1
|
Sofeo N, Toi MG, Ee EQG, Ng JY, Busran CT, Lukito BR, Thong A, Hermansen C, Peterson EC, Glitsos R, Arumugam P. Sustainable production of lipids from cocoa fatty acid distillate fermentation driven by adaptive evolution in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2024; 394:130302. [PMID: 38199440 DOI: 10.1016/j.biortech.2024.130302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Single cell oil production using oleaginous yeasts is a promising alternative to animal and plant-derived lipids. But substrate costs for microbial fermentation are a major bottleneck. Using side streams as alternative to substrates like glucose, for growing yeast, is a potential cost-effective solution. By combining a previously reported process of growing yeasts on a solid cocoa fatty acid distillate side stream with adaptive evolution techniques, the growth of oleaginous yeast Yarrowia lipolytica was improved by 2-fold. The lipid titre was also boosted by more than 3-fold. Using transcriptomics, key genes were identified that are possibly involved in tailoring of lipid composition, side stream utilisation and enhancement of lipid titres. Candidate genes were also identified that might enable efficient growth and utilization of fatty acids and triacylglycerides found in cocoa fatty acid distillate. In summary, this research has improved the understanding of side stream utilisation for lipid production in oleaginous yeast.
Collapse
Affiliation(s)
- Naazneen Sofeo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore.
| | - Min Gin Toi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - En Qi Grace Ee
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Jing Yang Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Coleen Toledo Busran
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Benedict Ryan Lukito
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Aaron Thong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Christian Hermansen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Eric Charles Peterson
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore; Institut National de la Recherche Scientifique - Eau Terre Environnement (INRS-ETE), 490 Rue de la Couronne, Quebec City, QC G1K 9A9, Canada
| | - Renata Glitsos
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Prakash Arumugam
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| |
Collapse
|
2
|
Lv J, Liu Y, Tang J, Xiao H, Hu R, Wang G, Niu D, Shao PL, Yang J, Jin Z, Xu Z, Zhang B. A Novel Cell Membrane-Associated RNA Extraction Method and Its Application in the Discovery of Breast Cancer Markers. Anal Chem 2023; 95:11706-11713. [PMID: 37459193 DOI: 10.1021/acs.analchem.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Cell membrane-associated RNA (mem-RNA) has been demonstrated to be cell-specific and disease-related and are considered as potential biomarkers for disease diagnostics, drug delivery, and cell screening. However, there is still a lack of methods specifically designed to extract mem-RNA from cells, limiting the discovery and applications of mem-RNA. In this study, we propose the first all-in-one solution for high-purity mem-RNA isolation based on two types of magnetic nanoparticles, named MREMB (Membrane-associated RNA Extraction based on Magnetic Beads), which achieved ten times enrichment of cell membrane components and over 90% recovery rate of RNA extraction. To demonstrate MREMB's potential in clinical research, we extracted and sequenced mem-RNA of typical breast cancer MCF-7, MDA-MB-231, and SKBR-3 cell lines and non-neoplastic breast epithelial cell MCF-10A. Compared to total RNA, sequencing results revealed that membrane/secreted protein-encoding mRNAs and long noncoding RNAs (lncRNAs) were enriched in the mem-RNA, some of which were significantly overexpressed in the three cancer cell lines, including extracellular matrix-related genes COL5A1 and lncRNA TALAM1. The results indicated that MREMB could enrich membrane/secreted protein-coding RNA and amplify the expression differences of related RNAs between cancer and non-neoplastic cells, promising for cancer biomarker discovery.
Collapse
Affiliation(s)
- Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Pan-Lin Shao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Jin
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
3
|
Yue Y, Deng J, Wang H, Lv T, Dou W, Jiao Y, Peng X, Zhang Y. Two Secretory T2 RNases Act as Cytotoxic Factors Contributing to the Virulence of an Insect Fungal Pathogen. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7069-7081. [PMID: 37122240 DOI: 10.1021/acs.jafc.3c01617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNase T2 members are secreted by several pathogens or parasites during infection, playing various roles in pathogen-host interaction. However, functions of those members in biocontrol microbes targeting their hosts are still unknown. Here, we report that an insect fungal pathogen, Beauveria bassiana, produces two secretory RNase T2 members that act as cytotoxic factors, which were examined by insect bioassays using the targeted gene(s) disruption and overexpression strains. Overexpression strains displayed dramatically increased virulence, which was concurrent with few fungal cells and hemocytes in hemocoel, suggesting a cytotoxicity of the overexpressed gene products. In vitro assays using yeast-expressed proteins verified the cytotoxicity of the two members against insect cells, to which the cytotoxic effect was dependent on their RNases enzyme activities and glycosylation modification. Moreover, the excessive humoral immune responses triggered by the two ribonucleases were examined. These results suggested prospects of these two T2 ribonucleases for improvement of biocontrol agents.
Collapse
Affiliation(s)
- Yong Yue
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Juan Deng
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Huifang Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Ting Lv
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Wei Dou
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Yufei Jiao
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Xinxin Peng
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| | - Yongjun Zhang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Biotechnology Research Center, Southwest University, Chongqing 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Southwest University, Chongqing 400715, People's Republic of China
| |
Collapse
|
4
|
Choi W, Kim YH, Min J. Inhibition of Enveloped Virus Surrogate Phi6 Infection Using Yeast-Derived Vacuoles. Microbiol Spectr 2023; 11:e0266122. [PMID: 36688634 PMCID: PMC9927162 DOI: 10.1128/spectrum.02661-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The periodic emergence of infectious disease poses a serious threat to human life. Among the causative agents, including pathogenic bacteria and fungi, enveloped viruses have caused global pandemics. In the last 10 years, outbreaks of severe acute respiratory syndrome coronavirus 2 disease, severe acute respiratory syndrome, and Middle East respiratory syndrome have all been caused by enveloped viruses. Among several paths of secondary transmission, inhalation of aerosols containing saliva with sputum droplets from infected patients is the major path. To prevent these infectious diseases, mass use of antiviral agents is essential. The yeast-derived vacuole is a small organelle in which hydrolytic enzymes are concentrated. It is an intracellular organ with an excellent ability to process old organelles and bacteria and viruses that have invaded from the outside and can be present in sufficient quantity to be called a kind of enzyme bomb. We confirmed the inhibition of virus infection and structural collapse by vacuole treatment. Among several enzymes, proteases affected Phi6 infectivity. This study tried to isolate these vacuoles from yeast and use them as an antiviral agent for virus treatment, which is a recent issue. We confirmed that viral infectivity was inactivated, and structure collapsed through vacuole treatment. This paper is meaningful in that extracellularly isolated yeast-derived vacuoles are a first attempt to utilize vacuoles for viral treatment. IMPORTANCE The study assesses the vacuoles isolated from the yeast Saccharomyces cerevisiae as green antiviral agents to decrease the concerns about massive use of chemical antiviral agents and its side effects. To prevent the spreading of infectious diseases, personal or public use of antiviral agents is encouraged. The concern about the active compounds of these chemical antiviral agents has grown. Active compounds of antiviral agents have potential side effects on human health and the environment. Our proposed approach suggests effective and green antivirus material from a nonhazardous yeast strain. Also, large-scale production using a fermentation process can allow cost-effectiveness. The results showed sufficient reduced infectivity by vacuole treatment. The exposed vacuole can play the roles of both enzyme bomb to the virus and renewable nutrient source in the ecosystem.
Collapse
Affiliation(s)
- Wooil Choi
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, Jeonbuk, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, Cheongju, South Korea
| | - Jiho Min
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, Jeonbuk, South Korea
| |
Collapse
|
5
|
Azizkhani N, Mirzaei S, Torkzadeh-Mahani M. Genome-wide identification and characterization of legume T2 Ribonuclease gene family and analysis of GmaRNS9, a soybean T2 Ribonuclease gene, function in nodulation. 3 Biotech 2021; 11:495. [PMID: 34881158 DOI: 10.1007/s13205-021-03025-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/08/2021] [Indexed: 01/30/2023] Open
Abstract
T2 ribonuclease family (RNaseT2) proteins are secretory and nonspecific endoribonucleases that have a large conserved biological role. Family members of RNaseT2 are found in every organism and carry out important biological functions. However, little is known about the functions of these proteins in legumes, including potential roles in symbiotic nodulation. This study aimed to characterize and perform bioinformatic analysis of RNaseT2 genes in four legume species that their genome was sequenced. In total, 60 RNaseT2 genes were identified and characterized. By analyzing their phylogeny, we divided these RNaseT2 into five clades. Expression analysis of RNaseT2 genes indicated that these genes are expressed in various tissues, and the most expression level was related to the pod, flower, and root. Moreover, GmaRNS9 expression analysis in soybean was consistent with in silico studies and demonstrated that this gene usually has high root tip expression. GmaRNS9 expression was reduced by Bradyrhizobium japonicum inoculation and nodule formation. Reduced expression of this gene was possibly controlled by the GmNARK gene either directly or pleiotropically through increased phosphorus requirements during increased nodulation. However, the nutrient stress (phosphate and nitrate starvation) led to an increase in the expression level of GmRNS9. In silico and quantitative gene expression analyses showed that RNaseT2 genes could play important roles in the growth and development of legumes as well as nodulation.
