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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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2
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Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [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: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
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Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
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3
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Li H, Guo Z, Xu M, Zhao J, Xu D. Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108524. [PMID: 38518432 DOI: 10.1016/j.plaphy.2024.108524] [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: 01/27/2024] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.
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Affiliation(s)
- Hongwei Li
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Ziyi Guo
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Mengwei Xu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China
| | - Juanjuan Zhao
- Department of Immunology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China.
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China; Department of Medical Instrumental Analysis, Zunyi Medical University, No.6 Xuefuxi Road, Xinpu District, Zunyi City, Guizhou Province, 563099, China.
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4
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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5
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Zhou L, John Martin JJ, Li R, Zeng X, Wu Q, Li Q, Fu D, Li X, Liu X, Ye J, Cao H. Catalase (CAT) Gene Family in Oil Palm ( Elaeis guineensis Jacq.): Genome-Wide Identification, Analysis, and Expression Profile in Response to Abiotic Stress. Int J Mol Sci 2024; 25:1480. [PMID: 38338758 PMCID: PMC10855858 DOI: 10.3390/ijms25031480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Catalases (CATs) play crucial roles in scavenging H2O2 from reactive oxygen species, controlling the growth and development of plants. So far, genome-wide identification and characterization of CAT genes in oil palm have not been reported. In the present study, five EgCAT genes were obtained through a genome-wide identification approach. Phylogenetic analysis divided them into two subfamilies, with closer genes sharing similar structures. Gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the EgCAT genes. Several cis-acting elements related to hormone, stress, and defense responses were identified in the promoter regions of EgCATs. Tissue-specific expression of EgCAT genes in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Stress-responsive expression analysis showed that five EgCAT genes were significantly expressed under cold, drought, and salinity stress conditions. Collectively, this study provided valuable information on the oil palm CAT gene family and the validated EgCAT genes can be used as potential candidates for improving abiotic stress tolerance in oil palm and other related crops.
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Affiliation(s)
- Lixia Zhou
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jerome Jeyakumar John Martin
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Rui Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xianhai Zeng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qiufei Wu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qihong Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Dengqiang Fu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xinyu Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xiaoyu Liu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jianqiu Ye
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Hongxing Cao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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6
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Lai T, Yu Q, Pan J, Wang J, Tang Z, Bai X, Shi L, Zhou T. The Identification and Comparative Analysis of Non-Coding RNAs in Spores and Mycelia of Penicillium expansum. J Fungi (Basel) 2023; 9:999. [PMID: 37888255 PMCID: PMC10607695 DOI: 10.3390/jof9100999] [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: 06/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Penicillium expansum is the most popular post-harvest pathogen and causes blue mold disease in pome fruit and leads to significant economic losses worldwide every year. However, the fundamental regulation mechanisms of growth in P. expansum are unclear. Recently, non-coding RNAs (ncRNAs) have attracted more attention due to critical roles in normalizing gene expression and maintaining cellular genotypes in organisms. However, the research related to ncRNAs in P. expansum have not been reported. Therefore, to provide an overview of ncRNAs on composition, distribution, expression changes, and potential targets in the growth process, a comparative transcriptomic analysis was performed on spores and mycelia of P. expansum in the present study. A total of 2595 novel mRNAs, 3362 long non-coding RNAs (lncRNAs), 10 novel microRNAs (miRNAs), 86 novel small interfering RNAs (siRNAs), and 11,238 circular RNAs (circRNAs) were predicted and quantified. Of these, 1482 novel mRNAs, 5987 known mRNAs, 2047 lncRNAs, 40 miRNAs, 38 novel siRNAs, and 9235 circRNAs were differentially expressed (DE) in response to the different development stages. Afterward, the involved functions and pathways of DE RNAs were revealed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database enrichment analysis. The interaction networks between mRNAs, lncRNAs, and miRNAs were also predicted based on their correlation coefficient of expression profiles. Among them, it was found that miR168 family members may play important roles in fungal growth due to their central location in the network. These findings will contribute to a better understanding on regulation machinery at the RNA level on fungal growth and provide a theoretical basis to develop novel control strategies against P. expansum.
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Affiliation(s)
- Tongfei Lai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Qinru Yu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Pan
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Zhenxing Tang
- School of Culinary Arts, Tourism College of Zhejiang, Hangzhou 311231, China;
| | - Xuelian Bai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Lue Shi
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Ting Zhou
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
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7
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Jaiswal M, Kumar S. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species. J Biomol Struct Dyn 2023:1-13. [PMID: 37464885 DOI: 10.1080/07391102.2023.2235605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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8
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Ku YS. Partners in crime: MicroRNA408 and peptide miPEP408 negatively regulate arsenic and low sulfur tolerance. PLANT PHYSIOLOGY 2023; 192:685-687. [PMID: 36879411 DOI: 10.1093/plphys/kiad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/01/2023]
Affiliation(s)
- Yee-Shan Ku
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists, USA
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
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9
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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Regulatory miPEP Open Reading Frames Contained in the Primary Transcripts of microRNAs. Int J Mol Sci 2023; 24:ijms24032114. [PMID: 36768436 PMCID: PMC9917039 DOI: 10.3390/ijms24032114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
This review aims to consider retrospectively the available data on the coding properties of pri-microRNAs and the regulatory functions of their open reading frames (ORFs) and the encoded peptides (miPEPs). Studies identifying miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed together with a brief description of the methods to identify pri-miRNA ORFs and the encoded protein products. Generally, miPEPs have been identified in many plant species of several families and in a few animal species. Importantly, molecular mechanisms of the miPEP action are often quite different between flowering plants and metazoan species. Requirement for the additional studies in these directions is highlighted by alternative findings concerning negative or positive regulation of pri-miRNA/miRNA expression by miPEPs in plants and animals. Additionally, the question of how miPEPs are distributed in non-flowering plant taxa is very important for understanding the evolutionary origin of such micropeptides. Evidently, further extensive studies are needed to explore the functions of miPEPs and the corresponding ORFs and to understand the full set of their roles in eukaryotic organisms. Thus, we address the most recent integrative views of different genomic, physiological, and molecular aspects concerning the expression of miPEPs and their possible fine functions.
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Affiliation(s)
- Tatiana N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitriy Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey Y. Morozov
- Belozersky Institute of Physico-Chemical Biology and Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence:
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10
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Bajczyk M, Jarmolowski A, Jozwiak M, Pacak A, Pietrykowska H, Sierocka I, Swida-Barteczka A, Szewc L, Szweykowska-Kulinska Z. Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020342. [PMID: 36679055 PMCID: PMC9864873 DOI: 10.3390/plants12020342] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 05/27/2023]
Abstract
MicroRNAs are small RNAs, 20-22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic and biotic factors. Therefore, the deficiency or excess of individual miRNAs is detrimental to particular aspects of a plant's life. In consequence, the miRNA levels must be appropriately adjusted. To obtain proper expression of each miRNA, their biogenesis is controlled at multiple regulatory layers. Here, we addressed processes discovered to influence miRNA steady-state levels, such as MIR transcription, co-transcriptional pri-miRNA processing (including splicing, polyadenylation, microprocessor assembly and activity) and miRNA-encoded peptides synthesis. MiRNA stability, RISC formation and miRNA export out of the nucleus and out of the plant cell also define the levels of miRNAs in various plant tissues. Moreover, we show the evolutionary conservation of miRNA biogenesis core proteins across the plant kingdom.
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11
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Yang J, Liu M, Fang X, Zhang H, Ren Q, Zheng Y, Wang Y, Zhou Y. Advances in peptides encoded by non-coding RNAs: A cargo in exosome. Front Oncol 2022; 12:1081997. [PMID: 36620552 PMCID: PMC9822543 DOI: 10.3389/fonc.2022.1081997] [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: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.
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Affiliation(s)
- Jing Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengxiao Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xidong Fang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qian Ren
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
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12
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Zhang Y, Zhou Y, Zhu W, Liu J, Cheng F. Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:965745. [PMID: 36311129 PMCID: PMC9597485 DOI: 10.3389/fpls.2022.965745] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/26/2022] [Indexed: 05/24/2023]
Abstract
To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.
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Affiliation(s)
- Yingying Zhang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ye Zhou
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Weimin Zhu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Fang Cheng
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
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13
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Zhang F, Yang J, Zhang N, Wu J, Si H. Roles of microRNAs in abiotic stress response and characteristics regulation of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:919243. [PMID: 36092392 PMCID: PMC9459240 DOI: 10.3389/fpls.2022.919243] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.
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Affiliation(s)
- Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Leong AZX, Lee PY, Mohtar MA, Syafruddin SE, Pung YF, Low TY. Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures. J Biomed Sci 2022; 29:19. [PMID: 35300685 PMCID: PMC8928697 DOI: 10.1186/s12929-022-00802-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises ≤ 100 amino acids. Traditionally dismissed by genome annotation pipelines as meaningless noise, sORFs were found to possess coding potential with ribosome profiling (RIBO-Seq), which unveiled sORF-based transcripts at various genome locations. Nonetheless, the existence of corresponding microproteins that are stable and functional was little substantiated by experimental evidence initially. With recent advancements in multi-omics, the identification, validation, and functional characterisation of sORFs and microproteins have become feasible. In this review, we discuss the history and development of an emerging research field of sORFs and microproteins. In particular, we focus on an array of bioinformatics and OMICS approaches used for predicting, sequencing, validating, and characterizing these recently discovered entities. These strategies include RIBO-Seq which detects sORF transcripts via ribosome footprints, and mass spectrometry (MS)-based proteomics for sequencing the resultant microproteins. Subsequently, our discussion extends to the functional characterisation of microproteins by incorporating CRISPR/Cas9 screen and protein–protein interaction (PPI) studies. Our review discusses not only detection methodologies, but we also highlight on the challenges and potential solutions in identifying and validating sORFs and their microproteins. The novelty of this review lies within its validation for the functional role of microproteins, which could contribute towards the future landscape of microproteomics.
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Affiliation(s)
- Alyssa Zi-Xin Leong
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Semenyih, 43500, Selangor, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia.
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Katsarou K, Adkar-Purushothama CR, Tassios E, Samiotaki M, Andronis C, Lisón P, Nikolaou C, Perreault JP, Kalantidis K. Revisiting the Non-Coding Nature of Pospiviroids. Cells 2022; 11:265. [PMID: 35053381 PMCID: PMC8773695 DOI: 10.3390/cells11020265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/14/2022] Open
Abstract
Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study.
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Affiliation(s)
- Konstantina Katsarou
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
| | - Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; (C.R.A.-P.); (J.-P.P.)
| | - Emilios Tassios
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece;
| | - Martina Samiotaki
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece;
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València (UPV), Ciudad Politécnica de la Innovación (CPI) 8 E, Ingeniero Fausto Elio s/n, 46011 Valencia, Spain;
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece;
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; (C.R.A.-P.); (J.-P.P.)
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
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Yadav A, Kumar S, Verma R, Lata C, Sanyal I, Rai SP. microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2471-2485. [PMID: 34924705 PMCID: PMC8639965 DOI: 10.1007/s12298-021-01096-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.
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Affiliation(s)
- Ankita Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Sanoj Kumar
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005 India
| | - Rita Verma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067 India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shashi Pandey Rai
- Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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