Role of maltose enzymes in glycogen synthesis by Escherichia coli

Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection

Currently, the most cost-effective and efficient method for phosphorus (P) removal from wastewater is enhanced biological P removal (EPBR) via polyphosphate-accumulating organisms (PAOs). This study integrates a literature review with genomic analysis to uncover the phylogenetic and metabolic diversity of the relevant PAOs for wastewater treatment. The findings highlight significant differences in the metabolic capabilities of PAOs relevant to wastewater treatment. Notably, Candidatus Dechloromonas and Candidatus Accumulibacter can synthesize polyhydroxyalkanoates, possess specific enzymes for ATP production from polyphosphate, and have electrochemical transporters for acetate and C4-dicarboxylates. In contrast, Tetrasphaera, Candidatus Phosphoribacter, Knoellia, and Phycicoccus possess PolyP-glucokinase and electrochemical transporters for sugars/amino acids. Additionally, this review explores various detection methods for polyphosphate and PAOs in activated sludge wastewater treatment plants. Notably, FISH-Raman spectroscopy emerges as one of the most advanced detection techniques. Overall, this review provides critical insights into PAO research, underscoring the need for enhanced strategies in biological phosphorus removal.

Role of MalQ Enzyme in a Reconstructed Maltose/Maltodextrin Pathway in Actinoplanes sp. SE50/110

The pseudotetrasaccharide acarbose, produced by Actinoplanes sp. SE50/110, is a relevant secondary metabolite used in diabetes type II medication. Although maltose plays a crucial role in acarbose biosynthesis, the understanding of the maltose/maltodextrin metabolism and its involvement in acarbose production is at an early stage. Here, we reconstructed the predicted maltose-maltodextrin pathway that involves four enzymes AmlE, MalZ, MalP, and MalQ. An investigation of enzyme activities was conducted through in vitro assays, leading to an expansion of previously postulated substrate spectra. The maltose-induced α-glucosidase AmlE is noteworthy for its high hydrolysis rate of linear α-1,4-glucans, and its capability to hydrolyze various glycosidic bonds. The predicted maltodextrin glucosidase MalZ showed slow hydrolysis activity on linear α-glucans, but it was resistant to acarbose and capable of releasing glucose from acarbose. AmlE compensates for the low activity of MalZ to ensure glucose supply. We determined the enzyme activity of MalP and its dual function as maltodextrin and glycogen phosphorylase. The 4-α-glucanotransferase MalQ plays a central role in the maltose/maltodextrin metabolism, alongside MalP. This study confirmed the simultaneous degradation and synthesis of long-chain α-glucans. The product distribution showed that with an increasing number of glycosidic bonds, less glucose is formed. We found that MalQ, like its sequence homolog AcbQ from the acarbose biosynthetic gene cluster, is involved in the formation of elongated acarviosyl metabolites. However, MalQ does not participate in the elongation of acarbose 7-phosphate, which is likely the more readily available acceptor molecule in vivo. Accordingly, MalQ is not involved in the formation of acarviosyl impurities in Actinoplanes sp. SE50/110.

Mechanism of action of three different glycogen branching enzymes and their effect on bread quality

Bread staling adversely affects the quality of bread, but starch modification by enzymes can counteract this phenomenon. Glycogen branching enzymes (GBEs) used in this study were isolated from Deinococcus geothermalis (DgGBE), Escherichia coli (EcGBE), and Vibrio vulnificus (VvGBE). These enzymes were characterized and applied for starch dough modification to determine their role in improving bread quality. First, the branching patterns, activity on amylose and amylopectin, and thermostability of the GBEs were determined and compared. EcGBE and DgGBE exhibited better thermostable characteristics than VvGBE, and all GBEs exhibited preferential catalysis of amylopectin over amylose but different degrees. VvGBE and DgGBE produced a large number of short branches. Three GBEs degraded the starch granules and generated soluble polysaccharides. Moreover, the maltose was increased in the starch slurry but most significantly in the DgGBE treatment. Degradation of the starch granules by GBEs enhanced the maltose generation of internal amylases. When used in the bread-making process, DgGBE and VvGBE increased the dough and bread volume by 9 % and 17 %, respectively. The crumb firmness and retrogradation of the bread were decreased and delayed significantly more in the DgGBE bread. Consequently, this study can contribute to understanding the detailed roles of GBEs in the baking process.

Analysis of element yield, bacterial community structure and the impact of carbon sources for bioleaching rare earth elements from high grade monazite

Rare earth element (REE) recovery from waste streams, mine tailings or recyclable components using bioleaching is gaining traction due to the shortage and security of REE supply as well as the environmental problems that occur from processing and refining. Four heterotrophic microbial species with known phosphate solubilizing capabilities were evaluated for their ability to leach REE from a high-grade monazite when provided with either galactose, fructose or maltose. Supplying fructose resulted in the greatest amount of REE leached from the ore due to the largest amount of organic acid produced. Gluconic acid was the dominant organic acid identified produced by the cultures, followed by acetic acid. The monazite proved difficult to leach with the different carbon sources, with preferential release of Ce over La, Nd and Pr.

Enhanced production of maltobionic acid by a metabolically engineered Escherichia coli incapable of maltose utilization

To produce maltobionic acid (MBA) from maltose in Escherichia coli, we recombinantly expressed a glucose dehydrogenase gene (gdh1) from Enterobacter cloacae and a pyrroloquinoline quinone (PQQ) synthesis gene cluster (pqqFABCDEMIH) from Pseudomonas taetrolens. Although the recombinant E. coli strain (E. coli [pKK-ECGDH1 + pACYC-PQQ]) successfully produced MBA from maltose, the yield of MBA was rather low, indicating that E. coli has other maltose utilization pathways. Amylomaltase (MalQ) is the first enzyme in the maltose utilization pathway in E. coli. To investigate the potential role of MalQ on MBA production, E. coli malQ was inactivated. The culturing of the recombinant E. coli strain (E. coli ∆malQ [pKK-ECGDH1 + pACYC-PQQ]) in a flask resulted in higher MBA production titer, yield, and productivity (209.3 g/L, 100%, and 1.1 g/L/h, respectively) than those of E. coli [pKK-ECGDH1 + pACYC-PQQ] (162.1 g/L, 77.4%, and 0.5 g/L/h, respectively), indicating that the MalQ inactivation was highly effective in improving the MBA production ability of E. coli. After fermentation using 5-L bioreactor, MBA production titer, yield, and productivity of the recombinant E. coli strain were 209.3 g/L, 100%, and 1.5 g/L/h, respectively, which were 1.3-, 1.3-, 2.3-fold higher than those of E. coli [pKK-ECGDH1 + pACYC-PQQ] (167.3 g/L, 79.9%, and 0.65 g/L/h), respectively. Thus, our results provide an important foundation for efficient MBA production using recombinant E. coli strain.

