Bacterial amylases enable glycogen degradation by the vaginal microbiome.


Journal

Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869

Informations de publication

Date de publication:
09 2023
Historique:
received: 08 07 2021
accepted: 11 07 2023
medline: 31 8 2023
pubmed: 11 8 2023
entrez: 10 8 2023
Statut: ppublish

Résumé

The human vaginal microbiota is frequently dominated by lactobacilli and transition to a more diverse community of anaerobic microbes is associated with health risks. Glycogen released by lysed epithelial cells is believed to be an important nutrient source in the vagina. However, the mechanism by which vaginal bacteria metabolize glycogen is unclear, with evidence implicating both bacterial and human enzymes. Here we biochemically characterize six glycogen-degrading enzymes (GDEs), all of which are pullanases (PulA homologues), from vaginal bacteria that support the growth of amylase-deficient Lactobacillus crispatus on glycogen. We reveal variations in their pH tolerance, substrate preferences, breakdown products and susceptibility to inhibition. Analysis of vaginal microbiome datasets shows that these enzymes are expressed in all community state types. Finally, we confirm the presence and activity of bacterial and human GDEs in cervicovaginal fluid. This work establishes that bacterial GDEs can participate in the breakdown of glycogen, providing insight into metabolism that may shape the vaginal microbiota.

Identifiants

pubmed: 37563289
doi: 10.1038/s41564-023-01447-2
pii: 10.1038/s41564-023-01447-2
pmc: PMC10465358
doi:

Substances chimiques

Amylases EC 3.2.1.-
Glycogen 9005-79-2

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1641-1652

Subventions

Organisme : NIGMS NIH HHS
ID : DP2 GM136652
Pays : United States
Organisme : NIAID NIH HHS
ID : K08 AI130392
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States

Informations de copyright

© 2023. The Author(s).

