Multimeric states of starch phosphorylase determine protein-protein interactions with starch biosynthetic enzymes in amyloplasts

Genome-wide identification of starch phosphorylase gene family in Rosa chinensis and expression in response to abiotic stress

Chinese rose (Rosa chinensis) is an important ornamental plant, with economic, cultural, and symbolic significance. During the application of outdoor greening, adverse environments such as high temperature and drought are often encountered, which affect its application scope and ornamental quality. The starch phosphorylase (Pho) gene family participate in the synthesis and decomposition of starch, not only related to plant energy metabolism, but also plays an important role in plant stress resistance. The role of Pho in combating salinity and high temperature stress in R. chinensis remains unknown. In this work, 4 Phos from R. chinensis were detected with Pfam number of Pho (PF00343.23) and predicted by homolog-based prediction (HBP). The Phos are characterized by sequence lengths of 821 to 997 bp, and the proteins are predicted to subcellularly located in the plastid and cytoplasm. The regulatory regions of the Phos contain abundant stress and phytohormone-responsive cis-acting elements. Based on transcriptome analysis, the Phos were found to respond to abiotic stress factors such as drought, salinity, high temperature, and plant phytohormone of jasmonic acid and salicylic acid. The response of Phos to abiotic stress factors such as salinity and high temperature was confirmed by qRT-PCR analysis. To evaluate the genetic characteristics of Phos, a total of 69 Phos from 17 species were analyzed and then classified into 3 groups in phylogenetic tree. The collinearity analysis of Phos in R. chinensis and other species was conducted for the first time. This work provides a view of evolution for the Pho gene family and indicates that Phos play an important role in abiotic stress response of R. chinensis.

Initiation of B-type starch granules in wheat endosperm requires the plastidial α-glucan phosphorylase PHS1

The plastidial α-glucan phosphorylase (PHS1) can elongate and degrade maltooligosaccharides (MOSs), but its exact physiological role in plants is poorly understood. Here, we discover a specialized role of PHS1 in establishing the unique bimodal characteristic of starch granules in wheat (Triticum spp.) endosperm. Wheat endosperm contains large A-type granules that initiate at early grain development and small B-type granules that initiate in later grain development. We demonstrate that PHS1 interacts with B-GRANULE CONTENT1 (BGC1), a carbohydrate-binding protein essential for normal B-type granule initiation. Mutants of tetraploid durum wheat (Triticum turgidum) deficient in all homoeologs of PHS1 had normal A-type granules but fewer and larger B-type granules. Grain size and starch content were not affected by the mutations. Further, by assessing granule numbers during grain development in the phs1 mutant and using a double mutant defective in both PHS1 and BGC1, we demonstrate that PHS1 is exclusively involved in B-type granule initiation. The total starch content and number of starch granules per chloroplast in leaves were not affected by loss of PHS1, suggesting that its role in granule initiation in wheat is limited to the endosperm. We therefore propose that the initiation of A- and B-type granules occurs via distinct biochemical mechanisms, where PHS1 plays an exclusive role in B-type granule initiation.

Site-Directed Mutations at Phosphorylation Sites in Zea mays PHO1 Reveal Modulation of Enzymatic Activity by Phosphorylation at S566 in the L80 Region

Starch phosphorylase (PHO) is a pivotal enzyme within the GT35-glycogen-phosphorylase (GT; glycosyltransferases) superfamily. Despite the ongoing debate surrounding the precise role of PHO1, evidence points to its substantial influence on starch biosynthesis, supported by its gene expression profile and subcellular localization. Key to PHO1 function is the enzymatic regulation via phosphorylation; a myriad of such modification sites has been unveiled in model crops. However, the functional implications of these sites remain to be elucidated. In this study, we utilized site-directed mutagenesis on the phosphorylation sites of Zea mays PHO1, replacing serine residues with alanine, glutamic acid, and aspartic acid, to discern the effects of phosphorylation. Our findings indicate that phosphorylation exerts no impact on the stability or localization of PHO1. Nonetheless, our enzymatic assays unveiled a crucial role for phosphorylation at the S566 residue within the L80 region of the PHO1 structure, suggesting a potential modulation or enhancement of PHO1 activity. These data advance our understanding of starch biosynthesis regulation and present potential targets for crop yield optimization.

BE3 is the major branching enzyme isoform required for amylopectin synthesis in Chlamydomonas reinhardtii

Starch-branching enzymes (BEs) are essential for starch synthesis in both plants and algae where they influence the architecture and physical properties of starch granules. Within Embryophytes, BEs are classified as type 1 and type 2 depending on their substrate preference. In this article, we report the characterization of the three BE isoforms encoded in the genome of the starch producing green algae Chlamydomonas reinhardtii: two type 2 BEs (BE2 and BE3) and a single type 1 BE (BE1). Using single mutant strains, we analyzed the consequences of the lack of each isoform on both transitory and storage starches. The transferred glucan substrate and the chain length specificities of each isoform were also determined. We show that only BE2 and BE3 isoforms are involved in starch synthesis and that, although both isoforms possess similar enzymatic properties, BE3 is critical for both transitory and storage starch metabolism. Finally, we propose putative explanations for the strong phenotype differences evidenced between the C. reinhardtii be2 and be3 mutants, including functional redundancy, enzymatic regulation or alterations in the composition of multimeric enzyme complexes.

