Genome-wide multi-omics analysis reveals the nutrient-dependent metabolic features of mucin-degrading gut bacteria.

The prevalence and occurrence of mucin-degrading (MD) bacteria, such as Akkermansia muciniphila and Ruminococcus gnavus, is highly associated with human health and disease states. However, MD bacterial physiology and metabolism remain elusive. Here, we assessed functional modules of mucin catabolism, through a comprehensive bioinformatics-aided functional annotation, to identify 54 A. muciniphila genes and 296 R. gnavus genes. The reconstructed core metabolic pathways coincided with the growth kinetics and fermentation profiles of A. muciniphila and R. gnavus grown in the presence of mucin and its constituents. Genome-wide multi-omics analyses validated the nutrient-dependent fermentation profiles of the MD bacteria and identified their distinct mucolytic enzymes. The distinct metabolic features of the two MD bacteria induced differences in the metabolite receptor levels and inflammatory signals of the host immune cells. In addition, in vivo experiments and community-scale metabolic modeling demonstrated that different dietary intakes influenced the abundance of MD bacteria, their metabolic fluxes, and gut barrier integrity. Thus, this study provides insights into how diet-induced metabolic differences in MD bacteria determine their distinct physiological roles in the host immune response and the gut ecosystem.

Valorization of leftover green tea residues through conversion to bioactive peptides using probiotics-aided anaerobic digestion.

Bioactive peptides (BPs) are protein fragments that benefit human health. To assess whether leftover green tea residues (GTRs) can serve as a resource for new BPs, we performed in silico proteolysis of GTRs using the BIOPEP database, revealing a wide range of BPs embedded in GTRs. Comparative genomics and the percentage of conserved protein analyses enabled us to select a few probiotic strains for GTR hydrolysis. The selected probiotics digested GTRs anaerobically to yield GTR-derived peptide fractions. To examine whether green tea (GT) peptide fractions could be potential mediators of host-microbe interactions, we comprehensively screened agonistic and antagonistic activities of 168 human G protein-coupled receptors (GPCRs). NanoLC-MS/MS analysis and thin-layer chromatography allowed the identification of peptide sequences and the composition of glycan moieties in the GTRs. Remarkably, GT peptide fractions produced by Lactiplantibacillus plantarum APsulloc 331261, a strain isolated from GT, showed a potent-binding activity for P2RY6, a GPCR involved in intestinal homeostasis. Therefore, this study suggests the potential use of probiotics-aided GTR hydrolysates as postbiotic BPs, providing a biological process for recycling GTRs from agro-waste into renewable resources as health-promoting BPs.

A Genomics-Based Semirational Approach for Expanding the Postbiotic Potential of Collagen Peptides Using Lactobacillaceae.

Food-derived bioactive peptides (BPs) have received considerable attention as postbiotics for human gut health. Here we used a genomics-based semirational approach to expand the postbiotic potential of collagen peptides (CPs) produced from probiotic fermentation. In silico digestion revealed distinct BPs embedded in fish collagen in a protease-dependent manner. Anaerobic digestion of collagen by representative Lactobacillaceae species revealed differential substrate utilization and collagen degradation patterns. Nanoliquid chromatography-mass spectrometry analysis of CPs showed that each species exhibited different cleavage patterns and unique peptide profiles. Remarkably, the 1-10 kDa CPs produced by Lacticaseibacillus paracasei showed agonistic activities toward G protein-coupled receptor 35 (GPR35). These CPs could repair intestinal epithelium through the GPR35-mediated extracellular signal-regulated protein kinase (ERK) 1/2 signaling pathway, suggesting that probiotic-aided collagen hydrolysates can serve as postbiotics for host-microbe interactions. Therefore, this study provides an effective strategy for the rapid screening of CPs for gut health in the gastrointestinal tract.

Nutrient-specific proteomic analysis of the mucin degrading bacterium Akkermansia muciniphila.

