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Rosa roxburghii, a calciphilic species native to the mountainous regions of Southwest China, is renowned for its high vitamin C and bioactive components, making it valuable for culinary and medicinal uses. This species exhibits remarkable tolerance to the high-calcium conditions typical of karst terrains. However, the underlying mechanisms of this calcium resilience remain unclear. The Ca2+/cation antiporter (CaCA) superfamily plays a vital role in the transport of Ca2+ and other cations and is crucial for plant tolerance to metal stress. However, the roles and evolutionary significance of the CaCA superfamily members in R. roxburghii remain poorly understood. This study identified 22 CaCA superfamily genes in R. roxburghii, categorized into four subfamilies. The gene structures of these RrCaCAs show considerable conservation across related species. Selection pressure analysis revealed that all RrCaCAs are subject to purifying selection. The promoter regions of these genes contain numerous hormone-responsive and stress-related elements. qRT-PCR analyses demonstrated that H+/cation exchanger (CAX) RrCAX1a and RrCAX3a were highly responsive to Ca2+ stress, cation/Ca2+ exchanger (CCX) RrCCX4 to Mg2+ stress, and RrCCX11a to Na+ stress. Subcellular localization indicated that RrCAX1a is localized to the plant cell membrane, and its stable transformation in tobacco confirmed its ability to confer enhanced resistance to heavy Ca2+ stresses, highlighting its crucial role in the high-calcium tolerance mechanisms of R. roxburghii. This research establishes a foundation for further molecular-level functional analyses of the adaptation mechanisms of R. roxburghii to high-calcium environments. [ABSTRACT FROM AUTHOR]

Phospholipase C (PLC) is an essential enzyme involved in lipid signaling pathways crucial for regulating plant growth and responding to environmental stress. In sorghum, 11 PLC genes have been identified, comprising 6 PI-PLCs and 5 NPCs. Through phylogenetic and interspecies collinearity analyses, structural similarities between SbPLCs and ZmPLCs proteins have been observed, with a particularly strong collinearity between SbPLCs and OsPLCs. Promoter function analysis has shown that SbPLCs are significantly enriched under abiotic stress and hormonal stimuli, like ABA, jasmonic acid, drought, high temperature, and salt. Gene co-expression networks, constructed using a weighted gene co-expression network analysis (WGCNA), highlight distinct expression patterns of SbPLC1, SbPLC3a, and SbPLC4 in response to abiotic stress, providing further insights into the expression patterns and interactions of SbPLCs under various environmental stimuli. qRT-PCR results reveal variations in expression levels among most SbPLCs members under different stress conditions (drought, NaCl, NaHCO3), hormone treatments (ABA), and developmental stages, indicating both specific and overlapping expression patterns. This comprehensive analysis offers valuable insights into the roles of SbPLCs in sorghum, shedding light on their specific expression patterns, regulatory elements, and protein interactions across different environmental stimuli and developmental stages. [ABSTRACT FROM AUTHOR]

Peanut (Arachis hypogaea L.) is one of the most important oil and food legume crops worldwide. ASR (abscisic acid, stress, ripening) plays extremely important roles in plant growth and development, fruit ripening, pollen development, and stress. Here, six ASR genes were identified in peanut. Structural and conserved motif analyses were performed to identify common ABA/WDS structural domains. The vast majority of ASR genes encoded acidic proteins, all of which are hydrophilic proteins and localized on mitochondria and nucleus, respectively. The cis-element analysis revealed that some cis-regulatory elements were related to peanut growth and development, hormone, and stress response. Under normal growth conditions, AhASR4 and AhASR5 were expressed in all tissues of peanut plants. Quantitative real-time PCR (qRT-PCR) results indicated that peanut ASR genes exhibited complex expression patterns in response to abiotic stress. Notably, under drought and cadmium (Cd) stress, the expression levels of AhASR4 and AhASR5 were significantly upregulated, suggesting that these genes may play a crucial role in the peanut plant's resistance to such stressors. These results provide a theoretical basis for studying the evolution, expression, and function of the peanut ASR gene family and will provide valuable information in the identification and screening of genes for peanut stress tolerance breeding. [ABSTRACT FROM AUTHOR]

Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes. [ABSTRACT FROM AUTHOR]