Références

Kalia, N., Singh, J. & Kaur, M. Microbiota in vaginal health and pathogenesis of recurrent vulvovaginal infections: a critical review. Ann. Clin. Microbiol. Antimicrob. 19, 5 (2020).
pubmed: 31992328 pmcid: 6986042
Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA 108, 4680–4687 (2011).
pubmed: 20534435
Anahtar, M. N. et al. Inflammatory responses in the female genital tract. Immunity 42, 965–976 (2016).
Gosmann, C. et al. Lactobacillus-deficient cervicovaginal bacterial communities are associated with increased HIV acquisition in young South African women. Immunity 46, 29–37 (2017).
pubmed: 28087240 pmcid: 5270628
Dols, J. A. M. et al. Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis. Am. J. Obstet. Gynecol. 204, 305.e1–305.e7 (2011).
pubmed: 21272848
Hočevar, K. et al. Vaginal microbiome signature is associated with spontaneous preterm delivery. Front. Med. 6, 201 (2019).
Gajer, P. et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra52 (2012).
pubmed: 22553250 pmcid: 3722878
Foster, K. R., Schluter, J., Coyte, K. Z. & Rakoff-Nahoum, S. The evolution of the host microbiome as an ecosystem on a leash. Nature 548, 43–51 (2017).
pubmed: 28770836 pmcid: 5749636
Rakoff-Nahoum, S., Foster, K. R. & Comstock, L. E. The evolution of cooperation within the gut microbiota. Nature 533, 255–259 (2016).
pubmed: 27111508 pmcid: 4978124
Porter, N. T. & Martens, E. C. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu. Rev. Microbiol. 71, 349–369 (2017).
pubmed: 28657886
Rakoff-Nahoum, S., Coyne, M. J. & Comstock, L. E. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr. Biol. 24, 40–49 (2014).
pubmed: 24332541
Cruickshank, R. & Sharman, A. The biology of the vagina in the human subject. BJOG 41, 208–226 (1934).
Amabebe, E. & Anumba, D. O. C. The vaginal microenvironment: the physiologic role of Lactobacilli. Front. Med. 5, 181 (2018).
Mirmonsef, P. et al. Free glycogen in vaginal fluids is associated with Lactobacillus colonization and low vaginal pH. PLoS ONE 9, 26–29 (2014).
Stewart-Tull, D. E. S. Evidence that vaginal lactobacilli do not ferment glycogen. Am. J. Obstet. Gynecol. 88, 676–679 (1964).
pubmed: 14128200
Wylie, J. G. & Henderson, A. Identity and glycogen-fermenting ability of lactobacilli isolated from the vagina of pregnant women. J. Med. Microbiol. 2, 363–366 (1969).
pubmed: 4996481
Spear, G. T. et al. Human α-amylase present in lower-genital-tract mucosal fluid processes glycogen to support vaginal colonization by Lactobacillus. J. Infect. Dis. 210, 1019–1028 (2014).
pubmed: 24737800 pmcid: 4168305
Spear, G. T. et al. Effect of pH on cleavage of glycogen by vaginal enzymes. PLoS ONE 10, e0132646 (2015).
pubmed: 26171967 pmcid: 4501710
Huffman, R. D., Nawrocki, L. D., Wilson, W. A. & Brittingham, A. Digestion of glycogen by a glucosidase released by Trichomonas vaginalis. Exp. Parasitol. J. 159, 151–159 (2015).
Smith, R. W., Brittingham, A. & Wilson, W. A. Purification and identification of amylases released by the human pathogen Trichomonas vaginalis that are active towards glycogen. Mol. Biochem. Parasitol. 210, 22–31 (2016).
pubmed: 27506885
Nunn, K. L. et al. Amylases in the human vagina. mSphere https://doi.org/10.1128/msphere.00943-20 (2020).
van der Veer, C. et al. Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome 7, 49 (2019).
pubmed: 30925932 pmcid: 6441167
Hertzberger, R. et al. Genetic elements orchestrating Lactobacillus crispatus glycogen metabolism in the vagina. Int. J. Mol. Sci. 23, 5590 (2022).
pubmed: 35628398 pmcid: 9141943
Qiao, Y. et al. Gene cloning and enzymatic characterization of alkali-tolerant type I pullulanase from Exiguobacterium acetylicum. Lett. Appl. Microbiol. 60, 52–59 (2015).
pubmed: 25273816
Ma, B. et al. A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. Nat. Commun. 11, 940 (2020).
pubmed: 32103005 pmcid: 7044274
Chen, Y. et al. Activity-based protein profiling of retaining α-amylases in complex biological samples. J. Am. Chem. Soc. 143, 2423–2432 (2021).
pubmed: 33497208 pmcid: 7883350
von Heijne, G. The signal peptide. J. Membr. Biol. 115, 195–201 (1990).
