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Bhat A, Mishra S, Kaul S, Dhar MK. Comparative analysis of miRNA expression profiles in flowering and non-flowering tissue of Crocus sativus L. PROTOPLASMA 2024; 261:749-769. [PMID: 38340171 DOI: 10.1007/s00709-024-01931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Crocus sativus is a valuable plant due to the presence of apocarotenoids in its stigma. Considerable work has been done in the past to understand the apocarotenoid biosynthetic pathway in saffron. However, the reports on understanding the regulation of flowering at the post-transcriptional level are meagre. The study aimed to discover the candidate miRNAs, target genes, transcription factors (TFs), and apocarotenoid biosynthetic pathway genes associated with the regulation and transition of flowering in C. sativus. In the present investigation, miRNA profiling was performed in flowering and non-flowering corms of saffron, along with expression analysis of apocarotenoid genes and transcription factors involved in the synthesis of secondary metabolites. Significant modulation in the expression of miR156, miR159, miR166, miR172, miR395, miR396, miR399, and miR408 gene families was observed. We obtained 36 known miRNAs (26 in flowering and 10 in non-flowering) and 64 novel miRNAs (40 in flowering and 24 in non-flowering) unique to specific tissues in our analysis. TFs, including CsMADS and CsMYb, showed significant modulation in expression in flowering tissue, followed by CsHB. Additionally, the miRNAs were predicted to be involved in carbohydrate metabolism, phytohormone signalling, regulation of flower development, and response to stress, cold, and defence. The comprehensive study has enhanced our understanding of the regulatory machinery comprising factors like phytohormones, abiotic stress, apocarotenoid genes, transcription factors, and miRNAs responsible for the synthesis of apocarotenoids and developmental processes during and after flowering.
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Affiliation(s)
- Archana Bhat
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Sonal Mishra
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Manoj Kumar Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
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Chen D, Chen J, Dai R, Zheng X, Han Y, Chen Y, Xue T. Integration analysis of ATAC-seq and RNA-seq provides insight into fatty acid biosynthesis in Schizochytrium limacinum under nitrogen limitation stress. BMC Genomics 2024; 25:141. [PMID: 38311722 PMCID: PMC10840233 DOI: 10.1186/s12864-024-10043-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. RESULTS Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. CONCLUSIONS SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA.
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Affiliation(s)
- Duo Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jing Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Rongchun Dai
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xuehai Zheng
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yuying Han
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ting Xue
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China.
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Shor E, Skaliter O, Sharon E, Kitsberg Y, Bednarczyk D, Kerzner S, Vainstein D, Tabach Y, Vainstein A. Developmental and temporal changes in petunia petal transcriptome reveal scent-repressing plant-specific RING-kinase-WD40 protein. FRONTIERS IN PLANT SCIENCE 2023; 14:1180899. [PMID: 37360732 PMCID: PMC10286513 DOI: 10.3389/fpls.2023.1180899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/05/2023] [Indexed: 06/28/2023]
Abstract
In moth-pollinated petunias, production of floral volatiles initiates when the flower opens and occurs rhythmically during the day, for optimal flower-pollinator interaction. To characterize the developmental transcriptomic response to time of day, we generated RNA-Seq databases for corollas of floral buds and mature flowers in the morning and in the evening. Around 70% of transcripts accumulating in petals demonstrated significant changes in expression levels in response to the flowers' transition from a 4.5-cm bud to a flower 1 day postanthesis (1DPA). Overall, 44% of the petal transcripts were differentially expressed in the morning vs. evening. Morning/evening changes were affected by flower developmental stage, with a 2.5-fold larger transcriptomic response to daytime in 1DPA flowers compared to buds. Analyzed genes known to encode enzymes in volatile organic compound biosynthesis were upregulated in 1DPA flowers vs. buds-in parallel with the activation of scent production. Based on analysis of global changes in the petal transcriptome, PhWD2 was identified as a putative scent-related factor. PhWD2 is a protein that is uniquely present in plants and has a three-domain structure: RING-kinase-WD40. Suppression of PhWD2 (termed UPPER - Unique Plant PhEnylpropanoid Regulator) resulted in a significant increase in the levels of volatiles emitted from and accumulated in internal pools, suggesting that it is a negative regulator of petunia floral scent production.
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Affiliation(s)
- Ekaterina Shor
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Oded Skaliter
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Elad Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- The Institute for Medical Research, Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaarit Kitsberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dominika Bednarczyk
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shane Kerzner
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Danny Vainstein
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Tabach
- The Institute for Medical Research, Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander Vainstein
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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Chen D, Li H, Chen J, Han Y, Zheng X, Xiao Y, Chen X, Chen T, Chen J, Chen Y, Xue T. Combined analysis of chromatin accessibility and gene expression profiles provide insight into Fucoxanthin biosynthesis in Isochrysis galbana under green light. Front Microbiol 2023; 14:1101681. [PMID: 36846787 PMCID: PMC9950639 DOI: 10.3389/fmicb.2023.1101681] [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: 12/01/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Isochrysis galbana, as a potential accumulator of fucoxanthin, has become a valuable material to develop functional foods for humans. Our previous research revealed that green light effectively promotes the accumulation of fucoxanthin in I. galbana, but there is little research on chromatin accessibility in the process of transcriptional regulation. This study was conducted to reveal the mechanism of fucoxanthin biosynthesis in I. galbana under green light by analyzing promoter accessibility and gene expression profiles. Differentially accessible chromatin regions (DARs)-associated genes were enriched in carotenoid biosynthesis and photosynthesis-antenna protein formation, including IgLHCA1, IgLHCA4, IgPDS, IgZ-ISO, IglcyB, IgZEP, and IgVDE. The motifs for the MYB family were also identified as candidates controlling metabolic regulation responses to green light culture of I. galbana, including IgMYB1, IgMYB2, IgMYB33, IgMYB42, IgMYB98, IgMYB118, and IgMYB119. The results of differential expression analysis and WGCNA showed that several genes or transcription factors (TFs) related to carotenoid metabolism and photosynthesis exhibited a higher expression level and were significantly upregulated in A-G5d compared with A-0d and A-W5d, including IgMYB98, IgLHCA1, IgLHCX2, IgLHCB4, and IgLHCB5. This suggests that upregulation of these genes by green light may be the key factor leading to fucoxanthin accumulation by regulating the photosynthesis-antenna protein pathway. An integrated analysis of ATAC-seq and RNA-seq showed that 3 (IgphoA, IgPKN1, IgOTC) of 34 DARs-associated genes displayed obvious changes in their chromatin regions in ATAC-seq data, suggesting that these genes specific for green light may play a key role in fucoxanthin biosynthesis in I. galbana through a complex regulatory network of multiple metabolic pathways interacting with each other. These findings will facilitate in-depth understanding the molecular regulation mechanisms of fucoxanthin in I. galbana and its role in response to green light regulation, providing technical support for the construction of high fucoxanthin content strains.
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Affiliation(s)
| | | | | | - Yuying Han
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xuehai Zheng
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yixin Xiao
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xupeng Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Tao Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jiannan Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
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