Erik Vijgenboom
University lecturer / guest
- Name
- Dr. E. Vijgenboom
- Telephone
- +31 71 527 2727
- e.vijgenboom@biology.leidenuniv.nl
- ORCID iD
- 0000-0002-5059-069X
The filamentous microbe, Streptomyces lividans, is used to design cell factories for enzyme production and to study the role of redox-metal homeostasis in morphology.
Streptomyces lividans as cell factory for the expression and secretion of carbohydrate active enzymes (FilaZyme).
Design of Streptomyces lividans cell factories and expression cassettes for the efficient and high yield secretion of (heterologous) enzymes active in the decomposition of polysaccharides in biomass.
Production and characterization of LPMOs and chimeric enzymes in Streptomyces lividans
Lytic polysaccharide monooxygenases (LPMOs) are enzymes with the promise to play a major role in the initial decomposition of biomass. LPMOs active on substrates other than those currently listed in the CAZy database, are expressed and characterized. Furthermore, starch active LPMOs are designed for better performance using a combination of synthetic site evaluation libraries (SEL) and in vivo screening for LPMO variants that are more active on starch as substrate.
In another approach chimeric carbohydrate degrading enzymes are designed with the aim to create enzymes that perform better in complete breakdown of biomass.
Copper homeostasis and morphology in Streptomyces lividans
Morphological development of Streptomyces lividans is strongly dependent on the redox active metal copper. In these studies, the proteins active in Cu-homeostasis (trafficking, storage and Cu-chaperone delivery to enzymes) are investigated in relation to the morphology of Streptomyces on solid and liquid media. This research programme is carried out in collaboration with Dr J.A.R. Worrall, University of Essex, UK.
University lecturer / guest
- Science
- Instituut Biologie Leiden
- IBL Microbial Sciences
- Zhong X., Zhang L., Wezel G.P. van, Vijgenboom E. & Claessen D. (2022), Role for a lytic polysaccharide monooxygenase in cell wall remodeling in streptomyces coelicolor, mBio 13(2): e00456-22.
- Sidar A., Albuquerque E.D., Voshol G.P., Ram A.F.J., Vijgenboom E. & Punt P.J. (2020), Carbohydrate binding modules: diversity of domain architecture in amylases and cellulases from filamentous microorganisms , Frontiers in Bioengineering and Biotechnology 8: 871.
- Voshol G.P., Punt P.J. & Vijgenboom E. (2019), Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments, F1000Research 8: 1843.
- Straw M.L., Chaplin A.K., Hough M.A., Paps J., Bavro V.N., Wilson M.T., Vijgenboom E. & Worrall J.A.R. (2018), A cytosolic copper storage protein provides a second level of copper tolerance in Streptomyces lividans, Metallomics 10(1): 180-193.
- Voshol G., Vijgenboom E. & Punt P. (2017), The discovery of novel LPMO families with a new Hidden Markov model, BMC Research Notes 10(1): 105.
- Chaplin A.K., Svistunenko D.A., Hough M.A., Wilson M.T., Vijgenboom E. & Worrall J.A.R. (2017), Active-site maturation and activity of the copper-radical oxidase GlxA are governed by a tryptophan residue, Biochemical Journal 474(5): 809-825.
- Chaplin A.K., Wilson M.T., Hough M.A., Svistunenko D.A., Hemsworth G.R., Walton P.H., Vijgenboom E. & Worrall J.A.R. (2016), Heterogeneity in the Histidine-brace Copper Coordination Sphere in Auxiliary Activity Family 10 (AA10) Lytic Polysaccharide Monooxygenases, Journal of Biological Chemistry 291(24): 12838-12850.
- Sevillano L., Vijgenboom E., Wezel G.P. van, Diaz M. & Santamaria R.I. (2016), New approaches to achieve high level enzyme production in Streptomyces lividans, Microbial Cell Factories 15: 28.
- Petrus M.L.C., Vijgenboom E., Chaplin A.K., Worrall J.A.R., Wezel G.P. van & Claessen D. (2016), The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces, Open Biology 6(1): 150149.
- Chaplin A.K., Petrus M.L.C., Mangiameli G., Hough M.A., Svistunenko D.A., Nicholls P., Claessen D., Vijgenboom E. & Worrall J.A.R. (2015), GlxA is a new structural member of the radical copper oxidase family and is required for glycan deposition at hyphal tips and morphogenesis of Streptomyces lividans, Biochemical Journal 469(3): 433-444.
