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Basu A, Adams AN, Degnan PH, Vanderpool CK. Determinants of raffinose family oligosaccharide use in Bacteroides species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597959. [PMID: 38895307 PMCID: PMC11185731 DOI: 10.1101/2024.06.07.597959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Bacteroides species are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron. Examining the genomes of other Bacteroides species, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.
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Affiliation(s)
- Anubhav Basu
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Amanda N.D. Adams
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Patrick H. Degnan
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Carin K. Vanderpool
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Erban T, Sopko B. Understanding bacterial pathogen diversity: A proteogenomic analysis and use of an array of genome assemblies to identify novel virulence factors of the honey bee bacterial pathogen Paenibacillus larvae. Proteomics 2024:e2300280. [PMID: 38742951 DOI: 10.1002/pmic.202300280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 03/07/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024]
Abstract
Mass spectrometry proteomics data are typically evaluated against publicly available annotated sequences, but the proteogenomics approach is a useful alternative. A single genome is commonly utilized in custom proteomic and proteogenomic data analysis. We pose the question of whether utilizing numerous different genome assemblies in a search database would be beneficial. We reanalyzed raw data from the exoprotein fraction of four reference Enterobacterial Repetitive Intergenic Consensus (ERIC) I-IV genotypes of the honey bee bacterial pathogen Paenibacillus larvae and evaluated them against three reference databases (from NCBI-protein, RefSeq, and UniProt) together with an array of protein sequences generated by six-frame direct translation of 15 genome assemblies from GenBank. The wide search yielded 453 protein hits/groups, which UpSet analysis categorized into 50 groups based on the success of protein identification by the 18 database components. Nine hits that were not identified by a unique peptide were not considered for marker selection, which discarded the only protein that was not identified by the reference databases. We propose that the variability in successful identifications between genome assemblies is useful for marker mining. The results suggest that various strains of P. larvae can exhibit specific traits that set them apart from the established genotypes ERIC I-V.
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Affiliation(s)
- Tomas Erban
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
| | - Bruno Sopko
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
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Agnew HN, Brazel EB, Tikhomirova A, van der Linden M, McLean KT, Paton JC, Trappetti C. Streptococcus pneumoniae Strains Isolated From a Single Pediatric Patient Display Distinct Phenotypes. Front Cell Infect Microbiol 2022; 12:866259. [PMID: 35433506 PMCID: PMC9008571 DOI: 10.3389/fcimb.2022.866259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is the leading cause of bacterial paediatric meningitis after the neonatal period worldwide, but the bacterial factors and pathophysiology that drive pneumococcal meningitis are not fully understood. In this work, we have identified differences in raffinose utilization by S. pneumoniae isolates of identical serotype and sequence type from the blood and cerebrospinal fluid (CSF) of a single pediatric patient with meningitis. The blood isolate displayed defective raffinose metabolism, reduced transcription of the raffinose utilization pathway genes, and an inability to grow in vitro when raffinose was the sole carbon source. The fitness of these strains was then assessed using a murine intranasal infection model. Compared with the CSF isolate, mice infected with the blood isolate displayed higher bacterial numbers in the nose, but this strain was unable to invade the ears of infected mice. A premature stop codon was identified in the aga gene in the raffinose locus, suggesting that this protein likely displays impaired alpha-galactosidase activity. These closely related strains were assessed by Illumina sequencing, which did not identify any single nucleotide polymorphisms (SNPs) between the two strains. However, these wider genomic analyses identified the presence of an alternative alpha-galactosidase gene that appeared to display altered sequence coverage between the strains, which may account for the observed differences in raffinose metabolic capacity. Together, these studies support previous findings that raffinose utilization capacity contributes to disease progression, and provide insight into a possible alternative means by which perturbation of this pathway may influence the behavior of pneumococci in the host environment, particularly in meningitis.
