Transcription Factor B1 Research Articles

GDSL in Lilium pumilum (LpGDSL) Confers Saline-Alkali Resistance to the Plant by Enhancing the Lignin Content and Balancing the ROS.

In order to explore the response mechanism of Lilium pumilum (L. pumilum) to saline-alkali stress, we successfully cloned LpGDSL (GDSL lipase, Gly-Asp-Ser-Leu) from L. pumilum. The qRT-PCR results indicated that the LpGDSL expression was higher in the leaves of L. pumilum, and the expression of the LpGDSL reached the highest level at 12 h in leaves under 11 mM H2O2, 200 mM NaCl, 25 mM Na2CO3, and 20 mM NaHCO3. The bacteriophage overexpressing LpGDSL was more tolerant than the control under different NaHCO3 contents. Overexpressed and wild-type plants were analyzed for phenotype, chlorophyll content, O2- content, H2O2 content, lignin content, and so on. Overexpressed plants had significantly higher resistance than the wild type and were less susceptible to saline-alkali stress. The yeast two-hybrid and BiFC assays demonstrated the existence of an interaction between LpGDSL and LpBCP. The yeast one-hybrid assay and transcriptional activation assay confirmed that B3 transcription factors could act on LpGDSL promoters. Under saline-alkali stress, L. pumilum will promote the expression of LpGDSL, which will then promotes the accumulation of lignin and the scavenging of reactive oxygen species (ROS) to reduce its damage, thus improving the saline-alkali resistance of the plant.

HH5 double-carrier embryos fail to progress through early conceptus elongation

Massive genotyping in cattle has uncovered several deleterious haplotypes that cause preterm mortality. Holstein haplotype 5 (HH5) is a deleterious haplotype present in the Holstein Friesian population that involves the ablation of the transcription factor B1 mitochondrial (TFB1M) gene. The developmental stage at which HH5 double-carrier (DC, homozygous) embryos or fetuses die remains unknown and this is a relevant information to estimate the economic losses associated with the inadvertent cross between carriers. To determine whether HH5 DC survive to maternal recognition of pregnancy, embryonic day (E) 14 embryos were flushed from superovulated carrier cows inseminated with a carrier bull. Double-carrier E14 conceptuses were recovered at Mendelian rates but they failed to achieve early elongation, as evidenced by a drastic reduction of their extra-embryonic membranes, which were >26-fold shorter than those of carrier or noncarrier embryos. To assess development at earlier stages, TFB1M knockout (KO) embryos-functionally equivalent to DC embryos-were generated by clustered regularly interspaced short palindromic repeats (CRISPR) technology and cultured to the blastocyst stage, in vitro culture day (D) 8, and to the early embryonic disc stage, D12. No significant effect of TFB1M ablation was observed on the differentiation and proliferation of embryonic lineages and relative mitochondrial DNA (mtDNA) content up to D12. In conclusion, HH5 DC embryos are able to develop to early embryonic disc stage but fail to undergo early conceptus elongation, which is required for pregnancy recognition.

Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening

In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.

Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values.

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

Comprehensive analysis of B3 family genes in pearl millet (Pennisetum glaucum) and the negative regulator role of PgRAV-04 in drought tolerance.

Members of the plant-specific B3 transcription factor superfamily play crucial roles in various plant growth and developmental processes. Despite numerous valuable studies on B3 genes in other species, little is known about the B3 superfamily in pearl millet. Here, through comparative genomic analysis, we identified 70 B3 proteins in pearl millet and categorized them into four subfamilies based on phylogenetic affiliations: ARF, RAV, LAV, and REM. We also mapped the chromosomal locations of these proteins and analyzed their gene structures, conserved motifs, and gene duplication events, providing new insights into their potential functional interactions. Using transcriptomic sequencing and real-time quantitative PCR, we determined that most PgB3 genes exhibit upregulated expression under drought and high-temperature stresses, indicating their involvement in stress response regulation. To delve deeper into the abiotic stress roles of the B3 family, we focused on a specific gene within the RAV subfamily, PgRAV-04, cloning it and overexpressing it in tobacco. PgRAV-04 overexpression led to increased drought sensitivity in the transgenic plants due to decreased proline levels and peroxidase activity. This study not only adds to the existing body of knowledge on the B3 family's characteristics but also advances our functional understanding of the PgB3 genes in pearl millet, reinforcing the significance of these factors in stress adaptation mechanisms.

