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Jiadkong K, Fauzia AN, Yamaguchi N, Ueda A. Exogenous riboflavin (vitamin B2) application enhances salinity tolerance through the activation of its biosynthesis in rice seedlings under salinity stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111929. [PMID: 38007197 DOI: 10.1016/j.plantsci.2023.111929] [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: 07/22/2023] [Revised: 11/16/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
Salinity stress triggers the accumulation of reactive oxygen species (ROS), leading to impaired plant growth. Riboflavin (RIB; vitamin B2) is synthesized by plants, fungi, and microorganisms and is a precursor of the coenzymes, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), which are important for cellular metabolism. In this study, we aimed to elucidate the mechanistic basis of the RIB-mediated alleviation of salinity stress in rice. We observed higher biomass accumulation and lower concentrations of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in RIB-pretreated seedlings under salinity stress. In vitro assays showed that H2O2 was scavenged as the RIB concentration increased, implying that RIB may function as a non-enzymatic antioxidant in ROS detoxification. RIB-pretreated seedlings accumulated more Na+ in the roots than in the leaf blades because of the contributions of OsHKT2;1, OsNHX1, and OsHKT1;4 in the roots and leaf sheaths, respectively. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis revealed increased RIB concentration in roots and shoots and upregulation of key genes (OsRIBA1, OsGCHI, OsLS, and OsRS) involved in RIB biosynthesis in the roots of RIB-pretreated seedlings. Taken together, our findings suggest that RIB pretreatment ameliorates salinity stress in rice by improving (1) oxidative stress tolerance, as increased RIB concentration may function as a non-enzymatic antioxidant, and (2) ionic stress tolerance, as RIB pretreatment limits Na+ accumulation in the leaf blades and maintains a favorable Na+/K+ balance.
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Affiliation(s)
- Kamonthip Jiadkong
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Anisa Nazera Fauzia
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan; Department of Biology, Faculty of Science and Technology, Universitas Islam Negeri Sunan Kalijaga Yogyakarta, Jl. Laksda Adisucipto, Yogyakarta 55281, Indonesia
| | - Nobuo Yamaguchi
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Akihiro Ueda
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan.
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2
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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3
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Campomenosi P, Mortara L, Bassani B, Valli R, Porta G, Bruno A, Acquati F. The Potential Role of the T2 Ribonucleases in TME-Based Cancer Therapy. Biomedicines 2023; 11:2160. [PMID: 37626657 PMCID: PMC10452627 DOI: 10.3390/biomedicines11082160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
In recent years, there has been a growing interest in developing innovative anticancer therapies targeting the tumor microenvironment (TME). The TME is a complex and dynamic milieu surrounding the tumor mass, consisting of various cellular and molecular components, including those from the host organism, endowed with the ability to significantly influence cancer development and progression. Processes such as angiogenesis, immune evasion, and metastasis are crucial targets in the search for novel anticancer drugs. Thus, identifying molecules with "multi-tasking" properties that can counteract cancer cell growth at multiple levels represents a relevant but still unmet clinical need. Extensive research over the past two decades has revealed a consistent anticancer activity for several members of the T2 ribonuclease family, found in evolutionarily distant species. Initially, it was believed that T2 ribonucleases mainly acted as anticancer agents in a cell-autonomous manner. However, further investigation uncovered a complex and independent mechanism of action that operates at a non-cell-autonomous level, affecting crucial processes in TME-induced tumor growth, such as angiogenesis, evasion of immune surveillance, and immune cell polarization. Here, we review and discuss the remarkable properties of ribonucleases from the T2 family in the context of "multilevel" oncosuppression acting on the TME.
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Affiliation(s)
- Paola Campomenosi
- Laboratory of Molecular Genetics, Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy;
- Genomic Medicine Research Center, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (R.V.); (G.P.)
| | - Lorenzo Mortara
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, Via Monte Generoso 71, 21100 Varese, Italy;
| | - Barbara Bassani
- Laboratory of Innate Immunity, Unit of Molecular Pathology, Biochemistry, and Immunology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via G. Fantoli 16/15, 20138 Milan, Italy;
| | - Roberto Valli
- Genomic Medicine Research Center, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (R.V.); (G.P.)
- Department of Medicine and Surgery, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Giovanni Porta
- Genomic Medicine Research Center, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (R.V.); (G.P.)
- Department of Medicine and Surgery, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Antonino Bruno
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, Via Monte Generoso 71, 21100 Varese, Italy;
- Laboratory of Innate Immunity, Unit of Molecular Pathology, Biochemistry, and Immunology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via G. Fantoli 16/15, 20138 Milan, Italy;
| | - Francesco Acquati
- Genomic Medicine Research Center, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (R.V.); (G.P.)
- Human Genetics Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
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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.
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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
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Chen W, Wan H, Liu F, Du H, Zhang C, Fan W, Zhu A. Rapid evolution of T2/S-RNase genes in Fragaria linked to multiple transitions from self-incompatibility to self-compatibility. PLANT DIVERSITY 2023; 45:219-228. [PMID: 37069931 PMCID: PMC10105083 DOI: 10.1016/j.pld.2022.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 04/23/2022] [Indexed: 06/18/2023]
Abstract
The T2/RNase gene family is widespread in eukaryotes, and particular members of this family play critical roles in the gametophytic self-incompatibility (GSI) system in plants. Wild diploid strawberry (Fragaria) species have diversified their sexual systems via self-incompatible and self-compatible traits, yet how these traits evolved in Fragaria remains elusive. By integrating the published and de novo assembled genomes and the newly generated RNA-seq data, members of the RNase T2 gene family were systematically identified in six Fragaria species, including three self-incompatible species (Fragaria nipponica, Fragaria nubicola, and Fragaria viridis) and three self-compatible species (Fragaria nilgerrensis, Fragaria vesca, and Fragaria iinumae). In total, 115 RNase T2 genes were identified in the six Fragaria genomes and can be classified into three classes (I-III) according to phylogenetic analysis. The identified RNase T2 genes could be divided into 22 homologous gene sets according to amino acid sequence similarity and phylogenetic and syntenic relationships. We found that extensive gene loss and pseudogenization coupled with small-scale duplications mainly accounted for variations in the RNase T2 gene numbers in Fragaria. Multiple copies of homologous genes were mainly generated from tandem and segmental duplication events. Furthermore, we newly identified five S-RNase genes in three self-incompatible Fragaria genomes, including two in F. nipponica, two in F. viridis, and one in F. nubicola, which fit for typical features of a pistil determinant, including highly pistil-specific expression, highly polymorphic proteins and alkaline isoelectric point (pI), while no S-RNase genes were found in all three self-compatible Fragaria species. Surprisingly, these T2/S-RNase genes contain at least one large intron (>10 kb). This study revealed that the rapid evolution of T2/S-RNase genes within the Fragaria genus could be associated with its sexual mode, and repeated evolution of the self-compatible traits in Fragaria was convergent via losses of S-RNase.
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Affiliation(s)
- Wu Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Wan
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Luo Z, Zhang Y, Tian C, Wang L, Zhao X, Liu Z, Wang L, Wang L, Zhao J, Wang J, Liu M. Genome-wide screening of the RNase T2 gene family and functional analyses in jujube (Ziziphus jujuba Mill.). BMC Genomics 2023; 24:80. [PMID: 36803656 PMCID: PMC9940439 DOI: 10.1186/s12864-023-09165-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Ribonuclease (RNase T2) plays crucial roles in plant evolution and breeding. However, there have been few studies on the RNase T2 gene family in Ziziphus jujuba Mill., one of important dried fruit tree species. Recently, the released sequences of the reference genome of jujube provide a good chance to perform genome-wide identification and characterization of ZjRNase gene family in the jujube. RESULTS In this study, we identified four members of RNase T2 in jujube distributed on three chromosomes and unassembled chromosomes. They all contained two conserved sites (CASI and CASII). Analysis of the phylogenetic relationships revealed that the RNase T2 genes in jujube could be divided into two groups: ZjRNase1 and ZjRNase2 belonged to class I, while ZjRNase3 and ZjRNase4 belonged to class II. Only ZjRNase1 and ZjRNase2 expression were shown by the jujube fruit transcriptome analysis. So ZjRNase1 and ZjRNase2 were selected functional verification by overexpression transformation of Arabidopsis. The overexpression of these two genes led to an approximately 50% reduction in seed number, which deserve further attention. Moreover, the leaves of the ZjRNase1 overexpression transgenic lines were curled and twisted. Overexpression of ZjRNase2 resulted in shortened and crisp siliques and the production of trichomes, and no seeds were produced. CONCLUSION In summary, these findings will provide new insights into the molecular mechanisms of low number of hybrid seeds in jujube and a reference for the future molecular breeding of jujube.
