Publications in Scientific Journals

Nobrega FN, Lavigne R, Brouns SJJ. Revival of Phage therapy. In: Mighty Microbes. the amazing world of microorganisms. Eds. Oudega B et al. Oct 23, 2017.

This illustrated book aims to show that microorganisms are essential for our health, environment, the Earth and its sustainable future. Our chapter describes the past, present and future of bacteriophage therapy.

Jackson, SA, McKenzie RE, Fagerlund RD, Kieper SN, Fineran PC, Brouns SJJ. CRISPR-Cas: Adapting to change. Science, Apr 7, 2017.

This review paper summarises our understanding of how microbes change their CRISPR memories of invading viruses and plasmids.

Staals RH, Jackson SA, Biswas A, Brouns SJJ, Brown CM, Fineran PC.

Interference-driven spacer acquisition is dominant over naive and primed

adaptation in a native CRISPR-Cas system. Nat Commun. 2016 Oct 3;7:12853.

This paper describes that target interference is coupled to CRISPR adaptation in Type I-F CRISPR-Cas systems in Pectobacterium atrosepticum.

Künne T, Kieper SN, Bannenberg JW, Vogel AI, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJJ. Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation. Mol Cell. 2016 Aug 18.

This paper describes how CRISPR systems cleverly couple target interference to CRISPR memory update. The Cas3 nuclease fragments invader DNA into pieces of near-spacer length enriched for PAM sequences in their 3' ends to form ideal spacer precursors.

Xue C, Seetharam AS, Musharova O, Severinov K, J Brouns SJJ, Severin AJ, Sashital DG. CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Res. 2015 Dec 15;43(22):10831-47.

This paper describes how direct interference and priming are affected by spacer choice. In addition, the paper describes how CRISPR arrays avoid self-priming.

 

van der Oost J, Brouns SJJ. CRISPR sabotage. Genome Biol. 2015 Nov 9;16(1):248.

 

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015 Nov;13(11):722-36.

This paper presents the latest classification of CRISPR-Cas systems.

 

Künne T, Westra ER, Brouns SJJ. Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes. Methods Mol Biol. 2015; 1311:171-84.

 

Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C. Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol Cell. 2015 Apr 2;58(1):60-70.

This paper describes how Cascade recognizes targets using two distinct binding modes (PAM-seed dependent and PAM-seed independent) to trigger either direct interference or priming.

 

Swarts DC, Westra ER, Brouns SJJ, van der Oost. Purification and sequencing of DNA guides from prokaryotic Argonaute. Bio-protocol. 2014. 4(22).

 

Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B. Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science. 2014 Sep 19;345(6203):1473-9.

This paper presents the crystal structure of the Cascade complex from E. coli.

 

Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SAFT, Staals RHJ, Brouns SJJ. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38.

This paper reveals how direct interference and priming processes in deal with mutations in the target site.

 

Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders APL, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, Van der Oost J. DNA-guided DNA interference by a prokaryotic Argonaute. Nature. 2014 Mar 13;507(7491):258-61

This paper describes DNA-dependent DNA targeting by bacterial Argonaute proteins.

 

Künne T, Swarts DC, Brouns SJJ. Planting the seed: target recognition of short guide RNAs. Trends Microbiol. 2014 Feb;22(2):74-83.

This review highlights the importance of seed sequences in the initial interaction of small RNAs with their targets.

 

Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJJ. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet. 2013;9(9):e1003742.

This paper shows that PAM recognition by Cascade does not take place by direct interactions of the crRNA 5' handle with the PAM in target DNA.

 

Quax TEF, Wolf YI, Koehorst JJ, Wurtzel O, Van der Oost R, Ran W, Blombach F, Makarova KS, Brouns SJJ, Forster AC, Wagner EGH, Sorek R, Koonin EV, Van der Oost J. Differential translation tunes uneven production of operon-encoded proteins. Cell Rep. 2013 Sep 12;4(5):938-44.

This paper reveals how the translation of operon encoded proteins, for example Cascade, is regulated by codon usage.

