1
|
Kim J, Kim GL, Norambuena J, Boyd JM, Parker D. Impact of the pentose phosphate pathway on metabolism and pathogenesis of Staphylococcus aureus. PLoS Pathog 2023; 19:e1011531. [PMID: 37440594 PMCID: PMC10368262 DOI: 10.1371/journal.ppat.1011531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Staphylococcus aureus is an important pathogen that leads to significant disease through multiple routes of infection. We recently published a transposon sequencing (Tn-seq) screen in a mouse acute pneumonia model and identified a hypothetical gene (SAUSA300_1902, pgl) with similarity to a lactonase of Escherichia coli involved in the pentose phosphate pathway (PPP) that was conditionally essential. Limited studies have investigated the role of the PPP in physiology and pathogenesis of S. aureus. We show here that mutation of pgl significantly impacts ATP levels and respiration. RNA-seq analysis of the pgl mutant and parent strains identified compensatory changes in gene expression for glucose and gluconate as well as reductions in the pyrimidine biosynthesis locus. These differences were also evident through unbiased metabolomics studies and 13C labeling experiments that showed mutation of pgl led to reductions in pyrimidine metabolism including decreases in ribose-5P, UMP and GMP. These nucleotide reductions impacted the amount of extracellular DNA in biofilms and reduced biofilm formation. Mutation also limited the capacity of the strain to resist oxidant damage induced by hydrogen peroxide and paraquat and subsequent intracellular survival inside macrophages. Changes in wall teichoic acid impacted susceptibility to hydrogen peroxide. We demonstrated the importance of these changes on virulence in three different models of infection, covering respiratory, skin and septicemia, demonstrating the need for proper PPP function in all models. This work demonstrates the multifaceted role metabolism can play in multiple aspects of S. aureus pathogenesis.
Collapse
Affiliation(s)
- Jisun Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Gyu-Lee Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| |
Collapse
|
2
|
Sharma A, Sharma N, Gupta D, Lee HJ, Park YS. Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways. Comput Struct Biotechnol J 2022; 20:4771-4785. [PMID: 36147676 PMCID: PMC9465122 DOI: 10.1016/j.csbj.2022.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/30/2022] [Accepted: 08/13/2022] [Indexed: 11/03/2022] Open
Abstract
Comparative genomic analysis of four Leuconostoc strains was performed. Leuconostoc spp. shared genomic similarity, but their genetic content differed. Leuconostoc spp. showed different genes encoding CAZymes. Oligosaccharide’s utilization and folate biosynthesis pathways were investigated.
Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as Leuconostoc mesenteroides SG315 (LA), L. citreum SG255 (LB), L. lactis CCK940 (LC), and L. lactis SBC001 (LD). Comparative analysis was performed using their draft genome sequences. Differences among the four strains were analyzed using the average nucleotide identity, dot plot, and multiple alignments of conserved genomic sequences. Functional profiling revealed 2134, 1917, 1751, and 1816 open reading frames; 2023, 1823, 1655, and 1699 protein-coding genes; 60, 57, 83, and 82 RNA-coding genes; and GC content of 37.5 %, 38.8 %, 43.3 %, and 43.2 %, in LA, LB, LC, and LD, respectively. The total number of genes encoding carbohydrate-active enzymes was 76 (LA), 73 (LB), 57 (LC), and 67 (LD). These results indicate that the four strains shared a large number of genes, but their gene content is different. Furthermore, most genes with unknown functions were observed in the prophage regions of the genome. This study also elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. Taken together, our findings provide useful information on the genomic diversity of CAZymes in the four Leuconostoc strains and suggest that these species could be used for potent exploitation.