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Affiliation(s)
- Zhi Luo
- grid.274504.00000 0001 2291 4530College of Horticulture, Hebei Agricultural University, Baoding, 071001 China ,grid.274504.00000 0001 2291 4530Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Yu Zhang
- grid.274504.00000 0001 2291 4530College of Forestry, Hebei Agricultural University, Baoding, 071001 China
| | - Chunjiao Tian
- grid.274504.00000 0001 2291 4530College of Forestry, Hebei Agricultural University, Baoding, 071001 China
| | - Lihu Wang
- grid.412028.d0000 0004 1757 5708School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038 China
| | - Xuan Zhao
- grid.274504.00000 0001 2291 4530College of Horticulture, Hebei Agricultural University, Baoding, 071001 China ,grid.274504.00000 0001 2291 4530Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Zhiguo Liu
- grid.274504.00000 0001 2291 4530College of Horticulture, Hebei Agricultural University, Baoding, 071001 China ,grid.274504.00000 0001 2291 4530Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Lili Wang
- grid.274504.00000 0001 2291 4530College of Horticulture, Hebei Agricultural University, Baoding, 071001 China ,grid.274504.00000 0001 2291 4530Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Lixin Wang
- grid.274504.00000 0001 2291 4530College of Horticulture, Hebei Agricultural University, Baoding, 071001 China ,grid.274504.00000 0001 2291 4530Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, 071001, China.
| | - Jiurui Wang
- College of Forestry, Hebei Agricultural University, Baoding, 071001, China.
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding, 071001, China. .,Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071001, China.
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Wang C, Chen W, Aili M, Zhu L, Chen Y. tRNA-derived small RNAs in plant response to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1131977. [PMID: 36798699 PMCID: PMC9928184 DOI: 10.3389/fpls.2023.1131977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
tRNA-derived small RNAs (tsRNAs) represent a novel category of small non-coding RNAs and serve as a new regulator of gene expression at both transcriptional and post-transcriptional levels. Growing evidence indicates that tsRNAs can be induced by diverse stimuli and regulate stress-responsive target genes, allowing plants to adapt to unfavorable environments. Here, we discuss the latest developments about the biogenesis and classification of tsRNAs and highlight the expression regulation and potential function of tsRNAs in plant biotic and abiotic stress responses. Of note, we also collect useful bioinformatics tools and resources for tsRNAs study in plants. Finally, we propose current limitations and future directions for plant tsRNAs research. These recent discoveries have refined our understanding of whether and how tsRNAs enhance plant stress tolerance.
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Affiliation(s)
- Chaojun Wang
- Institute of Education Science, Leshan Normal University, Leshan, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Xinjiang Institute of Traditional Uyghur Medicine, Urumqi, China
| | - Maimaiti Aili
- Xinjiang Institute of Traditional Uyghur Medicine, Urumqi, China
| | - Lei Zhu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Chen
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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Li H, Schneider T, Tan Y, Zhang D. Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases. Protein Sci 2023; 32:e4531. [PMID: 36477982 PMCID: PMC9793965 DOI: 10.1002/pro.4531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Detection of homologous relationships among proteins and understanding their mechanisms of diversification are major topics in the fields of protein science, bioinformatics, and phylogenetics. Recent developments in sequence/profile-based and structural similarity-based methods have greatly facilitated the unification and classification of many protein families into superfamilies or folds, yet many proteins remain unclassified in current protein databases. As one of the three earliest identified RNases in biology, ribonuclease T2, also known as RNase I in Escherichia coli, RNase Rh in fungi, or S-RNase in plant, is thought to be an ancient RNase family due to its widespread distribution and distinct structure. In this study, we present evidence that RNase T2 represents a circularly permutated version of the BECR (Barnase-EndoU-Colicin E5/D-RelE) fold RNases. This subtle relationship cannot be detected by traditional methods such as sequence/profile-based comparisons, structure-similarity searches, and circular permutation detections. However, we were able to identify the structural similarity using rational reconstruction of a theoretical RNase T2 ancestor via a reverse circular permutation process, followed by structural modeling using AlphaFold2, and structural comparisons. This relationship is further supported by the fact that RNase T2 and other typical BECR RNases, namely Colicin D, RNase A, and BrnT, share similar catalytic site configurations, all involving an analogous set of conserved residues on the α0 helix and the β4 strand of the BECR fold. This study revealed a hidden root of RNase T2 in bacterial toxin systems and demonstrated that reconstruction and modeling of ancestral topology is an effective strategy to identify remote relationship between proteins.
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Affiliation(s)
- Huan Li
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
| | - Theresa Schneider
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
| | - Yongjun Tan
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
| | - Dapeng Zhang
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
- Program of Bioinformatics and Computational BiologySchool of Science and Engineering, Saint Louis UniversitySaint LouisMissouriUSA
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9
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Bartolo ND, Mortimer N, Manter MA, Sanchez N, Riley M, O'Malley TT, Hooker JM. Identification and Prioritization of PET Neuroimaging Targets for Microglial Phenotypes Associated with Microglial Activity in Alzheimer's Disease. ACS Chem Neurosci 2022; 13:3641-3660. [PMID: 36473177 DOI: 10.1021/acschemneuro.2c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Activation of microglial cells accompanies the progression of many neurodegenerative disorders, including Alzheimer's disease (AD). Development of molecular imaging tools specific to microglia can help elucidate the mechanism through which microglia contribute to the pathogenesis and progression of neurodegenerative disorders. Through analysis of published genetic, transcriptomic, and proteomic data sets, we identified 19 genes with microglia-specific expression that we then ranked based on association with the AD characteristics, change in expression, and potential druggability of the target. We believe that the process we used to identify and rank microglia-specific genes is broadly applicable to the identification and evaluation of targets in other disease areas and for applications beyond molecular imaging.
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Affiliation(s)
- Nicole D Bartolo
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
| | - Niall Mortimer
- Human Biology and Data Science, Eisai Center for Genetics Guided Dementia Discovery, 35 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Mariah A Manter
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
| | - Nicholas Sanchez
- Human Biology and Data Science, Eisai Center for Genetics Guided Dementia Discovery, 35 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Misha Riley
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
| | - Tiernan T O'Malley
- Human Biology and Data Science, Eisai Center for Genetics Guided Dementia Discovery, 35 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jacob M Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
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10
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Thompson CE, Brisolara-Corrêa L, Thompson HN, Stassen H, de Freitas LB. Evolutionary and structural aspects of Solanaceae RNases T2. Genet Mol Biol 2022; 46:e20220115. [PMID: 36534953 PMCID: PMC9762611 DOI: 10.1590/1678-4685-gmb-2022-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/20/2022] [Indexed: 12/23/2022] Open
Abstract
Plant RNases T2 are involved in several physiological and developmental processes, including inorganic phosphate starvation, senescence, wounding, defense against pathogens, and the self-incompatibility system. Solanaceae RNases form three main clades, one composed exclusively of S-RNases and two that include S-like RNases. We identified several positively selected amino acids located in highly flexible regions of these molecules, mainly close to the B1 and B2 substrate-binding sites in S-like RNases and the hypervariable regions of S-RNases. These differences between S- and S-like RNases in the flexibility of amino acids in substrate-binding regions are essential to understand the RNA-binding process. For example, in the S-like RNase NT, two positively selected amino acid residues (Tyr156 and Asn134) are located at the most flexible sites on the molecular surface. RNase NT is induced in response to tobacco mosaic virus infection; these sites may thus be regions of interaction with pathogen proteins or viral RNA. Differential selective pressures acting on plant ribonucleases have increased amino acid variability and, consequently, structural differences within and among S-like RNases and S-RNases that seem to be essential for these proteins play different functions.
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Affiliation(s)
- Claudia Elizabeth Thompson
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Departamento de Farmacociências, Porto Alegre, RS, Brazil
| | - Lauís Brisolara-Corrêa
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Porto Alegre, RS, Brazil
| | - Helen Nathalia Thompson
- Universidade Federal do Rio Grande do Sul, Instituto de Química,
Departamento de Fisico-Química, Laboratório de Química Teórica e Computacional,
Porto Alegre, RS, Brazil
| | - Hubert Stassen
- Universidade Federal do Rio Grande do Sul, Instituto de Química,
Departamento de Fisico-Química, Laboratório de Química Teórica e Computacional,
Porto Alegre, RS, Brazil
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11
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Thakur P, Atway J, Limbach PA, Addepalli B. RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site. Int J Mol Sci 2022; 23:7021. [PMID: 35806025 PMCID: PMC9266746 DOI: 10.3390/ijms23137021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/05/2023] Open
Abstract
Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. Here, we detail the cleavage specificity and efficiency of ribonuclease MC1 and cusativin using a customized RNA sequence that contained all dinucleotide combinations and homopolymer sequences. The sequencing of the oligonucleotide digestion products by a semi-quantitative liquid chromatography coupled with mass spectrometry (LC-MS) analysis documented as little as 0.5-1% cleavage levels for a given dinucleotide sequence combination. While RNase MC1 efficiently cleaved the [A/U/C]pU dinucleotide bond, no cleavage was observed for the GpU bond. Similarly, cusativin efficiently cleaved Cp[U/A/G] dinucleotide combinations along with UpA and [A/U]pU, suggesting a broader specificity of dinucleotide preferences. The molecular interactions between the substrate and active site as determined by the dinucleotide docking studies of protein models offered additional evidence and support for the observed substrate specificity. Targeted alteration of the key amino acid residues in the nucleotide-binding site confirms the utility of this in silico approach for the identification of key interactions. Taken together, the use of bioanalytical and computational approaches, involving LC-MS and ligand docking of tertiary structural models, can form a powerful combination to help explain the RNA cleavage behavior of RNases.
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Affiliation(s)
| | | | | | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (P.T.); (J.A.); (P.A.L.)
