Genome-wide screening of hexokinase gene family and functional elucidation of HXK2 response to cold stress in Jatropha curcas

The critical roles of three sugar-related proteins (HXK, SnRK1, TOR) in regulating plant growth and stress responses

Sugar signaling is one of the most critical regulatory signals in plants, and its metabolic network contains multiple regulatory factors. Sugar signal molecules regulate cellular activities and organism development by combining with other intrinsic regulatory factors and environmental inputs. HXK, SnRK1, and TOR are three fundamental proteins that have a pivotal role in the metabolism of sugars in plants. HXK, being the initial glucose sensor discovered in plants, is renowned for its multifaceted characteristics. Recent investigations have unveiled that HXK additionally assumes a significant role in plant hormonal signaling and abiotic stress. SnRK1 serves as a vital regulator of growth under energy-depleted circumstances, whereas TOR, a large protein, acts as a central integrator of signaling pathways that govern cell metabolism, organ development, and transcriptome reprogramming in response to diverse stimuli. Together, these two proteins work to sense upstream signals and modulate downstream signals to regulate cell growth and proliferation. In recent years, there has been an increasing amount of research on these three proteins, particularly on TOR and SnRK1. Furthermore, studies have found that these three proteins not only regulate sugar signaling but also exhibit certain signal crosstalk in regulating plant growth and development. This review provides a comprehensive overview and summary of the basic functions and regulatory networks of these three proteins. It aims to serve as a reference for further exploration of the interactions between these three proteins and their involvement in co-regulatory networks.

Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.

Identification and Expression Analysis of Hexokinases Family in Saccharum spontaneum L. under Drought and Cold Stresses

In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8-11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification.

Function of a non-enzymatic hexokinase LcHXK1 as glucose sensor in regulating litchi fruit abscission

Fruit abscission is a severe hindrance to commercial crop production, and a lack of carbohydrates causes fruit abscission to intensify in a variety of plant species. However, the precise mechanism by which carbohydrates affect fruit setting potential has yet to be determined. In the current study, we noticed negative correlation between hexose level and fruit setting by comparing different cultivars, bearing shoots of varying diameters, and girdling and defoliation treatments. The cumulative fruit-dropping rate was significantly reduced in response to exogenous glucose dipping. These results suggested that hexose, especially glucose, is the key player in lowering litchi fruit abscission. Moreover, five putative litchi hexokinase genes (LcHXKs) were isolated and the subcellular localization as well as activity of their expressed proteins in catalyzing hexose phosphorylation were investigated. LcHXK2 was only found in mitochondria and expressed catalytic protein, whereas the other four HXKs were found in both mitochondria and nuclei and had no activity in catalyzing hexose phosphorylation. LcHXK1 and LcHXK4 were found in the same cluster as previously reported hexose sensors AtHXK1 and MdHXK1. Furthermore, VIGS-mediated silencing assay confirms that LcHXK1 suppression increases fruit abscission. These findings revealed that LcHXK1 functions as hexose sensor, negatively regulating litchi fruit abscission.

Transcriptome reveals insights into biosynthesis of ginseng polysaccharides

BACKGROUND

Ginseng polysaccharides, have been used to treat various diseases as an important active ingredient. Nevertheless, the biosynthesis of ginseng polysaccharides is poorly understood. To elucidate the biosynthesis mechanism of ginseng polysaccharides, combined the transcriptome analysis and polysaccharides content determination were performed on the roots, stems, and leaves collected from four cultivars of ginseng.

RESULTS

The results indicated that the total contents of nine monosaccharides were highest in the roots. Moreover, the total content of nine monosaccharides in the roots of the four cultivars were different but similar in stems and leaves. Glucose (Glc) was the most component of all monosaccharides. In total, 19 potential enzymes synthesizing of ginseng polysaccharides were identified, and 17 enzymes were significantly associated with polysaccharides content. Among these genes, the expression of phosphoglucomutase (PGM), glucose-6-phosphate isomerase (GPI), UTP-glucose-1-phosphate uridylyltransferase (UGP2), fructokinase (scrK), mannose-1-phosphate guanylyltransferase (GMPP), phosphomannomutase (PMM), UDP-glucose 4-epimerase (GALE), beta-fructofuranosidase (sacA), and sucrose synthase (SUS) were correlated with that of MYB, AP2/ERF, bZIP, and NAC transcription factors (TFs). These TFs may regulate the expression of genes involved in ginseng polysaccharides synthesis.

