Degradation of Alginate by a Newly Isolated Marine Bacterium Agarivorans sp. B2Z047

Identification and Characterization of a Novel Alginate Lyase VSAly7C with Potential Application for Alginate Di- and Tri-Saccharide Preparation

Brown algae are the largest-producing macroalgae, and alginate lyase plays a key role in the green degradation and high-value conversion of brown algae. This study characterized a novel alginate lyase, VSAly7C, from the marine bacterium Vibrio sp. 8-14, which belongs to the PL7_5 subfamily. Biochemical analysis suggested that VSAly7C is medium-temperature, neutral, and polyG-preferred, with enzyme activities of 2608.3 ± 27.3, 1453.2 ± 50.2, and 2545.2 ± 13.2 U/mg toward polyG, polyM, and sodium alginate, respectively. The minimal oligosaccharides VSAly7C could degrade were tetrasaccharides, and its major products were disaccharides and trisaccharides. Structural bioinformatic analysis of the VSAly7C active groove showed that the -1 to +3 subsite interaction network is crucial for determining the minimal oligosaccharides it can degrade. This study elucidates the catalytic properties, modes of action, and substrate recognition mechanisms of a novel alginate lyase, VSAly7C, which may be potentially applicable in alginate disaccharide and trisaccharide preparation.

Insights into the mechanism of substrate specificity in a novel PL15_3 subfamily oligo-alginate lyase VBAly15A

Alginate is a major component of brown algae cell walls and can be degraded via β-elimination by alginate lyases. These enzymes are classified into polysaccharide lyases and oligo-alginate lyases (Oals), with Oals mainly represented by the PL15 and PL17 families. Unlike PL17 Oals, which are widely present in alginate-degrading microorganisms, PL15 enzymes are only identified in a limited number of microorganisms, and their biochemical characteristics remain poorly understood. In this research, a novel PL15 alginate lyase, VBAly15A, from the marine bacterium, Vibrio sp. B1Z05, was identified and characterized. It belongs to a new PL15_3 subfamily and exhibits high activity toward polyM substrates. VBAly15A is thermostable in medium temperatures, tolerant to alkaline up to 11.0, and polyM-specific Oal, and it can first degrade alginate polymers into disaccharides and subsequently catalyze disaccharides into monomers via an exolytic mode. Site-directed mutagenesis showed that Arg114, Tyr470, and Arg110 in the active groove are essential for the stable binding of the substrate. In addition, the amino acid His226 in VBAly15A, previously suggested to act as a catalytic base, is not essential for catalysis, whereas Tyr280, previously proposed to act as a catalytic acid, is required for enzyme activity. Structural bioinformatic and biochemical analyses revealed that His226 functions as a catalytic base, specifically abstracting protons from G-type substrates, while Tyr280 acts as both a catalytic acid and a base. This catalytic mechanism is likely conserved in PL15 family alginate lyases.IMPORTANCEAlginate, as a renewable resource for sustainability, has great application prospects. In addition to polysaccharide lyases, Oals are critical for the full degradation of alginate, a key prerequisite for biorefinery. So far, most identified and well-characterized Oals belong to the PL17 family. However, the catalytic mechanism of PL15 Oals is limited, and even the catalytic base and acid are not fully elucidated. The significance of this study lies in discovering and characterizing a novel Oal VBAly15A that divides into a new PL15 subfamily, PL15_3. Not only are key amino acid residues involved in enzyme activity identified, but residues acting as the catalytic base and acid are also demonstrated. The distance of the catalytic residues His and Tyr to the C5 proton of the sugar ring determines the substrate specificity. Therefore, this work provides new insights into the mechanism of substrate specificity in alginate lyases.

Molecular Engineering of Alginate Lyases and the Potential Agricultural Applications of Their Enzymatic Products

Alginate lyases, enzymes that degrade alginate into unsaturated oligosaccharides, have attracted significant attention for their potential applications across various fields, particularly in agriculture. This review focuses on the molecular engineering of alginate lyases to enhance their activity, stability, and specificity as well as the agricultural applications of the resulting enzymatic products, known as alginate oligosaccharides (AOS). We start by summarizing the sources and classification of alginate lyases, followed by recent advances in their engineering through directed evolution, rational design, truncation of noncatalytic domains, and conserved domain reconstruction. We then explore the diverse agricultural applications of AOS, including their ability to promote plant growth, to increase the content of active plant components, to extend fruit shelf life, and to enhance plant resistance to abiotic stresses. Furthermore, the potential value of AOS as feed additives and preservatives in shrimp-based products is also assessed. This review will not only lay a solid theoretical foundation but also serve as a catalyst for the innovative development and practical application of high-value enzymatic preparations and utilization of AOS-related products, providing new solutions for sustainable agriculture and the food industry.