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12
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Lv S, Qiao X, Zhang W, Li Q, Wang P, Zhang S, Wu J. The origin and evolution of RNase T2 family and gametophytic self-incompatibility system in plants. Genome Biol Evol 2022; 14:6609977. [PMID: 35714207 PMCID: PMC9250077 DOI: 10.1093/gbe/evac093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Ribonuclease (RNase) T2 genes are found widely in both eukaryotes and prokaryotes, and genes from this family have been revealed to have various functions in plants. In particular, S-RNase is known to be the female determinant in the S-RNase-based gametophytic self-incompatibility (GSI) system. However, the origin and evolution of the RNase T2 gene family and GSI system are not well understood. In this study, 785 RNase T2 genes were identified in 81 sequenced plant genomes representing broad-scale diversity and divided into three subgroups (Class I, II, and III) based on phylogenetic and synteny network analysis. Class I was found to be of ancient origin and to emerge in green algae, Class II was shown to originate with the appearance of angiosperms, while Class III was discovered to be eudicot-specific. Each of the three major classes could be further classified into several subclasses of which some subclasses were found to be lineage-specific. Furthermore, duplication, deletion, or inactivation of the S/S-like-locus was revealed to be linked to repeated loss and gain of self-incompatibility in different species from distantly related plant families with GSI. Finally, the origin and evolutionary history of S-locus in Rosaceae species was unraveled with independent loss and gain of S-RNase occurred in different subfamilies of Rosaceae. Our findings provide insights into the origin and evolution of the RNase T2 family and the GSI system in plants.
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Affiliation(s)
- Shouzheng Lv
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.,Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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13
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de Martin E, Schweizer M. Fifty Shades of Erns: Innate Immune Evasion by the Viral Endonucleases of All Pestivirus Species. Viruses 2022; 14:v14020265. [PMID: 35215858 PMCID: PMC8880635 DOI: 10.3390/v14020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
The genus Pestivirus, family Flaviviridae, includes four historically accepted species, i.e., bovine viral diarrhea virus (BVDV)-1 and -2, classical swine fever virus (CSFV), and border disease virus (BDV). A large number of new pestivirus species were identified in recent years. A common feature of most members is the presence of two unique proteins, Npro and Erns, that pestiviruses evolved to regulate the host’s innate immune response. In addition to its function as a structural envelope glycoprotein, Erns is also released in the extracellular space, where it is endocytosed by neighboring cells. As an endoribonuclease, Erns is able to cleave viral ss- and dsRNAs, thus preventing the stimulation of the host’s interferon (IFN) response. Here, we characterize the basic features of soluble Erns of a large variety of classified and unassigned pestiviruses that have not yet been described. Its ability to form homodimers, its RNase activity, and the ability to inhibit dsRNA-induced IFN synthesis were investigated. Overall, we found large differences between the various Erns proteins that cannot be predicted solely based on their primary amino acid sequences, and that might be the consequence of different virus-host co-evolution histories. This provides valuable information to delineate the structure-function relationship of pestiviral endoribonucleases.
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Affiliation(s)
- Elena de Martin
- Institute of Virology and Immunology, Länggass-Str. 122, POB, CH-3001 Bern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, CH-3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Matthias Schweizer
- Institute of Virology and Immunology, Länggass-Str. 122, POB, CH-3001 Bern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, CH-3012 Bern, Switzerland
- Correspondence:
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14
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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.
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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
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15
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Kettwig M, Ternka K, Wendland K, Krüger DM, Zampar S, Schob C, Franz J, Aich A, Winkler A, Sakib MS, Kaurani L, Epple R, Werner HB, Hakroush S, Kitz J, Prinz M, Bartok E, Hartmann G, Schröder S, Rehling P, Henneke M, Boretius S, Alia A, Wirths O, Fischer A, Stadelmann C, Nessler S, Gärtner J. Interferon-driven brain phenotype in a mouse model of RNaseT2 deficient leukoencephalopathy. Nat Commun 2021; 12:6530. [PMID: 34764281 PMCID: PMC8586222 DOI: 10.1038/s41467-021-26880-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/14/2021] [Indexed: 12/13/2022] Open
Abstract
Infantile-onset RNaseT2 deficient leukoencephalopathy is characterised by cystic brain lesions, multifocal white matter alterations, cerebral atrophy, and severe psychomotor impairment. The phenotype is similar to congenital cytomegalovirus brain infection and overlaps with type I interferonopathies, suggesting a role for innate immunity in its pathophysiology. To date, pathophysiological studies have been hindered by the lack of mouse models recapitulating the neuroinflammatory encephalopathy found in patients. In this study, we generated Rnaset2-/- mice using CRISPR/Cas9-mediated genome editing. Rnaset2-/- mice demonstrate upregulation of interferon-stimulated genes and concurrent IFNAR1-dependent neuroinflammation, with infiltration of CD8+ effector memory T cells and inflammatory monocytes into the grey and white matter. Single nuclei RNA sequencing reveals homeostatic dysfunctions in glial cells and neurons and provide important insights into the mechanisms of hippocampal-accentuated brain atrophy and cognitive impairment. The Rnaset2-/- mice may allow the study of CNS damage associated with RNaseT2 deficiency and may be used for the investigation of potential therapies.
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Affiliation(s)
- Matthias Kettwig
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany.
| | - Katharina Ternka
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Kristin Wendland
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Dennis Manfred Krüger
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Silvia Zampar
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Charlotte Schob
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Jonas Franz
- Institute of Neuropathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
- Campus Institute for Dynamics of Biological Networks, University of Göttingen, Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Anne Winkler
- Institute of Neuropathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - M Sadman Sakib
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Lalit Kaurani
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Robert Epple
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Hauke B Werner
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Samy Hakroush
- Institute of Pathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Julia Kitz
- Institute of Pathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Bartok
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Bonn, Germany
- Unit of Experimental Immunology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Bonn, Germany
| | - Simone Schröder
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Marco Henneke
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Susann Boretius
- Functional Imaging Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - A Alia
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Oliver Wirths
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Christine Stadelmann
- Institute of Neuropathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Stefan Nessler
- Institute of Neuropathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
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16
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Gu H, Lian B, Yuan Y, Kong C, Li Y, Liu C, Qi Y. A 5' tRNA-Ala-derived small RNA regulates anti-fungal defense in plants. SCIENCE CHINA-LIFE SCIENCES 2021; 65:1-15. [PMID: 34705222 DOI: 10.1007/s11427-021-2017-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022]
Abstract
Apart from their primordial role in protein synthesis, tRNAs can be cleaved to produce tRNA-derived small RNAs (tsRNAs). The biological functions of tsRNAs in plants remain largely unknown. In this study, we developed RtcB ligation-based small RNA (sRNA) sequencing, a method that captures and distinguishes between 3'-2',3'-cyclic-phosphate (cP)/phosphate (P)-terminated sRNAs and 3'-OH-terminated sRNAs, and profiled 5' tsRNAs and 5' tRNA halves in Arabidopsis thaliana. We found that Arabidopsis 5' tsRNAs and 5' tRNA halves predominantly contain a cP at the 3' end and require S-like RNase 1 (RNS1) and RNS3 for their production. One of the most abundant 5' tsRNAs, 5' tsR-Ala, by associating with AGO1, negatively regulates Cytochrome P450 71A13 (CYP71A13) expression and camalexin biosynthesis to repress anti-fungal defense. Interestingly, 5' tsR-Ala is downregulated upon fungal infection. Our study provides a global view of 5' tsRNAs and 5' tRNA halves in Arabidopsis and unravels an important role of a 5' tsRNA in regulating anti-fungal defense.
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Affiliation(s)
- Hanqing Gu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bi Lian
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuxiang Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ci Kong
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chang Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
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17
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Grünberg S, Coxam B, Chen TH, Dai N, Saleh L, Corrêa IR, Nichols NM, Yigit E. E. coli RNase I exhibits a strong Ca2+-dependent inherent double-stranded RNase activity. Nucleic Acids Res 2021; 49:5265-5277. [PMID: 33885787 PMCID: PMC8136782 DOI: 10.1093/nar/gkab284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/20/2021] [Accepted: 04/08/2021] [Indexed: 01/23/2023] Open
Abstract
Since its initial characterization, Escherichia coli RNase I has been described as a single-strand specific RNA endonuclease that cleaves its substrate in a largely sequence independent manner. Here, we describe a strong calcium (Ca2+)-dependent activity of RNase I on double-stranded RNA (dsRNA), and a Ca2+-dependent novel hybridase activity, digesting the RNA strand in a DNA:RNA hybrid. Surprisingly, Ca2+ does not affect the activity of RNase I on single stranded RNA (ssRNA), suggesting a specific role for Ca2+ in the modulation of RNase I activity. Mutation of a previously overlooked Ca2+ binding site on RNase I resulted in a gain-of-function enzyme that is highly active on dsRNA and could no longer be stimulated by the metal. In summary, our data imply that native RNase I contains a bound Ca2+, allowing it to target both single- and double-stranded RNAs, thus having a broader substrate specificity than originally proposed for this traditional enzyme. In addition, the finding that the dsRNase activity, and not the ssRNase activity, is associated with the Ca2+-dependency of RNase I may be useful as a tool in applied molecular biology.
