Gene

Bacteroides thetaiotaomicron

Bacteroides

Bacteria

Biology

ENCODE

Glycoprotein

Bacteroides fragilis

Biochemistry

Monosaccharide

Computational biology

Polysaccharide

Genetics

Microbiome

Glycan

Genome

Microbiology

Enzyme

Host (biology)

Ribose

Cell Host & Microbe

Bacteroides genomes encode a large repertoire of proteins dedicated to the utilization of diverse plant polysaccharides and host glycans. In this issue of Cell Host & Microbe, Glowacki et al., 2020Glowacki R. Pudlo N. Tuncil Y. Luis A. Sajjakulnukit P. Terekhov A. Lyssiotis C. Hamaker B. Martens E. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner.Cell Host Microbe. 2020; 27 (this issue): 79-92Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar show that B. thetaiotaomicron can also extract the monosaccharide ribose from nucleosides and characterize proteins necessary for its utilization. Bacteroides genomes encode a large repertoire of proteins dedicated to the utilization of diverse plant polysaccharides and host glycans. In this issue of Cell Host & Microbe, Glowacki et al., 2020Glowacki R. Pudlo N. Tuncil Y. Luis A. Sajjakulnukit P. Terekhov A. Lyssiotis C. Hamaker B. Martens E. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner.Cell Host Microbe. 2020; 27 (this issue): 79-92Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar show that B. thetaiotaomicron can also extract the monosaccharide ribose from nucleosides and characterize proteins necessary for its utilization. The success of the Bacteroides as abundant symbionts of the mammalian gut is in large part due to their ability to utilize a wide range of dietary polysaccharides and host glycans as nutrients. In fact, these saccharolytic bacteria devote a large percentage of their genome to the sensing, import, and hydrolysis of diverse glycans. There are numerous genomic regions designated polysaccharide utilization loci (PUL) (Bjursell et al., 2006Bjursell M.K. Martens E.C. Gordon J.I. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period.J. Biol. Chem. 2006; 281: 36269-36279Crossref PubMed Scopus (219) Google Scholar) that encode common classes of proteins involved in polysaccharide utilization. Analysis of the PULs of Bacteroides fragilis revealed that some encode predicted nucleases and/or phosphatases, suggesting their involvement in the utilization of nucleic acids (Cao et al., 2016Cao Y. Förstner K.U. Vogel J. Smith C.J. cis-Encoded Small RNAs, a conserved mechanism for repression of polysaccharide utilization in Bacteroides.J. Bacteriol. 2016; 198: 2410-2418Crossref PubMed Scopus (21) Google Scholar); however, experimental evidence demonstrating such activity has been lacking. In the study highlighted in this Preview, Glowacki et al., 2020Glowacki R. Pudlo N. Tuncil Y. Luis A. Sajjakulnukit P. Terekhov A. Lyssiotis C. Hamaker B. Martens E. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner.Cell Host Microbe. 2020; 27 (this issue): 79-92Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar identify and characterize a locus, designated rus, which is essential for utilization of ribose (Glowacki et al., 2020Glowacki R. Pudlo N. Tuncil Y. Luis A. Sajjakulnukit P. Terekhov A. Lyssiotis C. Hamaker B. Martens E. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner.Cell Host Microbe. 2020; 27 (this issue): 79-92Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar). In addition to being a component of the nucleotides of RNA, this pentose is also a constituent of diverse microbial glycans (Richards et al., 2018Richards E. Bouché L. Panico M. Arbeloa A. Vinogradov E. Morris H. Wren B. Logan S.M. Dell A. Fairweather N.F. The S-layer protein of a Clostridium difficile SLCT-11 strain displays a complex glycan required for normal cell growth and morphology.J. Biol. Chem. 2018; 293: 18123-18137Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar, Toukach, 2011Toukach P.V. Bacterial carbohydrate structure database 3: principles and realization.J. Chem. Inf. Model. 2011; 51: 159-170Crossref PubMed Scopus (67) Google Scholar) and other molecules such as NADH and ATP. In this study, the authors show that the type strain of Bacteroides thetaiotaomicron is able to use not only ribose, but also nucleosides, as a carbon and energy source in a ribose-utilization system (RUS)-dependent manner (Glowacki et al., 2020Glowacki R. Pudlo N. Tuncil Y. Luis A. Sajjakulnukit P. Terekhov A. Lyssiotis C. Hamaker B. Martens E. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner.Cell Host Microbe. 2020; 27 (this issue): 79-92Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar). The rus locus was identified based on its expression in a diet-dependent manner in a gnotobiotic mouse model. The locus is highly upregulated when B. thetaiotaomicron is grown on defined medium with ribose as the carbon source compared to glucose. Furthermore, a mutant harboring a deletion of the entire rus locus displayed a strong fitness defect relative to the wild type in a competitive colonization mouse model fed a fiber-rich diet, but not when fed a low fiber diet, and this was attributed to the presence of ribose in the mouse chow. RUS has many common features of Bacteroidetes PULs and comprises a seven gene locus with a predicted regulatory protein, RusR, encoded by an upstream gene (Figure 1). Notable proteins encoded in rus are SusCD orthologs that typically mediate import of oligosaccharides across the outer membrane, called RusCD, two predicted ribose kinases, a predicted ribose permease, and predicted nucleoside and glycoside hydrolases (Figure 1). Through a series of in vitro and in vivo analyses using wild-type and rus gene mutants, the two ribokinase genes (rusK1 and rusK2) were shown to be the only rus genes necessary for growth on ribose. Escherichia coli and many other bacteria use sugar phosphotransferase systems (PTSs) that phosphorylate monosaccharides as they are imported across the inner membrane. Bacteroides do not have sugar PTSs and instead use permeases to import monosaccharides to the cytoplasm where they are then phosphorylated by sugar kinases. In B. fragilis, two sugar kinases that phosphorylate a wide range of hexose and N-acetylated hexoses were previously described (Brigham and Malamy, 2005Brigham C.J. Malamy M.H. Characterization of the RokA and HexA broad-substrate-specificity hexokinases from Bacteroides fragilis and their role in hexose and N-acetylglucosamine utilization.J. Bacteriol. 2005; 187: 890-901Crossref PubMed Scopus (26) Google Scholar). RusK1 and K2 are the first experimentally confirmed sugar kinases of Bacteroides involved in pentose sugar phosphorylation. Enzymatic analyses of RusK1 and RusK2 demonstrated that each can convert ribose to ribose-5-phosphate. When ribose-1-phosphate was used as the substrate, both enzymes could convert it to ribose-1,5-bisphosphate, and RusK2 had the added activity of conversion of ribose-5-phosphate to ribose-1,5-bisphosphate. Importantly, these adjacent rusK genes encode both overlapping and distinct enzymatic functions and are required for growth on ribose. The ability of B. thetaiotaomicron to utilize nucleosides is more complex than its utilization of ribose. First, ribose was shown to be necessary for induction of rus locus expression and therefore, small amounts of ribose must be present for subsequent nucleoside utilization. Second, the RusNH nucleoside hydrolase was shown not to be involved in the utilization of nucleosides. Therefore, the investigators searched the B. thetaiotaomicron genome sequence for nucleoside scavenging systems and identified several genes predicted to encode enzymes that may be involved in nucleoside salvage and utilization. Mutational analyses uncovered an unlinked gene, BT4554, encoding a predicted nucleoside phosphorylase, which is necessary for growth on the nucleosides tested in this study. In a gnotobiotic mouse competitive colonization model in which ribose or ribose-containing molecules are components of the mouse food, the BT4554 mutant strain displayed the same competitive colonization defect as the rusK1/K2 deletion mutant. These data show that in this model system, the ability to harvest ribose from ribose-containing molecules confers a fitness advantage to this organism. Despite its ability to grow on nucleosides, B. thetaiotaomicron is unable to use RNA as a carbon source. Only when exogenous RNase and phosphatase were added to the medium to release nucleosides was B. thetaiotaomicron able to grow using RNA as the nutrient source. Bacteroides species have extensive diversity in their PUL content and in their ability to utilize various monosaccharides and dietary polysaccharides (Porter and Martens, 2017Porter N.T. Martens E.C. The critical roles of polysaccharides in gut microbial ecology and physiology.Annu. Rev. Microbiol. 