International Journal of Molecular Sciences

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Open AccessEditorial

Regulatory Mechanisms of Transcription Factors in Plant Morphology and Function

by Tomotsugu Koyama

Int. J. Mol. Sci. 2023, 24(8), 7039; https://doi.org/10.3390/ijms24087039 - 11 Apr 2023

Cited by 3 | Viewed by 1432

Abstract

Plants develop organs such as flowers and leaves with different morphologies [...] Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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23 pages, 4266 KiB

Open AccessArticle

The Non-JAZ TIFY Protein TIFY8 of Arabidopsis thaliana Interacts with the HD-ZIP III Transcription Factor REVOLUTA and Regulates Leaf Senescence

by Ana Gabriela Andrade Galan, Jasmin Doll, Svenja Corina Saile, Marieluise Wünsch, Edda von Roepenack-Lahaye, Laurens Pauwels, Alain Goossens, Justine Bresson and Ulrike Zentgraf

Int. J. Mol. Sci. 2023, 24(4), 3079; https://doi.org/10.3390/ijms24043079 - 4 Feb 2023

Cited by 10 | Viewed by 2678

Abstract

The HD-ZIP III transcription factor REVOLUTA (REV) is involved in early leaf development, as well as in leaf senescence. REV directly binds to the promoters of senescence-associated genes, including the central regulator WRKY53. As this direct regulation appears to be restricted to [...] Read more.

The HD-ZIP III transcription factor REVOLUTA (REV) is involved in early leaf development, as well as in leaf senescence. REV directly binds to the promoters of senescence-associated genes, including the central regulator WRKY53. As this direct regulation appears to be restricted to senescence, we aimed to characterize protein-interaction partners of REV which could mediate this senescence-specificity. The interaction between REV and the TIFY family member TIFY8 was confirmed by yeast two-hybrid assays, as well as by bimolecular fluorescence complementation in planta. This interaction inhibited REV’s function as an activator of WRKY53 expression. Mutation or overexpression of TIFY8 accelerated or delayed senescence, respectively, but did not significantly alter early leaf development. Jasmonic acid (JA) had only a limited effect on TIFY8 expression or function; however, REV appears to be under the control of JA signaling. Accordingly, REV also interacted with many other members of the TIFY family, namely the PEAPODs and several JAZ proteins in the yeast system, which could potentially mediate the JA-response. Therefore, REV appears to be under the control of the TIFY family in two different ways: a JA-independent way through TIFY8, which controls REV function in senescence, and a JA-dependent way through PEAPODs and JAZ proteins. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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13 pages, 2085 KiB

Open AccessArticle

Revisiting AGAMOUS-LIKE15, a Key Somatic Embryogenesis Regulator, Using Next Generation Sequencing Analysis in Arabidopsis

by Sanjay Joshi, Hadia Awan, Priyanka Paul, Ran Tian and Sharyn E. Perry

Int. J. Mol. Sci. 2022, 23(23), 15082; https://doi.org/10.3390/ijms232315082 - 1 Dec 2022

Cited by 3 | Viewed by 1809

Abstract

AGAMOUS-like 15 (AGL15) is a member of the MADS-domain transcription factor (TF) family. MADS proteins are named for a conserved domain that was originally from an acronym derived from genes expressed in a variety of eukaryotes (MCM1-AGAMOUS-DEFICIENS- [...] Read more.

AGAMOUS-like 15 (AGL15) is a member of the MADS-domain transcription factor (TF) family. MADS proteins are named for a conserved domain that was originally from an acronym derived from genes expressed in a variety of eukaryotes (MCM1-AGAMOUS-DEFICIENS-SERUM RESPONSE FACTOR). In plants, this family has expanded greatly, with more than one-hundred members generally found in dicots, and the proteins encoded by these genes have often been associated with developmental identity. AGL15 transcript and protein accumulate primarily in embryos and has been found to promote an important process called plant regeneration via somatic embryogenesis (SE). To understand how this TF performs this function, we have previously used microarray technologies to assess direct and indirect responsive targets of this TF. We have now revisited this question using next generation sequencing (NGS) to both characterize in vivo binding sites for AGL15 as well as response to the accumulation of AGL15. We compared these data to the prior microarray results to evaluate the different platforms. The new NGS data brought to light an interaction with brassinosteroid (BR) hormone signaling that was “missed” in prior Gene Ontology analysis from the microarray studies. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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20 pages, 6741 KiB