 

Douillard FP, Ribbera A, Kant R, Pietilä TE, Järvinen HM, Messing M, Randazzo CL, Paulin L, Laine P, Ritari J, Caggia C, Lähteinen T, Brouns SJJ, Satokari R, von Ossowski I, Reunanen J, Palva A, de Vos WM. Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet. 2013;9(8):e1003683.

 

Ruigrok VJB, Westra ER, Brouns SJJ, Escudé C, Smidt H, Van der Oost J. A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide. Nucleic Acids Res. 2013 May 1;41(10):e111.

This paper presents a method to capture double stranded DNA by forming a triple helix.

 

Westra ER, Staals RHJ, Gort G, Høgh S, Neumann S, de la Cruz F, Fineran PC, Brouns SJJ. CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biol. 2013 May;10(5):749-61.

This paper describes the observation that the E. coli CRISPR system is able to target conjugative plasmids.

 

Biswas A, Gagnon JN, Brouns SJJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013 May;10(5):817-27.

This paper describes a great tool for CRISPR target identification and PAM prediction.

 

Westra ER, Swarts DC, Staals RHJ, Jore MM, Brouns SJJ, Van der Oost J. The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu Rev Genet. 2012;46:311-39. Review

 

Westra ER, Nilges B, van Erp PB, Van der Oost J, Dame RT, Brouns SJJ. Cascade-mediated binding and bending of negatively supercoiled DNA. RNA Biol. 2012 Sep;9(9):1134-8.

 

van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJJ, Doudna JA, Van der Oost J, Heck AJR. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Mol Cell Proteomics. 2012 Nov;11(11):1430-41.

 

Brouns SJJ. Molecular biology. A Swiss army knife of immunity. Science. 2012. Aug 17;337(6096):808-9. Commentary

This is the accompanying commentary about the seminal paper by Charpentier and Doudna describing the function and programmability of the Cas9, which has opened the door for genome editing applications.

 

Westra ER, Brouns SJJ. The rise and fall of CRISPRs: dynamics of spacer acquisition and loss. Mol Microbiol. 2012 Sep;85(6):1021-5.

 

Swarts DC, Mosterd C, van Passel MW, Brouns SJJ. CRISPR interference directs strand specific spacer acquisition. PLoS One. 2012;7(4):e35888.

This paper describes naive and primed spacer acquisition in E. coli.

 

Westra ER, van Erp PB, Künne T, Wong SP, Staals RHJ, Seegers CL, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJJ, Van der Oost J. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell. 2012 Jun 8;46(5):595-605.

This paper shows that Cas3 is recruited to target-bound Cascade complexes to degrade the DNA.

 

Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, Van der Oost J, Doudna JA, Nogales E. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature. 2011 Sep 21;477(7365):486-9.

 

Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, Van der Oost J, Brouns SJJ, Severinov K. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10098-103.

This paper reveals the existence and importance of seed sequences in crRNA.

 

Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, Van der Oost J, Koonin EV. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011 Jun;9(6):467-77.

 

Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders APL, Dickman MJ, Doudna JA, Boekema EJ, Heck AJR, Van der Oost J, Brouns SJJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May;18(5):529-36.

This paper shows how crRNA effector complexes recognize target DNA by forming R-loops. Furthermore, this paper gives some first insights into the structural topology and stoichiometry of the Cascade complex from E. coli.

 

Jore MM, Brouns SJJ, Van der Oost J. RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb Perspect Biol. 2012 Jun 1;4(6). pii: a003657. Review.

 

Al-Attar S, Westra ER, Van der Oost J, Brouns SJJ. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem. 2011 Apr;392(4):277-89. Review

 

Blombach F, Brouns SJJ, Van der Oost J. Assembling the archaeal ribosome: roles for translation-factor-related GTPases. Biochem Soc Trans. 2011 Jan;39(1):45-50.

