Cloning and Functional Analysis of the Promoter of an Ascorbate Oxidase Gene from Gossypium hirsutum

Revisiting the role of ascorbate oxidase in plant systems

Ascorbic acid (AsA) plays an indispensable role in plants, serving as both an antioxidant and a master regulator of the cellular redox balance. Ascorbate oxidase (AO) is a blue copper oxidase that is responsible for the oxidation of AsA with the concomitant production of water. For many decades, AO was erroneously postulated as an enzyme without any obvious advantage, as it decreases the AsA pool size and thus is expected to weaken plant stress resistance. It was only a decade ago that this perspective shifted towards the fundamental role of AO in orchestrating both AsA and oxygen levels by influencing the overall redox balance in the extracellular matrix. Consistent with its localization in the apoplast, AO is involved in cell expansion, division, resource allocation, and overall plant yield. An increasing number of transgenic studies has demonstrated that AO can also facilitate communication between the surrounding environment and the cell, as its gene expression is highly responsive to factors such as hormonal signaling, oxidative stress, and mechanical injury. This review aims to describe the multiple functions of AO in plant growth, development, and stress resilience, and explore any additional roles the enzyme might have in fruits during the course of ripening.

Genome-wide identification of YABBY transcription factors in Brachypodium distachyon and functional characterization of Bd DROOPING LEAF

YABBY transcription factors (TFs) are plant-specific and are characterized by a C2-C2 zinc finger domain at the N-terminus and a YABBY domain at the C-terminus. In this study, eight YABBY genes were identified in the Brachypodium distachyon genome and were unevenly distributed across four chromosomes. Phylogenetic analysis classified BdYABBYs into FIL/YAB3, YAB2, CRC, and INO clades. Sixty-two putative cis-elements were identified in BdYABBY gene putative promoters, among them, CAAT-box, TATA-box, MYB, MYC, ARE, and Box_4 were shared by all. BdYABBY genes are highly expressed in inflorescences, and abiotic stresses regulate their expression. In addition, three transcripts of BdDL were identified. Over-expression in Arabidopsis has shown their different functions in reproductive development, as well as in response to cold stress. Our study lays the foundation for the functional elucidation of BdYABBY genes.

Isolation, cloning and functional analysis of a putative constitutive promoter of E3 ubiquitin- protein ligase RF4 from Coleus amboinicus Lour

Promoter is a region in the genome sequence located upstream of the transcription start site comprising cis acting elements, which initiates and regulates the transcription of an associated gene. As the need for genetically engineered plants has widened, the requirement to develop methods to optimize the control of transgene expression has also increased. Therefore, analyzing the functionality of the promoter is very important in understanding the target gene expression. The widespread use of viral constitutive promoters (Cauliflower mosaic virus - CaMV35) has raised concerns about the safety and containment of the transgene in the environment. Hence isolation and characterization of novel promoters using fast and efficient genetic engineering tools is the need of the hour. The present study, for the first time, describes the isolation and characterization of a novel constitutive promoter driving Ubiquitin E3 ligase from the plant Coleus amboinicus, a perennial herb, of Lamiaceae family. The functionality of the isolated promoter was demonstrated using the β Glucuronidase as a reporter in tobacco var Petit havana. Development of blue color in the tobacco leaves indicated the presence of a functional promoter. We describe for the first time the isolation and characterization of E3 ubiquitin- protein ligase RF4 promoter from Coleus amboinicus Lour. In silico analysis revealed the presence of core promoter elements and other responsive elements in the promoter. The functionality of the promoter was demonstrated in tobacco leaf discs via GUS staining. This article is protected by copyright. All rights reserved.

Expression profiling of the mitogen-activated protein kinase gene family reveals their diverse response pattern in two different salt-tolerant Glycyrrhiza species

BACKGROUND

Mitogen-activated protein kinases (MPKs) play important role in response to environmental stress as crucial signal receptors or sensors. Our previous study indicated that salt stress acts as a positive factor to stimulate the production of pharmacodynamic metabolites in the medicinal plant Glycyrrhiza uralensis. Currently, little is known about the MPK gene family and their functions in the medicinal plant G. uralensis.

OBJECTIVE

Identification, comprehensive bioinformatic analysis, expression profiling, and response pattern under salt stress of the G. uralensis GuMPK gene family.

METHODS

Genome-wide investigation and expression profiling of the MPK gene family in G. uralensis, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, promoter cis-acting element, and expression pattern under salt stress in two different salt-tolerant Glycyrrhiza species were performed.

