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Circadian Rhythms in Plants
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Circadian Rhythms in Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 9938

Special Issue Editors

Dr. Ana Jiménez

E-Mail Website1 Website2
Guest Editor
Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CSIC), Murcia, Spain
Interests: plant antioxidants; organellar antioxidants; abiotic stress; biotic stress; metabolic pathways; new antioxidants; protection; reactive oxygen
Special Issues, Collections and Topics in MDPI journals
Dr. María Carmen Martí Ruiz

E-Mail Website
Guest Editor
Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CSIC), Murcia, Spain
Interests: circadian rhythms; redox biology; abiotic stress; calcium signaling; reactive oxygen species; reactive nitrogen species
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants can measure time and predict and adapt to coming environmental changes thanks to their endogenous circadian clock. High-throughput expression analysis has led to the finding that the plant circadian clock accounts for one-third of Arabidopsis transcripts; therefore, it is involved in numerous biological and physiological processes, such as photoperiodic flowering, growth, metabolism, hormones signalling, and stress responses, among others. Furthermore, it has been shown that a majority of the signalling pathways regulated by the clock are able to modulate its function in return. Understanding how the circadian signalling network regulates these processes and vice versa and, therefore, how it affects productivity represents a pressing agronomic issue.

In this Special Issue of the International Journal of Molecular Science, papers advancing an improved understanding of the molecular mechanisms involved in the regulation of the circadian clock signalling network and its relationship with other biological pathways (e.g., hormones, stress responses, and metabolism) will be considered. Research papers, reviews, and feature/perspective articles are all welcome.

Dr. Ana Jiménez
Dr. María Carmen Martí Ruiz
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • circadian signalling
  • molecular mechanisms of circadian rhythms
  • epigenetic posttranscriptional
  • and posttranslational regulation of the clock

Published Papers (5 papers)

