Search Results (26)

The aromatic C₁₃ apocarotenoid β-ionone is a high-value natural-flavor and -fragrance compound derived from the oxidative cleavage of carotenoids. Carotenoid cleavage dioxygenases (CCDs) play a pivotal role in the biosynthesis of volatile apocarotenoids, particularly β-ionone. In this study, we report the identification, cloning, and functional characterization of two CCD1 homologs: OeCCD1 from Olea europaea and InCCD1 from Ipomoea nil. These two species, which, respectively, represent a woody perennial and a herbaceous annual, were selected to explore the potential functional divergence of CCD1 enzymes across different plant growth forms. These CCD1 genes were synthesized using codon optimization for Escherichia coli expression, followed by heterologous expression and purification using a GST-fusion system. In vitro assays confirmed that both enzymes cleave β-carotene at the 9,10 (9′,10′) double bond to yield β-ionone, but only OeCCD1 exhibits detectable activity on zeaxanthin; InCCD1 shows no in vitro cleavage of zeaxanthin. Kinetic characterization using β-apo-8′-carotenal as substrate revealed, for OeCCD1, a K_m of 0.82 mM, V_max of 2.30 U/mg (k_cat = 3.35 s⁻¹), and k_cat/K_m of 4.09 mM⁻¹·s⁻¹, whereas InCCD1 displayed K_m = 0.69 mM, V_max = 1.22 U/mg (k_cat = 1.82 s⁻¹), and k_cat/K_m = 2.64 mM⁻¹·s⁻¹. The optimization of expression parameters, as well as the systematic evaluation of temperature, pH, solvent, and metal ion effects, provided further insights into the stability and functional diversity within the plant CCD1 family. Overall, these findings offer promising enzymatic tools for the sustainable production of β-ionone and related apocarotenoids in engineered microbial cell factories. Full article

The Citrus clementina (citrus) plant produces various phytohormones due to the significant involvement of the carotenoid cleavage oxygenase (CCO) gene family in its growth and development. CCO genes can be divided into two main categories: NCED (9-cis-epoxy carotenoid dioxygenase), responsible for abscisic acid (ABA) production, and CCD (carotenoid cleavage dioxygenase), involved in pigment and strigolactone formation. To better understand the roles and positions of CcCCO gene members in relation to these hormones, researchers analyzed the clementine genome. To identify their structural features, they employed phylogenetic analysis, protein interactions, localization, structure, miRNA targets, evolutionary analysis, and transcriptome studies. The study revealed the presence of 15 CcCCO genes, including 11 NCED and 4 CCD genes, scattered across various chromosomes, with the majority located in chloroplasts. Promoter sequencing analysis indicated the presence of different cis-regulatory elements that likely interacted with phytohormones, such as auxin and abscisic acid among others. Notably, two genes, CcNCED1 and CcNCED3, were significantly expressed among the CCO genes, and these were found to be expressed during stress and played a crucial role in enabling optimal plant development. Furthermore, a comprehensive genome-wide comparison of CCO genes in C. Clementine and Arabidopsis thaliana models was conducted to understand their functional characteristics. This research provides a solid foundation for further exploration of the unique attributes of the C. clementina plant, contributing to a deeper understanding of its growth and development processes. Full article

Danshen (Salvia miltiorrhiza Bunge) is a perennial herbaceous plant of the Salvia genus in the family Lamiaceae. Its dry root is one of the important traditional Chinese herbal medicines with a long officinal history. The yield and quality of S. miltiorrhiza are influenced by various factors, among which drought is one of the most significant types of abiotic stress. Based on the transcriptome database of S. miltiorrhiza, our research group discovered a carotenoid cleavage dioxygenase gene, SmCCD4, belonging to the carotenoid cleavage oxygenase (CCO) gene family which is highly responsive to drought stress on the basis of our preceding work. Here, we identified 26 CCO genes according to the whole-genome database of S. miltiorrhiza. The expression pattern of SmCCD4 showed that this gene is strongly overexpressed in the aboveground tissue of S. miltiorrhiza. And by constructing SmCCD4 overexpression strains, it was shown that the overexpression of SmCCD4 not only promotes the synthesis of abscisic acid and increases plant antioxidant activity but also regulates the synthesis of the secondary metabolites tanshinone and phenolic acids in S. miltiorrhiza. In summary, this study is the first in-depth and systematic identification and investigation of the CCO gene family in S. miltiorrhiza. The results provide useful information for further systematic research on the function of CCO genes and provide a theoretical basis for improving the yield and quality of S. miltiorrhiza. Full article