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.

Functional characterization of maltodextrin glucosidase for maltodextrin and glycogen metabolism in Vibrio vulnificus MO6-24/O

Glycogen is important for transmission of V. vulnificus undergoing disparate environments of nutrient-rich host and nutrient-limited marine environment. The malZ gene of V. vulnificus encoding a maltodextrin glucosidase was cloned and over-expressed in E. coli to investigate its roles in glycogen/maltodextrin metabolism in the pathogen. The malZ gene encoded a protein with a predicted molecular mass of 70 kDa. The optimal pH and temperature of MalZ was 7.0 and 37 °C, respectively. MalZ hydrolyzed maltodextrin to glucose and maltose most efficiently, while hydrolyzed other substrates such as starch, maltose, β-cyclomaltodextrin, and glycogen less efficiently. The activity was enhanced greatly by Mn²⁺. It also exhibited transglycosylation activity toward excessive maltotriose. The malZ knock-out mutant accumulated 2.3-5.6-fold less glycogen than the wild type when excessive maltodextrin or glucose was added to LB medium, while it accumulated more glycogen than the wild type (3.5-fold) in the presence of excessive maltose. Growth and glycogen accumulation of the mutant were retarded most significantly in the M63 minimal medium supplemented with 0.5% maltodextrin. Side chain length distributions of glycogen molecules were varied by the malZ mutation and types of the excessive carbon source. Based on the results, MalZ of V. vulnificus was likely to be involved in maltose/maltodextrin metabolism, thereby balancing synthesis of glycogen and energy generation in the cell. The bacterium seemed to have multiple and unique pathways for glycogen metabolism according to carbon sources.

Characterization of a cold-adapted debranching enzyme and its role in glycogen metabolism and virulence of Vibrio vulnificus MO6-24/O

Vibrio vulnificus MO6-24/O has three genes annotated as debranching enzymes or pullulanase genes. Among them, the gene encoded by VVMO6_03032 (vvde1) shares a higher similarity at the amino acid sequence level to the glycogen debranching enzymes, AmyX of Bacillus subtilis (40.5%) and GlgX of Escherichia coli (55.5%), than those encoded by the other two genes. The vvde1 gene encoded a protein with a molecular mass of 75.56 kDa and purified Vvde1 efficiently hydrolyzed glycogen and pullulan to shorter chains of maltodextrin and maltotriose (G3), respectively. However, it hydrolyzed amylopectin and soluble starch far less efficiently, and β-cyclodextrin (β-CD) only rarely. The optimal pH and temperature of Vvde1 was 6.5 and 25°C, respectively. Vvde1 was a cold-adapted debranching enzyme with more than 60% residual activity at 5°C. It could maintain stability for 2 days at 25°C and 1 day at 35°C, but it destabilized drastically at 40°C. The Vvde1 activity was inhibited considerably by Cu²⁺, Hg²⁺, and Zn²⁺, while it was slightly enhanced by Co²⁺, Ca²⁺, Ni²⁺, and Fe²⁺. The vvde1 knock-out mutant accumulated more glycogen than the wild-type in media supplemented with 1.0% maltodextrin; however, the side chain length distribution of glycogen was similar to that of the wild-type except G3, which was much more abundant in the mutant. Therefore, Vvde1 seemed to debranch glycogen with the degree of polymerization 3 (DP3) as the specific target branch length. Virulence of the pathogen against Caenorhabditis elegans was attenuated significantly by the vvde1 mutation. These results suggest that Vvde1 might be a unique glycogen debranching enzyme that is involved in both glycogen utilization and shaping of glycogen molecules, and contributes toward virulence of the pathogen.

Production of Large-Ring Cyclodextrins by Amylomaltases

Amylomaltase is a well-known glucan transferase that can produce large ring cyclodextrins (LR-CDs) or so-called cycloamyloses via cyclization reaction. Amylomaltases have been found in several microorganisms and their optimum temperatures are generally around 60–70 °C for thermostable amylomaltases and 30–45 °C for the enzymes from mesophilic bacteria and plants. The optimum pHs for mesophilic amylomaltases are around pH 6.0–7.0, while the thermostable amylomaltases are generally active at more acidic conditions. Size of LR-CDs depends on the source of amylomaltases and the reaction conditions including pH, temperature, incubation time, and substrate. For example, in the case of amylomaltase from Corynebacterium glutamicum, LR-CD productions at alkaline pH or at a long incubation time favored products with a low degree of polymerization. In this review, we explore the synthesis of LR-CDs by amylomaltases, structural information of amylomaltases, as well as current applications of LR-CDs and amylomaltases.

Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BACKGROUND

The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment.

RESULTS

Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments.

