Breakdown Pathway Research Articles

Semi-global Chemical Kinetic Mechanism for FAME Combustion Modeling

ABSTRACT Modeling of combustion engines using computational fluid dynamics (CFD), to investigate and improve performance of biodiesel combustion, calls for development of small and efficient chemical kinetics mechanisms that accurately represent ignition and flame propagation of renewable fuels. In this work, a semi-global approach is used to develop a mechanism suitable for three-dimensional CFD of fatty acid methyl esters (FAME) in compression ignition engines. The mechanism includes five FAME fuel constituents that are the main compounds in FAME fuels such as rapeseed, palm and soybean. Each FAME fuel constituent is modeled using individual fuel breakdown pathways, creating a highly versatile and compact reaction mechanism, capable of modeling any constituent combination and hence almost any FAME fuel blend. The presented mechanism accurately represents the important ignition properties of the fuels and fuel constituents, including the low-temperature chemistry. It is validated against available experimental data as well as a highly detailed reaction mechanism. The presented mechanism offers a unique combination of fuel flexibility, mechanism performance and a low computational cost.

Exploration of Sugar and Starch Metabolic Pathway Crucial for Pollen Fertility in Rice.

Starch is the primary storage carbohydrate in mature pollen grains in many crop plants, including rice. Impaired starch accumulation causes male sterility because of the shortage of energy and building blocks for pollen germination and pollen tube growth. Thus, starch-defective pollen is applicable for inducing male sterility and hybrid rice production. Despite the importance of pollen starch, the details of the starch biosynthesis and breakdown pathway in pollen are still largely unknown. As pollen is isolated from the maternal tissue, photoassimilate transported from leaves must pass through the apoplastic space from the anther to the filial pollen, where it is stored as starch. Several sugar transporters and enzymes are involved in this process, but many are still unknown. Thus, the current review provides possible scenarios for sucrose transport and metabolic pathways that lead to starch biosynthesis and breakdown in rice pollen.

TMIC-38. CD39 EXPRESSION IN GLIOBLASTOMA TUMOR MICROENVIRONMENT DOES NOT AFFECT SURVIVAL OR T-CELL EXHAUSTION

Abstract Glioblastoma (GBM) is the most common malignant brain tumor with a median survival of 15 months. GBM is very difficult to treat due to numerous factors, including the paucity of immune infiltration of the tumor itself. Efforts to overcome this have led to use of immune checkpoint inhibitors such as PD-1 inhibitor, which have revolutionized treatment of many other solid tumors, and yet have not been successful in the treatment of GBM. This has led to many studies investigating various other similar markers. One such marker is CD39, which is highly upregulated in GBM and functions as the first enzyme in the metabolic pathway of ATP breakdown to adenosine. Additionally, CD39 is thought to contribute to T-cell exhaustion. Like PD-1, CD39 inhibition has had preliminary success in the treatment of other solid tumors. However, when tested on GBM, blocking the ATP breakdown pathway did not improve survival in mice, even in conjunction with PD-1 inhibition. Our team sought to determine if the expression of CD39 on the cell surface functioned as an exhaustion marker by injecting two different cell lines of GBM into CD39 global null mice. There was no survival benefit seen in either cell line when compared to wild type mice. Next, expression of known exhaustion markers such as PD-1, TIM3, and LAG3 on tumor infiltrating lymphocytes were analyzed. Expression of TIM3 and 2B4 were found to be increased in CD39KO mice in comparison to wild type (p < 0.01). Additionally, numerous exhaustion markers such as LAG3, TIGIT, and CTLA4 were decreased on tumor in comparison to peripheral blood (p < 0.01). These results demonstrate the complex nature of immune signaling in GBM tumor microenvironment that our team continues to investigate.