Open AccessArticle

Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean

by Ana M. González, Ricardo Lebrón, Fernando J. Yuste-Lisbona, Cristina Gómez-Martín, Ana Ortiz-Atienza, Michael Hackenberg, José L. Oliver, Rafael Lozano and Marta Santalla

Int. J. Mol. Sci. 2022, 23(23), 14783; https://doi.org/10.3390/ijms232314783 - 26 Nov 2022

Cited by 1 | Viewed by 1964

Abstract

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes [...] Read more.

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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18 pages, 3724 KiB

Open AccessArticle

Arabidopsis thaliana SHOOT MERISTEMLESS Substitutes for Medicago truncatula SINGLE LEAFLET1 to Form Complex Leaves and Petals

by Véronique Pautot, Ana Berbel, Thibaud Cayla, Alexis Eschstruth, Bernard Adroher, Pascal Ratet, Francisco Madueño and Patrick Laufs

Int. J. Mol. Sci. 2022, 23(22), 14114; https://doi.org/10.3390/ijms232214114 - 15 Nov 2022

Cited by 3 | Viewed by 1999

Abstract

LEAFY plant-specific transcription factors, which are key regulators of flower meristem identity and floral patterning, also contribute to meristem activity. Notably, in some legumes, LFY orthologs such as Medicago truncatula SINGLE LEAFLET (SGL1) are essential in maintaining an undifferentiated and proliferating fate [...] Read more.

LEAFY plant-specific transcription factors, which are key regulators of flower meristem identity and floral patterning, also contribute to meristem activity. Notably, in some legumes, LFY orthologs such as Medicago truncatula SINGLE LEAFLET (SGL1) are essential in maintaining an undifferentiated and proliferating fate required for leaflet formation. This function contrasts with most other species, in which leaf dissection depends on the reactivation of KNOTTED-like class I homeobox genes (KNOXI). KNOXI and SGL1 genes appear to induce leaf complexity through conserved downstream genes such as the meristematic and boundary CUP-SHAPED COTYLEDON genes. Here, we compare in M. truncatula the function of SGL1 with that of the Arabidopsis thaliana KNOXI gene, SHOOT MERISTEMLESS (AtSTM). Our data show that AtSTM can substitute for SGL1 to form complex leaves when ectopically expressed in M. truncatula. The shared function between AtSTM and SGL1 extended to the major contribution of SGL1 during floral development as ectopic AtSTM expression could promote floral organ identity gene expression in sgl1 flowers and restore sepal shape and petal formation. Together, our work reveals a function for AtSTM in floral organ identity and a higher level of interchangeability between meristematic and floral identity functions for the AtSTM and SGL1 transcription factors than previously thought. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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20 pages, 7090 KiB

Open AccessArticle

Genome-Wide Identification, Expression and Interaction Analysis of GmSnRK2 and Type A PP2C Genes in Response to Abscisic Acid Treatment and Drought Stress in Soybean Plant

by Xinjie Shen, Hong Nan, Yuzhuang Jiang, Yujia Zhou and Xuejun Pan

Int. J. Mol. Sci. 2022, 23(21), 13166; https://doi.org/10.3390/ijms232113166 - 29 Oct 2022

Cited by 6 | Viewed by 2221

Abstract

As a typical ancient tetraploid, soybean (Glycine max) is an important oil crop species and plays a crucial role in supplying edible oil, plant protein and animal fodder worldwide. As global warming intensifies, the yield of soybean in the field is [...] Read more.

