Cloning, characterization, and production of three α‐l‐fucosidases from Clostridium perfringens ATCC 13124
Abstract
α‐l‐Fucosidases are key enzymes for the degradation of intestinal glycans by gut microbes. In this work, three putative α‐l‐fucosidases (Afc1, Afc2, and Afc3) genes from Clostridium perfringens ATCC 13124 were cloned and expressed in Escherichia coli. Afc1 had the α‐l‐fucosidase domain of glycoside hydrolase (GH) 29 family but showed no enzyme activity toward all the substrates examined. The putative acid/base residue of Afc1, Ser205, was replaced by a glutamic acid which is conserved in GH29‐B α‐l‐fucosidases. However, the mutant Afc1‐S205E still failed to show enzyme activity. Afc2 and Afc3 were determined to be 1,3‐1,4‐α‐l‐fucosidase of GH29‐B subfamily and 1,2‐α‐l‐fucosidase of GH95 family, respectively, and both of them could release fucose from porcine gastric mucin (PGM). When C. perfringens ATCC 13124 grew with the presence of PGM, the transcription of afc 1 decreased slightly, while those of afc 2 and afc 3 increased to 2.2‐fold and 1.4‐fold, respectively, and the enzyme activities of Afc2 and Afc3 in the culture increased to 2.2‐fold and 2.6‐fold, respectively. These results suggest that Afc2 and Afc3 are involved in the degradation of intestinal fucosyl glycans by C. perfringens ATCC 13124.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Bacterial genes for alpha-l-fucosidase, alpha-galactosidase and glycosyltransferases were enriched in non-responders.
“Using a new binning approach to focus on candidate bacterial driver genes, we observed enrichment of bacterial genes encoding key enzymes: polysaccharide deacetylase (associated with reduction of polysaccharide immunogenicity42) in Rs; and alpha-l-fucosidase45 and alpha-galactosidase46 (associated with mucus degradation) and glycosyltransferases (associated with LPS synthesis57) in NRs.”
From Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1 (2022) · cites this paper as [45]
Unfavorable taxa had more genes for LPS synthesis and mucus-degrading enzymes like alpha-l-fucosidase and alpha-galactosidase.
“Conversely, within unfavorable taxa, genes encoding enzymes related to LPS synthesis and mucus degradation such as alpha-l-fucosidase45 and alpha-galactosidase46 were increased.”
From Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1 (2022) · cites this paper as [45]
Cites
Gut microbiota in health and disease
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182 · see citing works
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria
Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200 · see citing works
Johansson, M., Larsson, J. M. H., & Hansson, G. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006451107 · Cited by 1,459 · see citing works
How glycan metabolism shapes the human gut microbiota
Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419 · see citing works
Martens, E. C., Chiang, H. C., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.007 · Cited by 919 · see citing works
Human milk glycobiome and its impact on the infant gastrointestinal microbiota
Zivkovic, A. M., German, J. B., Lebrilla, C. B., & Mills, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000083107 · Cited by 679 · see citing works
Hatheway, C. L. (1990) · Clinical Microbiology Reviews · doi:10.1128/cmr.3.1.66 · Cited by 648 · see citing works
Clostridium perfringens: toxinotype and genotype
Petit, L., Gibert, M., & Popoff, M. R. (1999) · Trends in Microbiology · doi:10.1016/s0966-842x(98)01430-9 · Cited by 637 · see citing works
Human milk oligosaccharides are associated with protection against diarrhea in breast-fed infants
Morrow, A. L., Ruiz-Palacios, G. M., Altaye, M., Jiang, X., Guerrero, M. L., Meinzen‐Derr, J. K., Farkas, T., Chaturvedi, P., Pickering, L. K., & Newburg, D. S. (2004) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2004.04.054 · Cited by 467 · see citing works
Physiology of Consumption of Human Milk Oligosaccharides by Infant Gut-associated Bifidobacteria
Asakuma, S., Hatakeyama, E., Urashima, T., Yoshida, E., Katayama, T., Yamamoto, K., Kumagai, H., Ashida, H., Hirose, J., & Kitaoka, M. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.248138 · Cited by 442 · see citing works
Bifidobacteria and their role in human health
MITSUOKA, T. (1990) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/bf01575871 · Cited by 385 · see citing works
Fucosylated human milk oligosaccharides vary between individuals and over the course of lactation
