procedure for achieving a more significant treatment outcome for cancer patients. This review summarizes the role of miR-206 in several cancer types and the contributions made between miR-206 and the diagnosis, treatment, and drug resistance of solid tumors.
Collapse
Affiliation(s)
- Leila Bahari Khasraghi
- 15 khordad Educational Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Morteza Nouri
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoud Vazirzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Mehrdad Talebi
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran.
| | - Kambiz Kalhor
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, USA
| | - Poopak Farnia
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Mohsen Aghaei Zarch
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
16
|
Lin J, Chen Y, Zhang Y, Lin H, Ouyang Z. Deciphering the role of RNA structure in translation efficiency. BMC Bioinformatics 2022; 23:559. [PMID: 36564729 PMCID: PMC9783404 DOI: 10.1186/s12859-022-05037-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency. RESULTS Here, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3' untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5' UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3' UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5' UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish. CONCLUSIONS Our results suggest the openness of the 3' UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3' UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation.
Collapse
Affiliation(s)
- Jianan Lin
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Yang Chen
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Center for Quantitative Medicine, University of Connecticut, Farmington, CT, 06030, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University, New Haven, CT, 06520, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA.
| |
Collapse
|
17
|
Zhang Y, Yang M, Yang S, Hong F. Role of noncoding RNAs and untranslated regions in cancer: A review. Medicine (Baltimore) 2022; 101:e30045. [PMID: 35984196 PMCID: PMC9388041 DOI: 10.1097/md.0000000000030045] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023] Open
Abstract
Cancer is one of the most prevalent diseases worldwide, and poses a threat to human health. Noncoding RNAs (ncRNAs) constitute most transcripts, but they cannot be translated into proteins. Studies have shown that ncRNAs can act as tumor suppressors or oncogenes. This review describes the role of several ncRNAs in various cancers, including microRNAs (miRNAs) such as the miR-34 family, let-7, miR-17-92 cluster, miR-210, and long noncoding RNAs (lncRNAs) such as HOX transcript antisense intergenic RNA (HOTAIR), Metastasis associated lung adenocarcinoma transcript 1 (MALAT1), H19, NF-κB-interacting lncRNA (NKILA), as well as circular RNAs (circRNAs) and untranslated regions (UTRs), highlighting their effects on cancer growth, invasion, metastasis, angiogenesis, and apoptosis. They function as tumor suppressors or oncogenes that interfere with different axes and pathways, including p53 and IL-6, which are involved in the progression of cancer. The characteristic expression of some ncRNAs in cancer also allows them to be used as biomarkers for early diagnosis and therapeutic candidates. There is a complex network of interactions between ncRNAs, with some lncRNAs and circRNAs acting as competitive endogenous RNAs (ceRNAs) to decoy miRNAs and repress their expression. The ceRNA network is a part of the ncRNA network and numerous ncRNAs work as nodes or hubs in the network, and disruption of their interactions can cause cancer development. Therefore, the balance and stabilization of this network are important for cancer diagnosis and treatment.
Collapse
Affiliation(s)
- Yiping Zhang
- Experimental Centre of Pathogen Biology, Nanchang University, Nanchang, China
- Queen Mary College, School of Medicine, Nanchang University, Nanchang, China
| | - Meiwen Yang
- Department of Surgery, Fuzhou Medical College, Nanchang University, Fuzhou, China
| | - Shulong Yang
- Department of Physiology, Key Research Laboratory of Chronic Diseases, Fuzhou Medical College, Nanchang University, Fuzhou, China
- Department of Physiology, College of Medicine, Nanchang University, Nanchang, China
| | - Fenfang Hong
- Experimental Centre of Pathogen Biology, Nanchang University, Nanchang, China
| |
Collapse
|
18
|
Xu M, Risse J, Kormelink R. Cap-snatching as a possible contributor to photosynthesis shut-off. J Gen Virol 2022; 103. [PMID: 35947091 DOI: 10.1099/jgv.0.001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cap-snatching is a mechanism applied by segmented, negative strand (-) RNA viruses (NSVs) to initiate genome transcription. So far, the cap donor source of cytoplasmic-replicating NSVs has remained elusive. Recently, studies pointed to processing body (P body, PB) as the potential source for providing capped RNAs but conclusive evidence is still lacking. To attempt identifying these sources, here the 5' non-viral leader sequences of Tomato spotted wilt virus (TSWV) N mRNAs were analysed by high-throughput sequencing (HTS) from plants subjected to normal and heat-stress conditions, and subsequently mapped on host donor transcripts. The majority of non-viral heterogenous, host-derived leader sequences ranged in size between ~10-20 nt and contained A or AG residues at the cleavage site and the presence of certain sequence motifs. Mapping the capped-leader sequences to the 5' UTR region of genes encoded by the Nicotiana tabacum genome, identified 348 donor genes and which were specifically enriched in cellular photosynthesis pathway. Nineteen of those were clearly expressed differentially at normal condition versus heat-stress conditions. Although the results did not point towards snatching of capped-RNA leader sequences from certain cytoplasmic RNA granules in particular, they indicated photosynthesis downregulation (and development of disease symptoms) partially result from cap-snatching.
Collapse
Affiliation(s)
- Min Xu
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Judith Risse
- Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| |
Collapse
|
19
|
Review: RNA-based diagnostic markers discovery and therapeutic targets development in cancer. Pharmacol Ther 2022; 234:108123. [PMID: 35121000 DOI: 10.1016/j.pharmthera.2022.108123] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The present review aimed to outline different types of RNAs in cancer diagnostics and treatment, and to provide novel insights into their clinical applications. RNAs, including mRNA, long non-coding (lnc)RNA, circular (circ)RNA and micro (mi)RNA, are now increasingly utilized in the diagnosis and treatment of various cancers. Each aforementioned type of RNA possess their own unique characteristics and could be aberrantly expressed as diagnostic markers or therapeutic targets in different cancers. In addition to mRNAs, which have become a promising alternative in cancer diagnostics and therapy, the uses of lncRNA, circRNA and miRNA in predictive tumor diagnostics and therapy has rapidly increased in recent years. In the present review, the mechanisms of mRNA, lncRNA, circRNA and miRNA in regulating and participating in the development of different cancers were determined, and their potential capacity in cancer diagnostics and therapy were investigated. In addition, the present review analyzed the assoaciations between different RNAs and their subsequent potential in cancer prediction and treatment.
Collapse
|
20
|
Rajendran AK, Amirthalingam S, Hwang NS. A brief review of mRNA therapeutics and delivery for bone tissue engineering. RSC Adv 2022; 12:8889-8900. [PMID: 35424872 PMCID: PMC8985089 DOI: 10.1039/d2ra00713d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/15/2022] [Indexed: 11/21/2022] Open
Abstract
The therapeutics for bone tissue regeneration requires constant advancements owing to the steady increase in the number of patients suffering from bone-related disorders, and also to find efficient and cost-effective treatment modalities. One of the major advancements in the field of therapeutics is the development of mRNAs. mRNAs, which have been extensively tested for the vaccines, could be very well utilized as a potential inducer for bone regeneration. The ability of mRNAs to enter the cells and instruct the cellular machinery to produce the required native proteins such as BMP or VEGF is a great way to avoid the issues faced with growth factor deliveries such as the production cost, loss of biological function etc. However, there have been a few hurdles for using mRNAs as an effective therapeutic agent, such as proper dosing, tolerating the degradation by RNases, improving the half-life, controlling the spatio-temporal release and reducing the off-target effects. This brief review discusses the various developments in the field of mRNA therapeutics especially for bone tissue engineering, how nano-formulations are being developed to effectively deliver the mRNAs into the cells by evading the immune responses, how researchers have developed certain strategies to increase the half-life, to successfully deliver the mRNAs to specific bone defect area and bring about effective bone regeneration.