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Affiliation(s)
| | - Baptiste Coxam
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Tien-Hao Chen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Lana Saleh
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Nicole M Nichols
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Erbay Yigit
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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18
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Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides. Sci Rep 2021; 11:6900. [PMID: 33767357 PMCID: PMC7994793 DOI: 10.1038/s41598-021-86337-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/11/2021] [Indexed: 11/13/2022] Open
Abstract
The 2′,3′-cycling ribonuclease (RNase) genes are catalysts of RNA cleavage and include the RNase T2 gene family. RNase T2 genes perform important roles in plants and have been conserved in the genome of eukaryotic organisms. In this study we identified 21 EURNS genes in Eucommia ulmoides Oliver (E. ulmoides) and analyzed their structure, chromosomal location, phylogenetic tree, gene duplication, stress-related cis-elements, and expression patterns in different tissues. The length of 21 predicted EURNS proteins ranged from 143 to 374 amino acids (aa), their molecular weight (MW) ranged from 16.21 to 42.38 kDa, and their isoelectric point (PI) value ranged from 5.08 to 9.09. Two classifications (class I and class III) were obtained from the conserved domains analysis and phylogenetic tree. EURNS proteins contained a total of 15 motifs. Motif 1, motif 2, motif 3, and motif 7 were distributed in multiple sequences and were similar to the conserved domain of RNase T2. EURNS genes with similar structure and the predicted EURNS proteins with conserved motif compositions are in the same group in the phylogenetic tree. The results of RT-PCR and transcription data showed that EURNS genes have tissue-specific expression and exhibited obvious trends in different developmental stages. Gene duplication analysis results indicated that segment duplication may be the dominant duplication mode in this gene family. This study provides a theoretical basis for research on the RNase T2 gene family and lays a foundation for the further study of EURNS genes.
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19
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Arai N, Ohno Y, Jumyo S, Hamaji Y, Ohyama T. Organ-specific expression and epigenetic traits of genes encoding digestive enzymes in the lance-leaf sundew (Drosera adelae). JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1946-1961. [PMID: 33247920 PMCID: PMC7921302 DOI: 10.1093/jxb/eraa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/25/2020] [Indexed: 05/16/2023]
Abstract
Over the last two decades, extensive studies have been performed at the molecular level to understand the evolution of carnivorous plants. As fruits, the repertoire of protein components in the digestive fluids of several carnivorous plants have gradually become clear. However, the quantitative aspects of these proteins and the expression mechanisms of the genes that encode them are still poorly understood. In this study, using the Australian sundew Drosera adelae, we identified and quantified the digestive fluid proteins. We examined the expression and methylation status of the genes corresponding to major hydrolytic enzymes in various organs; these included thaumatin-like protein, S-like RNase, cysteine protease, class I chitinase, β-1, 3-glucanase, and hevein-like protein. The genes encoding these proteins were exclusively expressed in the glandular tentacles. Furthermore, the promoters of the β-1, 3-glucanase and cysteine protease genes were demethylated only in the glandular tentacles, similar to the previously reported case of the S-like RNase gene da-I. This phenomenon correlated with high expression of the DNA demethylase DEMETER in the glandular tentacles, strongly suggesting that it performs glandular tentacle-specific demethylation of the genes. The current study strengthens and generalizes the relevance of epigenetics to trap organ-specific gene expression in D. adelae. We also suggest similarities between the trap organs of carnivorous plants and the roots of non-carnivorous plants.
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Affiliation(s)
- Naoki Arai
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Ohno
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Shinya Jumyo
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Hamaji
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, Japan
- Correspondence:
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20
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Baranzini N, Pulze L, Reguzzoni M, Roncoroni R, Orlandi VT, Tettamanti G, Acquati F, Grimaldi A. 3D Reconstruction of HvRNASET2 Molecule to Understand Its Antibacterial Role. Int J Mol Sci 2020; 21:E9722. [PMID: 33352806 PMCID: PMC7767213 DOI: 10.3390/ijms21249722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Recent studies performed on the invertebrate model Hirudo verbana (medicinal leech) suggest that the T2 ribonucleic enzyme HvRNASET2 modulates the leech's innate immune response, promoting microbial agglutination and supporting phagocytic cells recruitment in challenged tissues. Indeed, following injection of both lipoteichoic acid (LTA) and Staphylococcus aureus in the leech body wall, HvRNASET2 is expressed by leech type I granulocytes and induces bacterial aggregation to aid macrophage phagocytosis. Here, we investigate the HvRNASET2 antimicrobial role, in particular assessing the effects on the Gram-negative bacteria Escherichia coli. For this purpose, starting from the three-dimensional molecule reconstruction and in silico analyses, the antibacterial activity was evaluated both in vitro and in vivo. The changes induced in treated bacteria, such as agglutination and alteration in wall integrity, were observed by means of light, transmission and scanning electron microscopy. Moreover, immunogold, AMPs (antimicrobial peptides) and lipopolysaccharide (LPS) binding assays were carried out to evaluate HvRNASET2 interaction with the microbial envelopes and the ensuing ability to affect microbial viability. Finally, in vivo experiments confirmed that HvRNASET2 promotes a more rapid phagocytosis of bacterial aggregates by macrophages, representing a novel molecule for counteracting pathogen infections and developing alternative solutions to improve human health.
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Affiliation(s)
- Nicolò Baranzini
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Laura Pulze
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy;
| | - Rossella Roncoroni
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Viviana Teresa Orlandi
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Francesco Acquati
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
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21
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Gho YS, Choi H, Moon S, Song MY, Park HE, Kim DH, Ha SH, Jung KH. Phosphate-Starvation-Inducible S-Like RNase Genes in Rice Are Involved in Phosphate Source Recycling by RNA Decay. FRONTIERS IN PLANT SCIENCE 2020; 11:585561. [PMID: 33424882 PMCID: PMC7793952 DOI: 10.3389/fpls.2020.585561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/02/2020] [Indexed: 05/16/2023]
Abstract
The fine-tuning of inorganic phosphate (Pi) for enhanced use efficiency has long been a challenging subject in agriculture, particularly in regard to rice as a major crop plant. Among ribonucleases (RNases), the RNase T2 family is broadly distributed across kingdoms, but little has been known on its substrate specificity compared to RNase A and RNase T1 families. Class I and class II of the RNase T2 family are defined as the S-like RNase (RNS) family and have showed the connection to Pi recycling in Arabidopsis. In this study, we first carried out a phylogenetic analysis of eight rice and five Arabidopsis RNS genes and identified mono-specific class I and dicot-specific class I RNS genes, suggesting the possibility of functional diversity between class I RNS family members in monocot and dicot species through evolution. We then compared the in silico expression patterns of all RNS genes in rice and Arabidopsis under normal and Pi-deficient conditions and further confirmed the expression patterns of rice RNS genes via qRT-PCR analysis. Subsequently, we found that most of the OsRNS genes were differentially regulated under Pi-deficient treatment. Association of Pi recycling by RNase activity in rice was confirmed by measuring total RNA concentration and ribonuclease activity of shoot and root samples under Pi-sufficient or Pi-deficient treatment during 21 days. The total RNA concentrations were decreased by < 60% in shoots and < 80% in roots under Pi starvation, respectively, while ribonuclease activity increased correspondingly. We further elucidate the signaling pathway of Pi starvation through upregulation of the OsRNS genes. The 2-kb promoter region of all OsRNS genes with inducible expression patterns under Pi deficiency contains a high frequency of P1BS cis-acting regulatory element (CRE) known as the OsPHR2 binding site, suggesting that the OsRNS family is likely to be controlled by OsPHR2. Finally, the dynamic transcriptional regulation of OsRNS genes by overexpression of OsPHR2, ospho2 mutant, and overexpression of OsPT1 lines involved in Pi signaling pathway suggests the molecular basis of OsRNS family in Pi recycling via RNA decay under Pi starvation.
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Affiliation(s)
- Yun-Shil Gho
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Heebak Choi
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Sunok Moon
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Min Yeong Song
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Ha Eun Park
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Doh-Hoon Kim
- Department of Life Science, College of Life Science and Natural Resources, Dong-A University, Busan, South Korea
| | - Sun-Hwa Ha
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
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22
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Mukherjee D, Gupta S, Ghosh A, Ghosh A. Ustilago maydis secreted T2 ribonucleases, Nuc1 and Nuc2 scavenge extracellular RNA. Cell Microbiol 2020; 22:e13256. [PMID: 32844528 DOI: 10.1111/cmi.13256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022]
Abstract
Ustilago maydis genome codes for many secreted ribonucleases. The contribution of two among these belonging to the T2 family (Nuc1 and Nuc2) in the pathogen virulence, has been assessed in this study. The nuc1 and nuc2 deletion mutants showed not only reduced pathogenicity compared to the SG200 WT strain but also exhibited significant delay in the completion of the pathogenic lifecycle. Both the proteins were also tested for their nucleolytic activities towards RNA substrates from maize and yeast. This also yielded valuable insights into the ability of the ribonucleases to utilise extracellular RNA as a nutrient source. Our study therefore established a role of two T2 type secreted ribonucleases of a phytopathogen in the acquisition of nutrient for the first time. This study also provides evidence that maize apoplast contains RNA, which can be utilised as a substrate by both Nuc1 and Nuc2.
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Affiliation(s)
- Dibya Mukherjee
- Division of Plant Biology, Bose Institute Centenary Campus, Kolkata, India
| | - Sayandeep Gupta
- Department of Biochemistry, Bose Institute Centenary Campus, Kolkata, India
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute Centenary Campus, Kolkata, India
| | - Anupama Ghosh
- Division of Plant Biology, Bose Institute Centenary Campus, Kolkata, India
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23
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Wu L, Xu Y, Zhao H, Li Y. RNase T2 in Inflammation and Cancer: Immunological and Biological Views. Front Immunol 2020; 11:1554. [PMID: 32903619 PMCID: PMC7438567 DOI: 10.3389/fimmu.2020.01554] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/12/2020] [Indexed: 01/13/2023] Open
Abstract
The RNase T2 family consists of evolutionarily conserved endonucleases that express in many different species, including animals, plants, protozoans, bacteria, and viruses. The main biological roles of these ribonucleases are cleaving or degrading RNA substrates. They preferentially cleave single-stranded RNA molecules between purine and uridine residues to generate two nucleotide fragments with 2'3'-cyclic phosphate adenosine/guanosine terminus and uridine residue, respectively. Accumulating studies have revealed that RNase T2 is critical for the pathophysiology of inflammation and cancer. In this review, we introduce the distribution, structure, and functions of RNase T2, its differential roles in inflammation and cancer, and the perspective for its research and related applications in medicine.
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Affiliation(s)
- Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China.,Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yanquan Xu
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Huakan Zhao
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China.,Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China.,Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, China
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24
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Rolland C, La Scola B, Levasseur A. How Tupanvirus Degrades the Ribosomal RNA of Its Amoebal Host? The Ribonuclease T2 Track. Front Microbiol 2020; 11:1691. [PMID: 32849355 PMCID: PMC7399046 DOI: 10.3389/fmicb.2020.01691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
Tupanviruses are giant viruses recently discovered in Brazil from extreme environments: Tupanvirus soda lake (TPV-SL) and Tupanvirus deep ocean (TPV-DO). Unexpected features in Tupanviruses is the cytotoxic effect observed during infection, where the virus degrades the ribosomal RNA (rRNA) of its amoebal host. Interestingly, only TPV-SL causes this rRNA shutdown. We performed a genomic comparison of the two strains to determine potential modifications explaining the absence of rRNA degradation by TPV-DO. Whole genome comparisons were performed as well as more in-depth analysis at the gene level. We also calculated selective pressure on the orthologous genes between the two viruses. Our computational and evolutionary investigations revealed a potential target: a ribonuclease T2. These enzymes are known to be involved in cellular RNA catabolism such as in lysosomal degradation of rRNA. Our results suggest a functional ribonuclease localized in acid compartment closely related to ribonuclease T2 from eukaryotes. Silencing of the RNAse T2 gene of TPV-SL abolished its rRNA shutdown ability thereby correlating in silico assumption to the experimental evidence. In conclusion, all our results pointed to RNAse T2 as a target for explaining the difference for rRNA degradation ability between both strains.
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Affiliation(s)
- Clara Rolland
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Institut Universitaire de France, Paris, France
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25
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Singh NK, Paz E, Kutsher Y, Reuveni M, Lers A. Tomato T2 ribonuclease LE is involved in the response to pathogens. MOLECULAR PLANT PATHOLOGY 2020; 21:895-906. [PMID: 32352631 PMCID: PMC7280031 DOI: 10.1111/mpp.12928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/05/2020] [Accepted: 02/15/2020] [Indexed: 05/16/2023]
Abstract
T2 ribonucleases (RNases) are RNA-degrading enzymes that function in various cellular processes, mostly via RNA metabolism. T2 RNase-encoding genes have been identified in various organisms, from bacteria to mammals, and are most diverse in plants. The existence of T2 RNase genes in almost every organism suggests an important biological function that has been conserved through evolution. In plants, T2 RNases are suggested to be involved in phosphate scavenging and recycling, and are implicated in defence responses to pathogens. We investigated the function of the tomato T2 RNase LE, known to be induced by phosphate deficiency and wounding. The possible involvement of LE in pathogen responses was examined. Expression analysis showed LE induction during fungal infection and by stimuli known to be associated with pathogen inoculation, including oxalic acid and hydrogen peroxide. Analysis of LE-suppressed transgenic tomato lines revealed higher susceptibility to oxalic acid, a cell death-inducing factor, compared to the wild type. This elevated sensitivity of LE-suppressed lines was evidenced by visual signs of necrosis, and increased ion leakage and reactive oxygen species levels, indicating acceleration of cell death. Challenge of the LE-suppressed lines with the necrotrophic pathogen Botrytis cinerea resulted in accelerated development of disease symptoms compared to the wild type, associated with suppressed expression of pathogenesis-related marker genes. The results suggest a role for plant endogenous T2 RNases in antifungal activity.
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Affiliation(s)
- Naveen Kumar Singh
- Department of Postharvest Science, Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
| | - Einat Paz
- Department of Postharvest Science, Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
- The Robert H. Smith Faculty of Agricultural, Food and Environment SciencesHebrew University of JerusalemRehovotIsrael
| | - Yaarit Kutsher
- Plant Science Institute, the Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
| | - Moshe Reuveni
- Plant Science Institute, the Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
| | - Amnon Lers
- Department of Postharvest Science, Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
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26
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Weber T, Schlotawa L, Dosch R, Hamilton N, Kaiser J, Schiller S, Wenske B, Gärtner J, Henneke M. Zebrafish disease model of human RNASET2-deficient cystic leukoencephalopathy displays abnormalities in early microglia. Biol Open 2020; 9:bio049239. [PMID: 32295832 PMCID: PMC7225086 DOI: 10.1242/bio.049239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/02/2020] [Indexed: 12/14/2022] Open
Abstract
Human infantile-onset RNASET2-deficient cystic leukoencephalopathy is a Mendelian mimic of in utero cytomegalovirus brain infection with prenatally developing inflammatory brain lesions. We used an RNASET2-deficient zebrafish model to elucidate the underlying disease mechanisms. Mutant and wild-type zebrafish larvae brain development between 2 and 5 days post fertilization (dpf) was examined by confocal live imaging in fluorescent reporter lines of the major types of brain cells. In contrast to wild-type brains, RNASET2-deficient larvae displayed increased numbers of microglia with altered morphology, often containing inclusions of neurons. Furthermore, lysosomes within distinct populations of the myeloid cell lineage including microglia showed increased lysosomal staining. Neurons and oligodendrocyte precursor cells remained unaffected. This study provides a first look into the prenatal onset pathomechanisms of human RNASET2-deficient leukoencephalopathy, linking this inborn lysosomal disease to the innate immune system and other immune-related childhood encephalopathies like Aicardi-Goutières syndrome (AGS).
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Affiliation(s)
- Thomas Weber
- Department of Pediatrics and Adolescent Medicine, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
| | - Lars Schlotawa
- Department of Pediatrics and Adolescent Medicine, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
| | - Roland Dosch
- Department of Human Genetics, University Medical Center Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Noémie Hamilton
- The Bateson Centre, University of Sheffield, Firth Court D31, Sheffield S10 2PT, United Kingdom
| | - Jens Kaiser
- Department of Pediatrics and Adolescent Medicine, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
| | - Stina Schiller
- Department of Pediatrics and Adolescent Medicine, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
| | - Britta Wenske
- Department of Haematology and Oncology, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
| | - Marco Henneke
- Department of Pediatrics and Adolescent Medicine, University Medical Center Goettingen, Robert- Koch- Str. 40, 37075 Goettingen, Germany
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27
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Baranzini N, De Vito A, Orlandi VT, Reguzzoni M, Monti L, de Eguileor M, Rosini E, Pollegioni L, Tettamanti G, Acquati F, Grimaldi A. Antimicrobial Role of RNASET2 Protein During Innate Immune Response in the Medicinal Leech Hirudo verbana. Front Immunol 2020; 11:370. [PMID: 32210967 PMCID: PMC7068815 DOI: 10.3389/fimmu.2020.00370] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/17/2020] [Indexed: 12/23/2022] Open
Abstract
The innate immune response represents a first-line defense against pathogen infection that has been widely conserved throughout evolution. Using the invertebrate Hirudo verbana (Annelida, Hirudinea) as an experimental model, we show here that the RNASET2 ribonuclease is directly involved in the immune response against Gram-positive bacteria. Injection of lipoteichoic acid (LTA), a key component of Gram-positive bacteria cell wall, into the leech body wall induced a massive migration of granulocytes and macrophages expressing TLR2 (the key receptor involved in the response to Gram-positive bacteria) toward the challenged/inoculated area. We hypothesized that the endogenous leech RNASET2 protein (HvRNASET2) might be involved in the antimicrobial response, as already described for other vertebrate ribonucleases, such as RNase3 and RNase7. In support of our hypothesis, HvRNASET2 was mainly localized in the granules of granulocytes, and its release in the extracellular matrix triggered the recruitment of macrophages toward the area stimulated with LTA. The activity of HvRNASET2 was also evaluated on Staphylococcus aureus living cells by means of light, transmission, and scanning electron microscopy analysis. HvRNASET2 injection triggered the formation of S. aureus clumps following a direct interaction with the bacterial cell wall, as demonstrated by immunogold assay. Taken together, our data support the notion that, during the early phase of leech immune response, granulocyte-released HvRNASET2 triggers bacterial clumps formation and, at the same time, actively recruits phagocytic macrophages in order to elicit a rapid and effective eradication of the infecting microorganisms from inoculated area.
