Publication list

  1. Paredes-Barrada, M., Mathissen, A., van der Molen, R.A., Jiménez-Huesa, P.J., Eduardo Polano, M, Donati, S., Abele, M., Ludwig, C., van Kranenburg, R., Claassens, N.J. 2025. Awakening of the RuMP cycle for partial methylotrophy in the thermophile Parageobacilllus thermoglucosidasius. Metab. Eng. 91:145-157.
  2. Lensch, A., Lindfors,, H.A., Duwenig, E.,, Fleischmann, T., Hjort, C., Kärenlampi, S.O., McMurtry, L., Melton, E.D., Rørdam Andersen, M., Skinner, R., Wyss, M., van Kranenburg, R. 2024. Safety aspects of microorganisms deliberately released into the environment. EFB Bioecon. J. 4:100061
  3. Paredes-Barrada, M., Kopsiaftis, P., Claassens, N.J., van Kranenburg, R. 2024. Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory. Metab. Eng. 83:39-51.
  4. Trasanidou, D., Potocnik, A., Barendse, P., Mohanraju, P., Bouzetos, E., Karpouzis, E., Desmet, A., van Kranenburg, R., van der Oost, J., Staals, R.H.J., Mougiakos, I. 2023. Characterization of the AcrIIC1 anti-CRISPR protein for Cas9-based genome engineering. Commun. Biol. 6:1042.
  5. Bruinsma, L., Martin-Pascual, M., Kurnia, K., Tack, M., Hendriks, S., van Kranenburg, R., Dos Santos, V.A.P.M. 2023. Increasing cellular fitness and product yields in Pseudomonas putida through an engineered phosphoketolase shunt. Microb. Cell. Fact. 22:14.
  6. Liang, J., van Kranenburg, R., Bolhuis, A., Leak, D.J. 2022. Removing carbon catabolite repression in Parageobacillus thermoglucosidasius DSM 2542. Front. Microbiol. 13:985465.
  7. Ganguly, J., Martin-Pascual, M., Montiel Ganzález, D., Bulut, A., Vermeulen, Bb., Tjalma, I., Vidaki, A., van Kranenburg, R. 2022. Breaking the restriction barriers and applying CRISPRi as a silencing tool in Pseudoclostridium thermosuccinogenes. Microorganisms 10:698.
  8. Liang, J., Roberts, A., van Kranenburg, R., Bolhuis, A., Leak, D.J. 2022. Relaxed control of sugar utilization in Parageobacillus thermoglucosidasius DSM 2542. Microb. Res. 256:126957.
  9. Asin-Garcia, E., Martin-Pascual, M., Garcia-Morales, van Kranenburg, R., Martins Dos Santos, V.A.P. 2021. ReScribe: An unrestrained tool combining multiplex recombineering and minimal-PAM ScCas9 for genome recoding Pseudomonas putida. ACS Synth. Biol. 10:2672-2688.
  10. Martin-Pascual, M., Batianis, C., Bruinsma, L., Asin-Garcia, E., Garcia-Morales, L., Weusthuis, R.A., van Kranenburg, R., Martins dos Santos, V.A.P. 2021. A navigation guide of synthetic biology tools for Pseudomonas putida. Biotechnol. Adv. 49:107732.
  11. Mohanraju, P., Mougiakos, I., Albers, J., Mabuchi, M., Fuchs, R.T., Curcuru, J.L., van Kranenburg, R., Robb, G.B., van der Oost, J. 2021. Development of a Cas12a-based genome editing tool for moderate thermophiles. CRISPR J. 4:82-91.
  12. Koendjbiharie, J.G., van Kranenburg, R., Kengen, S.W.M. 2021. The PEP-pyruvate-oxaloacetate node: Variation at the heart of metabolism. FEMS Microbiol. Rev. 45:fuaa061.
  13. Koendjbiharie, J.G., Post, W.B., Palmer, M.M., van Kranenburg, R. 2020. Effects of CO2 limitation on the metabolism of Pseudoclostridium thermosuccinogenes. BMC Microbiol. 20:149
  14. Ganguly, J., Tempelaars, M., Abee, T., van Kranenburg, R. 2020. Characterization of sporulation dynamics of Pseudoclostridium thermosuccinogenes using flow cytometry. Anaerobe 63:102208
  15. Koendjbiharie, J.G., Hon, S., Pabst, M., Hooftman, R., Stevenson, D.M., Cui, J. Amador-Noguez, D., Lynd, L.R., Olson, D.G., van Kranenburg, R. 2020. The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase. J. Biol. Chem. 295:1867-1878.
