ER as master regulator of membrane trafficking and organelle function.

The endoplasmic reticulum (ER), which occupies a large portion of the cytoplasm, is the cell's main site for the biosynthesis of lipids and carbohydrate conjugates, and it is essential for folding, assembly, and biosynthetic transport of secreted proteins and integral membrane proteins. The discovery of abundant membrane contact sites (MCSs) between the ER and other membrane compartments has revealed that, in addition to its biosynthetic and secretory functions, the ER plays key roles in the regulation of organelle dynamics and functions. In this review, we will discuss how the ER regulates endosomes, lysosomes, autophagosomes, mitochondria, peroxisomes, and the Golgi apparatus via MCSs. Such regulation occurs via lipid and Ca2+ transfer and also via control of in trans dephosphorylation reactions and organelle motility, positioning, fusion, and fission. The diverse controls of other organelles via MCSs manifest the ER as master regulator of organelle biology.

The SGNH hydrolase family: a template for carbohydrate diversity.

The substitution and de-substitution of carbohydrate materials are important steps in the biosynthesis and/or breakdown of a wide variety of biologically important polymers. The SGNH hydrolase superfamily is a group of related and well-studied proteins with a highly conserved catalytic fold and mechanism composed of 16 member families. SGNH hydrolases can be found in vertebrates, plants, fungi, bacteria, and archaea, and play a variety of important biological roles related to biomass conversion, pathogenesis, and cell signaling. The SGNH hydrolase superfamily is chiefly composed of a diverse range of carbohydrate-modifying enzymes, including but not limited to the carbohydrate esterase families 2, 3, 6, 12 and 17 under the carbohydrate-active enzyme classification system and database (CAZy.org). In this review, we summarize the structural and functional features that delineate these subfamilies of SGNH hydrolases, and which generate the wide variety of substrate preferences and enzymatic activities observed of these proteins to date.

Mutagenicity of Tectona grandis Wood Extracts and Their Ability to Improve Carbohydrate Yield for Kraft Cooking Eucalyptus Wood.

Considering the toxicity of the impurities of synthesized anthraquinone, this study clarified new catalytic compounds for kraft cooking with improved carbohydrate yield and delignification and less mutagenicity, which are important for ensuring the safety of paper products in contact with food. The 2-methylanthraquinone contents of teak (Tectona grandis) woods were 0.18-0.21%. Acetone extracts containing 2-methylanthraquinone from Myanmar and Indonesia teak woods as additives improved lignin removal during kraft cooking of eucalyptus wood, which resulted in kappa numbers that were 2.2-6.0 points lower than the absence of additive. Myanmar extracts and 2-methylanthraquinone improved carbohydrate yield in pulps with 1.7-2.2% yield gains. Indonesia extracts contained more deoxylapachol and its isomer than 2-methylanthraquinone. The residual content of 2-methylanthraquinone in the kraft pulp was trace. Although Ames tests showed that the Indonesia and Myanmar extracts were mutagenic to Salmonella typhimurium, 2-methylanthraquinone was not. The kraft pulp obtained with the additives should be safe for food-packaging applications, and the addition of 0.03% 2-methylanthraquinone to kraft cooking saves forest resources and fossil energy in industries requiring increased pulp yield.

Crosstalk during the Carbon-Nitrogen Cycle That Interlinks the Biosynthesis, Mobilization and Accumulation of Seed Storage Reserves.

Carbohydrates are the major storage reserves in seeds, and they are produced and accumulated in specific tissues during the growth and development of a plant. The storage products are hydrolyzed into a mobile form, and they are then translocated to the developing tissue following seed germination, thereby ensuring new plant formation and seedling vigor. The utilization of seed reserves is an important characteristic of seed quality. This review focuses on the seed storage reserve composition, source-sink relations and partitioning of the major transported carbohydrate form, i.e., sucrose, into different reserves through sucrolytic processes, biosynthetic pathways, interchanging levels during mobilization and crosstalk based on vital biochemical pathways that interlink the carbon and nitrogen cycles. Seed storage reserves are important due to their nutritional value; therefore, novel approaches to augmenting the targeted storage reserve are also discussed.