With the constant progress of urbanization and industrialization, cadmium (Cd) has emerged as one of the heavy metals that pollute soil and water. The presence of Cd has a substantial negative impact on the growth and development of both animals and plants. The allotetraploid Brasscia. carinata, an oil crop in the biofuel industry, is known to produce seeds with a high percentage of erucic acid; it is also known for its disease resistance and widespread adaptability. However, there is limited knowledge regarding the tolerance of B. carinata to Cd and its physiological responses and gene expressions under exposure to Cd. Here, we observed that the tested B. carinata exhibited a strong tolerance to Cd (1 mmol/L CdCl2 solution) and exhibited a significant ability to accumulate Cd, particularly in its roots, with concentrations reaching up to 3000 mg/kg. Additionally, we found that the total oil content of B. carinata seeds harvested from the Cd-contaminated soil did not show a significant change, but there were noticeable alterations in certain constituents. The activities of antioxidant enzymes, including catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX), were observed to significantly increase after treatment with different concentrations of CdCl2 solutions (0.25 mmol/L, 0.5 mmol/L, and 1 mmol/L CdCl2). This suggests that these antioxidant enzymes work together to enhance Cd tolerance. Comparative transcriptome analysis was conducted to identify differentially expressed genes (DEGs) in the shoots and roots of B. carinata when exposed to a 0.25 mmol/L CdCl2 solution for 7 days. A total of 631 DEGs were found in the shoots, while 271 DEGs were found in the roots. It was observed that these selected DEGs, which responded to Cd stress, also showed differential expression after exposure to PbCl2. This suggests that B. carinata may employ a similar molecular mechanism when tolerating these heavy metals. The functional annotation of the DEGs showed enrichment in the categories of 'inorganic ion transport and metabolism' and 'signal transduction mechanisms'. Additionally, the DEGs involved in 'tryptophan metabolism' and 'zeatin biosynthesis' pathways were found to be upregulated in both the shoots and roots of B. carinata, suggesting that the plant can enhance its tolerance to Cd by promoting the biosynthesis of plant hormones. These results highlight the strong Cd tolerance of B. carinata and its potential use as a Cd accumulator. Overall, our study provides valuable insights into the mechanisms underlying heavy metal tolerance in B. carinata. [ABSTRACT FROM AUTHOR]

Trisomy harbouring an extra copy of the chromosome generally causes a variety of physical and intellectual disabilities in mammals but is an extremely rare and important genetic stock in plants. In this study, a spontaneous trisomy plant in a Chinese kale accession (Brassica oleracea var. alboglabra, CC, 2n = 18) that showed significantly smaller plant architecture when compared to other normal plants was found and subsequently confirmed by cytological analysis in which the chromosome set of 2n = 19 and abnormal chromosome behaviour were observed. Then, based on the gene expression deviation determined by RNA-seq, the extra chromosome copy in this trisomy was identified as chromosome C2 (TC2). Compared to normal plants, TC2 not only showed generally upregulated differentially expressed genes (DEGs) on chromosome C2 (97.21% of 573 DEGs in chromosome C2) but also exhibited a whole-genome expression perturbation, in which 1329 DEGs (69.87% of total DEGs) were observed along two-copy chromosomes (trans-effect). The genes in the high (gene expression value > 100) and medium (100 > gene expression value > 10) groups were more prone to decreased gene expression, but the genes in the low group (10 > gene expression value > 0.1) showed upregulated expression deviation. In addition, GO (Gene ontology) annotation analysis revealed that the upregulated DEGs in the trans-effect group were overrepresented by the genes involved in the response to stress category, while the downregulated DEGs in the trans-effect group were mostly enriched in pathways related to DNA synthesis. In conclusion, we think our results can provide important resources for genetic analysis in B. oleracea and show some novel insights for understanding trisomy plant biology. [ABSTRACT FROM AUTHOR]