CONCLUSIONS

We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

Enzymes of an alternative pathway of glucose metabolism in obligate methanotrophs

Aerobic methanotrophic bacteria utilize methane as a growth substrate but are unable to grow on any sugars. In this study we have shown that two obligate methanotrophs, Methylotuvimicrobium alcaliphilum 20Z and Methylobacter luteus IMV-B-3098, possess functional glucose dehydrogenase (GDH) and gluconate kinase (GntK). The recombinant GDHs from both methanotrophs were homotetrameric and strongly specific for glucose preferring NAD⁺ over NADP⁺. GDH from Mtm. alcaliphilum was most active at pH 10 (V_max = 95 U/mg protein) and demonstrated very high K_m for glucose (91.8 ± 3.8 mM). GDH from Mb. luteus was most active at pH 8.5 (V_max = 43 U/mg protein) and had lower K_m for glucose (16 ± 0.6 mM). The cells of two Mtm. alcaliphilum double mutants with deletions either of the genes encoding GDH and glucokinase (gdh^─/glk^─) or of the genes encoding gluconate kinase and glucokinase (gntk^─/glk^─) had the lower glycogen level and the higher contents of intracellular glucose and trehalose compared to the wild type strain. The gntk^─/glk^─ knockout mutant additionally accumulated gluconic acid. These data, along with bioinformatics analysis, demonstrate that glycogen derived free glucose can enter the Entner–Doudoroff pathway or the pentose phosphate cycle in methanotrophs, bypassing glycolysis via the gluconate shunt.

Comparison of Catalyzing Properties of Bacterial 4-α-Glucanotransferases Focusing on Their Cyclizing Activity

A newly cloned 4-α-glucanotransferase (αGT) from Deinococcus geothermalis and two typical bacterial αGTs from Thermus scotoductus and Escherichia coli (MalQ) were investigated. Among 4 types of catalysis, the cyclization activity of αGTs that produces cycloamylose (CA), a valuable carbohydrate making inclusion complexes, was intensively studied. The new αGT, DgαGT, showed close protein sequence to the αGT from T. scotoductus (TsαGT). MalQ was clearly separated from the other two αGTs in the phylogenetic and the conserved regions analyses. The reaction velocities of disproportionation, cyclization, coupling, and hydrolysis of three αGTs were determined. Intriguingly, MalQ exhibited more than 100-fold lower cyclization activity than the others. To lesser extent, the disproportionation activity of MalQ was relatively low. DgαGT and TsαGT showed similar kinetics results, but TsαGT had nearly 10-fold lower hydrolysis activity than DgαGT. Due to the very low cyclizing activity of MalQ, DgαGT and TsαGT were selected for further analyses. When amylose was treated with DgαGT or TsαGT, CA with a broad DP range was generated immediately. The DP distribution of CA had a bimodal shape (DP 7 and 27 as peaks) for the both enzymes, but larger DPs of CA quickly decreased in the DgαGT. Cyclomaltopentaose, a rare cyclic sugar, was produced at early reaction stage and accumulated as the reactions went on in the both enzymes, but the increase was more profound in the TsαGT. Taken together, we clearly demonstrated the catalytic differences between αGT groups from thermophilic and pathogenic bacteria that and showed that αGTs play different roles depending on their lifestyle.

Glycogen Metabolism Impairment via Single Gene Mutation in the glgBXCAP Operon Alters the Survival Rate of Escherichia coli Under Various Environmental Stresses

Glycogen is a highly branched polysaccharide that is widely present in all life domains. It has been identified in many bacterial species and functions as an important energy storage compound. In addition, it plays important roles in bacterial transmission, pathogenicity, and environmental viability. There are five essential enzymes (coding genes) directly involved in bacterial glycogen metabolism, which forms a single operon glgBXCAP with a suboperonic promoter in glgC gene in Escherichia coli. Currently, there is no comparative study of how the disruptions of the five glycogen metabolism genes influence bacterial phenotypes, such as growth rate, biofilm formation, and environmental survival, etc. In this study, we systematically and comparatively studied five E. coli single-gene mutants (ΔglgC, ΔglgA, ΔglgB, ΔglgP, ΔglgX) in terms of glycogen metabolism and explored their phenotype changes with a focus on environmental stress endurance, such as nutrient deprivation, low temperature, desiccation, and oxidation, etc. Biofilm formation in wild-type and mutant strains was also compared. E. coli wild-type stores the highest glycogen content after around 20-h culture while disruption of degradation genes (glgP, glgX) leads to continuous accumulation of glycogen. However, glycogen primary structure was abnormally changed in ΔglgP and ΔglgX. Meanwhile, increased accumulation of glycogen facilitates the growth of E. coli mutants but reduces glucose consumption in liquid culture and vice versa. Glycogen metabolism disruption also significantly and consistently increases biofilm formation in all the mutants. As for environmental stress endurance, glycogen over-accumulating mutants have enhanced starvation viability and reduced desiccation viability while all mutants showed decreased survival rate at low temperature. No consistent results were found for oxidative stress resistance in terms of glycogen metabolism disruptions, though ΔglgA shows highest resistance toward oxidation with unknown mechanisms. In sum, single gene disruptions in glgBXCAP operon significantly influence bacterial growth and glucose consumption during culture. Accumulation and structure of intracellular glycogen were also significantly altered. In addition, we observed significant changes in E. coli environmental viabilities due to the deletions of certain genes in the operon. Further investigations shall be focused on the molecular mechanisms behind these phenotype changes.

Phosphorylase-catalyzed bottom-up synthesis of short-chain soluble cello-oligosaccharides and property-tunable cellulosic materials

Cellulose-based materials are produced industrially in countless varieties via top-down processing of natural lignocellulose substrates. By contrast, cellulosic materials are only rarely prepared via bottom up synthesis and oligomerization-induced self-assembly of cellulose chains. Building up a cellulose chain via precision polymerization is promising, however, for it offers tunability and control of the final chemical structure. Synthetic cellulose derivatives with programmable material properties might thus be obtained. Cellodextrin phosphorylase (CdP; EC 2.4.1.49) catalyzes iterative β-1,4-glycosylation from α-d-glucose 1-phosphate, with the ability to elongate a diversity of acceptor substrates, including cellobiose, d-glucose and a range of synthetic glycosides having non-sugar aglycons. Depending on the reaction conditions leading to different degrees of polymerization (DP), short-chain soluble cello-oligosaccharides (COS) or insoluble cellulosic materials are formed. Here, we review the characteristics of CdP as bio-catalyst for synthetic applications and show advances in the enzymatic production of COS and reducing end-modified, tailored cellulose materials. Recent studies reveal COS as interesting dietary fibers that could provide a selective prebiotic effect. The bottom-up synthesized celluloses involve chains of DP ≥ 9, as precipitated in solution, and they form ~5 nm thick sheet-like crystalline structures of cellulose allomorph II. Solvent conditions and aglycon structures can direct the cellulose chain self-assembly towards a range of material architectures, including hierarchically organized networks of nanoribbons, or nanorods as well as distorted nanosheets. Composite materials are also formed. The resulting materials can be useful as property-tunable hydrogels and feature site-specific introduction of functional and chemically reactive groups. Therefore, COS and cellulose obtained via bottom-up synthesis can expand cellulose applications towards product classes that are difficult to access via top-down processing of natural materials.