- Chaplin A.K., Tan B.G., Vijgenboom E. & Worall J.A.R. (2015), Copper trafficking in the CsoR regulon of Streptomyces lividans, Metallomics 7(1): 145-155.
- Tan B.G., Vijgenboom E. & Worrall J.A. (2014), Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans, Nucleic Acids Research 42(2): 1326-1340.
- Blundell K.L., Hough M.A., Vijgenboom E. & Worrall J.A. (2014), Structural and mechanistic insights into an extracytoplasmic copper trafficking pathway in Streptomyces lividans, Biochemical Journal 459(3): 515-538.
- Cruz-Morales P., Vijgenboom E., Iruegas-Bocardo F., Girard G., Yañez-Guerra L.A., Ramos-Aboites H.E., Pernodet J.L., Anné J., Wezel G.P. van & Barona-Gómez F. (2013), The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island, Genome Biology and Evolution 5(6): 1165-1175.
- Blundell K.L., Wilson M.T., Svistunenko D.A., Vijgenboom E. & Worrall J.A. (2013), Morphological development and cytochrome c oxidase activity in Streptomyces lividans are dependent on the action of a copper bound Sco protein, Open Biology 3(1): 120163.
- Blundell K.L.I.M., Wilson M.T., Vijgenboom E. & Worrall J.A.R. (2013), The role of the Cys-X-X-X-Cys motif on the kinetics of cupric ion loading to the Streptomyces lividans Sco Q1 protein, Dalton Transactions 42(29): 10608-10616.
- Jong W. de, Vijgenboom E., Dijkhuizen L., Wösten H.A.B. & Claessen D. (2012), SapB and the rodlins are required for development of Streptomyces coelicolor in high osmolarity media, FEMS Microbiology Letters 329(2): 154-159.
- Dwarakanath S., Chaplin A.K., Hough M.A., Rigali S., Vijgenboom E. & Worrall J.A.R. (2012), Response to copper stress in Streptomyces lividans extends beyond genes under direct control of a copper-sensitive operon repressor protein (CsoR), Journal of Biological Chemistry 287(21): 17833-17847.
- Barends S., Zehl M., Bialek S., Waal E. de, Traag B.A., Willemse J., Nørregaard Jensen O., Vijgenboom E. & Wezel G.P. van (2010), Transfer–messenger RNA controls the translation of cell-cycle and stress proteins in Streptomyces, EMBO Reports 11(2): 119-125.
- Worrall J.A.R. & Vijgenboom E. (2010), Copper mining in Streptomyces: enzymes, natural products and development, Natural Product Reports 27(5): 742-756.
- Tepper A.W.J.W., Milikisyants S., Sottini S., Vijgenboom E., Groenen E.J.J. & Canters G.W. (2009), Identification of a radical intermediate in the enzymatic reduction of oxygen by small laccase, Journal of the American Chemical Society 131(33): 11680-11682.
- Birkó Z., Swiatek M., Szájli E., Medzihradszky K.F., Vijgenboom E., Penyige A., Keserű J., Wezel G.P. van & Biró S. (2009), Lack of a-factor production induces the expression of nutrient scavenging and stress-related proteins in streptomyces griseus, Molecular and Cellular Proteomics 8(10): 2396-2403.
- Martin L.B., Nikodinovic J., Vijgenboom E., Mc Mahon A.M. & O’Connor K.E. (2008), Assessing the catalytic activity of three different sources of tyrosinase: a study of the oxidation of mono- and difluorinated monophenols, Enzyme and Microbial Technology 43(3): 297-301.
- Traag B.A., Seghezzi N., Vijgenboom E. & Wezel G.P. van (2007), Characterization of the sporulation control protein SsgA by use of an efficient method to create and screen random mutant libraries in streptomycetes, Applied and Environmental Microbiology 73(7): 2085-2092.
- Birko Z., Bialek S.M., Buzas K., Szajli E., Traag B.A., Medzihradszky K.F., Rigali S., Vijgenboom E., Penyige A., Kele Z., Wezel G.P. van & Biro S. (2007), The secreted signaling protein factor C triggers the A-factor response regulon in Streptomyces griseus: overlapping signaling routes, Molecular and Cellular Proteomics 6(7): 1248-1256.
- Wezel G.P. van, Krabben P., Traag B.A., Keijser B.J.F., Kerste R., Vijgenboom E., Heijnen J.J. & Kraal B. (2006), Unlocking Streptomyces spp. for Use as Sustainable Industrial Production Platforms by Morphological Engineering, Applied and Environmental Microbiology 72(8): 5283-5288.