CONCLUSION

Our findings could provide insight into a better understanding of the regulatory mechanism of polysaccharides biosynthesis, and would drive progress in genetic improvement and plantation development of ginseng.

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Low temperature is a major environmental factor, which limits rapeseed (Brassica napus L.) growth, development, and productivity. So far, the physiological and molecular mechanisms of rapeseed responses to cold stress are not fully understood. Here, we explored the transcriptome and metabolome profiles of two rapeseed genotypes with contrasting cold responses, i.e., XY15 (cold-sensitive) and GX74 (cold-tolerant). The global metabolome profiling detected 545 metabolites in siliques of both genotypes before (CK) and after cold-stress treatment (LW). The contents of several sugar metabolites were affected by cold stress with the most accumulated saccharides being 3-dehydro-L-threonic acid, D-xylonic acid, inositol, D-mannose, D-fructose, D-glucose, and L-glucose. A total of 1943 and 5239 differentially expressed genes were identified from the transcriptome sequencing in XY15CK_vs_XY15LW and GX74CK_vs_GX74LW, respectively. We observed that genes enriched in sugar metabolism and biosynthesis-related pathways, photosynthesis, reactive oxygen species scavenging, phytohormone, and MAPK signaling were highly expressed in GX74LW. In addition, several genes associated with cold-tolerance-related pathways, e.g., the CBF-COR pathway and MAPK signaling, were specifically expressed in GX74LW. Contrarily, genes in the above-mentioned pathways were mostly downregulated in XY15LW. Thus, our results indicate the involvement of these pathways in the differential cold-stress responses in XY15 and GX74.

Genome-Wide Survey and Expression Analyses of Hexokinase Family in Poplar (Populus trichocarpa)

Hexokinase (HXK) family proteins exert critical roles in catalyzing hexose phosphorylation, sugar sensing, and modulation of plant growth and stress adaptation. Nevertheless, a large amount remains unknown about the molecular profile of HXK enzymes in Populus trichocarpa, a woody model tree species. A genome-wide survey of HXK-encoding genes, including phylogenies, genomic structures, exon/intron organization, chromosomal distribution, and conserved features, was conducted, identifying six putative HXK isogenes (PtHXK1-6) in the Populus genome. The evolutionary tree demonstrated that 135 homologous HXKs between 17 plant species were categorized into four major subfamilies (type A, B, C, and D), clustering one plastidic (PtHXK3) and five mitochondrial PtHXKs grouped into type A and B, respectively. The in silico deduction prompted the presence of the conserved sugar-binding core (motif 4), phosphorylation sites (motif 2 and 3), and adenosine-binding domains (motif 7). The transcriptomic sequencing (RNA-seq) and the quantitative real-time PCR (qRT-PCR) assays revealed that three isogenes (PtHXK2, 3, and 6) were abundantly expressed in leaves, stems, and roots, while others appeared to be dominantly expressed in the reproductive tissues. Under the stress exposure, PtHXK2 and 6 displayed a significant induction upon the pathogenic fungi (Fusarium solani) infection and marked promotions by glucose feeding in roots. In contrast, the PtHXK3 and 6 are ABA-responsive genes, following a dose-dependent manner. The comprehensive analyses of the genomic patterns and expression profiling provide theoretical clues and lay a foundation for unraveling the physiological and signaling roles underlying the fine-tuned PtHXKs responding to diverse stressors.

