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Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. bioRxiv 2024:2024.03.29.587306. [PMID: 38617318 PMCID: PMC11014486 DOI: 10.1101/2024.03.29.587306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely (i) not triggered by microRNAs, (ii) not loaded by AGO18 proteins, and (iii) not capable of mediating cis-cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.
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Affiliation(s)
- Junpeng Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sébastien Bélanger
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- The James Hutton Institute, Dundee, Scotland DD2 5DA, UK
| | - Scott Lewis
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Michael A. Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Michael D. Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Zhang Y, Zeng Z, Hu H, Zhao M, Chen C, Ma X, Li G, Li J, Liu Y, Hao Y, Xu J, Xia R. MicroRNA482/2118 is lineage-specifically involved in gibberellin signalling via the regulation of GID1 expression by targeting noncoding PHAS genes and subsequently instigated phasiRNAs. Plant Biotechnol J 2024; 22:819-832. [PMID: 37966709 PMCID: PMC10955497 DOI: 10.1111/pbi.14226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 11/16/2023]
Abstract
MicroRNA482/2118 (miR482/2118) is a 22-nt miRNA superfamily, with conserved functions in disease resistance and plant development. It usually instigates the production of phased small interfering RNAs (phasiRNAs) from its targets to expand or reinforce its silencing effect. Using a new high-quality reference genome sequence and comprehensive small RNA profiling, we characterized a newly evolved regulatory pathway of miR482/2118 in litchi. In this pathway, miR482/2118 cleaved a novel noncoding trans-acting gene (LcTASL1) and triggered phasiRNAs to regulate the expression of gibberellin (GA) receptor gene GIBBERELLIN INSENSITIVE DWARF1 (GID1) in trans; another trans-acting gene LcTASL2, targeted by LcTASL1-derived phasiRNAs, produced phasiRNAs as well to target LcGID1 to reinforce the silencing effect of LcTASL1. We found this miR482/2118-TASL-GID1 pathway was likely involved in fruit development, especially the seed development in litchi. In vivo construction of the miR482a-TASL-GID1 pathway in Arabidopsis could lead to defects in flower and silique development, analogous to the phenotype of gid1 mutants. Finally, we found that a GA-responsive transcription factor, LcGAMYB33, could regulate LcMIR482/2118 as a feedback mechanism of the sRNA-silencing pathway. Our results deciphered a lineage-specifically evolved regulatory module of miR482/2118, demonstrating the high dynamics of miR482/2118 function in plants.
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Affiliation(s)
- Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Huimin Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Minglei Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Xingshuai Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Guanliang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Yanwei Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
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3
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Romero-Rodríguez B, Petek M, Jiao C, Križnik M, Zagorščak M, Fei Z, Bejarano ER, Gruden K, Castillo AG. Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato. BMC Plant Biol 2023; 23:651. [PMID: 38110861 PMCID: PMC10726652 DOI: 10.1186/s12870-023-04534-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/17/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). RESULTS We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. CONCLUSION We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.
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Affiliation(s)
- Beatriz Romero-Rodríguez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- The Key Lab of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Araceli G Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain.
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4
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Sharma S, Sett S, Das T, Prasad A, Prasad M. Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction. Plant Physiol Biochem 2023; 201:107852. [PMID: 37356385 DOI: 10.1016/j.plaphy.2023.107852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
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Affiliation(s)
| | - Susmita Sett
- National Institute of Plant Genome Research, New Delhi, India.
| | - Tuhin Das
- National Institute of Plant Genome Research, New Delhi, India.
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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5
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Abstract
Plant cells accumulate small RNA molecules that regulate plant development, genome stability, and environmental responses. These small RNAs fall into three major classes based on their function and mechanisms of biogenesis-microRNAs, heterochromatic small interfering RNAs, and secondary small interfering RNAs-plus several other less well-characterized categories. Biogenesis of each small RNA class requires a pathway of factors, some specific to each pathway and others involved in multiple pathways. Diverse sequenced plant genomes, along with rapid developments in sequencing, imaging, and genetic transformation techniques, have enabled significant progress in understanding the biogenesis, functions, and evolution of plant small RNAs, including those that had been poorly characterized because they were absent or had low representation in Arabidopsis (Arabidopsis thaliana). Here, we review recent findings about plant small RNAs and discuss our current understanding of their biogenesis mechanisms, targets, modes of action, mobility, and functions in Arabidopsis and other plant species, including economically important crops.
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Affiliation(s)
- Junpeng Zhan
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA;
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA;
- Division of Plant Science & Technology, University of Missouri-Columbia, Columbia, Missouri, USA
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6
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Zhang R, Zhang S, Li J, Gao J, Song G, Li W, Geng S, Liu C, Lin Y, Li Y, Li G. CRISPR/Cas9-targeted mutagenesis of TaDCL4, TaDCL5 and TaRDR6 induces male sterility in common wheat. Plant Biotechnol J 2023; 21:839-853. [PMID: 36597709 PMCID: PMC10037139 DOI: 10.1111/pbi.14000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Phased, small interfering RNAs (phasiRNAs) are important for plant anther development, especially for male sterility. PhasiRNA biogenesis is dependent on genes like RNA polymerase 6 (RDR6), DICER-LIKE 4 (DCL4), or DCL5 to produce 21- or 24 nucleotide (nt) double-strand small RNAs. Here, we generated mutants of DCL4, DCL5 and RDR6 using CRISPR/Cas9 system and studied their effects on plant reproductive development and phasiRNA production in wheat. We found that RDR6 mutation caused sever consequence throughout plant development starting from seed germination and the dcl4 mutants grew weaker with thorough male sterility, while dcl5 plants developed normally but exhibited male sterility. Correspondingly, DCL4 and DCL5, respectively, specified 21- and 24-nt phasiRNA biogenesis, while RDR6 contributed to both. Also, the three key genes evolved differently in wheat, with TaDCL5-A/B becoming non-functioning and TaRDR6-A being lost after polyploidization. Furthermore, we found that PHAS genes (phasiRNA precursors) identified via phasiRNAs diverged rapidly among sub-genomes of polyploid wheat. Despite no similarity being found among phasiRNAs of grasses, their targets were enriched for similar biological functions. In light of the important roles of phasiRNA pathways in gametophyte development, genetic dissection of the function of key genes may help generate male sterile lines suitable for hybrid wheat breeding.
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Affiliation(s)
- Rongzhi Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Shujuan Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Jihu Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Jie Gao
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Guoqi Song
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Wei Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Cheng Liu
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Yanxiang Lin
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Yulian Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Genying Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
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Si F, Luo H, Yang C, Gong J, Yan B, Liu C, Song X, Cao X. Mobile ARGONAUTE 1d binds 22-nt miRNAs to generate phasiRNAs important for low-temperature male fertility in rice. Sci China Life Sci 2023; 66:197-208. [PMID: 36239908 DOI: 10.1007/s11427-022-2204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Phased small interfering RNAs (phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice (Oryza sativa) low temperature-induced Argonaute (AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis; it also binds 21-nt phasiRNAs with a 5' terminal U. In total, phasiRNAs from 972 loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.
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Affiliation(s)
- Fuyan Si
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haofei Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Gong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bin Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Innovative Academy of Seed Design (INASEED), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100039, China. .,CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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8
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Shi C, Zhang J, Wu B, Jouni R, Yu C, Meyers BC, Liang W, Fei Q. Temperature-sensitive male sterility in rice determined by the roles of AGO1d in reproductive phasiRNA biogenesis and function. New Phytol 2022; 236:1529-1544. [PMID: 36031742 DOI: 10.1111/nph.18446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants, with spatial-temporal specificity. However, the ARGONAUTE (AGO) proteins associated with phasiRNAs and their miRNA triggers remain elusive. Here, through histological and high-throughput sequencing analyses, we show that rice AGO1d, which is specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. AGO1d preferentially binds to miR2118-triggered 21-nucleotide (nt) phasiRNAs with a 5'-terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes a reduction of 21- and 24-nt phasiRNAs and temperature-sensitive male sterility. At lower temperatures, anthers of the ago1d mutant predominantly show excessive tapetal cells with little starch accumulation during pollen formation, possibly caused by the dysregulation of cell metabolism. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function.