Chaturvedi, P., Warren, C. D., Altaye, M., Morrow, A. L., Ruiz-Palacios, G. M., Pickering, L. K., & Newburg, D. S. (2001) · Glycobiology · doi:10.1093/glycob/11.5.365 · Cited by 370 · see citing works
Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringensPreprint
Myers, G. S. A., Rasko, D. A., Cheung, J. K., Ravel, J., Seshadri, R., DeBoy, R. T., Ren, Q., Varga, J. J., Awad, M. M., Brinkac, L. M., et al. (2006) · Genome Research · doi:10.1101/gr.5238106 · Cited by 323 · see citing works
Katayama, T., Sakuma, A., Kimura, T., Makimura, Y., Hiratake, J., Sakata, K., Yamanoi, T., Kumagai, H., & Yamamoto, K. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.15.4885-4893.2004 · Cited by 263 · see citing works
Sela, D. A., Garrido, D. A., Lerno, L., Wu, S., Tan, K., Eom, H., Joachimiak, A., Lebrilla, C. B., & Mills, D. A. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.06762-11 · Cited by 255 · see citing works
Ashida, H., Miyake, A., Kiyohara, M., Wada, J., Yoshida, E., Kumagai, H., Katayama, T., & Yamamoto, K. (2009) · Glycobiology · doi:10.1093/glycob/cwp082 · Cited by 241 · see citing works
Evidence of Regio-specific Glycosylation in Human Intestinal Mucins
Masselot, C. R., Capon, C., Maes, E., Rousset, M., Zweibaum, A., Zanetta, J., & Michalski, J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m302529200 · Cited by 232 · see citing works
Mucin Degradation by Bifidobacterium Strains Isolated from the Human Intestinal Microbiota
Ruas‐Madiedo, P., Gueimonde, M., Fernández-García, M., Reyes‐Gavilán, C. G. D. L., & Margollés, A. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02509-07 · Cited by 222 · see citing works
Asha, N. J., Tompkins, D. S., & Wilcox, M. H. (2006) · Journal of Clinical Microbiology · doi:10.1128/jcm.00165-06 · Cited by 194 · see citing works
Nagae, M., Tsuchiya, A., Katayama, T., Yamamoto, K., Soichi Wakatsuki, A., & Kato, R. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702246200 · Cited by 131 · see citing works
Sakurama, H., Tsutsumi, E., Ashida, H., Katayama, T., Yamamoto, K., & Kumagai, H. (2012) · Bioscience Biotechnology and Biochemistry · doi:10.1271/bbb.111004 · Cited by 101 · see citing works
Rodríguez‐Díaz, J., Monedero, V., & Yebra, M. J. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.01906-10 · Cited by 101 · see citing works
1,3-1,4-α-l-Fucosynthase That Specifically Introduces Lewis a/x Antigens into Type-1/2 Chains
Sakurama, H., Fushinobu, S., Hidaka, M., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.333781 · Cited by 99 · see citing works
Ficko‐Blean, E., & Boraston, A. B. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m606126200 · Cited by 98 · see citing works
Enzymes That Destroy Blood Group Specificity
Aminoff, D., & Furukawa, K. (1970) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)77143-9 · Cited by 96 · see citing works
Karlsson, N. G., NORDMAN, H., Karlsson, H., Carlstedt, I., & Hansson, G. C. (1997) · Biochemical Journal · doi:10.1042/bj3260911 · Cited by 84 · see citing works
Ashida, H., Maki, R. G., Ozawa, H., Tani, Y., Kiyohara, M., Fujita, M., Imamura, A., Ishida, H., Kiso, M., & Yamamoto, K. (2008) · Glycobiology · doi:10.1093/glycob/cwn053 · Cited by 71 · see citing works
Substrate specificity and other properties of alpha-L-fucosidase from human serum.
DiCioccio, R. A., Barlow, J. J., & Matta, K. L. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)68254-2 · Cited by 61 · see citing works
Divergent Modes of Glycan Recognition by a New Family of Carbohydrate-binding Modules
Gregg, K. J., Finn, R. M., Abbott, D. W., & Boraston, A. B. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m709865200 · Cited by 55 · see citing works
Ogawa, H. K., Muramatsu, H., Kobayashi, T., Morozumi, K., Yokoyama, I., Kurosawa, N., Nakao, A., & Muramatsu, T. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m001888200 · Cited by 53 · see citing works
Purification and characterization of alpha-L-fucosidase from Streptomyces species.
Sano, M., Hayakawa, K., & Kato, I. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)45977-7 · Cited by 51 · see citing works
Rodríguez‐Díaz, J., Rubio‐del‐Campo, A., & Yebra, M. J. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.00474-12 · Cited by 51 · see citing works
A Clostridial Endo-β-galactosidase That Cleaves Both Blood Group A and B Glycotopes
Anderson, K. M., Ashida, H., Maskos, K., et al. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m414099200 · Cited by 50 · see citing works
Diversity in the Properties of Two Sialidase Isoenzymes Produced byClostridium perfringensspp.
