1
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Huang J, Yang P, Pan W, Wu F, Qiu J, Ma Z. The role of polypeptides encoded by ncRNAs in cancer. Gene 2024; 928:148817. [PMID: 39098512 DOI: 10.1016/j.gene.2024.148817] [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: 04/12/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
It was previously thought that ncRNA could not encode polypeptides, but recent reports have challenged this notion. As research into ncRNA progresses, it is increasingly clear that it serves roles beyond traditional mechanisms, playing significant regulatory roles in various diseases, notably cancer, which is responsible for 70% of human deaths. Numerous studies have highlighted the diverse regulatory mechanisms of ncRNA that are pivotal in cancer initiation and progression. The role of ncRNA-encoded polypeptides in cancer regulation has gained prominence. This article explores the newly identified regulatory functions of these polypeptides in three types of ncRNA-lncRNA, pri-miRNA, and circRNA. These polypeptides can interact with proteins, influence signaling pathways, enhance miRNA stability, and regulate cancer progression, malignancy, resistance, and other clinical challenges. Furthermore, we discuss the evolutionary significance of these polypeptides in the transition from RNA to protein, examining their emergence and conservation throughout evolution.
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Affiliation(s)
- Jiayuan Huang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Ping Yang
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming 650118,China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Fan Wu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jianhua Qiu
- Department of Anesthesiology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 201800, China.
| | - Zhongliang Ma
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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2
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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs. PLANTS (BASEL, SWITZERLAND) 2024; 13:1137. [PMID: 38674546 PMCID: PMC11055055 DOI: 10.3390/plants13081137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.
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Affiliation(s)
- T. N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - D. Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. Y. Morozov
- Biological Faculty, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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3
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Zhang L, Ma X, Tong P, Zheng B, Zhu M, Peng B, Wang J, Liu Y. RNA-Seq analysis of long non-coding RNA in human intestinal epithelial cells infected by Shiga toxin-producing Escherichia coli. Cytokine 2024; 173:156421. [PMID: 37944420 DOI: 10.1016/j.cyto.2023.156421] [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: 08/14/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND The Shiga toxin-producing Escherichia coli (STEC) infects animals and induces acute intestinal inflammation. Long non-coding RNAs (lncRNAs) are known to play crucial roles in modulating inflammation response. However, it is not clear whether lncRNAs are involved in STEC-induced inflammation. METHODS AND RESULTS To understand the association of lncRNAs with STEC infection, we used RNA-seq technology to analyze the profiles of lncRNAs in Mock-infected and STEC-infected human intestinal epithelial cells (HIECs). We detected a total of 702 lncRNAs differentially expressed by STEC infection. 583 differentially expressed lncRNAs acted as competitive microRNAs (miRNAs) binding elements in regulating the gene expression involved in TNF signaling pathway, IL-17 signaling pathway, PI3K-Akt signaling pathway, and apoptosis pathways. We analyzed 3 targeted genes, TRADD, TRAF1 and TGFB2, which were differentially regulated by mRNA-miRNA-lncRNA interaction network, potentially involved in the inflammatory and apoptotic response to STEC infection. Functional analysis of up/downstream genes associated with differentially expressed lncRNAs revealed their role in adheres junction and endocytosis. We also used the qRT-PCR technique to validate 8 randomly selected differentially expressed lncRNAs and mRNAs in STEC-infected HIECs. CONCLUSION Our results, for the first time, revealed differentially expressed lncRNAs induced by STEC infection of HIECs. The results will help investigate the molecular mechanisms for the inflammatory responses induced by STEC.
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Affiliation(s)
- Liuqing Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Xuelian Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Panpan Tong
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Baili Zheng
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Mingyue Zhu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Bin Peng
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Jinquan Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Yingyu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
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4
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Zhang L, Fan D, Li H, Chen Q, Zhang Z, Liu M, Liu J, Song Y, He J, Xu W, Song S, Liu H, Ren Y, Ma C. Characterization and identification of grapevine heat stress-responsive microRNAs revealed the positive regulated function of vvi-miR167 in thermostability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111623. [PMID: 36750140 DOI: 10.1016/j.plantsci.2023.111623] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/19/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
High temperature stress is one of the primary abiotic stresses that restrict fruit tree production. Grapevine (Vitis vinifera) with high economic value throughout the world is a cultivated fruit crop, and its growth and development is often influenced by high temperature stress. Studying the heat stress-response mechanism of grapevine has great significance for understanding the acclimation to heat stress. In this study, we identified a series of heat stress responsive miRNAs and analyzed their function during the heat tolerance response. CK (control group, 25 °C) and heat treatment stress (TS, 45 °C) small RNA (sRNA) libraries were constructed and sequenced by high-throughput sequencing in 'Thompson seedless' grapevine. 873 known-miRNAs and 86 novel-miRNAs were identified, of which 88 known and three novel miRNAs were expressed differentially under heat stress. 322 genes were predicted to be targeted by the miRNAs. Eight selected miRNAs and its targets were confirmed by real time quantitative PCR (RT - qPCR), indicating that these "miRNA - target" were responsive to heat stress. In addition, most of the predicted target genes were negatively regulated by corresponding miRNAs. Gene function and pathway analyses indicated that these genes probably play crucial roles in heat stress tolerance. Vvi-miR167b transiently overexpression in grapevine leaves decreased target gene vvARF6, vvARF6-like and vvARF8 expression. The function of vvi-miR167 was verified by ectopic transformation in Arabidopsis thaliana, and the heat tolerance in transgenic lines was enhanced significantly, suggesting that the vvi-miR167 plays a positive regulatory role in grape thermostability. Comparison of miRNA expression patterns between heat treatment stress and CK can help elucidate the heat stress response and resistance mechanisms in grapes. In conclusion, these results gave us useful information to better understand the heat stress-response during domestication as well as for breeding new cultivars with heat stress resistance in fruit trees.
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Affiliation(s)
- Lipeng Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China
| | - Dongying Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiuju Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Zhen Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Minying Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingjing Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China
| | - Yue Song
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan He
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenping Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiren Song
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaifeng Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China
| | - Yi Ren
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Chao Ma
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Gorgues L, Li X, Maurel C, Martinière A, Nacry P. Root osmotic sensing from local perception to systemic responses. STRESS BIOLOGY 2022; 2:36. [PMID: 37676549 PMCID: PMC10442022 DOI: 10.1007/s44154-022-00054-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/28/2022] [Indexed: 09/08/2023]
Abstract
Plants face a constantly changing environment, requiring fine tuning of their growth and development. Plants have therefore developed numerous mechanisms to cope with environmental stress conditions. One striking example is root response to water deficit. Upon drought (which causes osmotic stress to cells), plants can among other responses alter locally their root system architecture (hydropatterning) or orientate their root growth to optimize water uptake (hydrotropism). They can also modify their hydraulic properties, metabolism and development coordinately at the whole root and plant levels. Upstream of these developmental and physiological changes, plant roots must perceive and transduce signals for water availability. Here, we review current knowledge on plant osmotic perception and discuss how long distance signaling can play a role in signal integration, leading to the great phenotypic plasticity of roots and plant development.