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Affiliation(s)
- Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bingjin Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Rachel Jouni
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University, Saint Louis, MI, 63130, USA
- Donald Danforth Plant Science Center, Saint Louis, MI, 63132, USA
| | - Changxiu Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MI, 63132, USA
- Division of Plant Sciences and Technology, University of Missouri-Columbia, Columbia, MI, 65211, USA
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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9
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Liao L, Xie B, Guan P, Jiang N, Cui J. New insight into the molecular mechanism of miR482/2118 during plant resistance to pathogens. Front Plant Sci 2022; 13:1026762. [PMID: 36388487 PMCID: PMC9650292 DOI: 10.3389/fpls.2022.1026762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
MicroRNAs (miRNAs), a group of small noncoding RNAs (approximately 20-24 nucleotides), act as essential regulators affecting endogenous gene expression in plants. MiR482/2118 is a unique miRNA superfamily in plants and represses NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT (NBS-LRR) genes to function in plant resistance to pathogens. In addition, over the past several years, it has been found that miR482/2118 not only targets NBS-LRRs but also acts on other molecular mechanisms to affect plant resistance. miR482/2118-5ps, phased small interfering RNAs (phasiRNAs) and long noncoding RNAs (lncRNAs) play important roles in plant disease resistance. This review summarizes the current knowledge of the interactions and links between miR482/2118 and its new interacting molecules, miR482/2118-5p, phasiRNAs and lncRNAs, in plant disease resistance. Here, we aim to provide a comprehensive view describing the new molecular mechanism associated with miR482/2118 in the plant immune system.
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Affiliation(s)
- Lijuan Liao
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, Changsha, China
| | - Biao Xie
- College of Life Science, Hunan Normal University, Changsha, China
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, Changsha, China
| | - Peipei Guan
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, Changsha, China
| | - Ning Jiang
- Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jun Cui
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, Changsha, China
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10
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Dey S, Sarkar A, Chowdhury S, Singh R, Mukherjee A, Ghosh Z, Kundu P. Heightened miR6024-NLR interactions facilitate necrotrophic pathogenesis in tomato. Plant Mol Biol 2022; 109:717-739. [PMID: 35499677 DOI: 10.1007/s11103-022-01270-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
miR6024 acts as a negative regulator of R genes, hence of Tomato plant immunity, and facilitates disease by the necrotrophic pathogen A. solani. Plant resistance genes or Nucleotide-binding leucine-rich repeat (NLR) genes, integral components of plant disease stress-signaling are targeted by variable groups of miRNAs. However, the significance of miRNA-mediated regulation of NLRs during a pathogen stress response, specifically for necrotrophic fungus, is poorly understood. A thorough examination of Tomato NLRs and miRNAs could map substantial interactions of which half the annotated NLRs were targets of Solanaceae-specific and conserved miRNAs, at the NB subdomain. The Solanaceae-specific miR6024 and its NLR targets analysed in different phytopathogenic stresses revealed differential and mutually antagonistic regulation. Interestingly, miR6024-targeted cleavage of a target NLR also triggered the generation of secondary phased siRNAs which could potentially amplify the defense signal. RNA-seq analysis of leaf tissues from miR6024 overexpressing Tomato plants evidenced a perturbation in the defense transcriptome with the transgenics showing unwarranted immune response-related genes' expression with or without infection with necrotrophic Alternaria solani, though no adverse effect could be observed in the growth and development of the transgenic plants. Transgenic plants exhibited constitutive downregulation of the target NLRs, aggravated disease phenotype with an enhanced lesion, greater ROS generation and hypersusceptibility to A. solani infection, thus establishing that miR6024 negatively impacts plant immune response during necrotrophic pathogenesis. Limited knowledge about the outcome of NLR-miRNA interaction during necrotrophic pathogenesis is a hindrance to the deployment of miRNAs in crop improvement programs. With the elucidation of the necrotrophic disease-synergistic role played by miR6024, it becomes a potent candidate for biotechnological manipulation for the rapid development of pathogen-tolerant solanaceous plants.
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Affiliation(s)
- Sayani Dey
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Arijita Sarkar
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Shreya Chowdhury
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Raghuvir Singh
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Mukherjee
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Pallob Kundu
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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11
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Wang WQ, Moss SMA, Zeng L, Espley RV, Wang T, Lin-Wang K, Fu BL, Schwinn KE, Allan AC, Yin XR. The red flesh of kiwifruit is differentially controlled by specific activation-repression systems. New Phytol 2022; 235:630-645. [PMID: 35348217 DOI: 10.1111/nph.18122] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Anthocyanins are visual cues for pollination and seed dispersal. Fruit containing anthocyanins also appeals to consumers due to its appearance and health benefits. In kiwifruit (Actinidia spp.) studies have identified at least two MYB activators of anthocyanin, but their functions in fruit and the mechanisms by which they act are not fully understood. Here, transcriptome and small RNA high-throughput sequencing were used to comprehensively identify contributors to anthocyanin accumulation in kiwifruit. Stable overexpression in vines showed that both 35S::MYB10 and MYB110 can upregulate anthocyanin biosynthesis in Actinidia chinensis fruit, and that MYB10 overexpression resulted in anthocyanin accumulation which was limited to the inner pericarp, suggesting that repressive mechanisms underlie anthocyanin biosynthesis in this species. Furthermore, motifs in the C-terminal region of MYB10/110 were shown to be responsible for the strength of activation of the anthocyanic response. Transient assays showed that both MYB10 and MYB110 were not directly cleaved by miRNAs, but that miR828 and its phased small RNA AcTAS4-D4(-) efficiently targeted MYB110. Other miRNAs were identified, which were differentially expressed between the inner and outer pericarp, and cleavage of SPL13, ARF16, SCL6 and F-box1, all of which are repressors of MYB10, was observed. We conclude that it is the differential expression and subsequent repression of MYB activators that is responsible for variation in anthocyanin accumulation in kiwifruit species.
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Affiliation(s)
- Wen-Qiu Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Horticulture Department, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Sarah M A Moss
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston North, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Bei-Ling Fu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Horticulture Department, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kathy E Schwinn
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston North, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Xue-Ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Horticulture Department, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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12
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Qing Y, Zheng Y, Mlotshwa S, Smith HN, Wang X, Zhai X, van der Knaap E, Wang Y, Fei Z. Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication. Plant J 2022; 110:1536-1550. [PMID: 35514123 DOI: 10.1111/tpj.15798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/23/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
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Affiliation(s)
- You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | | | - Heather N Smith
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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13
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Pokhrel S, Meyers BC. Heat-responsive microRNAs and phased small interfering RNAs in reproductive development of flax. Plant Direct 2022; 6:e385. [PMID: 35224420 PMCID: PMC8845017 DOI: 10.1002/pld3.385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 05/05/2023]
Abstract
Plants will face increased heat stress due to rising global temperatures. Heat stress affects plant reproductive development and decreases productivity; however, the underlying molecular mechanisms of these processes are poorly characterized. Plant small RNAs (sRNAs) have important regulatory roles in plant reproductive development following abiotic stress responses. We generated sRNA transcriptomes of reproductive bud stages at three different time points to identify sRNA-mediated pathways responsive to heat stress in flax (Linum usitatissimum). With added sRNA transcriptomes of vegetative tissues, we comprehensively annotated miRNA and phasiRNA-encoding genes (PHAS) in flax. We identified 173 miRNA genes, of which 42 are newly annotated. Our analysis revealed that 141 miRNA genes were differentially accumulated between tissue types, while 18 miRNA genes were differentially accumulated in reproductive tissues following heat stress, including members of miR482/2118 and miR2275 families, known triggers of reproductive phasiRNAs. Furthermore, we identified 68 21-PHAS flax loci from protein-coding and noncoding regions, four 24-PHAS loci triggered by miR2275, and 658 24-PHAS-like loci with unknown triggers, derived mostly from noncoding regions. The reproductive phasiRNAs are mostly downregulated in response to heat stress. Overall, we found that several previously unreported miRNAs and phasiRNAs are responsive to heat stress in flax reproductive tissues.
