Glycogen with short average chain length enhances bacterial durability

α-Glucan-type exopolysaccharides with varied linkage patterns: Mitigating post-prandial glucose spike and prolonging the glycemic response

Microbial exopolysaccharides (EPSs) are traditionally known as prebiotics that foster colon health by serving as microbiota nutrients, while remaining undigested in the small intestine. However, recent findings suggest that α-glucan structures in EPS, with their varied α-linkage types, can be hydrolyzed by mammalian α-glucosidases at differing rates. This study explores α-glucan-type EPSs, including dextran, alternan, and reuteran, assessing their digestive properties both in vitro and in vivo. Notably, while fungal amyloglucosidase - a common in vitro tool for carbohydrate digestibility analysis - shows limited efficacy in breaking down these structures, mammalian intestinal α-glucosidases can partially degrade them into glucose, albeit slowly. In vivo experiments with mice revealed that various EPSs elicited a significantly lower glycemic response (p < 0.05) than glucose, indicating their nature as carbohydrates that are digested slowly. This leads to the conclusion that different α-glucan-type EPSs may serve as ingredients that attenuate post-prandial glycemic responses. Furthermore, rather than serving as mere dietary fibers, they hold the potential for blood glucose regulation, offering new avenues for managing obesity, Type 2 diabetes, and other related-chronic diseases.

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.

Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli

Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacterium Escherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and 13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.

The Synergistic Effect of GH13 and GH57 GBEs of Petrotoga mobilis Results in α-Glucan Molecules with a Higher Branch Density

Glycogen is a biopolymer consisting of glycosyl units, with a linear backbone connected by α-1,4-linkages and branches attached via α-1,6-linkages. In microorganisms, glycogen synthesis involves multiple enzymes, with glycogen branching enzymes (GBEs) being vital for creating α-1,6-linkages. GBEs exist in two families: glycoside hydrolase (GH) 13 and GH57. Some organisms possess either a single GH13 or GH57 GBE, while others, such as Petrotoga mobilis, have both types of GBEs. In this study, the simultaneous use of a GH13 and GH57 GBE each from Petrotoga mobilis for α-glucan modification was investigated using a linear maltodextrin substrate with a degree of polymerization of 18 (DP18). The products from modifications by one or both GBEs in various combinations were analyzed and demonstrated a synergistic effect when both enzymes were combined, leading to a higher branch density in the glycogen structure. In this cooperative process, PmGBE13 was responsible for creating longer branches, whereas PmGBE57 hydrolyzed these branches, resulting in shorter lengths. The combined action of the two enzymes significantly increased the number of branched chains compared to when they acted individually. The results of this study therefore give insight into the role of PmGBE13 and PmGBE57 in glycogen synthesis, and show the potential use of both enzymes in a two-step modification to create an α-glucan structure with short branches at a high branch density.

Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats

Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between habitats is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate pathogen adaptation to water and soil, two environments that act as bacterial reservoirs, and compare this information with gene expression in planta. Gene expression in water resembled that observed during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). Alkaline pH and nutrient scarcity-conditions also encountered during late infection stages-were identified as the triggers for this T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and genes for the use of alternate carbon sources, such as phenylacetate catabolism and the glyoxylate cycle, and downregulated virulence-associated genes. We proved through gain- and loss-of-function experiments that genes associated with the oxidative stress response, such as the regulator OxyR and the catalase KatG, are key for bacterial survival in soil, as their deletion cause a decrease in culturability associated with a premature induction of the viable but non culturable state (VBNC). This work identifies essential factors necessary for R. solanacearum to complete its life cycle and is the first comprehensive gene expression analysis in all environments occupied by a bacterial plant pathogen, providing valuable insights into its biology and adaptation to unexplored habitats.

Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes

Planktonic bacteria can be grouped into 'high nucleic acid content (HNA) bacteria' and 'low nucleic acid content (LNA) bacteria.' Nutrient input modes vary in environments, causing nutrient availability heterogeneity. We incubated them with equal amounts of total glucose added in a continuous/pulsed mode. The pulse-treated LNA bacteria exhibited twice the cell abundance and four times the viability of the continuous-treated LNA, while HNA did not show an adaptation to pulsed treatment. In structural equation modelling, LNA bacteria had higher path coefficients than HNA, between growth and carbon-saving metabolic pathways, intracellular ATP and the inorganic energy storage polymer, polyphosphate, indicating their low-cost growth, and flexible energy storage and utilisation. After incubation, the pulse-treated LNA bacteria contained more proteins and polysaccharides (0.00064, 0.0012 ng cell-1 ) than the continuous-treated LNA (0.00014, 0.00014 ng cell-1 ), conferring endurance and rapid response to pulses. Compared to LNA, HNA keystone taxa had stronger correlations with the primary glucose metabolism step, glycolysis, and occupied leading positions to explain the random forest model. They are essential to introduce glucose into the element cycling of the whole community under both treatments. Our work outlines a systematic bacterial response to carbon input.

Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota

Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.

Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland

Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.

Genomic evidence for the first symbiotic Deferribacterota, a novel gut symbiont from the deep-sea hydrothermal vent shrimp Rimicaris kairei

The genus Rimicaris is the dominant organism living in hydrothermal vents. However, little research has been done on the functions of their intestinal flora. Here, we investigated the potential functions of Deferribacterota, which is dominant in the intestine of Rimicaris kairei from the Central Indian Ridge. In total, six metagenome-assembled genomes (MAGs) of Deferribacterota were obtained using the metagenomic approach. The six Deferribacterota MAGs (Def-MAGs) were clustered into a new branch in the phylogenetic tree. The six Def-MAGs were further classified into three species, including one new order and two new genera, based on the results of phylogenetic analysis, relative evolutionary divergence (RED), average nucleotide identity (ANI), average amino acid identity (AAI) and DNA-DNA hybridization (DDH) values. The results of the energy metabolism study showed that these bacteria can use a variety of carbon sources, such as glycogen, sucrose, salicin, arbutin, glucose, cellobiose, and maltose. These bacteria have a type II secretion system and effector proteins that can transport some intracellular toxins to the extracellular compartment and a type V CRISPR-Cas system that can defend against various invasions. In addition, cofactors such as biotin, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) synthesized by R. kairei gut Deferribacterota may also assist their host in surviving under extreme conditions. Taken together, the potential function of Deferribacterota in the hydrothermal R. kairei gut suggests its long-term coevolution with the host.

Alpha-1,4-transglycosylation Activity of GH57 Glycogen Branching Enzymes Is Higher in the Absence of a Flexible Loop with a Conserved Tyrosine Residue

Starch-like polymers can be created through the use of enzymatic modification with glycogen branching enzymes (GBEs). GBEs are categorized in the glycoside hydrolase (GH) family 13 and 57. Both GH13 and GH57 GBEs exhibit branching and hydrolytic activity. While GH13 GBEs are also capable of α-1,4-transglycosylation, it is yet unknown whether GH57 share this capability. Among the four crystal structures of GH57 GBEs that have been solved, a flexible loop with a conserved tyrosine was identified to play a role in the branching activity. However, it remains unclear whether this flexible loop is also involved in α-1,4-transglycosylation activity. We hypothesize that GH57 GBEs with the flexible loop and tyrosine are also capable of α-1,4-transglycosylation, similar to GH13 GBEs. The aim of the present study was to characterize the activity of GH57 GBEs to investigate a possible α-1,4-transglycosylation activity. Three GH57 GBEs were selected, one from Thermococcus kodakarensis with the flexible loop and two beta-strands; one from Thermotoga maritima, missing the flexible loop and beta-strands; and one from Meiothermus sp., missing the flexible loop but with the two beta-strands. The analysis of chain length distribution over time of modified maltooctadecaose, revealed, for the first time, that all three GH57 GBEs can generate chains longer than the substrate itself, showing that α-1,4-transglycosylation activity is generally present in GH57 GBEs.

The Structure of Maltooctaose-Bound Escherichia coli Branching Enzyme Suggests a Mechanism for Donor Chain Specificity

Glycogen is the primary storage polysaccharide in bacteria and animals. It is a glucose polymer linked by α-1,4 glucose linkages and branched via α-1,6-linkages, with the latter reaction catalyzed by branching enzymes. Both the length and dispensation of these branches are critical in defining the structure, density, and relative bioavailability of the storage polysaccharide. Key to this is the specificity of branching enzymes because they define branch length. Herein, we report the crystal structure of the maltooctaose-bound branching enzyme from the enterobacteria E. coli. The structure identifies three new malto-oligosaccharide binding sites and confirms oligosaccharide binding in seven others, bringing the total number of oligosaccharide binding sites to twelve. In addition, the structure shows distinctly different binding in previously identified site I, with a substantially longer glucan chain ordered in the binding site. Using the donor oligosaccharide chain-bound Cyanothece branching enzyme structure as a guide, binding site I was identified as the likely binding surface for the extended donor chains that the E. coli branching enzyme is known to transfer. Furthermore, the structure suggests that analogous loops in branching enzymes from a diversity of organisms are responsible for branch chain length specificity. Together, these results suggest a possible mechanism for transfer chain specificity involving some of these surface binding sites.

Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme

In humans, glycogen storage diseases result from metabolic inborn errors, and can lead to severe phenotypes and lethal conditions. Besides these rare diseases, glycogen is also associated to widely spread societal burdens such as diabetes. Glycogen is a branched glucose polymer synthesised and degraded by a complex set of enzymes. Over the past 50 years, the structure of glycogen has been intensively investigated. Yet, the interplay between the detailed three-dimensional glycogen structure and the related enzyme activity is only partially characterised and still to be fully understood. In this article, we develop a stochastic coarse-grained and spatially resolved model of branched polymer biosynthesis following a Gillespie algorithm. Our study largely focusses on the role of the branching enzyme, and first investigates the properties of the model with generic parameter values, before comparing it to in vivo experimental data in mice. It arises that the ratio of glycogen synthase over branching enzyme reaction rates drastically impacts the structure of the granule. We deeply investigate the mechanism of branching and parametrise it using distinct lengths. Not only do we consider various possible sets of values for these lengths, but also distinct rules to apply them. We show how combining various values for these lengths finely tunes glycogen macromolecular structure. Comparing the model with experimental data confirms that we can accurately reproduce glycogen chain length distributions in wild type mice. Additional granule properties obtained for this fit are also in good agreement with typically reported values in the experimental literature. Nonetheless, we find that the mechanism of branching must be more flexible than usually reported. Overall, our model provides a theoretical basis to quantify the effect that single enzymatic parameters, in particular of the branching enzyme, have on the chain length distribution. Our generic model and methods can be applied to any glycogen data set, and could in particular contribute to characterise the mechanisms responsible for glycogen storage disorders.

Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows

Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (r_test = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals.

Designing starch derivatives with desired structures and functional properties via rearrangements of glycosidic linkages by starch-active transglycosylases

Modification of starch by transglycosylases from glycoside hydrolase families has attracted much attention recently; these enzymes can produce starch derivatives with novel properties, i.e. processability and functionality, employing highly efficient and safe methods. Starch-active transglycosylases cleave starches and transfer linear fragments to acceptors introducing α-1,4 and/or linear/branched α-1,6 glucosidic linkages, resulting in starch derivatives with excellent properties such as complexing and resistance to digestion characteristics, and also may be endowed with new properties such as thermo-reversible gel formation. This review summarizes the effects of variations in glycosidic linkage composition on structure and properties of modified starches. Starch-active transglycosylases are classified into 4 groups that form compounds: (1) in cyclic with α-1,4 glucosidic linkages, (2) with linear chains of α-1,4 glucosidic linkages, (3) with branched α-1,6 glucosidic linkages, and (4) with linear chains of α-1,6 glucosidic linkages. We discuss potential processability and functionality of starch derivatives with different linkage combinations and structures. The changes in properties caused by rearrangements of glycosidic linkages provide guidance for design of starch derivatives with desired structures and properties, which promotes the development of new starch products and starch processing for the food industry.

Genome analysis revealed a repertoire of oligosaccharide utilizing CAZymes in Weissella confusa CCK931 and Weissella cibaria YRK005

Weissella bacteria are gram-positive, anaerobic, fermentative, and have probiotic potential. This study aimed to compare the genomes of W. cibaria YRK005 and W. confusa CCK931 isolated from young radish and kimchi, respectively. The genomic size of W. cibaria YRK005 and W. confusa CCK931 with GC content is 2.36 Mb (45%) and 2.28 Mb (44.67%), respectively. The genome study identified 92 and 83 CAZymes genes, respectively, for W. cibaria YRK005 and W. confusa CCK931, that are responsible for 26 and 27 glycoside hydrolases (GH) and 21 and 27 glycosyl transferases. Both species have one gene for carbohydrate esterases and three genes for carbohydrate-binding modules. The primary CAZymes found in both species that are involved in oligosaccharide utilization are GH1, GH2, GH30, GH13_30, GH13_31, GH42, GH43, and GH65. The study also details the production pathways for glycogen and folate. Both strains include a unique repertoire of genes, including hypothetical proteins, showing adaptability to diverse ecological niches and evolution over time.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01232-7.