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Affiliation(s)
- Lucille Gorgues
- IPSiM, CNRS, INRAE, Institut Agro, Univ Montpellier, 34060 Montpellier, France
| | - Xuelian Li
- IPSiM, CNRS, INRAE, Institut Agro, Univ Montpellier, 34060 Montpellier, France
| | - Christophe Maurel
- IPSiM, CNRS, INRAE, Institut Agro, Univ Montpellier, 34060 Montpellier, France
| | | | - Philippe Nacry
- IPSiM, CNRS, INRAE, Institut Agro, Univ Montpellier, 34060 Montpellier, France
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6
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Zhang P, Chen H, Shang Q, Chen G, He J, Shen G, Yu X, Zhang Z, Zhao W, Zhu G, Huang J, Liang D, Tang J, Cui J, Liu Z, Jiang X, Ren H. Zuogui Pill Ameliorates Glucocorticoid-Induced Osteoporosis through ZNF702P-Based ceRNA Network: Bioinformatics Analysis and Experimental Validation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:8020182. [PMID: 39280960 PMCID: PMC11401717 DOI: 10.1155/2022/8020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/08/2022] [Accepted: 08/07/2022] [Indexed: 09/18/2024]
Abstract
Glucocorticoid-induced osteoporosis (GIOP) is a musculoskeletal disease with increased fracture risk caused by long-term application of glucocorticoid, but there exist few effective interventions. Zuogui Pill (ZGP) has achieved clinical improvement for GIOP as an ancient classical formula, but its molecular mechanisms remain unclear due to scanty relevant studies. This study aimed to excavate the effective compounds and underlying mechanism of ZGP in treating GIOP and construct relative ceRNA network by using integrated analysis of bioinformatics analysis and experimental validation. Results show that ZNF702P is significantly upregulated in GIOP than normal cases based on gene chip sequencing analysis. Totally, 102 ingredients and 535 targets of ZGP as well as 480 GIOP-related targets were selected, including 122 common targets and 8 intersection targets with the predicted mRNAs. The ceRNA network contains one lncRNA (ZNF702P), 6 miRNAs, and 8 mRNAs. Four hub targets including JUN, CCND1, MAPK1, and MAPK14 were identified in the PPI network. Six ceRNA interaction axes including ZNF702P-hsa-miR-429-JUN, ZNF702P-hsa-miR-17-5p/hsa-miR-20b-5p-CCND1, ZNF702P-hsa-miR-17-5p/hsa-miR-20b-5p-MAPK1, and ZNF702P-hsa-miR-24-3p-MAPK14 were obtained. By means of molecular docking, we found that all the hub targets could be effectively combined with related ingredients. GO enrichment analysis showed 649 biological processes, involving response to estrogen, response to steroid hormone, inflammatory response, macrophage activation, and osteoclast differentiation, and KEGG analysis revealed 102 entries with 36 relative signaling pathways, which mainly contained IL-17 signaling pathway, T cell receptor signaling pathway, FoxO signaling pathway, the PD-L1 expression and PD-1 checkpoint pathway, MAPK signaling pathway, TNF signaling pathway, Estrogen signaling pathway, and Wnt signaling pathway. Our experiments confirmed that ZNF702P exhibited gradually increasing expression levels during osteoclast differentiation of human peripheral blood monocytes (HPBMs) induced by RANKL, while ZGP could inhibit osteoclast differentiation of HPBMs induced by RANKL in a concentration-dependent manner. Therefore, by regulating inflammatory response, osteoclast differentiation, and hormone metabolism, ZGP may treat GIOP by regulating hub target genes, such as JUN, CCND1, MAPK1, and MAPK14, and acting on numerous key pathways, which involve the ZNF702P-based ceRNA network.
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Affiliation(s)
- Peng Zhang
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Honglin Chen
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Qi Shang
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Guifeng Chen
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Jiahui He
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Gengyang Shen
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Xiang Yu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Zhida Zhang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Wenhua Zhao
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Guangye Zhu
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jinglin Huang
- The First Clinical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - De Liang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Jingjing Tang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Jianchao Cui
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Zhixiang Liu
- Affiliated Huadu Hospital, Southern Medical University, Guangzhou 510800, China
| | - Xiaobing Jiang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
| | - Hui Ren
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Lingnan Medical Research Center of Guangzhou Univercity of Chinese Medicine, Guangzhou 510405, China
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7
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Dozier C, Montigny A, Viladrich M, Culerrier R, Combier JP, Besson A, Plaza S. Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila. Int J Mol Sci 2022; 23:5764. [PMID: 35628573 PMCID: PMC9144653 DOI: 10.3390/ijms23105764] [Citation(s) in RCA: 2] [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: 04/25/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). However, several lnc pri-miRNAs contain translatable small open reading frames (smORFs). If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis-regulatory elements involved in lncRNA decay. Here, we investigated the possible involvement of smORFs in the regulation of lnc pri-miRNAs in Human and Drosophila, focusing on pri-miRNAs previously shown to contain translatable smORFs. We show that smORFs regulate the expression levels of human pri-miR-155 and pri-miR-497, and Drosophila pri-miR-8 and pri-miR-14, and also affect the expression and activity of their associated miRNAs. This smORF-dependent regulation is independent of the nucleotidic and amino acidic sequences of the smORFs and is sensitive to the ribosome-stalling drug cycloheximide, suggesting the involvement of translational events. This study identifies smORFs as new cis-acting elements involved in the regulation of pri-miRNAs and miRNAs expression, in both Human and Drosophila melanogaster.