Integrated Isoform Sequencing and Dynamic Transcriptome Analysis Reveals Diverse Transcripts Responsible for Low Temperature Stress at Anther Meiosis Stage in Rice

Low temperatures stress is one of the important factors limiting rice yield, especially during rice anther development, and can cause pollen sterility and decrease grain yield. In our study, low-temperature stress decreased pollen viability and spikelet fertility by affecting the sugar, nitrogen and amino acid contents of anthers. We performed RNA-seq and ISO-seq experiments to study the genome-wide transcript expression profiles in low-temperature anthers. A total of 4,859 differentially expressed transcripts were detected between the low-temperature and control groups. Gene ontology enrichment analysis revealed significant terms related to cold tolerance. Hexokinase and glutamate decarboxylase participating in starch and sucrose metabolism may play important roles in the response to cold stress. Using weighted gene co-expression network analysis, nine hub transcripts were found that could improve cold tolerance throughout the meiosis period of rice: Os02t0219000-01 (interferon-related developmental regulator protein), Os01t0218350-00 (tetratricopeptide repeat-containing thioredoxin), Os08t0197700-00 (luminal-binding protein 5), Os11t0200000-01 (histone deacetylase 19), Os03t0758700-01 (WD40 repeat domain-containing protein), Os06t0220500-01 (7-deoxyloganetin glucosyltransferase), Pacbio.T01382 (sucrose synthase 1), Os01t0172400-01 (phospholipase D alpha 1), and Os01t0261200-01 (NAC domain-containing protein 74). In the PPI network, the protein minichromosome maintenance 4 (MCM4) may play an important role in DNA replication induced by cold stress.

Moonlighting Proteins: The Case of the Hexokinases

Moonlighting proteins are defined as proteins with two or more functions that are unrelated and independent to each other, so that inactivation of one of them should not affect the second one and vice versa. Intriguingly, all the glycolytic enzymes are described as moonlighting proteins in some organisms. Hexokinase (HXK) is a critical enzyme in the glycolytic pathway and displays a wide range of functions in different organisms such as fungi, parasites, mammals, and plants. This review discusses HXKs moonlighting functions in depth since they have a profound impact on the responses to nutritional, environmental, and disease challenges. HXKs’ activities can be as diverse as performing metabolic activities, as a gene repressor complexing with other proteins, as protein kinase, as immune receptor and regulating processes like autophagy, programmed cell death or immune system responses. However, most of those functions are particular for some organisms while the most common moonlighting HXK function in several kingdoms is being a glucose sensor. In this review, we also analyze how different regulation mechanisms cause HXK to change its subcellular localization, oligomeric or conformational state, the response to substrate and product concentration, and its interactions with membrane, proteins, or RNA, all of which might impact the HXK moonlighting functions.

Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

BACKGROUND

Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants. Camellia sinensis, a perennial evergreen tree that is the source of tea, is mainly grown in warm areas. Camellia sinensis var. sinensis (CSS) has greater cold tolerance than Camellia sinensis var. assamica (CSA). To gain deep insight into the molecular mechanisms underlying cold adaptation, we investigated the physiological responses and transcriptome profiles by RNA-Seq in two tea varieties, cold resistant SCZ (classified as CSS) and cold susceptible YH9 (classified as CSA), during cold acclimation.

RESULTS

Under freezing stress, lower relative electrical conductivity and higher chlorophyll fluorescence (Fv/Fm) values were detected in SCZ than in YH9 when subjected to freezing acclimation. During cold treatment, 6072 and 7749 DEGs were observed for SCZ and YH9, respectively. A total of 978 DEGs were common for both SCZ and YH9 during the entire cold acclimation process. DEGs were enriched in pathways of photosynthesis, hormone signal transduction, and transcriptional regulation of plant-pathogen interactions. Further analyses indicated that decreased expression of Lhca2 and higher expression of SnRK2.8 are correlated with cold tolerance in SCZ.

CONCLUSIONS

Compared with CSA, CSS was significantly more resistant to freezing after cold acclimation, and this increased resistance was associated with an earlier expression of cold-induced genes. Because the greater transcriptional differentiation during cold acclimation in SCZ may contribute to its greater cold tolerance, our studies identify specific genes involved in photoinhibition, ABA signal conduction, and plant immunity that should be studied for understanding the processes involved in cold tolerance. Marker-assisted breeding focused on the allelic variation at these loci provides an avenue for the possible generation of CSA cultivars that have CSS-level cold tolerance.