1
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Zhuomeng L, Ji T, Chen Q, Xu C, Liu Y, Yang X, Li J, Yang F. Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant. PeerJ 2024; 12:e17341. [PMID: 38827281 PMCID: PMC11141551 DOI: 10.7717/peerj.17341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/15/2024] [Indexed: 06/04/2024] Open
Abstract
Phosphorus is one of the lowest elements absorbed and utilized by plants in the soil. SPX domain-containing genes family play an important role in plant response to phosphate deficiency signaling pathway, and related to seed development, disease resistance, absorption and transport of other nutrients. However, there are no reports on the mechanism of SPX domain-containing genes in response to phosphorus deficiency in eggplant. In this study, the whole genome identification and functional analysis of SPX domain-containing genes family in eggplant were carried out. Sixteen eggplant SPX domain-containing genes were identified and divided into four categories. Subcellular localization showed that these proteins were located in different cell compartments, including nucleus and membrane system. The expression patterns of these genes in different tissues as well as under phosphate deficiency with auxin were explored. The results showed that SmSPX1, SmSPX5 and SmSPX12 were highest expressed in roots. SmSPX1, SmSPX4, SmSPX5 and SmSPX14 were significantly induced by phosphate deficiency and may be the key candidate genes in response to phosphate starvation in eggplant. Among them, SmSPX1 and SmSPX5 can be induced by auxin under phosphate deficiency. In conclusion, our study preliminary identified the SPX domain genes in eggplant, and the relationship between SPX domain-containing genes and auxin was first analyzed in response to phosphate deficiency, which will provide theoretical basis for improving the absorption of phosphorus in eggplants through molecular breeding technology.
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Affiliation(s)
- Li Zhuomeng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Tuo Ji
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai an, China
| | - Qi Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Chenxiao Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Yuqing Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Xiaodong Yang
- Weifang Academy of Agricultural Science, Weifang, China
| | - Jing Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai an, China
| | - Fengjuan Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai an, China
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2
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Azad MF, Dawar P, Esim N, Rock CD. Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1278320. [PMID: 38023835 PMCID: PMC10656695 DOI: 10.3389/fpls.2023.1278320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.
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Affiliation(s)
- Md. Fakhrul Azad
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Nevzat Esim
- Department of Molecular Biology and Genetics, Bіngöl University, Bingöl, Türkiye
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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3
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Yadav B, Majhi A, Phagna K, Meena MK, Ram H. Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing. Funct Integr Genomics 2023; 23:317. [PMID: 37837547 DOI: 10.1007/s10142-023-01244-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.
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Affiliation(s)
- Banita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashis Majhi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Phagna
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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4
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Chandra T, Jaiswal S, Iquebal MA, Singh R, Gautam RK, Rai A, Kumar D. Revitalizing miRNAs mediated agronomical advantageous traits improvement in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107933. [PMID: 37549574 DOI: 10.1016/j.plaphy.2023.107933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/04/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - R K Gautam
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India; Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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5
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Huang C, Wang J, Wang D, Chang J, Chen H, Chen D, Deng W, Tian C. Genome-Wide Identification and Analysis of OsSPXs Revealed Its Genetic Influence on Cold Tolerance of Dongxiang Wild Rice (DXWR). Int J Mol Sci 2023; 24:ijms24108755. [PMID: 37240100 DOI: 10.3390/ijms24108755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1, OsSPX2, OsSPX4, and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs, which is helpful for the gene-function research of DXWR and genetic improvements during breeding.
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Affiliation(s)
- Cheng Huang
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jilin Wang
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Dianwen Wang
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hongping Chen
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Dazhou Chen
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Wei Deng
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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6
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Singh NRR, Roychowdhury A, Srivastava R, Gaganan GA, Parida AP, Kumar R. Silencing of SlSPX1 and SlSPX2 promote growth and root mycorrhization in tomato (Solanum lycopersicum L.) seedlings. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 333:111723. [PMID: 37142098 DOI: 10.1016/j.plantsci.2023.111723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/10/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Owing to the essential requirement of phosphorus (P) for growth and development, plants tightly control inorganic phosphate (Pi) homeostasis. SPX-PHR regulatory circuit not only control phosphate homeostasis responses but also root mycorrhization by arbuscular mycorrhiza (AM) fungi. Besides sensing Pi deficiency, SPX (SYG1/Pho81/XPR1) proteins also control the transcription of P starvation inducible (PSI) genes by blocking the activity of PHR1 (PHOSPHATE STARVATION RESPONSE1) homologs in plants under Pi-sufficient conditions. However, the roles of SPX members in Pi homeostasis and AM fungi colonization remain to be fully recognized in tomato. In this study, we identified 17 SPX-domain containing members in the tomato genome. Transcript profiling revealed the high Pi-specific nature of their activation. Four SlSPX members have also induced in AM colonized roots. Interestingly, we found that SlSPX1 and SlSPX2 are induced by P starvation and AM colonization. Further, SlSPX1 and SlSPX2 exhibited varying degrees of interaction with the PHR homologs in this study. Virus-induced gene silencing-based (VIGS) transcript inhibition of these genes alone or together promoted the accumulation of higher total soluble Pi in tomato seedlings and improved their growth. It also enhanced AM fungi colonization in the roots of SlSPX1 and SlSPX2 silenced seedlings. Overall, the present study provides evidence in support of SlSPX members being good candidates for improving AM fungi colonization potential in tomato.
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Affiliation(s)
| | | | - Rajat Srivastava
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | | | - Adwaita Prasad Parida
- Department of Entomology, Texas A&M University, College Station, Texas 77843-2475, USA
| | - Rahul Kumar
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
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7
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Sun Y, Wu Q, Xie Z, Huang J. Transcription factor OsNAC016 negatively regulates phosphate-starvation response in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111618. [PMID: 36738935 DOI: 10.1016/j.plantsci.2023.111618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/11/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Phosphate (Pi), the main form of inorganic phosphorus that can be absorbed by plants, is one of the most limiting macro-nutrients in plants. However, the underlying molecular mechanism determining how plants sense external Pi levels and reprogram transcriptional and adaptive responses is incompletely understood. At present, few rice NAC members have been reported to be involved in the signaling pathways of Pi homeostasis in plants. Here, our research demonstrated that OsNAC016, a Pi-starvation responsive gene in rice, was regulated by PHOSPHATE STARVATION RESPONSE protein 1 (OsPHR1) and OsPHR4. Under Pi-starvation stress, the root growth of OsNAC016-overexpression lines was inhibited more severely, and overexpression plants had lower Pi content than wild type, while osnac016 mutant was hyposensitive to Pi starvation, indicating that OsNAC016 negatively modulates rice Pi-starvation response. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) analysis and transient transactivation assays indicated that OsNAC016 could activate the SPX-domain-containing protein 2 (OsSPX2) gene through binding to its promoter. Further, we found that Pi starvation enhanced OsNAC016 binding to the OsSPX2 promoter, thus strongly promoting OsSPX2 expression. At the same time, Pi starvation induced OsNAC016 protein accumulation in plants. Moreover, similar to OsSPX2, OsNAC016 negatively regulates leaf inclination by repressing the cell elongation in lamina joint in rice under Pi-starvation stress. Together, our findings demonstrate that OsNAC016 negatively regulates rice phosphate-starvation response and leaf inclination by activating OsSPX2 expression under Pi-starvation conditions. These data provide a strategy to create smart crops with ideal shoot architecture and high phosphorus utilization efficiency.
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Affiliation(s)
- Ying Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Qi Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Zizhao Xie
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
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8
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Lu H, Wang F, Wang Y, Lin R, Wang Z, Mao C. Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1104-1119. [PMID: 36208118 DOI: 10.1111/pce.14457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is a macronutrient required for plant growth and reproduction. Orthophosphate (Pi), the preferred P form for plant uptake, is easily fixed in the soil, making it unavailable to plants. Limited phosphate rock resources, low phosphate fertilizer use efficiency and high demands for green agriculture production make it important to clarify the molecular mechanisms underlying plant responses to P deficiency and to improve plant phosphate efficiency in crops. Over the past 20 years, tremendous progress has been made in understanding the regulatory mechanisms of the plant P starvation response. Here, we systematically review current research on the mechanisms of Pi acquisition, transport and distribution from the rhizosphere to the shoot; Pi redistribution and reuse during reproductive growth; and the molecular mechanisms of arbuscular mycorrhizal symbiosis in rice (Oryza sativa L.) under Pi deficiency. Furthermore, we discuss several strategies for boosting P utilization efficiency and yield in rice.