Tracking down carbon inputs underground from an arid zone Australian calcrete

Freshwater ecosystems play a key role in shaping the global carbon cycle and maintaining the ecological balance that sustains biodiversity worldwide. Surficial water bodies are often interconnected with groundwater, forming a physical continuum, and their interaction has been reported as a crucial driver for organic matter (OM) inputs in groundwater systems. However, despite the growing concerns related to increasing anthropogenic pressure and effects of global change to groundwater environments, our understanding of the dynamics regulating subterranean carbon flows is still sparse. We traced carbon composition and transformations in an arid zone calcrete aquifer using a novel multidisciplinary approach that combined isotopic analyses of dissolved organic carbon (DOC) and inorganic carbon (DIC) (δ13CDOC, δ13CDIC, 14CDOC and 14CDIC) with fluorescence spectroscopy (Chromophoric Dissolved OM (CDOM) characterisation) and metabarcoding analyses (taxonomic and functional genomics on bacterial 16S rRNA). To compare dynamics linked to potential aquifer recharge processes, water samples were collected from two boreholes under contrasting rainfall: low rainfall ((LR), dry season) and high rainfall ((HR), wet season). Our isotopic results indicate limited changes and dominance of modern terrestrial carbon in the upper part (northeast) of the bore field, but correlation between HR and increased old and 13C-enriched DOC in the lower area (southwest). CDOM results show a shift from terrestrially to microbially derived compounds after rainfall in the same lower field bore, which was also sampled for microbial genetics. Functional genomic results showed increased genes coding for degradative pathways-dominated by those related to aromatic compound metabolisms-during HR. Our results indicate that rainfall leads to different responses in different parts of the bore field, with an increase in old carbon sources and microbial processing in the lower part of the field. We hypothesise that this may be due to increasing salinity, either due to mobilisation of Cl- from the soil, or infiltration from the downstream salt lake during HR. This study is the first to use a multi-technique assessment using stable and radioactive isotopes together with functional genomics to probe the principal organic biogeochemical pathways regulating an arid zone calcrete system. Further investigations involving extensive sampling from diverse groundwater ecosystems will allow better understanding of the microbiological pathways sustaining the ecological functioning of subterranean biota.

Starch and Glycogen Analyses: Methods and Techniques

For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included.

Recent progress in the structure of glycogen serving as a durable energy reserve in bacteria

Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length g_c in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.

Essentiality of the Maltase AmlE in Maltose Utilization and Its Transcriptional Regulation by the Repressor AmlR in the Acarbose-Producing Bacterium Actinoplanes sp. SE50/110

Actinoplanes sp. SE50/110 is the wild type of industrial production strains of the fine-chemical acarbose (acarviosyl-maltose), which is used as α-glucosidase inhibitor in the treatment of type II diabetes. Although maltose is an important building block of acarbose, the maltose/maltodextrin metabolism has not been studied in Actinoplanes sp. SE50/110 yet. Bioinformatic analysis located a putative maltase gene amlE (ACSP50_2474, previously named malL; Wendler et al., 2015a), in an operon with an upstream PurR/LacI-type transcriptional regulator gene, named amlR (ACSP50_2475), and a gene downstream (ACSP50_2473) encoding a GGDEF-EAL-domain-containing protein putatively involved in c-di-GMP signaling. Targeted gene deletion mutants of amlE and amlR were constructed by use of the CRISPR/Cas9 technology. By growth experiments and functional assays of ΔamlE, we could show that AmlE is essential for the maltose utilization in Actinoplanes sp. SE50/110. Neither a gene encoding a maltose phosphorylase (MalP) nor MalP enzyme activity were detected in the wild type. By this, the maltose/maltodextrin system appears to be fundamentally different from other described prokaryotic systems. By sequence similarity analysis and functional assays from the species Streptomyces lividans TK23, S. coelicolor A3(2) and S. glaucescens GLA.O, first hints for a widespread lack of MalP and presence of AmlE in the class Actinobacteria were given. Transcription of the aml operon is significantly repressed in the wild type when growing on glucose and repression is absent in an ΔamlR deletion mutant. Although AmlR apparently is a local transcriptional regulator of the aml operon, the ΔamlR strain shows severe growth inhibitions on glucose and – concomitantly – differential transcription of several genes of various functional classes. We ascribe these effects to ACSP50_2473, which is localized downstream of amlE and presumably involved in the metabolism of the second messenger c-di-GMP. It can be assumed, that maltose does not only represent the most important carbon source of Actinoplanes sp. SE50/110, but that its metabolism is coupled to the nucleotide messenger system of c-di-GMP.

Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation

Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.

Omnipresent Maxwell's demons orchestrate information management in living cells

The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.

Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria

In bacteria, glycogen plays important roles in carbon and energy storage. Its structure has recently been linked with bacterial environmental durability. Among the essential genes for bacterial glycogen metabolism, the glgB-encoded branching enzyme GBE plays an essential role in forming α-1,6-glycosidic branching points, and determines the unique branching patterns in glycogen. Previously, evolutionary analysis of a small sets of GBEs based on their N-terminal domain organization revealed that two types of GBEs might exist: (1) Type 1 GBE with both N1 and N2 (also known as CBM48) domains and (2) Type 2 GBE with only the N2 domain. In this study, we initially analyzed N-terminal domains of 169 manually reviewed bacterial GBEs based on hidden Markov models. A previously unreported group of GBEs (Type 3) with around 100 amino acids ahead of the N1 domains was identified. Phylogenetic analysis found clustered patterns of GBE types in certain bacterial phyla, with the shorter, Type 2 GBEs predominantly found in Gram-positive species, while the longer Type 1 GBEs are found in Gram-negative species. Several in vitro studies have linked N1 domain with transfer of short oligosaccharide chains during glycogen formation, which could lead to small and compact glycogen structures. Compact glycogen degrades more slowly and, as a result, may serve as a durable energy reserve, contributing to the enhanced environmental persistence for bacteria. We were therefore interested in classifying GBEs based on their N-terminal domain via large-scale sequence analysis. In addition, we set to understand the evolutionary patterns of different GBEs through phylogenetic analysis at species and sequence levels. Three-dimensional modeling of GBE N-termini was also performed for structural comparisons. A further study of 9,387 GBE sequences identified 147 GBEs that might belong to a possibly novel group of Type 3 GBE, most of which fall into the phylum of Actinobacteria. We also attempted to correlate glycogen average chain length (ACL) with GBE types. However, no significant conclusions were drawn due to limited data availability. In sum, our study systematically investigated bacterial GBEs in terms of domain organizations from evolutionary point of view, which provides guidance for further experimental study of GBE N-terminal functions in glycogen structure and bacterial physiology.

Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics

Toward the elucidation of the advanced mechanism of l-valine production by Corynebacterium glutamicum, a highly developed industrial strain VWB-1 was analyzed, employing the combination of transcriptomics and proteomics methods. The transcriptional level of 1155 genes and expression abundance of 96 proteins were changed significantly by the transcriptome and proteome comparison of VWB-1 and ATCC 13869. It was indicated that the key genes involved in the biosynthesis of l-valine, ilvBN, ilvC, ilvD, ilvE were up-regulated in VWB-1, which together made prominent contributions in improving the carbon flow towards l-valine. The l-leucine and l-isoleucine synthesis ability were weakened according to the down-regulation of leuB and ilvA. The up-regulation of the branched chain amino acid transporter genes brnFE promoted the l-valine secretion capability of VWB-1. The NADPH and ATP generation ability of VWB-1 were strengthened through the up-regulation of the genes involved in phosphate pentose pathway and TCA pathway. Pyruvate accumulation was achieved through the weakening of the l-lactate, acetate and l-alanine pathways. The up-regulation of the genes coding for elongation factors and ribosomal proteins were beneficial for l-valine synthesis in C. glutamicum. All information acquired were useful for the genome breeding of better industrial l-valine producing strains.

Maltose Utilization as a Novel Selection Strategy for Continuous Evolution of Microbes with Enhanced Metabolite Production

We have developed a novel selection circuit based on carbon source utilization that establishes and sustains growth-production coupling over several generations in a medium with maltose as the sole carbon source. In contrast to traditional antibiotic resistance-based circuits, we first proved that coupling of cell fitness to metabolite production by our circuit was more robust with a much lower escape risk even after many rounds of selection. We then applied the selection circuit to the optimization of L-tryptophan (l-Trp) production. We demonstrated that it enriched for specific mutants with increased l-Trp productivity regardless of whether it was applied to a small and defined mutational library or a relatively large and undefined one. From the latter, we identified four novel mutations with enhanced l-Trp output. Finally, we used it to select for several high l-Trp producers with randomly generated genome-wide mutations and obtained strains with up to 65% increased l-Trp production. This selection circuit provides new perspectives for the optimization of microbial cell factories for diverse metabolite production and the discovery of novel genotype-phenotype associations at the single-gene and whole-genome levels.

Enzymes Required for Maltodextrin Catabolism in Enterococcus faecalis Exhibit Novel Activities

Maltose and maltodextrins are formed during the degradation of starch or glycogen. Maltodextrins are composed of a mixture of maltooligosaccharides formed by α-1,4- but also some α-1,6-linked glucosyl residues. The α-1,6-linked glucosyl residues are derived from branching points in the polysaccharides. In Enterococcus faecalis, maltotriose is mainly transported and phosphorylated by a phosphoenolpyruvate:carbohydrate phosphotransferase system. The formed maltotriose-6″-phosphate is intracellularly dephosphorylated by a specific phosphatase, MapP. In contrast, maltotetraose and longer maltooligosaccharides up to maltoheptaose are taken up without phosphorylation via the ATP binding cassette transporter MdxEFG-MsmX. We show that the maltose-producing maltodextrin hydrolase MmdH (GenBank accession no. EFT41964) in strain JH2-2 catalyzes the first catabolic step of α-1,4-linked maltooligosaccharides. The purified enzyme converts even-numbered α-1,4-linked maltooligosaccharides (maltotetraose, etc.) into maltose and odd-numbered (maltotriose, etc.) into maltose and glucose. Inactivation of mmdH therefore prevents the growth of E. faecalis on maltooligosaccharides ranging from maltotriose to maltoheptaose. Surprisingly, MmdH also functions as a maltogenic α-1,6-glucosidase, because it converts the maltotriose isomer isopanose into maltose and glucose. In addition, E. faecalis contains a glucose-producing α-1,6-specific maltodextrin hydrolase (GenBank accession no. EFT41963, renamed GmdH). This enzyme converts panose, another maltotriose isomer, into glucose and maltose. A gmdH mutant had therefore lost the capacity to grow on panose. The genes mmdH and gmdH are organized in an operon together with GenBank accession no. EFT41962 (renamed mmgT). Purified MmgT transfers glucosyl residues from one α-1,4-linked maltooligosaccharide molecule to another. For example, it catalyzes the disproportionation of maltotriose by transferring a glucosyl residue to another maltotriose molecule, thereby forming maltotetraose and maltose together with a small amount of maltopentaose.IMPORTANCE The utilization of maltodextrins by Enterococcus faecalis has been shown to increase the virulence of this nosocomial pathogen. However, little is known about how this organism catabolizes maltodextrins. We identified two enzymes involved in the metabolism of various α-1,4- and α-1,6-linked maltooligosaccharides. We found that one of them functions as a maltose-producing α-glucosidase with relaxed linkage specificity (α-1,4 and α-1,6) and exo- and endoglucosidase activities. A third enzyme, which resembles amylomaltase, exclusively transfers glucosyl residues from one maltooligosaccharide molecule to another. Similar enzymes are present in numerous other Firmicutes, such as streptococci and lactobacilli, suggesting that these organisms follow the same maltose degradation pathway as E. faecalis.

