Evolution and diversity of invertase genes in Populus trichocarpa

Genomic identification and expression analysis of acid invertase (AINV) gene family in Dendrobium officinale Kimura et Migo

BACKGROUND

Dendrobium officinale Kimura et Migo, a renowned traditional Chinese orchid herb esteemed for its significant horticultural and medicinal value, thrives in adverse habitats and contends with various abiotic or biotic stresses. Acid invertases (AINV) are widely considered enzymes involved in regulating sucrose metabolism and have been revealed to participate in plant responses to environmental stress. Although members of AINV gene family have been identified and characterized in multiple plant genomes, detailed information regarding this gene family and its expression patterns remains unknown in D. officinale, despite their significance in polysaccharide biosynthesis.

RESULTS

This study systematically analyzed the D. officinale genome and identified four DoAINV genes, which were classified into two subfamilies based on subcellular prediction and phylogenetic analysis. Comparison of gene structures and conserved motifs in DoAINV genes indicated a high-level conservation during their evolution history. The conserved amino acids and domains of DoAINV proteins were identified as pivotal for their functional roles. Additionally, cis-elements associated with responses to abiotic and biotic stress were found to be the most prevalent motif in all DoAINV genes, indicating their responsiveness to stress. Furthermore, bioinformatics analysis of transcriptome data, validated by quantitative real-time reverse transcription PCR (qRT-PCR), revealed distinct organ-specific expression patterns of DoAINV genes across various tissues and in response to abiotic stress. Examination of soluble sugar content and interaction networks provided insights into stress release and sucrose metabolism.

CONCLUSIONS

DoAINV genes are implicated in various activities including growth and development, stress response, and polysaccharide biosynthesis. These findings provide valuable insights into the AINV gene amily of D. officinale and will aid in further elucidating the functions of DoAINV genes.

The potential roles of acid invertase family in Dendrobium huoshanense: Identification, evolution, and expression analyses under abiotic stress

Dendrobium huoshanense, a traditional Chinese medicine prized for its horticultural and medicinal properties, thrives in an unfavorable climate and is exposed to several adverse environmental conditions. Acid invertase (AINV), a widely distributed enzyme that has been demonstrated to play a significant role in response to environmental stresses. However, the identification of the AINV gene family in D. huoshanense, the collinearity between relative species, and the expression pattern under external stress have yet to be resolved. We systematically retrieved the D. huoshanense genome and screened out four DhAINV genes, which were further classified into two subfamilies by the phylogenetic analysis. The evolutionary history of AINV genes in D. huoshanense was uncovered by comparative genomics investigations. The subcellular localization predicted that the DhVINV genes may be located in the vacuole, while the DhCWINV genes may be located in the cell wall. The exon/intron structures and conserved motifs of DhAINV genes were found to be highly conserved in two subclades. The conserved amino acids and catalytic motifs in DhAINV proteins were determined to be critical to their function. Notably, the cis-acting elements in all DhAINV genes were mainly relevant to abiotic stresses and light response. In addition, the expression profile coupled with qRT-PCR revealed the typical expression patterns of DhAINV in response to diverse abiotic stresses. Our findings could be beneficial to the characterization and further investigation of AINV functions in Dendrobium plants.

Structure and Expression Analysis of PtrSUS, PtrINV, PtrHXK, PtrPGM, and PtrUGP Gene Families in Populus trichocarpa Torr. and Gray

Exogenous nitrogen and carbon can affect plant cell walls, which are composed of structural carbon. Sucrose synthase (SUS), invertase (INV), hexokinase (HXK), phosphoglucomutase (PGM), and UDP-glucose pyrophosphorylase (UGP) are the key enzymes of sucrose metabolism involved in cell wall synthesis. To understand whether these genes are regulated by carbon and nitrogen to participate in structural carbon biosynthesis, we performed genome-wide identification, analyzed their expression patterns under different carbon and nitrogen treatments, and conducted preliminary functional verification. Different concentrations of nitrogen and carbon were applied to poplar (Populus trichocarpa Torr. and Gray), which caused changes in cellulose, lignin, and hemicellulose contents. In poplar, 6 SUSs, 20 INVs, 6 HXKs, 4 PGMs, and 2 UGPs were identified. Moreover, the physicochemical properties, collinearity, and tissue specificity were analyzed. The correlation analysis showed that the expression levels of PtrSUS3/5, PtrNINV1/2/3/5/12, PtrCWINV3, PtrVINV2, PtrHXK5/6, PtrPGM1/2, and PtrUGP1 were positively correlated with the cellulose content. Meanwhile, the knockout of PtrNINV12 significantly reduced the cellulose content. This study could lay the foundation for revealing the functions of SUSs, INVs, HXKs, PGMs, and UGPs, which affected structural carbon synthesis regulated by nitrogen and carbon, proving that PtrNINV12 is involved in cell wall synthesis.

The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis

INTRODUCTION

Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear.

OBJECTIVE

To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation.

METHODS

PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation.

RESULTS

A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids.

CONCLUSION

Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation.

MeNINV1: An Alkaline/Neutral Invertase Gene of Manihot esculenta, Enhanced Sucrose Catabolism and Promoted Plant Vegetative Growth in Transgenic Arabidopsis

Alkaline/neutral invertase (A/N-INV) is an invertase that irreversibly decomposes sucrose into fructose as well as glucose and plays a role in plant growth and development, starch synthesis, abiotic stress, and other plant-life activities. Cassava is an economically important starch crop in tropical regions. During the development of cassava tuber roots, A/N-INV activity is relatively high, which indicates that it may participate in sucrose metabolism and starch synthesis. In this study, MeNINV1 was confirmed to function as invertase to catalyze sucrose decomposition in yeast. The optimal enzymatic properties of MeNINV1 were a pH of 6.5, a reaction temperature of 40 °C, and sucrose as its specific catalytic substrate. VB6, Zn2+, and Pb2+ at low concentrations as well as EDTA, DTT, Tris, Mg2+, and fructose inhibited A/N-INV enzymic activity. In cassava, the MeNINV1 gene was mainly expressed in the fibrous roots and the tuber root phloem, and its expression decreased as the tuber root grew. MeNINV1 was confirmed to localize in chloroplasts. In Arabidopsis, MeNINV1-overexpressing Arabidopsis had higher A/N-INV activity, and the increased glucose, fructose, and starch content in the leaves promoted plant growth and delayed flowering time but did not change its resistance to abiotic stress. Our results provide new insights into the biological function of MeNINV1.

Mobile forms of carbon in trees: metabolism and transport

Plants constitute 80% of the biomass on earth, and almost two-thirds of this biomass is found in wood. Wood formation is a carbon (C)-demanding process and relies on C transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here, we review the molecules and mechanisms used to transport and allocate C in trees. Sucrose is the major form in which C is transported in plants, and it is found in the phloem sap of all tree species investigated so far. However, in several tree species, sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Furthermore, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular C recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C-carrying molecules in trees reveals no consistent differences in C transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate-related environmental factors will not explain the diversity of C transport forms. However, the consideration of C-transport mechanisms in relation to tree-rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.