Collapse
Affiliation(s)
- Arun Kumar Rajendran
- School of Chemical and Biological Engineering, The Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Sivashanmugam Amirthalingam
- School of Chemical and Biological Engineering, The Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Nathaniel S Hwang
- School of Chemical and Biological Engineering, The Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University Seoul 08826 Republic of Korea
- Bio-MAX/N-Bio Institute, Institute of Bio-Engineering, Seoul National University Seoul 08826 Republic of Korea
- Institute for Engineering Research, Seoul National University Seoul 08826 Republic of Korea
| |
Collapse
|
21
|
Dong Z, Liao Z, He Y, Wu C, Meng Z, Qin B, Xu G, Li Z, Sun T, Wen Y, Li G. Advances in the Biological Functions and Mechanisms of miRNAs in the Development of Osteosarcoma. Technol Cancer Res Treat 2022; 21:15330338221117386. [PMID: 35950243 PMCID: PMC9379803 DOI: 10.1177/15330338221117386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Osteosarcoma is one of the most common primary malignant bone tumors, mainly
occurring in children and adolescents, and is characterized by high morbidity
and poor prognosis. MicroRNAs, a class of noncoding RNAs consisting of 19 to 25
nucleotides, are involved in cell proliferation, invasion, metastasis, and
apoptosis to regulate the development and progression of osteosarcoma. Studies
have found that microRNAs are closely related to the diagnosis, treatment, and
prognosis of osteosarcoma patients and have an important role in improving drug
resistance in osteosarcoma. This paper reviews the role of microRNAs in the
pathogenesis of osteosarcoma and their clinical value, aiming to provide a new
research direction for diagnosing and treating osteosarcoma and achieving a
better prognosis.
Collapse
Affiliation(s)
- Zihe Dong
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Zhipeng Liao
- The Second School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Yonglin He
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Chengye Wu
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Zixiang Meng
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Baolong Qin
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Ge Xu
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Zeyang Li
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Tianxin Sun
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Yuyan Wen
- The First School of Clinical Medicine, 12426Lanzhou University, Lanzhou, Gansu, China
| | - Guangjie Li
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| |
Collapse
|
22
|
Naik R, Peden K. Regulatory Considerations on the Development of mRNA Vaccines. Curr Top Microbiol Immunol 2022; 440:187-205. [PMID: 32638114 DOI: 10.1007/82_2020_220] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Developing traditional viral vaccines for infectious diseases usually takes years, as these are usually produced either by chemical inactivation of the virus or attenuation of the pathogen, processes that can take considerable time to validate and also require the live pathogen. With the advent of nucleic-acid vaccines (DNA and mRNA), the time to vaccine design and production is considerably shortened, since once the platform has been established, all that is required is the sequence of the antigen gene, its synthesis and insertion into an appropriate expression vector; importantly, no infectious virus is required. mRNA vaccines have some advantages over DNA vaccines, such as expression in non-dividing cells and the absence of the perceived risk of integration into host genome. Also, generally lower doses are required to induce the immune response. Based on experience in recent clinical trials, mRNA-based vaccines are a promising novel platform that might be useful for the development of vaccines against emerging pandemic infectious diseases. This chapter discusses some of the specific issues that mRNA vaccines raise with respect to production, quality, safety and efficacy, and how they have been addressed so as to allow their evaluation in clinical trials.
Collapse
Affiliation(s)
- Ramachandra Naik
- Division of Vaccines and Related Products Applications, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 71, Room 3045, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Keith Peden
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 52/72, Room 1220, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
| |
Collapse
|
23
|
Masson T, Landras Guetta C, Laigre E, Cucchiarini A, Duchambon P, Teulade-Fichou MP, Verga D. BrdU immuno-tagged G-quadruplex ligands: a new ligand-guided immunofluorescence approach for tracking G-quadruplexes in cells. Nucleic Acids Res 2021; 49:12644-12660. [PMID: 34875077 PMCID: PMC8682774 DOI: 10.1093/nar/gkab1166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes (G4s) are secondary structures forming in G-rich nucleic acids. G4s are assumed to play critical roles in biology, nonetheless their detection in cells is still challenging. For tracking G4s, synthetic molecules (G4 ligands) can be used as reporters and have found wide application for this purpose through chemical functionalization with a fluorescent tag. However, this approach is limited by a low-labeling degree impeding precise visualization in specific subcellular regions. Herein, we present a new visualization strategy based on the immuno-recognition of 5-bromo-2′-deoxyuridine (5-BrdU) modified G4 ligands, functionalized prior- or post-G4-target binding by CuAAC. Remarkably, recognition of the tag by antibodies leads to the detection of the modified ligands exclusively when bound to a G4 target both in vitro, as shown by ELISA, and in cells, thereby providing a highly efficient G4-ligand Guided Immunofluorescence Staining (G4-GIS) approach. The obtained signal amplification revealed well-defined fluorescent foci located in the perinuclear space and RNase treatment revealed the preferential binding to G4-RNA. Furthermore, ligand treatment affected significantly BG4 foci formation in cells. Our work headed to the development of a new imaging approach combining the advantages of immunostaining and G4-recognition by G4 ligands leading to visualization of G4/ligands species in cells with unrivaled precision and sensitivity.
Collapse
Affiliation(s)
- Thibaut Masson
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Corinne Landras Guetta
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Eugénie Laigre
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Anne Cucchiarini
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| |
Collapse
|
24
|
Prieto A, Bernabeu M, Sánchez-Herrero JF, Pérez-Bosque A, Miró L, Bäuerl C, Collado C, Hüttener M, Juárez A. Modulation of AggR levels reveals features of virulence regulation in enteroaggregative E. coli. Commun Biol 2021; 4:1295. [PMID: 34785760 PMCID: PMC8595720 DOI: 10.1038/s42003-021-02820-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) strains are one of the diarrheagenic pathotypes. EAEC strains harbor a virulence plasmid (pAA2) that encodes, among other virulence determinants, the aggR gene. The expression of the AggR protein leads to the expression of several virulence determinants in both plasmids and chromosomes. In this work, we describe a novel mechanism that influences AggR expression. Because of the absence of a Rho-independent terminator in the 3'UTR, aggR transcripts extend far beyond the aggR ORF. These transcripts are prone to PNPase-mediated degradation. Structural alterations in the 3'UTR result in increased aggR transcript stability, leading to increased AggR levels. We therefore investigated the effect of increased AggR levels on EAEC virulence. Upon finding the previously described AggR-dependent virulence factors, we detected novel AggR-regulated genes that may play relevant roles in EAEC virulence. Mutants exhibiting high AggR levels because of structural alterations in the aggR 3'UTR show increased mobility and increased pAA2 conjugation frequency. Furthermore, among the genes exhibiting increased fold change values, we could identify those of metabolic pathways that promote increased degradation of arginine, fatty acids and gamma-aminobutyric acid (GABA), respectively. In this paper, we discuss how the AggR-dependent increase in specific metabolic pathways activity may contribute to EAEC virulence.
