Identification and genes expression analysis of ATP-dependent phosphofructokinase family members among three Saccharum species

The function of an apple ATP-dependent Phosphofructokinase gene MdPFK5 in regulating salt stress

Salt stress severely affects the growth and yield of apples (Malus domestica Borkh). Although salt-tolerant genes have been extensively studied, documentation on the role of the ATP-dependent phosphofructokinase gene MdPFK5 in salt stress is limited. This study conducted an evolutionary tree and three-dimensional structure analysis of the PFK gene family in Arabidopsis thaliana and MdPFK (MD01G1037400), revealing a close phylogenetic relationship between MdPFK (MD01G1037400) and AtPFK5. Given the similarity in their protein tertiary structures, MdPFK was designated as MdPFK5, suggesting functional similarities with AtPFK5. Further investigation revealed elevated expression levels of MdPFK5 in apple leaves and flowers, particularly showing significant upregulation 120 days after blooming and differential expression beginning at 3 hours of salt stress. Overexpression of MdPFPK5 conferred salt tolerance in both apple calli and transgenic lines of Arabidopsis thaliana. Moreover, NaCl treatment promoted soluble sugar accumulation in apple calli and transgenic lines of Arabidopsis thaliana overexpressing MdPFK5. This study provides new insights into the salt tolerance function of MdPFK5.

Characterization of ATP-dependent phosphofructokinase genes during ripening and their modulation by phytohormones during postharvest storage of citrus fruits (Citrus reticulata Blanco.)

The level of sweetness in citrus fruit is crucial for consumer appeal and market competitiveness, determined mainly by soluble sugars and organic acids. ATP-dependent 6-phosphofructokinase is central to regulating sugar metabolism, yet its role in citrus fruit ripening and postharvest storage remains underexplored. We characterized phosphofructokinase genes in citrus, identifying eight genes classified into pyrophosphate-dependent phosphofructokinase (PFP) and ATP-dependent 6-phosphofructokinase (PFK) subgroups using phylogenetic analysis, genomic architectures, and protein motifs. Comparative genomic analysis with other plants highlighted significant protein homology among CitPFKs. The motif analysis indicated conserved phosphofructokinase domains in CitPFK sequences, with upstream promoter regions containing diverse cis-regulatory elements, most notably light-responsive (LREs). The gene expression profiling throughout fruit development and ripening revealed differential patterns, with responses to gibberellic acid and salicylic acid phytohormones during postharvest indicating their roles in regulating CitPFK genes. The analysis of the transcriptome showed high expression of ATP-dependent 6-phosphofructokinase 3 (CitPFK3) during fruit development, indicating a positive role in fruit maturation. Consequently, silencing CitPFK3 through virus-induced gene silencing (VIGS) increased hexose sugar content, suggesting its function in sugar accumulation. These findings improve our understanding of PFKs in citrus, particularly CitPFK3's pivotal role in regulating hexose sugar dynamics and their modulation by exogenous phytohormones after harvest. This study provides a foundation for optimizing soluble sugar regulation to enhance fruit quality and postharvest handling in citrus production.

Genome-wide survey of the phosphofructokinase family in cassava and functional characterization in response to oxygen-deficient stress

BACKGROUND

Glycolytic pathway is common in all plant organs, especially in oxygen-deficient tissues. Phosphofructokinase (PFK) is a rate-limiting enzyme in the glycolytic pathway and catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. Cassava (M. esculenta) root is a huge storage organ with low amount of oxygen. However, less is known about the functions of PFK from M. esculenta (MePFK). We conducted a systematic analysis of MePFK genes to explore the function of the MePFK gene family under hypoxic stress.

RESULTS

We identified 13 MePFK genes and characterised their sequence structure. The phylogenetic tree divided the 13 genes into two groups: nine were MePFKs and four were pyrophosphate-fructose-6-phosphate phosphotransferase (MePFPs). We confirmed by green fluorescent protein fusion protein expression that MePFK03 and MePFPA1 were localised in the chloroplast and cytoplasm, respectively. The expression profiles of the 13 MePFKs detected by quantitative reverse transcription polymerase chain reaction revealed that MePFK02, MePFK03, MePFPA1, MePFPB1 displayed higher expression in leaves, root and flower. The expression of MePFK03, MePFPA1 and MePFPB1 in tuber root increased gradually with plant growth. We confirmed that hypoxia occurred in the cassava root, and the concentration of oxygen was sharply decreasing from the outside to the inside root. The expression of MePFK03, MePFPA1 and MePFPB1 decreased with the decrease in the oxygen concentration in cassava root. Waterlogging stress treatment showed that the transcript level of PPi-dependent MePFP and MeSuSy were up-regulated remarkably and PPi-dependent glycolysis bypass was promoted.