Collapse
Affiliation(s)
- Negin Azizkhani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, 7631885356 Kerman, Iran
| | - Saeid Mirzaei
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, 7631885356 Kerman, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, 7631885356 Kerman, Iran
| |
Collapse
|
6
|
Kumaran G, Michaeli S. Eating the messenger (RNA): autophagy shapes the cellular RNA landscape. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6803-6807. [PMID: 34468738 PMCID: PMC8547149 DOI: 10.1093/jxb/erab385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
This article comments on: Hickl D, Drews F, Girke C, Zimmer D, Mühlhaus T, Hauth J, Nordström K, Trentmann O, Neuhaus EH, Scheuring D, Fehlmann T, Keller A, Simon M, Möhlmann T. 2021. Differential degradation of RNA species by autophagy-related pathways in Arabidopsis. Journal of Experimental Botany 72, 6867–6881.
Collapse
Affiliation(s)
- Girishkumar Kumaran
- Institute of Postharvest and Food Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Simon Michaeli
- Institute of Postharvest and Food Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| |
Collapse
|
7
|
Zhao H, Song Y, Li J, Zhang Y, Huang H, Li Q, Zhang Y, Xue Y. Primary restriction of S-RNase cytotoxicity by a stepwise ubiquitination and degradation pathway in Petunia hybrida. THE NEW PHYTOLOGIST 2021; 231:1249-1264. [PMID: 33932295 PMCID: PMC8361771 DOI: 10.1111/nph.17438] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/20/2021] [Indexed: 05/15/2023]
Abstract
In self-incompatible Petunia species, the pistil S-RNase acts as cytotoxin to inhibit self-pollination but is polyubiquitinated by the pollen-specific nonself S-locus F-box (SLF) proteins and subsequently degraded by the ubiquitin-proteasome system (UPS), allowing cross-pollination. However, it remains unclear how S-RNase is restricted by the UPS. Using biochemical analyses, we first show that Petunia hybrida S3 -RNase is largely ubiquitinated by K48-linked polyubiquitin chains at three regions, R I, R II and R III. R I is ubiquitinated in unpollinated, self-pollinated and cross-pollinated pistils, indicating its occurrence before PhS3 -RNase uptake into pollen tubes, whereas R II and R III are exclusively ubiquitinated in cross-pollinated pistils. Transgenic analyses showed that removal of R II ubiquitination resulted in significantly reduced seed sets from cross-pollination and that of R I and R III to a lesser extent, indicating their increased cytotoxicity. Consistent with this, the mutated R II of PhS3 -RNase resulted in a marked reduction of its degradation, whereas that of R I and R III resulted in less reduction. Taken together, we demonstrate that PhS3 -RNase R II functions as a major ubiquitination region for its destruction and R I and R III as minor ones, revealing that its cytotoxicity is primarily restricted by a stepwise UPS mechanism for cross-pollination in P. hybrida.
Collapse
Affiliation(s)
- Hong Zhao
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yanzhai Song
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Junhui Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Huaqiu Huang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Qun Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Yu’e Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, and The Innovation Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Beijing Institute of GenomicsChinese Academy of Sciences and National Centre for BioinformationBeijing100101China
- Jiangsu Co‐Innovation Centre for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou225009China
| |
Collapse
|
8
|
Abstract
Increased proliferation and protein synthesis are characteristics of transformed and tumor cells. Although the components of the translation machinery are often dysregulated in cancer, the role of tRNAs in cancer cells has not been well studied. Nevertheless, the number of related studies has recently started increasing. With the development of high throughput technologies such as next-generation sequencing, genome-wide differential tRNA expression patterns in breast cancer-derived cell lines and breast tumors have been investigated. The genome-wide transcriptomics analyses have been linked with many studies for functional and phenotypic characterization, whereby tRNAs or tRNA-related fragments have been shown to play important roles in breast cancer regulation and as promising prognostic biomarkers. Here, we review their expression patterns, functions, prognostic value, and potential therapeutic use as well as related technologies.
Collapse
|
9
|
Castro J, Ribó M, Vilanova M, Benito A. Strengths and Challenges of Secretory Ribonucleases as AntiTumor Agents. Pharmaceutics 2021; 13:82. [PMID: 33435285 PMCID: PMC7828032 DOI: 10.3390/pharmaceutics13010082] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/25/2022] Open
Abstract
Approaches to develop effective drugs to kill cancer cells are mainly focused either on the improvement of the currently used chemotherapeutics or on the development of targeted therapies aimed at the selective destruction of cancer cells by steering specific molecules and/or enhancing the immune response. The former strategy is limited by its genotoxicity and severe side effects, while the second one is not always effective due to tumor cell heterogeneity and variability of targets in cancer cells. Between these two strategies, several approaches target different types of RNA in tumor cells. RNA degradation alters gene expression at different levels inducing cell death. However, unlike DNA targeting, it is a pleotropic but a non-genotoxic process. Among the ways to destroy RNA, we find the use of ribonucleases with antitumor properties. In the last few years, there has been a significant progress in the understanding of the mechanism by which these enzymes kill cancer cells and in the development of more effective variants. All the approaches seek to maintain the requirements of the ribonucleases to be specifically cytotoxic for tumor cells. These requirements start with the competence of the enzymes to interact with the cell membrane, a process that is critical for their internalization and selectivity for tumor cells and continue with the downstream effects mainly relying on changes in the RNA molecular profile, which are not only due to the ribonucleolytic activity of these enzymes. Although the great improvements achieved in the antitumor activity by designing new ribonuclease variants, some drawbacks still need to be addressed. In the present review, we will focus on the known mechanisms used by ribonucleases to kill cancer cells and on recent strategies to solve the shortcomings that they show as antitumor agents, mainly their pharmacokinetics.
Collapse
Affiliation(s)
- Jessica Castro
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 40, 17003 Girona, Spain; (J.C.); (M.R.)
- Institut d’Investigació Biomèdica de Girona Josep Trueta, (IdIBGi), Hospital de Santa Caterina, Carrer del Dr. Castany, s/n, 17190 Salt, Spain
| | - Marc Ribó
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 40, 17003 Girona, Spain; (J.C.); (M.R.)
- Institut d’Investigació Biomèdica de Girona Josep Trueta, (IdIBGi), Hospital de Santa Caterina, Carrer del Dr. Castany, s/n, 17190 Salt, Spain
| | - Maria Vilanova
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 40, 17003 Girona, Spain; (J.C.); (M.R.)
- Institut d’Investigació Biomèdica de Girona Josep Trueta, (IdIBGi), Hospital de Santa Caterina, Carrer del Dr. Castany, s/n, 17190 Salt, Spain
| | - Antoni Benito
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, Carrer Maria Aurèlia Capmany, 40, 17003 Girona, Spain; (J.C.); (M.R.)
- Institut d’Investigació Biomèdica de Girona Josep Trueta, (IdIBGi), Hospital de Santa Caterina, Carrer del Dr. Castany, s/n, 17190 Salt, Spain
| |
Collapse
|
10
|
Link AJ, Niu X, Weaver CM, Jennings JL, Duncan DT, McAfee KJ, Sammons M, Gerbasi VR, Farley AR, Fleischer TC, Browne CM, Samir P, Galassie A, Boone B. Targeted Identification of Protein Interactions in Eukaryotic mRNA Translation. Proteomics 2020; 20:e1900177. [PMID: 32027465 DOI: 10.1002/pmic.201900177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 12/13/2019] [Indexed: 11/09/2022]
Abstract
To identify protein-protein interactions and phosphorylated amino acid sites in eukaryotic mRNA translation, replicate TAP-MudPIT and control experiments are performed targeting Saccharomyces cerevisiae genes previously implicated in eukaryotic mRNA translation by their genetic and/or functional roles in translation initiation, elongation, termination, or interactions with ribosomal complexes. Replicate tandem affinity purifications of each targeted yeast TAP-tagged mRNA translation protein coupled with multidimensional liquid chromatography and tandem mass spectrometry analysis are used to identify and quantify copurifying proteins. To improve sensitivity and minimize spurious, nonspecific interactions, a novel cross-validation approach is employed to identify the most statistically significant protein-protein interactions. Using experimental and computational strategies discussed herein, the previously described protein composition of the canonical eukaryotic mRNA translation initiation, elongation, and termination complexes is calculated. In addition, statistically significant unpublished protein interactions and phosphorylation sites for S. cerevisiae's mRNA translation proteins and complexes are identified.