Insights into putative alginate lyases from epipelagic and mesopelagic communities of the global ocean

Alginate lyases and oligoalginate lyases catalyze the cleavage of the glycosidic bonds of alginate, an acidic polysaccharide synthesized by brown algae and other organisms. These enzymes are highly diverse, currently classified into 15 families of the Carbohydrate-Active Enzyme (CAZy) database. We explored the structural and taxonomic diversity, the biogeographic distribution of the genes and transcripts, and the potential environmental drivers of putative alginate-degrading enzymes from picoplanktonic communities of the upper layers of the global ocean. The identified sequences were first analyzed using sequence similarity networks to assess their relationship with CAZy members. Sequences related to the PL5, PL6, PL7, PL17, and PL38 families had higher gene and transcript abundances, with temperature being a key driver of the structuring of the community members carrying putative alginate lyase genes. PL5 homologs included variants in a key residue of the active site, and sequences assigned to 'Candidatus Pelagibacter' showed high gene and transcript abundances that negatively correlated with inorganic phosphorus concentrations. Sequences assigned to Flavobacteriia and/or Gammaproteobacteria classes dominated the PL6, PL7, and PL17 families, in particular those closely related to sequences from uncultured Polaribacter and Alteromonas australica. In the PL38 family, while sequences assigned to taxa from the Planctomycetota, Verrucomicrobiota, and Bacteroidota phyla showed the highest relative gene abundance at most regions and depths, high expression levels were observed at high latitudes in sequences assigned to Eukaryota (e.g., Phaeocystis antarctica). Overall, the putative enzymes uncovered in this study could be involved in various physiological processes, including alginate assimilation and biosynthesis.

Direct Influence of the Conserved Motif in PL7 Family Alginate Lyases on Enzyme Cold Adaptability

Alginate lyase, a vital component of polysaccharide lyases, is instrumental in the efficient degradation of alginate and the production of single oligosaccharides. Although numerous alginate lyases have been characterized, only a few display extreme cold adaptability in the range of 0-20 °C. In this study, we identified a novel cold-adapted alginate lyase, Aly423, from Tamlana laminarinivorans PT2-4 isolated from Sargassum. Phylogenetic classification, enzyme structure, and catalytic property analyses confirmed that Aly423 could be classified as a member of subfamily 5 of the PL7 family and exhibited significant cold adaptability at low temperatures. Further analysis of the secondary structure and homology modeling of several cold-adapted enzymes revealed two variable amino acid sites in the conserved amino acid motif (YFK*G*Y) of Aly423, which may affect the cold adaptation mechanism. Point mutation experiments demonstrated that mutant A304T significantly altered the temperature adaptation of Aly423, highlighting the critical role of this amino acid site in the cold-adaptation mechanism of the enzyme. In summary, we effectively enhanced the enzymatic activity of the PL7 alginate cold-adapted enzyme through a rational design using computational methods. This advancement is of significant importance for the efficient utilization of sodium alginate in the food, agricultural, and pharmaceutical industries under low-temperature conditions.

Genome Analysis of a Polysaccharide-Degrading Bacterium Microbulbifer sp. HZ11 and Degradation of Alginate

Marine bacteria are crucial sources of alginate lyases, which play an essential role in alginate oligosaccharide (AOS) production. This study reports the biochemical characteristics of a new species of the Microbulbifer genus, Microbulbifer sp. HZ11. The strain HZ11 is Gram-negative, aerobic, flagellate-free, and rod-shaped. The genome of strain HZ11 is a 4,248,867 bp circular chromosome with an average GC content of 56.68%. HZ11 can degrade alginate and other polysaccharides. The carbohydrate-active enzyme (CAZyme) genes account for 4.57% of the total protein-coding genes of HZ11. Its alginate metabolism process is consistent with the characteristics of the polysaccharide utilization locus (PUL) system. The alginate lyase produced by strain HZ11 showed the highest activity at 50 °C, pH 8.5, and 0.1 M NaCl. The substrate preference was as follows: sodium alginate > poly mannuronic acid > poly guluronic acid. The thin layer chromatography (TLC) results revealed that the main enzymatic degradation products were monosaccharides or AOSs with a degree of polymerization (DP) of 2-3. These results help clarify the metabolism and utilization mechanism of alginate by marine bacteria and provide a theoretical reference for its application in the degradation of alginate and other polysaccharides.