RNASeq analysis of drought-stressed guayule reveals the role of gene transcription for modulating rubber, resin, and carbohydrate synthesis.

The drought-adapted shrub guayule (Parthenium argentatum) produces rubber, a natural product of major commercial importance, and two co-products with potential industrial use: terpene resin and the carbohydrate fructan. The rubber content of guayule plants subjected to water stress is higher compared to that of well-irrigated plants, a fact consistently reported in guayule field evaluations. To better understand how drought influences rubber biosynthesis at the molecular level, a comprehensive transcriptome database was built from drought-stressed guayule stem tissues using de novo RNA-seq and genome-guided assembly, followed by annotation and expression analysis. Despite having higher rubber content, most rubber biosynthesis related genes were down-regulated in drought-stressed guayule, compared to well-irrigated plants, suggesting post-transcriptional effects may regulate drought-induced rubber accumulation. On the other hand, terpene resin biosynthesis genes were unevenly affected by water stress, implying unique environmental influences over transcriptional control of different terpene compounds or classes. Finally, drought induced expression of fructan catabolism genes in guayule and significantly suppressed these fructan biosynthesis genes. It appears then, that in guayule cultivation, irrigation levels might be calibrated in such a regime to enable tunable accumulation of rubber, resin and fructan.

Regulation of secondary antioxidants and carbohydrates by gamma-aminobutyric acid under salinity-alkalinity stress in rice (Oryza sativa L.).

Gamma-aminobutyric acid (GABA) is known to improve tolerance against abiotic stresses but less studied for salinity-alkalinity stress (SAS). In the present study, GABA regulation of secondary antioxidants and carbohydrates was studied in rice in the presence and absence of SAS. About 1.5 mM GABA, 200 mM SAS, GABA + SAS were applied to 5-day old seedlings, and thereafter measurements were done in shoots and roots at 24, 48, 72 h in rice cultivars CSR 43 (tolerant) and Pusa 44 (susceptible). SAS was applied in molar ratio of 1:9:9:1 of NaCl:Na2SO4:NaHCO3:Na2CO3. Peroxidases (POX), polyphenol oxidases (PPO), lignin, flavonoids and phenolics from secondary metabolism and invertases, hexoses, sucrose and starch from carbohydrate metabolism were studied. Pusa 44 increased soluble POX, lignin, flavonoids in shoots but deficient in roots during stress period but improved under GABA + SAS. CSR 43 increased soluble POX, lignin, flavonoids in roots consistently throughout the stress period and also improved under GABA + SAS. Early increase in cell wall POX/PPO under SAS was seen in CSR 43 only, while Pusa 44 improved this under GABA + SAS. During stress period, CSR 43 showed an increasing trend of cell wall invertase activity, sucrose, sucrose-to-hexose ratio and starch in roots but Pusa 44 showed poor such response but Pusa 44 improved starch, sucrose, sucrose-to-hexose ratio by significant amount in both shoots and roots under GABA + SAS. The overall study indicated GABA as an important regulator of secondary and carbohydrate metabolisms. Besides improving secondary antioxidants, GABA under stress may improve cellular reserves like starch and protective sugars like sucrose.

GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases.