Collapse
Affiliation(s)
- Alejandro Prieto
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Manuel Bernabeu
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | | | - Anna Pérez-Bosque
- Department of Biochemistry and Physiology, Universitat de Barcelona, Barcelona, Spain
- Institut de Nutrició i Seguretat Alimentària, Universitat de Barcelona, Barcelona, Spain
| | - Lluïsa Miró
- Department of Biochemistry and Physiology, Universitat de Barcelona, Barcelona, Spain
- Institut de Nutrició i Seguretat Alimentària, Universitat de Barcelona, Barcelona, Spain
| | - Christine Bäuerl
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Carmen Collado
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Mário Hüttener
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain.
| | - Antonio Juárez
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain.
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain.
| |
Collapse
|
25
|
Cao L, Pechan T, Lee S, Cheng WH. Identification of Selenoprotein H Isoforms and Impact of Selenoprotein H Overexpression on Protein But Not mRNA Levels of 2 Other Selenoproteins in 293T Cells. J Nutr 2021; 151:3329-3338. [PMID: 34510207 PMCID: PMC9034323 DOI: 10.1093/jn/nxab290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/16/2021] [Accepted: 08/06/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Selenoprotein H (SELONOH), a member of the thioredoxin-like family proteins, is prioritized to degradation in selenium (Se) insufficiency. Recent studies implicate protective roles of SELENOH in oxidative stress, cellular senescence, and intestinal tumorigenesis. Although the nonselenoprotein H0YE28 is suggested as shortened SELENOH according to genomic and proteomic data repositories, this variant has not been verified biochemically. OBJECTIVES We sought to identify SELENOH isoforms and explore the impact of Se flux on selenoprotein expression in SELENOH-overexpressing cells. METHODS A vector expressing a FLAG (the DYKDDDDK sequence) tag on the N-terminal end of wild-type SELENOH was constructed and transiently transfected into 293T cells incubated with graded concentrations of Na2SeO3 (0-200 nM). Cells were subjected to immunoprecipitation, LC-MS/MS protein analysis, immunoblotting, qRT-PCR, and senescence assays. Data were analyzed by 1-way or 2-way ANOVA. RESULTS Results of anti-FLAG immunoblotting showed that FLAG-SELENOH transfection increased (3.7-fold; P < 0.05) protein levels of the long, but not the short, SELENOH variants in the presence of Na2SeO3 (100 nM). By contrast, SELENOH mRNA levels were increased by 53-fold upon FLAG-SELENOH transfection but were comparable with or without supplemental Se (100 nM). LC-MS/MS analyses of anti-FLAG immunoprecipitates designated both anti-FLAG bands as SELENOH and co-identified three 60S ribosomal and 9 other proteins. Overexpression of FLAG-SELENOH 1) reduced glutathione peroxidase 1 and thioredoxin reductase 1 expression at the protein rather than the mRNA level in the absence but not presence of supplemental Se (100 nM; P < 0.05); 2) increased mRNA levels of 3 heat shock proteins (HSP27, HSP70-1A, and HSP70-1B; P < 0.05); and 3) reduced senescence induced by H2O2 (20 μM, 4 hours; P < 0.05). CONCLUSIONS These cellular studies demonstrate a Se-independent, shortened SELENOH variant and suggest competition of overexpressed FLAG-SELENOH with 2 other selenoproteins for the expression at the protein but not the mRNA level in Se insufficiency.
Collapse
Affiliation(s)
- Lei Cao
- Departments of Food Science, Nutrition, and Health Promotion, Mississippi
State University, Mississippi State, MS, USA,Institute of Marine Life Science, Pukyong National
University, Busan, Republic
of Korea
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State
University, Mississippi State, MS, USA
| | - Sanggil Lee
- Department of Food Science and Nutrition, Pukyong National
University, Busan, Republic
of Korea
| | | |
Collapse
|
26
|
A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. Nat Commun 2021; 12:5120. [PMID: 34433827 PMCID: PMC8387416 DOI: 10.1038/s41467-021-25361-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. Intriguingly, substantial amount of SARS-CoV-2 translation initiates at a novel translation initiation site (TIS) located in the leader sequence, termed TIS-L. Since TIS-L is included in all the genomic and subgenomic RNAs, the SARS-CoV-2 translatome may be regulated by a sophisticated interplay between TIS-L and downstream TISs. TIS-L functions as a strong translation enhancer for ORF S, and as translation suppressors for most of the other ORFs. Our global temporal atlas provides compelling insight into unique regulation of the SARS-CoV-2 translatome and helps comprehensively evaluate its impact on the human genome. Here, Kim et al. apply various sequencing techniques (RPF-seq, QTI-seq, mRNA-seq, sRNA-seq) to unravel the high-resolution, longitudinal translatome and transcriptome of SARS-CoV-2. They identify a translation initiation site in the leader sequence of all genomic and subgenomic RNAs and show its relevance for the SARS-CoV-2 translatome.
Collapse
|
27
|
Duan N, Arroyo M, Deng W, Cardoso MC, Leonhardt H. Visualization and characterization of RNA-protein interactions in living cells. Nucleic Acids Res 2021; 49:e107. [PMID: 34313753 PMCID: PMC8501972 DOI: 10.1093/nar/gkab614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/14/2021] [Accepted: 07/07/2021] [Indexed: 12/26/2022] Open
Abstract
RNA–protein interactions are the structural and functional basis of significant numbers of RNA molecules. RNA–protein interaction assays though, still mainly depend on biochemical tests in vitro. Here, we establish a convenient and reliable RNA fluorescent three-hybrid (rF3H) method to detect/interrogate the interactions between RNAs and proteins in cells. A GFP tagged highly specific RNA trap is constructed to anchor the RNA of interest to an artificial or natural subcellular structure, and RNA–protein interactions can be detected and visualized by the enrichment of RNA binding proteins (RBPs) at these structures. Different RNA trapping systems are developed and detection of RNA–protein complexes at multiple subcellular structures are assayed. With this new toolset, interactions between proteins and mRNA or noncoding RNAs are characterized, including the interaction between a long noncoding RNA and an epigenetic modulator. Our approach provides a flexible and reliable method for the characterization of RNA–protein interactions in living cells.