Akkermansia muciniphila is a prominent mucin-degrading bacterium that acts as a keystone species in regulating the human gut microbiota. Despite recently increasing research into this bacterium and its relevance to human health, a high-resolution database of its functional proteins remains scarce. Here, we provide a proteomic overview of A. muciniphila grown in different nutrient conditions ranging from defined to complex. Of 2318 protein-coding genes in the genome, we identified 841 (40%) that were expressed at the protein level. Overall, proteins involved in energy production and carbohydrate metabolism indicate that A. muciniphila relies mainly on the Embden-Meyerhof-Parnas pathway, and produces short-chain fatty acids through anaerobic fermentation in a nutrient-specific manner. Moreover, this bacterium possesses a broad repertoire of glycosyl hydrolases, together with putative peptidases and sulfatases, to cleave O-glycosylated mucin. Of them, putative mucin-degrading enzymes (Amuc_1220, Amuc_1120, Amuc_0052, Amuc_0480, and Amuc_0060) are highly abundant in the mucin-supplemented media. Furthermore, A. muciniphila uses mucin-derived monosaccharides as sources of energy and cell wall biogenesis. Our dataset provides nutrient-dependent global proteomes of A. muciniphila ATCC BAA-835 to offer insights into its metabolic functions that shape the composition of the human gut microbiota via mucin degradation.

The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation.

Most extremophilic anaerobes possess a sulfur formation (Suf) system for Fe-S cluster biogenesis. In addition to its essential role in redox chemistry and stress responses of Fe-S cluster proteins, the Suf system may play an important role in keratin degradation by Fervidobacterium islandicum AW-1. Comparative genomics of the order Thermotogales revealed that the feather-degrading F. islandicum AW-1 has a complete Suf-like machinery (SufCBDSU) that is highly expressed in cells grown on native feathers in the absence of elemental sulfur (S0 ). On the other hand, F. islandicum AW-1 exhibited a significant retardation in the Suf system-mediated keratin degradation in the presence of S0 . Detailed differential expression analysis of sulfur assimilation machineries unveiled the mechanism by which an efficient sulfur delivery from persulfurated SufS to SufU is achieved during keratinolysis under sulfur starvation. Indeed, addition of SufS-SufU to cell extracts containing keratinolytic proteases accelerated keratin decomposition in vitro under reducing conditions. Remarkably, mass spectrometric analysis of extracellular and intracellular levels of amino acids suggested that redox homeostasis within cells coupled to extracellular cysteine and cystine recycling might be a prerequisite for keratinolysis. Taken together, these results suggest that the Suf-like machinery including the SufS-SufU complex may contribute to sulfur availability for an extracellular reducing environment as well as intracellular redox homeostasis through cysteine released from keratin hydrolysate under starvation conditions.

Identification of keratinases from Fervidobacterium islandicum AW-1 using dynamic gene expression profiling.

Keratin degradation is of great interest for converting agro-industrial waste into bioactive peptides and is directly relevant for understanding the pathogenesis of superficial infections caused by dermatophytes. However, the mechanism of this process remains unclear. Here, we obtained the complete genome sequence of a feather-degrading, extremely thermophilic bacterium, Fervidobacterium islandicum AW-1 and performed bioinformatics-based functional annotation. Reverse transcription PCR revealed that 57 putative protease-encoding genes were differentially expressed in substrate-dependent manners. Consequently, 16 candidate genes were highly expressed under starvation conditions, when keratin degradation begun. Subsequently, the dynamic expression profiles of these 16 selected genes in response to feathers, as determined via quantitative real-time PCR, suggested that they included four metalloproteases and two peptidases including an ATP-dependent serine protease, all of which might act as key players in feather decomposition. Furthermore, in vitro keratinolytic assays supported the notion that recombinant enzymes enhanced the decomposition of feathers in the presence of cell extracts. Therefore, our genome-based systematic and dynamic expression profiling demonstrated that these identified metalloproteases together with two additional peptidases might be primarily associated with the decomposition of native feathers, suggesting that keratin degradation can be achieved via non-canonical catalysis of several membrane-associated metalloproteases in cooperation with cytosolic proteases.

Identification of Matrix Metalloproteinase-1-Suppressive Peptides in Feather Keratin Hydrolysate.

Inhibition of matrix metalloproteinases (MMPs), which degrade collagen and elastin in the dermis of normal skin, is a key strategy for anti-skin aging. In this study, we identified five low-molecular-weight (LMW, <1 kDa) MMP-1-suppressive peptides in feather keratin hydrolysate (FKH) obtained by anaerobic digestion with an extremophilic bacterium. FKH was first subjected to ultrafiltration, followed by size-exclusion chromatography and liquid chromatography/electrospray ionization tandem mass spectrometry analysis. Chemically synthesized peptides identical to the sequences identified suppressed MMP expression in human dermal fibroblasts (HDFs). To investigate the impact of the MMP-1-suppressive peptides on the signaling pathway, we performed antibody array phosphorylation profiling of HDFs. The results suggested that the peptide GGFDL regulates ultraviolet-B-induced MMP-1 expression by inhibiting mitogen-activated protein kinases and nuclear factor κB signaling pathways as well as histone modification. Thus, LMW feather keratin peptides could serve as novel bioactive compounds to protect the skin against intrinsic and extrinsic factors.

