Search Results (354)

Background: Translational regulation constitutes a critical layer of gene expression control in plants, yet the contribution of endogenous 5′ untranslated regions (5′ UTRs) to translational efficiency remains incompletely defined. While viral and synthetic leader sequences have been widely used to enhance protein production, comparatively few native plant 5′ UTRs have been systematically characterised. The objective of this study was to identify and functionally evaluate endogenous plant 5′ UTR elements that promote translation through post-transcriptional mechanisms. Methods: A 79-nucleotide fragment (CYSTM α) derived from the 5′ UTR of Arabidopsis thaliana CYSTM1 (AT1G05340) was cloned upstream of reporter genes and assessed using dual-luciferase assays in transient expression systems (Nicotiana benthamiana and A. thaliana) and in stable transgenic Arabidopsis lines. Translational activity was further evaluated in monocot wheat germ extract and in Escherichia coli. Transcript abundance was quantified by qRT-PCR. Publicly available ribosome profiling and m⁶A datasets were analysed to assess translational efficiency and RNA modification status. Results: In N. benthamiana and A. thaliana, CYSTM α increases reporter protein production 3–7 fold relative to the control and 30–130% above the benchmark Tobacco Mosaic Virus (TMV) Ω leader, without altering mRNA abundance. The CYSTM α sequence also enhances luciferase translation in monocot wheat germ extract and elevates translation 5-fold in E. coli. CYSTM α contains three motifs that may promote translation, namely three CAA repeats that are associated with translation initiation, an AMAYAA motif that is associated with eIF3 binding, and two N6-adenosine DRACH sites that are associated with cap-independent translation. Additionally, ribosome profiling revealed high translational efficiency (TE = 3.25) of native CYSTM1. Conclusions: CYSTM α represents a compact endogenous 5′ UTR element that enhances translation across multiple experimental systems. These findings expand the repertoire of plant-derived translational enhancers and provide insight into sequence features associated with efficient mRNA translation in plants. Full article

Grain number and size are important agronomic traits determining grain yield, and yield improvement depends on exploring functional variations of key regulatory genes. Mitogen-activated protein kinase 6 (MAPK6) plays a key role in crop development; however, its function and variation in wheat remain largely unclear. In this study, we aimed to characterize the function and haplotype variations of TaMAPK6-7A in wheat and develop functional molecular markers for marker assisted breeding. We identified three TaMAPK6 homoeologs on 7A, 7B, and 7D in wheat through bioinformatics analysis and revealed their evolutionary trajectory by phylogenetic analysis, with clear monocot-dicot lineage divergence and TaMAPK6 homoeolog clustering matching with hexaploid wheat’s allopolyploid origin. Spatiotemporal expression analysis showed that the TaMAPK6 homoeologs constitutively expressed in wheat tissues and were highly abundant in endosperm, spike, grain, and anther, with TaMAPK6-7A showing slightly higher transcript levels. In an ethyl methanesulfonate (EMS)-induced Jing411 mutant library, we identified a loss-of-function mutant of TaMAPK6-7A (J7633452), which exhibited severely reduced grain number per spike, impaired anther fertility, and increased grain size. Natural variation analysis of a large set of wheat accessions identified two major haplotypes of TaMAPK6-7A, with Type I was identical to the reference genome cultivar ‘Chinese Spring’, and Type II was consistent with the elite wheat cultivar ‘AK58’. We developed a PCR marker to accurately distinguish the two haplotypes and genotyped 192 wheat cultivars and elite breeding lines. Phenotypic evaluation indicated that Type II was an elite haplotype significantly associated with higher grain number per spike. This study characterizes TaMAPK6-7A as a key regulator of grain number per spike, providing a gene and molecular marker for marker-assisted breeding to improve grain yield. Full article