Collapse
|
3
|
Bhalla A, Arce J, Ubanwa B, Singh G, Sani RK, Balan V. Thermophilic Geobacillus WSUCF1 Secretome for Saccharification of Ammonia Fiber Expansion and Extractive Ammonia Pretreated Corn Stover. Front Microbiol 2022; 13:844287. [PMID: 35694290 PMCID: PMC9176393 DOI: 10.3389/fmicb.2022.844287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
A thermophilic Geobacillus bacterial strain, WSUCF1 contains different carbohydrate-active enzymes (CAZymes) capable of hydrolyzing hemicellulose in lignocellulosic biomass. We used proteomic, genomic, and bioinformatic tools, and genomic data to analyze the relative abundance of cellulolytic, hemicellulolytic, and lignin modifying enzymes present in the secretomes. Results showed that CAZyme profiles of secretomes varied based on the substrate type and complexity, composition, and pretreatment conditions. The enzyme activity of secretomes also changed depending on the substrate used. The secretomes were used in combination with commercial and purified enzymes to carry out saccharification of ammonia fiber expansion (AFEX)-pretreated corn stover and extractive ammonia (EA)-pretreated corn stover. When WSUCF1 bacterial secretome produced at different conditions was combined with a small percentage of commercial enzymes, we observed efficient saccharification of EA-CS, and the results were comparable to using a commercial enzyme cocktail (87% glucan and 70% xylan conversion). It also opens the possibility of producing CAZymes in a biorefinery using inexpensive substrates, such as AFEX-pretreated corn stover and Avicel, and eliminates expensive enzyme processing steps that are used in enzyme manufacturing. Implementing in-house enzyme production is expected to significantly reduce the cost of enzymes and biofuel processing cost.
Collapse
Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
| | - Jessie Arce
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Bryan Ubanwa
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, India
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkatesh Balan
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
- *Correspondence: Venkatesh Balan,
| |
Collapse
|
4
|
Sawicka-Smiarowska E, Bondarczuk K, Bauer W, Niemira M, Szalkowska A, Raczkowska J, Kwasniewski M, Tarasiuk E, Dubatowka M, Lapinska M, Szpakowicz M, Stachurska Z, Szpakowicz A, Sowa P, Raczkowski A, Kondraciuk M, Gierej M, Motyka J, Jamiolkowski J, Bondarczuk M, Chlabicz M, Bucko J, Kozuch M, Dobrzycki S, Bychowski J, Musial WJ, Godlewski A, Ciborowski M, Gyenesei A, Kretowski A, Kaminski KA. Gut Microbiome in Chronic Coronary Syndrome Patients. J Clin Med 2021; 10:jcm10215074. [PMID: 34768594 PMCID: PMC8584954 DOI: 10.3390/jcm10215074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023] Open
Abstract
Despite knowledge of classical coronary artery disease (CAD) risk factors, the morbidity and mortality associated with this disease remain high. Therefore, new factors that may affect the development of CAD, such as the gut microbiome, are extensively investigated. This study aimed to evaluate gut microbiome composition in CAD patients in relation to the control group. We examined 169 CAD patients and 166 people in the control group, without CAD, matched in terms of age and sex to the study group. Both populations underwent a detailed health assessment. The microbiome analysis was based on the V3-V4 region of the 16S rRNA gene (NGS method). Among 4074 identified taxonomic units in the whole population, 1070 differed between study groups. The most common bacterial types were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Furthermore, a higher Firmicutes/Bacteroidetes ratio in the CAD group compared with the control was demonstrated. Firmicutes/Bacteroidetes ratio, independent of age, sex, CAD status, LDL cholesterol concentration, and statins treatment, was related to altered phosphatidylcholine concentrations obtained in targeted metabolomics. Altered alpha-biodiversity (Kruskal-Wallis test, p = 0.001) and beta-biodiversity (Bray-Curtis metric, p < 0.001) in the CAD group were observed. Moreover, a predicted functional analysis revealed some taxonomic units, metabolic pathways, and proteins that might be characteristic of the CAD patients' microbiome, such as increased expressions of 6-phospho-β-glucosidase and protein-N(pi)-phosphohistidine-sugar phosphotransferase and decreased expressions of DNA topoisomerase, oxaloacetate decarboxylase, and 6-beta-glucosidase. In summary, CAD is associated with altered gut microbiome composition and function.
Collapse
Affiliation(s)
- Emilia Sawicka-Smiarowska
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
- Department of Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.T.); (A.S.); (W.J.M.)