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Affiliation(s)
- Nicolò Baranzini
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Annarosaria De Vito
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | | | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Laura Monti
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Magda de Eguileor
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Francesco Acquati
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
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28
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Diaz-Baena M, Galvez-Valdivieso G, Delgado-Garcia E, Pineda M, Piedras P. Nuclease and ribonuclease activities in response to salt stress: Identification of PvRNS3, a T2/S-like ribonuclease induced in common bean radicles by salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:235-241. [PMID: 31881432 DOI: 10.1016/j.plaphy.2019.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 05/28/2023]
Abstract
The increase in soil salinization due to global climate change could cause large losses in crop productivity affecting, among other biological processes, to germination and seedling development. We have studied how salt stress affects nucleic acid degrading activities in radicles of common bean during seedling development. In radicles of common bean, a main nuclease of 37 kDa and two ribonucleases of 17 and 19 kDa were detected. Saline stress did not alter these three activities but induced a new ribonuclease of 16 kDa. All three ribonucleases are acidic enzymes that were inhibited by Zn. The 16 and 17 kDa ribonucleases are inhibited by guanilates. In the genome of common bean, we have identified 13 genes belonging to the T2 ribonuclease family and that are grouped in the 3 classes of T2 ribonucleases. The analysis of the expression of the 3 genes belonging to Class I (PvRNS1 to 3) and the unique gene from Class II (PvRNS4) in radicles showed that PvRNS3 is highly induced under salt stress.
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Affiliation(s)
- Mercedes Diaz-Baena
- Departamento de Botánica, Ecología y Fisiología Vegetal, Plants Molecular Physiology and Biotechnology Group, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Gregorio Galvez-Valdivieso
- Departamento de Botánica, Ecología y Fisiología Vegetal, Plants Molecular Physiology and Biotechnology Group, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Elena Delgado-Garcia
- Departamento de Botánica, Ecología y Fisiología Vegetal, Plants Molecular Physiology and Biotechnology Group, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Manuel Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal, Plants Molecular Physiology and Biotechnology Group, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Pedro Piedras
- Departamento de Botánica, Ecología y Fisiología Vegetal, Plants Molecular Physiology and Biotechnology Group, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain.
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29
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Megel C, Hummel G, Lalande S, Ubrig E, Cognat V, Morelle G, Salinas-Giegé T, Duchêne AM, Maréchal-Drouard L. Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis. Nucleic Acids Res 2019; 47:941-952. [PMID: 30462257 PMCID: PMC6344867 DOI: 10.1093/nar/gky1156] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
RNA fragments deriving from tRNAs (tRFs) exist in all branches of life and the repertoire of their biological functions regularly increases. Paradoxically, their biogenesis remains unclear. The human RNase A, Angiogenin, and the yeast RNase T2, Rny1p, generate long tRFs after cleavage in the anticodon region. The production of short tRFs after cleavage in the D or T regions is still enigmatic. Here, we show that the Arabidopsis Dicer-like proteins, DCL1-4, do not play a major role in the production of tRFs. Rather, we demonstrate that the Arabidopsis RNases T2, called RNS, are key players of both long and short tRFs biogenesis. Arabidopsis RNS show specific expression profiles. In particular, RNS1 and RNS3 are mainly found in the outer tissues of senescing seeds where they are the main endoribonucleases responsible of tRNA cleavage activity for tRFs production. In plants grown under phosphate starvation conditions, the induction of RNS1 is correlated with the accumulation of specific tRFs. Beyond plants, we also provide evidence that short tRFs can be produced by the yeast Rny1p and that, in vitro, human RNase T2 is also able to generate long and short tRFs. Our data suggest an evolutionary conserved feature of these enzymes in eukaryotes.
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Affiliation(s)
- Cyrille Megel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Stéphanie Lalande
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Geoffrey Morelle
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Anne-Marie Duchêne
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Laurence Maréchal-Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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30
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Ou J, Peng Y, Yang W, Zhang Y, Hao J, Li F, Chen Y, Zhao Y, Xie X, Wu S, Zha L, Luo X, Xie G, Wang L, Sun W, Zhou Q, Li J, Liang H. ABHD5 blunts the sensitivity of colorectal cancer to fluorouracil via promoting autophagic uracil yield. Nat Commun 2019; 10:1078. [PMID: 30842415 PMCID: PMC6403256 DOI: 10.1038/s41467-019-08902-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 02/05/2019] [Indexed: 12/18/2022] Open
Abstract
The efficacy of Fluorouracil (FU) in the treatment of colorectal cancer (CRC) is greatly limited by drug resistance. Autophagy has been implicated in chemoresistance, but the role of selective autophagic degradation in regulating chemoresistance remains unknown. In this study, we revealed a critical role of ABHD5 in charging CRC sensitivity to FU via regulating autophagic uracil yield. We demonstrated that ABHD5 localizes to lysosome and interacts with PDIA5 to prevent PDIA5 from interacting with RNASET2 and inactivating RNASET2. ABHD5 deficiency releases PDIA5 to directly interact with RNASET2 and leave RNASET2 in an inactivate state, which impairs RNASET2-mediated autophagic uracil yield and promotes CRC cells to uptake FU as an exogenous uracil, thus increasing their sensitivity to FU. Our findings for the first time reveal a novel role of ABHD5 in regulating lysosome function, highlighting the significance of ABHD5 as a compelling biomarker predicting the sensitivity of CRCs to FU-based chemotherapy.
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Affiliation(s)
- Juanjuan Ou
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China.
| | - Yuan Peng
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Weiwen Yang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Yue Zhang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Jie Hao
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Fu Li
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Yanrong Chen
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Yang Zhao
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Xiong Xie
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Shuang Wu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Lin Zha
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Xi Luo
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Ganfeng Xie
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Wei Sun
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Qi Zhou
- Department of Oncology, Fuling Central Hospital, Chongqing, 408099, China
| | - Jianjun Li
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China.
| | - Houjie Liang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, China.
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31
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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.
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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
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32
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Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE. A planarian nidovirus expands the limits of RNA genome size. PLoS Pathog 2018; 14:e1007314. [PMID: 30383829 PMCID: PMC6211748 DOI: 10.1371/journal.ppat.1007314] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/02/2018] [Indexed: 12/28/2022] Open
Abstract
RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is in the 100–300 kb range. This large difference presents a daunting gap for the transition from primordial RNP to contemporary DNA-RNP-based life. Whether or not RNA viruses represent transitional steps towards DNA-based life, studies of larger RNA viruses advance our understanding of the size constraints on RNP entities and the role of genome size in virus adaptation. For example, emergence of the largest previously known RNA genomes (20–34 kb in positive-stranded nidoviruses, including coronaviruses) is associated with the acquisition of a proofreading exoribonuclease (ExoN) encoded in the open reading frame 1b (ORF1b) in a monophyletic subset of nidoviruses. However, apparent constraints on the size of ORF1b, which encodes this and other key replicative enzymes, have been hypothesized to limit further expansion of these viral RNA genomes. Here, we characterize a novel nidovirus (planarian secretory cell nidovirus; PSCNV) whose disproportionately large ORF1b-like region including unannotated domains, and overall 41.1-kb genome, substantially extend the presumed limits on RNA genome size. This genome encodes a predicted 13,556-aa polyprotein in an unconventional single ORF, yet retains canonical nidoviral genome organization and expression, as well as key replicative domains. These domains may include functionally relevant substitutions rarely or never before observed in highly conserved sites of RdRp, NiRAN, ExoN and 3CLpro. Our evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and acquired additional genes, including those typical of large DNA viruses or hosts, e.g. Ankyrin and Fibronectin type II, which might modulate virus-host interactions. PSCNV's greatly expanded genome, proteomic complexity, and unique features–impressive in themselves–attest to the likelihood of still-larger RNA genomes awaiting discovery. RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication. The upper genome size for such entities was assumed to be <35 kb; conversely, the minimal cellular DNA genome is in the 100–300 kilobase (kb) range. This large difference presents a daunting gap for the proposed evolution of contemporary DNA-RNP-based life from primordial RNP entities. Here, we describe a nidovirus from planarians, named planarian secretory cell nidovirus (PSCNV), whose 41.1 kb genome is 23% larger than any riboviral genome yet discovered. This increase is nearly equivalent in size to the entire poliovirus genome, and it equips PSCNV with an unprecedented extra coding capacity to adapt. PSCNV has broken apparent constraints on the size of the genomic subregion that encodes core replication machinery in other nidoviruses, including coronaviruses, and has acquired genes not previously observed in RNA viruses. This virus challenges and advances our understanding of the limits to RNA genome size.