Structure and Expression Analysis of Sucrose Phosphate Synthase, Sucrose Synthase and Invertase Gene Families in Solanum lycopersicum

Sucrose phosphate synthase (SPS), sucrose synthase (SUS) and invertase (INV) are all encoded by multigene families. In tomato (Solanum lycopersicum), a comprehensive analysis of structure characteristics of these family genes is still lacking, and the functions of individual isoforms of these families are mostly unclear under stress. Here, the structure characteristics of the three families in tomato were analyzed; moreover, as a first step toward understanding the functions of isoforms of these proteins under stress, the tissue expression pattern and stress response of these genes were also investigated. The results showed that four SPS genes, six SUS genes and nineteen INV genes were identified in tomato. The subfamily differentiation of SlSPS and SlSUS might have completed before the split of monocotyledons and dicotyledons. The conserved motifs were mostly consistent within each protein family/subfamily. These genes demonstrated differential expressions among family members and tissues, and in response to polyethylene glycerol, NaCl, H₂O₂, abscisic acid or salicylic acid treatment. Our results suggest that each isoform of these families may have different functions in different tissues and under environmental stimuli. SlSPS1, SlSPS3, SlSUS1, SlSUS3, SlSUS4, SlINVAN5 and SlINVAN7 demonstrated consistent expression responses and may be the major genes responding to exogenous stimuli.

Transcriptomic Profiling of Populus Roots Challenged with Fusarium Reveals Differential Responsive Patterns of Invertase and Invertase Inhibitor-Like Families within Carbohydrate Metabolism

Fusarium solani (Fs) is one of the notorious necrotrophic fungal pathogens that cause root rot and vascular wilt, accounting for the severe loss of Populus production worldwide. The plant-pathogen interactions have a strong molecular basis. As yet, the genomic information and transcriptomic profiling on the attempted infection of Fs remain unavailable in a woody model species, Populus trichocarpa. We used a full RNA-seq transcriptome to investigate the molecular interactions in the roots with a time-course infection at 0, 24, 48, and 72 h post-inoculation (hpi) of Fs. Concomitantly, the invertase and invertase inhibitor-like gene families were further analyzed, followed by the experimental evaluation of their expression patterns using quantitative PCR (qPCR) and enzyme assay. The magnitude profiles of the differentially expressed genes (DEGs) were observed at 72 hpi inoculation. Approximately 839 genes evidenced a reception and transduction of pathogen signals, a large transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related genes, and secondary and carbohydrate metabolism changes. Among these, a total of 63 critical genes that consistently appear during the entire interactions of plant-pathogen had substantially altered transcript abundance and potentially constituted suitable candidates as resistant genes in genetic engineering. These data provide essential clues in the developing new strategies of broadening resistance to Fs through transcriptional or translational modifications of the critical responsive genes within various analyzed categories (e.g., carbohydrate metabolism) in Populus.

The acid invertase gene family is involved in internode elongation in Phyllostachys heterocycla cv. pubescens

Acid invertases (INVs) play a pivotal role in both vegetative and reproductive growth of plants. However, their possible functions in fast-growing plants such as bamboo are largely unknown. Here, we report the molecular characterization of acid INVs in Phyllostachys heterocycla cv. pubescens, a fast-growing bamboo species commercially grown worldwide. Nine acid INVs (PhINVs), including seven cell wall INVs (PhCWINV1, PhCWINV2, PhCWINV3, PhCWINV4, PhCWINV5, PhCWINV6 and PhCWINV7) and two vacuolar INVs (PhVINV11 and PhVINV12) were isolated. Bioinformatic analyses demonstrated that they all share high amino acid identity with other INVs from different plant species and contain the motifs typically conserved in acid INV. Enzyme activity assays revealed a significantly higher INV activity in the fast-growing tissues, such as the elongating internodes of stems. Detailed quantitative reverse-transcription PCR analyses showed various expression patterns of PhINVs at different developmental stages of the elongating stems. With the exception of PhCWINV6, all PhINVs were ubiquitously expressed in a developmental-specific manner. Further studies in Arabidopsis exhibited that constitutive expression of PhCWINV1, PhCWINV4 or PhCWINV7 increased the biomass production of transgenic plants, as indicated by augmented plant heights and shoot dry weights than the wild-type plants. All these results suggest that acid INVs play a crucial role in the internode elongation of P. heterocycla cv. pubescens and would provide valuable information for the dissection of their exact biological functions in the fast growth of bamboo.

Systematic Analysis of Alkaline/Neutral Invertase Genes Reveals the Involvement of Smi-miR399 in Regulation of SmNINV3 and SmNINV4 in Salvia miltiorrhiza

Alkaline/neutral invertases (NINVs), which irreversibly catalyze the hydrolysis of sucrose into fructose and glucose, play crucial roles in carbohydrate metabolism and plant development. Comprehensive insights into NINV genes are lacking in Salvia miltiorrhiza, a well-known traditional Chinese medicinal (TCM) plant with significant medicinal and economic value. Through genome-wide prediction, nine putative SmNINV genes, termed SmNINV1-SmNINV9, were identified. Integrated analysis of gene structures, sequence features, conserved domains, conserved motifs and phylogenetic trees revealed the conservation and divergence of SmNINVs. The identified SmNINVs were differentially expressed in roots, stems, leaves, flowers, and different root tissues. They also responded to drought, salicylic acid, yeast extract, and methyl jasmonate treatments. More importantly, computational prediction and experimental validation showed that SmNINV3 and SmNINV4 were targets of Smi-miR399, a conserved miRNA previously shown to affect Pi uptake and translocation through the cleavage of PHOSPHATE2 (PHO2). Consistently, analysis of 43 NINV genes and 26 miR399 sequences from Arabidopsis thaliana, Populus trichocarpa, Manihot esculenta, and Solanum lycopersicum showed that various AtNINV, PtNINV, MeNINV, and SlNINV genes were regulated by miR399. It indicates that the miR399-NINV module exists widely in plants. Furthermore, Smi-miR399 also cleaved SmPHO2 transcripts in S. miltiorrhiza, suggesting the complexity of NINVs, PHO2, and miR399 networks.