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-269 Bialystok, Poland; (K.B.); (M.K.); (M.B.)
| | - Witold Bauer
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Anna Szalkowska
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Justyna Raczkowska
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-269 Bialystok, Poland; (K.B.); (M.K.); (M.B.)
| | - Ewa Tarasiuk
- Department of Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.T.); (A.S.); (W.J.M.)
| | - Marlena Dubatowka
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Magda Lapinska
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Malgorzata Szpakowicz
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Zofia Stachurska
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Anna Szpakowicz
- Department of Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.T.); (A.S.); (W.J.M.)
| | - Pawel Sowa
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Andrzej Raczkowski
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Marcin Kondraciuk
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Magdalena Gierej
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Joanna Motyka
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Jacek Jamiolkowski
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
| | - Mateusz Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-269 Bialystok, Poland; (K.B.); (M.K.); (M.B.)
| | - Malgorzata Chlabicz
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
- Department of Invasive Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (M.K.); (S.D.)
| | - Jolanta Bucko
- Department of Cardiology, Bialystok Regional Hospital, 15-950 Bialystok, Poland; (J.B.); (J.B.)
| | - Marcin Kozuch
- Department of Invasive Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (M.K.); (S.D.)
| | - Slawomir Dobrzycki
- Department of Invasive Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (M.K.); (S.D.)
| | - Jerzy Bychowski
- Department of Cardiology, Bialystok Regional Hospital, 15-950 Bialystok, Poland; (J.B.); (J.B.)
| | - Wlodzimierz Jerzy Musial
- Department of Cardiology, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.T.); (A.S.); (W.J.M.)
| | - Adrian Godlewski
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Attila Gyenesei
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, 15-269 Bialystok, Poland; (W.B.); (M.N.); (A.S.); (J.R.); (A.G.); (M.C.); (A.G.); (A.K.)
| | - Karol Adam Kaminski
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, 15-269 Bialystok, Poland; (E.S.-S.); (M.D.); (M.L.); (M.S.); (Z.S.); (P.S.); (A.R.); (M.K.); (M.G.); (J.M.); (J.J.); (M.C.)
- Correspondence: ; Tel.: +48-85-8318-656
| |
Collapse
|
5
|
Veldman W, Liberato MV, Souza VP, Almeida VM, Marana SR, Tastan Bishop Ö, Polikarpov I. Differences in Gluco and Galacto Substrate-Binding Interactions in a Dual 6Pβ-Glucosidase/6Pβ-Galactosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis. J Chem Inf Model 2021; 61:4554-4570. [PMID: 34423980 DOI: 10.1021/acs.jcim.1c00413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial glycoside hydrolase 1 (GH1) enzymes with 6-phospho-β-galactosidase and 6-phospho-β-glucosidase activities have the important task of releasing phosphorylated and nonphosphorylated monosaccharides into the cytoplasm. Curiously, dual 6-phospho-β-galactosidase/6-phospho-β-glucosidase (dual-phospho) enzymes have broad specificity and are able to hydrolyze galacto- and gluco-derived substrates. This study investigates the structure and substrate specificity of a GH family 1 enzyme from Bacillus licheniformis, hereafter known as BlBglC. The enzyme structure has been solved, and sequence analysis, molecular dynamics simulations, and binding free energy calculations offered evidence of dual-phospho activity. Both test ligands p-nitrophenyl-β-d-galactoside-6-phosphate (PNP6Pgal) and p-nitrophenyl-β-d-glucoside-6-phosphate (PNP6Pglc) demonstrated strong binding to BlBglC although the pose and interactions of the PNP6Pglc triplicates were slightly more consistent. Interestingly, known specificity-inducing residues, Gln23 and Trp433, bind strongly to the ligand O3 hydroxyl group in the PNP6Pgal-BlBglC complex and to the ligand O4 hydroxyl group in the PNP6Pglc-BlBglC complex. Additionally, the BlBglC-His124 residue is a major contributor of hydrogen bonds to the PNP6Pgal O3 hydroxyl group but does not form any hydrogen bonds with PNP6Pglc. On the other hand, BlBglC residues Tyr173, Tyr301, Gln302, and Thr321 form hydrogen bonds with PNP6Pglc but not PNP6Pgal. These findings provide important details of the broad specificity of dual-phospho activity GH1 enzymes.