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Affiliation(s)
- Suresh Pokhrel
- Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Blake C. Meyers
- Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
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14
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Abstract
Small RNAs (sRNAs) are short noncoding RNAs involved in the regulation of a wide range of biological processes in plants. Advances in high-throughput sequencing and development of new computational tools had facilitated the discovery of different classes of sRNAs, their quantification, and elucidation of their functional role in gene expression regulation by target transcript predictions. The workflow presented here allows identification of different sRNA species: known and novel potato miRNAs, and their sequence variants (isomiRs), as well as identification of phased small interfering RNAs (phasiRNAs). Moreover, it includes steps for differential expression analysis to search for regulated sRNAs across different tested biological conditions. In addition, it describes two different methods for predicting sRNA targets, in silico prediction, and degradome sequencing data analysis. All steps of the workflow are written in a clear and user-friendly way; thus they can be followed also by the users with minimal bioinformatics knowledge. We also included several in-house scripts together with valuable notes to facilitate data (pre)processing steps and to reduce the analysis time.
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15
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Abstract
Since co-suppression was discovered as a pioneer silencing phenomenon of RNA interference (RNAi) in petunia in 1990, many types of small RNAs have been identified in the RNAi pathway among various eukaryotes. In plants, a large number of 21- or 24-nucleotide (nt) phased small interfering RNAs (phasiRNAs) are produced via processing of long RNA precursors by Dicer-like proteins. However, the roles of phasiRNAs remain largely unknown. The development of imaging technology and RNA profiling has clarified the spatiotemporal regulation of phasiRNAs, and subsequently the different functions of 21-nt trans-acting phasiRNAs and 24-nt cis-regulatory phasiRNAs during male organ development. This review focuses on the biogenesis, diversification, spatiotemporal expression pattern and function of phasiRNAs in plants.
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Affiliation(s)
- Reina Komiya
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST).,PRESTO, Japan Science and Technology Agency (JST)
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16
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Wang L, Zhu T, Rodriguez JC, Deal KR, Dubcovsky J, McGuire PE, Lux T, Spannagl M, Mayer KFX, Baldrich P, Meyers BC, Huo N, Gu YQ, Zhou H, Devos KM, Bennetzen JL, Unver T, Budak H, Gulick PJ, Galiba G, Kalapos B, Nelson DR, Li P, You FM, Luo MC, Dvorak J. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 (Bethesda) 2021; 11:6369516. [PMID: 34515796 PMCID: PMC8664484 DOI: 10.1093/g3journal/jkab325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.
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Affiliation(s)
- Le Wang
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Juan C Rodriguez
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.,University of Missouri, Columbia, Division of Plant Sciences, Columbia, Missouri 65211, USA
| | - Naxin Huo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, California 94710, USA
| | - Yong Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, California 94710, USA
| | - Hongye Zhou
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Dept. of Crop & Soil Sciences) and Dept. of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | | | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara 06374, Turkey
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, Montana 59801, USA
| | - Patrick J Gulick
- Department of Biology, Concordia University, Montreal, Quebec H3G 1M8, Canada
| | - Gabor Galiba
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, H-2462 Martonvásár, Hungary.,Department of Environmental Sustainability, IES, Hungarian University of Agriculture and Life Sciences, H-8360 Keszthely, Hungary
| | - Balázs Kalapos
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, H-2462 Martonvásár, Hungary
| | - David R Nelson
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C5, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C5, Canada
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
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17
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Iwakawa HO, Lam AYW, Mine A, Fujita T, Kiyokawa K, Yoshikawa M, Takeda A, Iwasaki S, Tomari Y. Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants. Cell Rep 2021; 35:109300. [PMID: 34192539 DOI: 10.1016/j.celrep.2021.109300] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/10/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
The path of ribosomes on mRNAs can be impeded by various obstacles. One such example is halting of ribosome movement by microRNAs, but the exact mechanism and physiological role remain unclear. Here, we find that ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates production of secondary small interfering RNAs (siRNAs) in plants. We show that the double-stranded RNA-binding protein SGS3 interacts directly with the 3' end of the microRNA in an Argonaute protein, resulting in ribosome stalling. Importantly, microRNA-mediated ribosome stalling correlates positively with efficient production of secondary siRNAs from target mRNAs. Our results illustrate a role of paused ribosomes in regulation of small RNA function that may have broad biological implications across the plant kingdom.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan.
| | - Andy Y W Lam
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akira Mine
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan; Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Kanagawa 226-8503, Japan
| | - Kaori Kiyokawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Manabu Yoshikawa
- Division of Crop Growth Mechanism, Research Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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18
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Dermastia M, Škrlj B, Strah R, Anžič B, Tomaž Š, Križnik M, Schönhuber C, Riedle-Bauer M, Ramšak Ž, Petek M, Kladnik A, Lavrač N, Gruden K, Roitsch T, Brader G, Pompe-Novak M. Differential Response of Grapevine to Infection with ' Candidatus Phytoplasma solani' in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes. Int J Mol Sci 2021; 22:3531. [PMID: 33805429 DOI: 10.3390/ijms22073531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.
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19
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Tian P, Zhang X, Xia R, Liu Y, Wang M, Li B, Liu T, Shi J, Wing RA, Meyers BC, Chen M. Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytol 2021; 229:2970-2983. [PMID: 33111313 DOI: 10.1111/nph.17035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 05/20/2023]
Abstract
In grasses, two types of phased, small interfering RNAs (phasiRNAs) are expressed largely in young, developing anthers. They are 21 or 24 nucleotides (nt) in length and are triggered by miR2118 or miR2275, respectively. However, most of their functions and activities are not fully understood. We performed comparative genomic analysis of their source loci (PHAS) in five Oryza genomes and combined this with analysis of high-throughput sRNA and degradome datasets. In total, we identified 8216 21-PHAS and 626 24-PHAS loci. Local tandem and segmental duplications mainly contributed to the expansion and supercluster distribution of the 21-PHAS loci. Despite their relatively conserved genomic positions, PHAS sequences diverged rapidly, except for the miR2118/2275 target sites, which were under strong selection for conservation. We found that 21-nt phasiRNAs with a 5'-terminal uridine (U) demonstrated cis-cleavage at PHAS precursors, and these cis-acting sites were also variable among close species. miR2118 could trigger phasiRNA production from its own antisense transcript and the derived phasiRNAs might reversibly regulate miR2118 precursors. We hypothesised that successful initiation of phasiRNA biogenesis is conservatively maintained, while phasiRNA products diverged quickly and are not individually conserved. In particular, phasiRNA production is under the control of multiple reciprocal regulation mechanisms.
