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Studies on mannan-degrading enzymes from termite symbionts and a filamentous fungus

徐, 韻涵 東京大学 DOI:10.15083/0002002068

2021.10.04

概要

Introduction
　Lignocellulosic biomass has been considered as a renewable resource for biorefinery to contribute to the future production of biofuels. Among the constituents of biomass, mannan is widely distributed as the third most abundant component of hemicellulose in the plant cell wall. Endo-1,4-β-mannanase (EC 3.2.1.78) is one of the major plant mannan-degrading enzymes and is capable of cleaving internal β-1,4-linkage of two mannose moieties or between mannose and glucose. Another key group of enzymes in mannan hydrolysis are β-mannosidases (EC 3.2.1.25), exo-acting enzymes that catalyze the hydrolysis of β-1,4-linked mannosides, releasing mannose from the non-reducing end of mannans and manno-oligosaccharides produced by β-mannanase. Symbiotic protists in the gut of termites are prominent natural enzymatic resources for efficient lignocellulose degradation. However, the catalytic mechanism and enzymatic properties of β-mannanases from termite hindgut still remain unclear. Previous studies conducted in our laboratory reported the biochemical characterization of GH26 endo-β-mannanases, RsMan26C and RsMan26H, isolated from a cDNA library of symbiotic protists of the lower termite, Reticulitermes speratus. RsMan26C was a typical endo-mode mannanase, whereas RsMan26H was demonstrated to be an endo-processive mannobiohydrolase. Since these were the only two studies conducted on mannanases from termite symbionts, in this study I heterologously expressed and characterized two additional protistan GH26 endo-β- mannanases, RsMan26A and RsMan26B, together with RsMan26C. In addition, the catalytic process of RsMan26H was also analyzed in more detail based on the molecular modeling studies.
　Although the enzymatic properties of mannanases were analyzed by these in vitro analyses, their roles in vivo, especially those in termite symbionts, cannot be studied due to the unculturable nature of these microorganisms. Instead, the filamentous fungus Neurospora crassa grows easily and has a unique haploid life cycle which significantly simplifies the genetic analysis. Along with its well-annotated genome sequence and robust growth on lignocellulose, I used this fungus as a model for the analysis of mannan utilization mechanism in vivo. The physiological role(s) of mannan-degrading enzymes in N. crassa were investigated by growing the wild-type and the mutant strains in the medium containing various carbon sources. In the course of the study one β-mannanase and one β-mannosidase were heterologously expressed and characterized. The results revealed the novel insights into the mannan degradation in N. crassa.

Chapter 1: Expression and characterization of protistan β-mannanases RsMan26A, RsMan26B, and RsMan26C
　Two novel β-mannanases, RsMan26A and RsMan26B, from a symbiotic protist community of the lower termite, R. speratus, were successfully expressed in the methylotrophic yeast, Pichia pastoris, using the strong constitutive GAP promoter and the prepro-α-factor signal sequence. Purification of RsMan26A and RsMan26B was done by Ni2+-NTA affinity and then anion exchange chromatographies. Deglycosylation assay suggested that RsMan26A was heterologously modified by either one or two N-glycans, while RsMan26B was modified at both sites of potential N-glycosylation. RsMan26A and RsMan26B displayed similar temperature and pH optima of 50°C and pH 5.0, respectively. Regarding the substrate specificity, TLC analysis and kinetic study suggested that RsMan26A, RsMan26B, and RsMan26C displayed similar substrate preference, exhibiting higher activity to konjac glucomannan and locust bean gum with lower degree of galactosyl substitution.
　The crystal structure of RsMan26C and the homology modeling of RsMan26A and RsMan26B imply that the tryptophan residue (Trp79, Trp79, and Trp80 in RsMan26A, RsMan26B, and RsMan26C, respectively) located at subsite -5 of the enzyme forms a hydrophobic stacking interaction with a sugar ring of the substrate, which is consistent with the increase in Km values by substituting the Trp residue with alanine in these three protistan mannanases. Furthermore, substitution of the first residue of conserved WFWWG sequence at subsite +1 in RsMan26C, Trp182, caused a substantial reduction in the catalytic activity, displaying the importance of this residue as well as the large influence caused by modification of the residues proximal to the catalytic site. In contrast, although Tyr 294 was proposed to form a hydrophobic stacking interaction with the sugar ring at subsite -2, Y294A mutation caused limited decrease in the catalytic efficiency than other mutations, such as W80A and W182A, suggesting that the effect of hydrophobic stacking interaction at subsite -2 is less crucial than those at subsites -5 or +1. Another possible explanation is that the tyrosine residue may cause weaker hydrophobic stacking interaction than the tryptophan residue.