Nitrogen-dependent binding of the transcription factor PBF1 contributes to the balance of protein and carbohydrate storage in maize endosperm

Fluctuations in nitrogen (N) availability influence protein and starch levels in maize (Zea mays) seeds, yet the underlying mechanism is not well understood. Here, we report that N limitation impacted the expression of many key genes in N and carbon (C) metabolism in the developing endosperm of maize. Notably, the promoter regions of those genes were enriched for P-box sequences, the binding motif of the transcription factor prolamin-box binding factor 1 (PBF1). Loss of PBF1 altered accumulation of starch and proteins in endosperm. Under different N conditions, PBF1 protein levels remained stable but PBF1 bound different sets of target genes, especially genes related to the biosynthesis and accumulation of N and C storage products. Upon N-starvation, the absence of PBF1 from the promoters of some zein genes coincided with their reduced expression, suggesting that PBF1 promotes zein accumulation in the endosperm. In addition, PBF1 repressed the expression of sugary1 (Su1) and starch branching enzyme 2b (Sbe2b) under normal N supply, suggesting that, under N-deficiency, PBF1 redirects the flow of C skeletons for zein toward the formation of C compounds. Overall, our study demonstrates that PBF1 modulates C and N metabolism during endosperm development in an N-dependent manner.

Dynamic Change in Starch Biosynthetic Enzymes Complexes during Grain-Filling Stages in BEIIb Active and Deficient Rice

Starch is the predominant reserve in rice (Oryza sativa L.) endosperm, which is synthesized by the coordinated efforts of a series of starch biosynthetic-related enzymes in the form of a multiple enzyme complex. Whether the enzyme complex changes during seed development is not fully understood. Here, we investigated the dynamic change in multi-protein complexes in an indica rice variety IR36 (wild type, WT) and its BEIIb-deficient mutant (be2b) at different developmental stages. Gel permeation chromatography (GPC) and Western blotting analysis of soluble protein fractions revealed most of the enzymes except for SSIVb were eluted in smaller molecular weight fractions at the early developing stage and were transferred to higher molecular weight fractions at the later stage in both WT and be2b. Accordingly, protein interactions were enhanced during seed development as demonstrated by co-immunoprecipitation analysis, suggesting that the enzymes were recruited to form larger protein complexes during starch biosynthesis. The converse elution pattern from GPC of SSIVb may be attributed to its vital role in the initiation step of starch synthesis. The number of protein complexes was markedly decreased in be2b at all development stages. Although SSIVb could partially compensate for the role of BEIIb in protein complex formation, it was hard to form a larger protein complex containing over five proteins in be2b. In addition, other proteins such as PPDKA and PPDKB were possibly present in the multi-enzyme complexes by proteomic analyses of high molecular weight fractions separated from GPC. Two putative protein kinases were found to be potentially associated with starch biosynthetic enzymes. Collectively, our findings unraveled a dynamic change in the protein complex during seed development, and potential roles of BEIIb in starch biosynthesis via various protein complex formations, which enables a deeper understanding of the complex mechanism of starch biosynthesis in rice.

Comparative Study of Starch Phosphorylase Genes and Encoded Proteins in Various Monocots and Dicots with Emphasis on Maize

Starch phosphorylase (PHO) is a multimeric enzyme with two distinct isoforms: plastidial starch phosphorylase (PHO1) and cytosolic starch phosphorylase (PHO2). PHO1 specifically resides in the plastid, while PHO2 is found in the cytosol. Both play a critical role in the synthesis and degradation of starch. This study aimed to report the detailed structure, function, and evolution of genes encoding PHO1 and PHO2 and their protein ligand-binding sites in eight monocots and four dicots. "True" orthologs of PHO1 and PHO2 of Oryza sativa were identified, and the structure of the enzyme at the protein level was studied. The genes controlling PHO2 were found to be more conserved than those controlling PHO1; the variations were mainly due to the variable sequence and length of introns. Cis-regulatory elements in the promoter region of both genes were identified, and the expression pattern was analyzed. The real-time quantitative polymerase chain reaction indicated that PHO2 was expressed in all tissues with a uniform pattern of transcripts, and the expression pattern of PHO1 indicates that it probably contributes to the starch biosynthesis during seed development in Zea mays. Under abscisic acid (ABA) treatment, PHO1 was found to be downregulated in Arabidopsis and Hordeum vulgare. However, we found that ABA could up-regulate the expression of both PHO1 and PHO2 within 12 h in Zea mays. In all monocots and dicots, the 3D structures were highly similar, and the ligand-binding sites were common yet fluctuating in the position of aa residues.