2017; 71: 349-369Crossref PubMed Scopus (124) Google Scholar). Even within a species, there are strain level differences in nutrient utilization. To better understand the importance of ribose utilization and rus loci among diverse members of the Bacteroidales order, the investigators performed a comprehensive analysis of ribose utilization in 354 Bacteroidales strains of 29 species. These data revealed that the ability to utilize ribose is not a trait of all Bacteroidales, but rather there is variability among species and, for some species, strain level variation. For example, all but two of the 58 B. thetaiotaomicron strains analyzed were able to utilize ribose, whereas none of the 56 B. fragilis strains tested could utilize this monosaccharide. In addition, there was a rather even distribution of utilizers and non-utilizers among Bacteroides uniformis strains, with some of the utilizing strains growing poorly on this nutrient and others achieving high density. A search of the genomic sequences of the ribose-utilizing strains demonstrated that all contain rus-like PULs, whereas no strains unable to utilize ribose contained such a locus. However, these rus-like loci, though maintaining some conserved genes such as the ribokinase(s) and permease, demonstrated extensive variability in other encoded functions. In all, they identified 70 different rus configurations, with some loci encompassing as many as 36 genes. Such variability suggests that there is an extensive array of ribose-containing molecules that serve as nutrients for these gut symbionts. This study has illuminated new and exciting biology of these important gut symbionts, but there are many unresolved questions for future investigation. The functions of the other B. thetaiotaomicron rus products that were shown not to be necessary for growth on ribose, nucleosides, or RNA remain unknown. These include the RusCD outer membrane complex, orthologs of which import molecules such as oligo- and polysaccharides, and the rus-encoded nucleoside and glycoside hydrolases. RNA is just one example of a ribose-containing molecule, and the authors predict these genes may be involved in the import and hydrolysis of other ribose-containing molecules. The glycoside hydrolase encoded by the rus locus suggests the nutrient may be a ribose-containing glycan, which could be of eukaryotic or bacterial origin. Although many Bacteroidales strains and species were demonstrated to grow on ribose, the ability of these diverse organisms to utilize nucleosides was not investigated in this study. It will be interesting to determine if these bacteria, which have largely evolved a saccharolytic lifestyle, are generally able to utilize ribose from nucleic acids and whether the nucleobase component of the nucleoside is salvaged. Other gut symbionts of diverse taxa can also utilize ribose (Bernstein, 1953Bernstein I.A. Fermentation of ribose-C14 by Lactobacillus pentosus.J. Biol. Chem. 1953; 205: 309-316PubMed Google Scholar, Pokusaeva et al., 2010Pokusaeva K. Neves A.R. Zomer A. O'Connell-Motherway M. MacSharry J. Curley P. Fitzgerald G.F. van Sinderen D. Ribose utilization by the human commensal Bifidobacterium breve UCC2003.Microb. Biotechnol. 2010; 3: 311-323Crossref PubMed Scopus (48) Google Scholar) and therefore, this nutrient may be an important commodity in the mammalian gut. As with the utilization of most nutrients in the human gut, and as shown here for B. thetaiotaomicron, the contribution of ribose utilization to the fitness of these bacteria should be dependent on the diet of the host. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific MannerGlowacki et al.Cell Host & MicrobeDecember 31, 2019In BriefGlowacki et al. show that the ability of Bacteroides thetaiotaomicron to use ribose derived from nucleosides is an important function in vivo on a plant-fiber-rich diet. Ribokinases encoded in a ribose-utilization system (RUS) and an unlinked nucleoside phosphorylase mediate this effect in vivo through generation of ribose-1,5-bisphosphate. Full-Text PDF Open Archive

Utilizing Ribose Compounds: How Bacteroides PUL It Off