Arabis paniculata has been reported as a hyperaccumulator and functions in cadmium (Cd) tolerance and accumulation. However, the genes involved in Cd stress resistance in A. paniculata are still unknown. In this work, genes of the natural resistance-associated macrophage proteins (NRAMPs) were characterized in A. paniculata, and their evolutionary relationship and expression patterns were analysed. Expression profiles indicated that ApNRAMPs showed large differences in response to Cd stress. It was highly induced by Cd in root and shoot tissues. To investigate the function of ApNRAMP4 under Cd stress, ApNRAMP4 was cloned and expressed in yeast and Arabidopsis. The results indicated that yeast and Arabidopsis expressing ApNRAMP4 showed normal growth under Cd stress. In addition, transgenic yeast and Arabidopsis showed the ability to concentrate Cd. Under 20 μM CdCl2, Cd concentrations in wild type (WT) and transgenic yeast were 3.11 and 5.92 mg/kg, respectively. Cd concentrations in root tissues of WT and transgenic Arabidopsis were 0.18 and 0.54 mg/kg, respectively. In shoot tissues of WT and transgenic Arabidopsis, Cd concentrations were 0.13 and 0.49 mg/kg, respectively. This report provides genomic information on hyperaccumulator A. paniculata. In addition, the present work identified key NRAMP genes that may serve as resources for heavy metal phytoremediation. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a toxic heavy metal that is absorbed from the soil through roots and transmitted through the food chain, posing a serious threat to human health and food security. Exogenous NaCl can reduce the uptake of Cd by plants, but the underlying molecular mechanism is still unclear. In this study, we elucidated the molecular mechanism by which exogenous NaCl inhibited Cd absorption in wheat seedlings. Notably, 50 mM NaCl altered the wheat physiological response and reduce the Cd uptake by plants. Overexpression of the NaCl–responsive gene TaNHX2 increased the levels of chlorophyll and proline, enhanced antioxidant enzyme (CAT, POD, and SOD) activity, decreased the MDA content, and improved tolerance to Cd stress in transgenic wheat plants. We further found that TaWRKY13 binds directly to the TaNHX2 promoter to regulate its transcription. Subsequent research found that TaWRKY13 can also bind to the promoter of the heavy metal transporter gene TaHMA2 to activate its expression. TaNHX2 overexpression obviously downregulated the expression of TaHMA2 in the presence of both NaCl and Cd. In vivo and in vitro assays revealed that NaCl inhibited the binding of TaWRKY13 to the TaHMA2 promoter. This work reveals that NaCl and Cd antagonize uptake at the molecular level and provides new insights for future reductions in Cd accumulation in wheat. [Display omitted] • Exogenous NaCl can reduce the uptake of Cd by wheat plants. • Overexpression of TaNHX2 improved tolerance to Cd stress in wheat. • TaWRKY13 binds the promoters of TaNHX2 and TaHMA2. • NaCl promoted the binding of TaWRKY13 to the TaNHX2 promoter. • NaCl inhibited the binding of TaWRKY13 to the TaHMA2 promoter. [ABSTRACT FROM AUTHOR]

Soil and water are increasingly at risk of contamination from the toxic heavy metals lead (Pb) and cadmium (Cd). Arabis paniculata (Brassicaceae) is a hyperaccumulator of heavy metals (HMs) found widely distributed in areas impacts by mining activities. However, the mechanism by which A. paniculata tolerates HMs is still uncharacterized. For this experiment, we employed RNA sequencing (RNA-seq) in order to find Cd (0.25 mM)- and Pb (2.50 mM)-coresponsive genes A. paniculata. In total, 4490 and 1804 differentially expressed genes (DEGs) were identified in root tissue, and 955 and 2209 DEGs were identified in shoot tissue, after Cd and Pb exposure, respectively. Interestingly in root tissue, gene expression corresponded similarly to both Cd and Pd exposure, of which 27.48% were co-upregulated and 41.00% were co-downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the co-regulated genes were predominantly involved in transcription factors (TFs), cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. Many critical Pb/Cd-induced DEGs involved in phytohormone biosynthesis and signal transduction, HM transport, and transcription factors were also identified. Especially the gene ABCC9 was co-downregulated in root tissues but co-upregulated in shoot tissues. The co-downregulation of ABCC9 in the roots prevented Cd and Pb from entering the vacuole rather than the cytoplasm for transporting HMs to shoots. While in shoots, the ABCC9 co-upregulated results in vacuolar Cd and Pb accumulation, which may explain why A. paniculata is a hyperaccumulator. These results will help to reveal the molecular and physiological processes underlying tolerance to HM exposure in the hyperaccumulator A. paniculata , and aid in future efforts to utilize this plant in phytoremediation. [Display omitted] • RNA sequencing was used for the first time to find the Cd- and Pb- coresponsive genes in Arabis paniculata. • Arabis paniculata is a hyperaccumulator of heavy metals found widely distributed in areas impacts by mining activities. • The co-regulated genes were predominantly involved in TFs, cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. • Many critical Cd/Pb-induced DEGs, such as HAI2 , ABF3 , YSL3 , ZIP11 , ABCC9 , NRAMP4 , EIN3 , WRKY19 , and WRKY40 , were also identified. • The creation of a PPI network facilitated the identification of key genes, such as PI4KG4 , MPK1 and XLG2. [ABSTRACT FROM AUTHOR]