Starch synthase II plays a crucial role in starch biosynthesis and the formation of multienzyme complexes in cassava storage roots

Starch is a glucose polymer synthesized by green plants for energy storage and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis and the formation of protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII, and MeISAII. MeSSII-RNAi cassava lines showed increased amylose content and reduced biosynthesis of the intermediate chain of amylopectin (B1 type) in their storage roots, leading to altered starch physicochemical properties. Furthermore, gel permeation chromatography analysis of starch biosynthetic enzymes between wild type and MeSSII-RNAi lines confirmed the key role of MeSSII in the organization of heteromeric starch synthetic protein complexes. The lack of MeSSII in cassava also reduced the capacity of MeSSI, MeSBEII, MeISAI, and MeISAII to bind to starch granules. These findings shed light on the key components of the starch biosynthesis machinery in root crops.

Molecular Functions and Pathways of Plastidial Starch Phosphorylase (PHO1) in Starch Metabolism: Current and Future Perspectives

Starch phosphorylase is a member of the GT35-glycogen-phosphorylase superfamily. Glycogen phosphorylases have been researched in animals thoroughly when compared to plants. Genetic evidence signifies the integral role of plastidial starch phosphorylase (PHO1) in starch biosynthesis in model plants. The counterpart of PHO1 is PHO2, which specifically resides in cytosol and is reported to lack L80 peptide in the middle region of proteins as seen in animal and maltodextrin forms of phosphorylases. The function of this extra peptide varies among species and ranges from the substrate of proteasomes to modulate the degradation of PHO1 in Solanum tuberosum to a non-significant effect on biochemical activity in Oryza sativa and Hordeum vulgare. Various regulatory functions, e.g., phosphorylation, protein–protein interactions, and redox modulation, have been reported to affect the starch phosphorylase functions in higher plants. This review outlines the current findings on the regulation of starch phosphorylase genes and proteins with their possible role in the starch biosynthesis pathway. We highlight the gaps in present studies and elaborate on the molecular mechanisms of phosphorylase in starch metabolism. Moreover, we explore the possible role of PHO1 in crop improvement.

Starch biosynthesis in cereal endosperms: An updated review over the last decade

Starch is a vital energy source for living organisms and is a key raw material and additive in the food and non-food industries. Starch has received continuous attention in multiple research fields. The endosperm of cereals (e.g., rice, corn, wheat, and barley) is the most important site for the synthesis of storage starch. Around 2010, several excellent reviews summarized key progress in various fields of starch research, serving as important references for subsequent research. In the past 10 years, many achievements have been made in the study of starch synthesis and regulation in cereals. The present review provides an update on research progress in starch synthesis of cereal endosperms over the past decade, focusing on new enzymes and non-enzymatic proteins involved in starch synthesis, regulatory networks of starch synthesis, and the use of elite alleles of starch synthesis-related genes in cereal breeding programs. We also provide perspectives on future research directions that will further our understanding of cereal starch biosynthesis and regulation to support the rational design of ideal quality grain.

The Associated With Carbon Conversion Rate and Source-Sink Enzyme Activity in Tomato Fruit Subjected to Water Stress and Potassium Application

Carbon metabolism in higher plants is a basic physiological metabolism, and carbon allocation and conversion require the activity of various enzymes in metabolic processes that alter the content and overall composition of sugars in the sink organ. However, it is not known how various enzymes affect carbon metabolism when tomato plants are subjected to water stress or treated with potassium. Although the process of carbon metabolism is very complex, we used the carbon conversion rate to compare and analyze the enzyme activities related to sugar metabolism and find out which carbon conversion rate are the most important. Results showed that water stress and potassium increased carbon import flux in the fruit, which was beneficial to carbon accumulation. Water deficit increased the activity of sucrose synthase (SuSy) and starch phosphorylase (SP) and decreased the activity of sucrose phosphate synthase (SPS) and adenosine diphosphate glucose pyrophosphorylase (AGPase) in the source. Water stress increased the activity of acid invertase (AI), SuSy and SP but decreased the activity of AGPase in the sink. Potassium modified the balance of enzymes active in sugar and starch metabolism by increasing the activity of AI, SuSy, SPS and SP and significantly decreasing the activity of AGPase, resulting in increase of hexose. Canonical correlational analysis revealed that the carbon conversion rate was mainly affected by the relative rate of conversion of sucrose to fructose and glucose [p1(t)] and glucose to starch [p5m(t)]. SuSy and AGPase had the greatest effect on enzyme activity in the fruit; respectively regulated p 1(t) and p 5m(t).