- Worrall J.A.R., Machczynski M.C., Keijser B.J.F., Rocco G. di, Ceola S., Ubbink M., Vijgenboom E. & Canters G.W. (2006), Spectroscopic characterization of a high-potential lipo-cupredoxin found in Streptomyces coelicolor, Journal of the American Chemical Society 128(45): 14579-14589.
- Machczynski M.C., Vijgenboom E., Samyn B. & Canters G.W. (2004), Characterization of SLAC: a small laccase from Streptomyces coelicolor with unprecedented activity, Protein Science 13(9): 2388-2397.
- Wezel G.P. van & Vijgenboom E. (2004), Novel aspects of signaling in Streptomyces development, Advances in Applied Microbiology 56: 65-88.
- Bubacco L., Gastel M. van, Groenen E.J.J., Vijgenboom E. & Canters G.W. (2003), Spectroscopic characterization of the electronic changes in the active site of Streptomyces antibioticus tyrosinase upon binding of transition state analogue inhibitors, Journal of Biological Chemistry 278(9): 7381-7389.
- Boer A.L. de, Neerken S., Wijn R. de, Permentier H.P., Gast P., Vijgenboom E. & Hoff A.J. (2002), B-branch electron transfer in reaction centers of Rhodobacter sphaeroides assessed with site-directed mutagenesis, Photosynthesis Research 71(3): 221-239.
- Boer A.L. de, Neerken S., Wijn R. de, Permentier H.P., Gast P., Vijgenboom E. & Hoff A.J. (2002), High yield of B-branch electron transfer in a quadruple reaction center mutant of the photosynthetic bacterium Rhodobacter sphaeroides, Biochemistry 41(9): 3081-3088.
- Keijser B.J.F., Wezel G.P. van, Canters G.W. & Vijgenboom E. (2002), Developmental regulation of the Streptomyces lividans ram genes: involvement of RamR in regulation of the ramCSAB operon, Journal of Bacteriology 184(16): 4420-4429.
- Machczynski M.C., Canters G.W. & Vijgenboom E. (2001), Soft-metal chaperones in Streptomyces coelicolour: expression, disruption, and regulation, Journal of Inorganic Biochemistry 86(1): 323-323.
- Streffer K., Vijgenboom E., Tepper A.W.J.W., Makower A., Scheller F.W., Canters G.W. & Wollenberger U. (2001), Determination of phenolic compounds using recombinant tyrosinase from Streptomyces antibioticus, Analytica Chimica Acta 427(2): 201-210.
- Keijser B.J.F., Wezel G.P. van, Canters G.W., Kieser T. & Vijgenboom E. (2000), The ram dependence of Streptomyces lividans differentiation is by-passed by copper, Journal of Molecular Microbiology and Biotechnology 2(4): 565-574.
- Brouwers G.J., Vijgenboom E., Corstjens P.L.A.M., Vrind J.P.M. de & Vrind-de Jong E.W. de (2000), Bacterial Mn2+ oxidizing systems and multicopper oxidases: an overview of mechanisms and functions, Geomicrobiology Journal 17(1): 1-24.
- Bubacco L., Vijgenboom E., Gobin C., Tepper A.W.J.W., Salgado J. & Canters G.W. (2000), Kinetic and paramagnetic NMR investigations of the inhibition of Streptomyces antibioticus tyrosinase, Journal of Molecular Catalysis B: Enzymatic 8(1-3): 27-35.
- Gastel M. van, Bubacco L., Groenen E.J.J., Vijgenboom E. & Canters G.W. (2000), EPR study of the dinuclear active copper site of tyrosinase from Streptomyces antibioticus, FEBS Letters 474(2-3): 228-232.
- Price N.J., Brennan L., Faria T.Q., Vijgenboom E., Canters G.W., Turner D.L. & Santos H. (2000), High yield of Methylophillus methylotrophus cytochrome c by coexpression with cytochrome c maturation gene cluster from Eschericia coli, Protein Expression and Purification 20(3): 444-450.
- Price N.J., Vijgenboom E., Ribeiro G., Costa J.V., Canters G.W. & Santos H. (1999), Cloning and sequence analysis of the gene encoding Methylophilus methyltrophus cytochrome c: a unique protein with a perpendicular orientation of the histidinyl ligands, Biochimica et Biophysica Acta. Bioenergetics 1413(1): 55-61.
- Bubacco L., Salgado J., Tepper W.J.W., Vijgenboom E. & Canters G.W. (1999), 1H NMR spectroscopy of the binuclear CU(ll) active site of streptomyces antibioticus tyrosinase, FEBS Letters 442(2-3): 215-220.