Indole enhances the survival of Pantoea ananatis YJ76 in face of starvation conditions

Pantoea ananatis YJ76 is an indole-producing predominant diazotrophic endophyte isolated from rice having multiple growth-promoting effects on host plant. As a decomposition metabolite of L-tryptophan (L-Trp), indole is confirmed to regulate various physiological processes of bacteria. In this research, we found that indole significantly improves the survival of YJ76 in face of starvation conditions and the promoting effect is related to the glycogen accumulation promoted by indole, which is much more significant in the middle decline phase than in other growth phases. Since carbon storage regulator CsrA is a key inhibiting factor on the storage of glycogen in bacteria, we explored the relation between indole-enhanced glycogen accumulation and csrA expression and found that there is a positive correlation between indole-enhanced glycogen accumulation and the indole-inhibited csrA expression in YJ76, which implies the potential relation between CsrA regulation and indole regulatory pathway.

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.

Role of N-terminal region of Escherichia coli maltodextrin glucosidase in folding and function of the protein

Maltodextrin glucosidase (MalZ) hydrolyses short malto-oligosaccharides from the reducing end releasing glucose and maltose in Escherichia coli. MalZ is a highly aggregation prone protein and molecular chaperonins GroEL and GroES assist in the folding of this protein to a substantial level. The N-terminal region of this enzyme appears to be a unique domain as seen in sequence comparison studies with other amylases as well as through homology modelling. The sequence and homology model analysis show a probability of disorder in the N-Terminal region of MalZ. The crystal structure of this enzyme has been reported in the present communication. Based on the crystallographic structure, it has been interpreted that the N-terminal region of the enzyme (Met1-Phe131) might be unstructured or flexible. To understand the role of the N-terminal region of MalZ in its enzymatic activity, and overall stability, a truncated version (Ala111-His616) of MalZ was created. The truncated version failed to fold into an active enzyme both in E. coli cytosol and in vitro even with the assistance of chaperonins GroEL and GroES. Furthermore, the refolding effort of N-truncated MalZ in the presence of isolated N-terminal domain didn't succeed. Our studies suggest that while the structural rigidity or orientation of the N-terminal region of the MalZ protein may not be essential for its stability and function, but the said domain is likely to play an important role in the formation of the native structure of the protein when present as an integral part of the protein.

The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive response in the zoonotic Streptococcus suis

The (p)ppGpp signal molecules play a central role in the stringent response (SR) to adapt to nutrient starvation in bacteria, yet the carbohydrate starvation induced adaptive response and the roles of SR in this response is not well characterized, especially in Gram-positives. Here, two (p)ppGpp synthetases RelA and RelQ are identified in Streptococcus suis, an important emerging zoonotic Gram-positive bacterium, while only RelA is functional under glucose starvation. To characterize the roles of RelA/(p)ppGpp in glucose starvation response in S. suis, the growth curves and transcriptional profiles were compared between the mutant strain ΔrelA [a (p)ppGpp⁰ strain under glucose starvation] and its parental strain SC-19 [(p)ppGpp⁺]. The results showed great difference between SC-19 and ΔrelA on adaptive responses when suffering glucose starvation, and demonstrated that RelA/(p)ppGpp plays important roles in adaptation to glucose starvation. Besides the classic SR including inhibition of growth and related macromolecular synthesis, the extended adaptive response also includes inhibited glycolysis, and carbon catabolite repression (CCR)-mediated carbohydrate-dependent metabolic switches. Collectively, the pheno- and genotypic characterization of the glucose starvation induced adaptive response in S. suis makes a great contribution to understanding better the mechanism of SR.

Characterization and Application of BiLA, a Psychrophilic α-Amylase from Bifidobacterium longum

In this study, a novel α-amylase was cloned from Bifidobacterium longum and named BiLA. The enzyme exhibited optimal activity at 20 °C and a pH value of 5.0. Kinetic analysis using various carbohydrate substrates revealed that BiLA had the highest k(cat/)K(m) value for amylose. Interestingly, analysis of the enzymatic reaction products demonstrated that BiLA specifically catalyzed the hydrolysis of oligosaccharides and starches up to G5 from the nonreducing ends. To determine whether BiLA can be used to generate slowly digestible starch (SDS), starch was treated with BiLA, and the kinetic parameters were analyzed using porcine pancreatic α-amylase (PPA) and amyloglucosidase (AMG). Compared to normal starch, BiLA-treated starch showed lower k(cat)/K(m) values with PPA and AMG, suggesting that BiLA is a potential candidate for the production of SDS.

Glycogen: Biosynthesis and Regulation

Glycogen accumulation occurs in Escherichia coli and Salmonella enterica serovar Typhimurium as well as in many other bacteria. Glycogen will be formed when there is an excess of carbon under conditions in which growth is limited because of the lack of a growth nutrient, e.g., a nitrogen source. This review describes the enzymatic reactions involved in glycogen synthesis and the allosteric regulation of the first enzyme, ADP-glucose pyrophosphorylase. The properties of the enzymes involved in glycogen synthesis, ADP-glucose pyrophosphorylase, glycogen synthase, and branching enzyme are also characterized. The data describing the genetic regulation of the glycogen synthesis are also presented. An alternate pathway for glycogen synthesis in mycobacteria is also described.

Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli

Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. To elucidate the molecular basis of transglycosylation by MalQ, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine-glucose-acarbose, at resolutions down to 2.1 Å. MalQ represents the first example of a mesophilic bacterial amylomaltase with known structure and exhibits an N-terminal extension of about 140 residues, in contrast with previously described thermophilic enzymes. This moiety seems unique to amylomaltases from Enterobacteriaceae and folds into two distinct subdomains that associate with different parts of the catalytic core. Intriguingly, the three MalQ crystal structures appear to correspond to distinct states of this enzyme, revealing considerable conformational changes during the catalytic cycle. In particular, the inhibitor complex highlights the requirement of both a 3-OH group and a 4-OH group (or α1-4-glycosidic bond) at the acceptor subsite +1 for the catalytically competent orientation of the acid/base catalyst Glu-496. Using an HPLC-based MalQ enzyme assay, we could demonstrate that the equilibrium concentration of maltodextrin products depends on the length of the initial substrate; with increasing numbers of glycosidic bonds, less glucose is formed. Thus, both structural and enzymatic data are consistent with the extremely low hydrolysis rates observed for amylomaltases and underline the importance of MalQ for the metabolism of maltodextrins in E. coli.

Influence of in situ progressive N-terminal is still controversial truncation of glycogen branching enzyme in Escherichia coli DH5α on glycogen structure, accumulation, and bacterial viability

BACKGROUND

Glycogen average chain length (ACL) has been linked with bacterial durability, but this was on the basis of observations across different species. We therefore wished to investigate the relationship between bacterial durability and glycogen ACL by varying glycogen average chain length in a single species. It has been shown that progressive shortening of the N-terminus of glycogen branching enzyme (GBE) leads to a lengthening of oligosaccharide inter-α-1,6-glycosidic chain lengths, so we sought to harness this to create a set of Escherichia coli DH5α strains with a range of glycogen average chain lengths, and assess these strains for durability related attributes, such as starvation, cold and desiccation stress resistance, and biofilm formation.

RESULTS

A series of Escherichia coli DH5α mutants were created with glgB genes that were in situ progressively N-terminus truncated. N-terminal truncation shifted the distribution of glycogen chain lengths from 5-11 DP toward 13-50 DP, but the relationship between glgB length and glycogen ACL was not linear. Surprisingly, removal of the first 270 nucleotides of glgB (glgBΔ270) resulted in comparatively high glycogen accumulation, with the glycogen having short ACL. Complete knockout of glgB led to the formation of amylose-like glycogen containing long, linear α1,4-glucan chains with significantly reduced branching frequency. Physiologically, the set of mutant strains had reduced bacterial starvation resistance, while minimally increasing bacterial desiccation resistance. Finally, although there were no obvious changes in cold stress resistance or biofilm forming ability, one strain (glgBΔ180) had significantly increased biofilm formation in favourable media.

CONCLUSIONS

Despite glgB being the first gene of an operon, it is clear that in situ mutation is a viable means to create more biologically relevant mutant strains. Secondly, there was the suggestion in the data that impairments of starvation, cold and desiccation resistance were worse for the strain lacking glgB, though the first of these was not statistically significant. The results provide prima facie evidence linking abiotic stress tolerance with shorter glycogen ACL. However, further work needs to be done, perhaps in a less labile species. Further work is also required to tease out the complex relationship between glycogen abundance and glycogen structure.

The α-glucan phosphorylase MalP of Corynebacterium glutamicum is subject to transcriptional regulation and competitive inhibition by ADP-glucose

α-Glucan phosphorylases contribute to degradation of glycogen and maltodextrins formed in the course of maltose metabolism in bacteria. Accordingly, bacterial α-glucan phosphorylases are classified as either glycogen or maltodextrin phosphorylase, GlgP or MalP, respectively. GlgP and MalP enzymes follow the same catalytic mechanism, and thus their substrate spectra overlap; however, they differ in their regulation: GlgP genes are constitutively expressed and the enzymes are controlled on the activity level, whereas expression of MalP genes are transcriptionally controlled in response to the carbon source used for cultivation. We characterize here the modes of control of the α-glucan phosphorylase MalP of the Gram-positive Corynebacterium glutamicum. In accordance to the proposed function of the malP gene product as MalP, we found transcription of malP to be regulated in response to the carbon source. Moreover, malP transcription is shown to depend on the growth phase and to occur independently of the cell glycogen content. Surprisingly, we also found MalP activity to be tightly regulated competitively by the presence of ADP-glucose, an intermediate of glycogen synthesis. Since the latter is considered a typical feature of GlgPs, we propose that C. glutamicum MalP acts as both maltodextrin and glycogen phosphorylase and, based on these findings, we question the current system for classification of bacterial α-glucan phosphorylases.

IMPORTANCE

Bacterial α-glucan phosphorylases have been classified conferring to their purpose as either glycogen or maltodextrin phosphorylases. We found transcription of malP in C. glutamicum to be regulated in response to the carbon source, which is recognized as typical for maltodextrin phosphorylases. Surprisingly, we also found MalP activity to be tightly regulated competitively by the presence of ADP-glucose, an intermediate of glycogen synthesis. The latter is considered a typical feature of GlgPs. These findings, taken together, suggest that C. glutamicum MalP is the first α-glucan phosphorylase that does not fit into the current system for classification of bacterial α-glucan phosphorylases and exemplifies the complex mechanisms underlying the control of glycogen content and maltose metabolism in this model organism.

Comparative genomic and phylogenetic analyses of Gammaproteobacterial glg genes traced the origin of the Escherichia coli glycogen glgBXCAP operon to the last common ancestor of the sister orders Enterobacteriales and Pasteurellales

Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria.

Analysis of the functional interaction of Arabidopsis starch synthase and branching enzyme isoforms reveals that the cooperative action of SSI and BEs results in glucans with polymodal chain length distribution similar to amylopectin

Starch synthase (SS) and branching enzyme (BE) establish the two glycosidic linkages existing in starch. Both enzymes exist as several isoforms. Enzymes derived from several species were studied extensively both in vivo and in vitro over the last years, however, analyses of a functional interaction of SS and BE isoforms are missing so far. Here, we present data from in vitro studies including both interaction of leaf derived and heterologously expressed SS and BE isoforms. We found that SSI activity in native PAGE without addition of glucans was dependent on at least one of the two BE isoforms active in Arabidopsis leaves. This interaction is most likely not based on a physical association of the enzymes, as demonstrated by immunodetection and native PAGE mobility analysis of SSI, BE2, and BE3. The glucans formed by the action of SSI/BEs were analysed using leaf protein extracts from wild type and be single mutants (Atbe2 and Atbe3 mutant lines) and by different combinations of recombinant proteins. Chain length distribution (CLD) patterns of the formed glucans were irrespective of SSI and BE isoforms origin and still independent of assay conditions. Furthermore, we show that all SS isoforms (SSI-SSIV) were able to interact with BEs and form branched glucans. However, only SSI/BEs generated a polymodal distribution of glucans which was similar to CLD pattern detected in amylopectin of Arabidopsis leaf starch. We discuss the impact of the SSI/BEs interplay for the CLD pattern of amylopectin.