Collapse
Affiliation(s)
- Andrew J Link
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xinnan Niu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Connie M Weaver
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jennifer L Jennings
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Dexter T Duncan
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - K Jill McAfee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Morgan Sammons
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Vince R Gerbasi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Adam R Farley
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Tracey C Fleischer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | | | - Parimal Samir
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Allison Galassie
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Braden Boone
- Department of Bioinformatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| |
Collapse
|
11
|
The Ins and Outs of Autophagic Ribosome Turnover. Cells 2019; 8:cells8121603. [PMID: 31835634 PMCID: PMC6952998 DOI: 10.3390/cells8121603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosomes are essential for protein synthesis in all organisms and their biogenesis and number are tightly controlled to maintain homeostasis in changing environmental conditions. While ribosome assembly and quality control mechanisms have been extensively studied, our understanding of ribosome degradation is limited. In yeast or animal cells, ribosomes are degraded after transfer into the vacuole or lysosome by ribophagy or nonselective autophagy, and ribosomal RNA can also be transferred directly across the lysosomal membrane by RNautophagy. In plants, ribosomal RNA is degraded by the vacuolar T2 ribonuclease RNS2 after transport by autophagy-related mechanisms, although it is unknown if a selective ribophagy pathway exists in plants. In this review, we describe mechanisms of turnover of ribosomal components in animals and yeast, and, then, discuss potential pathways for degradation of ribosomal RNA and protein within the vacuole in plants.
Collapse
|
12
|
Ueda S, Ozaki R, Kaneko A, Akizuki R, Katsuta H, Miura A, Matsuura A, Ushimaru T. TORC1, Tel1/Mec1, and Mpk1 regulate autophagy induction after DNA damage in budding yeast. Cell Signal 2019; 62:109344. [DOI: 10.1016/j.cellsig.2019.109344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 02/08/2023]
|
13
|
Neupane A, Feng C, Mochama PK, Saleem H, Lee Marzano SY. Roles of Argonautes and Dicers on Sclerotinia sclerotiorum Antiviral RNA Silencing. FRONTIERS IN PLANT SCIENCE 2019; 10:976. [PMID: 31440265 PMCID: PMC6694225 DOI: 10.3389/fpls.2019.00976] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/11/2019] [Indexed: 05/30/2023]
Abstract
RNA silencing or RNA interference (RNAi) is an essential mechanism in animals, fungi, and plants that functions in gene regulation and defense against foreign nucleic acids. In fungi, RNA silencing has been shown to function primarily in defense against invasive nucleic acids. We previously determined that mycoviruses are triggers and targets of RNA silencing in Sclerotinia sclerotiorum. However, recent progresses in RNAi or dsRNA-based pest control requires more detailed characterization of the RNA silencing pathways in S. sclerotiorum to investigate the utility of dsRNA-based strategy for white mold control. This study elucidates the roles of argonaute enzymes, agl-2 and agl-4, in small RNA metabolism in S. sclerotiorum. Gene disruption mutants of agl-2 and agl-4 were compared for changes in phenotype, virulence, viral susceptibility, and small RNA profiles. The Δagl-2 mutant but not the Δagl-4 mutant had significantly slower growth and virulence prior to virus infection. Similarly, the Δagl-2 mutant but not the Δagl-4 mutant, showed greater debilitation under virus infection compared to uninfected strains. The responses were confirmed in complementation studies and revealed the antiviral role of agl-2. Gene disruption mutants of agl-2, agl-4, Dicer-like (dcl)-1, and dcl-2 did not change the stability of the most abundant endogenous small RNAs, which suggests the existence of alternative enzymes/pathways for small RNA biogenesis in S. sclerotiorum. Furthermore, in vitro synthesized dsRNA targeting agl-2 showed a significantly reduced average lesion diameter (P < 0.05) on canola leaves with agl-2 down-regulated compared to controls. This is the first report describing the effectiveness of RNA pesticides targeting S. sclerotiorum RNA silencing pathway for the control of the economically important pathogen.
Collapse
Affiliation(s)
- Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Chenchen Feng
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Pauline K. Mochama
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Huma Saleem
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Shin-Yi Lee Marzano
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| |
Collapse
|
14
|
Parzych KR, Klionsky DJ. Vacuolar hydrolysis and efflux: current knowledge and unanswered questions. Autophagy 2018; 15:212-227. [PMID: 30422029 DOI: 10.1080/15548627.2018.1545821] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Hydrolysis within the vacuole in yeast and the lysosome in mammals is required for the degradation and recycling of a multitude of substrates, many of which are delivered to the vacuole/lysosome by autophagy. In humans, defects in lysosomal hydrolysis and efflux can have devastating consequences, and contribute to a class of diseases referred to as lysosomal storage disorders. Despite the importance of these processes, many of the proteins and regulatory mechanisms involved in hydrolysis and efflux are poorly understood. In this review, we describe our current knowledge of the vacuolar/lysosomal degradation and efflux of a vast array of substrates, focusing primarily on what is known in the yeast Saccharomyces cerevisiae. We also highlight many unanswered questions, the answers to which may lead to new advances in the treatment of lysosomal storage disorders. Abbreviations: Ams1: α-mannosidase; Ape1: aminopeptidase I; Ape3: aminopeptidase Y; Ape4: aspartyl aminopeptidase; Atg: autophagy related; Cps1: carboxypeptidase S; CTNS: cystinosin, lysosomal cystine transporter; CTSA: cathepsin A; CTSD: cathepsin D; Cvt: cytoplasm-to-vacuole targeting; Dap2: dipeptidyl aminopeptidase B; GS-bimane: glutathione-S-bimane; GSH: glutathione; LDs: lipid droplets; MVB: multivesicular body; PAS: phagophore assembly site; Pep4: proteinase A; PolyP: polyphosphate; Prb1: proteinase B; Prc1: carboxypeptidase Y; V-ATPase: vacuolar-type proton-translocating ATPase; VTC: vacuolar transporter chaperone.
Collapse
Affiliation(s)
- Katherine R Parzych
- a Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Daniel J Klionsky
- a Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| |
Collapse
|
15
|
Lin C, Yang L. Long Noncoding RNA in Cancer: Wiring Signaling Circuitry. Trends Cell Biol 2018; 28:287-301. [PMID: 29274663 PMCID: PMC5869122 DOI: 10.1016/j.tcb.2017.11.008] [Citation(s) in RCA: 386] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Long noncoding RNAs (lncRNAs), which are encoded by a vast less explored region of the human genome, may hold missing drivers of cancer and have gained attention recently as a potentially crucial layer of cancer cell regulation. lncRNAs are aberrantly expressed in a broad spectrum of cancers, and they play key roles in promoting and maintaining tumor initiation and progression, demonstrating their clinical potential as biomarkers and therapeutic targets. Recent discoveries have revealed that lncRNAs act as key signal transduction mediators in cancer signaling pathways by interacting with proteins, RNA, and lipids. Here, we review the mechanisms by which lncRNAs regulate cellular responses to extracellular signals and discuss their clinical potential as diagnostic indicators, stratification markers, and therapeutic targets of combinatorial treatments.