High-entropy assisted BaTiO3-based ceramic capacitors for energy storage

The market-dominating material BaTiO 3 is highly crucial in advanced electronics and electric power systems owing to its fast charging/discharging speed and superior cycle life. However, the low energy storage efficiency and breakdown strength hinder further device miniaturization for energy storage applications. Herein, we design a high configurational entropy (HCE) material BaTiO 3 -BiFeO 3 -CaTiO 3 with rational microstructural engineering that demonstrates an ultrahigh energy density of 7.2 J cm −3 . The HCE design leads to the increased solubility of CaTiO 3 in the matrix, which enhances the resistivity and polarization. Simultaneously, the nano-segregations around the grains can enhance the breakdown strength obviously due to strongly scattering of electron carriers and impeding of electrical breakdown pathways. Furthermore, the multilayer ceramic capacitors (MLCCs) using such dielectrics were constructed with energy density of 16.6 J cm −3 and efficiency of 83%. This work offers a route to explore new dielectric materials that are expected to benefit dielectric devices' compactness and high performance. • High-entropy relaxor-ferroelectric is designed and synthesized • Special microstructure related to the improvement of electric breakdown strength • High energy storage density of 16.6 Jcm −3 is achieved in the MLCC Qi et al. report a high-entropy relaxor-ferroelectric material BaTiO 3 -BiFeO 3 -CaTiO 3 with rational microstructural engineering. They achieve an ultrahigh energy density of 16.6 J cm −3 , and efficiency of 83% in a prototype MLCC device.

Identification of a S-(2-succino)cysteine breakdown pathway that uses a novel S-(2-succino) lyase

Succination is the spontaneous reaction between the respiratory intermediate fumarate and cellular thiols that forms stable S-(2-succino)-adducts such as S-(2-succino)cysteine (2SC). 2SC is a biomarker for conditions associated with elevated fumarate levels, including diabetes, obesity, and certain cancers, and succination likely contributes to disease progression. Bacillus subtilis has a yxe operon-encoded breakdown pathway for 2SC that involves three distinct enzymatic conversions. The first step is N-acetylation of 2SC by YxeL to form N-acetyl-2SC (2SNAC). YxeK catalyzes the oxygenation of 2SNAC, resulting in its breakdown to oxaloacetate and N-acetylcysteine, which is deacetylated by YxeP to give cysteine. The monooxygenase YxeK is key to the pathway but is rare, with close homologs occurring infrequently in prokaryote and fungal genomes. The existence of additional 2SC breakdown pathways was not known prior to this study. Here, we used comparative genomics to identify a S-(2-succino) lyase (2SL) that replaces yxeK in some yxe gene clusters. 2SL genes from Enterococcus italicus and Dickeya dadantii complement B.subtilis yxeK mutants. We also determined that recombinant 2SL enzymes efficiently break down 2SNAC into fumarate and N-acetylcysteine, can perform the reverse reaction, and have minor activity against 2SC and other small molecule thiols. The strong preferences both YxeK and 2SL enzymes have for 2SNAC indicate that 2SC acetylation is a conserved breakdown step. The identification of a second naturally occurring 2SC breakdown pathway underscores the importance of 2SC catabolism and defines a general strategy for 2SC breakdown involving acetylation, breakdown, and deacetylation.

Plant N-glycan breakdown by human gut Bacteroides

The major nutrients available to the human colonic microbiota are complex glycans derived from the diet. To degrade this highly variable mix of sugar structures, gut microbes have acquired a huge array of different carbohydrate-active enzymes (CAZymes), predominantly glycoside hydrolases, many of which have specificities that can be exploited for a range of different applications. Plant N-glycans are prevalent on proteins produced by plants and thus components of the diet, but the breakdown of these complex molecules by the gut microbiota has not been explored. Plant N-glycans are also well characterized allergens in pollen and some plant-based foods, and when plants are used in heterologous protein production for medical applications, the N-glycans present can pose a risk to therapeutic function and stability. Here we use a novel genome association approach for enzyme discovery to identify a breakdown pathway for plant complex N-glycans encoded by a gut Bacteroides species and biochemically characterize five CAZymes involved, including structures of the PNGase and GH92 α-mannosidase. These enzymes provide a toolbox for the modification of plant N-glycans for a range of potential applications. Furthermore, the keystone PNGase also has activity against insect-type N-glycans, which we discuss from the perspective of insects as a nutrient source.