Collapse
Affiliation(s)
- Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | | | - Valquiria P Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Vitor M Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Sandro R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, Brazil
| |
Collapse
|
6
|
Pell LG, Horne RG, Huntley S, Rahman H, Kar S, Islam MS, Evans KC, Saha SK, Campigotto A, Morris SK, Roth DE, Sherman PM. Antimicrobial susceptibilities and comparative whole genome analysis of two isolates of the probiotic bacterium Lactiplantibacillus plantarum, strain ATCC 202195. Sci Rep 2021; 11:15893. [PMID: 34354117 PMCID: PMC8342526 DOI: 10.1038/s41598-021-94997-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/13/2021] [Indexed: 12/24/2022] Open
Abstract
A synbiotic containing Lactiplantibacillus plantarum [American Type Culture Collection (ATCC) strain identifier 202195] and fructooligosaccharide was reported to reduce the risk of sepsis in young infants in rural India. Here, the whole genome of two isolates of L. plantarum ATCC 202195, which were deposited to the ATCC approximately 20 years apart, were sequenced and analyzed to verify their taxonomic and strain-level identities, identify potential antimicrobial resistant genes and virulence factors, and identify genetic characteristics that may explain the observed clinical effects of L. plantarum ATCC 202195. Minimum inhibitory concentrations for selected antimicrobial agents were determined using broth dilution and gradient strip diffusion techniques. The two L. plantarum ATCC 202195 isolates were genetically identical with only three high-quality single nucleotides polymorphisms identified, and with an average nucleotide identity of 99.99%. In contrast to previously published reports, this study determined that each isolate contained two putative plasmids. No concerning acquired or transferable antimicrobial resistance genes or virulence factors were identified. Both isolates were sensitive to several clinically important antibiotics including penicillin, ampicillin and gentamicin, but resistant to vancomycin. Genes involved in stress response, cellular adhesion, carbohydrate metabolism and vitamin biosynthesis are consistent with features of probiotic organisms.
Collapse
Affiliation(s)
- Lisa G Pell
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Rachael G Horne
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Stuart Huntley
- International Flavors & Fragrances Inc., Madison, WI, USA
| | | | - Sanchita Kar
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Kara C Evans
- International Flavors & Fragrances Inc., Madison, WI, USA
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Aaron Campigotto
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Microbiology, Hospital for Sick Children, Toronto, ON, Canada
| | - Shaun K Morris
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Division of Infectious Diseases, Hospital for Sick Children, Toronto, ON, Canada
| | - Daniel E Roth
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Paediatric Medicine and Child Health Evaluative Sciences, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
| | - Philip M Sherman
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
| |
Collapse
|
7
|
Veldman W, Liberato MV, Almeida VM, Souza VP, Frutuoso MA, Marana SR, Moses V, Tastan Bishop Ö, Polikarpov I. X-ray Structure, Bioinformatics Analysis, and Substrate Specificity of a 6-Phospho-β-glucosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis. J Chem Inf Model 2020; 60:6392-6407. [PMID: 33166469 DOI: 10.1021/acs.jcim.0c00759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In bacteria, mono- and disaccharides are phosphorylated during the uptake processes through the vastly spread transport system phosphoenolpyruvate-dependent phosphotransferase. As an initial step in the phosphorylated disaccharide metabolism pathway, 6-phospho-β-glucosidases and 6-phospho-β-galactosidases play a crucial role by releasing phosphorylated and nonphosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. Here, an X-ray structure of a glycoside hydrolase family 1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was determined at 2.2 Å resolution, and its substrate specificity was investigated. The sequence of BlBglH was compared to the sequences of 58 other GH1 enzymes using sequence alignments, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Motif and structural observations highlighted the importance of loop L8 in 6-phospho-β-glucosidase activity enzymes. To further affirm enzyme specificity, molecular docking and molecular dynamics simulations were performed using the crystallographic structure of BlBglH. Docking was carried out with a 6-phospho-β-glucosidase enzyme activity positive and negative control ligand, followed by 400 ns of MD simulations. The positive and negative control ligands were PNP6Pglc and PNP6Pgal, respectively. PNP6Pglc maintained favorable interactions within the active site until the end of the MD simulation, while PNP6Pgal exhibited instability. The favorable binding of substrate stabilized the loops that surround the active site. Binding free energy calculations showed that the PNP6Pglc complex had a substantially lower binding energy compared to the PNP6Pgal complex. Altogether, the findings of this study suggest that BlBglH possesses 6-phospho-β-glucosidase enzymatic activity and revealed sequence and structural differences between bacterial GH1 enzymes of various activities.