CONCLUSION

A systematic survey of phylogenetic relation, molecular characterisation, chromosomal and subcellular localisation and cis-element prediction of MePFKs were performed in cassava. The expression profiles of MePFKs in different development stages, organs and under waterlogging stress showed that MePFPA1 plays an important role during the growth and development of cassava. Combined with the transcriptional level of MeSuSy, we found that pyrophosphate (PPi)-dependent glycolysis bypass was promoted when cassava was under waterlogging stress. The results would provide insights for further studying the function of MePFKs under hypoxic stress.

Planthopper Transmission of Ramu Stunt Virus, a Tenuivirus Causing the Sugarcane Disease Ramu Stunt, and its Distribution in Papua New Guinea

Ramu stunt is a serious disease of sugarcane, currently only reported from Papua New Guinea. It is found in both commercial sugarcane grown on the Ramu Agri Industries Limited (RAIL) estate and in chewing canes (Saccharum officinarum L.) grown in village gardens. The vector of Ramu stunt disease is the island sugarcane planthopper, Eumetopina flavipes Muir. Here we report on the successful transmission of Ramu stunt using E. flavipes and verify that the disease is caused by Ramu stunt virus, a virus with homology to the genus Tenuivirus. Diagnostic reverse transcription PCR screening, with partial genome sequencing and viral protein characterization, was used for confirmation. Disease surveys were undertaken on the RAIL estate, along roadsides, and in village gardens in parts of Papua New Guinea. When the disease was identified, partial genome sequencing of the virus was performed to assess the extent of genome variability among isolates. The disease was less common than predicted from early surveys based on symptoms alone, and genotypic variation was associated with geographic location.

Genome-wide identification, expression and functional analysis of the phosphofructokinase gene family in Chinese white pear (Pyrus bretschneideri)

Phosphofructokinase plays an essential role in sugar metabolism in plants. Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose-6-phosphate, the pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP), and the ATP-dependent phosphofructokinase (PFK). Until now, the gene evolution, expression patterns, and functions of phosphofructokinase proteins were unknown in pear. In this report, 14 phosphofructokinase genes were identified in pear. The phylogenetic tree indicated that the phosphofructokinase gene family could be grouped into two subfamilies, with 10 genes belonging to the PbPFK subfamily, and 4 genes belonging to the PbPFP subfamily. Conserved motifs and exon numbers of the phosphofructokinase were found in pear and other six species. The evolution analysis indicated that WGD/Segmental and dispersed duplications were the main duplication models for the phosphofructokinase genes expansion in pear and other six species. Analysis of cis-regulatory element sequences of all phosphofructokinase genes identified light regulation and the MYB binding site in the promoter of all pear phosphofructokinase genes, suggesting that phosphofructokinase might could be regulated by light and MYB transcription factors (TFs). Gene expression patterns revealed that PbPFP1 showed similar pattern with sorbitol contents, suggesting important contributions to sugar accumulation during fruit development. Further functional analysis indicated that the phosphofructokinase gene PbPFP1 was localized on plasma membrane compartment, indicating that PbPFP1 had function in plasma membrane. Transient transformation of PbPFP1 in pear fruits led to significant increases of fructose and sorbitol compared to controls. Overall, our study provides important insights into the gene expression patterns and important potential functions of phosphofructokinase for sugar accumulation in pear fruits, which will help to enrich understanding of sugar-related bio-pathways and lay the molecular basis for fruit quality improvement.

New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics

BACKGROUND

The SWEET (Sugars Will Eventually be Exported Transporters) gene family is a recently identified group of sugar transporters that play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction, nectar secretion, and reproductive tissue development. However, little information on Saccharum SWEET is available for this crop with a complex genetic background.

RESULTS

In this study, 22 SWEET genes were identified from Saccharum spontaneum Bacterial Artificial Chromosome libraries sequences. Phylogenetic analyses of SWEETs from 11 representative plant species showed that gene expansions of the SWEET family were mainly caused by the recent gene duplication in dicot plants, while these gene expansions were attributed to the ancient whole genome duplication (WGD) in monocot plant species. Gene expression profiles were obtained from RNA-seq analysis. SWEET1a and SWEET2s had higher expression levels in the transitional zone and maturing zone than in the other analyzed zones. SWEET1b was mainly expressed in the leaf tissues and the mature zone of the leaf of both S. spontaneum and S. officinarum, and displayed a peak in the morning and was undetectable in both sclerenchyma and parenchyma cells from the mature stalks of S. officinarum. SsSWEET4a\4b had higher expression levels than SWEET4c and were mainly expressed in the stems of seedlings and mature plants. SWEET13s are recently duplicated genes, and the expression of SWEET13s dramatically increased from the maturing to mature zones. SWEET16b's expression was not detected in S. officinarum, but displayed a rhythmic diurnal expression pattern.