  16. Ganguly, J., Martin-Pascual, M., van Kranenburg, R. 2020. CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313. Microb. Biotechnol. 13:33-349.
  17. Koendjbiharie, J.G., Wevers, K., van Kranenburg, R. 2019. Assessing cofactor usage in Pseudoclostridium thermosuccinogenes via heterologous expression of central metabolic enzymes. Front. Microbiol. 10:1162.
  18. Daas, M.J.A., Nijsse, B., van de Weijer, A.H.P., Groenendaal, B.W.A.J., Janssen, F., van der Oost, J., van Kranenburg, R. 2018. Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes. BMC Biotechnol. 18:42.
  19. Koendjbiharie, J.G., Wiersma, K., van Kranenburg, R. 2018. Investigating the central metabolism of Clostridium thermosuccinogenes. Appl. Environ. Microbiol. 84:e00363-18.
  20. Mougiakos, I., Bosma, E.F., Ganguly, J., van der Oost, J., van Kranenburg, R. 2018. Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects. Curr. Opin. Microbiol. 50:146-157.
  21. Frenzel, E., Legebeke, J., van Stralen, A., van Kranenburg, R., Kuipers, O.P. 2018. In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria. Biotechnol. Biofuels 11:8
  22. Daas, M.J.A., Vriesendorp, B., van de Weijer, A.H.P., van der Oost, J., van Kranenburg, R. 2018. Complete genome sequence of Geobacillus thermodenitrificans T12, a potential host for biotechnological applications. Curr. Microbiol. 75:49-56.
  23. Mougiakos, I., Mohanraju, P., Bosma, E.F., Vrouwe, V., Finger Bou, M., Naduthodi, M.I.S., Gussak, A., Brinkman, R.B.L., van Kranenburg, R., van der Oost, J. 2017. Characterizing a thermostable Cas9 for bacterial genome editing and silencing. Nat. Commun. 8:1647.
  24. Daas, M.J.A., Martínez, P.M., van de Weijer, A.H.P., van der Oost, J., de Vos, W.M., Kabel, M.A., van Kranenburg, R. 2017. Biochemical characterization of the xylan hydrolysis profile of the extracellular endo-xylanase from Geobacillus thermodenitrificans T12. BMC Biotechnol. 17:44.
  25. Mougiakos, I., Bosma, E.F., Weenink, K., Vossen, E., Goijvaerts, K., van der Oost, J., van Kranenburg, R. 2017. Efficient genome editing of a facultative thermophile using mesophilic spCas9. ACS Synth. Biol. 6:849-861.
  26. Daas, M.J.A., van de Weijer, A.H.P., de Vos, W.M., van der Oost, J., van Kranenburg, R. 2016. Isolation of a genetically accessible thermophilic xylan degrading bacterium from compost. Biotechnol. Biofuels. 9:210.
  27. Bosma, E.F., Koehorst, J.J., van Hijum, S.A.F.T., Renckens, B., Vriesendorp, B., van de Weijer, A.H.P., Schaap, P.J., de Vos, W.M., van der Oost, J., van Kranenburg, R. 2016. Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T. Standards Genomic Sci. 11:52.
  28. Mougiakos, I., Bosma, E.F., de Vos, W.M., van Kranenburg, R., van der Oost, J. 2016. Next generation prokaryotic engineering: the CRISPR-Cas toolkit. Trends Biotechnol. 34:575-587.
  29. Bosma, E.F., van de Weijer, A.H., van der Vlist, L., de Vos, W.M., van der Oost, J., van Kranenburg, R. 2015. Establishment of markerless gene deletion tools in thermophilic Bacillus smithii and construction of multiple mutant strains. Microb. Cell, Fact. 14:99.
  30. Bosma, E.F., van de Weijer, A.H., Daas, M.J., van der Oost, J., van Kranenburg, R. 2015. Isolation and screening of thermophilic bacilli from compost for electrotransformation and fermentation: Characterization of Bacillus smithii ET 138 as a new biocatalyst. Appl. Environ. Microbiol. 81:1874-1883.