Collapse
Affiliation(s)
- Ningjun Duan
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Maria Arroyo
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Wen Deng
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany
| |
Collapse
|
28
|
Qu X, Hou X, Chen Z, Chen G, Fan T, Yang X. Association analysis and functional study of COL6A1 single nucleotide polymorphisms in thoracic ossification of the ligamentum flavum in the Chinese Han population. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2021; 30:2782-2790. [PMID: 34287704 DOI: 10.1007/s00586-021-06932-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/09/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE Genetic factors play a crucial role in thoracic ossification of the ligamentum flavum (TOLF). This study aimed to better understand the association between single nucleotide polymorphisms (SNP) in functional regions of the collagen VI, alpha 1 gene (COL6A1) and TOLF, and to confirm COL6A1 as a TOLF susceptibility gene. METHODS Ten tag SNPs in COL6A1 were genotyped using the SNaPshot assay, and allele and genotype frequencies were compared between TOLF patients and control individuals. The function of SNPs associated with disease was studied. For COL6A1 promoter SNPs, the transcriptional activity of each haplotype was determined by luciferase reporter assays. For COL6A1 exonic SNPs, the effect of nucleotide substitutions on COL6A1 expression was determined by western blotting. COL6A1 mRNA expression in ligamentum flavum tissues from TOLF patients with different genotypes was examined using reverse transcription real-time PCR. RESULTS Four SNPs were associated or possibly associated with TOLF, with higher pathogenic allele and genotype frequencies seen in TOLF patients compared with controls. The rs17551710/rs7671-GG/GG genotype appeared to be related to disease severity. Nucleotide substitutions at rs17551710 and rs7671 increased COL6A1 transcriptional activity and nucleotide substitutions at rs1053312 and rs13051496 increased COL6A1 protein expression. COL6A1 mRNA expression was significantly up-regulated in individuals with rs17551710/rs7671-GG/GG and rs1053312/rs13051496-AA+AG/CC genotypes compared with other genotypes. CONCLUSION SNPs in the COL6A1 promoter and exonic regions are associated with TOLF in the Chinese Han population, and lead to up-regulated COL6A1 expression. We confirmed COL6A1 as a TOLF susceptibility gene that may be involved in TOLF pathology.
Collapse
Affiliation(s)
- Xiaochen Qu
- Department of Orthopaedics, First Affiliated Hospital of Dalian Medical University, Dalian, People's Republic of China. .,Key Laboratory of Molecular Mechanism for Repair and Remodeling of Orthopaedic Diseases, Dalian, 116011, Liaoning, People's Republic of China. .,Department of Orthopaedics, Peking University Third Hospital, Beijing, People's Republic of China.
| | - Xiaofei Hou
- Department of Orthopedics, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Zhongqiang Chen
- Department of Orthopaedics, Peking University Third Hospital, Beijing, People's Republic of China.
| | - Guanghui Chen
- Department of Orthopaedics, Peking University Third Hospital, Beijing, People's Republic of China
| | - Tianqi Fan
- Department of Orthopaedics, Peking University Third Hospital, Beijing, People's Republic of China
| | - Xiaoxi Yang
- Department of Orthopaedics, Peking University Third Hospital, Beijing, People's Republic of China
| |
Collapse
|
29
|
Qi T, Xu Y, Zhou T, Gu W. The Evolution of G-quadruplex Structure in mRNA Untranslated Region. Evol Bioinform Online 2021; 17:11769343211035140. [PMID: 34366661 DOI: 10.1177/11769343211035140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
The RNA G-quadruplex (rG4) is a kind of non-canonical high-order secondary structure with important biological functions and is enriched in untranslated regions (UTRs) of protein-coding genes. However, how rG4 structures evolve is largely unknown. Here, we systematically investigated the evolution of RNA sequences around UTR rG4 structures in 5 eukaryotic organisms. We found universal selection on UTR sequences, which facilitated rG4 formation in all the organisms that we analyzed. While G-rich sequences were preferred in the rG4 structural region, C-rich sequences were selectively not preferred. The selective pressure acting on rG4 structures in the UTRs of genes with higher G content was significantly smaller. Furthermore, we found that rG4 structures experienced smaller evolutionary selection near the translation initiation region in the 5' UTR, near the polyadenylation signals in the 3' UTR, and in regions flanking the miRNA targets in the 3' UTR. These results suggest universal selection for rG4 formation in the UTRs of eukaryotic genomes and the selection may be related to the biological functions of rG4s.
Collapse
Affiliation(s)
- Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Yuming Xu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China.,Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing, Jiangsu, China.,School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| |
Collapse
|
30
|
Hu Z, Ge L, Zhang H, Liu X. Expression of FKBP prolyl isomerase 5 gene in tissues of muscovy duck at different growth stages and its association with muscovy duck weight. Anim Biosci 2021; 35:1-12. [PMID: 34237933 PMCID: PMC8738923 DOI: 10.5713/ab.20.0649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/25/2021] [Indexed: 11/27/2022] Open
Abstract
Objective FKBP prolyl isomerase 5 (FKBP5) has been shown to play an important role in metabolically active tissues such as skeletal muscle. However, the expression of FKBP5 in Muscovy duck tissues and its association with body weight are still unclear. Methods In this study, real-time quantitative polymerase chain reaction was used to detect the expression of FKBP5 in different tissues of Muscovy duck at different growth stages. Further, single nucleotide polymorphisms (SNPs) were detected in the exon region of FKBP5 and were combined analyzed with the body weight of 334 Muscovy ducks. Results FKBP5 was highly expressed in various tissues of Muscovy duck at days 17, 19, 21, 24, and 27 of embryonic development. In addition, the expression of FKBP5 in the tissues of female adult Muscovy ducks was higher than that of male Muscovy ducks. Besides, an association analysis indicated that 3 SNPs were related to body weight trait. At the g.4819252 A>G, the body weight of AG genotype was significantly higher than that of the AA and the GG genotype. At the g.4821390 G>A, the genotype GA was extremely significantly related to body weight. At the g.4830622 T>G, the body weight of TT was significantly higher than GG and TG. Conclusion These findings indicate the possible effects of expression levels in various tissues and the SNPs of FKBP5 on Muscovy duck body weight trait. FKBP5 could be used as molecular marker for muscle development trait using early marker-assisted selection of Muscovy ducks.
Collapse
Affiliation(s)
- Zhigang Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Liyan Ge
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huilin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
31
|
Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Res 2021; 31:1136-1149. [PMID: 34187812 PMCID: PMC8256861 DOI: 10.1101/gr.269589.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g., transcription) and have been hypothesized to participate in others (e.g., firing of replication origins). Moreover, G4s differ in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase genome instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures, which has never been investigated. Here we conducted the first genome-wide analysis of G4 distribution, thermostability, and selection. We found an overrepresentation, high thermostability, and purifying selection for G4s within genic components in which they are expected to be functional-promoters, CpG islands, and 5' and 3' UTRs. A similar pattern was observed for G4s within replication origins, enhancers, eQTLs, and TAD boundary regions, strongly suggesting their functionality. In contrast, G4s on the nontranscribed strand of exons were underrepresented, were unstable, and evolved neutrally. In general, G4s on the nontranscribed strand of genic components had lower density and were less stable than those on the transcribed strand, suggesting that the former are avoided at the RNA level. Across the genome, purifying selection was stronger at stable G4s. Our results suggest that purifying selection preserves the sequences of functional G4s, whereas nonfunctional G4s are too costly to be tolerated in the genome. Thus, G4s are emerging as fundamental, functional genomic elements.
Collapse
Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, University Park, Pennsylvania 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Xiaoheng Cheng
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Kristin A Eckert
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Department of Pathology, Penn State University, College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| |
Collapse
|
32
|
Gong GH, Han S, Huang XL, Xie LP, Zhang W, Xu L, Hu YJ. The Expression of Recombinant Human Serum Albumin in the Mammary Gland of Transgenic Mice. PHARMACEUTICAL FRONTS 2021. [DOI: 10.1055/s-0041-1730985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
AbstractHuman serum albumin (HSA) is widely used in the clinic for the treatment of several diseases in large amount each year. With the increasing demands of HSA in clinic and limited blood resource, recombinant HSA (rHSA) is becoming an attractive and alternative source for HSA production. In this study, we aimed to express rHSA in the mammary glands of transgenic mice by using a tissue-specific promoter and other regulatory elements. An rHSA expression vector was constructed bearing the cDNA and first intron of HSA under the control of bovine αs1-casein promoter with a 2 × chicken β-globin insulator in the front. Transgenic mice were generated and reverse transcription polymerase chain reaction showed that rHSA was expressed only in the mammary gland, indicating the tissue specificity of the bovine αs1-casein promoter in directing transgene transcription in transgenic mice. Enzyme-linked immunosorbent assay test showed that rHSA was successfully secreted into the milk of transgenic mice with the highest level at 1.98 ± 0.12 g/L. Our results indicate the ability of the bovine αs1-casein promoter to induce successful expression of rHSA in the mammary gland of transgenic mice.