Low-molecular weight keratins with anti-skin aging activity produced by anaerobic digestion of poultry feathers with Fervidobacterium islandicum AW-1.

Bioactive peptides contribute to various cellular processes including improved skin physiology. Hence, bioactive keratins have attracted considerable attention as active cosmetic ingredients for skin health. Here, we obtained low molecular weight (LMW) keratins from native chicken feathers by anaerobic digestion with an extremely thermophilic bacterium Fervidobacterium islandicum AW-1, followed by stepwise fractionation through ultrafiltration. To assess the effects of the feather keratins on skin health, we performed in vitro and ex vivo assays to investigate their inhibitory effects on matrix metalloproteinases (MMPs). As results, LMW feather keratins marginally inhibited collagenase, elastase, and radical scavenging activities. On the other hand, LMW feather keratins significantly suppressed the expression of ultraviolet B (UVB)-induced MMP-1 and MMP-13 in human dermal fibroblasts. Furthermore, phospho-kinase antibody array revealed that LMW feather keratins suppressed UVB-induced phosphorylation of Akts, c-Jun N-terminal kinases 1, p38 beta, and RSK2, but not ERKs in human dermal fibroblast. Overall, these results suggest that LMW feather keratins are potential candidates as cosmeceutical peptides for anti-skin aging.

Development of a keratinase activity assay using recombinant chicken feather keratin substrates.

Poultry feathers consist mainly of the protein keratin, which is rich in ß-pleated sheets and consequently resistant to proteolysis. Although many keratinases have been identified, the reasons for their substrate specificity towards ß-keratin remain unclear due to difficulties in preparing a soluble feather keratin substrate for use in activity assays. In the present study, we overexpressed Gallus gallus chromosomes 2 and 27 ß-keratin-encoding genes in Escherichia coli, purified denatured recombinant proteins by Ni2+ affinity chromatography, and refolded by stepwise dialysis to yield soluble keratins. To assess the keratinolytic activity, we compared the proteolytic activity of crude extracts from the feather- degrading bacterium Fervidobacterium islandicum AW-1 with proteinase K, trypsin, and papain using purified recombinant keratin and casein as substrates. All tested proteases showed strong proteolytic activities for casein, whereas only F. islandicum AW-1 crude extracts and proteinase K exhibited pronounced keratinolytic activity for the recombinant keratin. Moreover, LC-MS/MS analysis of keratin hydrolysates allowed us to predict the P1 sites of keratinolytic enzymes in the F. islandicum AW-1 extracts, thereby qualifying and quantifying the extent of keratinolysis. The soluble keratin-based assay has clear therapeutic and industrial potential for the development of a high-throughput screening system for proteases hydrolyzing disease-related protein aggregates, as well as mechanically resilient keratin-based polymers.

Biochemical and structural characterization of a keratin-degrading M32 carboxypeptidase from Fervidobacterium islandicum AW-1.

Comparative genomics of the keratin-degrading extremophilic eubacterium Fervidobacterium islandicum AW-1 and the closely related Fervidobacterium nodosum with no keratinolytic activity suggested that the FIAW1_1600 gene encoding a carboxypeptidase (CP) plays an important role in keratin degradation. The presumptive 489 amino acid sequence of the gene showed a conserved HEXXH motif with low levels of sequence identity (<38%) to reported thermostable M32 CPs. To identify its functional role, the FIAW1_1600 gene was overexpressed in Escherichia coli, and the recombinant enzyme was purified and characterized in detail. F. islandicum AW-1 CP (FisCP) formed a homodimer with a molecular mass of 107 kDa, and its apoenzyme exhibited maximal activity at 80 °C and pH 7.0 in the presence of Co(2+). This metalloenzyme mainly cleaved the C-termini of peptides with a basic amino acid sequence. The crystal structure of FisCP at 2.2 Å resolution showed high levels of structural similarities (root-mean-square deviations of <1.7 Å) to those of other M32 CP homologs. Remarkably, the enzyme significantly enhanced the degradation of native chicken feathers. This study suggests that FisCP, a keratinolytic member of the thermostable M32 CP family, plays an important role in keratin degradation for cellular metabolism in F. islandicum AW-1.