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Affiliation(s)
- Peng Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xuemei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tieyan Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake C Meyers
- Division of Plant Sciences, 52 Agriculture Laboratory, University of Missouri, Columbia, Missouri, 65211, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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20
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Zhang M, Ma X, Wang C, Li Q, Meyers BC, Springer NM, Walbot V. CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers. New Phytol 2021; 229:2984-2997. [PMID: 33135165 DOI: 10.1111/nph.17060] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/14/2020] [Indexed: 05/23/2023]
Abstract
Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.
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Affiliation(s)
- Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Xuxu Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Li
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri-Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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21
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Yang X, You C, Wang X, Gao L, Mo B, Liu L, Chen X. Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes. Genome Biol 2021; 22:15. [PMID: 33402203 PMCID: PMC7784310 DOI: 10.1186/s13059-020-02242-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Background Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action. Results We investigate the cytoplasmic partitioning of sRNAs and their targets globally in maize (Zea mays, inbred line “B73”) and rice (Oryza sativa, cv. “Nipponbare”) by high-throughput sequencing of polysome-associated sRNAs and 3′ cleavage fragments, and find that both miRNAs and a subset of 21-nucleotide (nt)/22-nt siRNAs are enriched on membrane-bound polysomes (MBPs) relative to total polysomes (TPs) across different tissues. Most of the siRNAs are generated from transposable elements (TEs), and retrotransposons positively contributed to MBP overaccumulation of 22-nt TE-derived siRNAs (TE-siRNAs) as opposed to DNA transposons. Widespread occurrence of miRNA-mediated target cleavage is observed on MBPs, and a large proportion of these cleavage events are MBP-unique. Reproductive 21PHAS (21-nt phasiRNA-generating) and 24PHAS (24-nt phasiRNA-generating) precursors, which were commonly considered as noncoding RNAs, are bound by polysomes, and high-frequency cleavage of 21PHAS precursors by miR2118 and 24PHAS precursors by miR2275 is further detected on MBPs. Reproductive 21-nt phasiRNAs are enriched on MBPs as opposed to TPs, whereas 24-nt phasiRNAs are nearly completely devoid of polysome occupancy. Conclusions MBP overaccumulation is a conserved pattern for cytoplasmic partitioning of sRNAs, and endoplasmic reticulum (ER)-bound ribosomes function as an independent regulatory layer for miRNA-induced gene silencing and reproductive phasiRNA biosynthesis in maize and rice.
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Affiliation(s)
- Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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Bélanger S, Baldrich P, Lemay M, Marchand S, Esteves P, Meyers BC, Belzile F. The commitment of barley microspores into embryogenesis correlates with miRNA-directed regulation of members of the SPL, GRF and HD-ZIPIII transcription factor families. Plant Direct 2020; 4:e00289. [PMID: 36406053 PMCID: PMC9671080 DOI: 10.1002/pld3.289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/26/2020] [Accepted: 10/19/2020] [Indexed: 05/19/2023]
Abstract
Microspore embryogenesis is a model for developmental plasticity and cell fate decisions. To investigate the role of miRNAs in this development, we sequenced sRNAs and the degradome of barley microspores collected prior to (day 0) and after (days 2 and 5) the application of a stress treatment known to induce embryogenesis. Microspores isolated at these timepoints were uniform in both appearance and in their complements of sRNAs. We detected 68 miRNAs in microspores. The abundance of 51 of these miRNAs differed significantly during microspore development. One group of miRNAs was induced when the stress treatment was applied, prior to being repressed when microspores transitioned to embryogenesis. Another group of miRNAs were up-regulated in day-2 microspores and their abundance remained stable or increased in day-5 microspores, a timepoint at which the first clear indications of the transition toward embryogenesis were visible. Collectively, these miRNAs might play a role in the modulation of the stress response, the repression of gametic development, and/or the gain of embryogenic potential. A degradome analysis allowed us to validate the role of miRNAs in regulating 41 specific transcripts. We showed that the transition of microspores toward the embryogenesis pathway involves miRNA-directed regulation of members of the ARF, SPL, GRF, and HD-ZIPIII transcription factor families. We noted that 41.5% of these targets were shared between day-2 and day-5 microspores while 26.8% were unique to day-5 microspores. The former set may act to disrupt transcripts involved in pollen development while the latter set may drive the commitment to embryogenesis.
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Affiliation(s)
- Sébastien Bélanger
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | - Marc‐André Lemay
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Suzanne Marchand
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Patricio Esteves
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - François Belzile
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
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23
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Luan W, Dai Y, Li XY, Wang Y, Tao X, Li CX, Mao P, Ma XR. Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid. BMC Plant Biol 2020; 20:320. [PMID: 32635887 PMCID: PMC7339384 DOI: 10.1186/s12870-020-02528-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/26/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma. RESULTS Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5'terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated. CONCLUSIONS Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.
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Affiliation(s)
- Wei Luan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Yu Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cai-Xia Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
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24
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Corrigendum: Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. Front Plant Sci 2020; 11:653. [PMID: 32582234 PMCID: PMC7290127 DOI: 10.3389/fpls.2020.00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2016.00762.].
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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, St. Paul, MN, United States
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, United States
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
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25
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Sós‐Hegedűs A, Domonkos Á, Tóth T, Gyula P, Kaló P, Szittya G. Suppression of NB-LRR genes by miRNAs promotes nitrogen-fixing nodule development in Medicago truncatula. Plant Cell Environ 2020; 43:1117-1129. [PMID: 31834628 PMCID: PMC7317971 DOI: 10.1111/pce.13698] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/26/2019] [Accepted: 12/04/2019] [Indexed: 05/29/2023]
Abstract
Plant genomes contain two major classes of innate immune receptors to recognize different pathogens. The pattern recognition receptors perceive conserved pathogen-associated molecular patterns and the resistance genes with nucleotide-binding (NB) and leucine-rich repeat (LRR) domains recognize specific pathogen effectors. The precise regulation of resistance genes is important since the unregulated expression of NB-LRR genes can inhibit growth and may result in autoimmunity in the absence of pathogen infection. It was shown that a subset of miRNAs could target NB-LRR genes and act as an important regulator of plant immunity in the absence of pathogens. Plants not only interact with pathogens, but they can also establish symbiotic interactions with microbes. Nitrogen-fixing symbiotic interaction and nodule formation of legumes may also require the suppression of host defence to prevent immune responses. We found that upon symbiotic interactions, miRNAs repressing NB-LRR expression are upregulated in the developing nodules of Medicago truncatula. Furthermore, we show that the suppression of the activity of the NB-LRR genes targeted by these miRNAs is important during nodule development. Our results suggest that the downregulation of NB-LRR resistance genes in the developing nodule produces a suitable niche that facilitates bacterial colonization and the development of an N-fixing nodule.
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Affiliation(s)
- Anita Sós‐Hegedűs
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Ágota Domonkos
- Department of GeneticsAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Tamás Tóth
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Péter Gyula
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Péter Kaló
- Department of GeneticsAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
- Institute of Plant BiologyBiological Research CentreSzegedHungary
| | - György Szittya
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
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26
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Das S, Swetha C, Pachamuthu K, Nair A, Shivaprasad PV. Loss of function of Oryza sativa Argonaute 18 induces male sterility and reduction in phased small RNAs. Plant Reprod 2020; 33:59-73. [PMID: 32157461 DOI: 10.1007/s00497-020-00386-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/03/2020] [Indexed: 05/14/2023]
Abstract
In this manuscript, we show that Oryza sativa indica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position. Previous reports have implicated this protein in viral resistance as well as in gametogenesis, likely through its competition with AGO1 clade members for micro(mi)RNAs and other small (s)RNAs. Although expression of rice AGO18 in specific stages of male gametogenesis has been documented, its major functions in plant development remain poorly understood. Here, we show that Oryza sativa indica AGO18 is involved in male gametophyte development. Knockdown (KD) of AGO18 in transgenic rice lines resulted in stunted plants that are male sterile, whereas their carpels were functional. Transcriptome analysis revealed downregulation of several pollen development-associated genes in KD lines. sRNA sequencing in vegetative and reproductive tissues of KD lines indicated reduction of miRNAs and phased secondary sRNAs implicated in male gametophyte development. Our results indicate a distinct role for rice AGO18 in male fertility.