Collapse
Affiliation(s)
- Gui-Hua Gong
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Shu Han
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Xiao-Ling Huang
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Li-Ping Xie
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Wei Zhang
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Lei Xu
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - You-Jia Hu
- Biopharmaceutical Department, China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| |
Collapse
|
33
|
Semkum P, Kaewborisuth C, Thangthamniyom N, Theerawatanasirikul S, Lekcharoensuk C, Hansoongnern P, Ramasoota P, Lekcharoensuk P. A Novel Plasmid DNA-Based Foot and Mouth Disease Virus Minigenome for Intracytoplasmic mRNA Production. Viruses 2021; 13:1047. [PMID: 34205958 PMCID: PMC8229761 DOI: 10.3390/v13061047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Picornaviruses are non-enveloped, single-stranded RNA viruses that cause highly contagious diseases, such as polio and hand, foot-and-mouth disease (HFMD) in human, and foot-and-mouth disease (FMD) in animals. Reverse genetics and minigenome of picornaviruses mainly depend on in vitro transcription and RNA transfection; however, this approach is inefficient due to the rapid degradation of RNA template. Although DNA-based reverse genetics systems driven by mammalian RNA polymerase I and/or II promoters display the advantage of rescuing the engineered FMDV, the enzymatic functions are restricted in the nuclear compartment. To overcome these limitations, we successfully established a novel DNA-based vector, namely pKLS3, an FMDV minigenome containing the minimum cis-acting elements of FMDV essential for intracytoplasmic transcription and translation of a foreign gene. A combination of pKLS3 minigenome and the helper plasmids yielded the efficient production of uncapped-green florescent protein (GFP) mRNA visualized in the transfected cells. We have demonstrated the application of the pKLS3 for cell-based antiviral drug screening. Not only is the DNA-based FMDV minigenome system useful for the FMDV research and development but it could be implemented for generating other picornavirus minigenomes. Additionally, the prospective applications of this viral minigenome system as a vector for DNA and mRNA vaccines are also discussed.
Collapse
Affiliation(s)
- Ploypailin Semkum
- Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand;
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
- Center for Advanced Studies in Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Challika Kaewborisuth
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Nattarat Thangthamniyom
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
| | - Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Chalermpol Lekcharoensuk
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Payuda Hansoongnern
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
| | - Pongrama Ramasoota
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
- Center for Advanced Studies in Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| |
Collapse
|
34
|
Kuo S, Hu C, Huang Y, Lee C, Luo M, Tu C, Lee S, Lin N, Hsu Y. Argonaute 5 family proteins play crucial roles in the defence against Cymbidium mosaic virus and Odontoglossum ringspot virus in Phalaenopsis aphrodite subsp. formosana. MOLECULAR PLANT PATHOLOGY 2021; 22:627-643. [PMID: 33749125 PMCID: PMC8126185 DOI: 10.1111/mpp.13049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 05/27/2023]
Abstract
The orchid industry faces severe threats from diseases caused by viruses. Argonaute proteins (AGOs) have been shown to be the major components in the antiviral defence systems through RNA silencing in many model plants. However, the roles of AGOs in orchids against viral infections have not been analysed comprehensively. In this study, Phalaenopsis aphrodite subsp. formosana was chosen as the representative to analyse the AGOs (PaAGOs) involved in the defence against two major viruses of orchids, Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV). A total of 11 PaAGOs were identified from the expression profile analyses of these PaAGOs in P. aphrodite subsp. formosana singly or doubly infected with CymMV and/or ORSV. PaAGO5b was found to be the only one highly induced. Results from overexpression of individual PaAGO5 family genes revealed that PaAGO5a and PaAGO5b play central roles in the antiviral defence mechanisms of P. aphrodite subsp. formosana. Furthermore, a virus-induced gene silencing vector based on Foxtail mosaic virus was developed to corroborate the function of PaAGO5s. The results confirmed their importance in the defences against CymMV and ORSV. Our findings may provide useful information for the breeding of traits for resistance or tolerance to CymMV or ORSV infections in Phalaenopsis orchids.
Collapse
Affiliation(s)
- Song‐Yi Kuo
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Chung‐Chi Hu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
| | - Ying‐Wen Huang
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
| | - Chin‐Wei Lee
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
| | - Meng‐Jhe Luo
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Chin‐Wei Tu
- Microbial GenomicNational Chung Hsing University and Academia SinicaTaichungTaiwan
| | - Shu‐Chuan Lee
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Na‐Sheng Lin
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Yau‐Heiu Hsu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
| |
Collapse
|
35
|
Fernandes N, Buchan JR. RNAs as Regulators of Cellular Matchmaking. Front Mol Biosci 2021; 8:634146. [PMID: 33898516 PMCID: PMC8062979 DOI: 10.3389/fmolb.2021.634146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/22/2021] [Indexed: 12/30/2022] Open
Abstract
RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.
Collapse
Affiliation(s)
| | - J. Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
36
|
Degradation-Independent Inhibition of APOBEC3G by the HIV-1 Vif Protein. Viruses 2021; 13:v13040617. [PMID: 33916704 PMCID: PMC8066197 DOI: 10.3390/v13040617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
The ubiquitin–proteasome system plays an important role in the cell under normal physiological conditions but also during viral infections. Indeed, many auxiliary proteins from the (HIV-1) divert this system to its own advantage, notably to induce the degradation of cellular restriction factors. For instance, the HIV-1 viral infectivity factor (Vif) has been shown to specifically counteract several cellular deaminases belonging to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3 or A3) family (A3A to A3H) by recruiting an E3-ubiquitin ligase complex and inducing their polyubiquitination and degradation through the proteasome. Although this pathway has been extensively characterized so far, Vif has also been shown to impede A3s through degradation-independent processes, but research on this matter remains limited. In this review, we describe our current knowledge regarding the degradation-independent inhibition of A3s, and A3G in particular, by the HIV-1 Vif protein, the molecular mechanisms involved, and highlight important properties of this small viral protein.
Collapse
|
37
|
Time-Resolved Transcriptional Profiling of Epithelial Cells Infected by Intracellular Acinetobacter baumannii. Microorganisms 2021; 9:microorganisms9020354. [PMID: 33670223 PMCID: PMC7916935 DOI: 10.3390/microorganisms9020354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 12/22/2022] Open
Abstract
The rise in the number of antibiotic-resistant bacteria has become a serious threat to health, making it important to identify, characterize and optimize new molecules to help us to overcome the infections they cause. It is well known that Acinetobacter baumannii has a significant capacity to evade the actions of antibacterial drugs, leading to its emergence as one of the bacteria responsible for hospital and community-acquired infections. Nonetheless, how this pathogen infects and survives inside the host cell is unclear. In this study, we analyze the time-resolved transcriptional profile changes observed in human epithelial HeLa cells after infection by A. baumannii, demonstrating how it survives in host cells and starts to replicate 4 h post infection. These findings were achieved by sequencing RNA to obtain a set of Differentially Expressed Genes (DEGs) to understand how bacteria alter the host cells’ environment for their own benefit. We also determine common features observed in this set of genes and identify the protein–protein networks that reveal highly-interacted proteins. The combination of these findings paves the way for the discovery of new antimicrobial candidates for the treatment of multidrug-resistant bacteria.