- Schlarb B.G., Wagner M.J., Vijgenboom E., Ubbink M., Bendall D.S. & Howe C.J. (1999), Expression of plastocyanin and cytochrome f of the cyanobacterium Phormidium laminosum in escherichia coli and Paracoccus denitrificans and the role of leader peptides, Gene 234(2): 275-283.
- Dennison C., Canters G.W., Vries S. de, Vijgenboom E. & Spanning R.J. van (1998), The methylamine dehydrogenase electron transfer chain, Advances in Inorganic Chemistry 45: 351-407.
- Boer A.L. de, Neerken S., Permentier H.P., Vijgenboom E., Gast P., Aartsma T.J. & Hoff A.J. (1998), Spectroscopic characterization of two new reaction center mutants of the photosynthetic bacterium Rhodobacter sphaeroides. In: Garab G. (Ed.), Photosynthesis: Mechanisms and Effects. Dordrecht, The Netherlands: Kluwer Academic Publishers. 747-750.
- Vijgenboom E., Busch J.E. & Canters G.W. (1997), In vivo studies disprove an obligatory role of azurin in denitrification in Pseudomonas aeruginosa and show that azu expression is under control of RpoS and ANR, Microbiology 143(9): 2853-2863.
- Andrew C.R., Han J., Blaauwen T. den, Pouderoyen G. van, Vijgenboom E., Canters G.W., Loehr T.M. & Sanders-Loehr J. (1997), Cysteine ligand vibrations are responsible for the complex resonance Raman spectrum of azurin, Journal of Biological Inorganic Chemistry 2(1): 98-107.
- Dennison C., Vijgenboom E., Hagen W.R. & Canters G.W. (1996), Loop-directed mutagenesis converts amicyanin from Thiobacillus versutus into a novel blue copper protein, Journal of the American Chemical Society 118(31): 7406-7407.
- Bosch L., Vijgenboom E. & Zeef L.A.H. (1996), A revised bacterial polypeptide chain elongation cycle with a stepwise increase in restriction of unwanted ternary complexes by the ribosome, Biochemistry 35(39): 12647-12651.
- Dennison C., Vijgenboom E., Vries S. de, Oost J. van der & Canters G.W. (1995), Introduction of a Cu_A site into the blue copper protein amicyanin from thiobacillus-versutus , FEBS Letters 365(1): 92-94.
- Wezel G.P. van, Buttner M.J., Vijgenboom E., Bosch L., Hopwood D.A. & Kieser H.M. (1995), Mapping of genes involved in macromolecular-synthesis on the chromosome of Streptomyces-coelicolor A3(2), Journal of Bacteriology 177(2): 473-476.
- Shochat S., Gast P., Hoff A.J., Boender G.J., Leeuwen S. van, Liemt W.B.S. van, Vijgenboom E., Raap J., Lugtenburg J. & Groot H.J.M. de (1995), 13C MAS NMR evidence for a homogeneously ordered environment of tyrosine M210 in reaction centres of Rhodobacter sphaeroides, Spectrochimica Acta Part A : Molecular and Biomolecular Spectroscopy 51(1): 135-144.
- Wezel G.P. van, Takano E., Vijgenboom E., Bosch L. & Bibb M.J. (1995), The tuf3 gene of Streptomyces-coelicolor A3(2) encodes an inessential elongation-factor tu that is apparently subjest to positive stringent control , Microbiology 141(10): 2519-2528.
- Shochat S., Arlt T., Francke C., Gast P., Noort P.I. van, Otte S.C.M., Schelvis H.P.M., Schmidt S., Vijgenboom E., Vrieze J., Zinth W. & Hoff A.J. (1994), Spectroscopic characterization of reaction centers of the (M)Y210W mutant of the photosynthetic bacterium rhodobacter-spaeroides, Photosynthesis Research 40(1): 55-66.
- Wezel G.P. van, Woudt L.P., Vervenne R., Verdurmen M.L.A., Vijgenboom E. & Bosch L. (1994), Cloning and sequencing of the tuf genes of Streptomyces coelicolor A3(2), Biochimica et Biophysica Acta - Gene Structure and Expression 1219(2): 543-547.
- Vijgenboom E., Woudt L.P., Heinstra P.W.H., Rietveld K., Haarlem J. van, Wezel G.P. van, Shochat S. & Bosch L. (1994), Three tuf-like genes in the kirromycin producer Streptomyces ramocissimus, Microbiology 140(4): 983-998.