Chapter 2: Expression and structural analysis of a protistan β-mannanases RsMan26H
　Although another protistan β-mannanase RsMan26H was previously expressed in P. pastoris, the recombinant N-glycosylated RsMan26H could not be crystallized. Considering the effect of N-glycosylation on the crystal formation, the expression system of Escherichia coli was employed to express RsMan26H in this chapter. RsMan26H was produced in the soluble fraction of the cell lysates from BL21 (DE3) pLysS strain and was further purified by Ni2+-NTA and then anion exchange chromatographies. The purified protein displayed a single band of 42 kDa, which is nearly equal to the calculated size of hexahistidine-tagged RsMan26H.
　Homology modeling of RsMan26H was conducted by superimposition with an exo- mannobiohydrolase CjMan26C from Cellvibrio japonicus (34% identity) and an endo- processive mannobiohydrolase BoMan26A from Bacteroides ovatus (37% identity), respectively. In CjMan26C, loop 3 at subsite -2 is thought to close off the possibility of a -3 subsite, contributing to its exo-type mannobiohydrolase activity. This exo-loop is also conserved in RsMan26H and BoMan26A. Another loop region (loop 8) in BoMan26A, corresponding to a short α-helix turn in CjMan26C, was suggested to contribute to endo- activity due to its high flexibility. Although the amino acid sequence of loop 8 in BoMan26A was not highly conserved in the corresponding sequence of RsMan26H (only 6 conserved in about 20 residues), the modelled structures of two enzymes shared a long and winding loop region. In this study, although the crystallization screening was unsuccessful, mutagenesis analysis revealed that the conserved loop at subsite -2 is likely critical for the catalysis of RsMan26H because of the substantial reduction in the activity after replacing or deleting this loop region. Moreover, the retention of mannobiohydrolase activity in all the mutants indicated that this loop may not predominantly contribute to the mannobiohydrolase activity of RsMan26H. Taking into account the structural similarity with BoMan26A, I propose that the potential interaction between two equivalent loops around -2 and -3 subsites may instead account for the endo-processive mannobiohydrolase activity of RsMan26H.

Chapter 3: Physiological functions of mannan-degrading enzymes in Neurospora crassa
　In this chapter, in order to investigate the mannan degradation mechanism in N. crassa, I searched the genes encoding enzymes of GH2, GH5, and GH26 from the N. crassa genome database. As a result, three putative β-mannosidases (gh2-1, gh2-4, and gh2-5), one putative β- mannanase (gh5-7), and one putative hemicellulase (gh26-1) were found and heterologously expressed. Except gh2-1, all of the selected enzymes were expected as secretory proteins with N-terminal signal sequence. Among these five putative mannan-degrading enzymes, only the activities of gh5-7 and gh2-1 were confirmed, displaying endo-β-mannanase and exo-β- mannosidase activities, respectively. Real-time RT-PCR analyses indicated that the expression of gh5-7 is much higher than that of other genes when grown on mannan cultures, suggesting the critical role of gh5-7 in mannan degradation. β-mannanase gh5-7 displays a substrate preference on galactomannan by showing 10-times higher catalytic efficiency compared to β- mannan. Meanwhile the subcellular localization analysis indicated that the β-mannosidase gh2- 1 is an intracellular protein and localizes to the cytoplasm. Compared to the wild type strain, the growth of Δgh5-7 and Δgh5-7Δgh2-4 mutants was poor in the cultures containing galactomannan, β-mannan, or glucomannan as the sole carbon source, suggesting that β- mannanase gh5-7 plays a critical role in mannan degradation in vivo. On the other hand, Δgh2- 1, Δgh2-4, and Δgh2-1Δgh2-4 mutants grew normally when cultured with either galactomannan or glucomannan, while they showed significantly slow growth when grown on β-mannan as the sole carbon source, indicating that these two enzymes may play an important role in the degradation of unsubstituted β-mannan. Herein, I propose a following scheme of sequential actions by the enzymes involved in the mannan utilization in N. crassa: β-mannanase gh5-7 is the most powerful mannan degrader, releasing manno-oligosaccharides from the branched mannan. Subsequently, the short manno-oligosaccharides including mannobiose incorporated into the cells can be further converted to mannose by the intracellular β-mannosidase gh2-1. On the other hand, the functions of gh2-4, gh2-5, and gh26-1 were not clearly defined, indicating that further investigation is needed to fully understand the process of mannan utilization in N. crassa.

Conclusions:
　The present work reports the heterologous expression, purification, and biochemical characterization of four symbiotic protistan β-mannanases, RsMan26A, RsMan26B, RsMan26C, and RsMan26H. The significant binding of subsite -5 first reported in my study suggests a predominant mode of productive binding involving subsite -5 and the occupancy of at least 6 subsites for efficient hydrolytic activity in RsMan26A, RsMan26B, and RsMan26C. Homology modeling and mutagenesis study suggested that RsMan26H has a narrow cleft and two loops around -2 and -3 subsites, respectively. The potential flexibility of these two loops may account for the endo-processive mannobiohydrolase activity of RsMan26H. These data would provide insights into the catalytic process of mannanases from termite symbionts. Finally, the characterization and the physiological analyses of mannan-degrading enzymes from N. crassa were performed; the combination of in vitro and in vivo approaches would contribute to a better understanding of mannan degradation by N. crassa.

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