A novel agaro-oligosaccharide-lytic β-galactosidase from Agarivorans gilvus WH0801

Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer

This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.

A dual-signal fluorometric and colorimetric sensing platform based on gold-platinum bimetallic nanoclusters for the determination of β-galactosidase activity

Herein, a novel dual-signal sensing system for the determination of β-galactosidase (β-Gal) activity was established, which was based on a dual-emission probe assembled from gold-platinum bimetallic nanoclusters (Au-Pt NCs) and rhodamine B. Under the catalysis of β-Gal, 4-nitrophenyl β-D-galactopyranoside (PNPG) was rapidly hydrolyzed to generate p-nitrophenol (PNP), which has an obvious UV absorption peak at 400 nm. The hydrolyzed product PNP can quench the fluorescence of Au-Pt NCs effectively by inner filter effect (IFE), and PNP had no impact on the fluorescence of rhodamine B, which will change the emission intensity ratio of Au-Pt NCs and rhodamine B. Therefore, the ratiometric fluorescent and colorimetric dual-signal sensor based on Au-Pt NCs and rhodamine B was successfully constructed for sensitive detection of β-Gal activity. The linear detection range for the ratiometric fluorescence and colorimetric methods were 2.5-25 U/L and 15-55 U/L with detection limits of 1.2 U/L and 5.2 U/L, respectively. The developed assay method has been used for quantitative detection of β-Gal in spiked serum samples and showed good performance. And the detection platform has high reliability and excellent selectivity, which opens a new avenue for the further application of Au-Pt NCs in chemical sensing and biological analysis.

Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium

The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.

Characterization of Agarolytic Pathway in a Terrestrial Bacterium Cohnella sp. LGH

Previously, we have reported that an endo-type β-agarase AgaW was responsible for the hydrolysis of agarose into the major product neoagarotetraose in a terrestrial agar-degrading bacterium Cohnella sp. LGH. Here, we identify and characterize the following depolymerization pathway in strain LGH through the genomic and enzymatic analysis. In the pathway, neoagarotetraose was depolymerized by a novel α-neoagarooligosaccharide (NAOS) hydrolase CL5012 into 3,6-anhydro-α-L-galactose (L-AHG) and agarotriose; Agarotriose was further depolymerized by a novel agarolytic β-galactosidase CL4994 into D-galactose and neoagarobiose; Neoagarobiose was finally depolymerized by CL5012 into L-AHG and D-galactose. Although α-agarase has not been identified in strain LGH, the combined action of CL5012 and CL4994 unexpectedly plays a critical role in the depolymerization of agarotetraose, one theoretical product of α-agarase hydrolysis of agarose. In this pathway, agarotetraose was depolymerized by CL4994 into D-galactose and neoagarotriose; Neoagarotriose was then depolymerized by CL5012 into L-AHG and agarobiose. Furthermore, another novel endo-type β-agarase CL5055 was identified as an isozyme of AgaW with different pH preference in the hydrolysis of agarose into α-NAOSs. Strain LGH seemed to lack a common exo-type β-agarase responsible for the direct depolymerization of agarose or neoagarooligosaccharide into neoagarobiose. These results highlight the diversity of agarolytic manner in bacteria and provide a novel insight on the diversity of agarolytic pathways.

Cloning, expression, and characteristic analysis of the novel β-galactosidase from silkworm, Bombyx mori

β-Galactosidase is a critical exoglycosidase involved in the hydrolysis of lactose, the modification and degradation of glycoprotein in vivo. In this study, the β-galactosidase gene of silkworm (BmGal), whose cDNA comprises 11 exons and contains an intact ORF of 1,821 bp, was cloned. The protein sequence of BmGal showed high similarity with other known insect β-galactosidases. No activity of the BmGal expressed in Escherichia coli or Pichia pastoris was detected while it was successfully expressed with high enzyme activity in baculovirus expression system in silkworm, and the electrophoresis result revealed that the BmGal showed activity in oligomer mode. Enzyme activity assay showed that its optimum pH was 8.4 and its optimum temperature was 40 °C. What is more, we found that iron ions can stimulate the activity of the enzyme while cobalt, nickel, or lead ions can inhibit its activity significantly. Besides, the temporal-spatial transcription pattern of the BmGal mRNA level was analyzed, which showed that BmGal was transcribed at the highest level in the fifth larval instar but relatively low level in the pupal and adult stage, and the highest transcriptional level of BmGal was found in testis among all the tissues concerned.