Glycosyltransferases (GTs) play a central role in sustaining all forms of life through the biosynthesis of complex carbohydrates. Despite significant strides made in recent years to establish computational resources, databases and tools to understand the nature and role of carbohydrates and related glycoenzymes, a data analytics framework that connects the sequence-structure-function relationships to the evolution of GTs is currently lacking. This hinders the characterization of understudied GTs and the synthetic design of GTs for medical and biotechnology applications. Here, we present GTXplorer as an integrated platform that presents evolutionary information of GTs adopting a GT-A fold in an intuitive format enabling in silico investigation through comparative sequence analysis to derive informed hypotheses about their function. The tree view mode provides an overview of the evolutionary relationships of GT-A families and allows users to select phylogenetically relevant families for comparisons. The selected families can then be compared in the alignment view at the residue level using annotated weblogo stacks of the GT-A core specific to the selected clade, family, or subfamily. All data are easily accessible and can be downloaded for further analysis. GTXplorer can be accessed at https://vulcan.cs.uga.edu/gtxplorer/ or from GitHub at https://github.com/esbgkannan/GTxplorer to deploy locally. By packaging multiple data streams into an accessible, user-friendly format, GTXplorer presents the first evolutionary data analytics platform for comparative glycomics.

Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis.

It is now well established that the Gram-negative bacterium, Helicobacter pylori, causes gastritis in humans. In recent years, it has become apparent that the so-called non-pylori Helicobacters, normally infecting pigs, cats, and dogs, may also be involved in human pathology via zoonotic transmission. Indeed, more than 30 species of non-pylori Helicobacters have been identified thus far. One such organism is Helicobacter canadensis, an emerging pathogen whose genome sequence was published in 2009. Given our long-standing interest in the biosynthesis of N-formylated sugars found in the O-antigens of some Gram-negative bacteria, we were curious as to whether H. canadensis produces such unusual carbohydrates. Here, we demonstrate using both biochemical and structural techniques that the proteins encoded by the HCAN_0198, HCAN_0204, and HCAN_0200 genes in H. canadensis, correspond to a 3,4-ketoisomerase, a pyridoxal 5'-phosphate aminotransferase, and an N-formyltransferase, respectively. For this investigation, five high-resolution X-ray structures were determined and the kinetic parameters for the isomerase and the N-formyltransferase were measured. Based on these data, we suggest that the unusual sugar, 3-formamido-3,6-dideoxy-d-glucose, will most likely be found in the O-antigen of H. canadensis. Whether N-formylated sugars found in the O-antigen contribute to virulence is presently unclear, but it is intriguing that they have been observed in such pathogens as Francisella tularensis, Mycobacterium tuberculosis, and Brucella melitensis.

Implementation of kLa-Based Strategy for Scaling Up Porphyridium purpureum (Red Marine Microalga) to Produce High-Value Phycoerythrin, Fatty Acids, and Proteins.

Porphyridium purpureum is a well-known Rhodophyta that recently has attracted enormous attention because of its capacity to produce many high-value metabolites such as the pigment phycoerythrin and several high-value fatty acids. Phycoerythrin is a fluorescent red protein-pigment commercially relevant with antioxidant, antimicrobial activity, and fluorescent properties. The volumetric mass transfer coefficient (kLa) was kept constant within the different scaling-up stages in the present study. This scaling-up strategy was sought to maintain phycoerythrin production and other high-value metabolites by Porphyridium purpureum, using hanging-bag photobioreactors. The kLa was monitored to ensure the appropriate mixing and CO2 diffusion in the entire culture during the scaling process (16, 80, and 400 L). Then, biomass concentration, proteins, fatty acids, carbohydrates, and phycoerythrin were determined in each step of the scaling-up process. The kLa at 16 L reached a level of 0.0052 s-1, while at 80 L, a value of 0.0024 s-1 was achieved. This work result indicated that at 400 L, 1.22 g L-1 of biomass was obtained, and total carbohydrates (117.24 mg L-1), proteins (240.63 mg L-1), and lipids (17.75% DW) were accumulated. Regarding fatty acids production, 46.03% palmitic, 8.03% linoleic, 22.67% arachidonic, and 2.55% eicosapentaenoic acid were identified, principally. The phycoerythrin production was 20.88 mg L-1 with a purity of 2.75, making it viable for food-related applications. The results of these experiments provide insight into the high-scale production of phycoerythrin via the cultivation of P. purpureum in an inexpensive and straightforward culture system.