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Affiliation(s)
- Amir Saberi
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Anastasia A. Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John L. Brubacher
- Department of Biology, Canadian Mennonite University, Winnipeg, Canada
| | - Phillip A. Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- * E-mail: (PAN); (AEG)
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (PAN); (AEG)
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33
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Sinkevicius KW, Morrison TR, Kulkarni P, Caffrey Cagliostro MK, Iriah S, Malmberg S, Sabrick J, Honeycutt JA, Askew KL, Trivedi M, Ferris CF. RNaseT2 knockout rats exhibit hippocampal neuropathology and deficits in memory. Dis Model Mech 2018; 11:dmm.032631. [PMID: 29752287 PMCID: PMC6031352 DOI: 10.1242/dmm.032631] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/30/2018] [Indexed: 12/29/2022] Open
Abstract
RNASET2 deficiency in humans is associated with infant cystic leukoencephalopathy, which causes psychomotor impairment, spasticity and epilepsy. A zebrafish mutant model suggests that loss of RNASET2 function leads to neurodegeneration due to the accumulation of non-degraded RNA in the lysosomes. The goal of this study was to characterize the first rodent model of RNASET2 deficiency. The brains of 3- and 12-month-old RNaseT2 knockout rats were studied using multiple magnetic resonance imaging modalities and behavioral tests. While T1- and T2-weighted images of RNaseT2 knockout rats exhibited no evidence of cystic lesions, the prefrontal cortex and hippocampal complex were enlarged in knockout animals. Diffusion-weighted imaging showed altered anisotropy and putative gray matter changes in the hippocampal complex of the RNaseT2 knockout rats. Immunohistochemistry for glial fibrillary acidic protein (GFAP) showed the presence of hippocampal neuroinflammation. Decreased levels of lysosome-associated membrane protein 2 (LAMP2) and elevated acid phosphatase and β-N-acetylglucosaminidase (NAG) activities indicated that the RNASET2 knockout rats likely had altered lysosomal function and potential defects in autophagy. Object recognition tests confirmed that RNaseT2 knockout rats exhibited memory deficits. However, the Barnes maze, and balance beam and rotarod tests indicated there were no differences in spatial memory or motor impairments, respectively. Overall, patients with RNASET2 deficiency exhibited a more severe neurodegeneration phenotype than was observed in the RNaseT2 knockout rats. However, the vulnerability of the knockout rat hippocampus as evidenced by neuroinflammation, altered lysosomal function and cognitive defects indicates that this is still a useful in vivo model to study RNASET2 function. Summary: The authors characterize a rodent model of RNaseT2 deficiency, which offers insight into the susceptibility of the hippocampus to early inflammation caused by lysosome impairment due to loss of RNaseT2 function.
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Affiliation(s)
| | - Thomas R Morrison
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Praveen Kulkarni
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Martha K Caffrey Cagliostro
- Division of Developmental Neuroscience, Department of Psychiatry, Columbia University, New York, NY 10032, USA
| | - Sade Iriah
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Samantha Malmberg
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Julia Sabrick
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Jennifer A Honeycutt
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Kim L Askew
- Preclinical Pharmacology, Alexion Pharmaceuticals, Lexington, MA 02421, USA
| | - Malav Trivedi
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Craig F Ferris
- Center for Translational Neuroimaging, Department of Psychology and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
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34
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Muslimov AR, Timin AS, Petrova AV, Epifanovskaya OS, Shakirova AI, Lepik KV, Gorshkov A, Il'inskaja EV, Vasin AV, Afanasyev BV, Fehse B, Sukhorukov GB. Mesenchymal Stem Cells Engineering: Microcapsules-Assisted Gene Transfection and Magnetic Cell Separation. ACS Biomater Sci Eng 2017; 3:2314-2324. [PMID: 33445290 DOI: 10.1021/acsbiomaterials.7b00482] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stem cell engineering-the manipulation and functionalization of stem cells involving genetic modification-can significantly expand their applicability for cell therapy in humans. Toward this aim, reliable, standardized, and cost-effective methods for cell manipulation are required. Here we explore the potential of magnetic multilayer capsules to serve as a universal platform for nonviral gene transfer, stem cell magnetization, and magnetic cell separation to improve gene transfer efficiency. In particular, the following experiments were performed: (i) a study of the process of internalization of magnetic capsules into stem cells, including capsule co-localization with established markers of endo-lysosomal pathway; (ii) characterization and quantification of capsule uptake with confocal microscopy, electron microscopy, and flow cytometry; (iii) intracellular delivery of messenger RNA and separation of gene-modified cells by magnetic cell sorting (MACS); and (iv) analysis of the influence of capsules on cell proliferation potential. Importantly, based on the internalization of magnetic capsules, transfected cells became susceptible to external magnetic fields, which made it easy to enrich gene-modified cells using MACS (purity ∼95%), and also to influence their migration behavior. In summary, our results underline the high potential of magnetic capsules in stem cell functionalization, namely (i) to increase gene-transfer efficiency and (ii) to facilitate enrichment and targeting of transfected cells. Finally, we did not observe a negative impact of the capsules used on the proliferative capacity of stem cells, proving their high biocompatibility.
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Affiliation(s)
- Albert R Muslimov
- First Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation.,Research Institute of Influenza, Popova str., 15/17, 197376 Saint-Petersburg, Russian Federation.,RASA center in St. Petersburg, Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation
| | - Alexander S Timin
- First Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation.,RASA Center in Tomsk, Tomsk Polytechnic University, pros. Lenina, 30, 634050 Tomsk, Russian Federation
| | - Aleksandra V Petrova
- Research Institute of Influenza, Popova str., 15/17, 197376 Saint-Petersburg, Russian Federation.,Department of Molecular Biology, Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation
| | - Olga S Epifanovskaya
- First Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation
| | - Alena I Shakirova
- First Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation
| | - Kirill V Lepik
- First Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation.,RASA center in St. Petersburg, Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation
| | - Andrey Gorshkov
- Research Institute of Influenza, Popova str., 15/17, 197376 Saint-Petersburg, Russian Federation
| | - Eugenia V Il'inskaja
- Research Institute of Influenza, Popova str., 15/17, 197376 Saint-Petersburg, Russian Federation
| | - Andrey V Vasin
- Research Institute of Influenza, Popova str., 15/17, 197376 Saint-Petersburg, Russian Federation.,Department of Molecular Biology, Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russian Federation
| | - Boris V Afanasyev
- First Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022 St. Petersburg, Russian Federation
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246, Martinistraße 52, 20251 Hamburg, Germany
| | - Gleb B Sukhorukov
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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35
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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.
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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
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36
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Liu P, Huang J, Zheng Q, Xie L, Lu X, Jin J, Wang G. Mammalian mitochondrial RNAs are degraded in the mitochondrial intermembrane space by RNASET2. Protein Cell 2017; 8:735-749. [PMID: 28730546 PMCID: PMC5636749 DOI: 10.1007/s13238-017-0448-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 10/28/2022] Open
Abstract
Mammalian mitochondrial genome encodes a small set of tRNAs, rRNAs, and mRNAs. The RNA synthesis process has been well characterized. How the RNAs are degraded, however, is poorly understood. It was long assumed that the degradation happens in the matrix where transcription and translation machineries reside. Here we show that contrary to the assumption, mammalian mitochondrial RNA degradation occurs in the mitochondrial intermembrane space (IMS) and the IMS-localized RNASET2 is the enzyme that degrades the RNAs. This provides a new paradigm for understanding mitochondrial RNA metabolism and transport.
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Affiliation(s)
- Peipei Liu
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinliang Huang
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qian Zheng
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Leiming Xie
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinping Lu
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Jin
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Geng Wang
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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37
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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.
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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.
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38
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Liang M, Yang W, Su S, Fu L, Yi H, Chen C, Deng X, Chai L. Genome-wide identification and functional analysis of S-RNase involved in the self-incompatibility of citrus. Mol Genet Genomics 2016; 292:325-341. [PMID: 27933381 DOI: 10.1007/s00438-016-1279-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 12/03/2016] [Indexed: 11/25/2022]
Abstract
S-RNase-based self-incompatibility is found in Solanaceae, Rosaceae, and Scrophulariaceae, and is the most widespread mechanism that prevents self-fertilization in plants. Although 'Shatian' pummelo (Citrus grandis), a traditional cultivated variety, possesses the self-incompatible trait, the role of S-RNases in the self-incompatibility of 'Shatian' pummelo is poorly understood. To identify genes associated with self-incompatibility in citrus, we identified 16 genes encoding homologs of ribonucleases in the genomes of sweet orange (Citrus sinensis) and clementine mandarin (Citrus clementine). We preliminarily distinguished S-RNases from S-like RNases with a phylogenetic analysis that classified these homologs into three groups, which is consistent with the previous reports. Expression analysis provided evidence that CsRNS1 and CsRNS6 are S-like RNase genes. The expression level of CsRNS1 was increased during fruit development. The expression of CsRNS6 was increased during the formation of embryogenic callus. In contrast, we found that CsRNS3 possessed several common characteristics of the pistil determinant of self-incompatibility: it has an alkaline isoelectric point (pI), harbors only one intron, and is specifically expressed in style. We obtained a cDNA encoding CgRNS3 from 'Shatian' pummelo and found that it is homolog to CsRNS3 and that CgRNS3 exhibited the same expression pattern as CsRNS3. In an in vitro culture system, the CgRNS3 protein significantly inhibited the growth of self-pollen tubes from 'Shatian' pummelo, but after a heat treatment, this protein did not significantly inhibit the elongation of self- or non-self-pollen tubes. In conclusion, an S-RNase gene, CgRNS3, was obtained by searching the genomes of sweet orange and clementine for genes exhibiting sequence similarity to ribonucleases followed by expression analyses. Using this approach, we identified a protein that significantly inhibited the growth of self-pollen tubes, which is the defining property of an S-RNase.
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Affiliation(s)
- Mei Liang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wei Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shiying Su
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Fu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hualin Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Chuanwu Chen
- Guangxi Academy of Specialty Crops, Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, 541004, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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39
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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.
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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
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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.