SUPPRESSOR OF MAX2 1-LIKE (SMXL) proteins are negative regulators of strigolactone (SL) signal transduction that play an important role in regulating plant branching and responses to abiotic stress. Here, we studied the role of SMXL proteins in pear growth, development, and stress resistance. A total of 18 SMXL members were characterized in ‘duli’. All SMXL members were localized to chloroplasts. Chromosome mapping analysis showed that the members of this family were unevenly distributed on 14 chromosomes. Gene fragment replication analysis showed that there were no tandem repeat genes in PbSMXLs, and 12 pairs of homologous genes were fragment duplications. There were 30 pairs of homologous genes between ‘duli’ and apples, and 17 between ‘duli’ and Arabidopsis thaliana. Analysis of cis-acting elements showed that there was a large number of photo-effector elements, short-effector elements, hormone-responsive elements, and abiotic stress-responsive elements in the promoter sequences of this family. Analysis of enzyme activity and endogenous SL showed that β-carotenoid isomerase (D27), carotenoid cleavage dioxygenase 7 (CCD7), lateral branch oxidoreductase (LBO) levels, and SL content were higher in ‘duli’ roots and leaves compared in the control under exogenous GA₃ (gibberellin 3), IAA (indole-3-acetic acid), GR24 (synthetic SL analog), and NaCl. Most SMXL genes in ‘duli’ were highly expressed in branches and axillary lobes, but their expression was low in fruits. qRT-PCR analysis revealed that eight PbSMXL genes were responsive to GA₃, PAC (Paclobutrazol), IAA, ABA (abscisic acid), GR24, and Tis108 (SL biosynthesis inhibitor). PbSMXLs responded positively to salt stress. The expression of PbSMXL6 and PbSMXL15 was significantly induced under salt stress. The expression of PbSMXL7, PbSMXL10, and PbSMXL15 was significantly induced by Tis108 treatment. The results of this study enhance our understanding of the role of SMXL genes in the responses to plant growth regulators and salt stress. Our findings will also aid future studies of the functions of SMXL genes in ‘duli’. Full article

Carotenoid cleavage oxygenases (CCOs) cleave carotenoid molecules to produce bioactive products that influence the synthesis of hormones such as abscisic acid (ABA) and strigolactones (SL), which regulate plant growth, development, and stress adaptation. Here, to explore the molecular characteristics of all members of the OsCCO family in rice, fourteen OsCCO family genes were identified in the genome-wide study. The results revealed that the OsCCO family included one OsNCED and four OsCCD subfamilies. The OsCCO family was phylogenetically close to members of the maize ZmCCO family and the Sorghum SbCCO family. A collinearity relationship was observed between OsNCED3 and OsNCED5 in rice, as well as OsCCD7 and OsNCED5 between rice and Arabidopsis, Sorghum, and maize. OsCCD4a and OsCCD7 were the key members in the protein interaction network of the OsCCO family, which was involved in the catabolic processes of carotenoids and terpenoid compounds. miRNAs targeting OsCCO family members were mostly involved in the abiotic stress response, and RNA-seq data further confirmed the molecular properties of OsCCO family genes in response to abiotic stress and hormone induction. qRT-PCR analysis showed the differential expression patterns of OsCCO members across various rice organs. Notably, OsCCD1 showed relatively high expression levels in all organs except for ripening seeds and endosperm. OsNCED2a, OsNCED3, OsCCD1, OsCCD4a, OsCCD7, OsCCD8a, and OsCCD8e were potentially involved in plant growth and differentiation. Meanwhile, OsNCED2a, OsNCED2b, OsNCED5, OsCCD8b, and OsCCD8d were associated with reproductive organ development, flowering, and seed formation. OsNCED3, OsCCD4b, OsCCD4c, OsCCD8b, and OsCCD8c were related to assimilate transport and seed maturation. These findings provide a theoretical basis for further functional analysis of the OsCCO family. Full article