Collapse
Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
16
|
Morriss SC, Liu X, Floyd BE, Bassham DC, MacIntosh GC. Cell growth and homeostasis are disrupted in arabidopsis rns2-2 mutants missing the main vacuolar RNase activity. ANNALS OF BOTANY 2017; 120:911-922. [PMID: 28961890 PMCID: PMC5710523 DOI: 10.1093/aob/mcx099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/01/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND AIMS Enzymes belonging to the RNase T2 family are essential for normal rRNA turnover in eukaryotes. In Arabidopsis thaliana, this function is performed by RNS2. The null mutant rns2-2 has increased rRNA half-life and constitutive autophagy. The aim of this work was to determine the molecular changes that take place in the rns2-2 mutant that may lead to altered cellular homeostasis, manifested by the observed cellular phenotype. METHODS To determine the effect of defective rRNA turnover on cellular homeostasis, comparative transcriptome and metabolome analyses of 10-day-old wild-type and rns2-2 seedlings were used to identify molecular processes affected in the mutant. Bioinformatics analyses suggested additional phenotypes that were confirmed through direct plant size measurements and microscopy. KEY RESULTS Few genes were differentially expressed in the rns2-2 mutant, indicating that control of autophagy in this genotype is mainly achieved at the post-transcriptional level. Among differentially expressed genes, transcripts related to carbon flux processes, particularly the pentose phosphate pathway (PPP), were identified. Metabolite analyses confirmed changes in the levels of PPP intermediates. Genes related to cell wall loosening were also differentially expressed in the mutant, and a decrease in monosaccharide components of cell wall hemicellulose were found. As a potential effect of weaker cell walls, rns2-2 plants are larger than wild-type controls, due to larger cells and increased water content. Elevated levels of reactive oxygen species (ROS) were also measured in rns2-2, and the constitutive autophagy phenotype was blocked by preventing ROS production via NADPH oxidase. CONCLUSIONS Lack of rRNA recycling in rns2-2 cells triggers a change in carbon flux, which is redirected through the PPP to produce ribose-5-phosphate for de novo nucleoside synthesis. rRNA or ribosome turnover is thus essential for cellular homeostasis, probably through maintenance of nucleoside levels as part of the salvage pathway.
Collapse
Affiliation(s)
- Stephanie C Morriss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Xiaoyi Liu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Brice E Floyd
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Gustavo C MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| |
Collapse
|
17
|
Ramanauskas K, Igić B. The evolutionary history of plant T2/S-type ribonucleases. PeerJ 2017; 5:e3790. [PMID: 28924504 PMCID: PMC5598434 DOI: 10.7717/peerj.3790] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022] Open
Abstract
A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.
Collapse
Affiliation(s)
- Karolis Ramanauskas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| |
Collapse
|
18
|
Floyd BE, Mugume Y, Morriss SC, MacIntosh GC, Bassham DC. Localization of RNS2 ribonuclease to the vacuole is required for its role in cellular homeostasis. PLANTA 2017; 245:779-792. [PMID: 28025674 DOI: 10.1007/s00425-016-2644-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/21/2016] [Indexed: 05/28/2023]
Abstract
Localization of the RNase RNS2 to the vacuole via a C-terminal targeting signal is essential for its function in rRNA degradation and homeostasis. RNase T2 ribonucleases are highly conserved enzymes present in the genomes of nearly all eukaryotes and many microorganisms. Their constitutive expression in different tissues and cell types of many organisms suggests a housekeeping role in RNA homeostasis. The Arabidopsis thaliana class II RNase T2, RNS2, is encoded by a single gene and functions in rRNA degradation. Loss of RNS2 results in RNA accumulation and constitutive activation of autophagy, possibly as a compensatory mechanism. While the majority of RNase T2 enzymes is secreted, RNS2 is located within the vacuole and in the endoplasmic reticulum (ER), possibly within ER bodies. As RNS2 has a neutral pH optimum, and the endomembrane organelles are connected by vesicle transport, the site within the endomembrane system at which RNS2 functions is unclear. Here we demonstrate that localization to the vacuole is essential for the physiological function of RNS2. A mutant allele of RNS2, rns2-1, results in production of an active RNS2 RNase but with a mutation that removes a putative C-terminal vacuolar targeting signal. The mutant protein is, therefore, secreted from the cell. This results in a constitutive autophagy phenotype similar to that observed in rns2 null mutants. These findings illustrate that the intracellular retention of RNS2 and localization within the vacuole are critical for its cellular function.
Collapse
Affiliation(s)
- Brice E Floyd
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Yosia Mugume
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Stephanie C Morriss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gustavo C MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|
19
|
Lin A, Hu Q, Li C, Xing Z, Ma G, Wang C, Li J, Ye Y, Yao J, Liang K, Wang S, Park PK, Marks JR, Zhou Y, Zhou J, Hung MC, Liang H, Hu Z, Shen H, Hawke DH, Han L, Zhou Y, Lin C, Yang L. The LINK-A lncRNA interacts with PtdIns(3,4,5)P 3 to hyperactivate AKT and confer resistance to AKT inhibitors. Nat Cell Biol 2017; 19:238-251. [PMID: 28218907 PMCID: PMC5332298 DOI: 10.1038/ncb3473] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/12/2017] [Indexed: 12/13/2022]
Abstract
Phosphatidylinositol-3,4,5-trisphosphate (PIP3) mediates signaling pathways as a second messenger in response to extracellular signals. Although primordial functions of phospholipids and RNAs have been hypothesized in the “RNA world”, physiological RNA-phospholipid interactions and their involvement in essential cellular processes has remained a mystery. We explicate the contribution of lipid-binding long non-coding RNAs (lncRNAs) in cancer cells. Among them, Long Intergenic Noncoding RNA for Kinase Activation (LINK-A) directly interacts with AKT pleckstrin homology domain and PIP3 at the single nucleotide level, facilitating AKT-PIP3 interaction and consequent enzymatic activation. LINK-A-dependent AKT hyperactivation leads to tumorigenesis and resistance to AKT inhibitors. Genomic deletions of the LINK-A PIP3-binding motif dramatically sensitized breast cancer cells to AKT inhibitors. Furthermore, meta-analysis showed the correlation between LINK-A expression and incidence of a SNP (rs12095274: A>G), AKT phosphorylation status, and poor outcomes for breast and lung cancer patients. PIP3-binding lncRNA modulates AKT activation with broad clinical implications.
Collapse
Affiliation(s)
- Aifu Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chunlai Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhen Xing
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Cheng Wang
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yin Ye
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ke Liang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shouyu Wang
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Peter K Park
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeffrey R Marks
- Department of Surgery, Division of Surgical Science, Duke University, School of Medicine, Durham, North Carolina 27710, USA
| | - Yan Zhou
- Department of Oncology, Yixing People's Hospital, Yixing 214200, China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - David H Hawke
- Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
20
|
Xu WL, Yang Y, Wang YD, Qu LH, Zheng LL. Computational Approaches to tRNA-Derived Small RNAs. Noncoding RNA 2017; 3:E2. [PMID: 29657274 PMCID: PMC5832003 DOI: 10.3390/ncrna3010002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 12/12/2022] Open
Abstract
tRNA-derived small RNAs (tDRs) are a group of small, non-coding RNAs derived from transfer RNAs (tRNAs). They can be classified as tRNA halves and tRNA-derived small RNA fragments (tRFs). Accumulating experimental evidence suggests their functional roles in cells and in various biological processes. Advances in next-generation sequencing (NGS) techniques allow a large amount of small RNA deep-sequencing data to be generated. To investigate tDRs from these data, software to identify tDRs and databases to retrieve or manage tDR data have been devised. In this review, we summarized the tools and databases for tDR identification and collection, with the aim of helping researchers choose the best tools for their analysis and inspiring the invention or improvement of tools in the field.
Collapse
Affiliation(s)
- Wei-Lin Xu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Ye Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Yi-Dan Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| |
Collapse
|
21
|
Floyd BE, Morriss SC, MacIntosh GC, Bassham DC. Evidence for autophagy-dependent pathways of rRNA turnover in Arabidopsis. Autophagy 2016; 11:2199-212. [PMID: 26735434 DOI: 10.1080/15548627.2015.1106664] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Ribosomes account for a majority of the cell's RNA and much of its protein and represent a significant investment of cellular resources. The turnover and degradation of ribosomes has been proposed to play a role in homeostasis and during stress conditions. Mechanisms for the turnover of rRNA and ribosomal proteins have not been fully elucidated. We show here that the RNS2 ribonuclease and autophagy participate in RNA turnover in Arabidopsis thaliana under normal growth conditions. An increase in autophagosome formation was seen in an rns2-2 mutant, and this increase was dependent on the core autophagy genes ATG9 and ATG5. Autophagosomes and autophagic bodies in rns2-2 mutants contain RNA and ribosomes, suggesting that autophagy is activated as an attempt to compensate for loss of rRNA degradation. Total RNA accumulates in rns2-2, atg9-4, atg5-1, rns2-2 atg9-4, and rns2-2 atg5-1 mutants, suggesting a parallel role for autophagy and RNS2 in RNA turnover. rRNA accumulates in the vacuole in rns2-2 mutants. Vacuolar accumulation of rRNA was blocked by disrupting autophagy via an rns2-2 atg5-1 double mutant but not by an rns2-2 atg9-4 double mutant, indicating that ATG5 and ATG9 function differently in this process. Our results suggest that autophagy and RNS2 are both involved in homeostatic degradation of rRNA in the vacuole.