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Affiliation(s)
- Hong Lu
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rongbin Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuanzao Mao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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9
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Guo R, Zhang Q, Ying Y, Liao W, Liu Y, Whelan J, Chuanzao M, Shou H. Functional characterization of the three Oryza sativa SPX-MFS proteins in maintaining phosphate homoeostasis. PLANT, CELL & ENVIRONMENT 2023; 46:1264-1277. [PMID: 35909262 DOI: 10.1111/pce.14414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/15/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Plant vacuoles serve as the primary intracellular compartments for phosphorus (P) storage. The Oryza sativa genome contains three genes that encode SPX ( SYG1/ PHO81/ XPR1)-MFS ( Major Facility Superfamily) proteins (OsSPX-MFS1-3). The physiological roles of the three transporters under varying P conditions in laboratory and field are not known. To address this knowledge gap, we generated single, double and triple mutants for three OsSPX-MFS genes. All the mutants except Osspx-mfs2 display lower vacuolar Pi concentrations and OsSPX-MFSs overexpression plant display higher Pi accumulation, demonstrating that all OsSPX-MFSs are vacuolar Pi influx transporters. OsSPX-MFS3 plays the dominant role based on the phenotypes of single mutants in terms of growth, vacuolar and tissue Pi concentrations. OsSPX-MFS2 is the weakest and only functions as vacuole Pi sequestration in an Osspx-mfs1/3 background. The vacuolar Pi sequestration capacity was severely impaired in Osspx-mfs1/3 and Osspx-mfs1/2/3, which resulted in increased Pi allocation to aerial organs. High P in the panicle impaired panicle and fertility in Osspx-mfs1/3 and Osspx-mfs1/2/3. Osspx-mfs2 resulted in a more stable yield compared to the wild type under low P in field grown plants. The results suggest that alteration of vacuolar Pi sequestration may be a novel effective strategy to improve rice tolerance to low phosphorus in cropping systems.
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Affiliation(s)
- Runze Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Team of Seed Engineering and Industrialization, Hainan Institute, Zhejiang University, Sanya, China
| | - Qi Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Team of Seed Engineering and Industrialization, Hainan Institute, Zhejiang University, Sanya, China
| | - Yinghui Ying
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenying Liao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Team of Seed Engineering and Industrialization, Hainan Institute, Zhejiang University, Sanya, China
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - James Whelan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Animal, Plant and Soil Science, School of Life Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Melbourne, Victoria, Australia
| | - Mao Chuanzao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Team of Seed Engineering and Industrialization, Hainan Institute, Zhejiang University, Sanya, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Team of Seed Engineering and Industrialization, Hainan Institute, Zhejiang University, Sanya, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, China
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10
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Zhang YC, Yuan C, Chen YQ. Noncoding RNAs and their roles in regulating the agronomic traits of crops. FUNDAMENTAL RESEARCH 2023. [DOI: 10.1016/j.fmre.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
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11
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Brownlee C, Helliwell KE, Meeda Y, McLachlan D, Murphy EA, Wheeler GL. Regulation and integration of membrane transport in marine diatoms. Semin Cell Dev Biol 2023; 134:79-89. [PMID: 35305902 DOI: 10.1016/j.semcdb.2022.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Diatoms represent one of the most successful groups of marine phytoplankton and are major contributors to ocean biogeochemical cycling. They have colonized marine, freshwater and ice environments and inhabit all regions of the World's oceans, from poles to tropics. Their success is underpinned by a remarkable ability to regulate their growth and metabolism during nutrient limitation and to respond rapidly when nutrients are available. This requires precise regulation of membrane transport and nutrient acquisition mechanisms, integration of nutrient sensing mechanisms and coordination of different transport pathways. This review outlines transport mechanisms involved in acquisition of key nutrients (N, C, P, Si, Fe) by marine diatoms, illustrating their complexity, sophistication and multiple levels of control.
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Affiliation(s)
- Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Sciences, University of Southampton, Southampton SO14 3ZH, UK
| | - Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Yasmin Meeda
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Deirdre McLachlan
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Eleanor A Murphy
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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12
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Characterization and evolutionary analysis of phosphate starvation response genes in wheat and other major gramineous plants. Int J Biol Macromol 2023; 225:63-78. [PMID: 36481332 DOI: 10.1016/j.ijbiomac.2022.11.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
Developing cultivars with improved Pi use efficiency is essential for the sustainability of agriculture as well as the environment. Phosphate starvation response (PHR) regulators have not yet been systematically studied in wheat. This study provides the detailed characteristics of PHRs in hexaploid wheat as well as other major gramineous plants at the genome-wide level. The identified PHR proteins were divided into six subfamilies through phylogeny analysis, and a total of 63 paralogous TaPHR pairs were designated as arising from duplication events, with strong purifying selection. The promoters of TaPHRs were identified as stations for many transcription factors. Protein-protein interaction network and gene ontology enrichment analysis indicated a core biological process of cellular response to phosphate starvation. The three-dimensional structures of core PHR proteins showed a high phylogenetic relationship, but amino acid deletions in core protein domains may cause functional differentiation between rice and wheat. TaPHR3 could interact with TaSPX1 and TaSPX5 proteins, which is regarded as a novel interaction mode. Under different Pi gradient treatments, TaPHRs showed low inducible expression patterns among all subfamilies. Our study is the first to comprehensively clarify the basic properties of TaPHR proteins and might accumulate basic data for improving grain yield and environmental homeostasis.
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Yang Z, Yuan L, Zhu H, Jiang J, Yang H, Li L. Small RNA profiling reveals the involvement of microRNA-mediated gene regulation in response to symbiosis in raspberry. Front Microbiol 2022; 13:1082494. [PMID: 36620006 PMCID: PMC9810812 DOI: 10.3389/fmicb.2022.1082494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Dark septate endophytes (DSEs) can form reciprocal symbioses with most terrestrial plants, providing them with mineral nutrients in exchange for photosynthetic products. Although the mechanism of plant-DSEs is well understood at the transcriptional level, little is known about their post-transcriptional regulation, and microRNAs (miRNAs) for the symbiotic process of DSE infestation of raspberry have not been identified. In this study, we comprehensively identified the miRNAs of DSE-infested raspberry symbiosis using Illumina sequencing. A total of 361 known miRNAs and 95 novel miRNAs were identified in the roots. Similar to other dicotyledons, most of the identified raspberry miRNAs were 21 nt in length. Thirty-seven miRNAs were differentially expressed during colonization after inoculation with Phialocephala fortinii F5, suggesting a possible role for these miRNAs in the symbiotic process. Notably, two miRNAs (miR171h and miR396) previously reported to be responsive to symbiotic processes in alfalfa also had altered expression during raspberry symbiosis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggests that miRNAs are mainly involved in regulatory mechanisms, such as biological processes, cellular metabolic processes, biosynthesis of secondary metabolites, plant-pathogen interactions, and phytohormone signaling pathways. This study revealed the potential conservation of miRNA-mediated post-transcriptional regulation in symbiotic processes among plants and provides some novel miRNAs for understanding the regulatory mechanisms of DSE-raspberry symbiosis.
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Affiliation(s)
- Zhiyu Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Lianmei Yuan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Haifeng Zhu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Jing Jiang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Hongyi Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China,*Correspondence: Hongyi Yang,
| | - Lili Li
- Institute of Forestry Science of Heilongjiang Province, Harbin, China,Lili Li,
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Zhao Y, Li P, Wang H, Feng J, Li Y, Wang S, Li Y, Guo Y, Li L, Su Y, Sun Z. Genome-wide investigation and expression pattern of PHR family genes in cotton under low phosphorus stress. PeerJ 2022; 10:e14584. [PMID: 36540806 PMCID: PMC9760022 DOI: 10.7717/peerj.14584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Phosphorus starvation response (PHR) protein is an important transcription factor in phosphorus regulatory network, which plays a vital role in regulating the effective utilization of phosphorus. So far, the PHR genes have not been systematically investigated in cotton. In the present study, we have identified 22, 23, 41 and 42 PHR genes in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. Phylogenetic analysis showed that cotton PHR genes were classified into five distinct subfamilies. The gene structure, protein motifs and gene expression were further investigated. The PHR genes of G. hirsutum from the same subfamily had similar gene structures, all containing Myb_DNA-binding and Myb_CC_LHEQLE conserved domain. The structures of paralogous genes were considerably conserved in exons number and introns length. The cis-element prediction in their promoters showed that genes were not only regulated by light induction, but also were related to auxin, MeJA, abscisic acid-responsive elements, of which might be regulated by miRNA. The expression analysis showed that the GhPHR genes were differentially expressed in different tissues under various stresses. Furthermore, GhPHR6, GhPHR11, GhPHR18 and GhPHR38 were significantly changed under low phosphorus stress. The results of this study provide a basis for further cloning and functional verification of genes related to regulatory network of low phosphorus tolerance in cotton.
