Interrupted catalytic domain structures in xylanases from two distantly related strains of Prevotella ruminicola

doi:10.1016/S0167-4838(96)00213-0

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Volume 1337, Issue 2, 8 February 1997, Pages 161-165

Biochimica et Biophy...

https://doi.org/10.1016/S0167-4838(96)00213-0 Get rights and content

Abstract

Two xylanases from the rumen anaerobic bacterium Prevotella ruminicola were found to possess highly unusual structures in which family 10 catalytic domains are interrupted by unrelated sequences. XynC from P. ruminicola B₁4 carries a 160 amino-acid insertion, while a P. ruminicola D31d xylanase carries an unrelated region of 280 amino acids, containing an imperfect 130 amino-acid duplication. Both regions of family 10 similarity were shown to be essential for activity of the D31d enzyme.

References (23)

Dehority, B.A. (1991) Proc. Nutr. Soc. 50,...
Osborne, J.M. and Dehority, B.A. (1989) Appl. Env. Microbiol. 55,...
Avguštin, G., Flint, H.J. and Whitehead, T.R. (1992) FEMS Microbiol. Lett. 99,...
Avguštin, G., Wright, F. and Flint, H.J. (1994) Int. J. System. Bacteriol. 44,...
Whitehead, T.R. (1993) Curr. Microbiol. 27,...
Matsushita, O., Russell, J.B. and Wilson, D.B. (1990) J. Bacteriol. 172,...
Gasparic, A., Martin, J., Daniel, A. and Flint, H.J. (1995) Appl. Env. Microbiol. 61,...
Whitehead, T.R. and Lee, D.A. (1990) Curr. Microbiol. 23,...
Gasparic, A., Marinsek-Logar R., Martin, J., Wallace, R.J., Nekrep, F.V. and Flint, H.J. (1995) FEMS Microbiol. Lett....
Vercoe, P.E. and Gregg, K. (1992) Mol. Gen. Genet. 233,...

Gilkes, N.R., Henrissat, B., Kilburn, D.G., Miller, R.C. and Warren, R.A.J. (1991) Microbiol. Rev. 55,...

Cited by (35)