Advances in agaro-oligosaccharides preparation and bioactivities for revealing the structure-function relationship

Agaro-oligosaccharides originating from red algae have attracted increasing attention in both basic theoretical research and applied fields due to their excellent bioactivities, which indicates the wide prospects of agaro-oligosaccharides for application in the food, pharmaceutical and cosmetic industries. Thus, a considerable number of studies regarding functional agaro-oligosaccharides preparation as well as the bioactivities exploration have been carried out. Based on these studies, this review first introduced different methods that have been used in agar extraction from red algae, and further provided research progress on arylsulfatase. Then, different methods used for agaro-oligosaccharides production were summarized. Moreover, the abundant bioactivities of agaro-oligosaccharides were described in detail. Finally, this review has discussed current research problems and further provided critical aspects, which may be helpful for revealing the structure-function relationship of agaro-oligosaccharide.

Agarose degradation for utilization: Enzymes, pathways, metabolic engineering methods and products

Red algae are important renewable bioresources with very large annual outputs. Agarose is the major carbohydrate component of many red algae and has potential to be of value in the production of agaro-oligosaccharides, biofuels and other chemicals. In this review, we summarize the degradation pathway of agarose, which includes an upstream part involving transformation of agarose into its two monomers, D-galactose (D-Gal) and 3,6-anhydro-α-L-galactose (L-AHG), and a downstream part involving monosaccharide degradation pathways. The upstream part involves agarolytic enzymes such as α-agarase, β-agarase, α-neoagarobiose hydrolase, and agarolytic β-galactosidase. The downstream part includes the degradation pathways of D-Gal and L-AHG. In addition, the production of functional agaro-oligosaccharides such as neoagarobiose and monosaccharides such as L-AHG with different agarolytic enzymes is reviewed. Third, techniques for the setup, regulation and optimization of agarose degradation to increase utilization efficiency of agarose are summarized. Although heterologous construction of the whole agarose degradation pathway in an engineered strain has not been reported, biotechnologies applied to improve D-Gal utilization efficiency and construct L-AHG catalytic routes are reviewed. Finally, critical aspects that may aid in the construction of engineered microorganisms that can fully utilize agarose to produce agaro-oligosaccharides or as carbon sources for production of biofuels or other value-adding chemicals are discussed.

Cloning and Characterization of a New β-Galactosidase from Alteromonas sp. QD01 and Its Potential in Synthesis of Galacto-Oligosaccharides

As prebiotics, galacto-oligosaccharides (GOSs) can improve the intestinal flora and have important applications in medicine. β-galactosidases could promote the synthesis of GOSs in lactose and catalyze the hydrolysis of lactose. In this study, a new β-galactosidase gene (gal2A), which belongs to the glycoside hydrolase family 2, was cloned from marine bacterium Alteromonas sp. QD01 and expressed in Escherichia coli. The molecular weight of Gal2A was 117.07 kDa. The optimal pH and temperature of Gal2A were 8.0 and 40 °C, respectively. At the same time, Gal2A showed wide pH stability in the pH range of 6.0–9.5, which is suitable for lactose hydrolysis in milk. Most metal ions promoted the activity of Gal2A, especially Mn²⁺ and Mg²⁺. Importantly, Gal2A exhibited high transglycosylation activity, which can catalyze the formation of GOS from milk and lactose. These characteristics indicated that Gal2A may be ideal for producing GOSs and lactose-reducing dairy products.

Biochemical Characterization and Substrate Degradation Mode of a Novel α-Agarase from Catenovulum agarivorans

Agarose can be hydrolyzed into agarooligosaccharides (AOSs) by α-agarase, which is an important enzyme for efficient saccharification of agarose or preparation of bioactive oligosaccharides from agarose. Although many β-agarases have been reported and characterized, there are only a few studies on α-agarases. Here, we cloned a novel α-agarase named CaLJ96 with a molecular weight of approximately 200 kDa belonging to glycoside hydrolase family 96 from Catenovulum agarivorans. CaLJ96 has good pH stability and exhibits maximum activity at 37 °C and pH 7.0. The hydrolyzed products of agarose by CaLJ96 are analyzed as agarobiose (A2), agarotetraose (A4), and agarohexaose (A6), in which A4 is the dominant product. CaLJ96 can hydrolyze agaropentaose (A5) into A2 and agarotriose (A3) and A6 into A2 and A4 but cannot act on A2, A3, or A4. This is the first report to characterize the α-agarase action on AOSs in detail. Therefore, CaLJ96 has potential for the manufacture of bioactive AOSs.