Model simulation and mechanism of Fe(0/II/III) cycle activated persulfate degradation of methylparaben based on hydroxylamine enhanced nano-zero-valent iron

The mechanism of Fe2+-activated peroxodisulfate (PDS) by hydroxylamine (HA) has been investigated, however, nano zero-valent iron-activated persulfate (nZVI/PDS) has a more optimal effect and needs further investigation. This study investigated the addition of HA to nZVI/PDS to improve Fe2+ regeneration and accelerate methylparaben (MP) degradation by Fe (0/II/III) cycle. After 60 min of reaction, the HA-enhanced nZVI/PDS (HA/nZVI/PDS) system afforded a 21% increase in MP degradation, reaching 93.26% (1 mM HA, 1 mM nZVI, and 2 mM PDS). nZVI/PDS system was a second-order reaction, but after adding HA, the reaction was more suitable for the first-order reaction. The addition of HA effectively promoted the reduction of Fe3+ to Fe2+ to improve the effect and reaction rate of PDS degradation of MP (k increased from 0.0127 min−1 to 0.0198 min−1) and broadened the reaction pH range. The results of various characterizations of nZVI before and after the reaction revealed that nZVI changed from a spherical structure to a bundle structure and was slightly oxidized. Changes in the Fe2+ and Fe3+ concentrations as well as in the pH of the reaction systems were monitored and the possible reactions of the HA/nZVI/PDS system were derived for the first time (knZVI/PDS<3.7 × 106 M−1 s−1, kFe3+/NH2O· >4.2 min−1). 12 potential compounds were investigated and MP breakdown pathways were speculated; hydroxylation was determined to be the most important pathway of degradation. And the HA/nZVI/PDS system had universal applicability.

Poplar leaf abscission through induced chlorophyll breakdown by Mg-dechelatase

Chlorophyll breakdown is observed during senescence. The first step in chlorophyll breakdown is the removal of central Mg by Mg-dechelatase. This reaction is the rate-limiting step in the chlorophyll breakdown pathway. We evaluated the effect of induced chlorophyll breakdown on abscission through the removal of Mg by Mg-dechelatase. Poplar transformants carrying the dexamethasone-inducible Mg-dechelatase gene were prepared using the Arabidopsis Stay-Green1 cDNA. When leaves were treated with dexamethasone, chlorophyll was degraded, photosynthetic capacity was reduced, and an abscission zone was formed, resulting in leaf abscission. In addition, ethylene, which plays an important role during senescence, was produced in this process. Thus, chlorophyll breakdown induces the phenotype in the same way as commonly observed during leaf senescence. This study suggests a physiological role of chlorophyll breakdown in the leaf abscission of deciduous trees. Furthermore, this study shows that the dexamethasone-inducible gene expression system is an available option for deciduous tree studies.

Chemometric Quality Assessment of Doxylamine Succinate With Its Degradation Product: Implementation of Two Predictive Models on UV-Spectrophotometric Data of Anti-Emetic Binary Mixture.

The combination of pyridoxine hydrochloride (PYR) and doxylamine succinate (DOX) as an antiemetic binary mixture is used to treat nausea and vomiting during pregnancy. Two validated, accurate, and selective chemometric models were developed to assay binary mixture in the presence of DOX oxidative degradation product (DOX DEG) that could be characterized using LC-MS. Partial least squares (PLS) regression and principal component regression (PCR) were selected for the determination of our binary mixture in presence of degradation. To exhibit a training set of 25 mixtures that had various percentages of tested substances in five level 3 variables, an experimental design was chosen. A set of 18 synthetic mixtures in the concentration range 10.0-50.0 μg/mL, 12.00-20.0 μg/mL, and 6.0-30.0 μg/mL for PYR, DOX, and DOX DEG, respectively, were used in the construction of the calibration models.Then set of seven synthetic mixtures with different concentrations were used in the construction of the validation models. In validation samples with low root mean square error of prediction (RMSEP), the suggested models successfully predicted the concentrations of our drugs. The models developed were evaluated by RMSEP calculation, and the values obtained were 0.341, 0.196, and 0.388 for PYR, DOX, and DOX DEG, respectively, using PLS. While using PCR, RMSEP calculation and the values obtained were 0.400, 0.256, and 0.375 for PYR, DOX, and DOX DEG, respectively. The developed models were validated according to ICH strategies. The corresponding methods are suitable to determine PYR and DOX in pure form, pharmaceutical dosage form, and in the presence of DOX DEG product. The study of drug breakdown pathways is very important nowadays, so even in the presence of degradation and extreme spectral overlapping, the suggested PLS and PCR spectrophotometric approaches were able to identify PYR and DOX.