Functional Characterization of Invertase Inhibitors PtC/VIF1 and 2 Revealed Their Involvements in the Defense Response to Fungal Pathogen in Populus trichocarpa

In higher plants, cell wall invertase (CWI) and vacuolar invertase (VI) were considered to be essential coordinators in carbohydrate partitioning, sink strength determination, and stress responses. An increasing body of evidence revealed that the tight regulation of CWI and VI substantially depends on the post-translational mechanisms, which were mediated by small proteinaceous inhibitors (C/VIFs, Inhibitor of β-Fructosidases). As yet, the extensive survey of the molecular basis and biochemical property of C/VIFs remains largely unknown in black cottonwood (Populus trichocarpa Torr. & A. Gray), a model species of woody plants. In the present work, we have initiated a systematic review of the genomic structures, phylogenies, cis-regulatory elements, and conserved motifs as well as the tissue-specific expression, resulting in the identification of 39 genes encoding C/VIF in poplar genome. We characterized two putative invertase inhibitors PtC/VIF1 and 2, showing predominant transcript levels in the roots and highly divergent responses to the selected stress cues including fusarium wilt, drought, ABA, wound, and senescence. In silico prediction of the signal peptide hinted us that they both likely had the apoplastic targets. Based on the experimental visualization via the transient and stable transformation assays, we confirmed that PtC/VIF1 and 2 indeed secreted to the extracellular compartments. Further validation of their recombinant enzymes revealed that they displayed the potent inhibitory affinities on the extracted CWI, supporting the patterns that act as the typical apoplastic invertase inhibitors. To our knowledge, it is the first report on molecular characterization of the functional C/VIF proteins in poplar. Our results indicate that PtC/VIF1 and 2 may exert essential roles in defense- and stress-related responses. Moreover, novel findings of the up- and downregulated C/VIF genes and functional enzyme activities enable us to further unravel the molecular mechanisms in the promotion of woody plant performance and adapted-biotic stress, underlying the homeostatic control of sugar in the apoplast.

Genome-Wide Analysis, Expression Profile, and Characterization of the Acid Invertase Gene Family in Pepper

Catalytic decomposition of sucrose by acid invertases (AINVs) under acidic conditions plays an important role in the development of sink organs in plants. To reveal the function of AINVs in the development of pepper fruits, nine AINV genes of pepper were identified. Protein sequencing and phylogenetic analysis revealed that the CaAINV family may be divided into cell wall invertases (CaCWINV1⁻7) and vacuolar invertases (CaVINV1⁻2). CaAINVs contain conserved regions and protein structures typical of the AINVs in other plants. Gene expression profiling indicated that CaCWINV2 and CaVINV1 were highly expressed in reproductive organs but differed in expression pattern. CaCWINV2 was mainly expressed in buds and flowers, while CaVINV1 was expressed in developmental stages, such as the post-breaker stage. Furthermore, invertase activity of CaCWINV2 and CaVINV1 was identified via functional complementation in an invertase-deficient yeast. Optimum pH for CaCWINV2 and CaVINV1 was found to be 4.0 and 4.5, respectively. Gene expression and enzymatic activity of CaCWINV2 and CaVINV1 indicate that these AINV enzymes may be pivotal for sucrose hydrolysis in the reproductive organs of pepper.

Sucrose transport and carbon fluxes during wood formation

Wood biosynthesis defines the chemical and structural properties of wood. The metabolic pathways that produce the precursors of wood cell wall polymers have a central role in defining wood properties. To make rational design of wood properties feasible, we need not only to understand the cell wall biosynthetic machinery, but also how sucrose transport and metabolism in developing wood connect to cell wall biosynthesis and how they respond to genetic and environmental cues. Here, we review the current understanding of the sucrose transport and primary metabolism pathways leading to the precursors of cell wall biosynthesis in woody plant tissues. We present both old, persistent questions and new emerging themes with a focus on wood formation in trees and draw upon evidence from the xylem tissues of herbaceous plants when it is relevant.

Genome-Wide Survey of Invertase Encoding Genes and Functional Characterization of an Extracellular Fungal Pathogen-Responsive Invertase in Glycine max

Invertases are essential enzymes that irreversibly catalyze the cleavage of sucrose into glucose and fructose. Cell wall invertase (CWI) and vacuolar invertase (VI) are glycosylated proteins and exert fundamental roles in plant growth as well as in response to environmental cues. As yet, comprehensive insight into invertase encoding genes are lacking in Glycine max. In the present study, the systematic survey of gene structures, coding regions, regulatory elements, conserved motifs, and phylogenies resulted in the identification of thirty⁻two putative invertase genes in soybean genome. Concomitantly, impacts on gene expression, enzyme activities, proteins, and soluble sugar accumulation were explored in specific tissues upon stress perturbation. In combination with the observation of subcellular compartmentation of the fluorescent fusion protein that indeed exported to apoplast, heterologous expression, and purification in using Pichia pastoris system revealed that GmCWI4 was a typical extracellular invertase. We postulated that GmCWI4 may play regulatory roles and be involved in pathogenic fungi defense. The experimental evaluation of physiological significance via phenotypic analysis of mutants under stress exposure has been initiated. Moreover, our paper provides theoretical basis for elucidating molecular mechanisms of invertase in association with inhibitors underlying the stress regime, and will contribute to the improvement of plant performance to a diverse range of stressors.

Cell wall invertase activity regulates the expression of the transfer cell-specific transcription factor ZmMRP-1

Studies in cell wall bound invertase mutants indicate that the promoter of the transfer cell-specific transcription factor, ZmMRP - 1 , is modulated by the carbohydrate balance. Transfer cells are highly specialized plant cells located at the surfaces that need to support an intensive exchange of nutrients, such as the entrance of fruits, seeds and nodules or the young branching points along the stem. ZmMRP-1 is a one-domain MYB-related transcription factor specifically expressed at the transfer cell layer of the maize endosperm. Previous studies demonstrated that this factor regulates the expression of a large number of transfer cell-specific genes, and suggested that ZmMRP-1 is a key regulator of the differentiation of this tissue. The expression of this gene is largely dominated by positional cues, but within the ZmMRP-1 expressing cells the promoter appears to be modulated by sugars. Here we have investigated in vivo this modulation. Using maize and Arabidopsis mutants for cell wall invertase genes, we found that the absence of cell wall invertase activity is a major inductive signal of the ZmMRP-1 expression.

Genome-Wide Identification, Expression, and Functional Analysis of the Alkaline/Neutral Invertase Gene Family in Pepper

Alkaline/neutral invertase (NINV) proteins irreversibly cleave sucrose into fructose and glucose, and play important roles in carbohydrate metabolism and plant development. To investigate the role of NINVs in the development of pepper fruits, seven NINV genes (CaNINV1-7) were identified. Phylogenetic analysis revealed that the CaNINV family could be divided into α and β groups. CaNINV1-6 had typical conserved regions and similar protein structures to the NINVs of other plants, while CaNINV7 lacked amino acid sequences at the C-terminus and N-terminus ends. An expression analysis of the CaNINV genes in different tissues demonstrated that CaNINV5 is the dominant NINV in all the examined tissues (root, stem, leaf, bud, flower, and developmental pepper fruits stage). Notably, the expression of CaNINV5 was found to gradually increase at the pre-breaker stages, followed by a decrease at the breaker stages, while it maintained a low level at the post-breaker stages. Furthermore, the invertase activity of CaNINV5 was identified by functional complementation of the invertase-deficient yeast strain SEY2102, and the optimum pH of CaNINV5 was found to be ~7.5. The gene expression and enzymatic activity of CaNINV5 suggest that it might be the main NINV enzyme for hydrolysis of sucrose during pepper fruit development.