CONCLUSIONS

Our study revealed the gene evolutionary history of SWEETs in Saccharum and SWEET1b was found to be a sucrose starvation-induced gene involved in the sugar transportation in the high photosynthetic zones. SWEET13c was identified as the key player in the efflux of sugar transportation in mature photosynthetic tissues. SWEET4a\4b were found to be mainly involved in sugar transportation in the stalk. SWEET1a\2a\4a\4b\13a\16b were suggested to be the genes contributing to the differences in sugar contents between S. spontaneum and S. officinarum. Our results are valuable for further functional analysis of SWEET genes and utilization of the SWEET genes for genetic improvement of Saccharum for biofuel production.

Confirmation that the Novel Cercozoa Phytocercomonas venanatans Is the Cause of the Disease Chlorotic Streak in Sugarcane

A cercomonad, named Phytocercomonas venanatans, is confirmed as the cause of the sugarcane disease chlorotic streak. This was achieved by establishing aseptic liquid cultures of the pathogen isolated from internal pieces of sugarcane stalk tissue. Actively motile cultures of the pathogen were inoculated into sugarcane roots, stalks, and leaf whorls. Infected plants subsequently developed the characteristic symptoms of chlorotic streak. Infection was confirmed by PCR screening of plant tissues and by reisolation of the pathogen into aseptic culture followed by PCR and microscopic confirmation. P. venanatans is the first reported pathogenic cercomonad able to systemically infect higher plants and the first plant pathogenic cercozoan able to be successfully grown in axenic culture on common microbiological media.

Evolution and expression of the fructokinase gene family in Saccharum

BACKGROUND

Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity.

RESULTS

In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress.

CONCLUSIONS

Our study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane.

Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum

BACKGROUND

Sugarcane is an economically important crop contributing to about 80% of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane's complicated genomes, it is still challenging to study the genetic basis of traits, such as sucrose accumulation. Sucrose transporters (SUTs) are critical for both phloem loading in source tissue and sucrose uptaking in sink tissue, and are considered to be the control points for regulating sucrose storage. However, no genomic study for sugarcane sucrose transporter (SsSUT) families has been reported up to date.

RESULTS

By using comparative genomics and bacterial artificial chromosomes (BACs), six SUT genes were identified and characterized in S. spontaenum. Phylogenetic analyses revealed that the two pairs SsSUTs (SsSUT1/SsSUT3 and SsSUT5/SsSUT6) could be clustered together into two separate monocot specific SUT groups, while SsSUT2 and SsSUT4 were separated into the other two groups, with members from both dicot and monocot species. Gene structure comparison demonstrated that the number and position of exons/introns in SUTs were highly conserved among the close orthologs; in contrast, there were variations among the paralogous SUTs in Sacchuarm. Though with the high polyploidy level, gene allelic haplotype comparative analysis showed that the examined four SsSUT members exhibited conservations of gene structures and amino acid sequences among the allelic haplotypes accompanied by variations of intron sizes. Gene expression analyses were performed for tissues from seedlings under drought stress and mature plants of three Saccharum species (S.officinarnum, S.spotaneum and S.robustum). Both SUT1 and SUT4 expressed abundantly at different conditions. SUT2 had similar expression level in all of the examined tissues, but SUT3 was undetectable. Both of SUT5 and SUT6 had lower expression level than other gene member, and expressed stronger in source leaves and are likely to play roles in phloem loading. In the seeding plant leave under water stress, four genes SUT1, SUT2, SUT4 and SUT5 were detectable. In these detectable genes, SUT1 and SUT4 were down regulated, while, SUT2 and SUT5 were up regulated.

CONCLUSIONS

In this study, we presented the first comprehensive genomic study for a whole gene family, the SUT family, in Saccharum. We speculated that there were six SUT members in the S. spotaneum genome. Out of the six members, SsSUTs, SsSUT5 and SsSUT6 were recent duplication genes accompanied by rapid evolution, while, SsSUT2 and SsSUT4 were the ancient members in the families. Despite the high polypoidy genome, functional redundancy may not exist among the SUTs allelic haplotypes supported by the evidence of strong purifying selection of the gene allele. SUT3 could be a low active member in the family because it is undetectable in our study, but it might not be a pseudogene because it harbored integrated gene structure. SUT1 and SUT4 were the main members for the sucrose transporter, while, these SUTs had sub-functional divergence in response to sucrose accumulation and plant development in Saccharum.