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Soumya PR, Vengavasi K, Pandey R. Adaptive strategies of plants to conserve internal phosphorus under P deficient condition to improve P utilization efficiency. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1981-1993. [PMID: 36573147 PMCID: PMC9789281 DOI: 10.1007/s12298-022-01255-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Phosphorus (P) is one of the limiting factors for plant growth and productivity due to its slow diffusion and immobilization in the soil which necessitates application of phosphatic fertilizers to meet the crop demand and obtain maximum yields. However, plants have evolved mechanisms to adapt to low P stress conditions either by increasing acquisition (alteration of belowground processes) or by internal inorganic P (Pi) utilization (cellular Pi homeostasis) or both. In this review, we have discussed the adaptive strategies that conserve the use of P and maintain cellular Pi homeostasis in the cytoplasm. These strategies involve modification in membrane lipid composition, flavanol/anthocyanin level, scavenging and reutilization of Pi adsorbed in cell wall pectin, remobilization of Pi during senescence by enzymes like RNases and purple acid phosphatases, alternative mitochondrial electron transport, and glycolytic pathways. The remobilization of Pi from senescing tissues and its internal redistribution to various cellular organelles is mediated by various Pi transporters. Although much efforts have been made to enhance P acquisition efficiency, an understanding of the physiological mechanisms conserving internal Pi and their manipulation would be useful for plants that can utilize P more efficiently to produce optimum growth per unit P uptake.
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Affiliation(s)
- Preman R. Soumya
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
- Present Address: Regional Agricultural Research Station, Kerala Agricultural University, Ambalavayal, Wayanad, Kerala 673593 India
| | - Krishnapriya Vengavasi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
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Lu Y, Zhang J, Han Z, Han Z, Li S, Zhang J, Ma H, Han Y. Screening of differentially expressed microRNAs and target genes in two potato varieties under nitrogen stress. BMC PLANT BIOLOGY 2022; 22:478. [PMID: 36207676 PMCID: PMC9547441 DOI: 10.1186/s12870-022-03866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. In recent years, some of the mechanisms of miRNAs have been elucidated via the analysis of the correlation between the expression levels of potato miRNA target genes and regulated genes under conditions of stress, but the role of miRNAs in the inhibition/expression of key genes regulating N metabolism under N stress is still unclear. Our study aimed to identify the role played by specific enzymes and miRNAs in the responses of plants to N stress. RESULTS The roots and leaves of the N-efficient potato variety, Yanshu4 ("Y"), and N-inefficient potato variety, Atlantic ("D"), were collected at the seedling and budding stages after they were exposed to different N fertilizer treatments. The miRNAs expressed differentially under the two types of N stress and their corresponding target genes were first predicted using miRNA and degradome analysis. Then, quantitative polymerase chain reaction (qRT-PCR) was performed to verify the expression of differential miRNAs that were closely related to N metabolism. Finally, the shearing relationship between stu-miR396-5p and its target gene StNiR was determined by analyzing luciferase activity levels. The results showed that NiR activity increased significantly with an increase in the applied N levels from the seedling stage to the budding stage, and NiR responded significantly to different N treatments. miRNA sequencing enabled us to predict 48 families with conserved miRNAs that were mainly involved in N metabolism, carbon metabolism, and amino acid biosynthesis. The differences in the expression of the following miRNAs were identified via screening (high expression levels and P < 0.05): stu-miR396-5p, stu-miR408b-3p_R-1, stu-miR3627-3p, stu-miR482a-3p, stu-miR8036-3p, stu-miR482a-5p, stu-miR827-5p, stu-miR156a_L-1, stu-miR827-3p, stu-miR172b-5p, stu-miR6022-p3_7, stu-miR398a-5p, and stu-miR166c-5p_L-3. Degradome analysis showed that most miRNAs had many-to-many relationships with target genes. The main target genes involved in N metabolism were NiR, NiR1, NRT2.5, and NRT2.7. qRT-PCR analysis showed that there were significant differences in the expression levels of stu-miR396-5p, stu-miR8036-3p, and stu-miR482a-3p in the leaves and roots of the Yanshu4 and Atlantic varieties at the seedling and budding stages under conditions that involved no N and excessive N application; the expression of these miRNAs was induced in response to N stress. The correlation between the differential expression of stu-miR396-5p and its corresponding target gene NiR was further verified by determining the luciferase activity level and was found to be strongly negative. CONCLUSION The activity of NiR was significantly positively correlated with N application from the seedling to the budding stage. Differential miRNAs and target genes showed a many-to-many relationship with each other. The expression of stu-miR396-5p, stu-miR482a-3p, and stu-miR8036-3p in the roots and leaves of the Yanshu4 and Atlantic varieties at the seedling and budding stages was notably different under two types of N stress. Under two types of N stress, stu-miR396-5p was down-regulated in Yanshu4 in the seedling-stage and shoot-stage roots, and up-regulated in seedling-stage roots and shoot-stage leaves; stu-miR482a-3p was up-regulated in the seedling and shoot stages. The expression of stu-miR8036-3p was up-regulated in the leaves and roots at the seedling and budding stages, and down-regulated in roots under both types of N stress. The gene expressing the key enzyme involved in N metabolism, StNiR, and the stu-miR396-5p luciferase assay reporter gene had a strong regulatory relationship with each other. This study provides candidate miRNAs related to nitrogen metabolism and highlights that differential miRNAs play a key role in nitrogen stress in potato, providing insights for future research on miRNAs and their target genes in nitrogen metabolic pathways and breeding nitrogen-efficient potatoes.
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Affiliation(s)
- Yue Lu
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Jingying Zhang
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
- College of Resources and Environment, Jilin Agricultural University, Changchun City, 130118, P.R. China
| | - Zhijun Han
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Zhongcai Han
- Jilin Provincial Research Institute of Vegetables and Flowers, Changchun City, 130052, People's Republic of China
| | - Shuang Li
- Teaching and Research Base Management Office, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Jiayue Zhang
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Haoran Ma
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Yuzhu Han
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China.
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Xue H, Liu J, Oo S, Patterson C, Liu W, Li Q, Wang G, Li L, Zhang Z, Pan X, Zhang B. Differential Responses of Wheat ( Triticum aestivum L.) and Cotton ( Gossypium hirsutum L.) to Nitrogen Deficiency in the Root Morpho-Physiological Characteristics and Potential MicroRNA-Mediated Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:928229. [PMID: 35845660 PMCID: PMC9281546 DOI: 10.3389/fpls.2022.928229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Understanding the mechanism of crop response to nitrogen (N) deficiency is very important for developing sustainable agriculture. In addition, it is unclear if the microRNA-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under N deficiency. Therefore, the root morpho-physiological characteristics and microRNA-mediated mechanisms were studied under N deficiency in wheat (Triticum aestivum L.) and cotton (Gossypium hirsutum L.). For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of N deficiency. Although N deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton. After 8 days of treatment with N deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton. At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of N deficiency treatment. Additionally, the two crops had different root regulatory mechanisms of microRNAs (miRNAs) to N deficiency. In wheat, the expressions of miR167, miR319, miR390, miR827, miR847, and miR165/166 were induced by N treatment; these miRNAs inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate N deficiency. In cotton, the expressions of miR156, miR167, miR171, miR172, miR390, miR396 were induced and the expressions of miR162 and miR393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the N deficiency. In conclusion, N deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by miRNAs, but the miRNA-mediated mechanisms were different in wheat and cotton.