Collapse
|
38
|
Reichert D, Mootz HD, Rentmeister A. Light-control of cap methylation and mRNA translation via genetic code expansion of Ecm1. Chem Sci 2021; 12:4383-4388. [PMID: 34163701 PMCID: PMC8179545 DOI: 10.1039/d1sc00159k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
Gene expression is tightly regulated in all domains of life, with post-transcriptional regulation being more pronounced in higher eukaryotes. Optochemical and optogenetic approaches enable the actuation of many underlying processes by light, which is an excellent tool to exert spatio-temporal control. However, light-mediated control of eukaryotic mRNA processing and the respective enzymes has not been reported. We used genetic code expansion to install a photo-caged tyrosine (Y) in the active site of the cap methyltransferase Ecm1. This enzyme is responsible for guanine N7 methylation of the 5' cap, which is required for translation. Substituting Y284 with the photocaged ortho-nitrobenzyl-tyrosine (ONBY) almost completely abrogated the methylation activity of Ecm1. Irradiation with light removed the ONB group, restoring the native tyrosine and Ecm1 activity, yielding up to 97% conversion of the minimal substrate GpppA within 60 min after activation. Using luciferase- and eGFP-mRNAs as reporters, we could show that light actuates translation by inducing activation of Ecm1 ONBY284 in a eukaryotic in vitro translation system.
Collapse
Affiliation(s)
- Dennis Reichert
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
- Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
| | - Henning D Mootz
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
- Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
| |
Collapse
|
39
|
Markus BM, Waldman BS, Lorenzi HA, Lourido S. High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii. Front Cell Infect Microbiol 2021; 10:617998. [PMID: 33553008 PMCID: PMC7854901 DOI: 10.3389/fcimb.2020.617998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Toxoplasma gondii is a common parasite of humans and animals, causing life-threatening disease in the immunocompromized, fetal abnormalities when contracted during gestation, and recurrent ocular lesions in some patients. Central to the prevalence and pathogenicity of this protozoan is its ability to adapt to a broad range of environments, and to differentiate between acute and chronic stages. These processes are underpinned by a major rewiring of gene expression, yet the mechanisms that regulate transcription in this parasite are only partially characterized. Deciphering these mechanisms requires a precise and comprehensive map of transcription start sites (TSSs); however, Toxoplasma TSSs have remained incompletely defined. To address this challenge, we used 5'-end RNA sequencing to genomically assess transcription initiation in both acute and chronic stages of Toxoplasma. Here, we report an in-depth analysis of transcription initiation at promoters, and provide empirically-defined TSSs for 7603 (91%) protein-coding genes, of which only 1840 concur with existing gene models. Comparing data from acute and chronic stages, we identified instances of stage-specific alternative TSSs that putatively generate mRNA isoforms with distinct 5' termini. Analysis of the nucleotide content and nucleosome occupancy around TSSs allowed us to examine the determinants of TSS choice, and outline features of Toxoplasma promoter architecture. We also found pervasive divergent transcription at Toxoplasma promoters, clustered within the nucleosomes of highly-symmetrical phased arrays, underscoring chromatin contributions to transcription initiation. Corroborating previous observations, we asserted that Toxoplasma 5' leaders are among the longest of any eukaryote studied thus far, displaying a median length of approximately 800 nucleotides. Further highlighting the utility of a precise TSS map, we pinpointed motifs associated with transcription initiation, including the binding sites of the master regulator of chronic-stage differentiation, BFD1, and a novel motif with a similar positional arrangement present at 44% of Toxoplasma promoters. This work provides a critical resource for functional genomics in Toxoplasma, and lays down a foundation to study the interactions between genomic sequences and the regulatory factors that control transcription in this parasite.
Collapse
Affiliation(s)
- Benedikt M. Markus
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Benjamin S. Waldman
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
40
|
Varchenko OI, Kuchuk MV, Parii MF, Symonenko YV. Comparison of gfp Gene Expression Levels after Agrobacterium-Mediated Transient Transformation of Nicotiana rustica L. by Constructs with Different Promoter Sequences. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452720060110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
41
|
Liu XM, Zhou J. Multifaceted regulation of translation by the epitranscriptomic modification N 6-methyladenosine. Crit Rev Biochem Mol Biol 2021; 56:137-148. [PMID: 33412937 DOI: 10.1080/10409238.2020.1869174] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Translation occurring on cytoplasmic mRNA is precisely governed at three consecutive stages, including initiation, elongation and termination. A growing body of evidence has revealed that an emerging epitranscriptomic code N6-methyladenosine (m6A), asymmetrically present in a large subset of coding and non-coding transcripts, is crucially required for mediating the translatomic stability. Through recruiting translation machinery proteins, serving as a physical barrier, or directing RNA structural rearrangement and mRNA looping formation, m6A has been decoded to modulate translational dynamics through potentially influencing the progress of different stages, thereby forming an additional layer of complexity to the regulation of translation. In this review, we summarize the current understanding of how m6A guides mRNA translation under normal and stress conditions, highlighting the divergent molecular mechanisms of multifarious regulation of m6A-mediated translation.
Collapse
Affiliation(s)
- Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
42
|
Ahammad I, Lira SS. Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach. Int J Biol Macromol 2020; 162:820-837. [PMID: 32599237 PMCID: PMC7319648 DOI: 10.1016/j.ijbiomac.2020.06.213] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 is the deadly virus behind COVID-19, the disease that went on to ravage the world and caused the biggest pandemic 21st century has witnessed so far. On the face of ongoing death and destruction, the urgent need for the discovery of a vaccine against the virus is paramount. This study resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. Various immunoinformatics tools were utilized to predict T and B lymphocyte epitopes. The epitopes were channeled through a filtering pipeline comprised of antigenicity, toxicity, allergenicity, and cytokine inducibility evaluation with the goal of selecting epitopes capable of generating both T and B cell-mediated immune responses. Molecular docking simulation between the epitopes and their corresponding MHC molecules was carried out. 13 epitopes, a highly immunogenic adjuvant, elements for proper sub-cellular trafficking, a secretion booster, and appropriate linkers were combined for constructing the vaccine. The vaccine was found to be antigenic, almost neutral at physiological pH, non-toxic, non-allergenic, capable of generating a robust immune response and had a decent worldwide population coverage. Based on these parameters, this design can be considered a promising choice for a vaccine against SARS-CoV-2.