RESULTS

A total of 20 G. uralensis GuMPK genes were identified and categorized into five groups, and had conserved gene structure and motif distribution. Expression profiling of GuMPK genes suggested their potentially diverse functions in plant growth and in response to phytohormones and environmental stress, particularly GuMPK1, 2, 5, and 10 as key components for G. uralensis in response to abiotic stress. Further expression analysis under NaCl treatment in two different salt-tolerant Glycyrrhiza species displayed the MPKs' different response patterns, emphasizing the role of MPK2, 5, 7, and 16 as potentially crucial genes for Glycyrrhiza to respond to salt stress.

CONCLUSION

Our results provide a genome-wide identification and expression profiling of MPK gene family in G. uralensis, and establish the foundation for screening key responsive genes and understanding the potential function and regulatory mechanism of GuMPKs in salt responsiveness.

Molecular dissection of genes and promoters involved in glycyrrhizin biosynthesis revealed phytohormone induced modulation in Glycyrrhiza glabra L

The study reports cloning and characterization of complete biosynthetic gene cluster committed to glycyrrhizin biosynthesis along with their corresponding promoter regions from Glycyrrhiza glabra. The identified genes namely, β-amyrin synthase, β-amyrin-11-oxidase, 11-oxo-beta-amyrin 30-oxidase and UDP-dependent glucosyltransferase, were hetrologously expressed in Nicotiana benthamiana for functional validation. The phyto-hormone, naphthalene acetic acid was shown to prompt maximum up regulation (1.3-14.0 folds) of all the genes, followed by gibberellic acid (0.001-10.0 folds) and abscisic acid (0.2-7.7 folds) treatments. The promoter-GUS fusion constructs infiltrated leaves of the identified genes exhibited enhanced promoter activity of β-amyrin synthase (3.9 & 3.0 folds) and 11-oxo-beta-amyrin 30-oxidase (3.6 & 3.2 folds) under the GA₃ and NAA treatments, respectively as compared to their respective untreated controls. The transcriptional control of the three phytohormones studied could be correlated to the cis-responsive elements present in the upstream regions of the individual genes. The study provided an insight into the intricate interaction between hormone-responsive motifs with the corresponding co-expression of the glycyrrhizin biosynthetic pathway genes. The study will help in understanding the phytohormones-mediated regulation of glycyrrhizin biosynthesis and its modulation in the plant.

Genome-Wide Identification of the Eucalyptus urophylla GATA Gene Family and Its Diverse Roles in Chlorophyll Biosynthesis

GATA transcription factors have been demonstrated to play key regulatory roles in plant growth, development, and hormonal response. However, the knowledge concerning the evolution of GATA genes in Eucalyptus urophylla and their trans-regulatory interaction is indistinct. Phylogenetic analysis and study of conserved motifs, exon structures, and expression patterns resolved the evolutionary relationships of these GATA proteins. Phylogenetic analysis showed that EgrGATAs are broadly distributed in four subfamilies. Cis-element analysis of promoters revealed that EgrGATA genes respond to light and are influenced by multiple hormones and abiotic stresses. Transcriptome analysis revealed distinct temporal and spatial expression patterns of EgrGATA genes in various tissues of E. urophylla S.T.Blake, which was confirmed by real-time quantitative PCR (RT-qPCR). Further research revealed that EurGNC and EurCGA1 were localized in the nucleus, and EurGNC directly binds to the cis-element of the EurGUN5 promoter, implying its potential roles in the regulation of chlorophyll synthesis. This comprehensive study provides new insights into the evolution of GATAs and could help to improve the photosynthetic assimilation and vegetative growth of E. urophylla at the genetic level.

Plant Copper Metalloenzymes As Prospects for New Metabolism Involving Aromatic Compounds

Copper is an important transition metal cofactor in plant metabolism, which enables diverse biocatalysis in aerobic environments. Multiple classes of plant metalloenzymes evolved and underwent genetic expansions during the evolution of terrestrial plants and, to date, several representatives of these copper enzyme classes have characterized mechanisms. In this review, we give an updated overview of chemistry, structure, mechanism, function and phylogenetic distribution of plant copper metalloenzymes with an emphasis on biosynthesis of aromatic compounds such as phenylpropanoids (lignin, lignan, flavonoids) and cyclic peptides with macrocyclizations via aromatic amino acids. We also review a recent addition to plant copper enzymology in a copper-dependent peptide cyclase called the BURP domain. Given growing plant genetic resources, a large pool of copper biocatalysts remains to be characterized from plants as plant genomes contain on average more than 70 copper enzyme genes. A major challenge in characterization of copper biocatalysts from plant genomes is the identification of endogenous substrates and catalyzed reactions. We highlight some recent and future trends in filling these knowledge gaps in plant metabolism and the potential for genomic discovery of copper-based enzymology from plants.