 

de Koning B, Blombach F, Brouns SJJ, Van der Oost J. Fidelity in archaeal information processing. Archaea. 2010 Sep 5;2010. pii: 960298. Review

 

Westra ER, Pul Ü, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner EGH, Schnetz K, Van der Oost J, Wagner R, Brouns SJJ. H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol. 2010 Sep;77(6):1380-93.

Commentary by: Mojica FJM, Díez-Villaseñor C. The on–off switch of CRISPR immunity against phages in Escherichia coli, Mol Microbiol. 2010, 77, 6

 

Van der Oost J, Brouns SJJ. RNAi: prokaryotes get in on the act. Cell. 2009 Nov 25;139(5):863-5.

 

Wu H, Sun L, Blombach F, Brouns SJJ, Snijders APL, Lorenzen K, van den Heuvel RHH, Heck AJ, Fu S, Li X, Zhang XC, Rao Z, Van der Oost J. Structure of the ribosome associating GTPase HflX. Proteins. 2010 Feb 15;78(3):705-13.

 

Van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci. 2009 Aug;34(8):401-7. Review

de Koning B, Blombach F, Wu H, Brouns SJJ, Van der Oost J. Role of multiprotein bridging factor 1 in archaea: bridging the domains? Biochem Soc Trans. 2009 Feb;37(Pt1):52-7. Review

 

Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, Van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008 Aug 15;321(5891):960-4.

This paper describes the discovery of the Cascade complex and how crRNAs are formed and loaded into the Cascade complex. It also shows that Cas3 is required for phage resistance. A hypothesis is presented that CRISPR systems act on the DNA level.

Perspective in Science, Secret Weapon, Young RF. 2008. 321, 922-3

Molecular Biology Select in Cell, CRISPR insights into prokaryotic antiviral defense, Bao MZ. 2008. 135, 7

Research Highlight in Nat Struct Mol Biol, Cascade defense, Chen I, Eggleston AK, Finkelstein JM, Lall S. 2008. 15, 901

Faculty of 1000 Biology

 

Machielsen R, Leferink NG, Hendriks A, Brouns SJJ, Hennemann HG, Daussmann T, Van der Oost J. Laboratory evolution of Pyrococcus furiosus alcohol dehydrogenase to improve the production of (2S,5S)-hexanediol at moderate temperatures. Extremophiles. 2008 Jul;12(4):587-94.

 

Brouns SJJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, Van der Oost J. Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J Mol Biol. 2008 May 30;379(2):357-71.

 

Ortmann AC, Brumfield SK, Walther J, McInnerney K, Brouns SJJ, van de Werken HJG,

Bothner B, Douglas T, van de Oost J, Young MJ. Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with Sulfolobus turreted icosahedral virus. J Virol. 2008 May;82(10):4874-83.

 

Brouns SJJ, Turnbull AP, Willemen HLDM, Akerboom J, Van der Oost J. Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus. J Mol Biol. 2007 Aug 31;371(5):1249-60.

 

Wu H, Sun L, Brouns SJJ, Fu S, Akerboom J, Li X, Van der Oost J. Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Mar 1;63(Pt 3):239-41.

 

van den Heuvel RHH, van Duijn E, Mazon HFM, Synowsky SA, Lorenzen K, Versluis C, Brouns SJJ, Langridge D, Van der Oost J, Hoyes J, Heck AJR. Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal Chem. 2006 Nov 1;78(21):7473-83.

 

Brouns SJJ, Walther J, Snijders APL, van de Werken HJG, Willemen HL, Worm P, de Vos MGJ, Andersson A, Lundgren M, Mazon HFM, van den Heuvel RHH, Nilsson P, Salmon L, de Vos WM, Wright PC, Bernander R, Van der Oost J. Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J Biol Chem. 2006 Sep 15;281(37):27378-88.

This paper reveals a pentose sugar degradation pathway in hyperthermophilic archaea.