As a crucial member of the gene family involved in the biosynthesis of strigolactones, D27 plays an important regulatory role in plant branching and root development, which is essential for field management and yield increase in peppers (Capsicum annuum L.). To comprehensively understand the characteristics of the pepper D27 gene family, we identified three CaD27 genes. By analyzing their physicochemical properties, phylogenetic relationships, gene structures, promoters, and expression patterns in different tissues, the characteristics of the CaD27 gene family were revealed. The research results showed that these three CaD27 genes are located in three different chromosomes. Evolutionary analysis divided the members of CaD27 into three groups, and gene collinearity analysis did not find any duplicates, indicating the diversity and non-redundancy of the CaD27 gene family members. In addition, we identified and classified cis-elements in the promoter regions of CaD27 genes, with a relatively high proportion related to light and plant hormone responses. Expression pattern analysis showed that CaD27.1 is expressed in leaves, while CaD27.2 is expressed in roots, indicating tissue specificity. Furthermore, protein interaction predictions revealed an interaction between D27.2 and CCD7. This study provided important insights into the function and regulatory mechanisms of the CaD27 gene family and the role of strigolactones in plant growth and development. Full article

Cerasus humilis, a small shrub of the Cerasus genus within the Rosaceae family, is native to China and renowned for its highly nutritious and medicinal fruits, robust root system, and remarkable drought resistance. This study primarily employed association transcriptome and metabolome analyses to assess changes in abscisic acid (ABA) levels and identify key regulatory genes in C. humilis subjected to varying degrees of drought stress. Notably, we observed distinct alterations in transcription factors across different drought intensities. Specifically, our transcriptome data indicated noteworthy shifts in GATA, MYB, MYC, WRKY, C2H2, and bHLH transcription factor families. Furthermore, combined transcriptomic and metabolomic investigations demonstrated significant enrichment of metabolic pathways, such as ‘Carbon metabolism’, ‘Biosynthesis of amino acids’, ‘Biosynthesis of cofactors’, ‘Phenylpropanoid biosynthesis’, ‘Starch and sucrose metabolism’, and ‘Plant hormone signal transduction’ under moderate (Mod) or severe (Sev) drought conditions. A total of 11 candidate genes involved in ABA biosynthesis and signaling pathways were identified. The down-regulated genes included secoisolariciresinol dehydrogenase-like and PYL2. Conversely, genes including FAD-dependent urate hydroxylase-like, cytochrome P450 97B2, carotenoid cleavage dioxygenase 4 (CCD4), SnRK2.2, ABI 5-like protein 5, PP2C 51, and SnRK2.3, were up-regulated under Mod or Sev drought stress. This study lays the genetic foundation for ABA biosynthesis to enhance drought tolerance and provides genetic resources for plant genetic engineering and breeding efforts. Full article