Fission yeast Schizosaccharomyces pombe shares various important properties with higher eukaryotes and is now considered a useful host for elevated production of mammalian proteins for medicinal applications. The full-length nmt1 promoter has been widely used as a strong promoter in S. pombe expression system. In the present study, the promoters of the eno101 and gpd3 genes in S. pombe were identified as strong constitutive promoters. For convenient applications in the plasmids of S. pombe, these promoters were refined to 276-bp eno and 273-bp gpd promoters by deleting undesired sequences and examining the expression of reporter genes including lacZ and xynA. Both the refined eno and gpd promoters provided approximately 1.5-fold higher expression of LacZ than nmt1 promoter. Furthermore, gene expression under the control of the eno or gpd promoter was not repressed by the components of YES medium while nmt1 promoter was inhibited by thiamine in yeast extract. Therefore, both eno and gpd promoters offer opportunities for efficient production of recombinant proteins by S. pombe in high cell-density fermentation. [ABSTRACT FROM AUTHOR]

Focuses on the construction of hepatocellular carcinoma (HCC) cDNAs into ZAP cDNA expression library. Positive clones; Number of genes of HCC-associated tumor antigens identified; RNA transcription and splicing p-associated molecules; Protein metabolism-associated molecules; Energy synthesis-associated molecules; Cell adhesion molecules.

• The progeny plants AR(2n=19) harboring the genomes of radish (Raphanus sativus, RR, 2n=18) and cabbage (Brassica pekinensis, AA, 2n=20) were identified by fluorescence in situ hybridization. • The gene expression bias of AR leaf and flower tissues was in favor of A genome, and the proportion was 26.03 % and 32.74 %. ELD results showed that all of them were favorable to R genome, and the proportion was 15.41 % and 18.61 %. • Gene silencing and expression of new genes in the two tissues were observed in the progeny AR. Polyploidization is an evolutionarily and mechanistically intriguing process, that requires harmonization of genomic and regulatory interactions among divergent genome groups. Here, we examined gene expression pattern changes in the leaves and petals of Raphanobrassica, a new synthetic amphidiploid generated by a distant cross between radish (RR, 2n = 18) and purple cabbage (AA, 2n = 20). The degree and direction of expression level dominance (ELD), defined as the total expression level of two homoeologous genes, was assessed, and homoeologous expression bias (HEB) analyzed, to assess the relative contributions of homoeologous genes to the transcriptome. Comparative analysis between Raphanobrassica and its parental species revealed that most differentially expressed genes were additive (leaves, 81.63 %; flowers, 82.71 %). ELD favors the R genome in both Raphanobrassica tissues, primarily driven by up- or down-regulation of non-dominant parent genes, with radish (RR) as the dominant parent in ELD-R and cabbage (AA) in ELD-A HEB indicated a preference for the A genome in both tissues (leaves, 26.03 %; flowers, 32.74 %). To further elucidate the ELD phenomenon, we compared expression levels of individual homoeologous genes with those in the diploid parents. ELD toward genes expressed at higher levels in parents was mediated either by down-regulation of genes from the dominant parent or up-regulation of those from the non-dominant parent, whereas ELD toward genes expressed at lower levels in parents was attributable solely to down-regulation of non-dominant parent homoeologous genes. Our findings provide novel insights into gene expression changes in heterodiploids generated by hybridization prior to polyploidization, laying a foundation for understanding genome-wide expression pattern alterations during polyploid formation. [ABSTRACT FROM AUTHOR]

In contrast with the past, the water buffalo is now not only a draft animal, but also an important food source of milk and meat. It is increasingly apparent that the water buffalo have huge potential for meat production, but its breeding needs to be investigated. Regarding the molecular mechanisms involved in the meat quality difference between the buffalo ( Bubalus bulabis ) and yellow cattle ( Bos taurus ), 12 chemical-physical characteristics related to the meat quality of longissimus thoracis muscles (LTM) have been compared at the age of 36 months. Intramuscular lipid and b* (yellowness) were greater in cattle than the buffalo, whereas a* (redness) was greater in the buffalo. Gene expression profiles were constructed by bovine genome array. A total of 8884 and 10,960 probes were detected in buffalo and cattle, respectively, with 1580 genes being differentially expressed. Over 400 probes were upregulated and nearly 1200 were downregulated in LTM of the buffalo, most being involved in ribosomal RNA (rRNA) processing, cholesterol homeostasis, regulation of transcription, response to hypoxia, and glycolysis. Quantitative real-time PCR was used to validate the microarray data. Enriched GO analyses of highly expressed genes in LTM showed that protein biosynthesis, striated muscle contraction, iron homeostasis, iron transport, glycolysis and glucose metabolism were similar between the buffalo and cattle. High protein content, low fat content and deep meat color of buffalo LTM may be closely associated with the increased expression of genes involved in cholesterol and iron homeostasis, while also reducing the expression of genes involved in ubiquitin-mediated proteolysis and protein oxidative phosphorylation. These results establish the groundwork for further studies on buffalo meat quality and will be beneficial in improving water buffalo breeding by molecular biotechnology. [ABSTRACT FROM AUTHOR]