Faculty of 1000 Biology

 

Berrisford JM, Hounslow AM, Akerboom J, Hagen WR, Brouns SJJ, Van der Oost J, Murray IA, Michael Blackburn G, Waltho JP, Rice DW, Baker PJ. Evidence supporting a cis-enediol-based mechanism for Pyrococcus furiosus phosphoglucose isomerase. J Mol Biol. 2006 May 19;358(5):1353-66.

 

Brouns SJJ, Smits N, Wu H, Snijders APL, Wright PC, de Vos WM, Van der Oost J. Identification of a novel alpha-galactosidase from the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol. 2006 Apr;188(7):2392-9.

 

Snijders APL, Walther J, Peter S, Kinnman I, de Vos MGJ, van de Werken HJG, Brouns SJJ, Van der Oost J, Wright PC. Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis. Proteomics. 2006 Mar;6(5):1518-29.

 

Gödde C, Sahm K, Brouns SJJ, Kluskens LD, Van der Oost J, de Vos WM, Antranikian G. Cloning and expression of islandisin, a new thermostable subtilisin from Fervidobacterium islandicum, in Escherichia coli. Appl Environ Microbiol. 2005 Jul;71(7):3951-8.

 

Brouns SJJ, Wu H, Akerboom J, Turnbull AP, de Vos WM, Van der Oost J. Engineering a selectable marker for hyperthermophiles. J Biol Chem. 2005 Mar 25;280(12):11422-31.

This paper presents a directed evolution and in vivo selection approach to create a thermostable antibiotic resistance marker for (hyper) thermophilic bacteria and archaea.

Faculty of 1000 Biology

 

Berrisford JM, Akerboom J, Brouns SJJ, Sedelnikova SE, Turnbull AP, Van der Oost J, Salmon L, Hardré R, Murray IA, Blackburn GM, Rice DW, Baker PJ. The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis. J Mol Biol. 2004 Oct 22;343(3):649-57.

 

Kaper T, Brouns SJJ, Geerling AC, De Vos WM, Van der Oost J. DNA family shuffling of hyperthermostable beta-glycosidases. Biochem J. 2002 Dec 1;368(Pt2):461-70.


Publications in Books

Künne T, Westra ER, Brouns SJJ. Electrophoretic mobility shift assay of DNA and CRISPR-Cas ribonucleoprotein complexes. In Lundgren M, Fineran P, Charpentier E (ed.) In: Methods in Molecular Biology. Springer Verlag, 2015.

 

Staals RHJ, Brouns SJJ. Distribution and mechanism of Type I CRISPR-Cas systems. In: Barrangou R, Van der Oost J (ed.) CRISPR-Cas Immune systems, Springer Verlag, 2013. 145-69. Review

 

Westra ER, Jore MM, Al-Attar S, Brouns SJJ, Van der Oost J. Small RNAs in Bacteria. Encyclopedia of Biological Chemistry 2nd Edition. Elsevier. 2013. 249-55. Review

Westra ER, Van der Oost J, Brouns SJJ (2011) McGraw-Hill Encyclopedia of Science and Technology 2010, 10th ed. 63-6. Review

 

Jore MM, Brouns SJJ, Van der Oost J RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. In: Atkins JF, Gesteland RF and Cech TR (ed.), RNA Worlds: from life's origins to diversity in gene regulation. Cold Spring Harbor Laboratory Press. 2010. 231-42. Review

 

Van de Werken HJGG, Brouns SJJ, and Van der Oost J. Pentose metabolism in Archaea. In: Blum P (ed.) Archaea: new models for prokaryotic biology. Horizon Scientific Press. 2008. 71-94. Review

 

Brouns SJJ, Ettema TJG, Stedman KM, Walther J, Smidt H, Snijders APL, Young M, Bernander R, Wright PC, Siebers B, Van der Oost J. The hyperthermophilic archaeon Sulfolobus solfataricus: from exploration to exploitation. In: Inskeep WP and McDermott TR (ed.), Geothermal biology and geochemistry in Yellowstone national park. Thermal Biology Institute, Montana State University, Bozeman, United States. 2005. 261-76. Review