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Affiliation(s)
- Huiyun Xue
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Jia Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Sando Oo
- Department of Biology, East Carolina University, Greenville, NC, United States
- Department of Biology, Elizabeth City State University, Elizabeth City, NC, United States
| | - Caitlin Patterson
- Department of Biology, East Carolina University, Greenville, NC, United States
- Department of Biology, Elizabeth City State University, Elizabeth City, NC, United States
| | - Wanying Liu
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qian Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Guo Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Lijie Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
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Ma X, Tang K, Tang Z, Dong A, Xiao H, Meng Y, Wang P. An organ-specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein-coding genes, microRNAs, and regulatory networks. THE PLANT GENOME 2022; 15:e20210. [PMID: 35475547 DOI: 10.1002/tpg2.20210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
As one of the important species belonging to the Bletilla genus of Orchidaceae, Bletilla striata (Thunb.) Rchb. f., possesses both ornamental and medicinal values. Its dried tubers are used as a traditional Chinese medicine, and several secondary metabolites have been indicated to be the active ingredients. However, the molecular mechanisms related to the regulation of secondary metabolism have not been characterized in B. striata. In this study, integrated analysis of RNA sequencing (RNA-seq), small RNA sequencing (sRNA-seq), and degradome sequencing (degradome-seq) data from three organs (leaf, root, and tuber) of B. striata provided us with a comprehensive view of the microRNA (miRNA)-mediated regulatory network. Firstly, based on the RNA-seq data, the organ-specific expression patterns of the protein-coding genes, especially for those related to secondary metabolism, were investigated. Secondly, 342 conserved miRNA candidates were identified from B. striata. These miRNAs were assigned to 88 families, some of which were selected for expression pattern analysis. Additionally, 31 hairpin-structured precursors encoding 23 novel miRNAs were uncovered from the transcriptome assembly. Thirdly, based on the degradome signatures, 1,142 validated miRNA-target pairs (involving 167 conserved miRNAs and six novel miRNAs and 51 target genes) were included in the regulatory network. Organ-specific expression level comparison between the miRNAs and their targets revealed some interesting miRNA-target pairs. Fourthly, some valuable subnetworks were extracted for further functional studies. Additionally, some regulatory pathways were indicated to be monocot specific. Summarily, our results lay a solid basis for in-depth studies on the regulatory mechanisms underlying the production of the medicinal ingredients in B. striata.
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Affiliation(s)
- Xiaoxia Ma
- College of Pharmaceutical Science, Zhejiang Univ. of Technology, Hangzhou, 310014, China
- School of Pharmacy, Hangzhou Normal Univ., Hangzhou, 311121, China
| | - Kehua Tang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou Univ., Zhangjiajie, 427000, China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural Univ., Changsha, 410128, China
| | - Aiwen Dong
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou Univ., Zhangjiajie, 427000, China
| | - Hang Xiao
- Dep. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, USA
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal Univ., Hangzhou, 311121, China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang Univ. of Technology, Hangzhou, 310014, China
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Abstract
As sessile organisms, plants have developed sophisticated mechanism to sense and utilize nutrients from the environment, and modulate their growth and development according to the nutrient availability. Research in the past two decades revealed that nutrient assimilation is not occurring spontaneously, but nutrient signaling networks are complexly regulated and integrate sensing and signaling, gene expression, and metabolism to ensure homeostasis and coordination with plant energy conversion and other processes. Here, we review the importance of the macronutrient sulfur (S) and compare the knowledge of S signaling with other important macronutrients, such as nitrogen (N) and phosphorus (P). We focus on key advances in understanding sulfur sensing and signaling, uptake and assimilation, and we provide new analysis of published literature, to identify core genes regulated by the key transcriptional factor in S starvation response, SLIM1/EIL3, and compare the impact on other nutrient deficiency and stresses on S-related genes.
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Affiliation(s)
- Daniela Ristova
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Stanislav Kopriva
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Str. 47b, 50674 Cologne, Germany
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20
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Abstract
Nutrients are scarce and valuable resources, so plants developed sophisticated mechanisms to optimize nutrient use efficiency. A crucial part of this is monitoring external and internal nutrient levels to adjust processes such as uptake, redistribution, and cellular compartmentation. Measurement of nutrient levels is carried out by primary sensors that typically involve either transceptors or transcription factors. Primary sensors are only now starting to be identified in plants for some nutrients. In particular, for nitrate, there is detailed insight concerning how the external nitrate status is sensed by members of the nitrate transporter 1 (NRT1) family. Potential sensors for other macronutrients such as potassium and sodium have also been identified recently, whereas for micronutrients such as zinc and iron, transcription factor type sensors have been reported. This review provides an overview that interprets and evaluates our current understanding of how plants sense macro and micronutrients in the rhizosphere and root symplast.
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21
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Prathap V, Kumar A, Maheshwari C, Tyagi A. Phosphorus homeostasis: acquisition, sensing, and long-distance signaling in plants. Mol Biol Rep 2022; 49:8071-8086. [PMID: 35318578 DOI: 10.1007/s11033-022-07354-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/09/2022] [Indexed: 12/29/2022]
Abstract
Phosphorus (P), an essential nutrient required by plants often becomes the limiting factor for plant growth and development. Plants employ various mechanisms to sense the continuously changing P content in the soil. Transcription factors, such as SHORT ROOT (SHR), AUXIN RESPONSE FACTOR19 (ARF19), and ETHYLENE-INSENSITIVE3 (EIN3) regulate the growth of primary roots, root hairs, and lateral roots under low P. Crop improvement strategies under low P depend either on improving P acquisition efficiency or increasing P utilization. The various phosphate transporters (PTs) are involved in the uptake and transport of P from the soil to various plant cellular organelles. A plethora of regulatory elements including transcription factors, microRNAs and several proteins play a critical role in the regulation of coordinated cellular P homeostasis. Among these, the well-established P starvation signaling pathway comprising of central transcriptional factor phosphate starvation response (PHR), microRNA399 (miR399) as a long-distance signal molecule, and PHOSPHATE 2 (PHO2), an E2 ubiquitin conjugase is crucial in the regulation of phosphorus starvation responsive genes. Under PHR control, several classes of PHTs, microRNAs, and proteins modulate root architecture, and metabolic processes to enable plants to adapt to low P. Even though sucrose and inositol phosphates are known to influence the phosphorus starvation response genes, the exact mechanism of regulation is still unclear. In this review, a basic understanding of P homeostasis under low P in plants and all the above aspects are discussed.
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Affiliation(s)
- V Prathap
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anuj Kumar
- ICAR- Indian Agricultural Statistical Research Institute, New Delhi, India
| | - Chirag Maheshwari
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Aruna Tyagi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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22
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The Genetic Basis of Phosphorus Utilization Efficiency in Plants Provide New Insight into Woody Perennial Plants Improvement. Int J Mol Sci 2022; 23:ijms23042353. [PMID: 35216469 PMCID: PMC8877309 DOI: 10.3390/ijms23042353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 01/01/2023] Open
Abstract
Soil nutrient restrictions are the main environmental conditions limiting plant growth, development, yield, and quality. Phosphorus (P), an essential macronutrient, is one of the most significant factors that vastly restrains the growth and development of plants. Although the total P is rich in soil, its bio-available concentration is still unable to meet the requirements of plants. To maintain P homeostasis, plants have developed lots of intricate responsive and acclimatory mechanisms at different levels, which contribute to administering the acquisition of inorganic phosphate (Pi), translocation, remobilization, and recycling of Pi. In recent years, significant advances have been made in the exploration of the utilization of P in annual plants, while the research progress in woody perennial plants is still vague. In the meanwhile, compared to annual plants, relevant reviews about P utilization in woody perennial plants are scarce. Therefore, based on the importance of P in the growth and development of plants, we briefly reviewed the latest advances on the genetic and molecular mechanisms of plants to uphold P homeostasis, P sensing, and signaling, ion transporting and metabolic regulation, and proposed the possible sustainable management strategies to fasten the P cycle in modern agriculture and new directions for future studies.
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23
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Li C, You Q, Zhao P. Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum. PeerJ 2022; 9:e12689. [PMID: 35036163 PMCID: PMC8710047 DOI: 10.7717/peerj.12689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/03/2021] [Indexed: 01/24/2023] Open
Abstract
The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.
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Affiliation(s)
- Chunwei Li
- Nanchang Normal University, Nanchang, China
| | - Qiuye You
- Shanghai Center for Plant Stress Biology, Shanghai, China
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Nezamivand-Chegini M, Ebrahimie E, Tahmasebi A, Moghadam A, Eshghi S, Mohammadi-Dehchesmeh M, Kopriva S, Niazi A. New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean. BMC Genomics 2021; 22:915. [PMID: 34969367 PMCID: PMC8717665 DOI: 10.1186/s12864-021-08242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/09/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. RESULTS We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. CONCLUSION This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.