C. elegans as a model for inter-individual variation in metabolism.

Individuals can exhibit differences in metabolism that are caused by the interplay of genetic background, nutritional input, microbiota and other environmental factors1-4. It is difficult to connect differences in metabolism to genomic variation and derive underlying molecular mechanisms in humans, owing to differences in diet and lifestyle, among others. Here we use the nematode Caenorhabditis elegans as a model to study inter-individual variation in metabolism. By comparing three wild strains and the commonly used N2 laboratory strain, we find differences in the abundances of both known metabolites and those that have not to our knowledge been previously described. The latter metabolites include conjugates between 3-hydroxypropionate (3HP) and several amino acids (3HP-AAs), which are much higher in abundance in one of the wild strains. 3HP is an intermediate in the propionate shunt pathway, which is activated when flux through the canonical, vitamin-B12-dependent propionate breakdown pathway is perturbed5. We show that increased accumulation of 3HP-AAs is caused by genetic variation in HPHD-1, for which 3HP is a substrate. Our results suggest that the production of 3HP-AAs represents a 'shunt-within-a-shunt' pathway to accommodate a reduction-of-function allele in hphd-1. This study provides a step towards the development of metabolic network models that capture individual-specific differences of metabolism and more closely represent the diversity that is found in entire species.

Cold plasma treatment of porous scaffolds: Design principles

AbstractThree‐dimensional porous scaffolds have the potential to revolutionize a number of fields, including stem cell research, biomedical implants, tissue engineering, and regeneration, as well as energy technologies, filtration, and sensing. The ability to precisely engineer their surface properties is paramount to successful and enduring application. Plasma treatments promise to deliver homogeneous surfaces with tailored characteristics while generating few by‐products and not relying on the diffusion of liquids into a porous network. However, forming plasma inside complex interconnected pores is a significant challenge and requires much parameter fine‐tuning. This study uses numerical modeling to investigate key parameters which affect plasma breakdown and makes practical recommendations for achieving treatment homogeneity. We consider a dielectric barrier discharge (DBD) system, where nitrogen gas flows through a glass tube containing a porous scaffold, which is surrounded by a cylindrical electrode, with ground electrodes at either end of the tube. The parameters investigated include the scaffolds' pore size and porosity as well as electrode size and position. The results showed that homogeneous treatment is achieved by avoiding alternative breakdown pathways such as a poor seal between the scaffold and the glass containment tube, using a narrow supply electrode centered at the scaffold, and positioning ground electrodes as close as possible to the supply electrode without arcing. This strategy maximizes the electric field strength at a given voltage, allowing for higher pressures to be used, which in turn give a more homogeneous mean free path inside the pores.

Dietary vitamin B12 regulates chemosensory receptor gene expression via the MEF2 transcription factor in Caenorhabditis elegans.

Dynamic changes in chemoreceptor gene expression levels in sensory neurons are one strategy that an animal can use to modify their responses to dietary changes. However, the mechanisms underlying diet-dependent modulation of chemosensory gene expression are unclear. Here, we show that the expression of the srh-234 chemoreceptor gene localized in a single ADL sensory neuron type of Caenorhabditis elegans is downregulated when animals are fed a Comamonas aquatica bacterial diet, but not on an Escherichia coli diet. Remarkably, this diet-modulated effect on srh-234 expression is dependent on the micronutrient vitamin B12 endogenously produced by Comamonas aq. bacteria. Excess propionate and genetic perturbations in the canonical and shunt propionate breakdown pathways are able to override the repressive effects of vitamin B12 on srh-234 expression. The vitamin B12-mediated regulation of srh-234 expression levels in ADL requires the MEF-2 MADS domain transcription factor, providing a potential mechanism by which dietary vitamin B12 may transcriptionally tune individual chemoreceptor genes in a single sensory neuron type, which in turn may change animal responses to biologically relevant chemicals in their diet.

Organellar homeostasis and innate immune sensing.

A cell is delimited by numerous borders that define specific organelles. The walls of some organelles are particularly robust, such as in mitochondria or endoplasmic reticulum, but some are more fluid such as in phase-separated stress granules. Either way, all organelles can be damaged at times, leading their contents to leak out into the surrounding environment. Therefore, an elegant way to construct an innate immune defence system is to recognize host molecules that do not normally reside within a particular compartment. Here, we provide several examples where organellar homeostasis is lost, leading to the activation of a specific innate immune sensor; these include NLRP3 activation owing to a disrupted trans-Golgi network, Pyrin activation due to cytoskeletal damage, and cGAS-STING activation following the leakage of nuclear or mitochondrial DNA. Frequently, organelle damage is observed downstream of pathogenic infection but it can also occur in sterile settings as associated with auto-inflammatory disease. Therefore, understanding organellar homeostasis is central to efforts that will identify new innate immune pathways, and therapeutics that balance organellar homeostasis, or target the breakdown pathways that trigger innate immune sensors, could be useful treatments for infection and chronic inflammatory diseases.