Fibrillin-1 and fibrillin-2, encoded by FBN1 and FBN2, respectively, play significant roles in elastic fiber assembly, with pathogenic variants causing a diverse group of connective tissue disorders such as Marfan syndrome (MFS) and congenital contractural arachnodactyly (CCD). Different genomic variations may lead to heterogeneous phenotypic features and functional consequences. Recent high-throughput sequencing modalities have allowed detection of novel variants that may guide the care for patients and inform the genetic counseling for their families. We performed clinical phenotyping for two newborn infants with complex congenital heart defects. For genetic investigations, we employed next-generation sequencing strategies including whole-genome Single-Nucleotide Polymorphism (SNP) microarray for infant A with valvular insufficiency, aortic sinus dilatation, hydronephrosis, and dysmorphic features, and Trio whole-exome sequencing (WES) for infant B with dextro-transposition of the great arteries (D-TGA) and both parents. Infant A is a term male with neonatal marfanoid features, left-sided hydronephrosis, and complex congenital heart defects including tricuspid regurgitation, aortic sinus dilatation, patent foramen ovale, patent ductus arteriosus, mitral regurgitation, tricuspid regurgitation, aortic regurgitation, and pulmonary sinus dilatation. He developed severe persistent pulmonary hypertension and worsening acute hypercapnic hypoxemic respiratory failure, and subsequently expired on day of life (DOL) 10 after compassionate extubation. Cytogenomic whole-genome SNP microarray analysis revealed a deletion within the FBN1 gene spanning exons 7–30, which overlapped with the exon deletion hotspot region associated with neonatal Marfan syndrome. Infant B is a term male prenatally diagnosed with isolated D-TGA. He required balloon atrial septostomy on DOL 0 and subsequent atrial switch operation, atrial septal defect repair, and patent ductus arteriosus ligation on DOL 5. Trio-WES revealed compound heterozygous c.518C>T and c.8230T>G variants in the FBN2 gene. Zygosity analysis confirmed each of the variants was inherited from one of the parents who were healthy heterozygous carriers. Since his cardiac repair at birth, he has been growing and developing well without any further hospitalization. Our study highlights novel FBN1/FBN2 variants and signifies the phenotype–genotype association in two infants affected with complex congenital heart defects with and without dysmorphic features. These findings speak to the importance of next-generation high-throughput genomics for novel variant detection and the phenotypic variability associated with FBN1/FBN2 variants, particularly in the neonatal period, which may significantly impact clinical care and family counseling. Full article

Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and dental anomalies. It is a rare disease, with a prevalence of 1–9/1,000,000, high penetrance, and variable expression. The gene responsible for CCD is the Runt-related transcription factor 2 (RUNX2) gene. We characterize the clinical, genetic, and bioinformatic results of four CCD cases: two cases within Mexican families with six affected members, nine asymptomatic individuals, and two sporadic cases with CCD, with one hundred healthy controls. Genomic DNA analyses of the RUNX2 gene were performed for Sanger sequencing. Bioinformatics tools were used to predict the function, stability, and structural changes of the mutated RUNX2 proteins. Three novel heterozygous mutations (c.651_652delTA; c.538_539delinsCA; c.662T>A) and a previously reported mutation (c.674G>A) were detected. In silico analysis showed that all mutations had functional, stability-related, and structural alterations in the RUNX2 protein. Our results show novel mutations that enrich the pool of RUNX2 gene mutations with CCD. Moreover, the proband 1 presented clinical data not previously reported that could represent an expanded phenotype of severe expression. Full article

Variations in the petal color of Brassica napus are crucial for ornamental value, but the controlled loci for breeding remain to be unraveled. Here, we report a candidate locus, AGR-FC.C3, having conducted a bulked segregant analysis on a segregating population with different petal colors. Our results showed that the locus covers 9.46 Mb of the genome, harboring 951 genes. BnaC03.MYB4, BnaC03.MYB85, BnaC03.MYB73, BnaC03.MYB98, and BnaC03.MYB102 belonging to MYB TFs families that might regulate the petal color were observed. Next, a bulk RNA sequencing of white and orange-yellow petals on three development stages was performed to further identify the possible governed genes. The results revealed a total of 51 genes by overlapping the transcriptome data and the bulked segregant analysis data, and it was found that the expression of BnaC03.CCD4 was significantly up-regulated in the white petals at three development stages. Then, several novel candidate genes such as BnaC03.ENDO3, BnaC03.T22F8.180, BnaC03.F15C21.8, BnaC03.Q8GSI6, BnaC03.LSD1, BnaC03.MAP1Da, BnaC03.MAP1Db, and BnaC03G0739700ZS putative to controlling the petal color were identified through deeper analysis. Furthermo re, we have developed two molecular markers for the reported functional gene BnaC03.CCD4 to discriminate the white and orange-yellow petal colors. Our results provided a novel locus for breeding rapeseed with multi-color petals. Full article

