Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain

Abstract

Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential.

Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi

“…The long-type ulvan lyase from N. ulvanivorans PLR, which is smaller by 534 amino acids and has no similarity with Alteromonadales long ulvan lyases, is composed of two domains. 21) The N-terminal region contains the catalytic domain, and the C-terminus specifically binds to ulvan. The C-terminus of the long-type ulvan lyase from KUL17 contains 3-4 repeats with ca.…”

A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan

“…Furthermore, Rha3S can be modified by β-1,2-linked GlcA side chains and the GlcA-Rha3S or IdoA-Rha3S pattern can be interrupted by consecutive GlcA residues [7][8][9] . Increased interest in the enzymatic degradation of ulvan recently led to the description of several ulvan-active enzymes [10][11][12][13][14][15] . So far, and to the best of our knowledge, only two types of enzymes from different carbohydrate-active enzyme (CAZyme) families showed activity on ulvan.…”

Absorption, distribution, metabolism and elimination (ADME) and toxicity profile of marine sulfated polysaccharides used in bionanotechnology

“…Complex nature of ulvanolytic degradation into monosaccharides indicates participation of other lyases such as 6S-rhamnosidases, xylanases, and sulfatases (Collen et al, 2011). Enzymes acting on ulvan oligomers have also been identified such as β-glucuronidase, a glucuronanlyase, and an ulvan hydrolase (Melcher et al, 2017).…”

“…The sulfate content is 14.3 wt% and uronic acid is present at 19.3 wt%. Variations in molecular weight and rheological properties have been observed in different ulvans depending primarily on extraction conditions (Silva et al, 2013;Yoshimura et al, 2014;Cunha and Grenha, 2016;Collen et al, 2017;He et al, 2017;Melcher et al, 2017).…”

“…Ulvan-based intercalated and exfoliated nanoclays and nanofibres have also been developed (Robic et al, 2008;Melcher et al, 2017).…”