  31. Bosma, E.F., van der Oost, J., de Vos, W.M., van Kranenburg, R. 2013. Sustainable production of bio-based chemicals by extremophiles. Curr. Biotechnol. 2:360-379.
  32. Kovács, Á.T., Eckhardt, T.H., van Hartskamp, M., van Kranenburg, R., Kuipers, O.P. 2013. Functional analysis of the ComK protein in Bacillus coagulans. PLoS One 8:e53471.
  33. Remus, D.M., van Kranenburg, R., van Swam, I.I., Taverne, N., Bongers, R.S., Wels, M., Wells, J.M., Bron, P.A., Kleerebezem, M. 2012. Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signalling. Microb. Cell Fact. 11:149.
  34. Kovács, Á.T., van Hartskamp, M., Kuipers, O.P., van Kranenburg, R. 2010. Genetic tool development for a new host for biotechnology, the thermotolerant bacterium Bacillus coagulans. Appl. Environ. Microbiol. 76:4085-4088.
  35. Mols, M., van Kranenburg, R., van Melis, C.C., Moezelaar, R., Abee, T. 2010. Analysis of acid-stressed Bacillus cereus reveals a major oxidative response and inactivation-associated radical formation. Environ. Microbiol. 873-885.
  36. Mols, M., van Kranenburg, R., Tempelaars, M.H., van Schaik, W., Moezelaar, R., Abee, T. 2010. Comparative analysis of transcriptional and physiological responses of Bacillus cereus to organic and inorganic acid shocks. Int. J. Food Microbiol. 137:13-21.
  37. Siezen, R.J., Renckens, B., van Swam, I., Peters, S., van Kranenburg, R., Kleerebezem, M., de Vos, W.M. 2005. Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl. Environ. Microbiol. 71:8371-8382.
  38. van Kranenburg, R., Golic, N., Bongers, R., Leer, R.J., de Vos, W.M., Siezen, R.J., Kleerebezem, M. 2005. Functional analysis of three plasmids from Lactobacillus plantarum. Appl. Environ. Microbiol. 71:1223-1230.
  39. Golic, N., Schliekelmann, M., Fernández, M., Kleerebezem, M., van Kranenburg, R. 2005. Molecular characterization of the CmbR activator-binding site in the metC–cysK promoter region in Lactococcus lactis. Microbiology 151:439-446.
  40. Kleerebezem, M., Boekhorst, J., van Kranenburg, R., Molenaar, D., Kuipers, O.P., Leer, R., Tarchini, R., Peters, S.A., Sandbrink, H.M., Fiers, M.W., Stiekema, W., Lankhorst, R.M., Bron, P.A., Hoffer, S.M., Nierop Groot, M., Kerkhoven, R., de Vries, M., Ursing, B., de Vos, W.M., Siezen, R.J. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA. 100:1990-1995.
  41. Pastar, I., Tonic, I., Golic, N., Kojic, M., van Kranenburg, R., Kleerebezem, M., Topisirovic, L., Jovanovic, G. 2003. Identification and genetic characterization of a novel proteinase, PrtR, from the human isolate Lactobacillus rhamnosus BGT10. Appl. Environ. Microbiol. 69:5802-5811.
  42. Boels, I.C., van Kranenburg, R., Kanning, M.W., Chong, B.F., de Vos, W.M., Kleerebezem, M. 2003. Increased exopolysaccharide production in Lactococcus lactis due to increased levels of expression of the NIZO B40 eps gene cluster. Appl. Environ. Microbiol. 69:5029-5031.
  43. Rijnen, L., Yvon, M., van Kranenburg, R., Courtin, P., Verheul, A., Chambellon, E., Smit, G. 2003. Lactococcal aminotransferases AraT and BcaT are key enzymes for the formation of aroma compounds from amino acids in cheese. Int. Dairy J. 13:805-812.
  44. van Kranenburg, R., Kleerebezem, M., van Hylckama Vlieg, J., Ursing, B.M., Boekhorst, J., Smit, B.A., Ayad, E.H.E., Smit, G., Siezen, R.J. 2002. Flavour formation from amino acids by lactic acid bacteria: predictions from genome sequence analysis. Int. Dairy J. 12:111-121.