Aberrant seed development in Litchi chinensis is associated with the impaired expression of cell wall invertase genes

Cell wall invertase (CWIN) are known to play important roles in seed development. However, most reports to date have focused on a single gene family member, and have mainly investigated CWIN functions during the filling stage of seed development. In this study, we found significant lower levels of CWIN protein and activity associated with seed abortion in the Litchi chinensis cultivar "Nuomici." We identified five litchi CWIN genes and observed that the expression of LcCWIN5 was limited to the flower tissues and decreased sharply with fruit development. Silencing of LcCWIN5 expression before 28 DAA (cell division stage) resulted in perturbed liquid endosperm development, smaller seeds, and higher seed abortion rate, while silencing after 28 DAA (filling stage) had no effect on seed development. In contrast, LcCWIN2 was mostly expressed in the funicle and seed coat, and increased with fruit development. Decreased LcCWIN2 expression and CWIN activity during early seed filling coincided with smaller seeds in the cultivar "Feizixiao." Silencing of LcCWIN2 caused a reduction in the seed size without inducing seed abortion. We propose that CWIN activity in seed maternal tissues during cell division stage is likely due to LcCWIN5 expression, which regulates early seed development. On the other hand, CWIN activity during the filling stage is due to the expression of LcCWIN2, which may promote carbon import by creating a sucrose gradient. Comparable LcCWIN5 expression, but much lower CWIN activity, detected in the funicle of "Nuomici" is consistent with post-translational regulation.

The riddle of mitochondrial alkaline/neutral invertases: A novel Arabidopsis isoform mainly present in reproductive tissues and involved in root ROS production

Alkaline/neutral invertases (A/N-Inv), glucosidases that irreversibly hydrolyze sucrose into glucose and fructose, play significant roles in plant growth, development, and stress adaptation. They occur as multiple isoforms located in the cytosol or organelles. In Arabidopsis thaliana, two mitochondrial A/N-Inv genes (A/N-InvA and A/N-InvC) have already been investigated. In this study, we functionally characterized A/N-InvH, a third Arabidopsis gene coding for a mitochondrial-targeted protein. The phenotypic analysis of knockout mutant plants (invh) showed a severely reduced shoot growth, while root development was not affected. The emergence of the first floral bud and the opening of the first flower were the most affected stages, presenting a significant delay. A/N-InvH transcription is markedly active in reproductive tissues. It is also expressed in the elongation and apical meristem root zones. Our results show that A/N-InvH expression is not evident in photosynthetic tissues, despite being of relevance in developmental processes and mitochondrial functional status. NaCl and mannitol treatments increased A/N-InvH expression twofold in the columella root cap. Moreover, the absence of A/N-InvH prevented ROS formation, not only in invh roots of salt- and ABA-treated seedlings but also in invh control roots. We hypothesize that this isoform may take part in the ROS/sugar (sucrose or its hydrolysis products) signaling pathway network, involved in reproductive tissue development, cell elongation, and abiotic stress responses.

Molecular cloning, structure, phylogeny and expression analysis of the invertase gene family in sugarcane

BACKGROUND

Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism.

RESULTS

In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane. A comprehensive analysis of the invertase gene family was carried out, including gene structures, phylogenetic relationships, functional domains, conserved motifs of proteins. The results revealed that the 14 invertase members from sugarcane could be clustered into three subfamilies, including 6 neutral/alkaline invertases (ShN/AINVs), and 8 acid invertases (ShAINVs). Faster divergence occurred in acid INVs than in neutral/alkaline INVs after the split of sugarcane and sorghum. At least a one-time gene duplication event was observed to have occurred in the four groups of acid INVs, whereas ShN/AINV1 and ShN/AINV2 in the β8 lineage were revealed to be the most recently duplicated genes among their paralogous genes in the β group of N/AINVs. Furthermore, comprehensive expression analysis of these genes was performed in sugarcane seedlings subjected to five abiotic stresses (drought, low temperature, glucose, fructose, and sucrose) using Quantitative Real-time PCR. The results suggested a functional divergence of INVs and their potential role in response to the five different treatments. Enzymatic activity in sugarcane seedlings was detected under five abiotic stresses treatments, and showed that the activities of all INVs were significantly inhibited in response to five different abiotic stresses, and that the neutral/alkaline INVs played a more prominent role in abiotic stresses than the acid INVs.

CONCLUSIONS

In this study, we determined the INV gene family members of sugarcane by PCR cloning using sorghum as a reference, providing the first study of the INV gene family in sugarcane. Combining existing INV gene data from 7 plants with a comparative approach including a series of comprehensive analyses to isolate and identify INV gene family members proved to be highly successful. Moreover, the expression levels of INV genes and the variation of enzymatic activities associated with drought, low temperature, glucose, fructose, and sucrose are reported in sugarcane for the first time. The results offered useful foundation and framework for future research for understanding the physiological roles of INVs for sucrose accumulation in sugarcane.

TAI vacuolar invertase orthologs: the interspecific variability in tomato plants (Solanum section Lycopersicon)

Understanding the genetic mechanisms underlying carbohydrate metabolism can promote the development of biotechnological advances in fruit plants. The flesh tomato fruit represents an ideal system for examining the role of sucrose cleavage enzymes in fruit development, and wild tomato species differing in storage sugars serve as an excellent research material for this purpose. Plant vacuolar invertase is a key enzyme of sucrose metabolism in the sink organs. In the present study, we identified complete gene sequences encoding the TAI vacuolar invertase in 11 wild and one cultivated tomato accessions of the Solanum section Lycopersicon. The average level of interspecific polymorphism in TAI genes was 8.58%; however, in the green-fruited tomatoes, the TAI genes contained 100 times more SNPs than those in the red-fruited accessions. The TAI proteins demonstrated 8% variability, whereas the red-fruited species had none. A TAI-based phylogenetic tree revealed two main clusters containing self-compatible and self-incompatible species, which concurs with the previous crossability-based division and demonstrates that the TAI genes reflect the evolutionary relationships between the red- and green-fruited tomatoes. Furthermore, we detected differential expression patterns of the TAI genes in the fruits of wild and cultivated tomatoes, which corresponded to sugar composition. The polymorphism analysis of the TAI acid invertases of Solanum section Lycopersicon species will contribute to the understanding of the genetic potential of TAI genes to impact tomato breeding through genetic engineering of the carbohydrate composition in the fruit.

Cytosolic invertase contributes to the supply of substrate for cellulose biosynthesis in developing wood

Carbon for cellulose biosynthesis is derived from sucrose. Cellulose is synthesized from uridine 5'-diphosphoglucose (UDP-glucose), but the enzyme(s) responsible for the initial sucrose cleavage and the source of UDP-glucose for cellulose biosynthesis in developing wood have not been defined. We investigated the role of CYTOSOLIC INVERTASEs (CINs) during wood formation in hybrid aspen (Populus tremula × tremuloides) and characterized transgenic lines with reduced CIN activity during secondary cell wall biosynthesis. Suppression of CIN activity by 38-55% led to a 9-13% reduction in crystalline cellulose. The changes in cellulose were reflected in reduced diameter of acid-insoluble cellulose microfibrils and increased glucose release from wood upon enzymatic digestion of cellulose. Reduced CIN activity decreased the amount of the cellulose biosynthesis precursor UDP-glucose in developing wood, pointing to the likely cause of the cellulose phenotype. The findings suggest that CIN activity has an important role in the cellulose biosynthesis of trees, and indicate that cellulose biosynthesis in wood relies on a quantifiable UDP-glucose pool. The results also introduce a concept of altering cellulose microfibril properties by modifying substrate supply to cellulose biosynthesis.