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Affiliation(s)
- Christine Dozier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Mireia Viladrich
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Raphael Culerrier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
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8
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Kuromori T, Fujita M, Takahashi F, Yamaguchi‐Shinozaki K, Shinozaki K. Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:342-358. [PMID: 34863007 PMCID: PMC9300012 DOI: 10.1111/tpj.15619] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Plant response to drought stress includes systems for intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps entire plants acquire stress resistance. Plants sense water-deficit conditions both via the stomata of leaves and roots, and transfer water-deficit signals from roots to shoots via inter-organ signaling. Abscisic acid is an important phytohormone involved in the drought stress response and adaptation, and is synthesized mainly in vascular tissues and guard cells of leaves. In leaves, stress-induced abscisic acid is distributed to various tissues by transporters, which activates stomatal closure and expression of stress-related genes to acquire drought stress resistance. Moreover, the stepwise stress response at the whole-plant level is important for proper understanding of the physiological response to drought conditions. Drought stress is sensed by multiple types of sensors as molecular patterns of abiotic stress signals, which are transmitted via separate parallel signaling networks to induce downstream responses, including stomatal closure and synthesis of stress-related proteins and metabolites. Peptide molecules play important roles in the inter-organ signaling of dehydration from roots to shoots, as well as signaling of osmotic changes and reactive oxygen species/Ca2+ . In this review, we have summarized recent advances in research on complex plant drought stress responses, focusing on inter-tissue signaling in leaves and inter-organ signaling from roots to shoots. We have discussed the mechanisms via which drought stress adaptations and resistance are acquired at the whole-plant level, and have proposed the importance of quantitative phenotyping for measuring plant growth under drought conditions.
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Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science2‐1 HirosawaWakoSaitama351‐0198Japan
| | - Miki Fujita
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
| | - Fuminori Takahashi
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
- Department of Biological Science and TechnologyGraduate School of Advanced EngineeringTokyo University of Science6‐3‐1 Niijyuku, Katsushika‐kuTokyo125‐8585Japan
| | - Kazuko Yamaguchi‐Shinozaki
- Laboratory of Plant Molecular PhysiologyGraduate School of Agricultural and Life SciencesThe University of Tokyo1‐1‐1 Yayoi, Bunkyo‐kuTokyo113‐8657Japan
- Research Institute for Agricultural and Life SciencesTokyo University of Agriculture1‐1‐1 Sakuragaoka, Setagaya‐kuTokyo156‐8502Japan
| | - Kazuo Shinozaki
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science2‐1 HirosawaWakoSaitama351‐0198Japan
- Gene Discovery Research GroupRIKEN Center for Sustainable Resource Science3‐1‐1 KoyadaiTsukubaIbaraki305‐0074Japan
- Biotechonology CenterNational Chung Hsing University (NCHU)Taichung402Taiwan
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9
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Silveira GO, Coelho HS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. Parasitol Res 2021; 121:1091-1115. [PMID: 34859292 DOI: 10.1007/s00436-021-07384-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/14/2021] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) emerged in the past 20 years due to massive amounts of scientific data regarding transcriptomic analyses. They have been implicated in a plethora of cellular processes in higher eukaryotes. However, little is known about lncRNA possible involvement in parasitic diseases, with most studies only detecting their presence in parasites of human medical importance. Here, we review the progress on lncRNA studies and their functions in protozoans and helminths. In addition, we show an example of knockdown of one lncRNA in Schistosoma mansoni, SmLINC156349, which led to in vitro parasite adhesion, motility, and pairing impairment, with a 20% decrease in parasite viability and 33% reduction in female oviposition. Other observed phenotypes were a decrease in the proliferation rate of both male and female worms and their gonads, and reduced female lipid and vitelline droplets that are markers for well-developed vitellaria. Impairment of female worms' vitellaria in SmLINC156349-silenced worms led to egg development deficiency. All those results demonstrate the great potential of the tools and methods to characterize lncRNAs as potential new therapeutic targets. Further, we discuss the challenges and limitations of current methods for studying lncRNAs in parasites and possible solutions to overcome them, and we highlight the future directions of this exciting field.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Helena S Coelho