Biomass utilization and production of biofuels from carbon neutral materials

The availability of organic matters in vast quantities from the agricultural/industrial practices has long been a significant environmental challenge. These wastes have created global issues in increasing the levels of BOD or COD in water as well as in soil or air segments. Such wastes can be converted into bioenergy using a specific conversion platform in conjunction with the appropriate utilization of the methods such as anaerobic digestion, secondary waste treatment, or efficient hydrolytic breakdown as these can promote bioenergy production to mitigate the environmental issues. By the proper utilization of waste organics and by adopting innovative approaches, one can develop bioenergy processes to meet the energy needs of the society. Waste organic matters from plant origins or other agro-sources, biopolymers, or complex organic matters (cellulose, hemicelluloses, non-consumable starches or proteins) can be used as cheap raw carbon resources to produce biofuels or biogases to fulfill the ever increasing energy demands. Attempts have been made for bioenergy production by biosynthesizing, methanol, n-butanol, ethanol, algal biodiesel, and biohydrogen using different types of organic matters via biotechnological/chemical routes to meet the world's energy need by producing least amount of toxic gases (reduction up to 20-70% in concentration) in order to promote sustainable green environmental growth. This review emphasizes on the nature of available wastes, different strategies for its breakdown or hydrolysis, efficient microbial systems. Some representative examples of biomasses source that are used for bioenergy production by providing critical information are discussed. Furthermore, bioenergy production from the plant-based organic matters and environmental issues are also discussed. Advanced biofuels from the organic matters are discussed with efficient microbial and chemical processes for the promotion of biofuel production from the utilization of plant biomasses.

The Rice Plastidial Phosphorylase Participates Directly in Both Sink and Source Processes

The plastidial starch phosphorylase (Pho1) functions in starch metabolism. A distinctive structural feature of the higher Pho1 is a 50–82-amino-acid long peptide (L50–L82), which is absent in phosphorylases from non-plant organisms. To study the function of the rice Pho1 L80 peptide, we complemented a pho1− rice mutant (BMF136) with the wild-type Pho1 gene or with a Pho1 gene lacking the L80 region (Pho1ΔL80). While expression of Pho1 in BMF136 restored normal wild-type phenotype, the introduction of Pho1ΔL80 enhanced the growth rate and plant productivity above wild-type levels. Mass spectrometry analysis of proteins captured by anti-Pho1 showed the surprising presence of PsaC, the terminal electron acceptor/donor subunit of photosystem I (PSI). This unexpected interaction was substantiated by reciprocal immobilized protein pull-down assays of seedling extracts and supported by the presence of Pho1 on isolated PSI complexes resolved by blue-native gels. Spectrophotometric studies showed that Pho1ΔL80 plants exhibited modified PSI and enhanced CO2 assimilation properties. Collectively, these findings indicate that the higher plant Pho1 has dual roles as a potential modulator of source and sink processes.

Non-GMO potato lines, synthesizing increased amylose and resistant starch, are mainly deficient in isoamylase debranching enzyme

Solanum tuberosum potato lines with high amylose content were generated by crossing with the wild potato species Solanum sandemanii followed by repeated backcrossing to Solanum tuberosum lines. The trait, termed increased amylose (IAm), was recessive and present after three generations of backcrossing into S. tuberosum lines (6.25% S. sandemanii genes). The tubers of these lines were small, elongated and irregular with small and misshaped starch granules and high sugar content. Additional backcrossing resulted in less irregular tuber morphology, increased starch content (4.3%-9.5%) and increased amylose content (29%-37.9%) but indifferent sugar content. The amylose in the IAm starch granules was mainly located in peripheral spots, and large cavities were found in the granules. Starch pasting was suppressed, and the digestion-resistant starch (RS) content was increased. Comprehensive microarray polymer profiling (CoMPP) analysis revealed specific alterations of major pectic and glycoprotein cell wall components. This complex phenotype led us to search for candidate IAm genes exploiting its recessive trait. Hence, we sequenced genomic DNA of a pool of IAm lines, identified SNPs genome wide against the draft genome sequence of potato and searched for regions of decreased heterozygosity. Three regions, located on chromosomes 3, 7 and 10, respectively, displayed markedly less heterozygosity than average. The only credible starch metabolism-related gene found in these regions encoded the isoamylase-type debranching enzyme Stisa1. Decreased expression of mRNA (>500 fold) and reduced enzyme activity (virtually absent from IAm lines) supported Stisa1 as a candidate gene for IAm.

Starch phosphorylation and the in vivo regulation of starch metabolism and characteristics

Starch is the most significant carbon and energy reserve in plants and is also a sustainable feedstock for many industrial applications. Substantial research effort has been devoted to enhancing the yield and quality of starch. Over the past century, starch phosphorylation has aroused increasing interest as the only naturally occurring covalent modification in starch. Many studies have investigated the role of phosphorylation in starch metabolism and its impact on the starch granule. In this review, the two key enzymes involved in starch phosphorylation and their catalytic mechanisms are described at the molecular level; the vital roles of phosphorylation in starch degradation and biosynthesis are illuminated in detail; and the multiple influences of phosphorylation on starch composition, granule structure and physicochemical properties are discussed. This review systematically summarizes the importance of phosphorylation in starch metabolism, and describes the advanced methods used to precisely measure phosphate and increase the level of starch phosphorylation.