Fractional extraction and structural characterization of glycogen particles from the whole cultivated caterpillar fungus Ophiocordyceps sinensis

Ophiocordyceps sinensis (syn. Cordyceps sinensis) is a valuable medicinal fungus in traditional Chinese medicine, and one or more polysaccharides are the key constituents with important medical effects. Glycogen as a functional polysaccharide is widely identified in eukaryotes including fungi. However, there is no definitive report of glycogen presence in O. sinensis. In this study, we carefully fractionated polysaccharides from cultivated caterpillar fungus O. sinensis, which were then characterized via methods for glycogen analysis. According to the results, 1.03 ± 0.43 % of polysaccharides were quantified via amyloglucosidase digestion in the whole cultivated caterpillar fungus, which had a typical spherical shape under transmission electron microscope with an average peak radius of 37.63 ± 0.57 nm via size exclusion chromatography and an average chain length of 12.47 ± 0.94 degree of polymerization via fluorophore-assisted capillary electrophoresis. Taken together, this study confirmed that the polysaccharides extracted form O. sinensis were mostly glycogen.

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.

Molecular mechanisms of glycogen particle assembly in Escherichia coli

It has been reported that glycogen in Escherichia coli has two structural states, that is, fragility and stability, which alters dynamically. However, molecular mechanisms behind the structural alterations are not fully understood. In this study, we focused on the potential roles of two important glycogen degradation enzymes, glycogen phosphorylase (glgP) and glycogen debranching enzyme (glgX), in glycogen structural alterations. The fine molecular structure of glycogen particles in Escherichia coli and three mutants (ΔglgP, ΔglgX and ΔglgP/ΔglgX) were examined, which showed that glycogen in E. coli ΔglgP and E. coli ΔglgP/ΔglgX were consistently fragile while being consistently stable in E. coli ΔglgX, indicating the dominant role of GP in glycogen structural stability control. In sum, our study concludes that glycogen phosphorylase is essential in glycogen structural stability, leading to molecular insights into structural assembly of glycogen particles in E. coli.

Complete genome of Nakamurella sp. PAMC28650: genomic insights into its environmental adaptation and biotechnological potential

The mechanisms underlying the survival of bacteria in low temperature and high radiation are not yet fully understood. Nakamurella sp. PAMC28650 was isolated from a glacier of Rwenzori Mountain, Uganda, which species belonged to Nakamurella genus based on 16S rRNA phylogeny, ANI (average nucleotide identity), and BLAST Ring Image Generator (BRIG) analysis among Frankineae suborder. We conducted the whole genome sequencing and comparative genomics of Nakamurella sp. PAMC28650, to understand the genomic features pertaining to survival in cold environment, along with high UV (ultraviolet) radiation. This study highlights the role of polysaccharide in cold adaptation, mining of the UV protection-related secondary metabolites and other related to cold adaptation mechanism through different bioinformatics tools, and providing a brief overview of the genes present in DNA repair systems. Nakamurella sp. PAMC28650 contained glycogen and cellulose metabolism pathways, mycosporine-like amino acids and isorenieratene-synthesizing gene cluster, and a number of DNA repair systems. Also, the genome analysis showed osmoregulation-related genes and cold shock proteins. We infer these genomic features are linked to bacterial survival in cold and UV radiation.

Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways

(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.

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.

Effect of highly branched α-glucans synthesized by dual glycosyltransferases on the glucose release rate

Increasing α-1,6 linkages in starch molecules generates a large amount of α-limit dextrins (α-LDx) during α-amylolysis, which decelerate the release of glucose at the intestinal α-glucosidase level. This study synthesized highly branched α-glucans from sucrose using Neisseria polysaccharea amylosucrase and Rhodothermus obamensis glycogen branching enzyme to enhance those of slowly digestible property. The synthesized α-glucans (Mw: 1.7-4.9 × 10⁷ g mol^-1) were mainly composed of α-1,4 linkages and large proportions of α-1,6 linkages (7.5%-9.9%). After treating the enzymatically synthesized α-glucans with the human α-amylase, the quantity of branched α-LDx (36.2%-46.7%) observed was higher than that for amylopectin (26.8%) and oyster glycogen (29.1%). When the synthetic α-glucans were hydrolyzed by mammalin α-glucosidases, the glucose generation rate decreased because the amount of embedded branched α-LDx increased. Therefore, the macro-sized branched α-glucans with high α-LDx has the potential to be used as slowly digestible material to attenuate postprandial glycemic response.