Collapse
Affiliation(s)
- Brice E Floyd
- a Department of Genetics , Development and Cell Biology; Iowa State University ; Ames , IA , USA
| | - Stephanie C Morriss
- b Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology; Iowa State University ; Ames , IA USA
| | - Gustavo C MacIntosh
- b Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology; Iowa State University ; Ames , IA USA.,c Plant Sciences Institute; Iowa State University ; Ames , IA USA
| | - Diane C Bassham
- a Department of Genetics , Development and Cell Biology; Iowa State University ; Ames , IA , USA.,c Plant Sciences Institute; Iowa State University ; Ames , IA USA
| |
Collapse
|
22
|
Abstract
Macroautophagy/autophagy is a key catabolic process, essential for maintaining cellular homeostasis and survival through the removal and recycling of unwanted cellular material. Emerging evidence has revealed intricate connections between the RNA and autophagy research fields. While a majority of studies have focused on protein, lipid and carbohydrate catabolism via autophagy, accumulating data supports the view that several types of RNA and associated ribonucleoprotein complexes are specifically recruited to phagophores (precursors to autophagosomes) and subsequently degraded in the lysosome/vacuole. Moreover, recent studies have revealed a substantial number of novel autophagy regulators with RNA-related functions, indicating roles for RNA and associated proteins not only as cargo, but also as regulators of this process. In this review, we discuss widespread evidence of RNA catabolism via autophagy in yeast, plants and animals, reviewing the molecular mechanisms and biological importance in normal physiology, stress and disease. In addition, we explore emerging evidence of core autophagy regulation mediated by RNA-binding proteins and noncoding RNAs, and point to gaps in our current knowledge of the connection between RNA and autophagy. Finally, we discuss the pathological implications of RNA-protein aggregation, primarily in the context of neurodegenerative disease.
Collapse
Affiliation(s)
- Lisa B Frankel
- a Biotech Research and Innovation Centre , University of Copenhagen , Copenhagen , Denmark
| | - Michal Lubas
- a Biotech Research and Innovation Centre , University of Copenhagen , Copenhagen , Denmark
| | - Anders H Lund
- a Biotech Research and Innovation Centre , University of Copenhagen , Copenhagen , Denmark
| |
Collapse
|
23
|
Motoyoshi N, Kobayashi H, Itagaki T, Inokuchi N. Amino acid sequence analysis and characterization of a ribonuclease from starfish Asterias amurensis. J Biochem 2016; 160:131-9. [DOI: 10.1093/jb/mvw017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/06/2016] [Indexed: 11/13/2022] Open
|
24
|
Bayram Ö, Feussner K, Dumkow M, Herrfurth C, Feussner I, Braus GH. Changes of global gene expression and secondary metabolite accumulation during light-dependent Aspergillus nidulans development. Fungal Genet Biol 2016; 87:30-53. [DOI: 10.1016/j.fgb.2016.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/29/2015] [Accepted: 01/06/2016] [Indexed: 10/22/2022]
|
25
|
RNase T2 of Mortierella (phylum Zygomycota). MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2015.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
26
|
Rojas H, Floyd B, Morriss SC, Bassham D, MacIntosh GC, Goldraij A. NnSR1, a class III non-S-RNase specifically induced in Nicotiana alata under phosphate deficiency, is localized in endoplasmic reticulum compartments. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:250-9. [PMID: 26025538 DOI: 10.1016/j.plantsci.2015.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/11/2015] [Accepted: 04/18/2015] [Indexed: 05/28/2023]
Abstract
A combined strategy of phosphate (Pi) remobilization from internal and external RNA sources seems to be conserved in plants exposed to Pi starvation. Thus far, the only ribonucleases (RNases) reported to be induced in Nicotiana alata undergoing Pi deprivation are extracellular S-like RNase NE and NnSR1. NnSR1 is a class III non S-RNase of unknown subcellular location. Here, we examine the hypothesis that NnSR1 is an intracellular RNase derived from the self-incompatibility system with specific expression in self-incompatible Nicotiana alata. NnSR1 was not induced in self-compatible Nicotiana species exposed to Pi deprivation. NnSR1 conjugated with a fluorescent protein and transiently expressed in Arabidopsis protoplasts and Nicotiana leaves showed that the fusion protein co-localized with an endoplasmic reticulum (ER) marker. Subcellular fractionation by ultracentrifugation of roots exposed to Pi deprivation revealed that the native NnSR1 migrated in parallel with the BiP protein, a typical ER marker. To our knowledge, NnSR1 is the first class III RNase reported to be localized in ER compartments. The induction of NnSR1 was detected earlier than the extracellular RNase NE, suggesting that intracellular RNA may be the first source of Pi used by the cell under Pi stress.
Collapse
Affiliation(s)
- Hernán Rojas
- Dpto Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Brice Floyd
- Dept of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Stephanie C Morriss
- Dept of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane Bassham
- Dept of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Gustavo C MacIntosh
- Dept of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Ariel Goldraij
- Dpto Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina.
| |
Collapse
|
27
|
Huang H, Kawamata T, Horie T, Tsugawa H, Nakayama Y, Ohsumi Y, Fukusaki E. Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast. EMBO J 2014; 34:154-68. [PMID: 25468960 DOI: 10.15252/embj.201489083] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Autophagy is a catabolic process conserved among eukaryotes. Under nutrient starvation, a portion of the cytoplasm is non-selectively sequestered into autophagosomes. Consequently, ribosomes are delivered to the vacuole/lysosome for destruction, but the precise mechanism of autophagic RNA degradation and its physiological implications for cellular metabolism remain unknown. We characterized autophagy-dependent RNA catabolism using a combination of metabolome and molecular biological analyses in yeast. RNA delivered to the vacuole was processed by Rny1, a T2-type ribonuclease, generating 3'-NMPs that were immediately converted to nucleosides by the vacuolar non-specific phosphatase Pho8. In the cytoplasm, these nucleosides were broken down by the nucleosidases Pnp1 and Urh1. Most of the resultant bases were not re-assimilated, but excreted from the cell. Bulk non-selective autophagy causes drastic perturbation of metabolism, which must be minimized to maintain intracellular homeostasis.
Collapse
Affiliation(s)
- Hanghang Huang
- Department of Biotechnology, Osaka University, Suita Osaka, Japan
| | - Tomoko Kawamata
- Frontier Research Center, Tokyo Institute of Technology, Midori-ku Yokohama, Japan
| | - Tetsuro Horie
- Frontier Research Center, Tokyo Institute of Technology, Midori-ku Yokohama, Japan
| | - Hiroshi Tsugawa
- Department of Biotechnology, Osaka University, Suita Osaka, Japan
| | | | - Yoshinori Ohsumi
- Frontier Research Center, Tokyo Institute of Technology, Midori-ku Yokohama, Japan
| | | |
Collapse
|
28
|
Ambrosio L, Morriss S, Riaz A, Bailey R, Ding J, MacIntosh GC. Phylogenetic analyses and characterization of RNase X25 from Drosophila melanogaster suggest a conserved housekeeping role and additional functions for RNase T2 enzymes in protostomes. PLoS One 2014; 9:e105444. [PMID: 25133712 PMCID: PMC4136927 DOI: 10.1371/journal.pone.0105444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/18/2014] [Indexed: 11/25/2022] Open
Abstract
Ribonucleases belonging to the RNase T2 family are enzymes associated with the secretory pathway that are almost absolutely conserved in all eukaryotes. Studies in plants and vertebrates suggest they have an important housekeeping function in rRNA recycling. However, little is known about this family of enzymes in protostomes. We characterized RNase X25, the only RNase T2 enzyme in Drosophila melanogaster. We found that RNase X25 is the major contributor of ribonuclease activity in flies as detected by in gel assays, and has an acidic pH preference. Gene expression analyses showed that the RNase X25 transcript is present in all adult tissues and developmental stages. RNase X25 expression is elevated in response to nutritional stresses; consistent with the hypothesis that this enzyme has a housekeeping role in recycling RNA. A correlation between induction of RNase X25 expression and autophagy was observed. Moreover, induction of gene expression was triggered by oxidative stress suggesting that RNase X25 may have additional roles in stress responses. Phylogenetic analyses of this family in protostomes showed that RNase T2 genes have undergone duplication events followed by divergence in several phyla, including the loss of catalytic residues, and suggest that RNase T2 proteins have acquired novel functions. Among those, it is likely that a role in host immunosuppression evolved independently in several groups, including parasitic Platyhelminthes and parasitoid wasps. The presence of only one RNase T2 gene in the D. melanogaster genome, without any other evident secretory RNase activity detected, makes this organism an ideal system to study the cellular functions of RNase T2 proteins associated with RNA recycling and maintenance of cellular homeostasis. On the other hand, the discovery of gene duplications in several protostome genomes also presents interesting new avenues to study additional biological functions of this ancient family of proteins.