The plastid phosphorylase as a multiple-role player in plant metabolism

The physiological roles of the plastidial phosphorylase in starch metabolism of higher plants have been debated for decades. While estimated physiological substrate levels favor a degradative role, genetic evidence indicates that the plastidial phosphorylase (Pho1) plays an essential role in starch initiation and maturation of the starch granule in developing rice grains. The plastidial enzyme contains a unique peptide domain, up to 82 residues in length depending on the plant species, not found in its cytosolic counterpart or glycogen phosphorylases. The role of this extra peptide domain is perplexing, as its complete removal does not significantly affect the in vitro catalytic or enzymatic regulatory properties of rice Pho1. This peptide domain may have a regulatory function as it contains potential phosphorylation sites and, in some plant Pho1s, a PEST motif, a substrate for proteasome-mediated degradation. We discuss the potential roles of Pho1 and its L80 domain in starch biosynthesis and photosynthesis.

Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.)

Background

Starch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism, determining amylopectin structure.

Methods

Full length coding sequences (CDS) of SBE genes were cloned using reverse transcription PCR (RT-PCR) technology, and neighbor-joining (NJ) tree was used for phylogenetic analysis. Single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyze the spatial and temporal expression of NnSBE genes. The effect of NnSBE genes on amylopectin’s fine structures was explored using affinity and the enzyme activity analysis of two isoforms in amylopectin and amylose.

Results

In this study, two SBE family genes, NnSBEI and NnSBEIII, were identified in lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis sorted NnSBEI into SBE family B and NnSBEIII into SBE family A. UPGMA phylogenetic tree divided 45 individuals of lotus into three classes. The homozygous haplotype (A G G A G) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in the middle of the development stage, while NnSBEI increased in the mid-late developmental stage. The different affinity activity of the two isozymes binding amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity.

Discussion

Genetic diversity showed that NnSBE genes received artificial selection during the process of cultivation and domestication in lotus seeds. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes were related to the chain length of amylopectin.

Starch granule initiation and morphogenesis-progress in Arabidopsis and cereals

Starch, the major storage carbohydrate in plants, is synthesized in plastids as semi-crystalline, insoluble granules. Many organs and cell types accumulate starch at some point during their development and maturation. The biosynthesis of the starch polymers, amylopectin and amylose, is relatively well understood and mostly conserved between organs and species. However, we are only beginning to understand the mechanism by which starch granules are initiated, and the factors that control the number of granules per plastid and the size/shape of granules. Here, we review recent progress in understanding starch granule initiation and morphogenesis. In Arabidopsis, granule initiation requires several newly discovered proteins with specific locations within the chloroplast, and also on the availability of maltooligosaccharides which act as primers for initiation. We also describe progress in understanding granule biogenesis in the endosperm of cereal grains-within which there is large interspecies variation in granule initiation patterns and morphology. Investigating whether this diversity results from differences between species in the functions of known proteins, and/or from the presence of novel, unidentified proteins, is a promising area of future research. Expanding our knowledge in these areas will lead to new strategies for improving the quality of cereal crops by modifying starch granule size and shape in vivo.

PII1: a protein involved in starch initiation that determines granule number and size in Arabidopsis chloroplast

The initiation of starch granule formation is still poorly understood. However, the soluble starch synthase 4 (SS4) appears to be a major component of this process since it is required to synthesize the correct number of starch granules in the chloroplasts of Arabidopsis thaliana plants. A yeast two-hybrid screen allowed the identification of several putative SS4 interacting partners. We identified the product of At4g32190 locus as a chloroplast-targeted PROTEIN INVOLVED IN STARCH INITIATION (named PII1). Arabidopsis mutants devoid of PII1 display an alteration of the starch initiation process and accumulate, on average, one starch granule per plastid instead of the five to seven granules found in plastids of wild-type plants. These granules are larger than in wild-type, and they remain flat and lenticular. pii1 mutants display wild-type growth rates and accumulate standard starch amounts. Moreover, starch characteristics, such as amylopectin chain length distribution, remain unchanged. Our results reveal the involvement of PII1 in the starch priming process in Arabidopsis leaves through interaction with SS4.