Collapse
Affiliation(s)
- Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | | | - Vitor M Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Valquiria P Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Maira A Frutuoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Sandro R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Vuyani Moses
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, Brazil
| |
Collapse
|
8
|
Shulami S, Zehavi A, Belakhov V, Salama R, Lansky S, Baasov T, Shoham G, Shoham Y. Cross-utilization of β-galactosides and cellobiose in Geobacillus stearothermophilus. J Biol Chem 2020; 295:10766-10780. [PMID: 32493770 DOI: 10.1074/jbc.ra120.014029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/02/2020] [Indexed: 11/06/2022] Open
Abstract
Strains of the Gram-positive, thermophilic bacterium Geobacillus stearothermophilus possess elaborate systems for the utilization of hemicellulolytic polysaccharides, including xylan, arabinan, and galactan. These systems have been studied extensively in strains T-1 and T-6, representing microbial models for the utilization of soil polysaccharides, and many of their components have been characterized both biochemically and structurally. Here, we characterized routes by which G. stearothermophilus utilizes mono- and disaccharides such as galactose, cellobiose, lactose, and galactosyl-glycerol. The G. stearothermophilus genome encodes a phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) for cellobiose. We found that the cellobiose-PTS system is induced by cellobiose and characterized the corresponding GH1 6-phospho-β-glucosidase, Cel1A. The bacterium also possesses two transport systems for galactose, a galactose-PTS system and an ABC galactose transporter. The ABC galactose transport system is regulated by a three-component sensing system. We observed that both systems, the sensor and the transporter, utilize galactose-binding proteins that also bind glucose with the same affinity. We hypothesize that this allows the cell to control the flux of galactose into the cell in the presence of glucose. Unexpectedly, we discovered that G. stearothermophilus T-1 can also utilize lactose and galactosyl-glycerol via the cellobiose-PTS system together with a bifunctional 6-phospho-β-gal/glucosidase, Gan1D. Growth curves of strain T-1 growing in the presence of cellobiose, with either lactose or galactosyl-glycerol, revealed initially logarithmic growth on cellobiose and then linear growth supported by the additional sugars. We conclude that Gan1D allows the cell to utilize residual galactose-containing disaccharides, taking advantage of the promiscuity of the cellobiose-PTS system.
Collapse
Affiliation(s)
- Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Valery Belakhov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Timor Baasov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
9
|
Hobbs JK, Meier EPW, Pluvinage B, Mey MA, Boraston AB. Molecular analysis of an enigmatic Streptococcus pneumoniae virulence factor: The raffinose-family oligosaccharide utilization system. J Biol Chem 2019; 294:17197-17208. [PMID: 31591266 PMCID: PMC6873169 DOI: 10.1074/jbc.ra119.010280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
Streptococcus pneumoniae is an opportunistic respiratory pathogen that can spread to other body sites, including the ears, brain, and blood. The ability of this bacterium to break down, import, and metabolize a wide range of glycans is key to its virulence. Intriguingly, S. pneumoniae can utilize several plant oligosaccharides for growth in vitro, including raffinose-family oligosaccharides (RFOs, which are α-(1→6)-galactosyl extensions of sucrose). An RFO utilization locus has been identified in the pneumococcal genome; however, none of the proteins encoded by this locus have been biochemically characterized. The enigmatic ability of S. pneumoniae to utilize RFOs has recently received attention because mutations in two of the RFO locus genes have been linked to the tissue tropism of clinical pneumococcal isolates. Here, we use functional studies combined with X-ray crystallography to show that although the pneumococcal RFO locus encodes for all the machinery required for uptake and degradation of RFOs, the individual pathway components are biochemically inefficient. We also demonstrate that the initiating enzyme in this pathway, the α-galactosidase Aga (a family 36 glycoside hydrolase), can cleave α-(1→3)-linked galactose units from a linear blood group antigen. We propose that the pneumococcal RFO pathway is an evolutionary relic that is not utilized in this streptococcal species and, as such, is under no selection pressure to maintain binding affinity and/or catalytic efficiency. We speculate that the apparent contribution of RFO utilization to pneumococcal tissue tropism may, in fact, be due to the essential role the ATPase RafK plays in the transport of other carbohydrates.