Degradation of xylan by human gut Bacteroides xylanisolvens XB1A
2023, Carbohydrate Polymers
Although many polysaccharides utilization loci (PULs) have been investigated by genomics and transcriptomics, the detailed functional characterization lags severely behind. We hypothesize that PULs on the genome of Bacteroides xylanisolvens XB1A (BX) dictate the degradation of complex xylan. To address, xylan S32 isolated from Dendrobium officinale was employed as a sample polysaccharide. We firstly showed that xylan S32 promoted the growth of BX which might degrade xylan S32 into monosaccharides and oligosaccharides. We further showed that this degradation was performed mainly via two discrete PULs in the genome of BX. Briefly, a new surface glycan binding protein (SGBP) BX_29290^SGBP was identified, and shown to be essential for the growth of BX on xylan S32. Two cell surface endo-xylanases Xyn10A and Xyn10B cooperated to deconstruct the xylan S32. Intriguingly, genes encoding Xyn10A and Xyn10B were mainly distributed in the genome of Bacteroides spp. In addition, BX metabolized xylan S32 to produce short chain fatty acids (SCFAs) and folate. Taken together, these findings provide new evidence to understand the food source of BX and the BX-directed intervention strategy by xylan.
Survival and retention of the probiotic properties of Bacillus sp. strains under marine stress starvation conditions and their potential use as a probiotic in Artemia culture
2012, Research in Veterinary Science
Citation Excerpt :
It is well established that bacteria evolve stress-sensing systems and defences against stress, which allow them to withstand harsh conditions and sudden environmental changes (Van de Guchte et al., 2002; Corcoran et al., 2008). The primary adhesion of microorganisms to abiotic materials is determined by both solid and cell surface properties (Flint et al., 1997). It has been reported that bacteria like Vibrio, Staphylococcus and Bacillus can be adhesive to abiotic surfaces (Arciola et al., 2002).
The probiotic properties of Bacillus strains isolated from Artemia culture and the effect of marine stress on viability and survival were investigated, as well as the changes occurring in their properties. Analyses showed that these bacteria corresponded to the genus Bacillus sp. Antagonism and adherence assays revealed that Bacillus strains have an inhibitory effect against tested pathogenic bacteria and are fairly adherent. Normal and starved cells showed different enzymatic profiles. Challenge tests performed with Artemia larvae provided evidence that the tested Bacillus strains were neither pathogenic nor toxic to the host and conferred protection for Artemia culture against pathogens. The tested strains maintained their viability and their probiotic properties during the period of study. The results suggest that the tested strains have suffered changes allowing them to survive in seawater in the absence of nutrients and outside their natural host, identifying them as potential probiotic candidates for Artemia culture.
Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes
2010, Journal of Biological Chemistry
Citation Excerpt :
Thus this bacterium can be used as a model to investigate the role of the hybrid two-component system in the catabolism of xylan. The xylan utilization gene cluster previously characterized by Gasparic et al. (7) was found to be part of a larger xylanolytic gene cluster that includes the previously characterized endoxylanase gene, xyn10C (10). The gene for Xyn10C (ORF1893) occurs in a group of six genes that the RNA-Seq data suggest are co-transcribed within a single polycistronic mRNA molecule.
Enzymatic depolymerization of lignocellulose by microbes in the bovine rumen and the human colon is critical to gut health and function within the host. Prevotella bryantii B₁4 is a rumen bacterium that efficiently degrades soluble xylan. To identify the genes harnessed by this bacterium to degrade xylan, the transcriptomes of P. bryantii cultured on either wheat arabinoxylan or a mixture of its monosaccharide components were compared by DNA microarray and RNA sequencing approaches. The most highly induced genes formed a cluster that contained putative outer membrane proteins analogous to the starch utilization system identified in the prominent human gut symbiont Bacteroides thetaiotaomicron. The arrangement of genes in the cluster was highly conserved in other xylanolytic Bacteroidetes, suggesting that the mechanism employed by xylan utilizers in this phylum is conserved. A number of genes encoding proteins with unassigned function were also induced on wheat arabinoxylan. Among these proteins, a hypothetical protein with low similarity to glycoside hydrolases was shown to possess endoxylanase activity and subsequently assigned to glycoside hydrolase family 5. The enzyme was designated PbXyn5A. Two of the most similar proteins to PbXyn5A were hypothetical proteins from human colonic Bacteroides spp., and when expressed each protein exhibited endoxylanase activity. By using site-directed mutagenesis, we identified two amino acid residues that likely serve as the catalytic acid/base and nucleophile as in other GH5 proteins. This study therefore provides insights into capture of energy by xylanolytic Bacteroidetes and the application of their enzymes as a resource in the biofuel industry.
Insights into the role of the (α + β) insertion in the TIM-barrel catalytic domain, regarding the stability and the enzymatic activity of Chitinase A from Serratia marcescens
2009, Biochimica et Biophysica Acta - Proteins and Proteomics
Chitinase A (ChiA) from Serratia marcescens is a mesophilic enzyme with high catalytic activity and high stability. The crystal structure of ChiA has revealed a TIM-barrel fold of the catalytic domain, an (α + β) insertion between the B7 β-strand and A7 α-helix of the TIM-barrel, an FnIII domain at the N-terminus of the molecule and a hinge region that connects the latter to the catalytic domain. In this study, the role of the (α + β) domain on the stability, catalytic activity and specificity of the enzyme was investigated by deleting this domain and studying the enzymatic and structural properties of the resulting truncated enzyme. The obtained data clearly show that by removing the (α + β) domain, the thermal stability of the enzyme is substantially reduced, with an apparent T_m of 42.0 ± 1.0 °C, compared to the apparent T_m of 58.1 ± 1.0 °C of ChiA at pH 9.0. The specific activity of ChiAΔ(α + β) was substantially decreased, the pH optimum was shifted from 6.5 to 5.0 and the substrate and product specificities were altered.
Polysaccharide breakdown by anaerobic microorganisms inhabiting the mammalian gut
2004, Advances in Applied Microbiology
Citation Excerpt :
Xylan degradation clusters identified in the xylan-utilizing species P. bryantii from the rumen (Gasparic et al., 1995a; Miyamoto et al., 2003) and B. ovatus from the human colon (Weaver et al., 1992) in both cases reveal a family 10 xylanase linked to a family 43 enzyme. P. bryantii (formerly P. ruminicola) possesses at least one other family 10 xylanase, with an unusual primary structure (Flint et al., 1997). Xylanase activity appears to be largely cell-associated both in Bacteroides (Hespell and Whitehead, 1990) and in rumen Prevotella bryantii, where assayable xylanase activity is increased fivefold by sonication (Miyazaki et al., 1997).
This chapter reviews the state of knowledge with particular emphasis on the utilization of dietary polysaccharides by anaerobic gut bacteria, drawing information from the rumen and large intestinal systems. The rumen and large intestine are the most densely colonized regions of the mammalian gut. The chapter discusses the main steps involved in the utilization of polysaccharides by individual micro-organisms. These steps include attachment to the substrate; disruption and enzymatic degradation of the substrate; transport of breakdown products into the cell—accompanied by further degradation, metabolism, and energy generation. Furthermore, the wealth of available ribosomal sequence data has allowed the development of techniques for microbial detection independent of cultivation that are based on oligonucleotide probes, quantitative polymerase chain reaction (QPCR), and molecular profiling. Finally, genome sequencing of further representative polysaccharide-degrading microorganisms—allied to gene expression studies—helps to reveal the transport systems, enzyme systems, and regulatory circuits that allow them to utilize polysaccharides.
Opportunities to improve fiber degradation in the rumen: Microbiology, ecology, and genomics
2003, FEMS Microbiology Reviews
The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.

View all citing articles on Scopus

View full text

Short sequence-paperInterrupted catalytic domain structures in xylanases from two distantly related strains of Prevotella ruminicola

Abstract

Short sequence-paper
Interrupted catalytic domain structures in xylanases from two distantly related strains of Prevotella ruminicola