A199 UTILIZATION OF MUCUS-DERIVED O-GLYCAN SUGARS BY THE PATHOGEN C. RODENTIUM FACILITATE ITS COLONIZATION OF THE MURINE GUT

BackgroundThe ability of enteric pathogens to colonize and expand within the mammalian gastrointestinal (GI) tract is determined by several factors, including the ability to find and acquire nutrients. The thick mucus layer that lines the inner surface of the large intestine is rich in sugars that can serve as nutrient sources for several members of the microbiota. Whether these sugars can also be used by invading bacterial pathogens to colonize the GI tract is still unclear, in particular for the family of attaching and effacing (A/E) bacterial pathogens, including the human diarrheal pathogens EHEC and EPEC.AimsTo investigate the ability of the murine A/E pathogen Citrobacter rodentium to use mucin-derived sugars as a nutrient source, and the importance of these sugars in the virulence of C. rodentium during in-vivo infection.MethodsTo identify which sugar(s) are required for C. rodentium to colonize and grow in the murine GI tract, we generated mutants lacking single or multiple genes involved in the uptake and catabolism of mucin-derived O-glycan sugars. This was followed by in-vitro growth assays in minimal media supplemented with mucin sugars to investigate the growth properties of C. rodentium and the generated mutants on mucin sugars.ResultsWe determined that C. rodentium was able to use three mucin O-glycan sugars: sialic acid, galactose, and N-acetylglucosamine (GlcNAc) as both carbon and nitrogen sources for in-vitro growth. C. rodentium exhibited the maximal growth rate and density on GlcNAc, followed by sialic acid, and finally galactose. A mutant C. rodentium strain carrying a deletion in the nagA gene was unable to grow on both GlcNAc and sialic acid, confirming that the breakdown pathways for these two sugars merge and are processed by shared suite of enzymes. As for galactose, combined deletions in the genes mglB and galP were required to abolish growth on this sugar. Notably, a mutant strain carrying simultaneous deletions in nagA, mglB, and galP was unable to grow on all three mucin sugars, as well as on purified mucin.ConclusionsOur results demonstrate that intestinal mucin sugars serve as potential nutrient sources for C. rodentium and that C. rodentium can catabolize three of these sugars. Future work will examine whether these sugar pathways contribute to C. rodentium colonization of the murine GI tract.Funding AgenciesCCC, CIHRCH.I.L.D. Fdn

Microbial communication during bioremediation of polyaromatic hydrocarbons

Human activity pollution has been shown to harm the environment, ecology, and health impacts. The polycyclic aromatic hydrocarbons (PAHs) produced by the industries such as tannery, distillery, pulp paper, and oil refineries are a major source of contaminant. PAHs are found all across the world, owing to long-term human pollution sources. PAHs' physico-chemical features, such as hydrophobicity and electrochemical stability, contribute to their environmental persistence and contribute to their carcinogenic and health effects. Numerous analytical and biological techniques for the qualitative and quantitative assessment of PAHs have been proposed. Bioaccumulation, adsorption, chemical oxidation, photolysis, volatilization, and microbiological degradation are the principal breakdown pathways of PAHs in the environment. Microbial populations, such as bacteria, fungi, and algae, play a crucial role in the biological elimination of PAHs. Oxidase, manganese peroxidases, lipases, and laccases are the enzymes involved in PAHs breakdown. The synthesis of surfactants by bacteria increases PAHs bioavailability and improves the elimination process of PAHs. Temperature, pH, aeration, moisture content, nutrition availability, absence of hazardous chemicals, and the kind and number of degrading microbial populations are all factors that influence PAHs decomposition. Microbial degradation mechanisms result in intermediate metabolites and carbon dioxide mineralization. The elimination of PAHs is improved by molecular approaches such as gene engineering and protein engineering. This review discussed the benefits of bioremediation strategies that were investigated for precise evaluation and were trusted at both the regulatory and scientific studies levels.