SmRAV1, an AP2 and B3 Transcription Factor, Positively Regulates Eggplant's Response to Salt Stress.

Salt stress is a lethal abiotic stress threatening global food security on a consistent basis. In this study, we identified an AP2 and B3 domain-containing transcription factor (TF) named SmRAV1, and its expression levels were significantly up-regulated by NaCl, abscisic acid (ABA), and hydrogen peroxide (H2O2) treatment. High expression of SmRAV1 was observed in the roots and sepal of mature plants. The transient expression assay in Nicotiana benthamiana leaves revealed that SmRAV1 was localized in the nucleus. Silencing of SmRAV1 via virus-induced gene silencing (VIGS) decreased the tolerance of eggplant to salt stress. Significant down-regulation of salt stress marker genes, including SmGSTU10 and SmNCED1, was observed. Additionally, increased H2O2 content and decreased catalase (CAT) enzyme activity were recorded in the SmRAV1-silenced plants compared to the TRV:00 plants. Our findings elucidate the functions of SmRAV1 and provide opportunities for generating salt-tolerant lines of eggplant.

Exploration of the B3 transcription factor superfamily in Aquilaria sinensis reveal their involvement in seed recalcitrance and agarwood formation.

The endangered tree species of the Aquilaria genus produce agarwood, a high value material produced only after wounding; however, conservation of Aquilaria seeds is difficult. The B3 transcription factor family has diverse important functions in plant development, especially in seed development, although their functions in other areas, such as stress responses, remain to be revealed. Here germination tests proved that the seeds of A. sinensis were recalcitrant seeds. To provide insights into the B3 superfamily, the members were identified and characterized by bioinformatic approaches and classified by phylogenetic analysis and domain structure. In total, 71 members were identified and classified into four subfamilies. Each subfamily not only had similar domains, but also had conserved motifs in their B3 domains. For the seed-related LAV subfamily, the B3 domain of AsLAV3 was identical to that of AsVALs but lacked a typical zf-CW domain such as VALs. AsLAV5 lacks a typical PHD-L domain present in Arabidopsis VALs. qRT-PCR expression analysis showed that the LEC2 ortholog AsLAV4 was not expressed in seeds. RAVs and REMs induced after wound treatment were also identified. These findings provide insights into the functions of B3 genes and seed recalcitrance of A. sinensis and indicate the role of B3 genes in wound response and agarwood formation.This is the first work to investigate the B3 family in A. sinensis and to provide insights of the molecular mechanism of seed recalcitrance.This will be a valuable guidance for studies of B3 genes in stress responses, secondary metabolite biosynthesis, and seed development.

Comparative transcriptome analysis of two varieties of common bean (Phaseolus vulgaris L.) to identify candidate drought resistance genes

In this work, we studied the physiological, biochemical and molecular mechanisms underlying the response to polyethylene glycol (PEG) in a drought-resistant variety ‘HZYTJ’ and the sensitive variety ‘WZWJD’ of common beans. The two bean varieties were subjected to a 10% PEG simulated drought stress treatment, and the resultant physiological and biochemical characteristics of the leaves and roots were compared. The superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and other indicators were higher in ‘HZYTJ’ than in ‘WZWJD’; additionally, the ‘HZYTJ’ exhibited slower changes in response to stress. The proline content in ‘HZYTJ’ changed slowly compared to that in ‘WZWJD’. The transcriptome analysis of the two varieties showed that 1,361 and 1,447 genes were differentially expressed in ‘HZYTJ’ and ‘WZWJD’, respectively. DEGs were also analyzed via the KEGG pathway database, and 10 significant metabolic pathways were found to be involved in ‘HZYTJ’, while nine were found in ‘WZWJD’. Using the GO function database, we found that 111 significant GO terms were involved in ‘HZYTJ’, whereas 125 were involved in ‘WZWJD’. Through analysis of transcription factors, 487 DEGs were identified, of which bHLH transcription factors were the most abundant, followed by ERF, MYB-related, B3 and other transcription factor families. The selected and screened genes with DEGs were validated by qRT–PCR. These results provide a basis for further research into the drought resistance of the common bean.