The CCD gene family plays a crucial role in the cleavage of carotenoids, converting them into apocarotenoids. This process not only impacts the physiology and development of plants but also enhances their tolerance toward different stresses. However, the character of the PmCCD gene family and its role in ornamental woody Prunus mume remain unclear. Here, ten non-redundant PmCCD genes were identified from the P. mume genome, and their physicochemical characteristics were predicted. According to the phylogenetic tree, PmCCD proteins were classified into six subfamilies: CCD1, CCD4, CCD7, CCD8, NCED and CCD-like. The same subfamily possessed similar gene structural patterns and numbers of conserved motifs. Ten PmCCD genes were concentrated on three chromosomes. PmCCD genes exhibited interspecific collinearity with P. armeniaca and P. persica. Additionally, PmCCD genes had obvious specificity in different tissues and varieties. Compared with white-flowered ‘ZLE’, PmCCD1 and PmCCD4 genes were low-expressed in ‘HJH’ with yellow petals, which suggested PmCCD1 and PmCCD4 might be related to the formation of yellow flowers in P. mume. Nine PmCCD genes could respond to NaCl or PEG treatments. These genes might play a crucial role in salt and drought resistance in P. mume. Moreover, PmVAR3 and PmSAT3/5 interacted with PmCCD4 protein in yeast and tobacco leaf cells. This study laid a foundation for exploring the role of the PmCCD gene family in flower coloration and stress response in P. mume. Full article

The B-BOX (BBX) gene family is widely distributed in animals and plants and is involved in the regulation of their growth and development. In plants, BBX genes play important roles in hormone signaling, biotic and abiotic stress, light-regulated photomorphogenesis, flowering, shade response, and pigment accumulation. However, there has been no systematic analysis of the BBX family in Platanus × acerifolia. In this study, we identified 39 BBX genes from the P. × acerifolia genome, and used TBtools, MEGA, MEME, NCBI CCD, PLANTCARE and other tools for gene collinearity analysis, phylogenetic analysis, gene structure, conserved domain analysis, and promoter cis-element analysis, and used the qRT-PCR and transcriptome data for analyzing expression pattern of the PaBBX genes. Collinearity analysis indicated segmental duplication was the main driver of the BBX family in P. × acerifolia, and phylogenetic analysis showed that the PaBBX family was divided into five subfamilies: I, II, III, IV and V. Gene structure analysis showed that some PaBBX genes contained super-long introns that may regulate their own expression. Moreover, the promoter of PaBBX genes contained a significant number of cis-acting elements that are associated with plant growth and development, as well as hormone and stress responses. The qRT-PCR results and transcriptome data indicated that certain PaBBX genes exhibited tissue-specific and stage-specific expression patterns, suggesting that these genes may have distinct regulatory roles in P. × acerifolia growth and development. In addition, some PaBBX genes were regularly expressed during the annual growth of P. × acerifolia, corresponding to different stages of flower transition, dormancy, and bud break, indicating that these genes may be involved in the regulation of flowering and/or dormancy of P. × acerifolia. This article provided new ideas for the study of dormancy regulation and annual growth patterns in perennial deciduous plants. Full article