- Wezel G.P. van, Krab I.M., Stephen D., Bibb M.J., Vijgenboom E. & Bosch L. (1994), Transcription analysis of the stretomyces-coelicolor A3(2) ribosomal-RNA operon, Microbiology 140(12): 3357-3365.
- Kraal B., Bosch L., Mesters J.R., Graaf J.M. de, Woudt L.P., Vijgenboom E., Heinstra P.W.H., Zeef L.A.H. & Boon C. (1993), Elongation factors in protein synthesis. In: Marsh J. & Goode J. (Eds.), Ciba Foundation Symposium 176 ‐ The GTPase Superfamily: The GTPase superfamily: Ciba Foundation Symposium 176. Novartis Foundation Symposia no. 176: Ciba Foundation 1993. 28-43.
- Lippmann C., Lindschau C., Vijgenboom E., Schröder W., Bosch L. & Erdmann V.A. (1993), Prokaryotic elongation factor-tu is phosphorylated invivo , Journal of Biological Chemistry 268(1): 601-607.
- Soliveri J., Vijgenboom E., Granozzi C., Plaskitt K.A. & Chater K.F. (1993), Functional and evolutionary implications of a survey of various actinomycetes for homologs of 2 strepomyces-coelicolor sporulation genes , Microbiology 139(11): 2569-2578.
- Nilsson L., Verbeek H., Vijgenboom E., Drunen C. van, Vanet A. & Bosch L. (1992), FIS-dependent transactivation of stable RNA operons of Escherichia-coli under various growth conditions , Journal of Bacteriology 174(3): 921-929.
- Boon K., Vijgenboom E., Madsen L.V., Talens A., Kraal B. & Bosch L. (1992), Isolation and functional analysis of histidine tagged elongation-factor Tu, European Journal of Biochemistry 210(1): 177-183.
- Wezel G.P. van, Vijgenboom E. & Bosch L. (1991), A comparative study of the ribosomal RNA operons of streptomyces coelicolor A3(2) and sequence analysis of rrnA, Nucleic Acids Research 19(16): 4399-4403.
- Schlaman W.R.M., Horvath B., Vijgenboom E., Okker R.J. & Lugtenberg E.J.J. (1991), Suppression of nodulation gene expression in bacteroids of Rhizobium leguminosarum biovar viciae, Journal of Bacteriology 173(14): 4277-4287.
- Nilsson L., Vanet A., Vijgenboom E. & Bosch L. (1990), The role of FIS in trans activation of stable RNA operons of E. coli , The EMBO Journal 9(3): 727-734.
- Bosch L., Nilsson L., Vijgenboom E. & Verbeek H. (1990), FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli , Biochimica et Biophysica Acta 1050(1-3): 293-301.
- Vijgenboom E. & Bosch L. (1989), Translational frameshifts induced by mutant species of the polypeptide-chain elongation factur-tu of escherichia-coli , Journal of Biological Chemistry 264(22): 13012-13017.
- Vijgenboom E., Nilsson L. & Bosch L. (1988), The elongation factor EF-Tu from E.coli binds to the upstream activator region of the transfer tRNA rna-tufB operon , Nucleic Acids Research 16(21): 10183-10197.
- Vijgenboom E. & Bosch L. (1987), Transfer of plasmid-borne tuf mutations to the chromosome as a genetic tool for studying the functioning of EF-TuA en EF-TuB in the E. coli cell , Biochimie 69(10): 1021-1030.
- Bosch L., Kraal B., Noort J.M. van, Delft J. van, Talens A. & Vijgenboom E. (1985), Novel RNA interactions with the elongation factor EF-Tu: consequences for protein synthesis and tuf gene expression, Trends in Biochemical Sciences 10(8): 313-316.
- Vijgenboom E., Vink T., Kraal B. & Bosch L. (1985), Mutants of the elongation factor EF-Tu, a new class of nonsense suppressors , The EMBO Journal 4(4): 1049-1052.
- Meide P.H. van der, Vijgenboom E., Talens A. & Bosch L. (1983), The role of EF-Tu in the expression of tufA and tufB genes , European Journal of Biochemistry 130(2): 397-407.
- Meide P.H. van der Kastelein R.A. Vijgenboom E. Bosch L. (1983), tuf Gene dosage effects on the intracellular concentration of EF-TuB, European Journal of Biochemistry 130(2): 409-417.
- Meide P.H. van der, Vijgenboom E., Dicke M. & Bosch L. (1982), Regulation of the expression of tufA and tufB, the 2 genes coding for the elongation factor EF-Tu in eschericia coli , FEBS Letters 139(2): 325-330.
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