Genome-Wide Investigation and Expression Profiling Under Abiotic Stresses of a Soybean Unknown Function (DUF21) and Cystathionine-β-Synthase (CBS) Domain-Containing Protein Family

Cystathionine-β-synthase (CBS) domain-containing proteins (CDCPs) constitute a large family in plants, and members of this family have been implicated in a variety of biological processes. However, the precise functions and the underlying mechanisms of most members of this family in plants remain to be elucidated. CBSDUF proteins belong to the CDCP superfamily, which contains one domain of unknown function (DUF21) and an N terminus that is adjacent to two intracellular CBS domains. In this study, a comprehensive genome database analysis of soybean was performed to investigate the role(s) of these CBSDUFs and to explore their nomenclature, classification, chromosomal distribution, exon-intron organization, protein structure, and phylogenetic relationships; the analysis identified a total of 18 putative CBSDUF genes. Using specific protein domains and phylogenetic analysis, the CBSDUF gene family was subdivided into eight groups. The soybean CBSDUF genes showed an uneven distribution on 12 chromosomes of Glycine max. RNA-seq transcriptome data from different tissues in public databases revealed tissue-specific and differential expression profiles of the GmCBSDUFs, and qPCR analysis revealed that certain groups of soybean CBSDUFs are likely involved in specific stress responses. In addition, GmCBSDUF3 transgenic Arabidopsis was subjected to phenotypic analysis under NaCl, PEG, and ABA stress treatments. The overexpression of GmCBSDUF3 could enhance tolerance to drought and salt stress in Arabidopsis. This study presents a first comprehensive look at soybean CBSDUF proteins and provides valuable resources for functionally elucidating this protein subgroup within the CBS domain-containing protein family.

Genome-Wide Identification and Expression Analysis of the Ascorbate Oxidase Gene Family in Gossypium hirsutum Reveals the Critical Role of GhAO1A in Delaying Dark-Induced Leaf Senescence

Ascorbate oxidase (AO) plays important roles in plant growth and development. Previously, we reported a cotton AO gene that acts as a positive factor in cell growth. Investigations on Gossypium hirsutum AO (GhAO) family genes and their multiple functions are limited. The present study identified eight GhAO family genes and performed bioinformatic analyses. Expression analyses of the tissue specificity and developmental feature of GhAOs displayed their diverse expression patterns. Interestingly, GhAO1A demonstrated the most rapid significant increase in expression after 1 h of light recovery from the dark. Additionally, the transgenic ao1-1/GhAO1AArabidopsis lines overexpressing GhAO1A in the Arabidopsisao1-1 late-flowering mutant displayed a recovery to the normal phenotype of wild-type plants. Moreover, compared to the ao1-1 mutant, the ao1-1/GhAO1A transgenic Arabidopsis presented delayed leaf senescence that was induced by the dark, indicating increased sensitivity to hydrogen peroxide (H₂O₂) under normal conditions that might be caused by a reduction in ascorbic acid (AsA) and ascorbic acid/dehydroascorbate (AsA/DHA) ratio. The results suggested that GhAOs are functionally diverse in plant development and play a critical role in light responsiveness. Our study serves as a foundation for understanding the AO gene family in cotton and elucidating the regulatory mechanism of GhAO1A in delaying dark-induced leaf senescence.

GhVTC1, the Key Gene for Ascorbate Biosynthesis in Gossypium hirsutum, Involves in Cell Elongation Under Control of Ethylene

L-Ascorbate (Asc) plays important roles in cell growth and plant development, and its de novo biosynthesis was catalyzed by the first rate-limiting enzyme VTC1. However, the function and regulatory mechanism of VTC1 involved in cell development is obscure in Gossypium hirsutum. Herein, the Asc content and AsA/DHA ratio were accumulated and closely linked with fiber development. The GhVTC1 encoded a typical VTC1 protein with functional conserved domains and expressed preferentially during fiber fast elongation stages. Functional complementary analysis of GhVTC1 in the loss-of-function Arabidopsis vtc1-1 mutants indicated that GhVTC1 is genetically functional to rescue the defects of mutants to normal or wild type (WT). The significant shortened primary root in vtc1-1 mutants was promoted to the regular length of WT by the ectopic expression of GhVTC1 in the mutants. Additionally, GhVTC1 expression was induced by ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), and the GhVTC1 promoter showed high activity and included two ethylene-responsive elements (ERE). Moreover, the 5'-truncted promoters containing the ERE exhibited increased activity by ACC treatment. Our results firstly report the cotton GhVTC1 function in promoting cell elongation at the cellular level, and serve as a foundation for further understanding the regulatory mechanism of Asc-mediated cell growth via the ethylene signaling pathway.