Action and cooperation in alginate degradation by three enzymes from the human gut bacterium Bacteroides eggerthii DSM 20697

Alginate is a polysaccharide consumed by humans in edible seaweed and different foods where it is applied as a texturizing hydrocolloid or in encapsulations of drugs and probiotics. While gut bacteria are found to utilize and ferment alginate to health-beneficial short-chain fatty acids, knowledge on the details of the molecular reactions is sparse. Alginates are composed of mannuronic acid (M) and its C-5 epimer guluronic acid (G). An alginate-related polysaccharide utilization locus (PUL) has been identified in the gut bacterium Bacteroides eggerthii DSM 20697. The PUL encodes two polysaccharide lyases (PLs) from the PL6 (BePL6) and PL17 (BePL17) families as well as a KdgF-like metalloprotein (BeKdgF) known to catalyze ring-opening of 4,5-unsaturated monouronates yielding 4-deoxy-l-erythro-5-hexoseulose uronate (DEH). B. eggerthii DSM 20697 does not grow on alginate, but readily proliferates with a lag phase of a few hours in the presence of an endo-acting alginate lyase A1-I from the marine bacterium Sphingomonas sp. A1. The B. eggerthii lyases are both exo-acting and while BePL6 is strictly G-block specific, BePL17 prefers M-blocks. BeKdgF retained 10-27% activity in the presence of 0.1-1 mM EDTA. X-ray crystallography was used to investigate the three-dimensional structure of BeKdgF, based on which a catalytic mechanism was proposed to involve Asp102, acting as acid/base having pKa of 5.9 as determined by NMR pH titration. BePL6 and BePL17 cooperate in alginate degradation with BeKdgF linearizing producing 4,5-unsaturated monouronates. Their efficiency of alginate degradation was much enhanced by the addition of the A1-I alginate lyase.

Enhanced algin oligosaccharide production through selective breeding and optimization of growth and degradation conditions in Cobetia sp. cqz5-12-M1

Algin oligosaccharides have been applied in diverse industries and could be innovative synthesized by alginate-degrading bacteria. For enhance the alginate degradation efficiency to produce more algin oligosaccharides, a mutant strain (Cobetia sp. cqz5-12-M1) was obtained through the complex mutagenesis using UV and the alkylating agent 1-methyl-3-nitro-1-nitrosoguanidine. The enzyme activity of the fermentation supernatant of mutant exhibited a significant 38.09% (53.98 ± 0.69 U/mL) increase, and its optimal growth conditions were determined as: 5 g/L sodium alginate, 5 g/L yeast powder, 30 g/L NaCl, 2 g/L K2HPO4, 2 g/L KH2PO4, 1 g/L MgSO4•7H2O, 0.01 g/L FeSO4•7H2O, pH 6.5, and 34 ℃. Moreover, its optimal degradation conditions were identified as: 5 g/L sodium alginate, 5 g/L yeast powder, 30 g/L NaCl, 2 g/L K2HPO4, 2 g/L KH2PO4, 1 g/L MgSO4•7H2O, 0.01 g/L FeSO4•7H2O, pH 6.5, 31 ℃ and 72 h, yielding an enzyme activity of 120.98 ± 1.40 U/mL in the fermentation supernatant. Conclusive experiments on reagent tolerance revealed the growth of the mutant strain was significantly inhibited by 3% hydrogen peroxide, 5% carbolic acid, and 10 mg/mL gatifloxacin. Additionally, the alginate degradation capacity of mutant strain was highly significantly inhibited by 75% ethanol and all tested antibiotics.

Genome Analysis of Multiple Polysaccharide-Degrading Bacterium Microbulbifer thermotolerans HB226069: Determination of Alginate Lyase Activity

Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from Qingge Port, Hainan, China. Results of the phylogenetic of the 16S rRNA gene and genotypic analysis indicated that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with a G+C content of 56.5%. Analysis of the predicted genes indicated that strain HB226069 encoded 161 carbohydrate-active enzymes (CAZymes), and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity of 117.4 U/mL at 50 °C, pH 7.0, and 0.05 M FeCl3, while exhibiting the best stability at 30 °C and pH 7.0. The Thin Layer Chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analyses indicated that the alginate oligosaccharides (AOSs) degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and supports its potential application in polysaccharide degradation.

Direct Degradation of Fresh and Dried Macroalgae by Agarivorans albus B2Z047

Marine macroalgae are increasingly recognized for their significant biological and economic potential. The key to unlocking this potential lies in the efficient degradation of all carbohydrates from the macroalgae biomass. However, a variety of polysaccharides (alginate, cellulose, fucoidan, and laminarin), are difficult to degrade simultaneously in a short time. In this study, the brown alga Saccharina japonica was found to be rapidly and thoroughly degraded by the marine bacterium Agarivorans albus B2Z047. This strain harbors a broad spectrum of carbohydrate-active enzymes capable of degrading various polysaccharides, making it uniquely equipped to efficiently break down both fresh and dried kelp, achieving a hydrolysis rate of up to 52%. A transcriptomic analysis elucidated the presence of pivotal enzyme genes implicated in the degradation pathways of alginate, cellulose, fucoidan, and laminarin. This discovery highlights the bacterium's capability for the efficient and comprehensive conversion of kelp biomass, indicating its significant potential in biotechnological applications for macroalgae resource utilization.

Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.

Current application of seaweed waste for composting and biochar: A review

To address the origins of ocean acidification, seaweed aquaculture is emerging as a key biosequestration strategy. Nevertheless, seaweed biomass is involved in developing food and animal feed, whereas seaweed waste from commercial hydrocolloid extraction is dumped in landfills, which together limit the carbon cycle and carbon sequestration. This work sought to evaluate the production, properties, and applications of seaweed compost and biochar to strengthen the "carbon sink" implications of aquaculture sectors. Due to their unique characteristics, the production of seaweed-derived biochar and compost, as well as their existing applications, are distinct when compared to terrestrial biomass. This paper outlines the benefits of composting and biochar production as well as proposes ideas and perspectives to overcome technical shortcomings. If properly synchronized, progression in the aquaculture sector, composting, and biochar production, potentially promote various Sustainable Development Goals.

Characterization of Multiple Alginate Lyases in a Highly Efficient Alginate-Degrading Vibrio Strain and Its Degradation Strategy

Alginate is an important polysaccharide in the ocean that supports the growth of marine microorganisms. Many widespread Vibrio species possess alginate lyases and can utilize alginate as a carbon source, but the detailed alginate degradation mechanism in Vibrio remains to be further explored. In this study, we obtained a highly efficient alginate-degrading strain, Vibrio pelagius WXL662, with 11 alginate lyases (VpAly-I to -XI) and further elucidated its molecular mechanism of alginate degradation. Three alginate utilization loci (AUL) were identified in different parts of WXL662's genome, comprising six alginate lyases (VpAly-I, -II, -VIII, -IX, -X, and -XI) and other genes related to alginate degradation. Most of the alginate-degrading genes are strongly induced when alginate is provided as the sole carbon source. Ten alginate lyases (VpAly-I to -X) had been purified and characterized, including six from polysaccharide lyase family 7 (PL7), three from PL17, and one from PL6. These recombinant alginate lyases existing in different cellular locations were active at a wide temperature (10 to 50°C) and pH (4.0 to 9.0) range, with different substrate preferences and diverse degradation products, enabling WXL662 to efficiently utilize alginate in a changing marine environment. Importantly, outer membrane vesicles (OMVs) can act as vectors for alginate lyases (VpAly-II, -V, and -VI) in WXL662. Further investigations of public Vibrio genomes revealed that most alginate-degrading vibrios possess one AUL instead of previously reported "scattered" system. These results emphasize the specific alginate degradation strategy in Vibrio pelagius WXL662, which can be used as a model strain to study the ecological importance of effective alginate-degrading vibrios in the ocean. IMPORTANCE Alginate is an important carbon source in the marine environment, and vibrios are major alginate utilizers. Previous studies focused only on the characteristics of individual alginate lyases in vibrios, but few of them discussed the comprehensive alginate-degrading strategy. Here, we depicted the alginate utilization mechanism and its ecological implications of a highly efficient alginate-degrading Vibrio strain, WXL662, which contained 11 alginate lyases with distinct enzymatic characteristics. Importantly, unlike other vibrios with only one alginate utilization locus (AUL) or the previously reported "scattered" system, three AUL were identified in WXL662. Additionally, the involvement of outer membrane vesicles (OMVs) in the secretion of alginate lyases is proposed for the first time.

Genome Analysis of a Novel Polysaccharide-Degrading Bacterium Paenibacillus algicola and Determination of Alginate Lyases

Carbohydrate-active enzymes (CAZymes) are an important characteristic of bacteria in marine systems. We herein describe the CAZymes of Paenibacillus algicola HB172198^T, a novel type species isolated from brown algae in Qishui Bay, Hainan, China. The genome of strain HB172198^T is a 4,475,055 bp circular chromosome with an average GC content of 51.2%. Analysis of the nucleotide sequences of the predicted genes shows that strain HB172198^T encodes 191 CAZymes. Abundant putative enzymes involved in the degradation of polysaccharides were identified, such as alginate lyase, agarase, carrageenase, xanthanase, xylanase, amylases, cellulase, chitinase, fucosidase and glucanase. Four of the putative polysaccharide lyases from families 7, 15 and 38 were involved in alginate degradation. The alginate lyases of strain HB172198^T exhibited the maximum activity 152 U/mL at 50 °C and pH 8.0, and were relatively stable at pH 7.0 and temperatures lower than 40 °C. The average degree of polymerization (DP) of the sodium alginate oligosaccharide (AOS) degraded by the partially purified alginate lyases remained around 14.2, and the thin layer chromatography (TCL) analysis indicated that it contained DP2-DP8 oligosaccharides. The complete genome sequence of P. algicola HB172198^T will enrich our knowledge of the mechanism of polysaccharide lyase production and provide insights into its potential applications in the degradation of polysaccharides such as alginate.