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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
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41
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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
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Hameş EE, Demir T. Microbial ribonucleases (RNases): production and application potential. World J Microbiol Biotechnol 2015; 31:1853-62. [PMID: 26433394 DOI: 10.1007/s11274-015-1945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/07/2015] [Indexed: 01/15/2023]
Abstract
Ribonuclease (RNase) is hydrolytic enzyme that catalyzes the cleavage of phosphodiester bonds in RNA. RNases play an important role in the metabolism of cellular RNAs, such as mRNA and rRNA or tRNA maturation. Besides their cellular roles, RNases possess biological activity, cell stimulating properties, cytotoxicity and genotoxicity. Cytotoxic effect of particular microbial RNases was comparable to that of animal derived counterparts. In this respect, microbial RNases have a therapeutic potential as anti-tumor drugs. The significant development of DNA vaccines and the progress of gene therapy trials increased the need for RNases in downstream processes. In addition, RNases are used in different fields, such as food industry for single cell protein preparations, and in some molecular biological studies for the synthesis of specific nucleotides, identifying RNA metabolism and the relationship between protein structure and function. In some cases, the use of bovine or other animal-derived RNases have increased the difficulties due to the safety and regulatory issues. Microbial RNases have promising potential mainly for pharmaceutical purposes as well as downstream processing. Therefore, an effort has been given to determination of optimum fermentation conditions to maximize RNase production from different bacterial and fungal producers. Also immobilization or strain development experiments have been carried out.
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Affiliation(s)
- E Esin Hameş
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Tuğçe Demir
- Department of Chemical Engineering, Kocaeli University, Umut Tepe Yerleşkesi, 41380, Kocaeli, Turkey
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43
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Nesiel-Nuttman L, Schwartz B, Shoseyov O. Human recombinant truncated RNASET2, devoid of RNase activity; A potential cancer therapeutic agent. Oncotarget 2015; 5:11464-78. [PMID: 25426551 PMCID: PMC4294338 DOI: 10.18632/oncotarget.2562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 10/01/2014] [Indexed: 01/16/2023] Open
Abstract
Human RNASET2 has been implicated in antitumorigenic and antiangiogenic activities, independent of its ribonuclease capacities. We constructed a truncated version of human RNASET2, starting at E50 (trT2-50) and devoid of ribonuclease activity. trT2-50 maintained its ability to bind actin and to inhibit angiogenesis and tumorigenesis. trT2-50 binds to cell surface actin and formed a complex with actin in vitro. The antiangiogenic effect of this protein was demonstrated in human umbilical vein endothelial cells (HUVECs) by its ability to arrest tube formation on Matrigel, induced by angiogenic factors. Immunofluorescence staining of HUVECs showed nuclear and cytosolic RNASET2 protein that was no longer detectable inside the cell following trT2-50 treatment. This effect was associated with disruption of the intracellular actin network. trT2-50 co-localized with angiogenin, suggesting that both molecules bind (or compete) for similar cellular epitopes. Moreover, trT2-50 led to a significant inhibition of tumor development. Histological analysis demonstrated abundant necrotic tissue and a substantial loss of endothelial structure in trT2-50-treated tumors. Collectively, the present results indicate that trT2-50, a molecule engineered to be deficient of its catalytic activity, still maintained its actin binding and anticancer-related biological activities. We therefore suggest that trT2-50 may serve as a potential cancer therapeutic agent.
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Affiliation(s)
- Liron Nesiel-Nuttman
- The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, ISRAEL
| | - Betty Schwartz
- School of Nutritional Sciences Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, ISRAEL
| | - Oded Shoseyov
- The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, ISRAEL
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Arai N, Nishimura E, Kikuchi Y, Ohyama T. Functional analyses of carnivorous plant-specific amino acid residues in S-like ribonucleases. Biochem Biophys Res Commun 2015; 465:108-12. [DOI: 10.1016/j.bbrc.2015.07.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
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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]
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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.
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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
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Human RNASET2 derivatives as potential anti-angiogenic agents: actin binding sequence identification and characterization. Oncoscience 2014; 2:31-43. [PMID: 25815360 PMCID: PMC4341462 DOI: 10.18632/oncoscience.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/26/2014] [Indexed: 02/02/2023] Open
Abstract
Human RNASET2 (hRNASET2) has been demonstrated to exert antiangiogenic and antitumorigenic effects independent of its ribonuclease capacity. We suggested that RNASET2 exerts its antiangiogenic and antitumorigenic activities via binding to actin and consequently inhibits cell motility. We focused herein on the identification of the actin binding site of hRNASET2 using defined sequences encountered within the whole hRNASET2 protein. For that purpose we designed 29 different hRNASET2-derived peptides. The 29 peptides were examined for their ability to bind immobilized actin. Two selected peptides-A103-Q159 consisting of 57 amino acids and peptide K108-K133 consisting of 26 amino acids were demonstrated to have the highest actin binding ability and concomitantly the most potent anti-angiogenic activity. Further analyses on the putative mechanisms associated with angiogenesis inhibition exerted by peptide K108-K133 involved its location during treatment within the HUVE cells. Peptide K108-K133 readily penetrates the cell membrane within 10 min of incubation. In addition, supplementation with angiogenin delays the entrance of peptide K108-K133 to the cell suggesting competition on the same cell internalization route. The peptide was demonstrated to co-localize with angiogenin, suggesting that both molecules bind analogous cellular epitopes, similar to our previously reported data for ACTIBIND and trT2-50.
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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.
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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)
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Zheng J, Wang Y, He Y, Zhou J, Li Y, Liu Q, Xie X. Overexpression of an S-like ribonuclease gene, OsRNS4, confers enhanced tolerance to high salinity and hyposensitivity to phytochrome-mediated light signals in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 214:99-105. [PMID: 24268167 DOI: 10.1016/j.plantsci.2013.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/26/2013] [Accepted: 10/05/2013] [Indexed: 05/15/2023]
Abstract
S-like ribonucleases (S-like RNases) are homologous to S-ribonucleases (S-RNases), but are not involved in self-incompatibility. In dicotyledonous plants, S-like RNases play an important role in phosphate recycling during senescence and are induced by inorganic phosphate-starvation and in response to defense and mechanical wounding. However, little information about the functions of the S-like RNase in monocots has been reported. Here, we investigated the expression patterns and roles of an S-like RNase gene, OsRNS4, in abscisic acid (ABA)-mediated responses and phytochrome-mediated light responses as well as salinity tolerance in rice. The OsRNS4 gene was expressed at relatively high levels in leaves although its transcripts were detected in various organs. OsRNS4 expression was regulated by salt, PEG and ABA. The seedlings overexpressing OsRNS4 had longer coleoptiles and first leaves than wild-type seedlings under red light (R) and far-red light (FR), suggesting negative regulation of OsRNS4 in photomorphogenesis in rice seedlings. Moreover, ABA-induced growth inhibition of rice seedlings was significantly increased in the OsRNS4-overexpression (OsRNS4-OX) lines compared with that in WT, suggesting that OsRNS4 probably acts as a positive regulator in ABA responses in rice seedlings. In addition, our results demonstrate that OsRNS4-OX lines have enhanced tolerance to high salinity compared to WT. Our findings supply new evidence on the functions of monocot S-like RNase in regulating photosensitivity and abiotic stress responses.
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Affiliation(s)
- Jun Zheng
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, 250100 Jinan, China.
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50
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Rojas HJ, Roldán JA, Goldraij A. NnSR1, a class III non-S-RNase constitutively expressed in styles, is induced in roots and stems under phosphate deficiency in Nicotiana alata. ANNALS OF BOTANY 2013; 112:1351-60. [PMID: 24047716 PMCID: PMC3806536 DOI: 10.1093/aob/mct207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/11/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Non-S-ribonucleases (non-S-RNases) are class III T2 RNases constitutively expressed in styles of species with S-RNase-based self-incompatibility. So far, no function has been attributed to these RNases. The aim of this work is to examine if NnSR1, a non-S-RNase from Nicotiana alata, is induced under conditions of phosphate (Pi) deprivation. The hypothesis is that under Pi-limited conditions, non-S-RNase functions may resemble the role of S-like RNases. To date, the only RNases reported to be induced by Pi deficiency are class I and class II S-like RNases, which are phylogenetically different from the class III clade of RNases. METHODS Gene and protein expression of NnSR1 were assayed in plants grown hydroponically with and without Pi, by combining RT-PCR, immunoblot and enzymatic activity approaches. KEY RESULTS NnSR1 transcripts were detected in roots 7 d after Pi deprivation and remained stable for several days. Transcript expression was correlated based on Pi availability in the culture medium. Antiserum against a peptide based on a hypervariable domain of NnSR1 recognized NnSR1 in roots and stems but not leaves exposed to Pi shortage. NnSR1 was not detected in culture medium and was pelleted with the microsomal fraction, suggesting that it was membrane-associated or included in large compartments. The anti-NnSR1 inhibited selectively the enzymatic activity of a 31-kDa RNase indicating that NnSR1 was induced in an enzymatically active form. CONCLUSIONS The induction of NnSR1 indicates that there is a general recruitment of all classes of T2 RNases in response to Pi shortage. NnSR1 appears to have regained ancestral functions of class III RNases related to strategies to cope with Pi limitation and also possibly with other environmental challenges. This constitutes the first report for a specific function of class III RNases other than S-RNases.
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Affiliation(s)
| | | | - Ariel Goldraij
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC–CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
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