Reaction kinetics of substrate transglycosylation catalyzed by TreX of Sulfolobus solfataricus and effects on glycogen breakdown

We studied the activity of a debranching enzyme (TreX) from Sulfolobus solfataricus on glycogen-mimic substrates, branched maltotetraosyl-β-cyclodextrin (Glc₄-β-CD), and natural glycogen to better understand substrate transglycosylation and the effect thereof on glycogen debranching in microorganisms. The validation test of Glc₄-β-CD as a glycogen mimic substrate showed that it followed the breakdown process of the well-known yeast and rat liver extract. TreX catalyzed both hydrolysis of α-1,6-glycosidic linkages and transglycosylation at relatively high (>0.5 mM) substrate concentrations. TreX transferred maltotetraosyl moieties from the donor substrate to acceptor molecules, resulting in the formation of two positional isomers of dimaltotetraosyl-α-1,6-β-cyclodextrin [(Glc₄)₂-β-CD]; these were 6(1),6(3)- and 6(1),6(4)-dimaltotetraosyl-α-1,6-β-CD. Use of a modified Michaelis-Menten equation to study substrate transglycosylation revealed that the kcat and Km values for transglycosylation were 1.78 × 10(3) s(-1) and 3.30 mM, respectively, whereas the values for hydrolysis were 2.57 × 10(3) s(-1) and 0.206 mM, respectively. Also, enzyme catalytic efficiency (the kcat/Km ratio) increased as the degree of polymerization of branch chains rose. In the model reaction system of Escherichia coli, glucose-1-phosphate production from glycogen by the glycogen phosphorylase was elevated ∼1.45-fold in the presence of TreX compared to that produced in the absence of TreX. The results suggest that outward shifting of glycogen branch chains via transglycosylation increases the number of exposed chains susceptible to phosphorylase action. We developed a model of the glycogen breakdown process featuring both hydrolysis and transglycosylation catalyzed by the debranching enzyme.

Identification and characterization of an archaeal kojibiose catabolic pathway in the hyperthermophilic Pyrococcus sp. strain ST04

A unique gene cluster responsible for kojibiose utilization was identified in the genome of Pyrococcus sp. strain ST04. The proteins it encodes hydrolyze kojibiose, a disaccharide product of glucose caramelization, and form glucose-6-phosphate (G6P) in two steps. Heterologous expression of the kojibiose-related enzymes in Escherichia coli revealed that two genes, Py04_1502 and Py04_1503, encode kojibiose phosphorylase (designated PsKP, for Pyrococcus sp. strain ST04 kojibiose phosphorylase) and β-phosphoglucomutase (PsPGM), respectively. Enzymatic assays show that PsKP hydrolyzes kojibiose to glucose and β-glucose-1-phosphate (β-G1P). The Km values for kojibiose and phosphate were determined to be 2.53 ± 0.21 mM and 1.34 ± 0.04 mM, respectively. PsPGM then converts β-G1P into G6P in the presence of 6 mM MgCl2. Conversion activity from β-G1P to G6P was 46.81 ± 3.66 U/mg, and reverse conversion activity from G6P to β-G1P was 3.51 ± 0.13 U/mg. The proteins are highly thermostable, with optimal temperatures of 90°C for PsKP and 95°C for PsPGM. These results indicate that Pyrococcus sp. strain ST04 converts kojibiose into G6P, a substrate of the glycolytic pathway. This is the first report of a disaccharide utilization pathway via phosphorolysis in hyperthermophilic archaea.

A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night

Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a “glucosyl buffer” to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway.

Biochemical characterization of 4-α-glucanotransferase from Saccharophagus degradans 2-40 and its potential role in glycogen degradation

4-α-Glucanotransferase, an enzyme encoded by malQ, transfers 1,4-α-glucan to an acceptor carbohydrate to produce long linear maltodextrins of varying lengths. To investigate the biochemical characteristics of the malQ gene (Sde0986) from Saccharophagus degradans 2-40 and to understand its physiological role in vivo, the malQ gene was cloned and expressed in Escherichia coli. The amino acid sequence of MalQ was found to be 36-47% identical to that of amylomaltases from gammaproteobacteria. MalQ is a monomeric enzyme that belongs to a family of 77 glycoside hydrolases, with a molecular mass of 104 kDa. The optimal pH and temperature for MalQ toward maltotriose were determined to be 8.5 and 35 °C, respectively. Furthermore, the enzyme displayed glycosyl transfer activity on maltodextrins of various sizes to yield glucose and long linear maltodextrins. MalQ, however, could be distinguished from other bacterial and archaeal amylomaltases in that it did not produce maltose and cyclic glucan. Reverse transcription PCR results showed that malQ was not induced by maltose and was highly expressed in the stationary phase. These data suggest that the main physiological role of malQ in S. degradans is in the degradation of glycogen, although the gene is commonly known to be involved in maltose metabolism in E. coli.

An expedient enzymatic route to isomeric 2-, 3- and 6-monodeoxy-monofluoro-maltose derivatives

2-Deoxy-2-fluoro-d-glucose, 3-deoxy-3-fluoro-D-glucose and 6-deoxy-6-fluoro-D-glucose were converted into the corresponding maltose derivatives using Arabidopsis thaliana DPE2-mediated trans-glycosylation reaction with glycogen acting as a glucosyl donor. (19)F NMR spectroscopy proved to be a valuable tool for monitoring the progress of these reactions and to assess the nature of resulting oligomeric products.