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Affiliation(s)
| | - Esmaeil Ebrahimie
- Institute of biotechnology, Shiraz university, Shiraz, Iran
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, VIC, 3086, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, 5371, Australia
| | | | - Ali Moghadam
- Institute of biotechnology, Shiraz university, Shiraz, Iran
| | - Saeid Eshghi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Ali Niazi
- Institute of biotechnology, Shiraz university, Shiraz, Iran.
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Jafari M, Shiran B, Rabiei G, Ravash R, Sayed Tabatabaei BE, Martínez-Gómez P. Identification and verification of seed development related miRNAs in kernel almond by small RNA sequencing and qPCR. PLoS One 2021; 16:e0260492. [PMID: 34851991 PMCID: PMC8635354 DOI: 10.1371/journal.pone.0260492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
Many studies have investigated the role of miRNAs on the yield of various plants, but so far, no report is available on the identification and role of miRNAs in fruit and seed development of almonds. In this study, preliminary analysis by high-throughput sequencing of short RNAs of kernels from the crosses between almond cultivars 'Sefid' × 'Mamaee' (with small and large kernels, respectively) and 'Sefid' × 'P. orientalis' (with small kernels) showed that the expressions of several miRNAs such as Pdu-miR395a-3p, Pdu-miR8123-5p, Pdu-miR482f, Pdu-miR6285, and Pdu-miR396a were significantly different. These miRNAs targeted genes encoding different proteins such as NYFB-3, SPX1, PGSIP3 (GUX2), GH3.9, and BEN1. The result of RT-qPCR revealed that the expression of these genes showed significant differences between the crosses and developmental stages of the seeds, suggesting that these genes might be involved in controlling kernel size because the presence of these miRNAs had a negative effect on their target genes. Pollen source can influence kernel size by affecting hormonal signaling and metabolic pathways through related miRNAs, a phenomenon known as xenia.
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Affiliation(s)
- Marjan Jafari
- Department of Horticulture, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Gholamreza Rabiei
- Department of Horticulture, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Roudabeh Ravash
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
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Chiou TJ. Editorial Feature: Meet the PCP Editor-Tzyy-Jen Chiou. PLANT & CELL PHYSIOLOGY 2021; 62:1357-1358. [PMID: 34405238 DOI: 10.1093/pcp/pcab096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/18/2021] [Accepted: 06/26/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
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Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci 2021; 22:ijms222011205. [PMID: 34681864 PMCID: PMC8539900 DOI: 10.3390/ijms222011205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023] Open
Abstract
Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.
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Wang Y, Wang F, Lu H, Liu Y, Mao C. Phosphate Uptake and Transport in Plants: An Elaborate Regulatory System. PLANT & CELL PHYSIOLOGY 2021; 62:564-572. [PMID: 33508131 DOI: 10.1093/pcp/pcab011] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/12/2021] [Indexed: 05/18/2023]
Abstract
Phosphorus (P) is an essential macronutrient for plant growth and development. Low inorganic phosphate (Pi) availability is a limiting factor for plant growth and yield. To cope with a complex and changing environment, plants have evolved elaborate mechanisms for regulating Pi uptake and use. Recently, the molecular mechanisms of plant Pi signaling have become clearer. Plants absorb Pi from the soil through their roots and transfer Pi to various organs or tissues through phosphate transporters, which are precisely controlled at the transcript and protein levels. Here, we summarize recent progress on the molecular regulatory mechanism of phosphate transporters in Arabidopsis and rice, including the characterization of functional transporters, regulation of transcript levels, protein localization and turnover of phosphate transporters. A more in-depth understanding of plant adaptation to a changing Pi environment will facilitate the genetic improvement of plant P efficiency.
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Affiliation(s)
- Yan Wang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, 572025, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fei Wang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, 572025, China
| | - Hong Lu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuanzao Mao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, 572025, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Srivastava S, Suprasanna P. MicroRNAs: Tiny, powerful players of metal stress responses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:928-938. [PMID: 34246107 DOI: 10.1016/j.plaphy.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/14/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.
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Affiliation(s)
- Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, Maharashtra, India
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Sharma S, Vengavasi K, Kumar MN, Yadav SK, Pandey R. Expression of potential reference genes in response to macronutrient stress in rice and soybean. Gene 2021; 792:145742. [PMID: 34051336 DOI: 10.1016/j.gene.2021.145742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023]
Abstract
Given the complexity of nutrient stress responses and the availability of a few validated reference genes, we aimed to identify robust and stable reference genes for macronutrient stress in rice and soybean. Ten potential reference genes were evaluated using geNorm, NormFinder, BestKeeper, Comparative ΔCt method, and RefFinder algorithms under low and completely starved conditions of nitrogen (N), phosphorus (P), potassium (K), and sulphur (S). Results revealed distinct sets of reference gene pairs, showing stable expression under different experimental conditions. The gene pairs TIP41/UBC(9/10/18) and F-box/UBC10 were most stable in rice and soybean, respectively under N stress. Under P stress, UBC9/UBC10 in rice and F-Box/UBC10 in soybean were most stable. Similarly, TIP41/UBC10 in rice and RING FINGER/UBC9 in soybean were the best gene pairs under K stress while F-Box/TIP41 in rice and UBC9/UBC10 in soybean were the most stable gene pairs under S stress. These reference gene pairs were validated by quantifying the expression levels of high-affinity transporters like NRT2.1/NRT2.5, PT1, AKT1, and SULTR1 for N, P, K, and S stress, respectively. This study reiterates the importance of choosing reference genes based on crop species and the experimental conditions, in order to obtain concrete answers to missing links of gene regulation in response to macronutrient deficiencies.
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Affiliation(s)
- Sandeep Sharma
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Krishnapriya Vengavasi
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - M Nagaraj Kumar
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Shiv Kumar Yadav
- Division of Seed Science and Technology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India.
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31
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Li H, Yu TT, Ning YS, Li H, Zhang WW, Yang HQ. Hydrogen Sulfide Alleviates Alkaline Salt Stress by Regulating the Expression of MicroRNAs in Malus hupehensis Rehd. Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:663519. [PMID: 34381471 PMCID: PMC8350742 DOI: 10.3389/fpls.2021.663519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/06/2021] [Indexed: 06/13/2023]
Abstract
Malus hupehensis Rehd. var. pingyiensis Jiang (Pingyi Tiancha, PYTC) is an excellent apple rootstock and ornamental tree, but its tolerance to salt stress is weak. Our previous study showed that hydrogen sulfide (H2S) could alleviate damage in M. hupehensis roots under alkaline salt stress. However, the molecular mechanism of H2S mitigation alkaline salt remains to be elucidated. MicroRNAs (miRNAs) play important regulatory roles in plant response to salt stress. Whether miRNAs are involved in the mitigation of alkaline salt stress mediated by H2S remains unclear. In the present study, through the expression analysis of miRNAs and target gene response to H2S and alkaline salt stress in M. hupehensis roots, 115 known miRNAs (belonging to 37 miRNA families) and 15 predicted novel miRNAs were identified. In addition, we identified and analyzed 175 miRNA target genes. We certified the expression levels of 15 miRNAs and nine corresponding target genes by real-time quantitative PCR (qRT-PCR). Interestingly, H2S pretreatment could specifically induce the downregulation of mhp-miR408a expression, and upregulated mhp-miR477a and mhp-miR827. Moreover, root architecture was improved by regulating the expression of mhp-miR159c and mhp-miR169 and their target genes. These results suggest that the miRNA-mediated regulatory network participates in the process of H2S-mitigated alkaline salt stress in M. hupehensis roots. This study provides a further understanding of miRNA regulation in the H2S mitigation of alkaline salt stress in M. hupehensis roots.