Collapse
Affiliation(s)
- Linda Ambrosio
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (LA); (GCM)
| | - Stephanie Morriss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Ayesha Riaz
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Ryan Bailey
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Jian Ding
- Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (LA); (GCM)
| |
Collapse
|
29
|
Steindorff AS, Ramada MHS, Coelho ASG, Miller RNG, Pappas GJ, Ulhoa CJ, Noronha EF. Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum. BMC Genomics 2014; 15:204. [PMID: 24635846 PMCID: PMC4004048 DOI: 10.1186/1471-2164-15-204] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/06/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The species of T. harzianum are well known for their biocontrol activity against plant pathogens. However, few studies have been conducted to further our understanding of its role as a biological control agent against S. sclerotiorum, a pathogen involved in several crop diseases around the world. In this study, we have used RNA-seq and quantitative real-time PCR (RT-qPCR) techniques in order to explore changes in T. harzianum gene expression during growth on cell wall of S. sclerotiorum (SSCW) or glucose. RT-qPCR was also used to examine genes potentially involved in biocontrol, during confrontation between T. harzianum and S. sclerotiorum. RESULTS Data obtained from six RNA-seq libraries were aligned onto the T. harzianum CBS 226.95 reference genome and compared after annotation using the Blast2GO suite. A total of 297 differentially expressed genes were found in mycelia grown for 12, 24 and 36 h under the two different conditions: supplemented with glucose or SSCW. Functional annotation of these genes identified diverse biological processes and molecular functions required during T. harzianum growth on SSCW or glucose. We identified various genes of biotechnological value encoding proteins with functions such as transporters, hydrolytic activity, adherence, appressorium development and pathogenesis. To validate the expression profile, RT-qPCR was performed using 20 randomly chosen genes. RT-qPCR expression profiles were in complete agreement with the RNA-Seq data for 17 of the genes evaluated. The other three showed differences at one or two growth times. During the confrontation assay, some genes were up-regulated during and after contact, as shown in the presence of SSCW which is commonly used as a model to mimic this interaction. CONCLUSIONS The present study is the first initiative to use RNA-seq for identification of differentially expressed genes in T. harzianum strain TR274, in response to the phytopathogenic fungus S. sclerotiorum. It provides insights into the mechanisms of gene expression involved in mycoparasitism of T. harzianum against S.sclerotiorum. The RNA-seq data presented will facilitate improvement of the annotation of gene models in the draft T. harzianum genome and provide important information regarding the transcriptome during this interaction.
Collapse
Affiliation(s)
- Andrei Stecca Steindorff
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, CEP 70.910-900 Brasília, DF, Brazil
| | | | - Alexandre Siqueira Guedes Coelho
- Escola de Agronomia e Engenharia de Alimentos, Universidade Federal de Goiás, Campus Samambaia, P.O. Box 131CEP 74001-970 Goiânia, GO, Brasil
| | - Robert Neil Gerard Miller
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, CEP 70.910-900 Brasília, DF, Brazil
| | - Georgios Joannis Pappas
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, CEP 70.910-900 Brasília, DF, Brazil
| | - Cirano José Ulhoa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Goiás, Campus Samambaia, Instituto de Ciências Biológicas, CEP 74.090-900 Goiânia, GO, Brazil
| | - Eliane Ferreira Noronha
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, CEP 70.910-900 Brasília, DF, Brazil
| |
Collapse
|
30
|
Ciesielska K, Van Bogaert I, Chevineau S, Li B, Groeneboer S, Soetaert W, Van de Peer Y, Devreese B. Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids. J Proteomics 2014; 98:159-74. [DOI: 10.1016/j.jprot.2013.12.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 12/30/2013] [Indexed: 01/25/2023]
|
31
|
Stress-induced RNASET2 overexpression mediates melanocyte apoptosis via the TRAF2 pathway in vitro. Cell Death Dis 2014; 5:e1022. [PMID: 24457966 PMCID: PMC4040706 DOI: 10.1038/cddis.2013.539] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/28/2013] [Accepted: 12/02/2013] [Indexed: 11/08/2022]
Abstract
The recent genome-wide association study identified a link between vitiligo and genetic variants in the ribonuclease T2 (RNASET2) gene; however, the functional roles of RNASET2 in vitiligo pathogenesis or in melanocyte apoptosis have yet to be determined. The current study was designed to investigate the vitiligo-related expression pattern of RNASET2 and its molecular function involving apoptosis-related signaling proteins and pathways. The results showed overexpression of RNASET2 in epidermis specimens from 40 vitiligo patients compared with that from matched healthy controls. In addition, in vitro analyses indicated that overexpression of RNASET2 was inducible in cultured primary human melanocytes and keratinocytes by stress conditions, that is, exposure to UV irradiation, hydrogen peroxide, and inflammatory factors, respectively, and led to increased cell apoptosis via the tumor necrosis factor receptor-associated factor 2 (TRAF2)-caspases pathway through the physical interaction of RNASET2 with TRAF2. Thus, RNASET2 may contribute to vitiligo pathogenesis by inhibiting TRAF2 expression and, as such, RNASET2 may represent a potential therapeutic target of vitiligo.
Collapse
|
32
|
Filipenko EA, Kochetov AV, Kanayama Y, Malinovsky VI, Shumny VK. PR-proteins with ribonuclease activity and plant resistance against pathogenic fungi. ACTA ACUST UNITED AC 2013. [DOI: 10.1134/s2079059713060026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
33
|
Shcherbik N. Golgi-mediated glycosylation determines residency of the T2 RNase Rny1p in Saccharomyces cerevisiae. Traffic 2013; 14:1209-27. [PMID: 24102742 DOI: 10.1111/tra.12122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/20/2022]
Abstract
The role of glycosylation in the function of the T2 family of RNases is not well understood. In this work, we examined how glycosylation affects the progression of the T2 RNase Rny1p through the secretory pathway in Saccharomyces cerevisiae. We found that Rny1p requires entering into the ER first to become active and uses the adaptor protein Erv29p for packaging into COPII vesicles and transport to the Golgi apparatus. While inside the ER, Rny1p undergoes initial N-linked core glycosylation at four sites, N37, N70, N103 and N123. Rny1p transport to the Golgi results in the further attachment of high-glycans. Whereas modifications with glycans are dispensable for the nucleolytic activity of Rny1p, Golgi-mediated modifications are critical for its extracellular secretion. Failure of Golgi-specific glycosylation appears to direct Rny1p to the vacuole as an alternative destination and/or site of terminal degradation. These data reveal a previously unknown function of Golgi glycosylation in a T2 RNase as a sorting and secretion signal.
Collapse
Affiliation(s)
- Natalia Shcherbik
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA.
| |
Collapse
|
34
|
Itagaki T, Motoyoshi N, Kobayashi H, Ogawa Y, Hirose D, Inokuchi N. Cloning and characterization of ribonuclease T2 gene (RNHe30) from the basidiomycete, Hericium erinaceum. MYCOSCIENCE 2013. [DOI: 10.1016/j.myc.2012.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
35
|
Durdevic Z, Schaefer M. tRNA modifications: necessary for correct tRNA-derived fragments during the recovery from stress? Bioessays 2013; 35:323-7. [PMID: 23315679 DOI: 10.1002/bies.201200158] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Endonuclease-mediated tRNA fragmentation has been observed in many species suggesting functional importance for tRNA fragments. The size distribution of tRNA-derived fragments indicates the existence of mechanisms that protect tRNAs and their fragments from total degradation by exonucleases. Could post-transcriptional modifications be important for the controlled processing of tRNAs?