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Affiliation(s)
- Hannah N. Agnew
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SAAustralia
| | - Erin B. Brazel
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SAAustralia
| | - Alexandra Tikhomirova
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SAAustralia
| | - Mark van der Linden
- German National Reference Center for Streptoccocci, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen, Germany
| | - Kimberley T. McLean
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SAAustralia
| | - James C. Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SAAustralia
- *Correspondence: Claudia Trappetti, ; James C. Paton,
| | - Claudia Trappetti
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SAAustralia
- *Correspondence: Claudia Trappetti, ; James C. Paton,
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Tangyu M, Fritz M, Ye L, Aragão Börner R, Morin-Rivron D, Campos-Giménez E, Bolten CJ, Bogicevic B, Wittmann C. Co-cultures of Propionibacterium freudenreichii and Bacillus amyloliquefaciens cooperatively upgrade sunflower seed milk to high levels of vitamin B 12 and multiple co-benefits. Microb Cell Fact 2022; 21:48. [PMID: 35346203 PMCID: PMC8959080 DOI: 10.1186/s12934-022-01773-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 01/12/2023] Open
Abstract
Background Sunflower seeds (Helianthus annuus) display an attractive source for the rapidly increasing market of plant-based human nutrition. Of particular interest are press cakes of the seeds, cheap residuals from sunflower oil manufacturing that offer attractive sustainability and economic benefits. Admittedly, sunflower seed milk, derived therefrom, suffers from limited nutritional value, undesired flavor, and the presence of indigestible sugars. Of specific relevance is the absence of vitamin B12. This vitamin is required for development and function of the central nervous system, healthy red blood cell formation, and DNA synthesis, and displays the most important micronutrient for vegans to be aware of. Here we evaluated the power of microbes to enrich sunflower seed milk nutritionally as well as in flavor. Results Propionibacterium freudenreichii NCC 1177 showed highest vitamin B12 production in sunflower seed milk out of a range of food-grade propionibacteria. Its growth and B12 production capacity, however, were limited by a lack of accessible carbon sources and stimulants of B12 biosynthesis in the plant milk. This was overcome by co-cultivation with Bacillus amyloliquefaciens NCC 156, which supplied lactate, amino acids, and vitamin B7 for growth of NCC 1177 plus vitamins B2 and B3, potentially supporting vitamin B12 production by the Propionibacterium. After several rounds of optimization, co-fermentation of ultra-high-temperature pre-treated sunflower seed milk by the two microbes, enabled the production of 17 µg (100 g)−1 vitamin B12 within four days without any further supplementation. The fermented milk further revealed significantly enriched levels of l-lysine, the most limiting essential amino acid, vitamin B3, vitamin B6, improved protein quality and flavor, and largely eliminated indigestible sugars. Conclusion The fermented sunflower seed milk, obtained by using two food-grade microbes without further supplementation, displays an attractive, clean-label product with a high level of vitamin B12 and multiple co-benefits. The secret of the successfully upgraded plant milk lies in the multifunctional cooperation of the two microbes, which were combined, based on their genetic potential and metabolic signatures found in mono-culture fermentations. This design by knowledge approach appears valuable for future development of plant-based milk products. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01773-w.
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Affiliation(s)
- Muzi Tangyu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michel Fritz
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lijuan Ye
- Nestlé Research Center, Lausanne, Switzerland
| | | | | | | | - Christoph J Bolten
- Nestlé Research Center, Lausanne, Switzerland.,Nestlé Product Technology Center Food, Singen, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Itoh T, Yaguchi M, Nakaichi A, Yoda M, Hibi T, Kimoto H. Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/ N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100049. [PMID: 34195603 PMCID: PMC8233162 DOI: 10.1016/j.yjsbx.2021.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 10/27/2022]
Abstract
The chitinolytic bacterium Paenibacillus sp. str. FPU-7 efficiently degrades chitin into oligosaccharides such as N-acetyl-D-glucosamine (GlcNAc) and disaccharides (GlcNAc)2 through multiple secretory chitinases. Transport of these oligosaccharides by P. str. FPU-7 has not yet been clarified. In this study, we identified nagB1, predicted to encode a sugar solute-binding protein (SBP), which is a component of the ABC transport system. However, the genes next to nagB1 were predicted to encode two-component regulatory system proteins rather than transmembrane domains (TMDs). We also identified nagB2, which is highly homologous to nagB1. Adjacent to nagB2, two genes were predicted to encode TMDs. Binding experiments of the recombinant NagB1 and NagB2 to several oligosaccharides using differential scanning fluorimetry and surface plasmon resonance confirmed that both proteins are SBPs of (GlcNAc)2 and (GlcNAc)3. We determined their crystal structures complexed with and without chitin oligosaccharides at a resolution of 1.2 to 2.0 Å. The structures shared typical SBP structural folds and were classified as subcluster D-I. Large domain motions were observed in the structures, suggesting that they were induced by ligand binding via the "Venus flytrap" mechanism. These structures also revealed chitin oligosaccharide recognition mechanisms. In conclusion, our study provides insight into the recognition and transport of chitin oligosaccharides in bacteria.