Bhandari, P., Tingley, J. P., Palmer, D. R. J., Abbott, D. W. & Hill, J. E. Characterization of an a-glucosidase enzyme conserved in Gardnerella spp. isolated from the human vaginal microbiome. J. Bacteriol. 203, e0021321 (2021).
pubmed: 34124938
Boot, H. J., Kolen, C. P. A. M. & Pouwels, P. H. Identification, cloning, and nucleotide sequence of a silent S-layer protein gene of Lactobacillus acidophilus ATCC 4356 which has extensive similarity with the S-layer protein gene of this species. J. Bacteriol. 177, 7222–7230 (1995).
pubmed: 8522531 pmcid: 177603
Willing, S. E. et al. Clostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII. Mol. Microbiol. 96, 596–608 (2015).
pubmed: 25649385 pmcid: 4973711
Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).
pubmed: 11152613
Cantarel, B. I. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, 20894 (2009).
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
pubmed: 30357350
Boraston, A. B. et al. A structural and functional analysis of α-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J. Biol. Chem. 281, 587–598 (2006).
pubmed: 16230347
Wiatrowski, H. A. et al. Mutations in the Gal83 glycogen-binding domain activate the Snf1/Gal83 kinase pathway by a glycogen-independent mechanism. Mol. Cell. Biol. 24, 352–361 (2004).
pubmed: 14673168 pmcid: 303368
Michelin, M. et al. Purification and biochemical characterization of a thermostable extracellular glucoamylase produced by the thermotolerant fungus Paecilomyces variotii. J. Ind. Microbiol. Biotechnol. 35, 17–25 (2008).
pubmed: 17938981
da Silva, T. M. et al. Purification and biochemical characterization of a novel α-glucosidase from Aspergillus niveus. Int. J. Gen. Mol. Microbiol. 96, 569–578 (2009).
Li, Y., Zhang, L., Ding, Z., Gu, Z. & Shi, G. Engineering of isoamylase: improvement of protein stability and catalytic efficiency through semi-rational design. J. Ind. Microbiol. Biotechnol. 43, 3–12 (2016).
pubmed: 26597030
Jung, J. H. et al. Characterization of a novel extracellular α-amylase from Ruminococcus bromii ATCC 27255 with neopullulanase-like activity. Int. J. Biol. Macromol. 130, 605–614 (2019).
pubmed: 30836186
Lee, H. W. et al. Characterization and application of BiLA, a psychrophilic α-amylase from Bifidobacterium longum. J. Agric. Food Chem. 64, 2709–2718 (2016).
pubmed: 26979859
Marie S. Møller, A. et al. An extracellular cell-attached pullulanase confers branched α-glucan utilization in human gut Lactobacillus acidophilus. Appl. Environ. Microbiol. 83, e00402-17 (2017).
pubmed: 28411221 pmcid: 5452828
Amsel, R. et al. Nonspecific vaginitis. Diagnostic criteria and microbial and epidemiologic associations. Am. J. Med. 74, 14–22 (1983).
pubmed: 6600371
Lin, F. P. & Leu, K. L. Cloning, expression, and characterization of thermostable region of amylopullulanase gene from Thermoanaerobacter ethanolicus 39E. Appl. Biochem. Biotechnol. 97, 33–44 (2002).
pubmed: 11900114
Nisha, M. & Satyanarayana, T. Characterization of recombinant amylopullulanase (gt-apu) and truncated amylopullulanase (gt-apuT) of the extreme thermophile Geobacillus thermoleovorans NP33 and their action in starch saccharification. Appl. Microbiol. Biotechnol. 97, 6279–6292 (2013).
pubmed: 23132347
Nisha, M. & Satyanarayana, T. Recombinant bacterial amylopullulanases: developments and perspectives. 4, 388–400 (2013).
Wang, M. et al. Discovery of a new microbial origin cold-active neopullulanase capable for effective conversion of pullulan to panose. Int. J. Mol. Sci. 23, 6928 (2022).
pubmed: 35805929 pmcid: 9267027
Hii, S. L., Tan, J. S., Ling, T. C. & Ariff, A. Bin Pullulanase: role in starch hydrolysis and potential industrial applications. Enzym. Res. 2012, 921362 (2012).
France, M. T. et al. Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. Genome Biol. 23, 66 (2022).
pubmed: 35232471 pmcid: 8886902
Kaminski, J. et al. Structure, function, and diversity of the healthy human microbiome with ShortBRED. Nature 486, 207–214 (2012).
Garcia, W. L. et al. Profiling how the gut microbiome modulates host xenobiotic metabolism in response to benzo[a]pyrene and 1-nitropyrene exposure. Chem. Res. Toxicol. 35, 585–596 (2022).
pubmed: 35347982 pmcid: 9878584
Bhandari, P., Tingley, J., Abbott, D. W. & Hill, J. E. Glycogen-degrading activities of catalytic domains of a-amylase and a-amylase-pullulanase enzymes conserved in Gardnerella spp. from the vaginal microbiome. J. Bacteriol. 205, e0039322 (2023).