Crop resistant starch and genetic improvement: a review of recent advances

Resistant starch (RS), as a healthy dietary fiber, meets with great human favor along with the rapid development and improvement of global living standards. RS shows direct effects in reducing postprandial blood glucose levels, serum cholesterol levels and glycemic index. Therefore, RS plays an important role in preventing and improving non-communicable diseases, such as obesity, diabetes, colon cancer, cardiovascular diseases and chronic kidney disease. In addition, RS leads to its potential applied value in the development of high-quality foodstuffs, such as bread, noodles and dumplings. This paper reviews the recent advances in RS research, focusing mainly on RS classification and measurement, formation, quantitative trait locus mapping, genome-wide association studies, molecular marker development and genetic improvement through induced mutations, plant breeding combined with marker-assisted selection and genetic transformation. Challenges and perspectives on further RS research are also discussed.

Evolutionary, structural and expression analysis of core genes involved in starch synthesis

Starch is the main storage carbohydrate in plants and an important natural resource for food, feed and industrial raw materials. However, the details regarding the pathway for starch biosynthesis and the diversity of biosynthetic enzymes involved in this process are poorly understood. This study uses a comprehensive phylogenetic analysis of 74 sequenced plant genomes to revisit the evolutionary history of the genes encoding ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch de-branching enzyme (DBE). Additionally, the protein structures and expression patterns of these four core genes in starch biosynthesis were studied to determine their functional differences. The results showed that AGPase, SS, SBE and DBE have undergone complicated evolutionary processes in plants and that gene/genome duplications are responsible for the observed differences in isoform numbers. A structure analysis of these proteins suggested that the deletion/mutation of amino acids in some active sites resulted in not only structural variation but also sub-functionalization or neo-functionalization. Expression profiling indicated that AGPase-, SS-, SBE- and DBE-encoding genes exhibit spatio-temporally divergent expression patterns related to the composition of functional complexes in starch biosynthesis. This study provides a comprehensive atlas of the starch biosynthetic pathway, and these data should support future studies aimed at increasing understanding of starch biosynthesis and the functional evolutionary divergence of AGPase, SS, SBE, and DBE in plants.

Proteome Analysis of Potato Starch Reveals the Presence of New Starch Metabolic Proteins as Well as Multiple Protease Inhibitors

Starch bound proteins mainly include enzymes from the starch biosynthesis pathway. Recently, new functions in starch molecular assembly or active protein targeting were also proposed for starch associated proteins. The potato genome sequence reveals 77 loci encoding starch metabolizing enzymes with the identification of previously unknown putative isoforms. Here we show by bottom-up proteomics that most of the starch biosynthetic enzymes in potato remain associated with starch even after washing with SDS or protease treatment of the granule surface. Moreover, our study confirmed the presence of PTST1 (Protein Targeting to Starch), ESV1 (Early StarVation1) and LESV (Like ESV), that have recently been identified in Arabidopsis. In addition, we report on the presence of a new isoform of starch synthase, SS6, containing both K-X-G-G-L catalytic motifs. Furthermore, multiple protease inhibitors were also identified that are cleared away from starch by SDS and thermolysin treatments. Our results indicate that SS6 may play a yet uncharacterized function in starch biosynthesis and open new perspectives both in understanding storage starch metabolism as well as breeding improved potato lines.

Starch Biosynthesis in the Developing Endosperms of Grasses and Cereals

The starch-rich endosperms of the Poaceae, which includes wild grasses and their domesticated descendents the cereals, have provided humankind and their livestock with the bulk of their daily calories since the dawn of civilization up to the present day. There are currently unprecedented pressures on global food supplies, largely resulting from population growth, loss of agricultural land that is linked to increased urbanization, and climate change. Since cereal yields essentially underpin world food and feed supply, it is critical that we understand the biological factors contributing to crop yields. In particular, it is important to understand the biochemical pathway that is involved in starch biosynthesis, since this pathway is the major yield determinant in the seeds of six out of the top seven crops grown worldwide. This review outlines the critical stages of growth and development of the endosperm tissue in the Poaceae, including discussion of carbon provision to the growing sink tissue. The main body of the review presents a current view of our understanding of storage starch biosynthesis, which occurs inside the amyloplasts of developing endosperms.

Characterization of starch phosphorylase from the marine green microalga (Chlorophyta) Tetraselmis subcordiformis reveals its potential role in starch biosynthesis

In a marine green starch-producing microalga Tetraselmis subcordiformis, the role of starch phosphorylase (SP) in the starch biosynthesis was disclosed by characterizing the enzyme properties and activity variations during the starch accumulation process. TsSP4, a SP isoform accounting for the major SP activity in T. subcordiformis, was unique to be active in a monomer form with a molecular weight of approximately 110kDa. It resembled one of the chloroplast-located SPs (PhoA) in Chlamydomonas reinhardtii with a similarity of 63.3% in sequence, though it possessed the typical L78/80 domain found in the plastidial SPs (Pho1) of higher plants that was absent in PhoA. TsSP4 exhibited moderate sensitivity to ADP-Glc inhibition and had a high activity for longer-chain linear maltooligosacchride (MOS) and amylopectin against highly branched glycogen as the substrates. TsSP4 had 2-fold higher affinity for Glc-1-P in the synthetic direction than for Pi in the phosphorolytic direction, and the catalytic constant k_cat for Glc-1-P was 2-fold of that for Pi. Collectively, TsSP4 preferred synthetic rather than phosphorolytic direction. TsSP4 could elongate MOSs even initially with Pi alone in the absence of Glc-1-P, which further supported its synthetic role in the starch biosynthesis. TsSP4 displayed increased activities in the developing and mature stage of starch biosynthesis under nitrogen-starvation conditions, indicating its possible contribution to the amylopectin amplification.