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Affiliation(s)
- Soumita Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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27
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Abstract
MicroRNAs (miRNAs) are a class of small RNAs (sRNAs) that repress gene expression via high complementary binding sites in target mRNAs (messenger RNAs). Many miRNAs are ancient, and their intricate integration into gene expression programs have been fundamental for plant life, controlling developmental programs and executing responses to biotic/abiotic cues. Additionally, there are many less conserved miRNAs in each plant species, raising the possibility that the functional impact of miRNAs extends into virtually every aspect of plant biology. This Special Issue of Plants presents papers that investigate the function and mechanism of miRNAs in controlling development and abiotic stress response. This includes how miRNAs adapt plants to nutrient availability, and the silencing machinery that is responsible for this. Several papers profile changes in miRNA abundances during stress, and another study raises the possibility of circular RNAs acting as endogenous decoys to sequester and inhibit plant miRNA function. These papers act as foundational studies for the more difficult task ahead of determining the functional significance of these changes to miRNA abundances, or the presence of these circular RNAs. Finally, how miRNAs trigger the production of secondary sRNAs is reviewed, along with the potential agricultural impact of miRNAs and these secondary sRNA in the exemplar crop maize.
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Affiliation(s)
- Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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28
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Liu Q, Ding C, Lang X, Guo G, Chen J, Su X. Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. Brief Bioinform 2019; 22:463-473. [PMID: 31885040 PMCID: PMC7820841 DOI: 10.1093/bib/bbz151] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 11/01/2019] [Indexed: 02/05/2023] Open
Abstract
Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Xiaoqiang Lang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ganggang Guo
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China 610041
| | - Jiafei Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Xiaohua Su
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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29
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Prigigallo MI, Križnik M, De Paola D, Catalano D, Gruden K, Finetti-Sialer MM, Cillo F. Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato. Viruses 2019; 11:v11121100. [PMID: 31783643 PMCID: PMC6950276 DOI: 10.3390/v11121100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/19/2019] [Accepted: 11/24/2019] [Indexed: 12/17/2022] Open
Abstract
Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype.
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Affiliation(s)
- Maria I. Prigigallo
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, G. Via Amendola 122/D, 70126 Bari, Italy;
| | - Maja Križnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (M.K.); (K.G.)
| | - Domenico De Paola
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, Via G. Amendola 165/A, 70126 Bari, Italy;
| | - Domenico Catalano
- Consiglio Nazionale delle Ricerche, Istituto di Tecnologie Biomediche, Via G. Amendola 122/D, 70126 Bari, Italy;
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (M.K.); (K.G.)
| | - Mariella M. Finetti-Sialer
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, Via G. Amendola 165/A, 70126 Bari, Italy;
- Correspondence: (M.M.F.-S.); (F.C.); Tel.: +39-080-55583400 (ext. 213) (M.M.F.-S.); +39-080-5443109 (F.C.)
| | - Fabrizio Cillo
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, G. Via Amendola 122/D, 70126 Bari, Italy;
- Correspondence: (M.M.F.-S.); (F.C.); Tel.: +39-080-55583400 (ext. 213) (M.M.F.-S.); +39-080-5443109 (F.C.)
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Li J, Hull JJ, Liang S, Wang Q, Chen L, Zhang Q, Wang M, Mansoor S, Zhang X, Jin S. Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction. Int J Mol Sci 2019; 20:E5357. [PMID: 31661835 DOI: 10.3390/ijms20215357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/14/2019] [Accepted: 10/25/2019] [Indexed: 01/10/2023] Open
Abstract
Although the regulatory function of miRNAs and their targets have been characterized in model plants, a possible underlying role in the cotton response to herbivore infestation has not been determined. To investigate this, we performed small RNA and degradome sequencing between resistant and susceptible cotton cultivar following infestation with the generalist herbivore whitefly. In total, the 260 miRNA families and 241 targets were identified. Quantitative-PCR analysis revealed that several miRNAs and their corresponding targets exhibited dynamic spatio-temporal expression patterns. Moreover, 17 miRNA precursors were generated from 29 long intergenic non-coding RNA (lincRNA) transcripts. The genome-wide analysis also led to the identification of 85 phased small interfering RNA (phasiRNA) loci. Among these, nine PHAS genes were triggered by miR167, miR390, miR482a, and two novel miRNAs, including those encoding a leucine-rich repeat (LRR) disease resistance protein, an auxin response factor (ARF) and MYB transcription factors. Through combined modeling and experimental data, we explored and expanded the miR390-tasiARF cascade during the cotton response to whitefly. Virus-induced gene silencing (VIGS) of ARF8 from miR390 target in whitefly-resistant cotton plants increased auxin and jasmonic acid (JA) accumulation, resulting in increased tolerance to whitefly infestation. These results highlight the provides a useful transcriptomic resource for plant-herbivore interaction.
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Dhaka N, Sharma S, Vashisht I, Kandpal M, Sharma MK, Sharma R. Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum. Genomics 2019; 112:1598-1610. [PMID: 31521711 DOI: 10.1016/j.ygeno.2019.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 02/06/2023]
Abstract
Understanding male gametophyte development is essential to augment hybrid production in sorghum. Although small RNAs are known to critically influence anther/pollen development, their roles in sorghum reproduction have not been deciphered yet. Here, we report small RNA profiling and high-confidence annotation of microRNAs (miRNAs) from meiotic and post-meiotic anthers in sorghum. We identified 262 miRNAs (82 known and 180 novel), out of which 58 (35 known and 23 novel) exhibited differential expression between two stages. Out of 35 differentially expressed known miRNAs, 13 are known to regulate anther/pollen development in other plant species. We also demonstrated conserved spatiotemporal patterns of 21- and 24-nt phasiRNAs and their respective triggers, miR2118 and miR2275, in sorghum anthers as evidenced in other monocots. miRNA target identification yielded 5622 modules, of which 46 modules comprising 16 known and 8 novel miRNA families with 38 target genes are prospective candidates for engineering male fertility in grasses.
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Affiliation(s)
- Namrata Dhaka
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Shalini Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Ira Vashisht
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manu Kandpal
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manoj Kumar Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India.