  45. Fernández, M., Kleerebezem, M., Kuipers, O.P., Siezen, R.J., van Kranenburg, R. 2002. Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis. J. Bacteriol. 184:82-90.
  46. Boels, I., van Kranenburg, R., Hugenholtz, J., Kleerebezem, M., de Vos, W.M. 2001. Sugar catabolism and its impact on the biosynthesis and engineering of exopolysaccharide production in lactic acid bacteria. Int. Dairy J. 11:723-732.
  47. Smit, G., Verheul, A., van Kranenburg, R., Ayad, E., Siezen, R., Engels, W. 2000. Cheese flavour development by enzymatic conversions of peptides and amino acids. Food Res. Int. 33:153-160.
  48. van Kranenburg, R., Kleerebezem, M., de Vos, W.M. 2000. Nucleotide sequence analysis of the lactococcal EPS plasmid pNZ4000. Plasmid 43:130-136.
  49. Fernández, M., van Doesburg, W., Rutten, G.A., Marugg, J.D., Alting, A.C., van Kranenburg, R., Kuipers, O.P. 1999. Molecular and functional analyses of the metC gene of Lactococcus lactis, encoding cystathionine g-lyase. Appl. Environ. Microbiol. 66:42-48.
  50. Kleerebezem, M., van Kranenburg, R., Tuinier, R., Boels, I.C., Zoon, P., Looijesteijn, E., Hugenholtz, J., de Vos, W.M. 1999. Exopolysaccharides produced by Lactococcus lactis: from genetic engineering to improved rheological properties? Antonie van Leeuwenhoek 76:357-365.
  51. van Kranenburg, R., Vos, H.R., van Swam, I.I., Kleerebezem, M., de Vos, W.M. 1999. Functional analysis of glycosyltransferase genes from Lactococcus lactis and other gram-positive cocci: complementation, expression, and diversity. J. Bacteriol. 181:6347-6353.
  52. van Kranenburg, R., Boels, I.C., Kleerebezem, M., de Vos, W.M. 1999. Genetics and engineering of microbial exopolysaccharides for food: approaches for the production of existing and novel polysaccharides. Curr. Opin. Biotechnol. 10:498-504.
  53. van Kranenburg, R., van Swam, I.I., Marugg, J.D., Kleerebezem, M., de Vos, W.M. 1999. Exopolysaccharide biosynthesis in Lactococcus lactis NIZO B40: functional analysis of the glycosyltransferase genes involved in synthesis of the polysaccharide backbone. J. Bacteriol. 181:338-340.
  54. van Kranenburg, R., de Vos, W.M. 1998. Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in Lactococcus lactis. J. Bacteriol 180:5285-5290.
  55. de Vos, W.M., Hols, P., van Kranenburg, R., Luesink, E.J., Kuipers, O.P., van der Oost, J., Kleerebezem, M., Hugenholtz, J. 1998. Making more of milk sugar by engineering lactic acid bacteria. Int. Dairy J. 8:227-233.
  56. van Kranenburg, R., Marugg, J.D., van Swam, I.I., Willem, N.J., de Vos, W.M. 1997. Molecular characterization of the plasmid-encoded eps gene cluster essential for exopolysaccharide biosynthesis in Lactococcus lactis. Mol. Microbiol. 24:387-397.
  57. Eggen, R.I., van Kranenburg, R., Vriesema, A.J., Geerling, A.C., Verhagen, M.F., Hagen, W.R., de Vos, W.M. 1996. Carbon monoxide dehydrogenase from Methanosarcina frisia Gö1. Characterization of the enzyme and the regulated expression of the two operon-like cdh gene clusters. J. Biol. Chem. 271:14256-14263.
  58. Marugg, J.D., van Kranenburg, R., Laverman, P., Rutten, G.A., de Vos, W.M. 1996. Identical transcriptional control of the divergently transcribed prtP and prtM genes that are required for proteinase production in Lactococcus lactis SK11. J. Bacteriol. 178:1525-1531.
  59. Marugg, J.D., Meijer, W., van Kranenburg, R., Laverman, P., Bruinenberg, P.G., de Vos, W.M. 1995. Medium-dependent regulation of proteinase gene expression in Lactococcus lactis: control of transcription initiation by specific dipeptides. J. Bacteriol. 177:2982-2989.