Collapse
Affiliation(s)
- Joanne K. Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Edward P. W. Meier
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Mackenzie A. Mey
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada, To whom correspondence should be addressed:
Dept. of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada. Tel.:
250-472-4168; Fax:
250-721-8855; E-mail:
| |
Collapse
|
10
|
Hobbs JK, Pluvinage B, Boraston AB. Glycan-metabolizing enzymes in microbe-host interactions: the Streptococcus pneumoniae paradigm. FEBS Lett 2018; 592:3865-3897. [PMID: 29608212 DOI: 10.1002/1873-3468.13045] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022]
Abstract
Streptococcus pneumoniae is a frequent colonizer of the upper airways; however, it is also an accomplished pathogen capable of causing life-threatening diseases. To colonize and cause invasive disease, this bacterium relies on a complex array of factors to mediate the host-bacterium interaction. The respiratory tract is rich in functionally important glycoconjugates that display a vast range of glycans, and, thus, a key component of the pneumococcus-host interaction involves an arsenal of bacterial carbohydrate-active enzymes to depolymerize these glycans and carbohydrate transporters to import the products. Through the destruction of host glycans, the glycan-specific metabolic machinery deployed by S. pneumoniae plays a variety of roles in the host-pathogen interaction. Here, we review the processing and metabolism of the major host-derived glycans, including N- and O-linked glycans, Lewis and blood group antigens, proteoglycans, and glycogen, as well as some dietary glycans. We discuss the role of these metabolic pathways in the S. pneumoniae-host interaction, speculate on the potential of key enzymes within these pathways as therapeutic targets, and relate S. pneumoniae as a model system to glycan processing in other microbial pathogens.
Collapse
Affiliation(s)
- Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| |
Collapse
|
11
|
Lansky S, Zehavi A, Belrhali H, Shoham Y, Shoham G. Structural basis for enzyme bifunctionality – the case of Gan1D fromGeobacillus stearothermophilus. FEBS J 2017; 284:3931-3953. [DOI: 10.1111/febs.14283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/31/2017] [Accepted: 09/28/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Shifra Lansky
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | | | - Yuval Shoham
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Gil Shoham
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
| |
Collapse
|
12
|
Pneumococcal 6-Phospho-β-Glucosidase (BglA3) Is Involved in Virulence and Nutrient Metabolism. Infect Immun 2015; 84:286-92. [PMID: 26527213 DOI: 10.1128/iai.01108-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
For the generation of energy, the important human pathogen Streptococcus pneumoniae relies on host-derived sugars, including β-glucoside analogs. The catabolism of these nutrients involves the action of 6-phospho-β-glucosidase to convert them into usable monosaccharaides. In this study, we characterized a 6-phospho-β-glucosidase (BglA3) encoded by SPD_0247. We found that this enzyme has a cell membrane localization and is active only against a phosphorylated substrate. A mutated pneumococcal ΔSPD0247 strain had reduced 6-phospho-glucosidase activity and was attenuated in growth on cellobiose and hyaluronic acid compared to the growth of wild-type D39. ΔSPD0247-infected mice survived significantly longer than the wild-type-infected cohort, and the colony counts of the mutant were lower than those of the wild type in the lungs. The expression of SPD_0247 in S. pneumoniae harvested from infected tissues was significantly increased relative to its expression in vitro on glucose. Additionally, ΔSPD0247 is severely impaired in its attachment to an abiotic surface. These results indicate the importance of β-glucoside metabolism in pneumococcal survival and virulence.
Collapse
|
13
|
Weiss PHE, Álvares ACM, Gomes AA, Miletti LC, Skoronski E, da Silva GF, de Freitas SM, Magalhães MLB. Beta glucosidase from Bacillus polymyxa is activated by glucose-6-phosphate. Arch Biochem Biophys 2015; 580:50-6. [PMID: 26116788 DOI: 10.1016/j.abb.2015.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/19/2015] [Accepted: 06/21/2015] [Indexed: 01/10/2023]
Abstract
Optimization of cellulose enzymatic hydrolysis is crucial for cost effective bioethanol production from lignocellulosic biomass. Enzymes involved in cellulose hydrolysis are often inhibited by their end-products, cellobiose and glucose. Efforts have been made to produce more efficient enzyme variants that are highly tolerant to product accumulation; however, further improvements are still necessary. Based on an alternative approach we initially investigated whether recently formed glucose could be phosphorylated into glucose-6-phosphate to circumvent glucose accumulation and avoid inhibition of beta-glucosidase from Bacillus polymyxa (BGLA). The kinetic properties and structural analysis of BGLA in the presence of glucose-6-phosphate (G6P) were investigated. Kinetic studies demonstrated that enzyme was not inhibited by G6P. In contrast, the presence of G6P activated the enzyme, prevented beta glucosidase feedback inhibition by glucose accumulation and improved protein stability. G6P binding was investigated by fluorescence quenching experiments and the respective association constant indicated high affinity binding of G6P to BGLA. Data reported here are of great impact for future design strategies for second-generation bioethanol production.
Collapse
Affiliation(s)
- Paulo H E Weiss
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Alice C M Álvares
- Biophysics Laboratory, Department of Cellular Biology, University of Brasília, Brasília 70910-900, Brazil
| | - Anderson A Gomes
- Water Treatment Laboratory, Department of Environmental Engineering, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Luiz C Miletti
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Everton Skoronski
- Water Treatment Laboratory, Department of Environmental Engineering, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Gustavo F da Silva
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil
| | - Sonia M de Freitas
- Biophysics Laboratory, Department of Cellular Biology, University of Brasília, Brasília 70910-900, Brazil
| | - Maria L B Magalhães
- Biochemistry Laboratory, Department of Food and Animal Production, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages, Santa Catarina 88520-000, Brazil.
| |
Collapse
|
14
|
Cordeiro RP, Doria JH, Zhanel GG, Sparling R, Holley RA. Role of glycoside hydrolase genes in sinigrin degradation by E. coli O157:H7. Int J Food Microbiol 2015; 205:105-11. [PMID: 25897994 DOI: 10.1016/j.ijfoodmicro.2015.04.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/01/2015] [Accepted: 04/04/2015] [Indexed: 11/24/2022]
Abstract
This work examined Escherichia coli O157:H7 strain 02-0304 for putative genes responsible for sinigrin hydrolysis. Sinigrin is a glucosinolate present in Oriental mustard (Brassica juncea), and its hydrolysis is mediated in plants by the enzyme myrosinase. Sinigrin hydrolysis by plant or bacterial myrosinase yields allyl isothiocyanate (AITC) which is bactericidal. In silico analysis using public databases found sequence similarity between plant myrosinase and enzymes encoded by genes from β-glucosidase families in E. coli O157:H7. Specifically, 6-phospho-β-glucosidase encoded by the genes bglA and ascB (family 1), and chbF (family 4) present in E. coli O157:H7 showed the highest similarity. Polymerase chain reaction (PCR) confirmed the presence of bglA, ascB, and chbF in the clinical E. coli strain tested. Disruption of these genes in wild-type E. coli O157:H7 strain 02-0304 using lambda-red replacement created single and double mutants. The relative importance of each gene in the hydrolysis of sinigrin by E. coli O157:H7 was also assessed by comparing gene expression and sinigrin degradation rates among the E. coli O157:H7 wild-type strain and its mutants. The results suggested that the genes bglA and ascB play a substantial role in the degradation of sinigrin by E. coli O157:H7 strain 02-0304.