Dietary tryptophan supplementation enhances mitochondrial function and reduces pyroptosis in the spleen and thymus of piglets after lipopolysaccharide challenge.

The thymus and spleen, the main reservoirs for T lymphocytes, modulate the innate immune response. Oxidative stress, excessive inflammation and abnormal pyroptosis can cause dysfunction of these organs. This study aimed to examine whether tryptophan supplementation can improve growth performance and mitochondrial function via the adenosine 5'-monophosphate-activated protein kinase (AMPK)/sirtuin1 (Sirt1)/peroxisome proliferator-activated receptor-γ coactivator-1α (PGC1α) signalling pathway and decrease pyroptosis via the nucleotidebinding oligomerisation domain-like receptor protein 3 (NLRP3)/caspase-1/gasderminD (GSDMD) signalling pathway in the spleen and thymus of piglets after lipopolysaccharide (LPS) challenge. Eighteen weaned piglets were allotted to three treatment groups: non-challenged control, LPS-challenged control and LPS+0.2% tryptophan. On day 35, the pigs in the LPS and LPS+0.2% tryptophan groups were injected with 100μg/kg BW LPS, whereas those in the control group were administered with sterile saline. At 4h postchallenge, the weaned piglets were sacrificed, and their thymuses and spleens were collected. Results showed that tryptophan enhanced growth performance and antioxidant status by increasing catalase, glutathione peroxidase and total superoxide dismutase activities and decreasing malondialdehyde and reactive oxygen species contents. Tryptophan also reduced the mRNA levels of proinflammatory cytokine genes and enhanced mitochondrial function by increasing the mRNA levels of mitochondrial transcription factor A, nuclear respiratory factor-1, mitochondria transcription factor B1, AMPKα1, AMPKα2, Sirt1 and PGC1α and the protein expression of phosphorylated AMPK, Sirt1 and PGC1α. It also reduced pyroptosis by decreasing the mRNA levels of NLRP3, apoptosis-associated speck-like protein containing CARD, caspase-1 and GSDMD and the protein expression of NLRP3, caspase-1 and GSDMD. These results indicate that tryptophan supplementation enhances growth performance and mitochondrial function via the AMPK/Sirt1/PGC1α signalling pathway and decreases pyroptosis via the NLRP3/caspase-1/GSDMD signalling pathway in the spleen and thymus of LPS-challenged piglets.

Dmrtb1 is involved in the testicular development in Larimichthys crocea.

dmrtb1 performs critical functions in sex determination/differentiation and gonadal development in many organisms, but its role in teleost is rarely studied. Through gene cloning, in situ hybridization, and RNA interference technology, the function of dmrtb1 in testicular development of large yellow croaker (Larimichthys crocea) was studied; our study will be helpful in understanding further the molecular regulation mechanism of Lcdmrtb1/Lcdmrt6 in testicular development in L. crocea, and our results enrich the theory of fish dmrts involved in reproductive regulation and provide a new idea for sex control breeding of L. crocea by manipulating reproductive pathway. Doublesex- and mab-3-related transcription factor B1 (dmrtb1/dmrt6) belongs to one of the members of DMRT family, which performs critical functions in sex determination and differentiation, gonadal development, and functional maintenance. However, knowledge of its exact mechanism remains unclear in teleost. Very little is known about the role of dmrtb1 in the gonad development of Larimichthys crocea. In this study, a dmrtb1 homolog in L. crocea named as Lcdmrtb1 with the full-length cDNA was isolated and characterized. Except for the conserved DM domain, the other regions had low homology. Of the tissues sampled, Lcdmrtb1 was only found to be highly expressed in the testis. In situ hybridization of testis revealed Lcdmrtb1 in both spermatogonia and spermatocytes. After Lcdmrtb1 interference in the testis cells (LYCT) of L. crocea, the expression levels of Lcdmrtb1 and Lcdmrt1 were significantly decreased; subsequently, testicular cell morphology changed from fibrous to round and their growth rate slowed. Similarly, the expression levels of Lcdmrtb1, Lcdmrt1, sox9a/b, and amh were significantly decreased after RNAi in the testis. Furthermore, it was discovered that the spermatogonia had disappeared, and the Sertoli cells had been reduced. The results of immunohistochemistry showed that the expression of Sox9 protein in the testis was not detected after dmrtb1 was knocked down. These results indicated that the absence of Lcdmrtb1 not only greatly inhibited cell growth and destroyed the morphology of testis cells but also down-regulated Lcdmrt1 expression in the testis. This study will be helpful in understanding further the molecular regulation mechanism of Lcdmrtb1/Lcdmrt6 in testicular development in L. crocea.