Understanding the roles of osmolytes for acclimatizing plants to changing environment: a review of potential mechanism.

Abiotic stresses are significant environmental issues that restrict plant growth, productivity, and survival while also posing a threat to global food production and security. Plants produce compatible solutes known as osmolytes to adapt themselves in such changing environment. Osmolytes contribute to homeostasis maintenance, provide the driving gradient for water uptake, maintain cell turgor by osmotic adjustment, and redox metabolism to remove excess level of reactive oxygen species (ROS) and reestablish the cellular redox balance as well as protect cellular machinery from osmotic stress and oxidative damage. Perceiving the mechanisms how plants interpret environmental signals and transmit them to cellular machinery to activate adaptive responses is important for crop improvement programs to get stress-tolerant varieties. A large number of studies conducted in the last few decades have shown that osmolytes accumulate in plants and have strong associations with abiotic stress tolerance. Production of abundant osmolytes is needed for tolerance in many plant species. In addition, transgenic plants overexpressing genes for different osmolytes showed enhanced tolerance to various abiotic stresses. Many important aspects of their mechanisms of action are yet to be largely identified, especially regarding the relevance and relative contribution of specific osmolytes to the stress tolerance of a given species. Therefore, more efforts and resources should be invested in the study of the abiotic stress responses of plants in their natural habitats. The present review focuses on the possible roles and mechanisms of osmolytes and their association toward abiotic stress tolerance in plants. This review would help the readers in learning more about osmolytes and how they behave in changing environments as well as getting an idea of how this knowledge could be applied to develop stress tolerance in plants.

Transgenic insertion of the cyanobacterial membrane protein ictB increases grain yield in Zea mays through increased photosynthesis and carbohydrate production.

The C4 crop maize (Zea mays) is the most widely grown cereal crop worldwide and is an essential feedstock for food and bioenergy. Improving maize yield is important to achieve food security and agricultural sustainability in the 21st century. One potential means to improve crop productivity is to enhance photosynthesis. ictB, a membrane protein that is highly conserved across cyanobacteria, has been shown to improve photosynthesis, and often biomass, when introduced into diverse C3 plant species. Here, ictB from Synechococcus sp. strain PCC 7942 was inserted into maize using Agrobacterium-mediated transformation. In three controlled-environment experiments, ictB insertion increased leaf starch and sucrose content by up to 25% relative to controls. Experimental field trials in four growing seasons, spanning the Midwestern United States (Summers 2018 & 2019) and Argentina (Winter 2018 & 2019), showed an average of 3.49% grain yield improvement, by as much as 5.4% in a given season and up to 9.4% at certain trial locations. A subset of field trial locations was used to test for modification of ear traits and ФPSII, a proxy for photosynthesis. Results suggested that yield gain in transgenics could be associated with increased ФPSII, and the production of longer, thinner ears with more kernels. ictB localized primarily to the microsome fraction of leaf bundle-sheath cells, but not to chloroplasts. Extramembrane domains of ictB interacted in vitro with proteins involved in photosynthesis and carbohydrate metabolism. To our knowledge, this is the first published evidence of ictB insertion into a species using C4 photosynthesis and the largest-scale demonstration of grain yield enhancement from ictB insertion in planta. Results show that ictB is a valuable yield gene in the economically important crop maize, and are an important proof of concept that transgenic manipulation of photosynthesis can be used to create economically viable crop improvement traits.

Recent progress in synthesis of carbohydrates with sugar nucleotide-dependent glycosyltransferases.

