The Distinctive Permutated Domain Structure of Periplasmic α-Amylase (MalS) from Glycoside Hydrolase Family 13 Subfamily 19

MalS, a periplasmic α-amylase in Escherichia coli, has a binding affinity to glycogen with unique substrate specificities

In this study, we investigated MalS, a periplasmic α-enzyme from Escherichia coli K12, known for its unique biochemical properties related to polysaccharide utilization. Evolutionarily, MalS has inherited the glycosyl hydrolase catalytic domain from the glycoside hydrolase family 13, with the protein sequences highly conserved across Enterobacteria, including Salmonella and Shigella. MalS exhibited optimal activity at 65 °C, significantly higher than other E. coli enzymes. Although its reaction pattern resembled that of typical α-amylases, its catalytic efficiency on polysaccharides was notably lower. Intriguingly, MalS demonstrated a strong binding affinity for various glucose polymers, including β-cyclodextrin and glycogen, which significantly enhanced its thermostability. Despite full-length MalS binding strongly to glycogen, neither its N-terminal domain, predicted by AlphaFold2 to belong to the Carbohydrate-Binding Module family 69, nor the remaining parts of the enzyme showed binding affinity toward polysaccharides. Kinetic studies revealed that MalS had a 2.5-fold lower Km and 1.4-fold higher catalytic efficiency toward glycogen compared to amylopectin, which contrasts starkly with pancreatic α-amylases. However, over prolonged reactions, glycogen hydrolysis by MalS was slower than that of amylopectin. In the early initial stage, MalS predominantly degraded glycogen to maltopentaose (G5) rather than maltohexaose (G6) as usual. Taken together, these findings suggest MalS may play a role in recognizing glycogen-type polysaccharides in the bacterial periplasm during adaptation to new environments. Given the crucial role of glycogen in the survival and infection processes of pathogenic bacteria, understanding MalS's interaction with glycogen-type polysaccharides could offer valuable insights into bacterial survival mechanisms and their ability to infect hosts. KEY POINTS: • MalS has unique structure and properties but conserved among many enterobacteria • Binding of MalS with polysaccharides significantly enhanced its thermostability • Unlike other amylases, MalS showed 2.5-fold lower Km on glycogen than amylopectin.

Comparative evaluation of amylases in the oral phase of the INFOGEST static simulation of oro-gastric digestion

Amylases are crucial enzymes for dietary starch hydrolysis and essential to human digestive physiology. To simulate gastrointestinal (GI) digestion in vitro, amylases may be included in a short oral phase to mimic human salivary amylase (HSA) activity. Due to the high procurement cost of HSA, alternate porcine or microbial sources of amylases have been used. The major objective of this study was to evaluate the suitability of porcine pancreatic amylase (PPA) as an alternative to HSA in the INFOGEST 2.0 static simulation of oro-gastric digestion. To start, a comprehensive literature review was conducted to categorize oral phase methodologies. We determined that 14.1 % and 5.2 % of 262 studies used PPA and microbial amylases, respectively, in the oral phase. Amylolytic activity was confirmed by HPLC analysis of free maltose after simulated potato digestion. PPA and HSA exhibited comparable starch hydrolysis, while a fungal amylase showed significantly higher activity (P < 0.0001). To investigate suspected proteolytic "side activity" of PPA, pea protein digestion was simulated with HSA, PPA, or no amylase in the oral phase. Proteolytic activity was evaluated in gastric digestas by measurement of free amino nitrogen (FAN) by UV spectroscopy and free amino acids by HPLC. Relative peptide hydrolysis patterns were evaluated by SDS-PAGE and size exclusion chromatography (SEC). PPA treatment showed significantly higher proteolytic activity based on FAN and free amino acid analysis compared to HSA (Both P < 0.0001, one-way ANOVA), and qualitatively greater protein hydrolysis by SDS-PAGE and SEC analyses. These data unanimously confirm the unintended proteolytic activity of PPA in the oral phase that carries over to the gastric phase, potentially confounding analyses of protein digestibility and nutrient bioavailability. These findings suggest PPA should be avoided in the oral phase and confirm that HSA remains the preferred amylase for simulating human oral digestion.

Heterologous Expression and Characterization of a Novel Mesophilic Maltogenic α-Amylase AmyFlA from Flavobacterium sp. NAU1659

A novel amylase AmyFlA from Flavobacterium sp. NAU1659, AmyFlA, was cloned and expressed in Esherichia coli. Based on phylogenetic and functional analysis, it was identified as a novel member of the subfamily GH13_46, sharing high sequence identity. The protein was predicted to consist of 620 amino acids, with a putative signal peptide of 25 amino acids. The enzyme was able to hydrolyze soluble starch with a specific activity of 352.97 U/mg at 50 °C in 50 mM phosphate buffer (pH 6.0). The Km and Vmax values of AmyFlA were respectively 3.15 mg/ml and 566.36 µmol·ml-1·min-1 under optimal conditions. Its activity towards starch was enhanced by 63% in the presence of 1 mM Ca2+, indicating that AmyFlA was a Ca2+-dependent amylase. Compared to the reported maltogenic amylases, AmyFlA produced a lower variety of intermediate oligosaccharides at the start of the reaction so that the product mixture contained a higher proportion of maltose. These results indicate that AmyFlA may be potential application value in the production of high-maltose syrup.

Unprecedented Diversity of the Glycoside Hydrolase Family 70: A Comprehensive Analysis of Sequence, Structure, and Function

The glycoside hydrolase family 70 (GH70) contains bacterial extracellular multidomain enzymes, synthesizing α-glucans from sucrose or starch-like substrates. A few dozen have been biochemically characterized, while crystal structures cover only the core domains and lack significant parts of auxiliary domains. Here we present a systematic overview of GH70 enzymes and their 3D structural organization and bacterial origin. A representative set of 234 permuted and 25 nonpermuted GH70 enzymes was generated, covering 12 bacterial families and 3 phyla and containing 185 predicted glucansucrases (GS), 15 branching sucrases (BrS), 8 "twin" GS-BrSs, and 51 α-glucanotransferases (α-GT). Analysis of AlphaFold models of all 259 entries showed that, apart from the core domains, the structural variation regarding auxiliary domains is far greater than anticipated, with nine different domain types. We analyzed the phylogenetic distribution and discuss the possible roles of auxiliary domains as well as possible correlations between enzyme specificity, auxiliary domain type, and bacterial origin.