Creation of intermuscular bone-free mutants in amphitriploid gibel carp by editing two duplicated runx2b homeologs

Intermuscular bones (IBs) are ubiquitous in most of freshwater farmed fishes, especially in cyprinid species, and the creation of IB-free mutants has become a hot issue in fish genetic breeding because of the potential beneficial for consumers and fish processing industry. Recently, significant progress in the mechanism underlying IB development has been achieved in zebrafish and a decisive player, runt-related transcription factor 2b (runx2b), has been identified. However, its role has not yet been validated in other farmed fishes. Amphitriploid gibel carp (Carassius gibelio) is an important aquaculture species in China, but the injuries threats with approximately 80 IBs have strongly restricted its industry development. In this study, we first identified two homeologs of runx2b (Cgrunx2b-A and Cgrunx2b-B) in gibel carp with about 91.8% identity, each of them possessing three alleles with 99.6% identities. Then, we traced the IB ossification process. Alizarin red S staining showed that gibel carp IB began to ossify at 14 approximately days post hatching (dph) and developed from the posterior to the anterior regions. Cgrunx2b-A and Cgrunx2b-B displayed similar expression pattern but differential expression level during IB development. Moreover, we applied an optimized protocol of CRISPR/Cas9 editing in the polyploid Carassius complex to disrupt the functions of CgRunx2b-A and CgRunx2b-B singly or simultaneously. IB development was unaffected by single deficiency of CgRunx2b-A or CgRunx2b-B, but simultaneous disruption of all alleles of both CgRunx2b-A and CgRunx2b-B leads to complete loss of IB. The results indicate that CgRunx2b-A and CgRunx2b-B cooperatively regulate IB development. Importantly, we created several gynogenetic gibel carp mutants, including IB-free Cgrunx2b-A−/−/−;Cgrunx2b-B−/−/− mutants and IB-less Cgrunx2b-A−/−/−;Cgrunx2b-B−/−/+ mutants. The current study not only confirms the cooperatively decisive role of two homeologs of runx2b in IB formation, but also provides a feasible gene editing-based approach to create IB-free mutants in gibel carp.

Reciprocal inhibition of expression between RAV1 and BES1 modulates plant growth and development in Arabidopsis.