Identification of the invertase gene family (INVs) in tea plant and their expression analysis under abiotic stress

Fourteen invertase genes were identified in the tea plant, all of which were shown to participate in regulating growth and development, as well as in responding to various abiotic stresses. Invertase (INV) can hydrolyze sucrose into glucose and fructose, which plays a principal role in regulating plant growth and development as well as the plants response to various abiotic and biotic stresses. However, currently, there is a lack of reported information, regarding the roles of INVs in either tea plant development or in the tea plants response to various stresses. In this study, 14 INV genes were identified from the transcriptome data of the tea plant (Camellia sinensis (L.) O. Kuntze), and named CsINV1-5 and CsINV7-15. Based on the results of a Blastx search and phylogenetic analysis, the CsINV genes could be clustered into 6 acid invertase (AI) genes and 8 alkaline/neutral invertase (A/N-Inv) genes. The results of tissue-specific expression analysis showed that the transcripts of all the identified CsINV genes are detectable in various tissues. Under various abiotic stress conditions, the expression patterns of the 14 CsINV genes were diverse in both the leaves and roots, and some of them were shown to be significantly expressed. Overall, we hypothesize that the identified CsINV genes all participate in regulating growth and development in the tea plant, and most likely through different signaling pathways that regulate the carbohydrate allocation and the ratio of hexose and sucrose for improving the resistance of the leaves and the roots of the tea plant to various abiotic stresses.

Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose

Background

Proteins in the Glycoside Hydrolase family 32 (GH32) are carbohydrate-active enzymes known as invertases that hydrolyse the glycosidic bonds of complex saccharides. Fungi rely on these enzymes to gain access to and utilize plant-derived sucrose. In fungi, GH32 invertase genes are found in higher copy numbers in the genomes of pathogens when compared to closely related saprophytes, suggesting an association between invertases and ecological strategy. The aim of this study was to investigate the distribution and evolution of GH32 invertases in the Ceratocystidaceae using a comparative genomics approach. This fungal family provides an interesting model to study the evolution of these genes, because it includes economically important pathogenic species such as Ceratocystis fimbriata, C. manginecans and C. albifundus, as well as saprophytic species such as Huntiella moniliformis, H. omanensis and H. savannae.

Results

The publicly available Ceratocystidaceae genome sequences, as well as the H. savannae genome sequenced here, allowed for the identification of novel GH32-like sequences. The de novo assembly of the H. savannae draft genome consisted of 28.54 megabases that coded for 7 687 putative genes of which one represented a GH32 family member. The number of GH32 gene family members appeared to be related to the ecological adaptations of these fungi. The pathogenic Ceratocystis species all contained two GH32 family genes (a putative cell wall and a putative vacuolar invertase), while the saprophytic Huntiella species had only one of these genes (a putative cell wall invertase). Further analysis showed that the evolution of the GH32 gene family in the Ceratocystidaceae involved transposable element-based retro-transposition and translocation. As an example, the activity of a Fot5-like element likely facilitated the assembly of the genomic regions harbouring the GH32 family genes in Ceratocystis.

Conclusions

This study provides insight into the evolutionary history of the GH32 gene family in Ceratocystidaceae. Our findings suggest that transposable elements shaped the evolution of the GH32 gene family, which in turn determines the sucrolytic activities and related ecological strategies of the Ceratocystidaceae species that harbour them. The study also provides insights into the role of carbohydrate-active enzymes in plant-fungal interactions and adds to our understanding of the evolution of these enzymes and their role in the life style of these fungi.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0550-7) contains supplementary material, which is available to authorized users.

Genome-Wide Identification of the Invertase Gene Family in Populus

Invertase plays a crucial role in carbohydrate partitioning and plant development as it catalyses the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families: acid invertases, which are targeted to the cell wall and vacuole; and neutral/alkaline invertases, which function in the cytosol. In this study, 5 cell wall invertase genes (PtCWINV1-5), 3 vacuolar invertase genes (PtVINV1-3) and 16 neutral/alkaline invertase genes (PtNINV1-16) were identified in the Populus genome and found to be distributed on 14 chromosomes. A comprehensive analysis of poplar invertase genes was performed, including structures, chromosome location, phylogeny, evolutionary pattern and expression profiles. Phylogenetic analysis indicated that the two sub-families were both divided into two clades. Segmental duplication is contributed to neutral/alkaline sub-family expansion. Furthermore, the Populus invertase genes displayed differential expression in roots, stems, leaves, leaf buds and in response to salt/cold stress and pathogen infection. In addition, the analysis of enzyme activity and sugar content revealed that invertase genes play key roles in the sucrose metabolism of various tissues and organs in poplar. This work lays the foundation for future functional analysis of the invertase genes in Populus and other woody perennials.

HbNIN2, a cytosolic alkaline/neutral-invertase, is responsible for sucrose catabolism in rubber-producing laticifers of Hevea brasiliensis (para rubber tree)

In Hevea brasiliensis, an alkaline/neutral invertase (A/N-Inv) is responsible for sucrose catabolism in latex (essentially the cytoplasm of rubber-producing laticifers, the source of natural rubber) and implicated in rubber yield. However, neither the gene encoding this enzyme nor its molecular and biochemical properties have been well documented. Three Hevea A/N-Inv genes, namely HbNIN1, 2 and 3, were first cloned and characterized in planta and in Escherichia coli. Cellular localizations of HbNIN2 mRNA and protein were probed. From latex, active A/N-Inv proteins were purified, identified, and explored for enzymatic properties. HbNIN2 was identified as the major A/N-Inv gene functioning in latex based on its functionality in E. coli, its latex-predominant expression, the conspicuous localization of its mRNA and protein in the laticifers, and its expressional correlation with rubber yield. An active A/N-Inv protein was partially purified from latex, and determined as HbNIN2. The enhancement of HbNIN2 enzymatic activity by pyridoxal is peculiar to A/N-Invs in other plants. We conclude that HbNIN2, a cytosolic A/N-Inv, is responsible for sucrose catabolism in rubber laticifers. The results contribute to the studies of sucrose catabolism in plants as a whole and natural rubber synthesis in particular.