Collapse
Affiliation(s)
- Roniele P Cordeiro
- Department of Food Science, Faculty of Agriculture and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Juan H Doria
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Richard Sparling
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Richard A Holley
- Department of Food Science, Faculty of Agriculture and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
| |
Collapse
|
15
|
Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D’Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol 2014; 9:2082-91. [PMID: 24984213 PMCID: PMC4168791 DOI: 10.1021/cb500244v] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 β-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different β-linked disaccharides. For some GH1s we also observed activity toward laminarin, a more complex oligosaccharide present as a major component of macroalgae. An area of particular interest was the identification of GH1 enzymes compatible with the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), a next-generation biomass pretreatment technology. We thus searched for GH1 enzymes active at 70 °C and 20% (v/v) [C2mim][OAc] over the course of a 24-h saccharification reaction. Using our unbiased approach, we identified multiple enzymes of different phylogentic origin with such activities. Our approach of characterizing sequence diversity through targeted gene synthesis coupled to high-throughput screening technologies is a broadly applicable paradigm for a wide range of biological problems.
Collapse
Affiliation(s)
- Richard A. Heins
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Xiaoliang Cheng
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Sangeeta Nath
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Kai Deng
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Dylan C. Chivian
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Supratim Datta
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Gregory D. Friedland
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Patrik D’Haeseleer
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Dongying Wu
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Mary Tran-Gyamfi
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Chessa S. Scullin
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Seema Singh
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Weibing Shi
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Matthew G. Hamilton
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Matthew L. Bendall
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Alexander Sczyrba
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - John Thompson
- NIDCR, NIH, Oral
Infection and Immunity Branch, 30 Convent
Drive, Bethesda, Maryland 20892, United States
| | - Taya Feldman
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Joel M. Guenther
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - John M. Gladden
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jan-Fang Cheng
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Paul D. Adams
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Edward M. Rubin
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Blake A. Simmons
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Kenneth L. Sale
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Trent R. Northen
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Samuel Deutsch
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| |
Collapse
|
16
|
Tamaki FK, Textor LC, Polikarpov I, Marana SR. Sets of covariant residues modulate the activity and thermal stability of GH1 β-glucosidases. PLoS One 2014; 9:e96627. [PMID: 24804841 PMCID: PMC4013033 DOI: 10.1371/journal.pone.0096627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/09/2014] [Indexed: 11/19/2022] Open
Abstract
The statistical coupling analysis of 768 β-glucosidases from the GH1 family revealed 23 positions in which the amino acid frequencies are coupled. The roles of these covariant positions in terms of the properties of β-glucosidases were investigated by alanine-screening mutagenesis using the fall armyworm Spodoptera frugiperda β-glycosidase (Sfβgly) as a model. The effects of the mutations on the Sfβgly kinetic parameters (kcat/Km) for the hydrolysis of three different p-nitrophenyl β-glycosides and structural comparisons of several β-glucosidases showed that eleven covariant positions (54, 98, 143, 188, 195, 196, 203, 398, 451, 452 and 460 in Sfβgly numbering) form a layer surrounding the active site of the β-glucosidases, which modulates their catalytic activity and substrate specificity via direct contact with the active site residues. Moreover, the influence of the mutations on the transition temperature (Tm) of Sfβgly indicated that nine of the coupled positions (49, 62, 143, 188, 223, 278, 309, 452 and 460 in Sfβgly numbering) are related to thermal stability. In addition to being preferentially occupied by prolines, structural comparisons indicated that these positions are concentrated at loop segments of the β-glucosidases. Therefore, due to these common biochemical and structural properties, these nine covariant positions, even without physical contacts among them, seem to jointly modulate the thermal stability of β-glucosidases.
Collapse
Affiliation(s)
- Fábio K. Tamaki
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Sandro R. Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| |
Collapse
|