Collapse
MESH Headings
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Drug Design
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Humans
- Immunogenicity, Vaccine
- Molecular Docking Simulation
- Pandemics/prevention & control
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- RNA, Messenger/immunology
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Vaccines, Synthetic/chemistry
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Viral Vaccines/chemistry
- Viral Vaccines/genetics
- Viral Vaccines/immunology
Collapse
Affiliation(s)
- Ishtiaque Ahammad
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh.
| | - Samia Sultana Lira
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| |
Collapse
|
43
|
Arif M, Atta S, Bashir MA, Hussain A, Khan MI, Farooq S, Hannan A, Islam SU, Umar UUD, Khan M, Lin W, Hashem M, Alamri S, Wu Z. Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses. Methods 2020; 183:43-49. [PMID: 31759050 DOI: 10.1016/j.ymeth.2019.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/16/2019] [Indexed: 12/31/2022] Open
Abstract
Geminiviruses constitute a family of plant viruses with characteristic twinned quasi-icosahedral virions and a small circular DNA genome. Geminiviruses, especially begomoviruses, cause substantial economic losses in tropical and subtropical regions globally. Geminiviruses use the host's transcriptional mechanisms to synthesize their mRNAs. They are considered as an attractive model to understand the transcription mechanism of their host plants. Experiments were conducted to identify transcriptional start sites (TSSs) of the three begomoviruses, i.e., Cotton leaf curl Multan virus (CLCuMuV), Corchorus yellow vein virus (CoYVV), and Ramie mosaic virus (RamV). We first rub-inoculated Rice stripe tenuivirus (RSV), a segmented negative-sense RNA virus that uses cap-snatching to produce capped viral mRNAs, into N. benthamiana. After the inoculation, RSV-infected N. benthamiana were super-infected by CoYVV, CLCuMuV, or RamV, respectively. The capped-RNA leaders snatched by RSV were obtained by determining the 5'-ends of RSV mRNA with high throughput sequencing. Afterwards, snatched capped-RNA leaders of RSV were mapped onto the genome of each begomovirus and those matching the begomoviral genome were considered to come from the 5' ends of assumed begomoviral mRNAs. In this way, TSSs of begomoviruses were obtained. After mapping these TSSs onto the genome of the respective begomovirus, it was found very commonly that a begomovirus can use many different TSSs to transcribe the same gene, producing many different mRNA isoforms containing the corresponding open reading frames (ORFs).
Collapse
Affiliation(s)
- Muhammad Arif
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Sagheer Atta
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Muhammad Amjad Bashir
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Ansar Hussain
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Muhammad Ifnan Khan
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Shahid Farooq
- Department of Plant Protection, Faculty of Agriculture, Harran University, Sanliurfa 63200, Turkey
| | - Abdul Hannan
- Department of Botany, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Saif Ul Islam
- Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ummad Ud Din Umar
- Department of Plant Pathology, Bahauddin Zakariya University, Multan, Punjab 60800, Pakistan
| | - Mehran Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Wenzhong Lin
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mohamed Hashem
- King Khalid University, College of Science, Department of Biology, Abha 61413, Saudi Arabia; Assiut University, Faculty of Science, Botany and Microbiology Department, Assiut, Egypt
| | - Saad Alamri
- King Khalid University, College of Science, Department of Biology, Abha 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| |
Collapse
|
44
|
Singh H, Kaur K, Singh M, Kaur G, Singh P. Plant Cyclophilins: Multifaceted Proteins With Versatile Roles. FRONTIERS IN PLANT SCIENCE 2020; 11:585212. [PMID: 33193535 PMCID: PMC7641896 DOI: 10.3389/fpls.2020.585212] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.
Collapse
Affiliation(s)
- Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- William Harvey Heart Centre, Queen Mary University of London, London, United Kingdom
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| |
Collapse
|
45
|
Babaylova ES, Kolobova AV, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data. Biochimie 2020; 177:68-77. [DOI: 10.1016/j.biochi.2020.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023]
|
46
|
Gong G, Zhang W, Xie L, Xu L, Han S, Hu Y. Expression of a recombinant anti-programed cell death 1 antibody in the mammary gland of transgenic mice. Prep Biochem Biotechnol 2020; 51:183-190. [PMID: 32808868 DOI: 10.1080/10826068.2020.1805755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nivolumab, a fully human IgG4 anti-programed cell death 1(PD-1)antibody, is recently one of the most popular and successful therapeutic monoclonal antibodies in clinical use. With the increasing demands for Nivolumab and other therapeutic monoclonal antibodies, the mammary gland bioreactor has been regarded as another choice for the production of recombinant monoclonal antibodies besides mammalian cell culture. Here, we expressed a recombinant human anti-PD-1 antibody in the mammary glands of transgenic mice. Two expression vectors were constructed bearing the heavy and light chains of anti-PD-1 antibody respectively under the control of bovine αs1-casein promoter. Transgenic mice were then generated by co-microinjection of the two expression cassettes. Three F0 founders with both heavy chain and light chain positive were obtained. Transgenes of both chains were detected to be stably transmitted to the offspring. The recombinant antibody was detected in the milk of transgenic mice with the highest expression level up to 80.52 ± 0.82 mg/L and could specifically binds to the human PD-1 antigen. Therefore, our results suggest the feasibility of anti-PD-1 antibody production in the milk of transgenic animals.
Collapse
Affiliation(s)
- Guihua Gong
- China State Institute of Pharmaceutical Industry, Shanghai, P. R. China
| | - Wei Zhang
- China State Institute of Pharmaceutical Industry, Shanghai, P. R. China
| | - Liping Xie
- China State Institute of Pharmaceutical Industry, Shanghai, P. R. China
| | - Lei Xu
- China State Institute of Pharmaceutical Industry, Shanghai, P. R. China
| | - Shu Han
- China State Institute of Pharmaceutical Industry, Shanghai, P. R. China
| | - Youjia Hu
- China State Institute of Pharmaceutical Industry, Shanghai, P. R. China
| |
Collapse
|
47
|
Dong ZY, Wang Q, Lin SP, Chen P, Liu JN, Liu SW, Cai GY, Chen XM, Hong Q. GLA missense and promoter variants co-segregating in a Chinese family with Fabry disease. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:865. [PMID: 32793709 DOI: 10.21037/atm-19-4510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Fabry disease (FD) is an X-linked recessive inheritance lysosomal storage disorder due to mutations in the GLA gene leading to deficiency of lysosomal α-galactosidase A (α-Gal A) and has a wide range of clinical presentations. Over 900 GLA gene mutations are currently known and of those most are thought not to be clinically significant, some with doubtful clinical significance, posing diagnostic and prognostic difficulties for the clinician. Methods Whole-exome sequencing (WES) was performed to detect the mutation in family members with Fabry disease. The function of g.1170C>T mutation was confirmed by dual luciferase system. Results A total of 1,375 variants were found in a Chinese family with FD. A missense variants c.1025C>T (p.Arg342Gln) which have been previously reported in association with FD and g.1170C>T single-nucleotide polymorphism (SNP) in the GLA gene were found in five patients. The g.1170C>T SNP affects transcription of GLA gene, presumably the transcription start site. Female patients only have hypohidrosis and neuropathic pain, while male patients have severe symptoms with simultaneous renal impairment. Conclusions Two simultaneous variants in cis of the GLA gene, c.1025C>T (p.Arg342Gln) and g.1170C>T, were verified in Chinese individuals, and the corresponding clinical symptoms were described. The disease severity in male patients is worse than in female patients. These results may be helpful for genetic counseling, diagnosis and prognosis of patients with FD.