Expression divergence of cellulose synthase (CesA) genes after a recent whole genome duplication event in Populus

Secondary cell wall-associated CesA genes in Populus have undergone a functional differentiation in expression pattern that may be attributable to evolutionary alteration of regulatory modules. Gene duplication is an important mechanism for functional divergence of genes. Secondary cell wall-associated cellulose synthase genes (CesA4, CesA7 and CesA8) are duplicated in Populus plants due to a recent whole genome duplication event. Here, we demonstrate that duplicate CesA genes show tissue-dependent expression divergence in Populus plants. Real-time PCR analysis of Populus CesA genes suggested that Pt × tCesA8-B was more highly expressed than Pt × tCesA8-A in phloem and secondary xylem tissue of mature stem. Histochemical and histological analyses of transformants expressing a GFP-GUS fusion gene driven by Populus CesA promoters revealed that the duplicate CesA genes showed different expression patterns in phloem fibers, secondary xylem, root cap and leaf trichomes. We predicted putative cis-regulatory motifs that regulate expression of secondary cell wall-associated CesA genes, and identified 19 motifs that are highly conserved in the CesA gene family of eudicotyledonous plants. Furthermore, a transient transactivation assay identified candidate transcription factors that affect levels and patterns of expression of Populus CesA genes. The present study reveals that secondary cell wall-associated CesA genes in Populus have undergone a functional differentiation in expression pattern that may be attributable to evolutionary alteration of regulatory modules.

Cloning, 3D modeling and expression analysis of three vacuolar invertase genes from cassava (Manihot Esculenta Crantz)

Vacuolar invertase is one of the key enzymes in sucrose metabolism that irreversibly catalyzes the hydrolysis of sucrose to glucose and fructose in plants. In this research, three vacuolar invertase genes, named MeVINV1-3, and with 653, 660 and 639 amino acids, respectively, were cloned from cassava. The motifs of NDPNG (β-fructosidase motif), RDP and WECVD, which are conserved and essential for catalytic activity in the vacuolar invertase family, were found in MeVINV1 and MeVINV2. Meanwhile, in MeVINV3, instead of NDPNG we found the motif NGPDG, in which the three amino acids GPD are different from those in other vacuolar invertases (DPN) that might result in MeVINV3 being an inactivated protein. The N-terminal leader sequence of MeVINVs contains a signal anchor, which is associated with the sorting of vacuolar invertase to vacuole. The overall predicted 3D structure of the MeVINVs consists of a five bladed β-propeller module at N-terminus domain, and forms a β-sandwich module at the C-terminus domain. The active site of the protein is situated in the β-propeller module. MeVINVs are classified in two subfamilies, α and β groups, in which α group members of MeVINV1 and 2 are highly expressed in reproductive organs and tuber roots (considered as sink organs), while β group members of MeVINV3 are highly expressed in leaves (source organs). All MeVINVs are highly expressed in leaves, while only MeVINV1 and 2 are highly expressed in tubers at cassava tuber maturity stage. Thus, MeVINV1 and 2 play an important role in sucrose unloading and starch accumulation, as well in buffering the pools of sucrose, hexoses and sugar phosphates in leaves, specifically at later stages of plant development.

Genome-wide identification, 3D modeling, expression and enzymatic activity analysis of cell wall invertase gene family from cassava (Manihot esculenta Crantz)

The cell wall invertases play a crucial role on the sucrose metabolism in plant source and sink organs. In this research, six cell wall invertase genes (MeCWINV1-6) were cloned from cassava. All the MeCWINVs contain a putative signal peptide with a predicted extracellular location. The overall predicted structures of the MeCWINV1-6 are similar to AtcwINV1. Their N-terminus domain forms a β-propeller module and three conserved sequence domains (NDPNG, RDP and WECP(V)D), in which the catalytic residues are situated in these domains; while the C-terminus domain consists of a β-sandwich module. The predicted structure of Pro residue from the WECPD (MeCWINV1, 2, 5, and 6), and Val residue from the WECVD (MeCWINV3 and 4) are different. The activity of MeCWINV1 and 3 were higher than other MeCWINVs in leaves and tubers, which suggested that sucrose was mainly catalyzed by the MeCWINV1 and 3 in the apoplastic space of cassava source and sink organs. The transcriptional levels of all the MeCWINVs and their enzymatic activity were lower in tubers than in leaves at all the stages during the cassava tuber development. It suggested that the major role of the MeCWINVs was on the regulation of carbon exportation from source leaves, and the ratio of sucrose to hexose in the apoplasts; the role of these enzymes on the sucrose unloading to tuber was weaker.

Steady sucrose degradation is a prerequisite for tolerance to root hypoxia

We investigated the role of glycolysis and sucrolysis in the difference in tolerance to root hypoxia between two Myrtaceae tree species, Melaleuca cajuputi (which shows superior tolerance to root hypoxia) and Eucalyptus camaldulensis (which does not). Analysis of the adenylate energy charge (AEC) in roots subjected to a 4-day hypoxic treatment (HT) in hydroponic culture revealed that the interspecies difference in tolerance corresponds to the ability to maintain energy status under root hypoxia: AEC was reduced by HT in E. camaldulensis, but not in M. cajuputi. The energy status in HT roots of E. camaldulensis was restored by feeding of glucose (Glc) but not sucrose (Suc). These data provide evidence that low substrate availability for glycolysis resulting from an impairment of sucrolysis suppresses ATP production under hypoxic conditions in this species. Measurements of the rates of O2 consumption and CO2 production in roots indicated that E. camaldulensis, but not M. cajuputi, failed to activate fermentation in HT roots. These results cannot be attributed to enzymatic dysfunction, because no inhibition of main glycolytic and fermentative enzymes was observed in both species, and Glc feeding had a beneficial effect on AEC of HT roots of E. camaldulensis. The impairment of sucrolysis was demonstrated by inhibited soluble acid invertase activity in HT roots of E. camaldulensis. In contrast, there was no inhibition in all sucrolytic enzymes tested in HT roots of M. cajuputi, suggesting that steady Suc degradation is essential for maintaining high energy status under root hypoxia. We conclude that root sucrolysis is one of the essential factors that determines the extent of tolerance to root hypoxia.

Metabolic and enzymatic changes associated with carbon mobilization, utilization and replenishment triggered in grain amaranth (Amaranthus cruentus) in response to partial defoliation by mechanical injury or insect herbivory

BACKGROUND

Amaranthus cruentus and A. hypochondriacus are crop plants grown for grain production in subtropical countries. Recently, the generation of large-scale transcriptomic data opened the possibility to study representative genes of primary metabolism to gain a better understanding of the biochemical mechanisms underlying tolerance to defoliation in these species. A multi-level approach was followed involving gene expression analysis, enzyme activity and metabolite measurements.