De-S-acylation enzymes mediate the reversible S-acylation cycle and play critical roles in plant development and stress responses. However, the precise origin and evolutionary dynamics of this gene family in plants remain poorly understood. In this study, a total of 718 ABAPT genes were identified across 73 plant genomes, including 622 ABHD17 and 96 ABHD13 homologs, which share only a 20–30% conserved sequence identity between them. We further performed comprehensive analyses of gene duplication and structure, protein properties, synteny networks, and expression profiles to establish a systematic framework by classifying ABAPT genes in land plants. Our results revealed that ABHD13 genes have been retained as a single copy in most angiosperm genomes, whereas ABHD17 genes have undergone extensive expansion. ABAPT genes formed three major evolutionary clades: Clade 1 contained ABHD13 homologs, while Clades 2 and 3 harbored ABHD17 homologs. The three clades showed distinct disparities in intron–exon structural patterns and IDR properties. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ABAPT subclades among the three clades, while Cluster4-Monocot was more dynamic and showed distinct lineage-specific duplication patterns restricted to Poaceae. ABHD13s exhibited constitutive expression patterns, while the tissue-specific expression genes were predominantly found within the ABHD17s subfamily. Notably, the ABAPT8/9 subgroups were specifically expressed in reproductive organs, and the weighted gene co-expression network identified specific groups to find ABAPT-specific regulatory features, implying the presence of potential modules for the protein S-acylation cycle during pollen development. Additionally, our results suggested that C-terminal Cys-rich region was required for ABAPT10 localization. Altogether, this study sheds light on the evolutionary divergence of the ABAPT subclades across major green plant lineages and emphasizes the need for future functional characterizations. Full article

Peptide deformylase (PDF) belongs to a conserved enzyme family critical for N-terminal methionine excision (NME), an essential protein maturation process in prokaryotes and eukaryotic organelles (chloroplasts, mitochondria). To explore the potential functions of OsPDFs in Oryza sativa, this study employed bioinformatics approaches and experimental validation to systematically identify and analyze the OsPDF gene family. Three OsPDF genes (OsPDF1A, OsPDF1B, OsPDF1B2) were identified in rice. These genes are exclusively distributed on chromosome 1. The biophysical properties of these proteins showed that OsPDF1A and OsPDF1B are alkaline proteins, while OsPDF1B2 is acidic, and all are hydrophilic with moderate thermostability potential. Synteny analysis revealed closer evolutionary relationships between Oryza sativa and the monocot Triticum aestivum than with dicots, reflecting conserved PDF function in gramineous plants. Analysis of cis-acting elements in the 2000 bp upstream region of OsPDF gene promoters revealed numerous elements associated with abiotic stress response and hormone regulation. Furthermore, quantitative real-time PCR (qRT-PCR) data supported these findings, indicating that OsPDF1A and OsPDF1B were upregulated under low-temperature stress, and all three OsPDF genes were transcriptionally activated by heat, salt and UV-B stresses, indicating their active involvement in rice growth, development, and abiotic stress tolerance. In summary, OsPDFs exhibit significant functions in rice’s stress adaptation, growth, and development. This study not only enhances our understanding of the OsPDF gene family’s genomic, evolutionary, and functional characteristics, but also provides new perspectives and foundational data for further exploring their regulatory mechanisms in protein maturation and abiotic stress responses, as well as their potential applications in rice stress tolerance breeding. Full article

The development of planar structures such as wings or leaves is a common feature among organisms and serves as a mechanism to increase surface to volume ratios. We wished to explore whether the recurrent and independent development of similar adaptive planar morphologies is the result of an activation of common genetic modules or toolkits. To test this, we focused on the developmental gene networks that are proposed to define leaf polarity in eudicots in phylloclades, leaf-like organs derived from branch primordia, in the monocot Ruscus aculeatus. Since branch primordia normally have a radial shape, this approach allowed us to examine the genetic changes required for the transformation from a round to a planar (flat) form. In our transcriptome analysis of phylloclade and stem tissue, we detected 76,085 annotated ORFs of which 87.2% were identified as complete out of 2026 BUSCO groups. Expression patterns clearly identify differentiation between phylloclade and stem tissues consistent with an enhanced photosynthetic function in the phylloclades. However, except for the AS1/AS2 and possibly STM module, we see little evidence that canonical leaf adaxial and abaxial modules are activated in the sampled phylloclades compared with the stems. Our results show that the unifacial nature of phylloclades is consistent with the observed lack of strong adaxial/abaxial molecular signatures. We propose that in R. aculeatus and plants with similar unifacial laminar leaves, adaxial/abaxial molecular identity may not be required for planar growth, and that lateral expansion of organ primordia and acropetal and intercalary cell division may be sufficient to generate planar versus radial organ shapes. Full article

AGL6 genes are critical floral regulators in diverse angiosperms, yet their roles in legumes remain poorly understood. This study aimed to characterize GmAGL6 genes in soybean (Glycine max [L.] Merr. cv. Williams 82). We identified four homologs (GmAGL6a–d) featuring conserved MADS-box and K-box domains that cluster within the AGL6 lineage. Tissue-specific expression profiling revealed significant transcript enrichment during flower bud differentiation and maturation. Using CRISPR/Cas9, we generated quadruple knockout lines to evaluate gene function. Phenotypic analysis showed that, unlike the homeotic transformations typical of AGL6 loss in monocots, Gmagl6 quadruple mutants retained a standard papilionaceous floral structure without keel petal aberrations. However, the mutants did not show significant changes in floral height or width, but exhibited a significantly increased floral height-to-width ratio and smaller mature seeds, while vegetative architecture and podding capacity remained unaffected. These results suggest that GmAGL6 genes in soybean may function primarily in the regulation of floral proportion and seed development rather than floral organ identity. This research provides insights into the evolution of specialized legume flowers and suggests candidate genes for seed size improvement. Full article