RAV1 (Related to ABI3/VP1) is a plant-specific B3 and AP2 domain-containing transcription factor that acts as a negative regulator of growth in many plant species. The expression of RAV1 is downregulated by brassinosteroids (BRs); large-scale transcriptome analyses have shown that the expression of RAV1 was previously targeted by BRI1-EMS-SUPPRESOR1 (BES1) and BRASSINAZOLE-RESISTANT1 (BZR1), which are critical transcription factors for the BR-signaling process. Using RAV1-overexpressing transgenic plants, we showed that RAV1 overexpression reduced the BR signaling capacity, resulting in the downregulation of BR biosynthetic genes and BES1 expression. Furthermore, we demonstrated that BES1, not BZR1, is directly bound to the RAV1 promoter and repressed RAV1 expression, and vice versa; RAV1 is also bound to the BES1 promoter and repressed BES1 expression. This mutual inhibition was specific to RAV1 and BES1 because RAV1 exhibited binding activity to the BZR1 promoter but did not repress BZR1 expression. We observed that constitutively activated BR signaling phenotypes in bes1-D were attenuated by the repression of endogenous BES1 expression in transgenic bes1-D plants overexpressing RAV1. RNA-sequencing analysis of RAV1-overexpressing transgenic plants and bes1-D mutant plants revealed differentially expressed genes by RAV1 and BES1 and genes that were oppositely co-regulated by RAV1 and BES1. RAV1 and BES1 regulated different transcriptomes but co-regulated a specific set of genes responsible for the balance between growth and defense. These results suggested that the mutual inhibitory transcriptional activities of RAV1 and BES1 provide fine regulatory mechanisms for plant growth and development.

Genome-Wide Analysis of the Molecular Functions of B3 Superfamily in Oil Biosynthesis in Olive (Olea europaea L.).

The plant B3 gene superfamily contains a large number of transcription factors playing a vital role in both vegetative growth and reproductive development in plants. Although several B3 genes have been well studied, molecular functions of the B3 genes in olive are largely unknown. In our study, a total of 200 B3 genes were identified in olive genome based on RNA-seq and comparative genomic analyses and further classified into five groups (i.e., REM, RAV, LAV, HSI, and ARF) based on phylogenetic analysis. Results of gene structure and motif composition analyses revealed diversified functions among these five groups of B3 genes. Results of genomic duplication and syntenic analyses indicated the gene expansion in the B3 genes. Results of gene expression based on both transcriptomics and relative expression revealed the tissue-biased expression patterns in B3 genes. The results of the comparative expression analysis of B3 genes between two olive cultivars with high and low oil contents identified several potential REM genes which may be involved in oil biosynthesis in olive. Based on the comprehensive characterization of the molecular structures and functions of B3 genes in olive genome, our study provided novel insights into the potential roles of B3 transcription factors in oil biosynthesis in olive and lays the groundwork for the functional explorations into this research field.

In Silico Genome-Wide Analysis of B3 Transcription Factors in Cannabis sativa L.

Introduction: The B3 transcription factor has been identified in Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum, among other species. This family of transcription factors regulates seed growth, development, and stress. Cannabis is a valuable crop with numerous applications; however, no B3 transcription factors have been identified in this plant. Materials and Methods: The cannabis B3 gene family was identified and analyzed using bioinformatics analysis tools, such as the NCBI database, plantTFDB website, TBtools, and MEGA software. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were used to confirm its function. Results: The cannabis B3 family contains 65 members spread across 10 chromosomes. The isoelectric point ranged from 10.03 to 4.65, and the molecular weight ranged from 99,542.88 to 14,310.9 Da. Most of the members were found in the nucleus. The upstream promoter region of the gene contains a variety of cis-acting elements related to the stress response. RNA-seq data and qRT-PCR results showed that CsB3 genes were expressed differently in five organs of female Diku plants and in glandular hairs of nine distinct types of female cannabis inflorescences. Collinearity analysis revealed that there were more homologous genes between cannabis and dicotyledons than monocotyledonous plants, which was consistent with the evolutionary relationship. Conclusions: Hormones and external environmental factors might influence CsB3 expression. Furthermore, some genes such as CsB3-02, CsB3-07, CsB3-50, CsB3-62, and CsB3-65 may participate in cannabis growth and development and play a role in secondary metabolite synthesis. This study provides a solid foundation for further research into the gene function of the cannabis B3 family.

Epigenetic stress memory: A new approach to study cold and heat stress responses in plants.

