Vibrio cholerae RbmB is an α-1,4-polysaccharide lyase with biofilm-disrupting activity against Vibrio polysaccharide (VPS)
Open accessPublished version of a preprint
Abstract
Many pathogenic bacteria form biofilms as a protective measure against environmental and host hazards. The underlying structure of the biofilm matrix consists of secreted macromolecules, often including exopolysaccharides. To escape the biofilm, bacteria may produce a number of matrix-degrading enzymes, including glycosidic enzymes that digest exopolysaccharide scaffolds. The human pathogen Vibrio cholerae assembles and secretes an exopolysaccharide called VPS ( V ibrio p oly s accharide) which is essential in most cases for the formation of biofilms and consists of a repeating tetrasaccharide unit. Previous studies have indicated that a secreted glycosidase called RbmB is involved in V . cholerae biofilm dispersal, although the mechanism by which this occurs is not understood. To approach the question of RbmB function, we recombinantly expressed and purified RbmB and tested its activity against purified VPS. Using a fluorescence-based biochemical assay, we show that RbmB specifically cleaves VPS in vitro under physiological conditions. Analysis of the cleavage process using mass spectrometry, solid-state NMR, and solution NMR indicates that RbmB cleaves VPS at a specific site (at the α-1,4 linkage between D-galactose and a modified L-gulose) into a mixture of tetramers and octamers. We demonstrate that the product of the cleavage contains a double bond in the modified guluronic acid ring, strongly suggesting that RbmB is cleaving using a glycoside lyase mechanism. Finally, we show that recombinant RbmB from V . cholerae and the related aquatic species Vibrio coralliilyticus are both able to disrupt living V . cholerae biofilms. Our results support the role of RbmB as a polysaccharide lyase involved in biofilm dispersal, as well as an additional glycolytic enzyme to add to the toolbox of potential therapeutic antibacterial enzymes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Database resources of the national center for biotechnology information
Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1112 · Cited by 2,812 · see citing works
A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates
Domon, B., & Costello, C. E. (1988) · Glycoconjugate Journal · doi:10.1007/bf01049915 · Cited by 2,762 · see citing works
Paysan‐Lafosse, T., Blum, M., Chuguransky, S., Grego, T., Pinto, B. L., Salazar, G. A., Bileschi, M. L., Peer Bork, B., Bridge, A. J., Colwell, L. J., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac993 · Cited by 2,371 · see citing works
Heteronuclear decoupling in rotating solids
Bennett, A. E., Rienstra, C. M., Auger, M., Lakshmi, K. V., & Griffin, R. G. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470372 · Cited by 2,127 · see citing works
SMART: recent updates, new developments and status in 2020
Letunic, I., Khedkar, S., & Bork, P. (2020) · Nucleic Acids Res. · doi:10.1093/nar/gkaa937 · Cited by 2,121 · see citing works
Carbon-13 nuclear magnetic resonance of polymers spinning at the magic angle
Schaefer, J., & Stejskal, E. O. (1976) · Journal of the American Chemical Society · doi:10.1021/ja00420a036 · Cited by 1,190 · see citing works
GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans
Ceroni, A., Maaß, K., Geyer, H., Geyer, R., Dell, A., & Haslam, S. M. (2008) · Journal of Proteome Research · doi:10.1021/pr7008252 · Cited by 1,059 · see citing works
The biofilm matrix: multitasking in a shared space
Flemming, H., van Hullebusch, E. D., Neu, T. R., Nielsen, P. H., Seviour, T. W., Stoodley, P., Wingender, J., & Wuertz, S. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00791-0 · Cited by 1,025 · see citing works
Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli
Whitfield, C. (2006) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.75.103004.142545 · Cited by 993 · see citing works
Rumbaugh, K. P., & Sauer, K. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0385-0 · Cited by 928 · see citing works
Chemical shift referencing in MAS solid state NMR
Morcombe, C. R., & Zilm, K. W. (2003) · Journal of Magnetic Resonance · doi:10.1016/s1090-7807(03)00082-x · Cited by 865 · see citing works
Carbohydrate-active enzymes (CAZymes) in the gut microbiome
Wardman, J. F., Bains, R. K., Rahfeld, P., & Withers, S. G. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00712-1 · Cited by 597 · see citing works
Yildiz, F. H., & Schoolnik, G. K. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.4028 · Cited by 589 · see citing works
CATH: increased structural coverage of functional space
Sillitoe, I., Bordin, N., Dawson, N., Waman, V. P., Ashford, P., Scholes, H. M., Pang, C. S. M., Woodridge, L., Rauer, C., Sen, N., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1079 · Cited by 509 · see citing works
New Domain Motif: the Structure of Pectate Lyase C, a Secreted Plant Virulence Factor
Yoder, M. D., Keen, N. T., & JURNAK, F. A. (1993) · Science · doi:10.1126/science.8502994 · Cited by 456 · see citing works
Living in the matrix: assembly and control of Vibrio cholerae biofilms
Teschler, J. K., Zamorano‐Sánchez, D., Utada, A. S., Warner, C. J. A., Wong, G. C. L., Linington, R. G., & Yildiz, F. H. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3433 · Cited by 412 · see citing works
Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms
Berk, V., Fong, J. C. N., Dempsey, G. T., Develïoğlu, Ö. N., Zhuang, X., Liphardt, J., Yildiz, F. H., & Chu, S. (2012) · Science · doi:10.1126/science.1222981 · Cited by 385 · see citing works
Reduction of cholera in Bangladeshi villages by simple filtration
Colwell, R. R., Huq, A., Islam, M. S., Aziz, K. M. A., Yunus, M., Khan, N. H., Mahmud, A. S., Sack, R. B., Nair, G. B., Chakraborty, J., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0237386100 · Cited by 381 · see citing works
Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein
Dong, C., Beis, K., Nesper, J., Brunkan-LaMontagne, A. L., Clarke, B. R., Whitfield, C., & Naismith, J. H. (2006) · Nature · doi:10.1038/nature05267 · Cited by 374 · see citing works
Kaplan, J. B., Ragunath, C., Ramasubbu, N., & Fine, D. H. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.16.4693-4698.2003 · Cited by 364 · see citing works
Carbohydrate-Based Macromolecular Biomaterials
Su, L., Feng, Y., Wei, K., Xu, X., Liu, R., & Chen, G. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01338 · Cited by 336 · see citing works
Sivashanmugam, A., Murray, V. L., Cui, C., Zhang, Y., Wang, J., & Li, Q. (2009) · Protein Science · doi:10.1002/pro.102 · Cited by 326 · see citing works
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases
Garron, M.-L., & Cygler, M. (2010) · Glycobiology · doi:10.1093/glycob/cwq122 · Cited by 287 · see citing works
Fong, J. C. N., Syed, K. A., Klose, K. E., & Yildiz, F. H. (2010) · Microbiology · doi:10.1099/mic.0.040196-0 · Cited by 245 · see citing works
Guilhen, C., Forestier, C., & Balestrino, D. (2017) · Molecular Microbiology · doi:10.1111/mmi.13698 · Cited by 226 · see citing works
Growth in a Biofilm Induces a Hyperinfectious Phenotype inVibrio cholerae
Tamayo, R., Patimalla, B., & Camilli, A. (2010) · Infection and Immunity · doi:10.1128/iai.00048-10 · Cited by 199 · see citing works
Characteristics and applications of alginate lyases: A review
Cheng, D., Jiang, C., Xu, J., Liu, Z., & Mao, X. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.07.199 · Cited by 187 · see citing works
Fong, J. C. N., & Yildiz, F. H. (2007) · Journal of Bacteriology · doi:10.1128/jb.01569-06 · Cited by 185 · see citing works
Ramasubbu, N., Thomas, L. M., Ragunath, C., & Kaplan, J. B. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.03.082 · Cited by 176 · see citing works