Collapse
Affiliation(s)
- Zeljko Durdevic
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | | |
Collapse
|
36
|
Teparić R, Didak B, Ščulac E, Mrša V. Genetic immobilization of RNase Rny1p at the Saccharomyces cerevisiae cell surface. J GEN APPL MICROBIOL 2013; 59:75-82. [DOI: 10.2323/jgam.59.75] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
37
|
Structure-function analysis of Rny1 in tRNA cleavage and growth inhibition. PLoS One 2012; 7:e41111. [PMID: 22829915 PMCID: PMC3400635 DOI: 10.1371/journal.pone.0041111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 06/18/2012] [Indexed: 01/05/2023] Open
Abstract
T2 ribonucleases are conserved nucleases that affect a variety of processes in eukaryotic cells including the regulation of self-incompatibility by S-RNases in plants, modulation of host immune cell responses by viral and schistosome T2 enzymes, and neurological development and tumor progression in humans. These roles for RNaseT2’s can be due to catalytic or catalytic-independent functions of the molecule. Despite this broad importance, the features of RNaseT2 proteins that modulate catalytic and catalytic-independent functions are poorly understood. Herein, we analyze the features of Rny1 in Saccharomyces cerevisiae to determine the requirements for cleaving tRNA in vivo and for inhibiting cellular growth in a catalytic-independent manner. We demonstrate that catalytic-independent inhibition of growth is a combinatorial property of the protein and is affected by a fungal-specific C-terminal extension, the conserved catalytic core, and the presence of a signal peptide. Catalytic functions of Rny1 are independent of the C-terminal extension, are affected by many mutations in the catalytic core, and also require a signal peptide. Biochemical flotation assays reveal that in rny1Δ cells, some tRNA molecules associate with membranes suggesting that cleavage of tRNAs by Rny1 can involve either tRNA association with, or uptake into, membrane compartments.
Collapse
|
38
|
Abstract
All RNA species in yeast cells are subject to turnover. Work over the past 20 years has defined degradation mechanisms for messenger RNAs, transfer RNAs, ribosomal RNAs, and noncoding RNAs. In addition, numerous quality control mechanisms that target aberrant RNAs have been identified. Generally, each decay mechanism contains factors that funnel RNA substrates to abundant exo- and/or endonucleases. Key issues for future work include determining the mechanisms that control the specificity of RNA degradation and how RNA degradation processes interact with translation, RNA transport, and other cellular processes.
Collapse
Affiliation(s)
- Roy Parker
- Department of Molecular and Cellular Biology, University of Arizona and Howard Hughes Medical Institute, Tucson, AZ 85721, USA.
| |
Collapse
|
39
|
Köthke S, Köck M. The Solanum lycopersicum RNaseLER is a class II enzyme of the RNase T2 family and shows preferential expression in guard cells. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:840-7. [PMID: 21237531 DOI: 10.1016/j.jplph.2010.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/12/2010] [Accepted: 11/08/2010] [Indexed: 05/30/2023]
Abstract
Ribonucleases (RNases) occur in different gene families, functioning in RNA processing and degradation. In this study, we report on cloning and characterization of RNaseLER, the first class II gene of the RNase T2 family in tomato (Solanum lycopersicum). The family also includes the class I members RNaseLE and RNaseLX, and the class III group of S-RNases acting in self incompatibility. The RNaseLER gene was cloned by polymerase chain reaction (PCR)-assisted methods. Structural analyses of RNaseLER and homologous genes revealed unique key features of class II RNase T2 genes. RNaseLER is a single copy gene in tomato and codes for a primary protein of 260 amino acids. Subcellular localization analyzed with a RNaseLER-eYFP fusion protein and co-localization experiments revealed an intracellular accumulation in the endoplasmic reticulum. Transgenic Nicotiana benthamiana plants carrying the uidA reporter gene under the control of a 900-bp RNaseLER promoter sequence express the reporter gene predominantly in guard cells and trichomes. This previously unknown spatial expression of a RNase T2 gene is consistent with ubiquitous detection of low RNaseLER transcript abundances in almost all parts of tomato plants. As revealed by quantitative real-time RT-PCR analysis treatments with abscisic acid, ethylene or other abiotic and biotic stress factors did not affect RNaseLER expression significantly. Unlike tomato class I genes, RNaseLER represents a constitutively expressed gene with a cell-specific role in stomata and trichomes and no involvement in stress responses.
Collapse
Affiliation(s)
- Sabine Köthke
- Martin-Luther-Universität Halle-Wittenberg, Biozentrum, Weinbergweg 22, D-06120 Halle, Germany
| | | |
Collapse
|
40
|
MacIntosh GC. RNase T2 Family: Enzymatic Properties, Functional Diversity, and Evolution of Ancient Ribonucleases. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2011. [DOI: 10.1007/978-3-642-21078-5_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
41
|
Luhtala N, Parker R. T2 Family ribonucleases: ancient enzymes with diverse roles. Trends Biochem Sci 2010; 35:253-9. [PMID: 20189811 DOI: 10.1016/j.tibs.2010.02.002] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/02/2010] [Accepted: 02/03/2010] [Indexed: 01/27/2023]
Abstract
Ribonucleases of the T2 family are found in the genomes of protozoans, plants, bacteria, animals and viruses. A broad range of biological roles for these ribonucleases have been suggested, including scavenging of nucleic acids, degradation of self-RNA, serving as extra- or intracellular cytotoxins, and modulating host immune responses. Recently, RNaseT2 family members have been implicated in human pathologies such as cancer and parasitic diseases. Interestingly, certain functions of RNaseT2 family members are independent of their nuclease activity, suggesting that these proteins have additional functions. Moreover, humans lacking RNASET2 manifest a defect in neurological development, perhaps due to aberrant control of the immune system. We review the basic structure and function of RNaseT2 family members and their biological roles.
Collapse
Affiliation(s)
- Natalie Luhtala
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721-0106, USA
| | | |
Collapse
|
42
|
RNase T2 genes from rice and the evolution of secretory ribonucleases in plants. Mol Genet Genomics 2010; 283:381-96. [PMID: 20182746 DOI: 10.1007/s00438-010-0524-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 02/02/2010] [Indexed: 12/31/2022]
Abstract
The plant RNase T2 family is divided into two different subfamilies. S-RNases are involved in rejection of self-pollen during the establishment of self-incompatibility in three plant families. S-like RNases, on the other hand, are not involved in self-incompatibility, and although gene expression studies point to a role in plant defense and phosphate recycling, their biological roles are less well understood. Although S-RNases have been subjects of many phylogenetic studies, few have included an extensive analysis of S-like RNases, and genome-wide analyses to determine the number of S-like RNases in fully sequenced plant genomes are missing. We characterized the eight RNase T2 genes present in the Oryza sativa genome; and we also identified the full complement of RNase T2 genes present in other fully sequenced plant genomes. Phylogenetics and gene expression analyses identified two classes among the S-like RNase subfamily. Class I genes show tissue specificity and stress regulation. Inactivation of RNase activity has occurred repeatedly throughout evolution. On the other hand, Class II seems to have conserved more ancestral characteristics; and, unlike other S-like RNases, genes in this class are conserved in all plant species analyzed and most are constitutively expressed. Our results suggest that gene duplication resulted in high diversification of Class I genes. Many of these genes are differentially expressed in response to stress, and we propose that protein characteristics, such as the increase in basic residues can have a defense role independent of RNase activity. On the other hand, constitutive expression and phylogenetic conservation suggest that Class II S-like RNases may have a housekeeping role.
Collapse
|
43
|
Shigematsu M, Ogawa T, Kido A, Kitamoto HK, Hidaka M, Masaki H. Cellular and transcriptional responses of yeast to the cleavage of cytosolic tRNAs induced by colicin D. Yeast 2009; 26:663-73. [PMID: 19877125 DOI: 10.1002/yea.1725] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
MESH Headings
- Base Sequence
- Cell Proliferation
- Cytosol/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Nucleic Acid Conformation
- Oligonucleotide Array Sequence Analysis
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- Pheromones/metabolism
- Plasmids/genetics
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- Signal Transduction
- Transcription, Genetic
- Transformation, Genetic
Collapse
Affiliation(s)
- Megumi Shigematsu
- Department of Biotechnology, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | | | | | | | | |
Collapse
|
44
|
Abstract
A conserved response to stress involves endonucleolytic cleavage of cytoplasmic transfer RNAs (tRNAs) by ribonucleases that are normally secreted or sequestered. Ribonuclease activation or release is an intriguing new aspect of cellular stress responses, with a potential impact on translation, apoptosis, cancer, and disease progression.
