Regulatory Properties of the ADP-Glucose Pyrophosphorylase from the Clostridial Firmicutes Member Ruminococcus albus

Study of two glycosyltransferases related to polysaccharide biosynthesis in Rhodococcus jostii RHA1

The bacterial genus Rhodococcus comprises organisms performing oleaginous behaviors under certain growth conditions and ratios of carbon and nitrogen availability. Rhodococci are outstanding producers of biofuel precursors, where lipid and glycogen metabolisms are closely related. Thus, a better understanding of rhodococcal carbon partitioning requires identifying catalytic steps redirecting sugar moieties to storage molecules. Here, we analyzed two GT4 glycosyl-transferases from Rhodococcus jostii (RjoGlgAb and RjoGlgAc) annotated as α-glucan-α-1,4-glucosyl transferases, putatively involved in glycogen synthesis. Both enzymes were produced in Escherichia coli cells, purified to homogeneity, and kinetically characterized. RjoGlgAb and RjoGlgAc presented the "canonical" glycogen synthase activity and were actives as maltose-1P synthases, although to a different extent. Then, RjoGlgAc is a homologous enzyme to the mycobacterial GlgM, with similar kinetic behavior and glucosyl-donor preference. RjoGlgAc was two orders of magnitude more efficient to glucosylate glucose-1P than glycogen, also using glucosamine-1P as a catalytically efficient aglycon. Instead, RjoGlgAb exhibited both activities with similar kinetic efficiency and preference for short-branched α-1,4-glucans. Curiously, RjoGlgAb presented a super-oligomeric conformation (higher than 15 subunits), representing a novel enzyme with a unique structure-to-function relationship. Kinetic results presented herein constitute a hint to infer on polysaccharides biosynthesis in rhodococci from an enzymological point of view.

A critical inter-subunit interaction for the transmission of the allosteric signal in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase

ADP-glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter-subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6-phosphate and pyruvate. Three pairs of distinct subunit-subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning mutagenesis showed that a mutation at the Arg11 position disrupted the activation of the enzyme. Considering the distance of these residues from the allosteric and catalytic sites, we hypothesized that the interaction between Arg11 and Asp141 is critical for allosteric signaling rather than effector binding. To prove our hypothesis, we mutated those two sites (D141A, D141E, D141N, D141R, R11D, and R11K) and performed kinetic and binding analysis. Mutations that altered the charge affected the regulation the most. To prove that the interaction per se (rather than the presence of specific residues) is critical, we partially rescued the R11D protein by introducing a second mutation (R11D/D141R). This could not restore the activator effect on kcat , but it did rescue the effect on substrate affinity. Our results indicate the critical functional role of Arg11 and Asp141 to relay the allosteric signal in this subunit interface.

Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait

The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.

Carbohydrate Metabolism in Bacteria: Alternative Specificities in ADP-Glucose Pyrophosphorylases Open Novel Metabolic Scenarios and Biotechnological Tools

We explored the ability of ADP-glucose pyrophosphorylase (ADP-Glc PPase) from different bacteria to use glucosamine (GlcN) metabolites as a substrate or allosteric effectors. The enzyme from the actinobacteria Kocuria rhizophila exhibited marked and distinctive sensitivity to allosteric activation by GlcN-6P when producing ADP-Glc from glucose-1-phosphate (Glc-1P) and ATP. This behavior is also seen in the enzyme from Rhodococcus spp., the only one known so far to portray this activation. GlcN-6P had a more modest effect on the enzyme from other Actinobacteria (Streptomyces coelicolor), Firmicutes (Ruminococcus albus), and Proteobacteria (Agrobacterium tumefaciens) groups. In addition, we studied the catalytic capacity of ADP-Glc PPases from the different sources using GlcN-1P as a substrate when assayed in the presence of their respective allosteric activators. In all cases, the catalytic efficiency of Glc-1P was 1-2 orders of magnitude higher than GlcN-1P, except for the unregulated heterotetrameric protein (GlgC/GgD) from Geobacillus stearothermophilus. The Glc-1P substrate preference is explained using a model of ADP-Glc PPase from A. tumefaciens based on the crystallographic structure of the enzyme from potato tuber. The substrate-binding domain localizes near the N-terminal of an α-helix, which has a partial positive charge, thus favoring the interaction with a hydroxyl rather than a charged primary amine group. Results support the scenario where the ability of ADP-Glc PPases to use GlcN-1P as an alternative occurred during evolution despite the enzyme being selected to use Glc-1P and ATP for α-glucans synthesis. As an associated consequence in such a process, certain bacteria could have improved their ability to metabolize GlcN. The work also provides insights in designing molecular tools for producing oligo and polysaccharides with amino moieties.