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Torres-Rodríguez JV, Salazar-Vidal MN, Chávez Montes RA, Massange-Sánchez JA, Gillmor CS, Sawers RJH. Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.). BMC PLANT BIOLOGY 2021; 21:259. [PMID: 34090337 PMCID: PMC8178920 DOI: 10.1186/s12870-021-02997-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential production. Fertilizer application increases nutrient availability, but is not available to all farmers, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized. RESULTS We characterized growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. We identified 1555 genes to respond to our nutrient treatments, in one or both tissues. A large group of genes, including many classical P starvation response genes, were regulated antagonistically between low N and P conditions. An additional experiment over a range of N availability indicated that a mild reduction in N levels was sufficient to repress the low P induction of P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under N limitation. CONCLUSIONS Transcriptional responses to low N or P were distinct, with few genes responding in a similar way to the two single stress treatments. In combined NP stress, the low N response dominated, and the P starvation response was largely suppressed. A mild reduction in N availability was sufficient to repress the induction of P starvation associated genes. We conclude that activation of the transcriptional response to P starvation in maize is contingent on N availability.
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Affiliation(s)
- J Vladimir Torres-Rodríguez
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
| | - M Nancy Salazar-Vidal
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Ricardo A Chávez Montes
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Julio A Massange-Sánchez
- Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ) Subsede Zapopan, Guadalajara, Mexico
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
| | - Ruairidh J H Sawers
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico.
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA.
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Ma C, Chen Q, Wang S, Lers A. Downregulation of GeBP-like α factor by MiR827 suggests their involvement in senescence and phosphate homeostasis. BMC Biol 2021; 19:90. [PMID: 33941183 PMCID: PMC8091714 DOI: 10.1186/s12915-021-01015-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/29/2021] [Indexed: 01/15/2023] Open
Abstract
Background Leaf senescence is a genetically controlled degenerative process intimately linked to phosphate homeostasis during plant development and responses to environmental conditions. Senescence is accelerated by phosphate deficiency, with recycling and mobilization of phosphate from senescing leaves serving as a major phosphate source for sink tissues. Previously, miR827 was shown to play a significant role in regulating phosphate homeostasis, and induction of its expression was also observed during Arabidopsis leaf senescence. However, whether shared mechanisms underlie potentially common regulatory roles of miR827 in both processes is not understood. Here, we dissect the regulatory machinery downstream of miR827. Results Overexpression or inhibited expression of miR827 led to an acceleration or delay in the progress of senescence, respectively. The transcriptional regulator GLABRA1 enhancer-binding protein (GeBP)-like (GPLα) gene was identified as a possible target of miR827. GPLα expression was elevated in miR827-suppressed lines and reduced in miR827-overexpressing lines. Furthermore, heterologous co-expression of pre-miR827 in tobacco leaves reduced GPLα transcript levels, but this effect was eliminated when pre-miR827 recognition sites in GPLα were mutated. GPLα expression is induced during senescence and its inhibition or overexpression resulted in senescence acceleration and inhibition, accordingly. Furthermore, GPLα expression was induced by phosphate deficiency, and overexpression of GPLα led to reduced expression of phosphate transporter 1 genes, lower leaf phosphate content, and related root morphology. The encoded GPLα protein was localized to the nucleus. Conclusions We suggest that MiR827 and the transcription factor GPLα may be functionally involved in senescence and phosphate homeostasis, revealing a potential new role for miR827 and the function of the previously unstudied GPLα. The close interactions between senescence and phosphate homeostasis are further emphasized by the functional involvement of the two regulatory components, miR827 and GPLα, in both processes and the interactions between them.
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Affiliation(s)
- Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Department of Postharvest Science, Agricultural Research Organization, Volcani Center, HaMaccabim Road 68, 7505101, Rishon LeZion, Israel
| | - Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Amnon Lers
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, HaMaccabim Road 68, 7505101, Rishon LeZion, Israel.
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Sega P, Kruszka K, Bielewicz D, Karlowski W, Nuc P, Szweykowska-Kulinska Z, Pacak A. Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses. BMC Genomics 2021; 22:165. [PMID: 33750301 PMCID: PMC7941915 DOI: 10.1186/s12864-021-07481-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/25/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are 20-30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. RESULTS In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value < 0.05) are represented by 15 molecules in shoot and 13 in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13% from the average of the unique small RNA expressed under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01%). More than 80% of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3'-5' exonuclease). This suggests that most small RNAs may be generated upon nucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools. CONCLUSIONS Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.
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Affiliation(s)
- Pawel Sega
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Wang Y, Chen YF, Wu WH. Potassium and phosphorus transport and signaling in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:34-52. [PMID: 33325114 DOI: 10.1111/jipb.13053] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/10/2020] [Indexed: 05/26/2023]
Abstract
Nitrogen (N), potassium (K), and phosphorus (P) are essential macronutrients for plant growth and development, and their availability affects crop yield. Compared with N, the relatively low availability of K and P in soils limits crop production and thus threatens food security and agricultural sustainability. Improvement of plant nutrient utilization efficiency provides a potential route to overcome the effects of K and P deficiencies. Investigation of the molecular mechanisms underlying how plants sense, absorb, transport, and use K and P is an important prerequisite to improve crop nutrient utilization efficiency. In this review, we summarize current understanding of K and P transport and signaling in plants, mainly taking Arabidopsis thaliana and rice (Oryza sativa) as examples. We also discuss the mechanisms coordinating transport of N and K, as well as P and N.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi-Fang Chen
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei-Hua Wu
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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Pabuayon ICM, Kitazumi A, Gregorio GB, Singh RK, de los Reyes BG. Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks. Front Genet 2020; 11:594569. [PMID: 33193743 PMCID: PMC7644915 DOI: 10.3389/fgene.2020.594569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
Genetic novelties are important nucleators of adaptive speciation. Transgressive segregation is a major mechanism that creates genetic novelties with morphological and developmental attributes that confer adaptive advantages in certain environments. This study examined the morpho-developmental and physiological profiles of recombinant inbred lines (RILs) from the salt-sensitive IR29 and salt-tolerant Pokkali rice, representing the total range of salt tolerance including the outliers at both ends of the spectrum. Morpho-developmental and physiological profiles were integrated with a hypothesis-driven interrogation of mRNA and miRNA transcriptomes to uncover the critical genetic networks that have been rewired for novel adaptive architecture. The transgressive super-tolerant FL510 had a characteristic small tiller angle and wider, more erect, sturdier, and darker green leaves. This unique morphology resulted in lower transpiration rate, which also conferred a special ability to retain water more efficiently for osmotic avoidance. The unique ability for water retention conferred by such adaptive morphology appeared to enhance the efficacy of defenses mediated by Na+ exclusion mechanism (SalTol-effects) inherited from Pokkali. The super-tolerant FL510 and super-sensitive FL499 had the smallest proportions of differentially expressed genes with little overlaps. Genes that were steadily upregulated in FL510 comprised a putative cytokinin-regulated genetic network that appeared to maintain robust growth under salt stress through well-orchestrated cell wall biogenesis and cell expansion, likely through major regulatory (OsRR23, OsHK5) and biosynthetic (OsIPT9) genes in the cytokinin signaling pathway. Meanwhile, a constitutively expressed cluster in FL510 prominently featured two transcription factors (OsIBH1, TAC3) that control tiller angle and growth habit through the brassinosteroid signaling pathway. Both the putative cytokinin-mediated and brassinosteroid-mediated clusters appeared to function as highly coordinated network synergies in FL510. In contrast, both networks appeared to be sub-optimal and inferior in the other RILs and parents as they were disjointed and highly fragmented. Transgressively expressed miRNAs (miR169, miR397, miR827) were also identified as prominent signatures of FL510, with functional implications to mechanisms that support robust growth, homeostasis, and osmotic stress avoidance. Results of this study demonstrate how genetic recombination creates novel morphology that complements inducible defenses hence transgressive adaptive phenotypes.
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Affiliation(s)
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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Grabowska A, Smoczynska A, Bielewicz D, Pacak A, Jarmolowski A, Szweykowska-Kulinska Z. Barley microRNAs as metabolic sensors for soil nitrogen availability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110608. [PMID: 32900446 DOI: 10.1016/j.plantsci.2020.110608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops in the world, ranking 4th in the worldwide production. Crop breeders are facing increasing environmental obstacles in the field, such as drought, salinity but also toxic over fertilization which not only impacts quality of the grain but also an yield. One of the most prevalent mechanisms of gene expression regulation in plants is microRNA-mediated silencing of target genes. We identified 13 barley microRNAs and 2 microRNAs* that are nitrogen excess responsive. Four microRNAs respond only in root, eight microRNAs only in shoot and one displays broad response in roots and shoots. We demonstrate that 2 microRNAs* are induced in barley shoot by nitrogen excess. For all microRNAs we identified putative target genes and confirmed microRNA-guided cleavage sites for ten out of thirteen mRNAs. None of the identified microRNAs or their target genes is known as nitrogen excess responsive. Analysis of expression pattern of thirteen target mRNAs and their cognate microRNAs showed expected correlations of their levels. The plant microRNAs analyzed are also known to respond to nitrogen deprivation and exhibit the opposite expression pattern when nitrogen excess/deficiency conditions are compared. Thus, they can be regarded as metabolic sensors of the regulation of nitrogen homeostasis in plants.