Color recycling: metabolization of apocarotenoid degradation products suggests carbon regeneration via primary metabolic pathways

Key messageAnalysis of carotenoid-accumulating roots revealed that oxidative carotenoid degradation yields glyoxal and methylglyoxal. Our data suggest that these compounds are detoxified via the glyoxalase system and re-enter primary metabolic pathways.Carotenoid levels in plant tissues depend on the relative rates of synthesis and degradation. We recently identified redox enzymes previously known to be involved in the detoxification of fatty acid-derived reactive carbonyl species which were able to convert apocarotenoids into corresponding alcohols and carboxylic acids. However, their subsequent metabolization pathways remain unresolved. Interestingly, we found that carotenoid-accumulating roots have increased levels of glutathione, suggesting apocarotenoid glutathionylation to occur. In vitro and in planta investigations did not, however, support the occurrence of non-enzymatic or enzymatic glutathionylation of β-apocarotenoids. An alternative breakdown pathway is the continued oxidative degradation of primary apocarotenoids or their derivatives into the shortest possible oxidation products, namely glyoxal and methylglyoxal, which also accumulated in carotenoid-accumulating roots. In fact, combined transcriptome and metabolome analysis suggest that the high levels of glutathione are most probably required for detoxifying apocarotenoid-derived glyoxal and methylglyoxal via the glyoxalase pathway, yielding glycolate and d-lactate, respectively. Further transcriptome analysis suggested subsequent reactions involving activities associated with photorespiration and the peroxisome-specific glycolate/glyoxylate transporter. Finally, detoxified primary apocarotenoid degradation products might be converted into pyruvate which is possibly re-used for the synthesis of carotenoid biosynthesis precursors. Our findings allow to envision carbon recycling during carotenoid biosynthesis, degradation and re-synthesis which consumes energy, but partially maintains initially fixed carbon via re-introducing reactive carotenoid degradation products into primary metabolic pathways.

Insights into ultrasound-promoted degradation of naphthenic acid compounds in oil sands process affected water. Part I: Accelerated H-abstraction and decarboxylation of aromatic and alicyclic compounds

Propelled by enormous increase in demand for fuel sources, Canadian oil sands are becoming increasingly important as a fuel source due to their abundance and upgrading capability. However, extraction of bitumen, a high acid crude (HAC) oil, requires 2–3 units of water per unit of oil resulting in naphthenic acid (NA)-rich oil sands process affected water (OSPW) collected in effluent ponds. This study illustrates the role of sonochemistry in the accelerated degradation through H-abstraction and subsequent decarboxylation of aromatic and alicyclic naphthenic acid model compounds. Benzoic acid and 3-methylcyclohexane carboxylic acid were selected as model NA compounds to investigate the mechanism of hydroxyl radical (OH•) initiated carboxylic acid degradation in 378 KHz sonochemical reactor. Established FTIR methods with low resolution LCMS spectroscopy confirmation were applied to determine the extent of carboxylic acid degradation and identify the formation of products. FTIR monitoring showed a non-linear degradation of carboxylic acids with formation of many intermediates highlighting the shift from cyclic carboxylic acids to cyclic alcohols during BA degradation. Subsequent decrease in carboxylic acid groups signifies scission of cyclic structures before complete mineralization. This is confirmed with the LCMS identification of products such as: 3-hydroxybenzoic acid and phenol. This study postulated new breakdown pathways for degradation of benzoic acid with complete mineralization at a sonochemical reaction time (SRT) of 4 h. A radical quenching process was also inferred through the formation of conglomerates during sonochemical degradation of BA. Extension of the study to 3-methylcyclohexane carboxylic acid (3mCHA) shows similar non-linearity with an increase in carboxylic acid groups indicating H-abstraction followed by ring-opened compounds. However, due to the complex nature of 3mCHA’s ring-opened compounds, complete mineralization is not achieved. The putative role of sonochemistry is a promising and sustainable degradation method for mitigating NAs in OSPW, but sonication periods need to be considered carefully to ensure adequate mineralization of their constituents and combinatorial methods with other advanced oxidation methods may be needed to enhance industrial application.In Part II, an in silico screening approach using first principles is reported to identify the breakdown of the organic compounds and determine molecular rates of reaction to confirm the mechanistic origins of the compounds formed.