Understanding plant stress memory under extreme temperatures such as cold and heat could contribute to plant development. Plants employ different types of stress memories, such as somatic, intergenerational and transgenerational, regulated by epigenetic changes such as DNA and histone modifications and microRNAs (miRNA), playing a key role in gene regulation from early development to maturity. In most cases, cold and heat stresses result in short-term epigenetic modifications that can return to baseline modification levels after stress cessation. Nevertheless, some of the modifications may be stable and passed on as stress memory, potentially allowing them to be inherited across generations, whereas some of the modifications are reactivated during sexual reproduction or embryogenesis. Several stress-related genes are involved in stress memory inheritance by turning on and off transcription profiles and epigenetic changes. Vernalization is the best example of somatic stress memory. Changes in the chromatin structure of the Flowering Locus C (FLC) gene, a MADS-box transcription factor (TF), maintain cold stress memory during mitosis. FLC expression suppresses flowering at high levels during winter; and during vernalization, B3 TFs, cold memory cis-acting element and polycomb repressive complex 1 and 2 (PRC1 and 2) silence FLC activation. In contrast, the repression of SQUAMOSA promoter-binding protein-like (SPL) TF and the activation of Heat Shock TF (HSFA2) are required for heat stress memory. However, it is still unclear how stress memory is inherited by offspring, and the integrated view of the regulatory mechanisms of stress memory and mitotic and meiotic heritable changes in plants is still scarce. Thus, in this review, we focus on the epigenetic regulation of stress memory and discuss the application of new technologies in developing epigenetic modifications to improve stress memory.

Mining for genes related to pistil abortion in Prunus sibirica L.

In Prunus sibirica, the phenomenon of pistil abortion is very common and seriously affects its fruit quality and yield; however, the molecular mechanisms of pistil abortion remains unclear. In this study, we identified differentially expressed genes (DEGs) and pathways associated with pistil abortion using transcriptome sequencing. After comparative analysis, a total of 1,950 DEGs were identified, of which 1,000 were upregulated, and 950 were downregulated. Gene Ontology (GO) functional enrichment analysis of DEGs showed that metabolic process, cellular process, single-organism process, membrane, membrane part, cell, binding, catalytic activity, and transporter activity contained the largest number of DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the plant-pathogen interaction, starch and sucrose metabolism, and plant hormone signal transduction pathways contained the largest number of DEGs. The NAC, bHLH, and B3 transcription factor families contained the largest number of DEGs. qRT-PCR detection confirmed that the gene expression levels were consistent with the transcriptome sequencing results. This study provides a theoretical basis and scientific basis for further research on the molecular mechanisms of P. sibirica pistil abortion.

Identification of Brachypodium distachyon B3 genes reveals that BdB3-54 regulates primary root growth.

B3 is a class of plant-specific transcription factors with important roles in plant development and growth. Here, we identified 69 B3 transcription factors in Brachypodium distachyon that were unevenly distributed across all five chromosomes. The ARF, REM, LAV, and RAV subfamilies were grouped based on sequence characteristics and phylogenetic relationships. The phylogenetically related members in the B3 family shared conserved domains and gene structures. Expression profiles showed that B3 genes were widely expressed in different tissues and varied in response to different abiotic stresses. BdB3-54 protein from the REM subfamily was located in the nucleus by subcellular localization and processed transcriptional activation activity. Overexpression of BdB3-54 in Arabidopsis increased primary root length. Our study provides a basis for further research on the functions of BdB3 genes.

Functional Analysis of ScABI3 from Syntrichia caninervis Mitt. in Medicago sativa L.

ABI3 (ABSCISIC ACID INSENSITIVE 3) is a family of B3 transcription factors essential for regulating the abscisic acid (ABA) signaling pathway involved in various biological processes and abiotic stress. Our previous studies demonstrated that ectopic expression of ScABI3 from a desiccation-tolerant moss (Syntrichia caninervis) into Arabidopsis thaliana enhanced abiotic stress tolerance. However, studies on plant transformation using the ABI3 gene are limited and other possible functions of ScABI3 are not known. Here, we transformed the ScABI3 into alfalfa (Medicago sativa L.) and analyzed the effects on phenotype, photosynthetic efficiency, and nutritional quality. The results showed that the endogenous ABA content of the transgenic plants was significantly higher than WT, and the leaf-stem ratio, leaf area, and branch number increased with ScABI3 overexpression in alfalfa. Further analysis of the gas exchange parameters showed that the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and water-use efficiency (WUE) of the transgenic alfalfa were significantly higher than WT; meanwhile, the protein content of the transgenic lines was higher than the WT, but the crude fat content was lower. Thus, these findings suggest that ScABI3 can be used as a potential candidate gene to manipulate alfalfa’s growth and nutritional quality. This study will provide a theoretical basis for breeding alfalfa varieties and assist in forage production and animal husbandry in the future.