Plastidial α-glucan phosphorylase 1 complexes with disproportionating enzyme 1 in Ipomoea batatas storage roots for elevating malto-oligosaccharide metabolism

It has been proposed that malto-oligosaccharides (MOSs) are possibly recycled back into amylopectin biosynthesis via the sequential reactions catalyzed by plastidial α-glucan phosphorylase 1 (Pho1) and disproportionating enzyme 1 (Dpe1). In the present study, the reciprocal co-immunoprecipitation experiments using specific antibodies against Pho1 and Dpe1 demonstrated that these two enzymes can form a complex (the PD complex) in Ipomoea batatas storage roots. The immunohistochemistry analyses also revealed the co-localization of Pho1 and Dpe1 in the amyloplasts, and the protein levels of Pho1 and Dpe1 increased gradually throughout sweet potato storage root development. A high molecular weight PD complex was co-purified from sweet potato storage root lysates by size exclusion chromatography. Enzyme kinetic analyses showed that the PD complex can catalyze maltotriose and maltotetraose to generate glucose-1-phosphate in the presence of inorganic phosphate, and it also performs greater Dpe1 activity toward MOSs than does free form Dpe1. These data suggest that Pho1 and Dpe1 may form a metabolon complex, which provides elevated metabolic fluxes for MOS metabolism via a direct transfer of sugar intermediates, resulting in recycling of glucosyl units back into amylopectin biosynthesis more efficiently.

Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development

The production of starch is essential for human nutrition and represents a major metabolic flux in the biosphere. The biosynthesis of starch in storage organs like barley endosperm operates via two main pathways using different substrates: starch synthases use ADP-glucose to produce amylose and amylopectin, the two major components of starch, whereas starch phosphorylase (Pho1) uses glucose-1-phosphate (G1P), a precursor for ADP-glucose production, to produce α-1,4 glucans. The significance of the Pho1 pathway in starch biosynthesis has remained unclear. To elucidate the importance of barley Pho1 (HvPho1) for starch biosynthesis in barley endosperm, we analyzed HvPho1 protein production and enzyme activity levels throughout barley endosperm development and characterized structure-function relationships of HvPho1. The molecular mechanisms underlying the initiation of starch granule biosynthesis, that is, the enzymes and substrates involved in the initial transition from simple sugars to polysaccharides, remain unclear. We found that HvPho1 is present as an active protein at the onset of barley endosperm development. Notably, purified recombinant protein can catalyze the de novo production of α-1,4-glucans using HvPho1 from G1P as the sole substrate. The structural properties of HvPho1 provide insights into the low affinity of HvPho1 for large polysaccharides like starch or amylopectin. Our results suggest that HvPho1 may play a role during the initiation of starch biosynthesis in barley.

Soluble Starch Synthase III-1 in Amylopectin Metabolism of Banana Fruit: Characterization, Expression, Enzyme Activity, and Functional Analyses

Soluble starch synthase (SS) is one of the key enzymes involved in amylopectin biosynthesis in plants. However, no information is currently available about this gene family in the important fruit crop banana. Herein, we characterized the function of MaSSIII-1 in amylopectin metabolism of banana fruit and described the putative role of the other MaSS family members. Firstly, starch granules, starch and amylopectin content were found to increase during banana fruit development, but decline during storage. The SS activity started to increase later than amylopectin and starch content. Secondly, four putative SS genes were cloned and characterized from banana fruit. Among them, MaSSIII-1 showed the highest expression in banana pulp during fruit development at transcriptional levels. Further Western blot analysis suggested that the protein was gradually increased during banana fruit development, but drastically reduced during storage. This expression pattern was highly consistent with changes in starch granules, amylopectin content, and SS activity at the late phase of banana fruit development. Lastly, overexpression of MaSSIII-1 in tomato plants distinctly changed the morphology of starch granules and significantly increased the total starch accumulation, amylopectin content, and SS activity at mature-green stage in comparison to wild-type. The findings demonstrated that MaSSIII-1 is a key gene expressed in banana fruit and responsible for the active amylopectin biosynthesis, this is the first report in a fresh fruit species. Such a finding may enable the development of molecular markers for banana breeding and genetic improvement of nutritional value and functional properties of banana fruit.