Surface Glucan Structures in Aeromonas spp

Aeromonas spp. are generally found in aquatic environments, although they have also been isolated from both fresh and processed food. These Gram-negative, rod-shaped bacteria are mostly infective to poikilothermic animals, although they are also considered opportunistic pathogens of both aquatic and terrestrial homeotherms, and some species have been associated with gastrointestinal and extraintestinal septicemic infections in humans. Among the different pathogenic factors associated with virulence, several cell-surface glucans have been shown to contribute to colonization and survival of Aeromonas pathogenic strains, in different hosts. Lipopolysaccharide (LPS), capsule and α-glucan structures, for instance, have been shown to play important roles in bacterial–host interactions related to pathogenesis, such as adherence, biofilm formation, or immune evasion. In addition, glycosylation of both polar and lateral flagella has been shown to be mandatory for flagella production and motility in different Aeromonas strains, and has also been associated with increased bacterial adhesion, biofilm formation, and induction of the host proinflammatory response. The main aspects of these structures are covered in this review.

Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity

Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this "rare" strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.

Metabolic control of nitrogen fixation in rhizobium-legume symbioses

Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N₂ into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD⁺ ratio than sugars. Modeling and ¹³C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N₂ fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.

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.

Soil microbiome predictability increases with spatial and taxonomic scale

Soil microorganisms shape ecosystem function, yet it remains an open question whether we can predict the composition of the soil microbiome in places before observing it. Furthermore, it is unclear whether the predictability of microbial life exhibits taxonomic- and spatial-scale dependence, as it does for macrobiological communities. Here, we leverage multiple large-scale soil microbiome surveys to develop predictive models of bacterial and fungal community composition in soil, then test these models against independent soil microbial community surveys from across the continental United States. We find remarkable scale dependence in community predictability. The predictability of bacterial and fungal communities increases with the spatial scale of observation, and fungal predictability increases with taxonomic scale. These patterns suggest that there is an increasing importance of deterministic versus stochastic processes with scale, consistent with findings in plant and animal communities, suggesting a general scaling relationship across biology. Biogeochemical functional groups and high-level taxonomic groups of microorganisms were equally predictable, indicating that traits and taxonomy are both powerful lenses for understanding soil communities. By focusing on out-of-sample prediction, these findings suggest an emerging generality in our understanding of the soil microbiome, and that this understanding is fundamentally scale dependent.

From Prokaryotes to Eukaryotes: Insights Into the Molecular Structure of Glycogen Particles

Glycogen is a highly-branched polysaccharide that is widely distributed across the three life domains. It has versatile functions in physiological activities such as energy reserve, osmotic regulation, blood glucose homeostasis, and pH maintenance. Recent research also confirms that glycogen plays important roles in longevity and cognition. Intrinsically, glycogen function is determined by its structure that has been intensively studied for many years. The recent association of glycogen α-particle fragility with diabetic conditions further strengthens the importance of glycogen structure in its function. By using improved glycogen extraction procedures and a series of advanced analytical techniques, the fine molecular structure of glycogen particles in human beings and several model organisms such as Escherichia coli, Caenorhabditis elegans, Mus musculus, and Rat rattus have been characterized. However, there are still many unknowns about the assembly mechanisms of glycogen particles, the dynamic changes of glycogen structures, and the composition of glycogen associated proteins (glycogen proteome). In this review, we explored the recent progresses in glycogen studies with a focus on the structure of glycogen particles, which may not only provide insights into glycogen functions, but also facilitate the discovery of novel drug targets for the treatment of diabetes mellitus.