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Sun W, Chen D, Xue Y, Zhai L, Zhang D, Cao Z, Liu L, Cheng C, Zhang Y, Zhang Z. Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq. BMC Genomics 2019; 20:656. [PMID: 31419938 PMCID: PMC6697968 DOI: 10.1186/s12864-019-6028-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Background Argonaute proteins (AGOs) are important players in the regulation of plant development by directing sRNAs to target mRNAs. In maize (Zea mays), AGO18b is a tassel-enriched and grass-specific AGO. Previous studies have shown that AGO18b is highly expressed in tassels during meiosis and negatively regulates determinacy of spikelet meristems. However, binding profile on RNAs and acting mechanisms of AGO18b remain unknown. Results In this study, we explored the binding profile of AGO18b in maize tassel by UV cross-linking RNA immunoprecipitation, followed by deep sequencing of these cDNA libraries (cRIP-seq), and systematically studied AGO18b-associated small RNAs and mRNAs by bioinformatics analysis. By globally analyzing the phased small-interfering RNA (phasiRNA) and miRNA abundance bound by AGO18b, we found AGO18b primarily binds to 21-nt phasiRNAs/miRNAs with a 5′-uridine and binds less strongly to 24-nt phasiRNAs with a 5′-adenosine in the premeiotic tassels. The abundance profile of AGO18b-associated miRNAs was different from their expression profile. Moreover, AGO18b strongly binds to miR166a-3p. We then obtained the AGO18b-bound mRNA targets of miR166a-3p by cRIP-seq, and confirmed the molecular function of AGO18b in regulating spikelet meristems. Conclusions Our results indicated that AGO18b binds to phasiRNAs with obvious 5 prime end bias under different sRNA length. MiRNAs and their target mRNAs associated with AGO18b indicated the molecular mechanisms of AGO18b as a negative regulator of inflorescence meristem and tassel development through integrating both phasiRNAs and miRNA pathways, which extended our view of sRNA regulation in flower development and provided potential methods to control pollination in the future. Electronic supplementary material The online version of this article (10.1186/s12864-019-6028-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Sun
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Yaqiang Xue
- Laboratory for Genome Regulation and Human Health, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Lihong Zhai
- Medical College of Hubei University of Arts and Science, Xiangyang, 441053, People's Republic of China
| | - Dan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zheng Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chao Cheng
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China. .,Laboratory for Genome Regulation and Human Health, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Zhang Z, Teotia S, Tang J, Tang G. Perspectives on microRNAs and Phased Small Interfering RNAs in Maize ( Zea mays L.): Functions and Big Impact on Agronomic Traits Enhancement. Plants (Basel) 2019; 8:E170. [PMID: 31212808 DOI: 10.3390/plants8060170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023]
Abstract
Small RNA (sRNA) population in plants comprises of primarily micro RNAs (miRNAs) and small interfering RNAs (siRNAs). MiRNAs play important roles in plant growth and development. The miRNA-derived secondary siRNAs are usually known as phased siRNAs, including phasiRNAs and tasiRNAs. The miRNA and phased siRNA biogenesis mechanisms are highly conserved in plants. However, their functional conservation and diversification may differ in maize. In the past two decades, lots of miRNAs and phased siRNAs have been functionally identified for curbing important maize agronomic traits, such as those related to developmental timing, plant architecture, sex determination, reproductive development, leaf morphogenesis, root development and nutrition, kernel development and tolerance to abiotic stresses. In contrast to Arabidopsis and rice, studies on maize miRNA and phased siRNA biogenesis and functions are limited, which restricts the small RNA-based fundamental and applied studies in maize. This review updates the current status of maize miRNA and phased siRNA mechanisms and provides a survey of our knowledge on miRNA and phased siRNA functions in controlling agronomic traits. Furthermore, improvement of those traits through manipulating the expression of sRNAs or their targets is discussed.
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de Felippes FF. Gene Regulation Mediated by microRNA-Triggered Secondary Small RNAs in Plants. Plants (Basel) 2019; 8:plants8050112. [PMID: 31035467 PMCID: PMC6572396 DOI: 10.3390/plants8050112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 01/18/2023]
Abstract
In plants, proper development and response to abiotic and biotic stimuli requires an orchestrated regulation of gene expression. Small RNAs (sRNAs) are key molecules involved in this process, leading to downregulation of their target genes. Two main classes of sRNAs exist, the small interfering RNAs (siRNAs) and microRNAs (miRNAs). The role of the latter class in plant development and physiology is well known, with many examples of how miRNAs directly impact the expression of genes in cells where they are produced, with dramatic consequences to the life of the plant. However, there is an aspect of miRNA biology that is still poorly understood. In some cases, miRNA targeting can lead to the production of secondary siRNAs from its target. These siRNAs, which display a characteristic phased production pattern, can act in cis, reinforcing the initial silencing signal set by the triggering miRNA, or in trans, affecting genes that are unrelated to the initial target. In this review, the mechanisms and implications of this process in the gene regulation mediated by miRNAs will be discussed. This work will also explore techniques for gene silencing in plants that are based on this unique pathway.
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Vargas-Asencio JA, Perry KL. A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs. Front Plant Sci 2019; 10:1710. [PMID: 32082334 PMCID: PMC7001039 DOI: 10.3389/fpls.2019.01710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 12/05/2019] [Indexed: 05/19/2023]
Abstract
Gene regulation involves the orchestrated action of multiple regulators to fine-tune the expression of genes. Hierarchical interactions and co-regulation among regulators are commonly observed in biological systems, leading to complex regulatory networks. Small RNA (sRNAs) have been shown to be important regulators of gene expression due to their involvement in multiple cellular processes. In plants, microRNA (miRNAs) and phased small interfering RNAs (phasiRNAs) correspond to two well-characterized types of sRNAs involved in the regulation of posttranscriptional gene expression, although information about their targets and interactions with other gene expression regulators is limited. We describe an extended sRNA-mediated regulatory network in Arabidopsis thaliana that provides a reference frame to understand sRNA biogenesis and activity at the genome-wide level. This regulatory network combines a comprehensive evaluation of phasiRNA production and sRNA targets supported by degradome data. The network includes ~17% of genes in the A. thaliana genome, representing ~50% annotated gene ontology (GO) functional categories. Approximately 14% of genes with GO annotations corresponding to regulation of gene expression were found to be under sRNA control. The unbiased bioinformatic approach used to produce the network was able to detect 107 PHAS loci (regions of phasiRNA production), 5,047 active phasiRNAs (~70% of which were non-canonical), and reconstruct 17 regulatory modules resulting from complex regulatory interactions between different sRNA-regulatory pathways. Known regulatory modules like miR173-TAS-PPR/TPR and miR390-TAS3-ARF/F-box were faithfully reconstructed and expanded, illustrating the accuracy and sensitivity of the methods and providing confidence for the validity of findings of previously unrecognized modules. The network presented here includes a 2X increase in the number of identified PHAS loci, a large complement (~70%) of non-canonical phasiRNAs, and the most comprehensive evaluation of sRNA cleavage activity in A. thaliana to date. Structural analysis showed similarities to networks of other biological systems and demonstrated connectivity between phasiRNA regulatory modules with extensive co-regulation of transcripts by miRNAs and phasiRNAs. The described regulatory network provides a reference that will facilitate global analyses of individual plant regulatory programs such as those that control homeostasis, development, and responses to biotic and abiotic environmental changes.
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Gyula P, Baksa I, Tóth T, Mohorianu I, Dalmay T, Szittya G. Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF-YA2 and YUC2. Plant Cell Environ 2018; 41:2404-2417. [PMID: 29856891 DOI: 10.1111/pce.13355] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Plants substantially alter their developmental programme upon changes in the ambient temperature. The 21-24 nt small RNAs (sRNAs) are important gene expression regulators, which play a major role in development and adaptation. However, little is known about how the different sRNA classes respond to changes in the ambient temperature. We profiled the sRNA populations in four different tissues of Arabidopsis thaliana plants grown at 15°C, 21°C, and 27°C. We found that only a small fraction (0.6%) of the sRNA loci are ambient temperature-controlled. We identified thermoresponsive microRNAs and identified their target genes using degradome libraries. We verified that the target of the thermoregulated miR169, NF-YA2, is also ambient temperature-regulated. NF-YA2, as the component of the conserved transcriptional regulator NF-Y complex, binds the promoter of the flowering time regulator FT and the auxin biosynthesis gene YUC2. Other differentially expressed loci include thermoresponsive phased siRNA loci that target various auxin pathway genes and tRNA fragments. Furthermore, a temperature-dependent 24-nt heterochromatic siRNA locus in the promoter of YUC2 may contribute to the epigenetic regulation of auxin homeostasis. This holistic approach facilitated a better understanding of the role of different sRNA classes in ambient temperature adaptation of plants.