Peter, R., Kleineidam Reinhard, G., & Roland, S. (1995) · Biological Chemistry Hoppe-Seyler · doi:10.1515/bchm3.1995.376.9.569 · Cited by 48 · see citing works
Identifying the Catalytic Acid/Base in GH29 α- l -Fucosidase Subfamilies
Shaikh, F. A., van Bueren, A. L., Davies, G. J., et al. (2013) · Biochemistry · doi:10.1021/bi400183q · Cited by 48 · see citing works
Léonard, R., Pabst, M., Bondili, J. S., Chambat, G., Veit, C., Strasser, R., & Altmann, F. (2008) · Phytochemistry · doi:10.1016/j.phytochem.2008.03.024 · Cited by 47 · see citing works
Zhao, W., Li, Y., Gao, P., et al. (2010) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-010-0906-3 · Cited by 45 · see citing works
Characterization of an α- l -fucosidase from the periodontal pathogenTannerella forsythia
Megson, Z. A., Koerdt, A., Schuster, H., Ludwig, R., Janesch, B., Frey, A. M., Naylor, K. L., Wilson, I., Stafford, G. P., Messner, P., et al. (2015) · Virulence · doi:10.1080/21505594.2015.1010982 · Cited by 41 · see citing works
Zeleny, R., LEONARD, R., Dorfner, G., Dalik, T., Kolarich, D., & Altmann, F. (2006) · Phytochemistry · doi:10.1016/j.phytochem.2006.01.021 · Cited by 39 · see citing works
Fujita, M., Tsuchida, A., Hirata, A., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.206722 · Cited by 33 · see citing works
An α-L-fucosidase from Thermus sp. with unusually broad specificity
Eneyskaya, E. V., Kulminskaya, A. A., Kalkkinen, N., et al. (2001) · Glycoconjugate Journal · doi:10.1023/a:1021163720282 · Cited by 32 · see citing works
An Unusual Mode of Galactose Recognition by a Family 32 Carbohydrate-Binding Module
Grondin, J. M., Chitayat, S., Ficko‐Blean, E., et al. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.11.029 · Cited by 23 · see citing works
Shvetsova, S. V., Zhurishkina, E. V., Bobrov, K. S., Ronzhina, N. L., Lapina, I. M., Ivanen, D. R., Gagkaeva, T. Y., & Kulminskaya, A. A. (2014) · Journal of Basic Microbiology · doi:10.1002/jobm.201400309 · Cited by 20 · see citing works
Ashida, H., Maskos, K., Li, S., et al. (2002) · Biochemistry · doi:10.1021/bi011940e · Cited by 18 · see citing works
Tsuji, Y., Yamamoto, K., Tochikura, T., et al. (1990) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a123046 · Cited by 15 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
McCulloch, J. A., Davar, D., Rodrigues, R. R., Badger, J. H., Fang, J. R., Cole, A. M., Balaji, A. K., Vetizou, M., Prescott, S. M., Fernandes, M. R., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01698-2 · Cited by 472 · see citing works
Facts and Hopes for Gut Microbiota Interventions in Cancer Immunotherapy
Davar, D., & Zarour, H. M. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-1129 · Cited by 40 · see citing works
- Authors
- Fan, S., Zhang, H., Chen, X., Lu, L., Xu, L., & Xiao, M.
- Affiliations
- Shandong University (CN)
- Corresponding author
- Xiao, Min
- Venue
- Journal of Basic Microbiology
- Publisher
- Wiley
- Published
- 2015-12-11
- Volume
- 56
- Issue
- 4
- Pages
- 347-357
- ISSN
- 0233-111X (ISSN-L)
- 1521-4028
- OpenAlex
- W2195422852
- Cited by
- 35
- References
- 45
- Citations by year
- 2025: 4 · 2024: 6 · 2023: 4 · 2022: 5 · 2020: 5 · 2019: 5 · 2018: 1 · 2017: 4 · 2016: 1
- FWCI
- 1.66
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Basic Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Major State Basic Research Development Program of China (2012CB822102)
- National High Technology Research and Development Program of China (2012AA021504)
- Key grant Project of Chinese Ministry of Education (313033)
- Science and Technology Development Project of Shandong Province (2014GSF121006)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Enzyme Production and Characterization
- Physical Sciences › Chemistry › Organic Chemistry › Carbohydrate Chemistry and Synthesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
- Keywords
- alpha-L-fucosidase, Clostridium perfringens, porcine gastric mucin, gene cloning, recombinant enzyme expression, gene expression regulation, gut microbiota
- MeSH terms
- Animals, Cloning, Molecular, Clostridium perfringens, Enzyme Activation, Escherichia coli, Fucose, alpha-L-Fucosidase, Gastric Mucins, Polysaccharides, Substrate Specificity, Swine, Mutagenesis, Site-Directed, Glutamic Acid
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