Increased particle size of goethite enhances the antibacterial effect on human pathogen Escherichia coli O157:H7: A Raman spectroscopic study

The persistence of Escherichia coli O157:H7 in soil is one of the most common causes of the food-borne outbreaks. Nano-sized iron oxide minerals in soil, especially goethite, have been found to reduce bacterial viability, which helps to control the spread of human pathogens. However, little is known about the antibacterial effects of iron oxides with different particle sizes. Our result revealed that the micro-sized goethite exhibited a more effective antibacterial activity against E. coli O157:H7 than the nano-sized goethite. The underlying antibacterial mechanisms were further investigated via single-cell Raman microspectroscopy. The exposure to nano-sized goethite increased the levels of ribonucleoside-related substances, phenylalanine and adenosine 5'-triphosphate, while decreased those of glycogen, protein and lipopolysaccharide & outer membrane porins (LPS & OMPs). Meanwhile, micro-sized goethite triggered less variation in ribonucleoside-related substances and induced more reduction in LPS & OMPs. Therefore, the antibacterial effects of nano-sized goethite were mediated by both ROS-dependent RNA damage and cell membrane destruction, whereas micro-sized goethite induced severer membrane damage and less ROS-dependent oxidative stress. This work demonstrates the role of particle sizes in antibacterial effects of iron oxides and provides implications for the pathogen control in soil.

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.

Characterization of glycogen molecular structure in the worm Caenorhabditis elegans

Glycogen, a glucose homopolymer with many glucose chains, is the primary blood-sugar reservoir in many organisms. It comprises β particles (∼20 nm) which can bind together to form large α particles with a rosette morphology. When dimethyl sulfoxide (DMSO) is added to glycogen from diabetic livers, α particles break apart to β particles ('fragility'), possibly due to H-bond disruption; this is not seen in healthy livers. Glycogen α and β particles, and α-particle fragility, are observed in mammals and bacteria, and are examined here in the worm Caenorhabditis elegans, with glycogen from two C. elegans strains, cultured in normal and high-glucose conditions. There were mainly β particles, with some large α particles. Most particles were fragile in DMSO. Growing in a high-glucose medium results in more long chains and more fragility, consistent with previous observations in diabetic animal models. Why high glucose levels facilitate fragility is worthy of further investigation.

Effects of fasting on liver glycogen structure in rats with type 2 diabetes

Liver glycogen, a highly branched glucose polymer, is important for blood sugar homeostasis. It comprises α particles which are made of linked β particles; the molecular structure changes diurnally. In diabetic liver, the α particles are fragile, easily breaking apart into β particles in chaotropic agents such as dimethyl sulfoxide. We here use size-exclusion chromatography to study how fasting changes liver-glycogen structure in vivo for mice in which type-2 diabetes had previously been induced. Diabetic glycogen degraded enzymatically more quickly in the fasted animals than did glycogen without fasting, with fewer α particles, which however were still fragile. The glycogen had fewer long chains and more shorter chains after fasting. This study gives an overview of the in vivo dynamic changes in α-particles under starvation conditions in both normal and diabetic livers.

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.

Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae

Nontypeable Haemophilus influenzae (NTHI) is a human-restricted pathogen with an essential requirement for heme-iron acquisition. We previously demonstrated that microevolution of NTHI promotes stationary phase survival in response to transient heme-iron restriction. In this study, we examine the metabolic contributions to biofilm formation using this evolved NTHI strain, RM33. Quantitative analyses identified 29 proteins, 55 transcripts, and 31 metabolites that significantly changed within in vitro biofilms formed by RM33. The synthesis of all enzymes within the tryptophan and glycogen pathways was significantly increased in biofilms formed by RM33 compared with the parental strain. In addition, increases were observed in metabolite transport, adhesin production, and DNA metabolism. Furthermore, we observed pyruvate as a pivotal point in the metabolic pathways associated with changes in cAMP phosphodiesterase activity during biofilm formation. Taken together, changes in central metabolism combined with increased stores of nutrients may serve to counterbalance nutrient sequestration.

Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.

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.

Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves

Previous bioinformatics studies have linked gain or loss of energy reserves with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the theoretical distribution patterns of energy reserves across bacterial species could provide a shortcut route to look into bacterial lifestyle and physiology. So far, five major energy reserves have been identified in bacteria due to their capacity to support bacterial persistence under nutrient deprivation conditions. These include polyphosphate (polyP), glycogen, wax ester (WE), triacylglycerol (TAG), and polyhydroxyalkanoates (PHAs). Although the enzymes related with metabolism of energy reserves are well understood, there is a lack of systematic investigations into the distribution of bacterial energy reserves from an evolutionary point of view. In this study, we sourced 8282 manually reviewed bacterial reference proteomes and combined a set of hidden Markov sequence models (HMMs) to search homologs of key enzymes related with the metabolism of energy reserves. Our results revealed that specific pathways like trehalose-related glycogen metabolism and enzymes such as wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) are mainly restricted within specific types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirms that loss of energy reserves like polyP metabolism absence in Mollicutes is correlated with bacterial genome reduction. Through this analysis, a clearer picture about the metabolism of energy reserves in bacteria is presented, which could serve as a guide for further theoretical and experimental analyses of bacterial energy metabolism.