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Affiliation(s)
- Péter Gyula
- Agricultural Biotechnology Institute, Epigenetics Group, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - Ivett Baksa
- Agricultural Biotechnology Institute, Epigenetics Group, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - Tamás Tóth
- Agricultural Biotechnology Institute, Epigenetics Group, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - Irina Mohorianu
- University of East Anglia, School of Biological Sciences, Norwich, UK
- University of East Anglia, School of Computing Sciences, Norwich, UK
| | - Tamás Dalmay
- University of East Anglia, School of Biological Sciences, Norwich, UK
| | - György Szittya
- Agricultural Biotechnology Institute, Epigenetics Group, National Agricultural Research and Innovation Center, Gödöllő, Hungary
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Ma W, Chen C, Liu Y, Zeng M, Meyers BC, Li J, Xia R. Coupling of microRNA-directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA-mediated gene silencing. New Phytol 2018; 217:1535-1550. [PMID: 29218722 DOI: 10.1111/nph.14934] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 10/31/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play vital regulatory roles in plant growth and development. Little is known about these small RNAs in litchi (Litchi chinensis), an economically important fruit crop widely cultivated in Southeast Asia. We profiled the litchi small RNA population with various deep-sequencing techniques and in-depth bioinformatic analyses. The genome-wide identification of miRNAs, their target genes, and phasiRNA-generating (PHAS) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function. We also discovered that, for 29 PHAS loci, miRNA-mediated phasiRNA production was coupled with alternative splicing (AS) and alternative polyadenylation (APA). Most of these loci encoded long noncoding RNAs. An miR482/2118 targeted locus gave rise to four main transcript isoforms through AS/APA, and diverse phasiRNAs generated from these isoforms appeared to target long terminal repeat (LTR) retrotransposons and other unrelated genes. This coupling enables phasiRNA production from different exons of noncoding PHAS genes and yields diverse phasiRNA populations, both broadening and altering the range of downstream phasiRNA-regulated genes. Our results reveal the diversity of miRNA and phasiRNA in litchi, and demonstrate AS/APA as a new layer of regulation in small RNA-mediated gene silencing.
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Affiliation(s)
- Wuqiang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Zeng
- Modern Education and Technology Center, South China Agricultural University, Guangzhou, 510642, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri - Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
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Abstract
Postranscriptional regulation has been widely shown to be regulated by several classes of small non-coding RNAs; most abundantly, microRNAs, which have been shown to be the first dominant class and has been widely characterized as post-transcriptional regulators. In addition to microRNAs, triggered by miRNAs, transcripts called as PHAS (or TAS) generate abundant class of small RNAs in 21-nt manner, which is a pattern formed by DICER-LIKE 4 (DCL4) processing. Although PHAS can be identified by aligning transcripts to reported PHAS in other species, the most sensitive and accurate way to discovery them is by mapping of the smallRNAs taking into account the transcript coordinates. Here, we describe a workflow that can be used for the identification PHAS and corresponding phasiRNAs in Brachypodium distachyon using publically availabe smallRNAs datasets.
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Abstract
Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs (phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long RNA precursors at intervals of 21 or 24 nt in plants, and they are produced from both protein-coding gene and long noncoding RNA genes. Different from those in eudicots, grass phasiRNAs include a special class of small RNAs that are specifically expressed in reproductive organs. These grass phasiRNAs are associated with gametogenesis, especially with anther development and male fertility. In this review, we summarized current knowledge on these small noncoding RNAs in male germ cells and their possible biological functions and mechanisms in grass species.
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Affiliation(s)
- Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yanfei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuchan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yueqin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Abstract
BACKGROUND Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs. RESULTS Here we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, supporting the wide range of species for which non-coding RNA reference sequences are available in the Ensembl databases (currently more than 800). unitas combines high quality annotation and numerous analysis features in a user-friendly manner. A complete annotation can be started with one simple shell command, making unitas particularly useful for researchers not having access to a bioinformatics facility. Noteworthy, the algorithms implemented in unitas are on par or even outperform comparable existing tools for small RNA annotation that map to publicly available ncRNA databases. CONCLUSIONS unitas brings together annotation and analysis features that hitherto required the installation of numerous different bioinformatics tools which can pose a challenge for the non-expert user. With this, unitas overcomes the problem of read normalization. Moreover, the high quality of sequence annotation and analysis, paired with the ease of use, make unitas a valuable tool for researchers in all fields connected to small RNA biology.
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Affiliation(s)
- Daniel Gebert
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099, Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099, Mainz, Germany.
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Fan Y, Yang J, Mathioni SM, Yu J, Shen J, Yang X, Wang L, Zhang Q, Cai Z, Xu C, Li X, Xiao J, Meyers BC, Zhang Q. PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice. Proc Natl Acad Sci U S A 2016; 113:15144-9. [PMID: 27965387 DOI: 10.1073/pnas.1619159114] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.
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Sun Y, Mui Z, Liu X, Yim AKY, Qin H, Wong FL, Chan TF, Yiu SM, Lam HM, Lim BL. Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages. Int J Mol Sci 2016; 17:E2043. [PMID: 27929436 PMCID: PMC5187843 DOI: 10.3390/ijms17122043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions. Based on a sliding window analysis workflow that we developed, 50 PHAS loci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41 PHAS loci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistant TIR-NB-LRR genes constitute a very large family of PHAS loci. PhasiRNAs were also generated from several loci that encode for NAC transcription factors, Dicer-like 2 (DCL2), Pentatricopeptide Repeat (PPR), and Auxin Signaling F-box 3 (AFB3) proteins. To investigate the possible involvement of miRNAs in initiating the PHAS-phasiRNA pathway, miRNA target predictions were performed and 17 C08 miRNAs and 15 W05 miRNAs were predicted to trigger phasiRNAs biogenesis. In summary, we provide a comprehensive description of the sRNA profiles of wild versus cultivated soybeans, and discuss the possible roles of sRNAs during soybean germination.
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Affiliation(s)
- Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Zeta Mui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xuan Liu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Aldrin Kay-Yuen Yim
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Hao Qin
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Fuk-Ling Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Siu-Ming Yiu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Fei Q, Yang L, Liang W, Zhang D, Meyers BC. Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways. J Exp Bot 2016; 67:6037-6049. [PMID: 27702997 PMCID: PMC5100018 DOI: 10.1093/jxb/erw361] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for examining traits of agronomic importance such as male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, plays an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein that acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wild-type rice, and from msp1 and ostdl1a mutants. Analysis of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of these OsAGO transcripts and phasiRNA accumulations.
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Affiliation(s)
- Qili Fei
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Li Yang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, South Australia 5064, Australia
| | - Blake C Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. Front Plant Sci 2016; 7:762. [PMID: 27313591 PMCID: PMC4889585 DOI: 10.3389/fpls.2016.00762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and micro RNAs (miRNAs) directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolated male meiocytes from maize (Zea mays) to investigate sRNA and DNA methylation landscapes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes take place. We discovered two novel miRNAs from meiocytes, zma-MIR11969 and zma-MIR11970, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 or 24 nt intervals, at a few hundred loci, specifically in male reproductive tissues in grasses. So far, the function of phasiRNAs remained elusive. Data from isolated meiocytes now revealed elevated DNA methylation at phasiRNA loci, especially in the CHH context, suggesting a role for phasiRNAs in cis DNA methylation. In addition, we consider a role of these phasiRNAs in chromatin remodeling/dynamics during meiosis. However, this is not well supported yet and will need more additional data. Here, we only lay out the idea due to other relevant literature and our additional observation of a peculiar GC content pattern at phasiRNA loci. Chromatin remodeling is also indicated by the discovery that histone genes were enriched for sRNA of 22 nt length. Taken together, we gained clues that lead us to hypothesize sRNA-driven DNA methylation and possibly chromatin remodeling during male meiosis in the monocot maize which is in line with and extends previous knowledge.