Calcium-Dependent Protein Kinase Genes in Glycyrrhiza Uralensis Appear to be Involved in Promoting the Biosynthesis of Glycyrrhizic Acid and Flavonoids under Salt Stress

As calcium signal sensors, calcium-dependent protein kinases (CPKs) play vital roles in stimulating the production of secondary metabolites to participate in plant development and response to environmental stress. However, investigations of the Glycyrrhiza uralensis CPK family genes and their multiple functions are rarely reported. In this study, a total of 23 GuCPK genes in G. uralensis were identified, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, and promoter cis-acting elements were analyzed. Ten GuCPKs showed root-specific preferential expressions, and GuCPKs indicated different expression patterns under treatments of CaCl2 and NaCl. In addition, under 2.5 mM of CaCl2 and 30 mM of NaCl treatments, the diverse, induced expression of GuCPKs and significant accumulations of glycyrrhizic acid and flavonoids suggested the possible important function of GuCPKs in regulating the production of glycyrrhizic acid and flavonoids. Our results provide a genome-wide characterization of CPK family genes in G. uralensis, and serve as a foundation for understanding the potential function and regulatory mechanism of GuCPKs in promoting the biosynthesis of glycyrrhizic acid and flavonoids under salt stress.

A Gossypium hirsutum GDSL lipase/hydrolase gene (GhGLIP) appears to be involved in promoting seed growth in Arabidopsis

GDSL lipase (GLIP) plays a pivotal role in plant cell growth as a multifunctional hydrolytic enzyme. Herein, a cotton (Gossypium hirsutum L. cv Xuzhou 142) GDSL lipase gene (GhGLIP) was obtained from developing ovules and fibers. The GhGLIP cDNA contained an open reading frame (ORF) of 1,143 base pairs (bp) and encodes a putative polypeptide of 380 amino acid residues. Sequence alignment indicated that GhGLIP includes four enzyme catalytic amino acid residue sites of Ser (S), Gly (G), Asn (N) and His (H), located in four conserved blocks. Phylogenetic tree analysis showed that GhGLIP belongs to the typical class IV lipase family with potential functions in plant secondary metabolism. Subcellular distribution analysis demonstrated that GhGLIP localized to the nucleus, cytoplasm and plasma membrane. GhGLIP was expressed predominantly at 5-15 day post anthesis (dpa) in developing ovules and elongating fibers, measured as mRNA levels and enzyme activity. Ectopic overexpression of GhGLIP in Arabidopsis plants resulted in enhanced seed development, including length and fresh weight. Meanwhile, there was increased soluble sugar and protein storage in transgenic Arabidopsis plants, coupled with the promotion of lipase activity. Moreover, the expression of cotton GhGLIP is induced by ethylene (ETH) treatment in vitro. A 1,954-bp GhGLIP promoter was isolated and expressed high activity in driving green fluorescence protein (GFP) expression in tobacco leaves. Cis-acting element analysis of the GhGLIP promoter (pGhGLIP) indicated the presence of an ethylene-responsive element (ERE), and transgenic tobacco leaves with ectopic expression of pGhGLIP::GFP-GUS showed increased GUS activity after ETH treatment. In summary, these results suggest that GhGLIP is a functional enzyme involved in ovule and fiber development and performs significant roles in seed development.

Calcium-Dependent Protein Kinase Family Genes Involved in Ethylene-Induced Natural Rubber Production in Different Hevea brasiliensis Cultivars

Natural rubber latex production can be improved by ethylene stimulation in the rubber tree (Hevea brasiliensis). However, the expression levels of most functional proteins for natural rubber biosynthesis are not induced after ethylene application, indicating that post-translational modifications, especially protein phosphorylation, may play important roles in ethylene signaling in Hevea. Here, we performed a comprehensive investigation on evolution, ethylene-induced expression and protein-protein interaction of calcium-dependent protein kinases (CPKs), an important serine/threonine protein kinase family, in Hevea. Nine duplication events were determined in the 30 identified HbCPK genes. Expression profiling of HbCPKs in three rubber tree cultivars with low, medium and high ethylene sensitivity showed that HbCPK6, 17, 20, 22, 24, 28 and 30 are induced by ethylene in at least one cultivar. Evolution rate analysis suggested accelerated evolution rates in two paralogue pairs, HbCPK9/18 and HbCPK19/20. Analysis of proteomic data for rubber latex after ethylene treatment showed that seven HbCPK proteins could be detected, including six ethylene-induced ones. Protein-protein interaction analysis of the 493 different abundant proteins revealed that protein kinases, especially calcium-dependent protein kinases, possess most key nodes of the interaction network, indicating that protein kinase and protein phosphorylation play important roles in ethylene signaling in latex of Hevea. In summary, our data revealed the expression patterns of HbCPK family members and functional divergence of two HbCPK paralogue pairs, as well as the potential important roles of HbCPKs in ethylene-induced rubber production improvement in Hevea.