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Murilo S Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil. .,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
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10
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Liang Y, Zhu W, Chen S, Qian J, Li L. Genome-Wide Identification and Characterization of Small Peptides in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:695439. [PMID: 34220917 PMCID: PMC8244733 DOI: 10.3389/fpls.2021.695439] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/20/2021] [Indexed: 05/06/2023]
Abstract
Small peptides (sPeptides), <100 amino acids (aa) long, are encoded by small open reading frames (sORFs) often found in the 5' and 3' untranslated regions (or other parts) of mRNAs, in long non-coding RNAs, or transcripts from introns and intergenic regions; various sPeptides play important roles in multiple biological processes. In this study, we conducted a comprehensive study of maize (Zea mays) sPeptides using mRNA sequencing, ribosome profiling (Ribo-seq), and mass spectrometry (MS) on six tissues (each with at least two replicates). To identify maize sORFs and sPeptides from these data, we set up a robust bioinformatics pipeline and performed a genome-wide scan. This scan uncovered 9,388 sORFs encoding peptides of 2-100 aa. These sORFs showed distinct genomic features, such as different Kozak region sequences, higher specificity of translation, and high translational efficiency, compared with the canonical protein-coding genes. Furthermore, the MS data verified 2,695 sPeptides. These sPeptides perfectly discriminated all the tissues and were highly associated with their parental genes. Interestingly, the parental genes of sPeptides were significantly enriched in multiple functional gene ontology terms related to abiotic stress and development, suggesting the potential roles of sPeptides in the regulation of their parental genes. Overall, this study lays out the guidelines for genome-wide scans of sORFs and sPeptides in plants by integrating Ribo-seq and MS data and provides a more comprehensive resource of functional sPeptides in maize and gives a new perspective on the complex biological systems of plants.
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Affiliation(s)
| | | | | | | | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Yadav A, Sanyal I, Rai SP, Lata C. An overview on miRNA-encoded peptides in plant biology research. Genomics 2021; 113:2385-2391. [PMID: 34022345 DOI: 10.1016/j.ygeno.2021.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are short (21-23 nt) regulatory RNA molecules present in plants and animals which are known for regulating the mRNA target gene expression either by cleavage or translational repression. With the advancements in miRNAs research in plants towards their biogenesis and applications has directed the recent discovery of pri-miRNAs encoding functional peptides or microRNA peptides (miPEPs). These miPEPs are encoded by 5' of pri-miRs containing short ORFs (miORFs). miPEPs are known to enhance the activity of their associated miRNAs by increasing their accumulation and hence downregulating the target genes. Since miPEPs are very specific for each miRNA, they are considered as novel and effective tools for improving traits of interest for plant growth promotion and plant-microbe interaction. Entire peptidome research is the need of the hour. This review thus summarizes recent advancements in miPEP research and its applications as a technology with important agronomical implications with miRNAs augmentation.
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Affiliation(s)
- Ankita Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Faculty of Science, Banaras Hindu University, Varanasi 221005, India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Shashi Pandey Rai
- Faculty of Science, Banaras Hindu University, Varanasi 221005, India
| | - Charu Lata
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi 110067, India.
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