ZmSIG2A is a nuclear-encoded plastid sigma factor 2A in maize (Zea mays L.) that is essential for plastid gene transcription and chloroplast biogenesis. As a key regulator of chloroplast development and function, ZmSIG2A may also contribute to the coordination of plant growth and environmental adaptation; however, its roles in root development and stress responses remain largely unclear. We compared two ZmSIG2A mutants, eal1-1 (hypomorphic) and ems110 (nonsense). eal1-1 had increased root number and longer roots, while ems110 had normal root number but shorter roots and failed to mature. The zmsig2a^Val480del transcript was upregulated in eal1-1, and the root-promoting effect of OsSIG2A in rice suggests a conserved role in monocot root growth. DAP-seq indicated that zmsig2a^Val480del targets are involved in metabolism, transport, signaling, and antioxidants, with Chr4 peak clustering near multiple LRR-RLKs, suggesting a ZmSIG2A–LRR-RLK module in root development and stress integration. Physiologically, eal1-1 showed increased antioxidant enzyme activities and reduced MDA, indicating enhanced ROS scavenging, while ems110 exhibited decreased enzyme activities and elevated MDA, indicating compromised ROS detoxification. Upstream, Y1H and dual-luciferase assays demonstrated that the Mediator subunit ZmMed31 positively regulates transcription from the ZmSIG2A promoter. Given Mediator’s role in bridging transcription factors and the core transcriptional machinery, ZmMed31 likely links hormone-responsive transcription factors to the ZmSIG2A regulatory network. Collectively, we propose a stress-responsive ZmMed31–ZmSIG2A–LRR-RLK module that underpins maize root development and drought adaptation, offering mechanistic insight and potential targets for stress-resilient breeding. Full article

Background/Objectives: NAC transcription factors are key regulators of stress responses, yet their roles in Narcissus tazetta L. var. chinensis remain uncharacterized. This study aimed to isolate and functionally analyze NtNACa, a NAC gene from the ‘Yunxiang’ narcissus variety, to evaluate its potential in enhancing abiotic stress tolerance. Methods: NtNACa was cloned and its expression pattern under heat, salt, and ABA treatments was assessed via qRT-PCR. Subcellular localization was determined using GFP fusion in tobacco. NtNACa was overexpressed in Arabidopsis thaliana through floral dip transformation, and transgenic lines were subjected to NaCl, ABA, and drought stress assays. Results: The results showed that NtNACa has high homology with monocot NAC family members and possesses typical NAC transcription factor features. Further analyses revealed that NtNACa localizes to the nucleus, and tissue-specific expression analysis indicated that it is highly expressed in leaves, followed by roots and bulbs. The transcriptional expression of NtNACa is differentially regulated in response to 100 mM NaCl, 100 μM ABA, and 50 °C temperature stress. Overexpression of NtNACa in A. thaliana produced transgenic lines with significantly higher germination rates under ABA and NaCl treatments. Soil-grown transgenic A. thaliana plants overexpressing NtNACa showed markedly increased drought stress. Moreover, NtNACa confers drought resilience by coordinately suppressing oxidative damage (via reduced O₂⁻· production rate and MDA accumulation and elevated AtCAT2 expression), enhancing osmotic adjustment (through AtP5CR-mediated proline biosynthesis), and activating core stress-signaling components such as AtRD29A and AtSnRK2.4. Conclusions: Taken together, these results indicate that heterologous overexpression of NtNACa from ‘Yunxiang’ (N. tazetta) confers enhanced drought and salt tolerance in A. thaliana. Full article