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Research

11 pages, 2395 KiB  
Article
Homologs of Ancestral CNNM Proteins Affect Magnesium Homeostasis and Circadian Rhythmicity in a Model Eukaryotic Cell
by Sergio Gil, Helen K. Feord and Gerben van Ooijen
Int. J. Mol. Sci. 2023, 24(3), 2273; https://doi.org/10.3390/ijms24032273 - 23 Jan 2023
Viewed by 1449
Abstract
Biological rhythms are ubiquitous across organisms and coordinate key cellular processes. Oscillations of Mg2+ levels in cells are now well-established, and due to the critical roles of Mg2+ in cell metabolism, they are potentially fundamental for the circadian control of cellular [...] Read more.
Biological rhythms are ubiquitous across organisms and coordinate key cellular processes. Oscillations of Mg2+ levels in cells are now well-established, and due to the critical roles of Mg2+ in cell metabolism, they are potentially fundamental for the circadian control of cellular activity. The identity of the transport proteins responsible for sustaining Mg2+ levels in eukaryotic cells remains hotly debated, and several are restricted to specific groups of higher eukaryotes. Here, using the eukaryotic minimal model cells of Ostreococcus tauri, we report two homologs of common descents of the Cyclin M (CNNM)/CorC protein family. Overexpression of these proteins leads to a reduction in the overall magnesium content of cells and a lengthening of the period of circadian gene expression rhythms. However, we observed a paradoxical increase in the magnesium content of the organelle fraction. The chemical inhibition of Mg2+ transport has a synergistic effect on circadian period lengthening upon the overexpression of one CNNM homolog, but not the other. Finally, both homologs rescue the deleterious effect of low extracellular magnesium on cell proliferation rates. Overall, we identified two CNNM proteins that directly affect Mg2+ homeostasis and cellular rhythms. Full article
(This article belongs to the Special Issue Circadian Rhythms in Plants)
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15 pages, 3734 KiB  
Article
Genomic Dissection and Diurnal Expression Analysis Reveal the Essential Roles of the PRR Gene Family in Geographical Adaptation of Soybean
by Peiguo Wang, Liwei Wang, Lixin Zhang, Tingting Wu, Baiquan Sun, Junquan Zhang, Enoch Sapey, Shan Yuan, Bingjun Jiang, Fulu Chen, Cunxiang Wu, Wensheng Hou, Shi Sun, Jiangping Bai and Tianfu Han
Int. J. Mol. Sci. 2022, 23(17), 9970; https://doi.org/10.3390/ijms23179970 - 01 Sep 2022
Cited by 2 | Viewed by 1590
Abstract
Pseudo-response regulator (PRR) family members serve as key components of the core clock of the circadian clock, and play important roles in photoperiodic flowering, stress tolerance, growth, and the development of plants. In this study, 14 soybean PRR genes were identified, and classified [...] Read more.
Pseudo-response regulator (PRR) family members serve as key components of the core clock of the circadian clock, and play important roles in photoperiodic flowering, stress tolerance, growth, and the development of plants. In this study, 14 soybean PRR genes were identified, and classified into three groups according to phylogenetic analysis and structural characteristics. Real-time quantitative PCR analysis revealed that 13 GmPRRs exhibited obvious rhythmic expression under long-day (LD) and short-day (SD) conditions, and the expression of 12 GmPRRs was higher under LD in leaves. To evaluate the effects of natural variations in GmPRR alleles on soybean adaptation, we examined the sequences of GmPRRs among 207 varieties collected across China and the US, investigated the flowering phenotypes in six environments, and analyzed the geographical distributions of the major haplotypes. The results showed that a majority of non-synonymous mutations in the coding region were associated with flowering time, and we found that the nonsense mutations resulting in deletion of the CCT domain were related to early flowering. Haplotype analysis demonstrated that the haplotypes associated with early flowering were mostly distributed in Northeast China, while the haplotypes associated with late flowering were mostly cultivated in the lower latitudes of China. Our study of PRR family genes in soybean provides not only an important guide for characterizing the circadian clock-controlled flowering pathway but also a theoretical basis and opportunities to breed varieties with adaptation to specific regions and farming systems. Full article
(This article belongs to the Special Issue Circadian Rhythms in Plants)
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17 pages, 3335 KiB  
Article
Evolutionary Analysis and Functional Identification of Clock-Associated PSEUDO-RESPONSE REGULATOR (PRRs) Genes in the Flowering Regulation of Roses
by Abdul Jalal, Jinrui Sun, Yeqing Chen, Chunguo Fan, Jinyi Liu and Changquan Wang
Int. J. Mol. Sci. 2022, 23(13), 7335; https://doi.org/10.3390/ijms23137335 - 30 Jun 2022
Cited by 7 | Viewed by 2075
Abstract
Pseudo-response regulators (PRRs) are the important genes for flowering in roses. In this work, clock PRRs were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw [...] Read more.