Collapse
Affiliation(s)
- Debrah M Thompson
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA
| | | |
Collapse
|
45
|
Pisani T, Munzi S, Paoli L, Backor M, Loppi S. Physiological effects of a geothermal element: boron excess in the epiphytic lichen Xanthoria parietina (L.) TH. FR. CHEMOSPHERE 2009; 76:921-926. [PMID: 19477478 DOI: 10.1016/j.chemosphere.2009.04.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/22/2009] [Accepted: 04/27/2009] [Indexed: 05/27/2023]
Abstract
The results of a study aimed at investigating the effects of boron excess on a set of ecophysiological parameters in the lichen Xanthoria parietina, to set up a monitoring system to trace early biological effects of boron pollution in geothermal areas, are reported. To this purpose, lichen thalli have been incubated for 24 h in solutions at boron concentrations of 0.1, 1, 10 and 100 ppm, which were within the range in bulk deposition and geothermal fluids. The results showed a general trend of decreasing sample viability and increasing cell membrane damage and membrane lipid peroxidation under increasing boron concentrations, while photosynthetic efficiency, chlorophyll degradation and the contents of H(2)O(2) and water-soluble proteins were not affected. It was argued that the fungal partner, that represents the large majority of the lichen biomass, is more sensitive to boron excess than the algal partner.
Collapse
Affiliation(s)
- Tommaso Pisani
- Department of Environmental Science G. Sarfatti, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy
| | | | | | | | | |
Collapse
|
46
|
Rossier O, Dao J, Cianciotto NP. A type II secreted RNase of Legionella pneumophila facilitates optimal intracellular infection of Hartmannella vermiformis. MICROBIOLOGY-SGM 2009; 155:882-890. [PMID: 19246759 DOI: 10.1099/mic.0.023218-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Type II protein secretion plays a role in a wide variety of functions that are important for the ecology and pathogenesis of Legionella pneumophila. Perhaps most dramatic is the critical role that this secretion pathway has in L. pneumophila intracellular infection of aquatic protozoa. Recently, we showed that virulent L. pneumophila strain 130b secretes RNase activity through its type II secretion system. We now report the cloning and mutational analysis of the gene (srnA) encoding that novel type of secreted activity. The SrnA protein was defined as being a member of the T2 family of secreted RNases. Supernatants from mutants inactivated for srnA completely lacked RNase activity, indicating that SrnA is the major secreted RNase of L. pneumophila. Although srnA mutants grew normally in bacteriological media and human U937 cell macrophages, they were impaired in their ability to grow within Hartmannella vermiformis amoebae. This finding represents the second identification of a L. pneumophila type II effector being necessary for optimal intracellular infection of amoebae, with the first being the ProA zinc metalloprotease. Newly constructed srnA proA double mutants displayed an even larger infection defect that appeared to be the additive result of losing both SrnA and ProA. Overall, these data represent the first demonstration of a secreted RNase promoting an intracellular infection event, and support our long-standing hypothesis that the infection defects of L. pneumophila type II secretion mutants are due to the loss of multiple secreted effectors.
Collapse
Affiliation(s)
- Ombeline Rossier
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, IL 60611, USA
| | - Jenny Dao
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, IL 60611, USA
| | - Nicholas P Cianciotto
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, IL 60611, USA
| |
Collapse
|
47
|
Thompson DM, Parker R. The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2009; 185:43-50. [PMID: 19332891 PMCID: PMC2700514 DOI: 10.1083/jcb.200811119] [Citation(s) in RCA: 246] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The cellular response to stress conditions involves a decision between survival or cell death when damage is severe. A conserved stress response in eukaryotes involves endonucleolytic cleavage of transfer RNAs (tRNAs). The mechanism and significance of such tRNA cleavage is unknown. We show that in yeast, tRNAs are cleaved by the RNase T2 family member Rny1p, which is released from the vacuole into the cytosol during oxidative stress. Rny1p modulates yeast cell survival during oxidative stress independently of its catalytic ability. This suggests that upon release to the cytosol, Rny1p promotes cell death by direct interactions with downstream components. Thus, detection of Rny1p, and possibly its orthologues, in the cytosol may be a conserved mechanism for assessing cellular damage and determining cell survival, analogous to the role of cytochrome c as a marker for mitochondrial damage.
Collapse
Affiliation(s)
- Debrah M Thompson
- Department of Molecular and Cellular Biology, and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721, USA
| | | |
Collapse
|
48
|
Trifonova EA, Sapotsky MV, Komarova ML, Scherban AB, Shumny VK, Polyakova AM, Lapshina LA, Kochetov AV, Malinovsky VI. Protection of transgenic tobacco plants expressing bovine pancreatic ribonuclease against tobacco mosaic virus. PLANT CELL REPORTS 2007; 26:1121-6. [PMID: 17242942 DOI: 10.1007/s00299-006-0298-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 12/25/2006] [Accepted: 12/31/2006] [Indexed: 05/13/2023]
Abstract
Transgenic tobacco plants (Nicotiana tabacum cv. SR1) expressing extracellular pancreatic ribonuclease from Bos taurus and characterized by an increased level of ribonuclease activity in leaf extracts were challenged with tobacco mosaic virus. The transgenic plants exhibited a significantly higher level of protection against the virus infection than the control non-transformed plants. The protection was evidenced by the absence (or significant delay) of the appearance of typical mosaic symptoms and the retarded accumulation of infectious virus and viral antigen. These results demonstrate that modulation of extracellular nuclease expression can be efficiently used in promoting protection against viral diseases.
Collapse
|
49
|
Lers A, Sonego L, Green PJ, Burd S. Suppression of LX ribonuclease in tomato results in a delay of leaf senescence and abscission. PLANT PHYSIOLOGY 2006; 142:710-21. [PMID: 16920876 PMCID: PMC1586048 DOI: 10.1104/pp.106.080135] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Although present in different organisms and conserved in their protein sequence, the biological functions of T2 ribonucleases (RNase) are generally unknown. Tomato (Lycopersicon esculentum) LX is a T2/S-like RNase and its expression is known to be associated with phosphate starvation, ethylene responses, and senescence and programmed cell death. In this study, LX function was investigated using antisense tomato plants in which the LX protein level was reduced. LX protein levels normally become elevated when leaves senesce and antisense inhibition of LX retarded the progression of senescence. Moreover, we observed a marked delay of leaf abscission in LX-deficient plants. This correlated with specific induction of LX protein in the tomato mature abscission zone tissue. LX RNase gene regulation and the consequences of antisense inhibition indicate that LX has an important functional role in both abscission and senescence.
Collapse
Affiliation(s)
- Amnon Lers
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel.
| | | | | | | |
Collapse
|
50
|
Campomenosi P, Salis S, Lindqvist C, Mariani D, Nordström T, Acquati F, Taramelli R. Characterization of RNASET2, the first human member of the Rh/T2/S family of glycoproteins. Arch Biochem Biophys 2006; 449:17-26. [PMID: 16620762 DOI: 10.1016/j.abb.2006.02.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 02/23/2006] [Accepted: 02/24/2006] [Indexed: 10/24/2022]
Abstract
Ribonucleases are ubiquitous enzymes involved in RNA metabolism and are classified in several families on the basis of their structural, catalytic, and biological properties. Here, we describe characterization of the only human member of the Rh/T2/S family of acid hydrolases so far described, named RNASET2. This protein was previously reported to have an interesting biological function in the control of tumourigenesis and metastatization. We show that RNASET2 is present in multiple forms in human cell lines and mouse tissues, one of which represents the full length, glycosylated and secreted form, while the others are proteolytic products. RNASET2 is endowed with catalytic activity as demonstrated with purified recombinant protein expressed in the Baculovirus Expression Vector System and in a human cell line ectopically expressing various types of constructs. Furthermore, we document for this protein a lysosomal localization as described for other members of the Rh/T2/S family of ribonucleases. The results presented herein represent a further advancement toward the molecular understanding of the tumour suppressive properties of the human RNASET2 protein.
Collapse
Affiliation(s)
- Paola Campomenosi
- Department of Biotechnology and Molecular Sciences, University of Insubria, Via JH Dunant, 3, 21100 Varese, Italy.
| | | | | | | | | | | | | |
Collapse
|