Sucrose phosphate synthase (SPS) is a key rate-limiting enzyme that regulates carbon partitioning and stress tolerance in plants. In this study, we systematically characterized the SPS gene family in maize (Zea mays L.) and identified key members and their interaction networks involved in drought responses. A total of seven ZmSPS genes were identified through genome-wide bioinformatics analyses. Motif composition, gene structure, phylogenetic relationships, and synteny analyses indicated that the ZmSPS gene family is highly conserved among monocot species. Promoter analysis revealed that the upstream regions of ZmSPS genes are enriched with multiple stress responsive cis-acting elements. Drought stress treatments combined with quantitative real-time PCR (RT-qPCR) analyses showed that the expression of ZmSPS3 was significantly upregulated with increasing stress duration. Furthermore, yeast two-hybrid assays demonstrated that ZmSPS3 physically interacts with protein kinases and F-box proteins. These interactions suggest a potential involvement of ZmSPS3 in post-translational modification and protein stability regulation during osmotic stress. As a potential candidate gene responsive to drought, ZmSPS3 provides a preliminary basis for understanding the complex drought-response networks in maize. Full article

Disparities in root fungal endophyte (RFE) communities are well documented among plant species, yet differences among plant functional groups (PFGs) remain unclear. Given that RFE community structure is influenced by host plant abundance and species-specific root functional traits, and that PFGs exhibit divergent relative abundances and root traits, we hypothesize that PFGs harbor unique RFE communities, potentially aligned with their functional traits. We investigated RFE communities in 45 alpine meadow species representing four PFGs (grasses, legumes, dicot forbs, and monocot forbs), using high-throughput sequencing. Ascomycota dominated all groups (>50%) except monocot forbs (38.9%). Distinct differences in the RFE community species composition were found among PFGs. In particular, the differences were significant between dicot forbs and monocot forbs, and between monocot forbs and grasses, which contradicted with conventional PFG classification that combined monocot and dicot forbs as a single PFG. Moreover, marker operational taxonomic units (OTUs) with symbiotic lifestyles were more abundant in legumes, and their functional composition differed significantly from grasses. Roots’ nitrogen concentration was the strongest predictor of RFE variation, followed by root length, biomass, and species abundance. These results emphasize the importance of integrating microbial partners into understanding plants’ functional diversity and ecosystem resilience in alpine environments. Full article

Current industrial sources of tocotrienols are almost entirely composed of tropical monocots. However, recent reports have observed significant tocotrienol (T3) contents in eudicot families, including Passifloraceae. While passion fruits are also tropical, their cultivation is not strictly limited to rainforests, and seeds are often a by-product of fruit processing. To elucidate tocochromanol production in the Passifloraceae family, seeds (54 samples representing 18 species) were gathered from botanical gardens worldwide. Ultrasound-assisted extraction in ethanol (UAEE) was compared with the standard saponification protocol as a greener alternative. Tocotrienols constituted a major percentage (48–91%) of Passifloraceae species’ seed tocochromanols, and γ-T3 (12–53%) and δ-T3 (8–68%) were major contributors. Although a higher δ-T3 content was observed in some Passiflora species, it was less consistent than the γ-T3 content between and within species. The highest total tocochromanol content was observed in P. subpeltata (28.98 ± 5.83 mg 100 g⁻¹ dry weight). The UAEE protocol recovered tocotrienols and tocopherols at degrees similar to those of saponification (100% and 93%, respectively). Therefore, UAEE could also be proposed for the effective recovery of these valuable phytochemicals from by-products of Passiflora fruits. Full article

Background: Plant mitochondrial genomes exhibit extreme variation in size and structure while maintaining a conserved set of core protein-coding genes. This combination of structural diversity and functional conservation provides valuable insights into evolutionary processes such as genome expansion, rearrangement, and intracellular DNA transfer. Curcuma longa, an economically and medicinally important species in the genus Curcuma (Zingiberaceae), has not yet been studied in terms of the organization and evolution of its mitochondrial genome. Methods: In this study, we assembled and annotated the mitochondrial and plastid genomes of C. longa using third-generation HiFi sequencing data, systematically analyzing their genomic structure, repetitive sequence content, and features of sequence transfer between nuclear and organellar genomes. Results: The mitochondrial genome of C. longa was assembled as a complex, network-like structure consisting of 12 contigs with a total length of approximately 7.7 Mb, making it one of the largest mitochondrial genomes reported in monocots to date. Comparative analysis revealed significant differences in repeat types, abundance, and length distribution between the two organellar genomes. Additionally, extensive intracellular DNA transfer events were identified among the nuclear, mitochondrial, and plastid genomes. Conclusions: Overall, this study provides the first comprehensive report on the giant mitochondrial genome of C. longa, detailing its structural organization, repeat content, and intergenomic transfers. These findings lay a foundation for understanding mitochondrial genome evolution in Curcuma and offer broader insights into the mechanisms driving extreme mitochondrial genome expansion in angiosperms and monocots specifically. Full article