Genome-wide identification of B3 superfamily in pecan (Carya illinoensis): In silico and experimental analyses

The B3 superfamily comprises a class of transcription factors containing B3 functional domains that play crucial roles in plant growth and development. However, the identification and analysis of the B3 superfamily have not been reported in pecans. In this study, 75 B3 superfamily members were identified and divided into four families, namely ARF (31), RAV (10), LAV (8), and REM (26). The gene structure, conserved motifs and domain analysis indicated that each family was highly similar. The Ka/Ks results indicated that the CiB3s underwent purifying selection. Several growth- and development-related cis-elements, such as Box 4, GATA-motif, and G-Box, were found in the promoter of the B3 transcription factor. The results obtained from the transcriptomic analysis of different kernel development stages and different tissues of pecan and qRT-PCR, indicated that several transcription factors, particularly CiABI3, CiFUS3, and CiLEC2, were involved in regulating kernel development. In particular, the expression of CiFUS3 changed significantly between S3 and S5. Additionally, CiFUS3 is localized in the nucleus and has no self-transcriptional activity. A yeast one-hybrid experiment showed that CiFUS3 could bind to the RY-motif related to seed development. Overall, our study provides a reference for the role of CiFUS3 in oil synthesis and the functional study of B3 genes in pecan.

Ellagic Acid Alters Muscle Fiber-Type Composition and Promotes Mitochondrial Biogenesis through the AMPK Signaling Pathway in Healthy Pigs.

Ellagic acid (EA), because of its remarkable health-promoting ability, has aroused widespread interest in the fields of nutrition and medicine. However, no reports showed that EA regulates mitochondrial biogenesis as well as muscle fiber-type composition in pigs. Our study found that dietary 75 and 150 mg/kg EA obviously augmented the slow myosin heavy chain (MyHC) protein level, the number of slow-twitch muscle fibers, and the activity of malate dehydrogenase (MDH) in the longissimus thoracis (LT) muscle of growing-finishing pigs. In contrast, dietary 75 and 150 mg/kg EA decreased the fast MyHC level, the number of fast-twitch muscle fibers, and the activity of lactate dehydrogenase (LDH) in the LT muscle. In addition, our further study found that dietary 75 and 150 mg/kg EA promoted the mitochondrial DNA (mtDNA) content, the mRNA expressions of ATP synthase (ATP5G), mtDNA transcription factor A (TFAM), AMP-activated protein kinase α1 (AMPKα1), peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) and sirtuin 1 (Sirt1), and the level of phospho-LKB1 (P-LKB1), phospho-AMPK (P-AMPK), Sirt1, and PGC-1α in the LT muscle. In vitro, 5, 10, and 20 μmol/L EA treatment upregulated the level of slow MyHC, but only 10 μmol/L EA treatment decreased fast MyHC protein expression in porcine skeletal muscle satellite cells (PSCs). In addition, our data again found that 10 μmol/L EA treatment promoted the mtDNA content, the mRNA levels of ATP5G, mitochondrial transcription factor b1 (TFB1M), citrate synthase (Cs), AMPKα1, PGC-1α, and Sirt1, and the protein expressions of P-AMPK, P-LKB1, PGC-1α, and Sirt1 in PSCs. What is more, inhibition of the AMPK signaling pathway by AMPKα1 siRNA significantly eliminated the improvement of EA on muscle fiber-type composition as well as the mtDNA content in PSCs. In conclusion, EA altered muscle fiber-type composition and promoted mitochondrial biogenesis through the AMPK signaling pathway.