Pseudo-response regulators (PRRs) are the important genes for flowering in roses. In this work, clock PRRs were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock PRRs in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock PRRs were significantly expanded in Rosaceae and were divided into three major clades, i.e., PRR5/9 (clade 1), PRR3/7 (clade 2), and TOC1/PRR1 (clade 3), based on their phylogeny. Within the clades, five clock PRRs were identified in Rosa chinensis. Clock PRRs had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock PRRs. The diverse cis elements and interaction of clock PRRs with miRNAs suggested their role in plant development. Co-expression network analysis showed that the clock PRRs from Rosa chinensis had a strong association with flowering controlling genes. Further silencing of RcPRR1b and RcPRR5 in Rosa chinensis using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between RcPRR1a/RcPRR5 and RcCO suggested that RcPRR1a/RcPRR5 may suppress flowering by interfering with the binding of RcCO to the promoter of RcFT. Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock PRRs in controlling flowering in roses. Full article
(This article belongs to the Special Issue Circadian Rhythms in Plants)
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15 pages, 5596 KiB  
Article
Identification and Characterization of PSEUDO-RESPONSE REGULATOR (PRR) 1a and 1b Genes by CRISPR/Cas9-Targeted Mutagenesis in Chinese Cabbage (Brassica rapa L.)
by Nan-Sun Kim, Jihyeon Yu, Sangsu Bae, Hyang Suk Kim, Soyoung Park, Kijong Lee, Soo In Lee and Jin A. Kim
Int. J. Mol. Sci. 2022, 23(13), 6963; https://doi.org/10.3390/ijms23136963 - 23 Jun 2022
Cited by 5 | Viewed by 1832
Abstract
The CRISPR/Cas9 site-directed gene-editing system offers great advantages for identifying gene function and crop improvement. The circadian clock measures and conveys day length information to control rhythmic hypocotyl growth in photoperiodic conditions, to achieve optimal fitness, but operates through largely unknown mechanisms. Here, [...] Read more.
The CRISPR/Cas9 site-directed gene-editing system offers great advantages for identifying gene function and crop improvement. The circadian clock measures and conveys day length information to control rhythmic hypocotyl growth in photoperiodic conditions, to achieve optimal fitness, but operates through largely unknown mechanisms. Here, we generated core circadian clock evening components, Brassica rapa PSEUDO-RESPONSE REGULATOR (BrPRR) 1a, 1b, and 1ab (both 1a and 1b double knockout) mutants, using CRISPR/Cas9 genome editing in Chinese cabbage, where 9–16 genetic edited lines of each mutant were obtained. The targeted deep sequencing showed that each mutant had 2–4 different mutation types at the target sites in the BrPRR1a and BrPRR1b genes. To identify the functions of BrPRR1a and 1b genes, hypocotyl length, and mRNA and protein levels of core circadian clock morning components, BrCCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) and BrLHY (LATE ELONGATED HYPOCOTYL) a and b were examined under light/dark cycles and continuous light conditions. The BrPRR1a and 1ab double mutants showed longer hypocotyls, lower core circadian clock morning component mRNA and protein levels, and a shorter circadian rhythm than wildtype (WT). On the other hand, the BrPRR1b mutant was not significantly different from WT. These results suggested that two paralogous genes may not be associated with the same regulatory function in Chinese cabbage. Taken together, our results demonstrated that CRISPR/Cas9 is an efficient tool for achieving targeted genome modifications and elucidating the biological functions of circadian clock genes in B. rapa, for both breeding and improvement. Full article
(This article belongs to the Special Issue Circadian Rhythms in Plants)
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10 pages, 2181 KiB  
Article
Crosstalk between the Circadian Clock and Histone Methylation
by Changhui Sun, Shihang Liu, Changcai He, Chao Zhong, Hongying Liu, Xu Luo, Ke Li, Kuan Zhang, Qian Wang, Congping Chen, Yulin Tang, Bin Yang, Xiaoqiong Chen, Peizhou Xu, Ting Zou, Shuangcheng Li, Peng Qin, Pingrong Wang, Chengcai Chu and Xiaojian Deng
Int. J. Mol. Sci. 2022, 23(12), 6465; https://doi.org/10.3390/ijms23126465 - 09 Jun 2022
Cited by 3 | Viewed by 2004
Abstract
The circadian clock and histone modifications could form a feedback loop in Arabidopsis; whether a similar regulatory mechanism exists in rice is still unknown. Previously, we reported that SDG724 and OsLHY are two rice heading date regulators in rice. SDG724 encodes a histone [...] Read more.
The circadian clock and histone modifications could form a feedback loop in Arabidopsis; whether a similar regulatory mechanism exists in rice is still unknown. Previously, we reported that SDG724 and OsLHY are two rice heading date regulators in rice. SDG724 encodes a histone H3K36 methyltransferase, and OsLHY is a vital circadian rhythm transcription factor. Both could be involved in transcription regulatory mechanisms and could affect gene expression in various pathways. To explore the crosstalk between the circadian clock and histone methylation in rice, we studied the relationship between OsLHY and SDG724 via the transcriptome analysis of their single and double mutants, oslhy, sdg724, and oslhysdg724. Screening of overlapped DEGs and KEGG pathways between OsLHY and SDG724 revealed that they could control many overlapped pathways indirectly. Furthermore, we identified three candidate targets (OsGI, OsCCT38, and OsPRR95) of OsLHY and one candidate target (OsCRY1a) of SDG724 in the clock pathway. Our results showed a regulatory relationship between OsLHY and SDG724, which paved the way for revealing the interaction between the circadian clock and histone H3K36 methylation. Full article
(This article belongs to the Special Issue Circadian Rhythms in Plants)
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