Glycogen synthase kinase 3 (GSK3/Shaggy-like) is a highly conserved serine/threonine kinase that orchestrates growth, hormone signaling, and abiotic stress responses in both animals and plants, yet its role in watermelon remains unexplored. In this study, we conducted a whole-genome identification, identifying a total of eight members of the GSK3 gene family (ClGSK3) distributed across seven chromosomes. Phylogenetic and synteny analyses resolved the eight ClGSK3s into four subfamilies that display one-to-one or one-to-many orthology with Arabidopsis and rice GSK3 genes, indicating conserved genomic micro-collinearity across dicots and monocots. Predictions of cis-acting elements and transcriptome data analysis indicate that ClGSK3s may be involved in hormone- and stress-responsive conditions. Protein–protein interaction networks predicted 53 candidate partners for five ClGSK3 proteins; yeast two-hybrid assays subsequently confirmed that ClSK21 associates with three of them—orthologs of the core brassinosteroid (BR)-signaling components BKI1 and BZR1. qRT-PCR revealed that ClSK21, ClSK31, and ClSK41 are rapidly and significantly reprogrammed by BR treatment. Collectively, our data suggest that ClGSK3s modulate fruit development and stress tolerance by integrating hormone-related pathways, especially BR signaling. Future studies are encouraged to integrate genetics and multi-omics approaches to systematically validate the roles of ClGSK3s in hormone signaling and abiotic stress responses. Full article

The organisation of hemicelluloses within the pollen intine of many monocots remains inadequately characterised, partly due to the masking of epitopes within complex wall matrices. In this study, mature pollen grains of Gagea lutea (L.) Ker-Gawl. were analysed using immunofluorescence and immunogold technique with a variety of monoclonal antibodies that target xyloglucan (LM15, LM24, LM25, CCRC-M48), heteroxylan (LM10, LM11), heteromannan (LM21, LM22), and xylan (CCRC-M138). Semithin sections of LR White were examined both untreated and following a sequential enzymatic pretreatment, which included alkaline de-esterification followed by treatment with pectate lyase (RbPel1A) and endo-β-mannanase 5A. In untreated pollen, xyloglucan-related epitopes were identified within the intine, accompanied by additional intracellular labelling for LM15, and LM25; while for LM24 signal was only to the intine ring. Conversely, CCRC-M48 exhibited a more punctate distribution. Neither xylan- nor mannan-related epitopes were detected in the wall or intracellularly. The enzymatic digestion significantly altered the detectability of epitopes, resulting in an increase in continuous wall labelling within the intine across multiple probes. These findings indicate that enzymatic modification of pectic and mannan components has a considerable impact on the apparent distribution of hemicellulose epitopes within the pollen wall of G. lutea. Together, these results expand the still limited in situ immunolocalisation evidence base for hemicellulose-related epitopes in pollen, and provide a practical framework for interpreting digestion-dependent changes primarily in terms of epitope accessibility within the intine matrix. Full article

Efficient in vitro regeneration remains a major constraint in the genetic transformation, genome editing, and molecular breeding of wheat (Triticum aestivum L.), largely due to strong genotype-dependent recalcitrance and limited activation of developmental programs required for somatic embryogenesis. Plant regeneration relies on extensive transcriptional reprogramming and epigenetic remodeling orchestrated by morphogenic regulators that modulate meristem identity, as well as cellular pluri- and totipotency. In this review, we synthesize current molecular knowledge on key transcription factors (BBM, WUS/WUS2, GRF-GIF, WOX, LAX1, SERK, WIND1/ERF115) and signaling peptides (CLE/CLV-WUS module, phytosulfokine/PSK) that regulate embryogenic competence in monocot cereals, with emphasis on their orthologs and functional relevance in wheat. We highlight how controlled expression of these morphogenic genes, promoter engineering, and transient or excisable induction systems can significantly enhance regeneration capacity, reduce chimerism in CRISPR-Cas-edited plants, and facilitate genotype-independent transformation. We also discuss epigenetic and metabolic constraints underlying wheat recalcitrance and their potential modulation to improve culture responsiveness. By integrating evidence from wheat, rice, maize, and barley, we outline conserved gene-regulatory networks that reinitiate totipotency and propose strategies to accelerate doubled haploid production and speed-breeding pipelines. Collectively, morphogenic factors emerge as central molecular tools for overcoming regeneration bottlenecks and enabling next-generation wheat improvement. The objective of this review is to synthesize and critically evaluate current molecular knowledge on morphogenic regulators controlling in vitro regeneration in wheat (Triticum aestivum L.), with particular emphasis on their roles in genetic transformation and genome editing. Full article