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Affiliation(s)
- Aleksandra Grabowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
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Systemic induction of phosphatidylinositol-based signaling in leaves of arbuscular mycorrhizal rice plants. Sci Rep 2020; 10:15896. [PMID: 32985595 PMCID: PMC7522983 DOI: 10.1038/s41598-020-72985-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/09/2020] [Indexed: 11/29/2022] Open
Abstract
Most land plants form beneficial associations with arbuscular mycorrhizal (AM) fungi which improves mineral nutrition, mainly phosphorus, in the host plant in exchange for photosynthetically fixed carbon. Most of our knowledge on the AM symbiosis derives from dicotyledonous species. We show that inoculation with the AM fungus Funneliformis mosseae stimulates growth and increases Pi content in leaves of rice plants (O. sativa, cv Loto, ssp japonica). Although rice is a host for AM fungi, the systemic transcriptional responses to AM inoculation, and molecular mechanisms underlying AM symbiosis in rice remain largely elusive. Transcriptomic analysis identified genes systemically regulated in leaves of mycorrhizal rice plants, including genes with functions associated with the biosynthesis of phospholipids and non-phosphorus lipids (up-regulated and down-regulated, respectively). A coordinated regulation of genes involved in the biosynthesis of phospholipids and inositol polyphosphates, and genes involved in hormone biosynthesis and signaling (jasmonic acid, ethylene) occurs in leaves of mycorrhizal rice. Members of gene families playing a role in phosphate starvation responses and remobilization of Pi were down-regulated in leaves of mycorrhizal rice. These results demonstrated that the AM symbiosis is accompanied by systemic transcriptional responses, which are potentially important to maintain a stable symbiotic relationship in rice plants.
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Takagi D, Miyagi A, Tazoe Y, Suganami M, Kawai-Yamada M, Ueda A, Suzuki Y, Noguchi K, Hirotsu N, Makino A. Phosphorus toxicity disrupts Rubisco activation and reactive oxygen species defence systems by phytic acid accumulation in leaves. PLANT, CELL & ENVIRONMENT 2020; 43:2033-2053. [PMID: 32281116 DOI: 10.1111/pce.13772] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Phosphorus (P) is an essential mineral nutrient for plants. Nevertheless, excessive P accumulation in leaf mesophyll cells causes necrotic symptoms in land plants; this phenomenon is termed P toxicity. However, the detailed mechanisms underlying P toxicity in plants have not yet been elucidated. This study aimed to investigate the molecular mechanism of P toxicity in rice. We found that under excessive inorganic P (Pi) application, Rubisco activation decreased and photosynthesis was inhibited, leading to lipid peroxidation. Although the defence systems against reactive oxygen species accumulation were activated under excessive Pi application conditions, the Cu/Zn-type superoxide dismutase activities were inhibited. A metabolic analysis revealed that excessive Pi application led to an increase in the cytosolic sugar phosphate concentration and the activation of phytic acid synthesis. These conditions induced mRNA expression of genes that are activated under metal-deficient conditions, although metals did accumulate. These results suggest that P toxicity is triggered by the attenuation of both photosynthesis and metal availability within cells mediated by phytic acid accumulation. Here, we discuss the whole phenomenon of P toxicity, beginning from the accumulation of Pi within cells to death in land plants.
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Affiliation(s)
- Daisuke Takagi
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Atsuko Miyagi
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Youshi Tazoe
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mao Suganami
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Akihiro Ueda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuji Suzuki
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Ko Noguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Naoki Hirotsu
- Faculty of Life Sciences, Toyo University, Itakura-machi, Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Xu L, Wang F, Li R, Deng M, Fu M, Teng H, Yi K. OsCYCP4s coordinate phosphate starvation signaling with cell cycle progression in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1017-1033. [PMID: 31697021 DOI: 10.1111/jipb.12885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Phosphate starvation leads to a strong reduction in shoot growth and yield in crops. The reduced shoot growth is caused by extensive gene expression reprogramming triggered by phosphate deficiency, which is not itself a direct consequence of low levels of shoot phosphorus. However, how phosphate starvation inhibits shoot growth in rice is still unclear. In this study, we determined the role of OsCYCP4s in the regulation of shoot growth in response to phosphate starvation in rice. We demonstrate that the expression levels of OsCYCP4s, except OsCYCP4;3, were induced by phosphate starvation. Overexpression of the phosphate starvation induced OsCYCP4s could compete with the other cyclins for the binding with cyclin-dependent kinases, therefore suppressing growth by reducing cell proliferation. The phosphate starvation induced growth inhibition in the loss-of-function mutants cycp4;1, cycp4;2, and cycp4;4 is partially compromised. Furthermore, the expression of some phosphate starvation inducible genes is negatively modulated by these cyclins, which indicates that these OsCYCP4s may also be involved in phosphate starvation signaling. We conclude that phosphate starvation induced OsCYCP4s might coordinate phosphate starvation signaling and cell cycle progression under phosphate starvation stress.
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Affiliation(s)
- Lei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ruili Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Minjuan Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Meilan Fu
- The Semi-arid Agriculture Engineering & Technology Research Center of P. R. China, Shijiazhuang, 050000, China
| | - Huiying Teng
- The Semi-arid Agriculture Engineering & Technology Research Center of P. R. China, Shijiazhuang, 050000, China
| | - Keke Yi
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Zhang Z, Gao S, Chu C. Improvement of nutrient use efficiency in rice: current toolbox and future perspectives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1365-1384. [PMID: 31919537 DOI: 10.1007/s00122-019-03527-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/24/2019] [Indexed: 05/03/2023]
Abstract
Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the "hidden hunger." Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.
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Affiliation(s)
- Zhihua Zhang
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Hou G, Du C, Gao H, Liu S, Sun W, Lu H, Kang J, Xie Y, Ma D, Wang C. Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels. BMC PLANT BIOLOGY 2020; 20:87. [PMID: 32103721 PMCID: PMC7045451 DOI: 10.1186/s12870-020-2296-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. RESULTS A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. CONCLUSIONS The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.
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Affiliation(s)
- Gege Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Du
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honghuan Gao
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sujun Liu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wan Sun
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongfang Lu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Kang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingxin Xie
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dongyun Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Chenyang Wang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
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Balyan S, Joseph SV, Jain R, Mutum RD, Raghuvanshi S. Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice. Funct Integr Genomics 2020; 20:509-522. [DOI: 10.1007/s10142-020-00731-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/04/2019] [Accepted: 01/02/2020] [Indexed: 11/28/2022]
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Huang Y, Xu PH, Hou BZ, Shen YY. Strawberry tonoplast transporter, FaVPT1, controls phosphate accumulation and fruit quality. PLANT, CELL & ENVIRONMENT 2019; 42:2715-2729. [PMID: 31151133 DOI: 10.1111/pce.13598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/26/2019] [Accepted: 05/28/2019] [Indexed: 05/13/2023]
Abstract
Phosphorus (P) is essential for plant growth and development, and the vacuole is an important organelle for phosphate storage. However, the tonoplast phosphate transporter in fleshy fruits remains unknown. In this study, based on the strawberry (Fragaria × ananassa) fruit transcriptome data, a tonoplast-localized vacuolar phosphate transporter with SPX and major facilitator superfamily domains, FaVPT1, was identified. FaVPT1 expression was highest in the fruits and could be induced by sucrose. Using transient transgenic systems in strawberry fruit, the downregulation and upregulation of FaVPT1 inhibited and promoted ripening, respectively, and affected phosphate contents, fruit firmness, sugar and anthocyanin contents, and ripening-related gene transcription. FaVPT1 could rescue Pi absorption in both yeast and the Arabidopsis atvpt1 mutant, confirming the similar function of FaVPT1 and AtVPT1, a previously identified tonoplast phosphate transporter in Arabidopsis. The Escherichia coli-expressed SPX domain of FaVPT1 could strongly bind to InsP6 with a Kd of 3.5 μM. The results demonstrate that FaVPT1 is a tonoplast phosphate transporter and regulates strawberry fruit ripening and quality, to a large extent, via sucrose.