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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
- *Correspondence: Changbin Chen,
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Xia R, Xu J, Arikit S, Meyers BC. Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants. Mol Biol Evol 2015; 32:2905-18. [PMID: 26318183 PMCID: PMC4651229 DOI: 10.1093/molbev/msv164] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In eudicot plants, the miR482/miR2118 superfamily regulates and instigates the production of phased secondary small interfering RNAs (siRNAs) from NB-LRR (nucleotide binding leucine-rich repeat) genes that encode disease resistance proteins. In grasses, this miRNA family triggers siRNA production specifically in reproductive tissues from long noncoding RNAs. To understand this functional divergence, we examined the small RNA population in the ancient gymnosperm Norway spruce (Picea abies). As many as 41 miRNA families in spruce were found to trigger phasiRNA (phased, secondary siRNAs) production from diverse PHAS loci, with a remarkable 19 miRNA families capable of targeting over 750 NB-LRR genes to generate phasiRNAs. miR482/miR2118, encoded in spruce by at least 24 precursor loci, targets not only NB-LRR genes to trigger phasiRNA production (as in eudicots) but also noncoding PHAS loci, generating phasiRNAs preferentially in male or female cones, reminiscent of its role in the grasses. These data suggest a dual function of miR482/miR2118 present in gymnosperms that was selectively yet divergently retained in flowering plants. A few MIR482/MIR2118 precursors possess an extremely long stem-loop structure, one arm of which shows significant sequence similarity to spruce NB-LRR genes, suggestive of an evolutionary origin from NB-LRR genes through gene duplication. We also characterized an expanded miR390-TAS3 (TRANS-ACTING SIRNA GENE 3)-ARF (AUXIN RESPONSIVE FACTOR) pathway, comprising 18 TAS3 genes of diverse features. Finally, we annotated spruce miRNAs and their targets. Taken together, these data expand our understanding of phasiRNA network in plants and the evolution of plant miRNAs, particularly miR482/miR2118 and its functional diversification.
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Affiliation(s)
- Rui Xia
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
| | - Jing Xu
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
| | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Nakhon Pathom, Thailand
| | - Blake C Meyers
- Department of Plant & Soil Sciences, University of Delaware Delaware Biotechnology Institute, University of Delaware
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Fei Q, Li P, Teng C, Meyers BC. Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances. Plant J 2015; 83:451-65. [PMID: 26042408 DOI: 10.1111/tpj.12900] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/23/2015] [Accepted: 05/28/2015] [Indexed: 05/04/2023]
Abstract
Small RNAs are a class of non-coding RNAs that are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and (typically) a microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasi-RNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3' terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3' terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this might be due to target inaccessibility determined by sequences flanking target sites. Our results suggest that target accessibility is an important component in miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA-target sites may be impacted.
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Affiliation(s)
- Qili Fei
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Pingchuan Li
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Chong Teng
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Blake C Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
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Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N, Nonomura KI. Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Plant J 2014; 78:385-97. [PMID: 24635777 DOI: 10.1111/tpj.12483] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/31/2014] [Accepted: 02/07/2014] [Indexed: 05/03/2023]
Abstract
Small RNAs that interact with Argonaute (AGO) proteins play central roles in RNA-mediated silencing. MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1), a rice AGO, has specific functions in the development of pre-meiotic germ cells and the progression of meiosis. Here, we show that MEL1, which is located mostly in the cytoplasm of germ cells, associates preferentially with 21-nucleotide phased small interfering RNAs (phasiRNAs) that bear a 5'-terminal cytosine. Most phasiRNAs are derived from 1171 intergenic clusters distributed on all rice chromosomes. From these clusters, over 700 large intergenic, non-coding RNAs (lincRNAs) that contain the consensus sequence complementary to miR2118 are transcribed specifically in inflorescences, and cleaved within the miR2118 site. Cleaved lincRNAs are processed via DICER-LIKE4 (DCL4) protein, resulting in production of phasiRNAs. This study provides the evidence that the miR2118-dependent and the DCL4-dependent pathways are both required for biogenesis of 21-nt phasiRNAs associated with germline-specific MEL1 AGO in rice, and over 700 lincRNAs are key factors for induction of this biogenesis during reproductive-specific stages.
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Affiliation(s)
- Reina Komiya
- Experimental Farm, National Institute of Genetics (NIG), Mishima, Shizuoka, 411-8540, Japan
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Ye CY, Xu H, Shen E, Liu Y, Wang Y, Shen Y, Qiu J, Zhu QH, Fan L. Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. Front Plant Sci 2014; 5:743. [PMID: 25566308 PMCID: PMC4274897 DOI: 10.3389/fpls.2014.00743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/05/2014] [Indexed: 05/19/2023]
Abstract
A wide range of RNA species interacting with microRNAs (miRNAs) form a complex gene regulation network and play vital roles in diverse biological processes. In this study, we performed a genome-wide identification of endogenous target mimics (eTMs) for miRNAs and phased-siRNA-producing loci (PHAS) in soybean with a focus on those involved in lipid metabolism. The results showed that a large number of eTMs and PHAS genes could be found in soybean. Additionally, we found that lipid metabolism related genes were potentially regulated by 28 miRNAs, and nine of them were potentially further regulated by a number of eTMs with expression evidence. Thirty-three miRNAs were found to trigger production of phasiRNAs from 49 PHAS genes, which were able to target lipid metabolism related genes. Degradome data supported miRNA- and/or phasiRNA-mediated cleavage of genes involved in lipid metabolism. Most eTMs for miRNAs involved in lipid metabolism and phasiRNAs targeting lipid metabolism related genes showed a tissue-specific expression pattern. Our bioinformatical evidences suggested that lipid metabolism in soybean is potentially regulated by a complex non-coding network, including miRNAs, eTMs, and phasiRNAs, and the results extended our knowledge on functions of non-coding RNAs.
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Affiliation(s)
- Chu-Yu Ye
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Hao Xu
- Guhe InformationHangzhou, China
| | - Enhui Shen
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yang Liu
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yu Wang
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yifei Shen
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Jie Qiu
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Qian-Hao Zhu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
| | - Longjiang Fan
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
- *Correspondence: Longjiang Fan, Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd., Hangzhou 310058, China e-mail:
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Abstract
Plant miRNAs can trigger the production of phased, secondary siRNAs from either non-coding or protein-coding genes. In this study, at least 864 and 3,961 loci generating 21-nt and 24-nt phased siRNAs (phasiRNAs),respectively, were identified in three tissues from wild rice. Of these phasiRNA-producing loci, or PHAS genes, biogenesis of phasiRNAs in at least 160 of 21-nt and 254 of 24-nt loci could be triggered by interaction with miRNA(s). Developing seeds had more PHAS genes than leaves and roots. Genetic constrain on miRNA-triggered PHAS genes suggests that phasiRNAs might be one of the driving forces contributed to rice domestication.
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Affiliation(s)
- Yang Liu
- Department of Agronomy & James D. Watson Institute of Genome Sciences; Zhejiang University; Hangzhou, PR China
| | - Yu Wang
- Department of Agronomy & James D. Watson Institute of Genome Sciences; Zhejiang University; Hangzhou, PR China
| | | | - Longjiang Fan
- Department of Agronomy & James D. Watson Institute of Genome Sciences; Zhejiang University; Hangzhou, PR China
- Correspondence to: Longjiang Fan,
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