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Key Words
- ABC transporter
- ABC, ATP-binding cassette
- Chitin oligosaccharide
- DSF, differential scanning fluorimetry
- GH, glycoside hydrolase
- GlcN, D-glucosamine
- GlcNAc, N-acetyl-D-glucosamine
- OD600, optical density at 600 nm
- PDB, Protein Data Bank
- PTS, phosphoenolpyruvate phosphotransferase system
- Paenibacillus
- RU, response unit
- SBP, solute binding protein
- Se-Met, selenomethionine
- Solute binding protein
- TMD, transmembrane domain
- Two-component regulatory system
- a.a., amino acid
- r.m.s.d., root mean-square deviation
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Misaki Yaguchi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Akari Nakaichi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Moe Yoda
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Hisashi Kimoto
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
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Lafond M, Tauzin AS, Bruel L, Laville E, Lombard V, Esque J, André I, Vidal N, Pompeo F, Quinson N, Perrier J, Fons M, Potocki-Veronese G, Giardina T. α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1. Front Microbiol 2020; 11:579521. [PMID: 33281771 PMCID: PMC7688924 DOI: 10.3389/fmicb.2020.579521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Plant α-galactosides belonging to the raffinose family oligosaccharides (RFOs) and considered as prebiotics, are commonly degraded by α-galactosidases produced by the human gut microbiome. In this environment, the Ruminococcus gnavus E1 symbiont-well-known for various benefit-is able to produce an original RgAgaSK bifunctional enzyme. This enzyme contains an hydrolytic α-galactosidase domain linked to an ATP dependent extra-domain, specifically involved in the α-galactoside hydrolysis and the phosphorylation of the glucose, respectively. However, the multi-modular relationships between both catalytic domains remained hitherto unexplored and has been, consequently, herein investigated. Biochemical characterization of heterologously expressed enzymes either in full-form or in separated domains revealed similar kinetic parameters. These results were supported by molecular modeling studies performed on the whole enzyme in complex with different RFOs. Further enzymatic analysis associated with kinetic degradation of various substrates followed by high pressure anionic exchange chromatography revealed that catalytic efficiency decreased as the number of D-galactosyl moieties branched onto the oligosaccharide increased, suggesting a preference of RgAgaSK for RFO's short chains. A wide prevalence and abundance study on a human metagenomic library showed a high prevalence of the RgAgaSK encoding gene whatever the health status of the individuals. Finally, phylogeny and synteny studies suggested a limited spread by horizontal transfer of the clusters' containing RgAgaSK to only few species of Firmicutes, highlighting the importance of these undispersed tandem activities in the human gut microbiome.
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Affiliation(s)
- Mickael Lafond
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Laetitia Bruel
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | | | - Jérémy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Isabelle André
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nicolas Vidal
- Yelen Analytics, Aix-Marseille Université, ICR, Marseille, France
| | | | - Nathalie Quinson
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Josette Perrier
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Michel Fons
- Aix-Marseille Université, CNRS, IMM, BIP, Marseille, France
| | | | - Thierry Giardina
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
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