Rice Endosperm Starch Phosphorylase (Pho1) Assembles with Disproportionating Enzyme (Dpe1) to Form a Protein Complex That Enhances Synthesis of Malto-oligosaccharides

Starch synthesis in cereal grain endosperm is dependent on the concerted actions of many enzymes. The starch plastidial phosphorylase (Pho1) plays an important role in the initiation of starch synthesis and in the maturation of starch granule in developing rice seeds. Prior evidence has suggested that the rice enzyme, OsPho1, may have a physical/functional interaction with other starch biosynthetic enzymes. Pulldown experiments showed that OsPho1 as well as OsPho1 devoid of its L80 region, a peptide unique to higher plant phosphorylases, captures disproportionating enzyme (OsDpe1). Interaction of the latter enzyme form with OsDpe1 indicates that the putative regulatory L80 is not responsible for multienzyme assembly. This heterotypic enzyme complex, determined at a molar ratio of 1:1, was validated by reciprocal co-immunoprecipitation studies of native seed proteins and by co-elution chromatographic and co-migration electrophoretic patterns of these enzymes in rice seed extracts. The OsPho1-OsDpe1 complex utilized a broader range of substrates for enhanced synthesis of larger maltooligosaccharides than each individual enzyme and significantly elevated the substrate affinities of OsPho1 at 30 °C. Moreover, the assembly with OsDpe1 enables OsPho1 to utilize products of transglycosylation reactions involving G1 and G3, sugars that it cannot catalyze directly.

Formation of starch in plant cells

Starch-rich crops form the basis of our nutrition, but plants have still to yield all their secrets as to how they make this vital substance. Great progress has been made by studying both crop and model systems, and we approach the point of knowing the enzymatic machinery responsible for creating the massive, insoluble starch granules found in plant tissues. Here, we summarize our current understanding of these biosynthetic enzymes, highlighting recent progress in elucidating their specific functions. Yet, in many ways we have only scratched the surface: much uncertainty remains about how these components function together and are controlled. We flag-up recent observations suggesting a significant degree of flexibility during the synthesis of starch and that previously unsuspected non-enzymatic proteins may have a role. We conclude that starch research is not yet a mature subject and that novel experimental and theoretical approaches will be important to advance the field.

Glycosyltransferase complexes in eukaryotes: long-known, prevalent but still unrecognized

Glycosylation is the most common and complex cellular modification of proteins and lipids. It is critical for multicellular life and its abrogation often leads to a devastating disease. Yet, the underlying mechanistic details of glycosylation in both health and disease remain unclear. Partly, this is due to the complexity and dynamicity of glycan modifications, and the fact that not all the players are taken into account. Since late 1960s, a vast number of studies have demonstrated that glycosyltransferases typically form homomeric and heteromeric complexes with each other in yeast, plant and animal cells. To propagate their acceptance, we will summarize here accumulated data for their prevalence and potential functional importance for glycosylation focusing mainly on their mutual interactions, the protein domains mediating these interactions, and enzymatic activity changes that occur upon complex formation. Finally, we will highlight the few existing 3D structures of these enzyme complexes to pinpoint their individual nature and to emphasize that their lack is the main obstacle for more detailed understanding of how these enzyme complexes interact and function in a eukaryotic cell.

A review of starch-branching enzymes and their role in amylopectin biosynthesis

Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and algae, and their activities play a crucial role in determining the structure and physical properties of starch granules. SBEs generate α-1,6-branch linkages in α-glucans through cleavage of internal α-1,4 bonds and transfer of the released reducing ends to C-6 hydroxyls. Starch biosynthesis in plants and algae requires multiple isoforms of SBEs and is distinct from glycogen biosynthesis in both prokaryotes and eukaryotes which uses a single branching enzyme (BE) isoform. One of the unique characteristics of starch structure is the grouping of α-1,6-branch points in clusters within amylopectin. This is a feature of SBEs and their interplay with other starch biosynthetic enzymes, thus facilitating formation of the compact water-insoluble semicrystalline starch granule. In this respect, the activity of SBE isoforms is pivotal in starch granule assembly. SBEs are structurally related to the α-amylase superfamily of enzymes, sharing three domains of secondary structure with prokaryotic Bes: the central (β/α)8 -barrel catalytic domain, an NH2 -terminal domain involved in determining the size of α-glucan chain transferred, and the C-terminal domain responsible for catalytic capacity and substrate preference. In addition, SBEs have conserved plant-specific domains, including phosphorylation sites which are thought to be involved in regulating starch metabolism. SBEs form heteromeric protein complexes with other SBE isoforms as well as other enzymes involved in starch synthesis, and assembly of these protein complexes is regulated by protein phosphorylation. Phosphorylated SBEIIb is found in multienzyme complexes with isoforms of glucan-elongating starch synthases, and these protein complexes are implicated in amylopectin cluster formation. This review presents a comparative overview of plant SBEs and includes a review of their properties, structural and functional characteristics, and recent developments on their post-translational regulation.