Molecular Structure of Glycogen in Escherichia coli

Glycogen, a randomly branched glucose polymer, provides energy storage in organisms. It forms small β particles which in animals bind to form composite α particles, which give better glucose release. Simulations imply β particle size is controlled only by activities and sizes of glycogen biosynthetic enzymes and sizes of polymer chains. Thus, storing more glucose requires forming more β particles, which are expected to sometimes form α particles. No α particles have been reported in bacteria, but the extraction techniques might have caused degradation. Using milder glycogen extraction techniques on Escherichia coli, transmission electron microscopy and size-exclusion chromatography showed α particles, consistent with this hypothesis for α-particle formation. Molecular density and size distributions show similarities with animal glycogen, despite very different metabolic processes. These general polymer constraints are such that any organism which needs to store and then release glucose will have similar α and β particle structures: a type of convergent evolution.

Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves

Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.

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.

Complex gene response of herbicide-resistant Enterobacter strain NRS-1 under different glyphosate stresses

Knowledge of biological evolution and genetic mechanisms is gained by studying the adaptation of bacteria to survive in adverse environmental conditions. In this regard, transcriptomic profiling of a glyphosate-tolerant Enterobacter strain NRS-1 was studied under four different treatments to investigate the gene-regulatory system for glyphosate tolerance. A total of 83, 83, 60 and 74 genes were up-regulated and 108, 87, 178 and 117 genes down-regulated under 60-NPG, 110-NPG, NaCl (355 mM) and HCl (pH 4.46) stress treatments, respectively. Complex gene network was identified to be involved in regulating tolerance to glyphosate. This study revealed that NRS-1 has gained glyphosate tolerance at the cost of osmotic and acidic resistance. The 25 differentially expressed genes are reported to may have partly changed the function for providing resistance to glyphosate directly, among them genes metK, mtbK, fdnG and wzb that might detoxify/degrade the glyphosate. However, under 110-NPG condition, NRS-1 might have utilized economical and efficient ways by depressing its metabolism and activity to pass through this stress. Hence, the present study provides insights into the genes involved in glyphosate tolerance, which can be effectively utilized to engineer herbicide-resistant crop varieties after their proper validation to manage weed growth.

Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence

Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.

The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence

The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence. However, no systematic study of these works is currently available and epidemiological analysis has not been updated for the sit-and-wait hypothesis since the publication of Walther and Ewald's (2004) review. In this article, we put experimental evidence, epidemiological data and theoretical analysis together to support the sit-and-wait hypothesis. According to the epidemiological data in terms of gain and loss of virulence (+/-) and durability (+/-) phenotypes, we classify bacteria into four groups, which are: sit-and-wait pathogens (++), vector-borne pathogens (+-), obligate-intracellular bacteria (--), and free-living bacteria (-+). After that, we dive into the abundant bacterial proteomic data with the assistance of bioinformatics techniques in order to investigate the two factors at molecular level thanks to the fast development of high-throughput sequencing technology. Sequences of durability-related genes sourced from Gene Ontology and UniProt databases and virulence factors collected from Virulence Factor Database are used to search 20 corresponding bacterial proteomes in batch mode for homologous sequences via the HMMER software package. Statistical analysis only identified a modest, and not statistically significant correlation between mortality and survival time for eight non-vector-borne bacteria with sit-and-wait potentials. Meanwhile, through between-group comparisons, bacteria with higher host-mortality are significantly more durable in the external environment. The results of bioinformatics analysis correspond well with epidemiological data, that is, non-vector-borne pathogens with sit-and-wait potentials have higher number of virulence and durability genes compared with other bacterial groups. However, the conclusions are constrained by the relatively small bacterial sample size and non-standardized experimental data.