Enrichment of chlorophyll catabolic enzymes in grana margins and their cooperation in catabolic reactions

During leaf senescence, chlorophyll a and b are degraded through several enzymatic reactions, including chlorophyll b reductase, 7-hydroxymethyl chlorophyll a reductase, and Mg-dechelatase. Considering that the intermediates of the chlorophyll breakdown pathway are highly photoreactive, cooperative and efficient reactions of chlorophyll metabolic enzymes may protect chloroplasts from potential photo-oxidative damage. Here, we investigated the sub-organellar localization and cooperative reactions of the enzymes involved in the chlorophyll breakdown pathway by the fractionation of thylakoid membranes and enzymatic assays using recombinant proteins. We found that these enzymes were enriched in the grana margin fraction. Furthermore, we found that chlorophyll b reductase and Mg-dechelatase efficiently catabolized chlorophylls bound to the chlorophyll–protein complexes when these two enzymes were mixed. These results suggest that the co-localization of chlorophyll catabolic enzymes enables efficient chlorophyll breakdown. The results from this study highlight a key step forward in the investigation of the photosystem breakdown process.

The Osmolyte Ties That Bind: Genomic Insights Into Synthesis and Breakdown of Organic Osmolytes in Marine Microbes

The production and consumption of organic matter by marine organisms plays a central role in the marine carbon cycle. Labile organic compounds (metabolites) are the major currency of energetic demands and organismal interaction, but these compounds remain elusive because of their rapid turnover and concomitant minuscule concentrations in the dissolved organic matter pool. Organic osmolytes are a group of small metabolites synthesized at high intracellular concentrations (mM) to regulate cellular osmolarity and have the potential to be released as abundant dissolved substrates. Osmolytes may represent an essential currency of exchange among heterotrophic prokaryotes and primary and secondary producers in marine food webs. For example, the well-known metabolite dimethylsulfoniopropionate (DMSP) is used as an osmolyte by some phytoplankton and can be subsequently metabolized by 60% of the marine bacterial community, supplying up to 13% of the bacterial carbon demand and 100% of the bacterial sulfur demand. While marine osmolytes have been studied for decades, our understanding of their cycling and significance within microbial communities is still far from comprehensive. Here, we surveyed the genes responsible for synthesis, breakdown, and transport of 14 key osmolytes. We systematically searched for these genes across marine bacterial genomes (n = 897) and protistan transcriptomes (n = 652) using homologous protein profiles to investigate the potential for osmolyte metabolisms. Using the pattern of gene presence and absence, we infer the metabolic potential of surveyed microbes to interact with each osmolyte. Specifically, we identify: (1) complete pathways for osmolyte synthesis in both prokaryotic and eukaryotic marine microbes, (2) microbes capable of transporting osmolytes but lacking complete synthesis and/or breakdown pathways, and (3) osmolytes whose synthesis and/or breakdown appears to be specialized and is limited to a subset of organisms. The analysis clearly demonstrates that the marine microbial loop has the genetic potential to actively recycle osmolytes and that this abundant group of small metabolites may function as a significant source of nutrients through exchange among diverse microbial groups that significantly contribute to the cycling of labile carbon.

Differential degradation of RNA species by autophagy-related pathways in Arabidopsis.

The plant vacuole recycles proteins and RNA delivered to it by autophagy. In this study, by isolating intact vacuoles from Arabidopsis plants, followed by subsequent RNA purification, and deep sequencing, we provide a comprehensive characterization of Arabidopsis vacuolar RNAome. In the vacuolar RNAome, we detected ribosomal RNAs, transfer RNAs, including those of chloroplast origin, and in addition small RNA types. As autophagy is a main mechanism for the transport of RNA to the vacuole, atg5-1 mutants deficient in autophagy were included in our analysis. We observed severely reduced amounts of most chloroplast-derived RNA species in these mutants. Comparisons with cellular RNA composition provided an indication of possible up-regulation of alternative RNA breakdown pathways. By contrast, vacuolar RNA processing and composition in plants lacking vacuolar ribonuclease 2, involved in cellular RNA homeostasis, only showed minor alterations, possibly because of the presence of further so far unknown vacuolar RNase species. Among the small RNA types, we detected mature miRNAs in all vacuolar preparations but at much lower frequency in atg5-1, raising the possibility of a biological role for vacuolar miRNAs.