A Communal Bacterial Adhesin Anchors Biofilm and Bystander Cells to Surfaces
Absalon, C., Dellen, K. L. V., & Watnick, P. I. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002210 · Cited by 157 · see citing works
Fong, J. C. N., Karplus, K. J., Schoolnik, G. K., & Yildiz, F. H. (2006) · Journal of Bacteriology · doi:10.1128/jb.188.3.1049-1059.2006 · Cited by 150 · see citing works
Xu, F., Dong, F., Wang, P., Cao, H., Li, C., Li, P., Pang, X., Zhang, Y., & Chen, X. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.766030 · Cited by 102 · see citing works
Mechanisms Underlying Vibrio cholerae Biofilm Formation and Dispersion
Teschler, J. K., Nadell, C. D., Drescher, K., & Yildiz, F. H. (2022) · Annual Review of Microbiology · doi:10.1146/annurev-micro-111021-053553 · Cited by 101 · see citing works
Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling
Yan, J. Q., Moreau, A., Khodaparast, S., Perazzo, A., Feng, J., Fei, C., Mao, S., Mukherjee, S., Košmrlj, A., Wingreen, N. S., et al. (2018) · Advanced Materials · doi:10.1002/adma.201804153 · Cited by 99 · see citing works
Self-citationStructural Characterization of the Extracellular Polysaccharide from Vibrio cholerae O1 El-Tor
Yildiz, F. H., Fong, J. C. N., Sadovskaya, I., Grard, T., & VINOGRADOV, E. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086751 · Cited by 94 · see citing works
Kato, T., & Kinoshita, T. (1980) · Analytical Biochemistry · doi:10.1016/0003-2697(80)90143-8 · Cited by 76 · see citing works
Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces
Jiang, Z., Nero, T., Mukherjee, S., Olson, R., & Yan, J. Q. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.686793 · Cited by 73 · see citing works
Self-citationUpregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity
Gallego-Hernández, A. L., DePas, W. H., Park, J. H., Teschler, J. K., Hartmann, R., Jeckel, H., Drescher, K., Beyhan, S., Newman, D. K., & Yildiz, F. H. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1916571117 · Cited by 73 · see citing works
Molecular Determinants of Mechanical Properties of V. cholerae Biofilms at the Air-Liquid Interface
Hollenbeck, E. C., Fong, J. C. N., Lim, J. Y., Yildiz, F. H., Fuller, G. G., & Cegelski, L. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.10.015 · Cited by 72 · see citing works
Self-citationBridges, A. A., Fei, C., & Bassler, B. L. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021166117 · Cited by 66 · see citing works
Efficacy and safety of biofilm dispersal by glycoside hydrolases in wounds
Redman, W. K., Welch, G. S., Williams, A. C., Damron, A. J., Northcut, W. O., & Rumbaugh, K. P. (2021) · Biofilm · doi:10.1016/j.bioflm.2021.100061 · Cited by 59 · see citing works
Environmental fluctuation governs selection for plasticity in biofilm production
Yan, J. Q., Nadell, C. D., & Bassler, B. L. (2017) · The ISME Journal · doi:10.1038/ismej.2017.33 · Cited by 56 · see citing works
Self-citationDifferential Efficacy of Glycoside Hydrolases to Disperse Biofilms
Redman, W. K., Welch, G. S., & Rumbaugh, K. P. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00379 · Cited by 47 · see citing works
Huang, X., Nero, T., Weerasekera, R., Matej, K., Hinbest, A., Jiang, Z., Lee, R. F., Wu, L., Chak, C., Nijjer, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37660-0 · Cited by 45 · see citing works
Self-citationSchwechheimer, C., Hebert, K. A., Tripathi, S. M., Singh, P. K., Floyd, K. A., Brown, E. R., Porcella, M. E., Osorio, J., Kiblen, J. T. M., Pagliai, F. A., et al. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008745 · Cited by 29 · see citing works
Kaus, K., Biester, A., Chupp, E., Lu, J., Visudharomn, C., & Olson, R. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.008335 · Cited by 26 · see citing works