As a typical ancient tetraploid, soybean (Glycine max) is an important oil crop species and plays a crucial role in supplying edible oil, plant protein and animal fodder worldwide. As global warming intensifies, the yield of soybean in the field is often strongly restricted by drought stress. SNF1-related protein kinase 2 (SnRK2) and type A protein phosphatase 2C (PP2C-A) family members are core components of the abscisic acid (ABA) signal transduction pathway in plants and have been suggested to play important roles in increasing plant tolerance to drought stress, but genetic information supporting this idea is still lacking in soybean. Here, we cloned the GmSnRK2s and GmPP2C-A family genes from the reference genome of Williams 82 soybean. The results showed that the expression patterns of GmSnRK2s and GmPP2C-As are spatiotemporally distinct. The expression of GmSnRK2s in response to ABA and drought signals is not strictly the same as that of Arabidopsis SnRK2 homologous genes. Moreover, our results indicated that the duplicate pairs of GmSnRK2s and GmPP2C-As have similar expression patterns, cis-elements and relationships. GmSnRK2.2 may have a distinct function in the drought-mediated ABA signaling pathway. Furthermore, the results of yeast two-hybrid (Y2H) assays between GmSnRK2s and GmPP2C-As revealed that GmSnRK2.17, GmSnRK2.18, GmSnRK2.22, GmPP2C5, GmPP2C7, GmPP2C10 and GmPP2C17 may play central roles in the crosstalk among ABA signals in response to drought stress. Furthermore, GmPP2C-As and GmSnRKs were targeted by miRNA and validated by degradome sequencing, which may play multiple roles in the crosstalk between ABA and drought signals and other stress signals. Taken together, these results indicate that GmSnRK2s and GmPP2C-As may play a variety of roles in the drought-mediated ABA signaling pathway. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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18 pages, 2865 KiB

Open AccessArticle

New Inhibitors of the Human p300/CBP Acetyltransferase Are Selectively Active against the Arabidopsis HAC Proteins

by Chiara Longo, Andrea Lepri, Andrea Paciolla, Antonella Messore, Daniela De Vita, Maria Carmela Bonaccorsi di Patti, Matteo Amadei, Valentina Noemi Madia, Davide Ialongo, Roberto Di Santo, Roberta Costi and Paola Vittorioso

Int. J. Mol. Sci. 2022, 23(18), 10446; https://doi.org/10.3390/ijms231810446 - 9 Sep 2022

Cited by 4 | Viewed by 2366

Abstract

Histone acetyltransferases (HATs) are involved in the epigenetic positive control of gene expression in eukaryotes. CREB-binding proteins (CBP)/p300, a subfamily of highly conserved HATs, have been shown to function as acetylases on both histones and non-histone proteins. In the model plant Arabidopsis thaliana [...] Read more.

Histone acetyltransferases (HATs) are involved in the epigenetic positive control of gene expression in eukaryotes. CREB-binding proteins (CBP)/p300, a subfamily of highly conserved HATs, have been shown to function as acetylases on both histones and non-histone proteins. In the model plant Arabidopsis thaliana among the five CBP/p300 HATs, HAC1, HAC5 and HAC12 have been shown to be involved in the ethylene signaling pathway. In addition, HAC1 and HAC5 interact and cooperate with the Mediator complex, as in humans. Therefore, it is potentially difficult to discriminate the effect on plant development of the enzymatic activity with respect to their Mediator-related function. Taking advantage of the homology of the human HAC catalytic domain with that of the Arabidopsis, we set-up a phenotypic assay based on the hypocotyl length of Arabidopsis dark-grown seedlings to evaluate the effects of a compound previously described as human p300/CBP inhibitor, and to screen previously described cinnamoyl derivatives as well as newly synthesized analogues. We selected the most effective compounds, and we demonstrated their efficacy at phenotypic and molecular level. The in vitro inhibition of the enzymatic activity proved the specificity of the inhibitor on the catalytic domain of HAC1, thus substantiating this strategy as a useful tool in plant epigenetic studies. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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9 pages, 1721 KiB

Open AccessArticle

Leaf Cell Morphology Alternation in Response to Environmental Signals in Rorippa aquatica

by Tomoaki Sakamoto, Shuka Ikematsu, Kazuki Namie, Hongwei Hou, Gaojie Li and Seisuke Kimura

Int. J. Mol. Sci. 2022, 23(18), 10401; https://doi.org/10.3390/ijms231810401 - 8 Sep 2022

Cited by 4 | Viewed by 1739

Abstract

Heterophylly, the phenomenon by which plants alter leaf forms to adapt to surrounding conditions, is apparent in amphibious plant species. In response to submergence, they emerge leaves with narrower blade areas. The pathway that receives the submergence signals and the mechanism regulating leaf [...] Read more.

Heterophylly, the phenomenon by which plants alter leaf forms to adapt to surrounding conditions, is apparent in amphibious plant species. In response to submergence, they emerge leaves with narrower blade areas. The pathway that receives the submergence signals and the mechanism regulating leaf form via cell proliferation and/or expansion systems have not yet been fully identified yet. Our anatomical study of Rorippa aquatica, an amphibious plant that exhibits heterophylly in response to various signals, showed that leaf thickness increased upon submergence; this was caused by the expansion of mesophyll cell size. Additionally, these submergence effects were inhibited under blue-light conditions. The ANGUSTIFOLIA3 (AN3)/GROWTH-REGULATING FACTOR (GRF) pathway regulating cell proliferation and cell expansion was downregulated in response to submergence; and the response was blocked under the blue-light conditions. These results suggest that submergence and light quality determine leaf cell morphology via the AN3/GRF pathway. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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13 pages, 3140 KiB

Open AccessArticle

Isolation and Functional Analysis of EPHEMERAL1-LIKE (EPH1L) Genes Involved in Flower Senescence in Cultivated Japanese Gentians

by Shigekazu Takahashi, Chiharu Yoshida, Hideyuki Takahashi and Masahiro Nishihara

Int. J. Mol. Sci. 2022, 23(10), 5608; https://doi.org/10.3390/ijms23105608 - 17 May 2022

Cited by 10 | Viewed by 2357

Abstract

The elongation of flower longevity increases the commercial value of ornamental plants, and various genes have been identified as influencing flower senescence. Recently, EPHEMERAL1 (EPH1), encoding a NAC-type transcription factor, was identified in Japanese morning glory as a gene that promotes [...] Read more.

The elongation of flower longevity increases the commercial value of ornamental plants, and various genes have been identified as influencing flower senescence. Recently, EPHEMERAL1 (EPH1), encoding a NAC-type transcription factor, was identified in Japanese morning glory as a gene that promotes flower senescence. Here we attempted to identify an EPH1 homolog gene from cultivated Japanese gentians and characterized the same with regard to its flower senescence. Two EPH1-LIKE genes (EPH1La and EPH1Lb), considered as alleles, were isolated from a gentian cultivar (Gentiana scabra × G. triflora). Phylogenetic analyses revealed that EPH1L belongs to the NAM subfamily. The transcript levels of EPH1L increased along with its senescence in the field-grown flowers. Under dark-induced senescence conditions, the gentian-detached flowers showed the peak transcription level of EPH1L earlier than that of SAG12, a senescence marker gene, suggesting the involvement of EPH1L in flower senescence. To reveal the EPH1L function, we produced eph1l-knockout mutant lines using the CRISPR/Cas9 system. When the flower longevity was evaluated using the detached flowers as described above, improved longevity was recorded in all genome-edited lines, with delayed induction of SAG12 transcription. The degradation analysis of genomic DNA matched the elongation of flower longevity, cumulatively indicating the involvement of EPH1L in the regulation of flower senescence in gentians. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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20 pages, 8956 KiB

Open AccessArticle

MYB2 Is Important for Tapetal PCD and Pollen Development by Directly Activating Protease Expression in Arabidopsis

by Xiaorui Guo, Lihong Li, Xiatong Liu, Chong Zhang, Xiaoyun Yao, Zhili Xun, Zhijing Zhao, Wenwen Yan, Yirong Zou, Di Liu, Hui Li and Hai Lu

Int. J. Mol. Sci. 2022, 23(7), 3563; https://doi.org/10.3390/ijms23073563 - 24 Mar 2022

Cited by 18 | Viewed by 3102

Abstract

Tapetal programmed cell death (PCD) is a complex biological process that plays an important role in pollen formation and reproduction. Here, we identified the MYB2 transcription factor expressed in the tapetum from stage 5 to stage 11 that was essential for tapetal PCD [...] Read more.