RESULTS

Defoliation by insect herbivory (HD) or mechanical damage (MD) led to a rapid and transient reduction of non-structural carbohydrates (NSC) in all tissues examined. This correlated with a short-term induction of foliar sucrolytic activity, differential gene expression of a vacuolar invertase and its inhibitor, and induction of a sucrose transporter gene. Leaf starch in defoliated plants correlated negatively with amylolytic activity and expression of a β-amylase-1 gene and positively with a soluble starch synthase gene. Fatty-acid accumulation in roots coincided with a high expression of a phosphoenolpyruvate/phosphate transporter gene. In all tissues there was a long-term replenishment of most metabolite pools, which allowed damaged plants to maintain unaltered growth and grain yield. Promoter analysis of ADP-glucose pyrophosphorylase and vacuolar invertase genes indicated the presence of cis-regulatory elements that supported their responsiveness to defoliation. HD and MD had differential effects on transcripts, enzyme activities and metabolites. However, the correlation between transcript abundance and enzymatic activities was very limited. A better correlation was found between enzymes, metabolite levels and growth and reproductive parameters.

CONCLUSIONS

It is concluded that a rapid reduction of NSC reserves in leaves, stems and roots followed by their long-term recovery underlies tolerance to defoliation in grain amaranth. This requires the coordinate action of genes/enzymes that are differentially affected by the way leaf damage is performed. Defoliation tolerance in grain is a complex process that can't be fully explained at the transcriptomic level only.

Global analysis of gene expression profiles in developing physic nut (Jatropha curcas L.) seeds

BACKGROUND

Physic nut (Jatropha curcas L.) is an oilseed plant species with high potential utility as a biofuel. Furthermore, following recent sequencing of its genome and the availability of expressed sequence tag (EST) libraries, it is a valuable model plant for studying carbon assimilation in endosperms of oilseed plants. There have been several transcriptomic analyses of developing physic nut seeds using ESTs, but they have provided limited information on the accumulation of stored resources in the seeds.

METHODOLOGY/PRINCIPAL FINDINGS

We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of developing physic nut seeds 14, 19, 25, 29, 35, 41, and 45 days after pollination (DAP). The acquired profiles reveal the key genes, and their expression timeframes, involved in major metabolic processes including: carbon flow, starch metabolism, and synthesis of storage lipids and proteins in the developing seeds. The main period of storage reserves synthesis in the seeds appears to be 29-41 DAP, and the fatty acid composition of the developing seeds is consistent with relative expression levels of different isoforms of acyl-ACP thioesterase and fatty acid desaturase genes. Several transcription factor genes whose expression coincides with storage reserve deposition correspond to those known to regulate the process in Arabidopsis.

CONCLUSIONS/SIGNIFICANCE

The results will facilitate searches for genes that influence de novo lipid synthesis, accumulation and their regulatory networks in developing physic nut seeds, and other oil seeds. Thus, they will be helpful in attempts to modify these plants for efficient biofuel production.

Molecular and functional characterization of novel fructosyltransferases and invertases from Agave tequilana

Fructans are the main storage polysaccharides found in Agave species. The synthesis of these complex carbohydrates relies on the activities of specific fructosyltransferase enzymes closely related to the hydrolytic invertases. Analysis of Agave tequilana transcriptome data led to the identification of ESTs encoding putative fructosyltransferases and invertases. Based on sequence alignments and structure/function relationships, two different genes were predicted to encode 1-SST and 6G-FFT type fructosyltransferases, in addition, 4 genes encoding putative cell wall invertases and 4 genes encoding putative vacuolar invertases were also identified. Probable functions for each gene, were assigned based on conserved amino acid sequences and confirmed for 2 fructosyltransferases and one invertase by analyzing the enzymatic activity of recombinant Agave protein s expressed and purified from Pichia pastoris. The genome organization of the fructosyltransferase/invertase genes, for which the corresponding cDNA contained the complete open reading frame, was found to be well conserved since all genes were shown to carry a 9 bp mini-exon and all showed a similar structure of 8 exons/7 introns with the exception of a cell wall invertase gene which has 7 exons and 6 introns. Fructosyltransferase genes were strongly expressed in the storage organs of the plants, especially in vegetative stages of development and to lower levels in photosynthetic tissues, in contrast to the invertase genes where higher levels of expression were observed in leaf tissues and in mature plants.

Systematic analysis of potato acid invertase genes reveals that a cold-responsive member, StvacINV1, regulates cold-induced sweetening of tubers

Acid invertase is believed to play a regulatory role during plant developmental processes and to respond to environmental stimuli. The expression profiles of the entire acid invertase family are not yet available for potato. By searching existing databases, it was determined that there are at least six acid invertase genes in potato, including four cell-wall invertase genes and two vacuolar invertase genes. They were subjected to comparative expression profiling in various organs of potato plants and in stored tubers to exploit their potential functions. The results revealed that each gene exhibited a unique expression pattern, which differed in transcript abundance or showed organ-specific features, pointing to the possible involvement of individual genes in plant development. The vacuolar invertase gene StvacINV1 had the highest expression level among three genes detected in the potato tubers. Further storage experiments showed that StvacINV1 was strongly induced by low temperatures, which is consistent with glucose accumulation in cold-stored tubers. Suppression of StvacINV1 by the antisense transformation in potato confirmed that lower StvacINV1 transcript abundance in transgenic tubers is related to lower reducing sugar content and lighter chip color in comparison with the wild type. The evidence strongly suggests that StvacINV1 is a gene involved in regulation of cold-induced sweetening of potato tubers. This provides an avenue for studying the mechanism involved in the regulation of the cold-induced sweetening trait and for agronomic enhancement.

Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of pseudo-response regulators

Background

Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages.

Results

In the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events.

Conclusions

Based on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

BACKGROUND

Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection.

RESULTS

Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process.

CONCLUSION

How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Photosynthetic and respiratory changes in leaves of poplar elicited by rust infection

Poplars are challenged by a wide range of pathogens during their lifespan, and have an innate immunity system that activates defence responses to restrict pathogen growth. Large-scale expression studies of poplar-rust interactions have shown concerted transcriptional changes during defence responses, as in other plant pathosystems. Detailed analysis of expression profiles of metabolic pathways in these studies indicates that photosynthesis and respiration are also important components of the poplar response to rust infection. This is consistent with our current understanding of plant pathogen interactions as defence responses impose substantive demands for resources and energy that are met by reorganization of primary metabolism. This review applies the results of poplar transcriptome analyses to current research describing how plants divert energy from plant primary metabolism for resistance mechanisms.

Glycosylation-mediated phenylpropanoid partitioning in Populus tremuloides cell cultures

BACKGROUND

Phenylpropanoid-derived phenolic glycosides (PGs) and condensed tannins (CTs) comprise large, multi-purpose non-structural carbon sinks in Populus. A negative correlation between PG and CT concentrations has been observed in several studies. However, the molecular mechanism underlying the relationship is not known.