Self-citationYang, Y., Yan, J. Q., Olson, R., & Jiang, X. (2025) · mSystems · doi:10.1128/msystems.00060-25 · Cited by 10 · see citing works
Self-citationA fluorescence assay for enzymes that cleave glycosidic linkages to produce reducing sugars
O’Neill, R. A., Darvill, A. G., & Albersheim, P. (1989) · Analytical Biochemistry · doi:10.1016/0003-2697(89)90004-3 · Cited by 10 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Moreau, A., Nguyen, D. H., Hinbest, A. J., Zamora, A., Weerasekera, R., Matej, K., Zhou, X., Sánchez, S., Rodriguez-Brenes, I. A., Tai, J. B., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-55602-2 · Cited by 21 · see citing works
Self-citationYang, Y., Yan, J. Q., Olson, R., & Jiang, X. (2025) · mSystems · doi:10.1128/msystems.00060-25 · Cited by 10 · see citing works
Self-citationDissecting the physics of bacterial biofilms with agent-based simulations
Nam, K.-M., Li, C., Cockx, B., Nguyen, D. T., Li, Y., Kreft, J., & Yan, J. Q. (2025) · Current Opinion in Solid State and Materials Science · doi:10.1016/j.cossms.2025.101228 · Cited by 6 · see citing works
Self-citationWeerasekera, R., Moreau, A., Huang, X., Potapova, A., Schwechheimer, C., Kandel, R., Huynh, Y., Cannizzo, O., Gordon, R., Gerace, E., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2534280123 · Cited by 3 · see citing works
Self-citationBiofilm formation: Regulatory mechanisms and therapeutic strategies
Ma, W., Zhang, J., Cheng, Y., Zhai, M., Zhou, J., & Qu, J. (2026) · Microbiological Research · doi:10.1016/j.micres.2026.128597 · Cited by 3 · see citing works
Structural basis of multimodal adsorption and infection initiation by Vibrio phage Peru-2Preprint
Yu, H., Zhao, J., Yue, J., Molineux, I. J., Liu, J., Robins, W. P., & Mekalanos, J. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.25.734500
Influence of cell–cell distance on the ecology and evolution of microbial communities
Huang, A., Ramesh, D., Nie, Y., Zhao, K., & Wang, M. (2026) · The ISME Journal · doi:10.1093/ismejo/wrag199
Hinbest, A. J., Nam, H. B., Liszczyk, E. D., Kandel, R., Gerace, E., Moreau, A., Weerasekera, R., Gordon, R., Yang, Y., Chen, J., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.03.742583
Self-citationGill, H. K., & Bassler, B. L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.20.745993
- Authors
- Weerasekera, R., Moreau, A., Huang, X., Nam, K.-M., Hinbest, A. J., Huynh, Y., Liu, X., Ashwood, C., Pepi, L. E., Paulson, E., Cegelski, L., Yan, J., & Olson, R.
- Affiliations
- Wesleyan University (US)
- Yale University (US)
- Stanford University (US)
- Beth Israel Deaconess Medical Center (US)
- Corresponding author
- Olson, Rich
- ORCID
- Venue
- PLOS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2024-12-02
- Volume
- 20
- Issue
- 12
- Pages
- e1012750
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- PMC
- PMC11637428
- OpenAlex
- W4404914127
- Cited by
- 9
- References
- 49
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 1
- FWCI
- 2.67
- Type
- journal article
- Language
- en
- Update notices
- new_version (2024-12-12)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Pathogens (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (R15GM152959, 1DP2GM146253, R01GM117278)
- National Science Foundation (2205006)
- Alfred P. Sloan Foundation (FG-2023-20857)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Vibrio bacteria research studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
- Life Sciences › Agricultural and Biological Sciences › Food Science › Polysaccharides Composition and Applications
- Keywords
- Vibrio cholerae, biofilm dispersal, biofilm matrix degradation, Vibrio coralliilyticus, antibacterial enzymes, glycolytic enzymes
- MeSH terms
- Bacterial Proteins, Cholera, Humans, Polysaccharide-Lyases, Polysaccharides, Bacterial, Vibrio cholerae, Biofilms
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