Tapetal programmed cell death (PCD) is a complex biological process that plays an important role in pollen formation and reproduction. Here, we identified the MYB2 transcription factor expressed in the tapetum from stage 5 to stage 11 that was essential for tapetal PCD and pollen development in Arabidopsis thaliana. Downregulation of MYB2 retarded tapetal degeneration, produced defective pollen, and decreased pollen vitality. EMSA and transcriptional activation analysis revealed that MYB2 acted as an upstream activator and directly regulated expression of the proteases CEP1 and βVPE. The expression of these proteases was lower in the buds of the myb2 mutant. Overexpression of either/both CEP1 or/and βVPE proteases partially recover pollen vitality in the myb2 background. Taken together, our results revealed that MYB2 regulates tapetal PCD and pollen development by directly activating expression of the proteases CEP1 and βVPE. Thus, a transcription factor/proteases regulatory and activated cascade was established for tapetal PCD during another development in Arabidopsis thaliana. Highlight: MYB2 is involved in tapetal PCD and pollen development by directly regulating expression of the protease CEP1 and βVPE and establishes a transcription factor/proteases regulatory and activated cascade. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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Review

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21 pages, 1525 KiB

Open AccessReview

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

by Ivana L. Viola, Antonela L. Alem, Rocío M. Jure and Daniel H. Gonzalez

Int. J. Mol. Sci. 2023, 24(6), 5437; https://doi.org/10.3390/ijms24065437 - 12 Mar 2023

Cited by 18 | Viewed by 3583

Abstract

TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and [...] Read more.

TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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12 pages, 1090 KiB

Open AccessReview

Mechanics of Reversible Deformation during Leaf Movement and Regulation of Pulvinus Development in Legumes

by Miyuki T. Nakata and Masahiro Takahara

Int. J. Mol. Sci. 2022, 23(18), 10240; https://doi.org/10.3390/ijms231810240 - 6 Sep 2022

Cited by 8 | Viewed by 2627

Abstract

Plant cell deformation is a mechanical process that is driven by differences in the osmotic pressure inside and outside of the cell and is influenced by cell wall properties. Legume leaf movements result from reversible deformation of pulvinar motor cells. Reversible cell deformation [...] Read more.

Plant cell deformation is a mechanical process that is driven by differences in the osmotic pressure inside and outside of the cell and is influenced by cell wall properties. Legume leaf movements result from reversible deformation of pulvinar motor cells. Reversible cell deformation is an elastic process distinct from the irreversible cell growth of developing organs. Here, we begin with a review of the basic mathematics of cell volume changes, cell wall function, and the mechanics of bending deformation at a macro scale. Next, we summarize the findings of recent molecular genetic studies of pulvinar development. We then review the mechanisms of the adaxial/abaxial patterning because pulvinar bending deformation depends on the differences in mechanical properties and physiological responses of motor cells on the adaxial versus abaxial sides of the pulvinus. Intriguingly, pulvini simultaneously encompass morphological symmetry and functional asymmetry along the adaxial/abaxial axis. This review provides an introduction to leaf movement and reversible deformation from the perspective of mechanics and molecular genetics. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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16 pages, 2232 KiB

Open AccessReview

BES1/BZR1 Family Transcription Factors Regulate Plant Development via Brassinosteroid-Dependent and Independent Pathways

by Hongyong Shi, Xiaopeng Li, Minghui Lv and Jia Li

Int. J. Mol. Sci. 2022, 23(17), 10149; https://doi.org/10.3390/ijms231710149 - 5 Sep 2022

Cited by 23 | Viewed by 4163

Abstract

The BES1/BZR1 family is a plant-specific small group of transcription factors possessing a non-canonical bHLH domain. Genetic and biochemical analyses within the last two decades have demonstrated that members of this family are key transcription factors in regulating the expression of brassinosteroid (BR) [...] Read more.

The BES1/BZR1 family is a plant-specific small group of transcription factors possessing a non-canonical bHLH domain. Genetic and biochemical analyses within the last two decades have demonstrated that members of this family are key transcription factors in regulating the expression of brassinosteroid (BR) response genes. Several recent genetic and evolutionary studies, however, have clearly indicated that the BES1/BZR1 family transcription factors also function in regulating several aspects of plant development via BR-independent pathways, suggesting they are not BR specific. In this review, we summarize our current understanding of this family of transcription factors, the mechanisms regulating their activities, DNA binding motifs, and target genes. We selectively discuss a number of their biological functions via BR-dependent and particularly independent pathways, which were recently revealed by loss-of-function genetic analyses. We also highlight a few possible future directions. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function)

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