Sugar nucleotide-dependent glycosyltransferases (GTs) are key enzymes that catalyze the formation of glycosidic bonds in nature. They have been increasingly applied in the synthesis of complex carbohydrates and glycoconjugates with or without in situ generation of sugar nucleotides. Human GTs are becoming more accessible and new bacterial GTs have been identified and characterized. An increasing number of crystal structures elucidated for GTs from mammalian and bacterial sources facilitate structure-based design of mutants as improved catalysts for synthesis. Automated platforms have also been developed for chemoenzymatic synthesis of carbohydrates. Recent progress in applying sugar nucleotide-dependent GTs in enzymatic and chemoenzymatic synthesis of mammalian glycans and glycoconjugates, bacterial surface glycans, and glycosylated natural products from bacteria and plants are reviewed.

Influence of Low Salt Concentration on Growth Behavior and General Biomass Composition in Lyngbya purpurem (Cyanobacteria).

Cyanobacteria are essential for the vast number of compounds they produce and the possible applications in the pharmaceutical, cosmetical, and food industries. As Lyngbya species' characterization is limited in the literature, we characterize this cyanobacterium's growth and biomass. L. purpureum was grown and analyzed under different salinities, culture media, and incubation times to determine the best conditions that favor its cell growth and the general production of proteins, carbohydrates, lipids, and some pigments as phycocyanin and chlorophyll a. In this study, each analyzed biomolecule's highest content was proteins 431.69 mg g-1, carbohydrates 301.45 mg g-1, lipids 131.5 mg g-1, chlorophyll a 4.09 mg g-1, and phycocyanin 40.4 mg g-1. These results can provide a general context of the possible uses that can be given to biomass and give an opening to investigate possible biocompounds or bio metabolites that can be obtained from it.

Application of Static Magnetic Fields on the Mixotrophic Culture of Chlorella minutissima for Carbohydrate Production.

Magnetic field (MF) can interact with the metabolism of microalgae and has an effect (positive or negative) on the synthesis of molecules. In addition to MF, the use of pentose as a carbon source for cultivating microalgae is an alternative to increase carbohydrate yield. This study aimed at evaluating the MF application on the mixotrophic culture of Chlorella minutissima in order to produce carbohydrates. MF of 30 mT was generated by ferrite magnets and applied diurnally for 12 days. The addition of 5% pentose, MF application of 30 mT, and nitrogen concentration reduced (1.25 mM of KNO3) was the best conditions to obtain higher carbohydrate concentrations. MF application of 30 mT increased biomass and carbohydrate contents in 30% and 163.1%, respectively, when compared with the assay without MF application. The carbohydrate produced can be used for bioethanol production.

Exploitation of carbohydrate processing enzymes in biocatalysis.

Exploitation of enzymes in biocatalytic processes provides scope both in the synthesis and degradation of molecules. Enzymes have power not only in their catalytic efficiency, but their chemoselectivity, regioselectivity, and stereoselectivity means the reactions they catalyze are precise and reproducible. Focusing on carbohydrate processing enzymes, this review covers advances in biocatalysis involving carbohydrates over the last 2-3 years. Given the notorious difficulties in the chemical synthesis of carbohydrates, the use of enzymes for synthesis has potential for significant impact in the future. The use of catabolic enzymes in the degradation of biomass, which can be exploited in the production of biofuels to provide a sustainable and greener source of energy, and the synthesis of molecules that have a range of applications including in the pharmaceutical and food industries will be explored.

Real-time hyperpolarized 13C magnetic resonance detects increased pyruvate oxidation in pyruvate dehydrogenase kinase 2/4-double knockout mouse livers.

The pyruvate dehydrogenase complex (PDH) critically regulates carbohydrate metabolism. Phosphorylation of PDH by one of the pyruvate dehydrogenase kinases 1-4 (PDK1-4) decreases the flux of carbohydrates into the TCA cycle. Inhibition of PDKs increases oxidative metabolism of carbohydrates, so targeting PDKs has emerged as an important therapeutic approach to manage various metabolic diseases. Therefore, it is highly desirable to begin to establish imaging tools for noninvasive measurements of PDH flux in rodent models. In this study, we used hyperpolarized (HP) 13C-magnetic resonance spectroscopy to study the impact of a PDK2/PDK4 double knockout (DKO) on pyruvate metabolism in perfused livers from lean and diet-induced obese (DIO) mice and validated the HP observations with high-resolution 13C-nuclear magnetic resonance (NMR) spectroscopy of tissue extracts and steady-state isotopomer analyses. We observed that PDK-deficient livers produce more HP-bicarbonate from HP-[1-13C]pyruvate than age-matched control livers. A steady-state 13C-NMR isotopomer analysis of tissue extracts confirmed that flux rates through PDH, as well as pyruvate carboxylase and pyruvate cycling activities, are significantly higher in PDK-deficient livers. Immunoblotting experiments confirmed that HP-bicarbonate production from HP-[1-13C]pyruvate parallels decreased phosphorylation of the PDH E1α subunit (pE1α) in liver tissue. Our findings indicate that combining real-time hyperpolarized 13C NMR spectroscopy and 13C isotopomer analysis provides quantitative insights into intermediary metabolism in PDK-knockout mice. We propose that this method will be useful in assessing metabolic disease states and developing therapies to improve PDH flux.

Ecotoxicological and biochemical effects of environmental concentrations of the plastic-bond pollutant dibutyl phthalate on Scenedesmus sp.

Phthalate esters are highly present in aquatic plastic litter, which can interfere with the biological processes in the wildlife. In this work, the commonly found freshwater microalga Scenedesmus sp. was exposed to environmental concentrations (0.02, 1 and 100 µg L-1) and to a higher concentration (500 µg L-1) of dibutyl phthalate (DBP), which is an environmental pollutant. The growth, pH variation, production of photosynthetic pigments, proteins and carbohydrates were evaluated. The main inhibition effect of DBP on the microalgal growth was observed in the first 48 h of the exposure (EC50: 41.88 µg L-1). A reduction in the photosynthetic pigment concentration was observed for the 0.02, 1 and 100 µg L-1 conditions indicating that the DBP downregulated the growth rate and affected the photosynthetic process. A significant increase in protein production was only observed under 500 µg L-1 DBP exposure. The extracellular carbohydrates production slightly decreased with the presence of DBP, with a stronger decrease occurring in the 500 µg L-1 condition. These results highlight the environmental risk evaluation and ecotoxicological effects of DBP on the production of biovaluable compounds by microalgae. The results also emphasize the importance of assessing the consequences of the environmental concentrations exposure as a result of the DBP dose-dependent correlation effects.

Carbon isotope measurements of foods containing sugar: A survey.

Over 200 sugars, high sugar content foods, and sugar-free alternative products found in Canadian supermarkets were analyzed for carbon isotope (δ13C) values, adding to the record of food items with reported δ13C values, which can aid in food authentication and human diet studies. The δ13C values of the products were mostly consistent with the photosynthetic pathway of the plant from which the main ingredients were derived. With the exception of those sugars and syrups derived from known C3 sources, all of the sugars and syrups and most of the sugar added to food products were from C4 plants such as sugar cane or corn syrup. Many sweeteners are chemically manufactured, and most reflect an intermediate δ13C value. A mixing model estimated the contribution of C3- and C4-based ingredients in foods with high sugar content, which may be used to evaluate the percentage of added sugar from C3- or C4-sources.

Optimizing real swine wastewater treatment with maximum carbohydrate production by a newly isolated indigenous microalga Parachlorella kessleri QWY28.

In this study, a newly discovered microalga Parachlorella kessleri QWY28 with a superior ability to treat real swine wastewater, was isolated and explored. The optimal culture conditions of 30 °C and 600 µmol/m2·s were set to improve the practical application potential, achieving maximum pollutant removal efficiencies of 88% COD, 95% TN and almost 100% TP, with carbohydrate production at 646 mg/L·d. These results present the highest efficiencies reported to date, for non-sterilized real swine wastewater without pretreatment. These findings support the practical feasibility of combined microalgal swine wastewater purification and energy production systems.