pubmed: 36744900
Andersch-Björkman, Y., Thomsson, K. A., Holmén Larsson, J. M., Ekerhovd, E. & Hansson, G. C. Large-scale identification of proteins, mucins and their O-glycosylation in the endocervical mucus during the menstrual cycle. Mol. Cell. Proteom. 6, 708–716 (2007).
Pereira, L. et al. Identification of novel protein biomarkers of preterm birth in human cervical−vaginal fluid. J. Proteome Res. 6, 1269–1276 (2007).
pubmed: 17373840
Kim, Y. E. et al. Quantitative proteomic profiling of cervicovaginal fluid from pregnant women with term and preterm birth. Proteome Sci. 19, 3 (2021).
pubmed: 33588889 pmcid: 7885372
Zhang, J., Li, L., Zhang, T. & Zhong, J. Characterization of a novel type of glycogen‑degrading amylopullulanase from Lactobacillus crispatus. Appl. Microbiol. Biotechnol. 106, 4053–4064 (2022).
Coyte, K. Z. & Rakoff-Nahoum, S. Understanding competition and cooperation within the mammalian gut microbiome. Curr. Biol. 29, R538–R544 (2019).
pubmed: 31163167 pmcid: 6935513
Lithgow, K. V, Cochinamogulos, A., Muirhead, K. & Oluoch, L. M. Resolving glycogen and related enzymes reveals correlates of Lactobacillus crispatus dominance in a cohort of young African women. Preprint at Res. Square https://doi.org/10.21203/rs.3.rs-1679828/v1 (2022).
Markowitz, V. M. et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 40, 115–122 (2012).
Almagro Armenteros, J. J. et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).
pubmed: 30778233
Nayfach, S. & Pollard, K. S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 16, 51 (2015).
pubmed: 25853934 pmcid: 4389708
Levin, B. J. et al. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline. Science 355, eaai8386 (2017).
pubmed: 28183913 pmcid: 5705181
Jiang, J. et al. Detection of active mammalian GH31 α-glucosidases in health and disease using in-class, broad-spectrum activity-based probes. ACS Cent. Sci. 2, 351–358 (2016).
pubmed: 27280170 pmcid: 4882745
Yu, F., Haynes, S. E. & Nesvizhskii, A. I. IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs. Mol. Cell. Proteom. 20, 100077 (2021).
Keller, A., Nesvizhskii, A. I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392 (2002).
pubmed: 12403597
Nesvizhskii, A. I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646–4658 (2003).
pubmed: 14632076
Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat. Methods 14, 513–520 (2017).
pubmed: 28394336 pmcid: 5409104
Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).
pubmed: 27348712
Zhang, H. et al. DbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95–W101 (2018).
pubmed: 29771380 pmcid: 6031026

Auteurs

Dominick J Jenkins (DJ)

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Benjamin M Woolston (BM)

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Department of Chemical Engineering, Northeastern University, Boston, MA, USA.

M Indriati Hood-Pishchany (MI)

Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
Department of Microbiology, Harvard Medical School, Boston, MA, USA.

Paula Pelayo (P)

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Alyssa N Konopaski (AN)

Department of Chemistry, Seattle University, Seattle, WA, USA.

M Quinn Peters (M)

Department of Chemistry, Seattle University, Seattle, WA, USA.

Michael T France (MT)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.

Jacques Ravel (J)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.

Caroline M Mitchell (CM)

Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA.
Harvard Medical School, Boston, MA, USA.

Seth Rakoff-Nahoum (S)

Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. seth.rakoff-nahoum@childrens.harvard.edu.
Department of Microbiology, Harvard Medical School, Boston, MA, USA. seth.rakoff-nahoum@childrens.harvard.edu.

Christopher Whidbey (C)

Department of Chemistry, Seattle University, Seattle, WA, USA. whidbeyc@seattleu.edu.

Emily P Balskus (EP)

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. balskus@chemistry.harvard.edu.
Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. balskus@chemistry.harvard.edu.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH