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New Insights into Plant Development and Signal Transduction

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (1 May 2021) | Viewed by 42363

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Dr. Ignacio Ezquer

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Guest Editor

Department of Biosciences, University of Milan, 20133 Milan, Italy
Interests: plant biotechnology; plant genetics; botany, evolution of plants; agricultural biotechnology; plant breeding; metabolism; carbohydrates; cell wall; seed and fruit development; sexual reproduction; transcriptional regulation and hybridization barriers
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Paola Vittorioso

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Co-Guest Editor

Department Biology and Biotechnology C. Darwin, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
Interests: arabidopsis thaliana; seed germination; light signaling; phtomorphogenesis; Dof proteins

Prof. Dr. Stefan de Folter

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Co-Guest Editor

UGA-LANGEBIO, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), 36670 Irapuato, Mexico
Interests: plant molecular biology; transcription factors; flower and fruit development; gene regulatory networks; cytokinin signaling; protein–protein interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Signal transduction is essential for almost all aspects of plant cell function and differentiation processes. In this special issue we propose to discuss the role of signalling cascades controlling both plant developmental processes, and plant response to biotic and abiotic external cues. Understanding how extracellular stimuli and intracellular signals are transmitted in an effective and proper manner inside a cell or between neighbouring cells, is vital to our understanding of such important biological processes in plants as cell expansion and proliferation, tissue differentiation, and organ function. Such responses include changes in the transcription or translation of genes, and post-translational and conformational changes in proteins, as well as changes in their localization which interplay in fine-tuning of plant growth and development. It is really difficult to include all relevant areas in a single issue. Indeed signal transduction is essential in many developmental processes like flower morphogenesis, gametogenesis, root development, seed germination, photomorphogenesis, as well as developmental plant responses to face biotic and abiotic stress. We welcome suggestions for research articles and submissions of reviews that provide good coverage of significant development in these and other areas within this exciting field.

Dr. Ignacio Ezquer
Prof. Paola Vittorioso
Prof. Stefan de Folter

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.

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Keywords

Plant development
Signalling
Gametogenesis
Fertilization
Embryogenesis
Plant polysaccharides and signalling
Hormonal regulation

Published Papers (12 papers)

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Editorial

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4 pages, 189 KiB

Open AccessEditorial

Developmental Signals in the 21st Century; New Tools and Advances in Plant Signaling

by Ignacio Ezquer, Paola Vittorioso and Stefan de Folter

Genes 2021, 12(11), 1708; https://doi.org/10.3390/genes12111708 - 27 Oct 2021

Viewed by 1250

Abstract

This special issue includes different research papers and reviews that studied the role of signaling cascades controlling both plant developmental processes and plant response mechanisms to biotic and abiotic stresses [...] Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

Research

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15 pages, 9221 KiB

Open AccessArticle

The PUB4 E3 Ubiquitin Ligase Is Responsible for the Variegated Phenotype Observed upon Alteration of Chloroplast Protein Homeostasis in Arabidopsis Cotyledons

by Nicolaj Jeran, Lisa Rotasperti, Giorgia Frabetti, Anna Calabritto, Paolo Pesaresi and Luca Tadini

Genes 2021, 12(9), 1387; https://doi.org/10.3390/genes12091387 - 6 Sep 2021

Cited by 14 | Viewed by 2884

Abstract

During a plant’s life cycle, plastids undergo several modifications, from undifferentiated pro-plastids to either photosynthetically-active chloroplasts, ezioplasts, chromoplasts or storage organelles, such as amyloplasts, elaioplasts and proteinoplasts. Plastid proteome rearrangements and protein homeostasis, together with intracellular communication pathways, are key factors for correct plastid differentiation and functioning. When plastid development is affected, aberrant organelles are degraded and recycled in a process that involves plastid protein ubiquitination. In this study, we have analysed the Arabidopsis gun1-102 ftsh5-3 double mutant, lacking both the plastid-located protein GUN1 (Genomes Uncoupled 1), involved in plastid-to-nucleus communication, and the chloroplast-located FTSH5 (Filamentous temperature-sensitive H5), a metalloprotease with a role in photosystem repair and chloroplast biogenesis. gun1-102 ftsh5-3 seedlings show variegated cotyledons and true leaves that we attempted to suppress by introgressing second-site mutations in genes involved in: (i) plastid translation, (ii) plastid folding/import and (iii) cytosolic protein ubiquitination. Different phenotypic effects, ranging from seedling-lethality to partial or complete suppression of the variegated phenotype, were observed in the corresponding triple mutants. Our findings indicate that Plant U-Box 4 (PUB4) E3 ubiquitin ligase plays a major role in the target degradation of damaged chloroplasts and is the main contributor to the variegated phenotype observed in gun1-102 ftsh5-3 seedlings. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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12 pages, 2996 KiB

Open AccessArticle

Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development

by Dario Paolo, Gregorio Orozco-Arroyo, Lisa Rotasperti, Simona Masiero, Lucia Colombo, Stefan de Folter, Barbara A. Ambrose, Elisabetta Caporali, Ignacio Ezquer and Chiara Mizzotti

Genes 2021, 12(8), 1189; https://doi.org/10.3390/genes12081189 - 30 Jul 2021

Cited by 6 | Viewed by 2801

Abstract

Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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21 pages, 8694 KiB

Open AccessArticle

Effects of the Developmental Regulator BOLITA on the Plant Metabolome

by Hugo Gerardo Lazcano-Ramírez, Roberto Gamboa-Becerra, Irving J. García-López, Ricardo A. Chávez Montes, David Díaz-Ramírez, Octavio Martínez de la Vega, José Juan Ordaz-Ortíz, Stefan de Folter, Axel Tiessen-Favier, Robert Winkler and Nayelli Marsch-Martínez

Genes 2021, 12(7), 995; https://doi.org/10.3390/genes12070995 - 29 Jun 2021

Cited by 3 | Viewed by 2082

Abstract

Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on specialized metabolism. For this, we used an Arabidopsis thaliana line in which the transcription factor activity can be induced. Fingerprinting metabolomic analyses of whole plantlets were performed at different times after induction. After 96 h, all induced replicas clustered as a single group, in contrast with all controls which did not cluster. Metabolomic analyses of shoot and root tissues enabled the putative identification of differentially accumulated metabolites in each tissue. Finally, the analysis of global gene expression in induced vs. non-induced root samples, together with enrichment analyses, allowed the identification of enriched metabolic pathways among the differentially expressed genes and accumulated metabolites after the induction. We concluded that the induction of BOL activity can modify the Arabidopsis metabolome. Future work should investigate whether its action is direct or indirect, and the implications of the metabolic changes for development regulation and bioprospection. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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23 pages, 6221 KiB

Open AccessArticle

Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation

by Oscar Arrey-Salas, José Carlos Caris-Maldonado, Bairon Hernández-Rojas and Enrique Gonzalez

Genes 2021, 12(2), 302; https://doi.org/10.3390/genes12020302 - 20 Feb 2021

Cited by 21 | Viewed by 3150

Abstract

Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte development, we performed a genome-wide identification and characterization of genes encoding ZFP (VviZFP family). A total of 98 genes were identified and renamed based on the gene distribution into grapevine genome. The analysis performed indicate significant changes throughout VviZFP genes evolution explained by high heterogeneity in sequence, length, number of ZF and presence of another conserved domains. Moreover, segmental duplication participated in the gene family expansion in grapevine. The VviZFPs were classified based on domain and phylogenetic analysis into three sets and different groups. Heat-map demonstrated differential and tissue-specific expression patterns of these genes and k-means clustering allowed to identify a group of putative orthologs to some ZFPs related to pollen development. In transgenic plants carrying the promVviZFP13::GUS and promVviZFP68::GUS constructs, GUS signals were detectable in the anther and mature pollen grains. Expression profiling of selected VviZFP genes showed differential expression pattern during flower development and provides a basis for deepening in the understanding of VviZFPs role on grapevine reproductive development. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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22 pages, 4910 KiB

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The Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE 1 Gene Is Involved in Anisotropic Root Growth during Osmotic Stress Adaptation

by María Belén Cuadrado-Pedetti, Inés Rauschert, María Martha Sainz, Vítor Amorim-Silva, Miguel Angel Botella, Omar Borsani and Mariana Sotelo-Silveira

Genes 2021, 12(2), 236; https://doi.org/10.3390/genes12020236 - 7 Feb 2021

Cited by 7 | Viewed by 2541

Abstract

Mutations in the Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE 1 (TTL1) gene cause reduced tolerance to osmotic stress evidenced by an arrest in root growth and root swelling, which makes it an interesting model to explore how root growth is controlled under stress conditions. We found that osmotic stress reduced the growth rate of the primary root by inhibiting the cell elongation in the elongation zone followed by a reduction in the number of cortical cells in the proximal meristem. We then studied the stiffness of epidermal cell walls in the root elongation zone of ttl1 mutants under osmotic stress using atomic force microscopy. In plants grown in control conditions, the mean apparent elastic modulus was 448% higher for live Col-0 cell walls than for ttl1 (88.1 ± 2.8 vs. 16.08 ± 6.9 kPa). Seven days of osmotic stress caused an increase in the stiffness in the cell wall of the cells from the elongation zone of 87% and 84% for Col-0 and ttl1, respectively. These findings suggest that TTL1 may play a role controlling cell expansion orientation during root growth, necessary for osmotic stress adaptation. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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24 pages, 4503 KiB

Open AccessArticle

Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii

by Alejandro Aragón-Raygoza, Alejandra Vasco, Ikram Blilou, Luis Herrera-Estrella and Alfredo Cruz-Ramírez

Genes 2020, 11(12), 1455; https://doi.org/10.3390/genes11121455 - 4 Dec 2020

Cited by 7 | Viewed by 6210

Abstract

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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Review

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16 pages, 1609 KiB

Open AccessReview

Building a Flower: The Influence of Cell Wall Composition on Flower Development and Reproduction

by José Erik Cruz-Valderrama, Judith Jazmin Bernal-Gallardo, Humberto Herrera-Ubaldo and Stefan de Folter

Genes 2021, 12(7), 978; https://doi.org/10.3390/genes12070978 - 26 Jun 2021

Cited by 6 | Viewed by 4660

Abstract

Floral patterning is a complex task. Various organs and tissues must be formed to fulfill reproductive functions. Flower development has been studied, mainly looking for master regulators. However, downstream changes such as the cell wall composition are relevant since they allow cells to divide, differentiate, and grow. In this review, we focus on the main components of the primary cell wall—cellulose, hemicellulose, and pectins—to describe how enzymes involved in the biosynthesis, modifications, and degradation of cell wall components are related to the formation of the floral organs. Additionally, internal and external stimuli participate in the genetic regulation that modulates the activity of cell wall remodeling proteins. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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40 pages, 1635 KiB

Open AccessReview

cROStalk for Life: Uncovering ROS Signaling in Plants and Animal Systems, from Gametogenesis to Early Embryonic Development

by Valentina Lodde, Piero Morandini, Alex Costa, Irene Murgia and Ignacio Ezquer

Genes 2021, 12(4), 525; https://doi.org/10.3390/genes12040525 - 3 Apr 2021

Cited by 11 | Viewed by 3223

Abstract

This review explores the role of reactive oxygen species (ROS)/Ca²⁺ in communication within reproductive structures in plants and animals. Many concepts have been described during the last years regarding how biosynthesis, generation products, antioxidant systems, and signal transduction involve ROS signaling, as well as its possible link with developmental processes and response to biotic and abiotic stresses. In this review, we first addressed classic key concepts in ROS and Ca²⁺ signaling in plants, both at the subcellular, cellular, and organ level. In the plant science field, during the last decades, new techniques have facilitated the in vivo monitoring of ROS signaling cascades. We will describe these powerful techniques in plants and compare them to those existing in animals. Development of new analytical techniques will facilitate the understanding of ROS signaling and their signal transduction pathways in plants and mammals. Many among those signaling pathways already have been studied in animals; therefore, a specific effort should be made to integrate this knowledge into plant biology. We here discuss examples of how changes in the ROS and Ca²⁺ signaling pathways can affect differentiation processes in plants, focusing specifically on reproductive processes where the ROS and Ca²⁺ signaling pathways influence the gametophyte functioning, sexual reproduction, and embryo formation in plants and animals. The study field regarding the role of ROS and Ca²⁺ in signal transduction is evolving continuously, which is why we reviewed the recent literature and propose here the potential targets affecting ROS in reproductive processes. We discuss the opportunities to integrate comparative developmental studies and experimental approaches into studies on the role of ROS/ Ca²⁺ in both plant and animal developmental biology studies, to further elucidate these crucial signaling pathways. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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17 pages, 602 KiB

Open AccessReview

The FLA4-FEI Pathway: A Unique and Mysterious Signaling Module Related to Cell Wall Structure and Stress Signaling

by Georg J. Seifert

Genes 2021, 12(2), 145; https://doi.org/10.3390/genes12020145 - 22 Jan 2021

Cited by 14 | Viewed by 2880

Abstract

Cell wall integrity control in plants involves multiple signaling modules that are mostly defined by genetic interactions. The putative co-receptors FEI1 and FEI2 and the extracellular glycoprotein FLA4 present the core components of a signaling pathway that acts in response to environmental conditions and insults to cell wall structure to modulate the balance of various growth regulators and, ultimately, to regulate the performance of the primary cell wall. Although the previously established genetic interactions are presently not matched by intermolecular binding studies, numerous receptor-like molecules that were identified in genome-wide interaction studies potentially contribute to the signaling machinery around the FLA4-FEI core. Apart from its function throughout the model plant Arabidopsis thaliana for the homeostasis of growth and stress responses, the FLA4-FEI pathway might support important agronomic traits in crop plants. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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17 pages, 1068 KiB

Open AccessReview

From the Outside to the Inside: New Insights on the Main Factors That Guide Seed Dormancy and Germination

by Chiara Longo, Soyanni Holness, Veronica De Angelis, Andrea Lepri, Sara Occhigrossi, Veronica Ruta and Paola Vittorioso

Genes 2021, 12(1), 52; https://doi.org/10.3390/genes12010052 - 31 Dec 2020

Cited by 18 | Viewed by 3987

Abstract

The transition from a dormant to a germinating seed represents a crucial developmental switch in the life cycle of a plant. Subsequent transition from a germinating seed to an autotrophic organism also requires a robust and multi-layered control. Seed germination and seedling growth are multistep processes, involving both internal and external signals, which lead to a fine-tuning control network. In recent years, numerous studies have contributed to elucidate the molecular mechanisms underlying these processes: from light signaling and light-hormone crosstalk to the effects of abiotic stresses, from epigenetic regulation to translational control. However, there are still many open questions and molecular elements to be identified. This review will focus on the different aspects of the molecular control of seed dormancy and germination, pointing out new molecular elements and how these integrate in the signaling pathways already known. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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18 pages, 302 KiB

Open AccessReview

Recent Development on Plant Aldehyde Dehydrogenase Enzymes and Their Functions in Plant Development and Stress Signaling

by Adesola J. Tola, Amal Jaballi, Hugo Germain and Tagnon D. Missihoun

Genes 2021, 12(1), 51; https://doi.org/10.3390/genes12010051 - 31 Dec 2020

Cited by 39 | Viewed by 4957

Abstract

Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilic α, β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)⁺-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development. Full article

(This article belongs to the Special Issue New Insights into Plant Development and Signal Transduction)

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