Structure, function, and evolution of plant ADP-glucose pyrophosphorylase

This review outlines research performed in the last two decades on the structural, kinetic, regulatory and evolutionary aspects of ADP-glucose pyrophosphorylase, the regulatory enzyme for starch biosynthesis. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the pathway of glycogen and starch synthesis in bacteria and plants, respectively. Plant ADP-Glc PPase is a heterotetramer allosterically regulated by metabolites and post-translational modifications. In this review, we focus on the three-dimensional structure of the plant enzyme, the amino acids that bind the regulatory molecules, and the regions involved in transmitting the allosteric signal to the catalytic site. We provide a model for the evolution of the small and large subunits, which produce heterotetramers with distinct catalytic and regulatory properties. Additionally, we review the various post-translational modifications observed in ADP-Glc PPases from different species and tissues. Finally, we discuss the subcellular localization of the enzyme found in grain endosperm from grasses, such as maize and rice. Overall, this work brings together research performed in the last two decades to better understand the multiple mechanisms involved in the regulation of ADP-Glc PPase. The rational modification of this enzyme could improve the yield and resilience of economically important crops, which is particularly important in the current scenario of climate change and food shortage.

The ADP-glucose pyrophosphorylase from Melainabacteria: a comparative study between photosynthetic and non-photosynthetic bacterial sources

Until recently, the cyanobacterial phylum only included oxygenic photosynthesizer members. The discovery of Melainabacteria as a group of supposed non-photosynthetic cyanobacteria asked to revisit such scenario. From metagenomic data, we were able to identify sequences encoding putative ADP-glucose pyrophosphorylases (ADP-GlcPPase) from free-living and intestinal Melainabacteria. The respective genes were de novo synthesized and over-expressed in Escherichia coli. The purified recombinant proteins from both Melainabacteria species were active as ADP-GlcPPases, exhibiting V_max values of 2.3 (free-living) and 7.1 U/mg (intestinal). The enzymes showed similar S_0.5 values (∼0.3 mM) for ATP, while the one from the intestinal source exhibited a 6-fold higher affinity toward glucose-1P. Both recombinant ADP-GlcPPases were sensitive to glucose-6P activation (A_0.5 ∼0.3 mM) and Pi and ADP inhibition (I_0.5 between 0.2 and 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. As far as we know, this is the first biochemical characterization of an active enzyme from Melainabacteria. This work contributes to a better understanding of the evolution of allosteric regulation in the ADP-GlcPPase family, which is critical for synthesizing the main reserve polysaccharide in prokaryotes (glycogen) and plants (starch). In addition, our results offer further information to discussions regarding the phylogenetic position of Melainabacteria.

Effects of pH on ex-situ biomethanation with hydrogenotrophic methanogens under thermophilic and extreme-thermophilic conditions

Ex-situ biogas upgrading based on hydrogenotrophic methanogenic process has attracted much attention with the depletion of fossil fuels. Consumption of CO₂ leads to the pH increase in the mixed cultures of biogas upgrading system. The hydrogenotrophic methanogens were enriched at pH 5.5-6.0, 7.0-7.5, and 8.5-9.0 and at 55°C and 70°C. The methane production activity and microbial community structure were evaluated. Semi-continuous experimental results showed that stable and similar methane production was obtained at pH 7.0-7.5 and 8.5-9.0. In addition, pH 8.5-9.0 presented higher maximum methane production rate compared to pH 7.0-7.5. pH below 6 obtained the longest lag phase time of about 17.4 h, more than twice the values at pH 7.0-7.5 (8.8 h) and pH 8.5-9.0 (6.9 h) at 55°C. The predominant methanogen was the genus Methanothermobacter, a hydrogenotrophic methanogen at higher temperatures. Methanobacterium became predominant at pH 8.5-9.0 and the abundance increased to 83.6% at 55°C. Coprothermobacter and Caldanaerobacter were identified as the core functional bacteria under alkaline condition and were likely involved in syntrophic acetate oxidation with hydrogenotrophic methanogens.

Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types

Background:

The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types.

Objective:

In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere microbiota prosperous at the root of Dangshan Su pear growing in sandy soil and clay soil.