The Csr System Regulates Escherichia coli Fitness by Controlling Glycogen Accumulation and Energy Levels

In the bacterium Escherichia coli, the posttranscriptional regulatory system Csr was postulated to influence the transition from glycolysis to gluconeogenesis. Here, we explored the role of the Csr system in the glucose-acetate transition as a model of the glycolysis-to-gluconeogenesis switch. Mutations in the Csr system influence the reorganization of gene expression after glucose exhaustion and disturb the timing of acetate reconsumption after glucose exhaustion. Analysis of metabolite concentrations during the transition revealed that the Csr system has a major effect on the energy levels of the cells after glucose exhaustion. This influence was demonstrated to result directly from the effect of the Csr system on glycogen accumulation. Mutation in glycogen metabolism was also demonstrated to hinder metabolic adaptation after glucose exhaustion because of insufficient energy. This work explains how the Csr system influences E. coli fitness during the glycolysis-gluconeogenesis switch and demonstrates the role of glycogen in maintenance of the energy charge during metabolic adaptation.IMPORTANCE Glycogen is a polysaccharide and the main storage form of glucose from bacteria such as Escherichia coli to yeasts and mammals. Although its function as a sugar reserve in mammals is well documented, the role of glycogen in bacteria is not as clear. By studying the role of posttranscriptional regulation during metabolic adaptation, for the first time, we demonstrate the role of sugar reserve played by glycogen in E. coli Indeed, glycogen not only makes it possible to maintain sufficient energy during metabolic transitions but is also the key component in the capacity of cells to resume growth. Since the essential posttranscriptional regulatory system Csr is a major regulator of glycogen accumulation, this work also sheds light on the central role of posttranscriptional regulation in metabolic adaptation.

The glycogen of Galdieria sulphuraria as alternative to starch for the production of slowly digestible and resistant glucose polymers

Highly branched glucose polymers produced from starch are applied in various products, such as peritoneal dialysis solutions and sports drinks. Due to its insoluble, granular nature, the use of native starch as substrate requires an energy consuming pre-treatment to achieve solubilization at the expense of process costs. Glycogen, like starch, is also a natural glucose polymer that shows more favorable features, since it is readily soluble in cold water and more accessible by enzymes. The extremophilic red microalga Galdieria sulphuraria accumulates large amounts of a small, highly branched glycogen that could represent a good alternative to starch as substrate for the production of highly branched glucose polymers. In the present work, we analyzed the structure-properties relationship of this glycogen in its native form and after treatment with amyloglucosidase and compared it to highly branched polymers produced from potato starch. Glycogen showed lower susceptibility to digestive enzymes and significantly decreased viscosity in solution compared to polymers derived from starch, properties conferred by its shorter side chains and higher branch density. The action of amyloglucosidase on native glycogen was somewhat limited due to the high branch density but resulted in the production of a hyperbranched polymer that was virtually resistant to digestive enzymes.

Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii

Glycogen branching enzyme (GBE) catalyzes the formation of α-1,6-branching points during glycogenesis by cleaving α-1,4 bonds and making new α-1,6 bonds. Most GBEs belong to the glycoside hydrolase 13 family (GH13), but new GBEs in the GH57 family have been isolated from Archaea. Here, we determined the crystal structure of a GH57 GBE from the hyperthermophilic archaeon Pyrococcus horikoshii (PhGBE) at a resolution of 2.3 Å. PhGBE exhibits both α-1,6-branching activity and endo-α-1,4 hydrolytic activity. PhGBE has a central (β/α)₇-barrel domain that contains an embedded helix domain and an α-helix-rich C-terminal domain. The active-site cleft is located at the interface of the central and C-terminal domains. Amino acid substitution at Trp22, which is separate from the catalytic nucleophilic residue, abolished both enzymatic activities, indicating that Trp22 might be responsible for substrate recognition. We also observed that shortening of the flexible loop near the catalytic residue changed branched chain lengths of the reaction products with increased hydrolytic activity. Taken together, our findings propose a molecular mechanism for how GH57 GBEs exhibit the two activities and where the substrate binds the enzyme.

Characterization of the highly branched glycogen from the thermoacidophilic red microalga Galdieria sulphuraria and comparison with other glycogens

The thermoacidophilic red microalga Galdieria sulphuraria synthesizes glycogen when growing under heterotrophic conditions. Structural characterization revealed that G. sulphuraria glycogen is the most highly branched glycogen described to date, with 18% of α-(1→6) linkages. Moreover, it differs from other glycogens because it is composed of short chains only and has a substantially smaller molecular weight and particle size. The physiological role of this highly branched glycogen in G. sulphuraria is discussed.