Collapse
Affiliation(s)
- Zhe-Yi Dong
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Qian Wang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Shu-Peng Lin
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Pu Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Jiao-Na Liu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Shu-Wen Liu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Guang-Yan Cai
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Xiang-Mei Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Quan Hong
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| |
Collapse
|
48
|
Sultana N, Hadas Y, Sharkar MTK, Kaur K, Magadum A, Kurian AA, Hossain N, Alburquerque B, Ahmed S, Chepurko E, Zangi L. Optimization of 5' Untranslated Region of Modified mRNA for Use in Cardiac or Hepatic Ischemic Injury. Mol Ther Methods Clin Dev 2020; 17:622-633. [PMID: 32300609 PMCID: PMC7150433 DOI: 10.1016/j.omtm.2020.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
Abstract
Modified mRNA (modRNA) is a gene-delivery platform for transiently introducing a single gene or several genes of interest to different cell types and tissues. modRNA is considered to be a safe vector for gene transfer, as it negligibly activates the innate immune system and does not compromise the genome integrity. The use of modRNA in basic and translational science is rising, due to the clinical potential of modRNA. We are currently using modRNA to induce cardiac regeneration post-ischemic injury. Major obstacles in using modRNA for cardiac ischemic disease include the need for the direct and single administration of modRNA to the heart and the inefficient translation of modRNA due to its short half-life. Modulation of the 5' untranslated region (5' UTR) to enhance translation efficiency in ischemic cardiac disease has great value, as it can reduce the amount of modRNA needed per delivery and will achieve higher and longer protein production post-single delivery. Here, we identified that 5' UTR, from the fatty acid metabolism gene carboxylesterase 1D (Ces1d), enhanced the translation of firefly luciferase (Luc) modRNA by 2-fold in the heart post-myocardial infarction (MI). Moreover, we identified, in the Ces1d, a specific RNA element (element D) that is responsible for the improvement of modRNA translation and leads to a 2.5-fold translation increment over Luc modRNA carrying artificial 5' UTR, post-MI. Importantly, we were able to show that 5' UTR Ces1d also enhances modRNA translation in the liver, but not in the kidney, post-ischemic injury, indicating that Ces1d 5' UTR and element D may play a wider role in translation of protein under an ischemic condition.
Collapse
Affiliation(s)
- Nishat Sultana
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yoav Hadas
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mohammad Tofael Kabir Sharkar
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keerat Kaur
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ajit Magadum
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ann Anu Kurian
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nadia Hossain
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bremy Alburquerque
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sakib Ahmed
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Chepurko
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lior Zangi
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
49
|
Kim B, Kim HM, Kang MK, Sohn DH, Han SJ. 5'-UTR and ORF elements, as well as the 3'-UTR regulate the translation of Cyclin. Biochem Biophys Res Commun 2020; 527:968-973. [PMID: 32439164 DOI: 10.1016/j.bbrc.2020.04.151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/29/2020] [Indexed: 12/25/2022]
Abstract
Mammalian oocyte maturation is wholly dependent on the translation of accumulated maternal transcripts. Therefore, measuring the translation of specific genes, especially Ccnb1 and Ccnb2, which are key regulators of the oocyte cell cycle in mice, is essential to monitor oocyte cell cycle progression. For this purpose, almost all previous research has used a reporter construct containing the 3'-untranslated region (UTR) of Ccnb. It is based on the concept that the 3'-UTR is the main modulator of translation. Here, we investigated the expression pattern of Renilla luciferase (RL) reporters combining the 5'-UTR and/or open reading frame (ORF) as well as the 3'-UTR (RL-3', 5'-RL-3', RL-ORF-3', and 5'-RL-ORF-3') of Ccnb1 and Ccnb2 in somatic cells and mouse oocytes. The addition of the 5'-UTR and/or ORF of Ccnb altered the expression of the RL-3' reporter in HEK293T cells and mouse oocytes. The ORF tended to suppress RL expression, whereas the 5'-UTR enhanced the expression in most cases. The increased rate in expression was the highest when only the 3'-UTR of Ccnb1 (RL-3') was used, whereas the 5'-RL-ORF-3' reporter showed a relatively lower increase during oocyte maturation. For Ccnb2, the RL-ORF-3' reporter showed the largest increase, and other reporters exhibited a similar increase in expression during oocyte maturation. Results show that the expression of these genes is modulated not only by the 3'-UTR but also by the 5'-UTR and ORF. Therefore, special caution should be taken when using only the 3'-UTR to monitor the expression of specific genes.
Collapse
Affiliation(s)
- Boram Kim
- Department of Biological Science, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea
| | - Hye Min Kim
- Department of Biological Science, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea; Institute of Digital Anti-Aging Healthcare, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea
| | - Min Kook Kang
- Department of Biological Science, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea; Department of Research Center, Dong Nam Institute of Radiological and Medical Sciences, 40 Jwadong-gil, Gijang-gun, Busan, 46033, Republic of Korea
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan, Gyeongnam, 50612, Republic of Korea
| | - Seung Jin Han
- Department of Biological Science, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea; Institute of Digital Anti-Aging Healthcare, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea; Department of Biotechnology, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea; Institute of Basic Science, Inje University, 197 Inje-ro, Gimhae, Gyeongnam, 50834, Republic of Korea.
| |
Collapse
|
50
|
Cai S, Lv Y, Huang K, Zhang W, Wang Q, Huang L, Wang J. Modulation on Glutamic Pathway of Frontal-Striatum-Thalamus by rs11146020 and rs3813296 Gene Polymorphism in First-Episode Negative Schizophrenia. Front Neurosci 2020; 14:351. [PMID: 32372910 PMCID: PMC7186427 DOI: 10.3389/fnins.2020.00351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
Objectives The frontal-striatum-thalamus pathway is important in the glutamic neural circuit. The hypofunction of GRIN1 and GRIA2 subunits from glutamic receptors has been hypothesized as the primary process in the etiology of schizophrenia. Identified gene polymorphism involved in the pathogenesis of schizophrenia may uncover relevant mechanism pathways. Methods We selected two loci of rs11146020 and rs3813296 distributed in GRIN1 and GRIA2 genes and tested their main and interaction effects on causality connections and structural characteristics in the frontal-striatum-thalamus pathway in 55 Han Chinese first-episode negative schizophrenia patients. Results We found that: (1) rs11146020 has a significant main effect on the causality connections between the bilateral dorsolateral prefrontal cortex, and rs3813296 mainly influences those of the descending pathway from the prefrontal cortex to the striatum; (2) interaction effect of rs11146020 and rs3813296 on causality connections are located in the ascending pathway from the pallidum to the dorsolateral prefrontal cortex; and (3) the two loci have effects on the volumes of several regions of this pathway. Conclusion Our results suggested there is modulation on glutamic frontal-striatum-thalamus pathway by rs11146020 and rs3813296 gene polymorphism. Patients with different genotypes have different neuroimaging characteristics, which indirectly reminded clinicians those patients should receive different clinical interventions.
Collapse
Affiliation(s)
- Suping Cai
- School of Life Sciences and Technology, Xidian University, Xi'an, China
| | - Yahui Lv
- School of Life Sciences and Technology, Xidian University, Xi'an, China
| | - Kexin Huang
- School of Life Sciences and Technology, Xidian University, Xi'an, China
| | - Wei Zhang
- School of Life Sciences and Technology, Xidian University, Xi'an, China
| | - Qiang Wang
- The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Liyu Huang
- School of Life Sciences and Technology, Xidian University, Xi'an, China
| | - Jijun Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|