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Affiliation(s)
- Yun Huang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bei Jing Bei Nong Enterprise Management Co., Ltd., Beijing, 102206, China
| | - Peng-Hao Xu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Bing-Zhu Hou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yuan-Yue Shen
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
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46
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Liu T, Tang J, Chen L, Zeng J, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Differential expression of miRNAs and their targets in wax-deficient rapeseed. Sci Rep 2019; 9:12201. [PMID: 31434948 PMCID: PMC6704058 DOI: 10.1038/s41598-019-48439-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022] Open
Abstract
The cuticle of a plant, composed of cutin and wax, is the outermost hydrophobic layer covering the epidermis of all its aerial organs, protecting it from many abiotic and biotic stresses. The biosynthesis and regulation pathways of wax components have been well studied, whereas there are fewer reports on the small RNA-involved post-transcriptional regulation of wax biosynthesis in plants, particularly in Brassica napus. Previously, we conducted a study on a glossy mutant of rapeseed, and we assumed that there was a dominant repressor to inhibit the expression of wax-related genes. To verify this hypothesis and investigate the function of small RNAs in wax biosynthesis in B. napus, we constructed four small RNA libraries from the stem epidermis of wax-deficient mutant and wild-type plants for sequencing. Subsequently, 43,840,451 clean reads were generated and 24 nt sequences represented the dominant percentage. In total, 300 unique known miRNAs were identified and eight of them showed differential expression. In addition, the expression levels of six novel miRNAs were altered. Surprisingly, we found that four up-regulated miRNAs in the wax-deficient plants, bna-miR408b-5p, bna-miR165b-5p, bna-miR160a-3p, and bna-miR398-5p, were all complementary strands of their corresponding mature strands. Stem-loop qRT-PCR verified that the expression of bna-miR165a-5p was increased in the mutant stems, while its putative target, BnaA06g40560D (CYP96A2), was down-regulated. In addition, the expression of bna-miR827a was detected to be down-regulated in glossy mutant. 5′ RACE experimental data showed that bna-miR827a cleaves three NITROGEN LIMITATION ADAPTATION (NLA) genes (BnaC08g45940D, BnaA10g01450D and BnaC05g01480D). The down-regulation of bna-miR827a resulted in decreased cleavage on its targets, and led to the up-regulation of its targets, especially BnaA10g01450D gene. These results showed that bna-miR165a-5p might participate in wax biosynthesis process by regulating its putative target BnaA06g40560D (CYP96A2). The expression levels of a phosphate (Pi)-related miRNA, bna-miR827a, and its target genes were affected in wax-deficient rapeseeds. These results will promote the study of post-transcriptional regulation mechanisms of wax biosynthesis in B. napus and provide new directions for further research.
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Affiliation(s)
- Tingting Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jingquan Tang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiayue Zeng
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
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Long L, Ma X, Ye L, Zeng J, Chen G, Zhang G. Root plasticity and Pi recycling within plants contribute to low-P tolerance in Tibetan wild barley. BMC PLANT BIOLOGY 2019; 19:341. [PMID: 31382871 PMCID: PMC6683381 DOI: 10.1186/s12870-019-1949-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Barley is a low phosphorus (P) demand cereal crop. Tibetan wild barley, as a progenitor of cultivated barley, has revealed outstanding ability of tolerance to low-P stress. However, the underlying mechanisms of low-P adaption and the relevant genetic controlling are still unclear. RESULTS We identified low-P tolerant barley lines in a doubled-haploid (DH) population derived from an elite Tibetan wild barley accession and a high-yield cultivar. The tolerant lines revealed greater root plasticity in the terms of lateral root length, compared to low-P sensitive lines, in response to low-P stress. By integrating the QTLs associated with root length and root transcriptomic profiling, candidate genes encoding isoflavone reductase, nitrate reductase, nitrate transporter and transcriptional factor MYB were identified. The differentially expressed genes (DEGs) involved the growth of lateral root, Pi transport within cells as well as from roots to shoots contributed to the differences between low-P tolerant line L138 and low-P sensitive lines L73 in their ability of P acquisition and utilization. CONCLUSIONS The plasticity of root system is an important trait for barley to tolerate low-P stress. The low-P tolerance in the elite DH line derived from a cross of Tibetan wild barley and cultivated barley is characterized by enhanced growth of lateral root and Pi recycling within plants under low-P stress.
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Affiliation(s)
- Lizhi Long
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Xinyi Ma
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Lingzhen Ye
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Jianbin Zeng
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Guang Chen
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
| | - Guoping Zhang
- Department of Agronomy, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058 China
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48
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Wu T, Li L, Jiang X, Yang Y, Song Y, Chen L, Xu X, Shen Y, Gu Y. Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater. Sci Rep 2019; 9:9514. [PMID: 31267025 PMCID: PMC6606587 DOI: 10.1038/s41598-019-45511-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due to the limited data and knowledge in genomics. In this study, we first investigated the differential growth rates among three wastewater-processing Chlorella strains: Chlorella sorokiniana BD09, Chlorella sorokiniana BD08 and Chlorella sp. Dachan, and the previously published Chlorella sorokiniana UTEX 1602, showing us that BD09 maintains the best tolerance in synthetic wastewater. We then performed genome sequencing and analysis, resulting in a high-quality assembly for each genome with scaffold N50 > 2 Mb and genomic completeness ≥91%, as well as genome annotation with 9,668, 10,240, 9,821 high-confidence gene models predicted for BD09, BD08, and Dachan, respectively. Comparative genomics study unravels that metabolic pathways, which are involved in nitrogen and phosphorus assimilation, were enriched in the faster-growing strains. We found that gene structural variation and genomic rearrangement might contribute to differential capabilities in wastewater tolerance among the strains, as indicated by gene copy number variation, domain reshuffling of orthologs involved, as well as a ~1 Mb-length chromosomal inversion we observed in BD08 and Dachan. In addition, we speculated that an associated bacterium, Microbacterium chocolatum, which was identified within Dachan, play a possible role in synergizing nutrient removal. Our three newly sequenced Chlorella genomes provide a fundamental foundation to understand the molecular basis of abiotic stress tolerance in wastewater treatment, which is essential for future genetic engineering and strain improvement.
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Affiliation(s)
- Tian Wu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaosen Jiang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China
| | - Yong Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China
| | - Yanzi Song
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, 40072, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China. .,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China.
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China. .,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China.
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49
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Xia Z, Zhao Z, Gao X, Jiao Z, Wu Y, Zhou T, Fan Z. Characterization of Maize miRNAs in Response to Synergistic Infection of Maize Chlorotic Mottle Virus and Sugarcane Mosaic Virus. Int J Mol Sci 2019; 20:ijms20133146. [PMID: 31252649 PMCID: PMC6650953 DOI: 10.3390/ijms20133146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 01/09/2023] Open
Abstract
The synergistic infection of maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) causes maize lethal necrosis, with considerable losses to global maize production. microRNAs (miRNAs) are conserved non-coding small RNAs that play essential regulatory roles in plant development and environmental stress responses, including virus infection. However, the characterization of maize miRNAs in response to synergistic infection of MCMV and SCMV remains largely unknown. In this study, the profiles of small RNAs from MCMV and SCMV single- and co-infected (S + M) maize plants were obtained by high-throughput sequencing. A total of 173 known miRNAs, belonging to 26 miRNA families, and 49 novel miRNAs were profiled. The expression patterns of most miRNAs in S + M-infected maize plants were similar to that in SCMV-infected maize plants, probably due to the existence of RNA silencing suppressor HC-Pro. Northern blotting and quantitative real-time PCR were performed to validate the accumulation of miRNAs and their targets in different experimental treatments, respectively. The down-regulation of miR159, miR393, and miR394 might be involved in antiviral defense to synergistic infection. These results provide novel insights into the regulatory networks of miRNAs in maize plants in response to the synergistic infection of MCMV and SCMV.
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Affiliation(s)
- Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| | - Zhenxing Zhao
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China
| | - Xinran Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhiyuan Jiao
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tao Zhou
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China
| | - Zaifeng Fan
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China.
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50
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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