RESULTS

Populus cell cultures produce CTs but not PGs under normal conditions. Feeding salicyl alcohol resulted in accumulation of salicins, the simplest PG, in the cells, but not higher-order PGs. Salicin accrual reflected the stimulation of a glycosylation response which altered a number of metabolic activities. We utilized this suspension cell feeding system as a model for analyzing the possible role of glycosylation in regulating the metabolic competition between PG formation, CT synthesis and growth. Cells accumulated salicins in a dose-dependent manner following salicyl alcohol feeding. Higher feeding levels led to a decrease in cellular CT concentrations (at 5 or 10 mM), and a negative effect on cell growth (at 10 mM). The competition between salicin and CT formation was reciprocal, and depended on the metabolic status of the cells. We analyzed gene expression changes between controls and cells fed with 5 mM salicyl alcohol for 48 hr, a time point when salicin accumulation was near maximum and CT synthesis was reduced, with no effect on growth. Several stress-responsive genes were up-regulated, suggestive of a general stress response in the fed cells. Salicyl alcohol feeding also induced expression of genes associated with sucrose catabolism, glycolysis and the Krebs cycle. Transcript levels of phenylalanine ammonia lyase and most of the flavonoid pathway genes were reduced, consistent with down-regulated CT synthesis.

CONCLUSIONS

Exogenous salicyl alcohol was readily glycosylated in Populus cell cultures, a process that altered sugar utilization and phenolic partitioning in the cells. Using this system, we identified candidate genes for glycosyltransferases that may mediate the glycosylation, and for transporters that mediate the subcellular compartmentalization of sugars and phenolic glycosides. The suspension cells appear to represent a facile system for dissecting the regulation of phenolic carbon partitioning, and in turn, its effects on growth in Populus.

A cytosolic invertase is required for normal growth and cell development in the model legume, Lotus japonicus

Neutral/alkaline invertases are a subgroup, confined to plants and cyanobacteria, of a diverse family of enzymes. A family of seven closely-related genes, LjINV1-LjINV7, is described here and their expression in the model legume, Lotus japonicus, is examined. LjINV1 previously identified as encoding a nodule-enhanced isoform is the predominant isoform present in all parts of the plant. Mutants for two isoforms, LjINV1 and LjINV2, were isolated using TILLING. A premature stop codon allele of LjINV2 had no effect on enzyme activity nor did it show a visible phenotype. For LjINV1, premature stop codon and missense mutations were obtained and the phenotype of the mutants examined. Recovery of homozygous mutants was problematic, but their phenotype showed a severe reduction in growth of the root and the shoot, a change in cellular development, and impaired flowering. The cellular organization of both roots and leaves was altered; leaves were smaller and thicker with extra layers of cells and roots showed an extended and broader zone of cell division. Moreover, anthers contained no pollen. Both heterozygotes and homozygous mutants showed decreased amounts of enzyme activity in nodules and shoot tips. Shoot tips also contained up to a 9-fold increased level of sucrose. However, mutants were capable of forming functional root nodules. LjINV1 is therefore crucial to whole plant development, but is clearly not essential for nodule formation or function.

Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2

LHY/CCA1 genes play a key role in the plant circadian clock system and are highly conserved among plant species. However, the evolutionary process of the LHY/CCA1 gene family remains unclear in angiosperms. To obtain details of the phylogeny of these genes, this study characterized LHY/CCA1 genes in a model woody plant,Populus tree.The evolutionary process of angiosperm LHY/CCA1 genes was elucidated using three approaches: comparison of exon–intron structures, reconstruction of phylogenetic trees and examination of syntenic relationships. In addition, the molecular evolutionary rates and the expression patterns of Populus LHYs were analyzed.Gene duplication events of Populus LHYs and Arabidopsis LHY/CCA1 had occurred independently by different chromosomal duplication events arising in each evolutionary lineage. Populus LHYs were under purifying selection by estimating substitution rates of these genes. Further, Populus LHYs conserved diurnal expressions in leaves and stems but the transcripts of LHY2 were more abundant than those of LHY1 in Populus plants.This study uncovered phylogenetic relationships of the LHY/CCA1 gene family in angiosperms. In addition, the transcript abundance and the evolutionary differences between Populus LHY1 and LHY2 imply that Populus LHY2, rather than LHY1, may have a major role in the Populus clock system.

Neutral invertases in grapevine and comparative analysis with Arabidopsis, poplar and rice

Neutral invertases (NIs, EC 3.2.1.26) cleave sucrose to glucose and fructose. They are encoded by a small gene family of 9 members in the Arabidopsis genome, 8 in rice, 16 in poplar and 9 in Vitis vinifera (L.). The grapevine NIs were identified in the 8.4X genome assembly of the quasi-homozygous line PN40024. In addition, alleles of three NIs were sequenced in the heterozygous cultivar 'Cabernet Sauvignon'. Analyses of sequence variation between alleles, homoeologous and paralogous copies in grapevine and their orthologues in Arabidopsis, poplar and rice are provided. In grapevine, NIs were classified into four alpha NIs and five beta NIs and subsequently grouped into hierarchical clades using a combination of evidence including amino acid identity, exon/intron structure, rate of synonymous substitutions (K (s)) and chromosomal distribution. Estimation of K (s) proved the ancient origin of all NIs and the lack of expansion by gene duplication past the event of polyploidisation. We then focused on transcription analysis of five NIs for which evidence of expression was available from expressed sequence tag databases. Among these, four NIs consisted of pairs of homoeologous copies, each pair lying on a pair of chromosomes duplicated by polyploidy. Unequal expression of homoeologous genes was observed by quantitative RT-PCR in leaf, flower, seed and root tissues. Since NIs might play significant roles in fruit and wine quality, NIs expression was monitored in flesh and skin of 'Merlot' berries and shown in parallel with the suite of changes that accompany fruit ripening, including glucose and fructose accumulation.

Heterologous expression and functional characterization of two hybrid poplar cell-wall invertases

The expression of two hybrid poplar cell-wall invertases (EC 3.2.1.26; PaxgINV1 and PaxgINV2) were previously shown to be spatially and temporally regulated in the vegetative tissues. The expression of PaxgINV1 was linked to processes relating to dormancy, while PaxgINV2 expression was prominent in tissues undergoing growth and expansion. In an effort to further elucidate the physiological roles of these key cell wall enzymes, PaxgINV1 and PaxgINV2 were heterologously expressed in the methylotrophic yeast Pichia pastoris. Three-dimensional predictive models of the poplar invertases revealed a structural channel containing both the conserved beta-fructofuranosidase and cell-wall invertase motifs, suggesting that this channel is the putative active site of these enzymes. Recombinant PaxgINV1 and PaxgINV2 had pH optima of 4.8 and 5.6 and temperature optima of 45 and 40 degrees C, respectively. Functional characterization revealed the ability for both enzymes to hydrolyze the fructose residue of sucrose, raffinose, stachyose and verbascose, with PaxgINV2 having higher specific activity for each of the substrates tested. The K(m) values of sucrose/raffinose/stachyose were 1.7/1.8/5.0 mM for PaxgINV1 and 1.6/1.7/1.9 mM for PaxgINV2, respectively. Activity analyses in the presence of various metal cations showed that PaxgINV2 was strongly inhibited by Cu(2+), Zn(2+) and Hg(2+), while PaxgINV1 was only weakly inhibited by these cations. The results from this study, coupled with previous expression data, suggest that PaxgINV1 and PaxgINV2 have distinct roles with respect to the physiology and development of hybrid poplar, specifically phloem unloading and processes related to dormancy and bud break.