Carotenoids are key metabolites in goji (Lycium), a traditional Chinese medicine plant; however, the carotenoid content varies in fruits of different goji species, and the mechanism of this variation is not clear. Carotenoids participate in signal transduction and photosynthesis, and function as colorants and photoprotectors. Members of the carotenoid cleavage oxygenase (CCO) gene family are involved in the regulation of phytohormones, pigments, and aromatic substances, such as abscisic acid (ABA), β-carotenoid, and α-ionone, by degrading carotenoids. Some CCO genes are also related to an abiotic stress response. Here, a total of 12 LbCCO genes were identified and analyzed from the L. barbarum genome. CCO genes were divided into six subfamilies based on the constructed phylogenetic tree, including LbNCEDs, LbCCD1, LbCCD3, LbCCD4, LbCCD7, and LbCCD8. Among them, CCD3 was reported for the first time. The gene structure and motif analysis revealed the conservation of CCO subfamilies. Pseudogene generation and the importance of each subfamily in CCOs were revealed by collinearity analysis. The spatiotemporal transcriptomes of L. barbarum and L. ruthenicum were compared, suggesting that CCD4-1 may dominate carotenoid degradation in goji fruits. Cis-acting elements prediction and environment responsive gene expression analyses indicated that salt-alkali stress and photothermal conditions might influence the expression of CCOs in goji. The results of this study enhance our understanding of the carotenoid degradation pathway, and the functions and responses of CCOs in goji species. Full article

Hormones act as master ripening regulators. In non-climacteric fruit, ABA plays a key role in ripening. Recently, we confirmed in Fragaria chiloensis fruit that in response to ABA treatment the fruit induces ripening-associated changes such as softening and color development. In consequence of these phenotypic changes, transcriptional variations associated with cell wall disassembly and anthocyanins biosynthesis were reported. As ABA stimulates the ripening of F. chiloensis fruit, the molecular network involved in ABA metabolism was analyzed. Therefore, the expression level of genes involved in ABA biosynthesis and ABA perception was quantified during the development of the fruit. Four NCED/CCDs and six PYR/PYLs family members were identified in F. chiloensis. Bioinformatics analyses confirmed the existence of key domains related to functional properties. Through RT-qPCR analyses, the level of transcripts was quantified. FcNCED1 codifies a protein that displays crucial functional domains, and the level of transcripts increases as the fruit develops and ripens, in parallel with the increment in ABA. In addition, FcPYL4 codifies for a functional ABA receptor, and its expression follows an incremental pattern during ripening. The study concludes that FcNCED1 is involved in ABA biosynthesis; meanwhile, FcPYL4 participates in ABA perception during the ripening of F. chiloensis fruit. Full article

Rose (Rosa sp.) is a widely used raw material for essential oil extraction and fragrance production. The carotenoid cleavage dioxygenases pathway is one of the main metabolic pathways for the degradation of carotenoids, which is located downstream of the terpenoids biosynthesis pathway and is closely related to the biosynthesis of volatile compounds. We performed a comprehensive genome-wide analysis of the rose CCD family genes (RcCCDs) in terms of phylogeny, sequence characterization, gene structure, gene duplication events, and transcriptome. Finally, 15 CCD family members were identified from the rose genome, and they were classified into three clades: nine for the CCD clade, four for the NCED clade, and two for the CCD-LIKE clade. The RcCCDs were distributed on chromosomes 1, 4, 5, 6, and 7, and were concentrated on both ends of the chromosomes. RcCCDs did not have paralogous genes or whole genome duplication events (WGD), eleven of them were single-copy genes, and their repetitive sequences were mainly dispersed and tandem. Ten RcCCDs were differentially expressed in the transcriptomes of different flowering stages. The expression of four of them increased and then decreased, which was the same process as the accumulation of volatile compounds, and it was speculated that these genes might be involved in the biosynthesis of volatile compounds. A total of fifteen modules were obtained by weighted gene co-expression network analysis of eighteen volatile compounds-related genes, of which six modules were a highly significant positive correlation with volatile compounds, and 20 hub genes in the modules were predicted. These hub genes all exercised their functions in the early flowering stage with strict temporal specificity. This study provided a theoretical basis for further exploring the biological functions of RcCCDs and hub genes regulating the synthesis and metabolism of volatile compounds in rose. Full article