Genome-wide investigation and expression profiling of APX gene family in Gossypium hirsutum provide new insights in redox homeostasis maintenance during different fiber development stages

Ascorbate peroxidase (APX) is a member of heme-containing peroxidases which catalyze the H₂O₂-dependent oxidation of a wide range of substrates in plants and animals. As is known, H₂O₂ acts as a signaling molecule in the regulation of fiber development. Our previous work reported that ascorbate peroxidase 1 (GhAPX1) was important for cotton fiber elongation. However, knowledge about APX gene family members and their evolutionary and functional characteristics in cotton is limited. Here, we report 26 GhAPX genes by genome-wide investigation of tetraploid cotton Gossypium hirsutum. Phylogenetic and gene structure analyses classified these APX members into five clades and syntenic analysis suggested two duplication events. Expression profiling of the 26 APXs revealed that ten members are expressed in cotton fibers. Notably, GhAPX10A, GhAPX10D, GhAPX12A, and GhAPX12D showed high expression levels in 30-day fiber, while GhAPX1A/D, GhAPX3A/D, and GhAPX6A/D showed very low expression levels. The enzyme activity and H₂O₂ content assays revealed that cotton fiber kept high enzyme activity and the lowest H₂O₂ level in 30-day fibers, indicating that other than GhAPX1, the newly reported APX members are responsible for the reactive oxygen species homeostasis in the cotton fiber maturation stages. Expression profiling of ten fiber-expressed APXs after phytohormone treatments revealed their regulation patterns by different stimuli, suggesting that GhAPX1, GhAPX12A, and GhAPX12D are responsible to most phytohormone treatments. Our data provided evolutionary and functional information of GhAPX gene family members and revealed that different members are responsible to redox homeostasis during different cotton fiber development stages.

Cotton Ascorbate Oxidase Promotes Cell Growth in Cultured Tobacco Bright Yellow-2 Cells through Generation of Apoplast Oxidation

Ascorbate oxidase (AO) plays an important role in cell growth through the modulation of reduction/oxidation (redox) control of the apoplast. Here, a cotton (Gossypium hirsutum) apoplastic ascorbate oxidase gene (GhAO1) was obtained from fast elongating fiber tissues. GhAO1 belongs to the multicopper oxidase (MCO) family and includes a signal peptide and several transmembrane regions. Analyses of quantitative real-time polymerase chain reaction (QRT-PCR) and enzyme activity showed that GhAO1 was expressed abundantly in 15-day post-anthesis (dpa) wild-type (WT) fibers in comparison with fuzzless-lintless (fl) mutant ovules. Subcellular distribution analysis in onion cells demonstrated that GhAO1 is localized in the cell wall. In transgenic tobacco bright yellow-2 (BY-2) cells with ectopic overexpression of GhAO1, the enhancement of cell growth with 1.52-fold increase in length versus controls was indicated, as well as the enrichment of both total ascorbate in whole-cells and dehydroascorbate acid (DHA) in apoplasts. In addition, promoted activities of AO and monodehydroascorbate reductase (MDAR) in apoplasts and dehydroascorbate reductase (DHAR) in whole-cells were displayed in transgenic tobacco BY-2 cells. Accumulation of H₂O₂, and influenced expressions of Ca2+ channel genes with the activation of NtMPK9 and NtCPK5 and the suppression of NtTPC1B were also demonstrated in transgenic tobacco BY-2 cells. Finally, significant induced expression of the tobacco NtAO gene in WT BY-2 cells under indole-3-acetic acid (IAA) treatment appeared; however, the sensitivity of the NtAO gene expression to IAA disappeared in transgenic BY-2 cells, revealing that the regulated expression of the AO gene is under the control of IAA. Taken together, these results provide evidence that GhAO1 plays an important role in fiber cell elongation and may promote cell growth by generating the oxidation of apoplasts, via the auxin-mediated signaling pathway.