Methods:

A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several common bacterial and fungal communities were found to be essential to Dangshan Su pear by using a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified through variance analysis and further characterized in the genus level.

Result:

Dangshan Su pears host rich and diverse microbial communities in thin layer of soil adhering to their roots. The composition of dominant microbial phyla is similar across different soil types, but the quantity of each microbial community varies significantly. Specially, the relative abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay to sandy, which can be not only conducive to the degradation of complex plant materials, but also responsible for the disinfestation of pathogens.

Conclusion:

Our results have a symbolic significance for the potential efforts of rhizosphere microbiota on the soil bioavailability and plant health. Through selecting soil types and altering microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be achieved.

The comparison of transcriptomic response of green microalga Chlorella sorokiniana exposure to environmentally relevant concentration of cadmium(II) and 4-n-nonylphenol

The transcriptomic response of green microalga Chlorella sorokiniana exposure to environmentally relevant concentration of cadmium(II) (Cd) and 4-n-nonylphenol (4-n-NP) was compared in the present study. Cd and 4-n-NP exposure showed a similar pattern of dys-regulated pathways. The photosystem was affected due to suppression of chlorophyll biosynthesis via down-regulation of Mg-protoporphyrin IX chelatase subunit ChlD (CHLD) and divinyl chlorophyllide a 8-vinyl-reductase (DVR) in Cd group and via down-regulation of DVR in 4-n-NP group. Furthermore, the reactive oxygen species (ROS) could be induced through down-regulation of solanesyl diphosphate synthase 1 (SPS1) and homogentisate phytyltransferase (HPT) in Cd group and via down-regulation of HPT in 4-n-NP group. Additionally, Cd and 4-n-NP would both cause the dys-regulation of carbohydrate metabolism and protein synthesis. On the other hand, there are some different responses or detoxification mechanism of C. sorokiniana to 4-n-NP stress compared to Cd exposure. The increased ROS would cause the DNA damage and protein destruction in Cd exposure group. Simultaneously, the RNA transcription was dys-regulated and a series of changes in gene expressions were observed. This included lipid metabolism, protein modification, and DNA repair, which involved in response of C. sorokiniana to Cd stress or detoxification of Cd. For 4-n-NP exposure, no effect on lipid metabolism and DNA repair was observed. The nucleotide metabolism including pyrimidine metabolism and purine metabolism was significantly up-regulated in the 4-n-NP exposure group, but not in the Cd exposure group. In addition, 4-n-NP would induce the ubiquitin-mediated proteolysis and proteasomal degradation to diminish the misfolded protein caused by ROS and down-regulation of heat shocking protein 40. In sum, the Cd and 4-n-NP could cause the same toxicological effects via the common pathways and possess similar detoxification mechanism. They also showed different responses in nucleotide metabolism, lipid metabolism, and DNA repair.

Mapping of a Regulatory Site of the Escherichia coli ADP-Glucose Pyrophosphorylase

The enzyme ADP-glucose pyrophosphorylase (ADP-Glc PPase) controls the biosynthesis of glycogen in bacteria and starch in plants. It is regulated by various activators in different organisms according to their metabolic characteristics. In Escherichia coli, the major allosteric activator is fructose 1,6-bisphosphate (FBP). Other potent activator analogs include 1,6-hexanediol bisphosphate (HBP) and pyridoxal 5'-phosphate (PLP). Recently, a crystal structure with FBP bound was reported (PDB ID: 5L6S). However, it is possible that the FBP site found is not directly responsible for the activation of the enzyme. We hypothesized FBP activates by binding one of its phosphate groups to another site ("P1") in which a sulfate molecule was observed. In the E. coli enzyme, Arg40, Arg52, and Arg386 are part of this "P1" pocket and tightly complex this sulfate, which is also present in the crystal structures of ADP-Glc PPases from Agrobacterium tumefaciens and Solanum tuberosum. To test this hypothesis, we modeled alternative binding conformations of FBP, HBP, and PLP into "P1." In addition, we performed a scanning mutagenesis of Arg residues near potential phosphate binding sites ("P1," "P2," "P3"). We found that Arg40 and Arg52 are essential for FBP and PLP binding and activation. In addition, mutation of Arg386 to Ala decreased the apparent affinity for the activators more than 35-fold. We propose that the activator binds at this "P1" pocket, as well as "P2." Arg40 and Arg52 are highly conserved residues and they may be a common feature to complex the phosphate moiety of different sugar phosphate activators in the ADP-Glc PPase family.