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Dr Edze Westra

Dr Edze Westra

Associate Professor / NERC Independent Research Fellow

 Not Known

 Environment and Sustainability Institute 2.34

 

Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK

Overview

I am a NERC funded Independent Research Fellow (Associate Professor), working on the evolutionary ecology of host-parasite interactions. My lab studies how ecological variables drive the evolution of various immune strategies in bacteria, with an emphasis on CRISPR-Cas adaptive immune systems, and examines their coevolutionary consequences. Bacteria encode lots of different immune mechanisms, and their molecular basis has been studied in great detail, which makes them an ideal model system to study more generally how ecology drives the evolution of different defenses. These bacterial defense mechanisms include CRISPR-Cas, which I studied at the molecular level during the start of my scientific career, surface modification, restriction modification, abortive infection and prokaryotic Argonaute.

I am a member of the Environment and Sustainability Institute and the Biosciences department of the College of Life and Environmental Sciences.

View my lab website here 

Qualifications

2016 Heineken Young Scientist Award for Biochemistry and Biophysics (awarded by the KNAW, the Dutch royal society for science)
2014 Westerdijk Award for best Ph.D. research in Microbiology in the Netherlands (awarded by the KNVM, the Dutch society for microbiology)
2013 Westenbrink Award for best Ph.D. research in Biochemistry in the Netherlands (awarded by the NVBMB, the Dutch society for biochemistry and molecular biology)
2013 PhD Microbiology (University of Wageningen)
2007 MSc Molecular Life Sciences (University of Wageningen)
2006 BSc Molecular Life Sciences (University of Wageningen)

Career

2017 Associate Professor / NERC Independent Research Fellow
2016 Senior Lecturer / NERC Independent Research Fellow
2015 Lecturer / NERC Independent Research Fellow
2013 Marie-Curie postdoctoral Research Fellow, University of Exeter
2013 Postdoctoral Research Fellow, University of Wageningen

Links

Research

Research interests

  • Evolutionary ecology of host-parasite interactions
  • Coevolution of bacteria and phage
  • Evolution of parasite host range and virulence

Research projects

My current work focuses on the evolution of different immune strategies in bacteria in response to phage, and the coevolutionary consequences. I am particularly interested in the way parasites drive diversity in host populations and the impact of various immune mechanisms on the evolution of phage life history traits.

Publications

Key publications | Publications by category | Publications by year

Publications by category


Journal articles

Pursey E, Sünderhauf D, Gaze WH, Westra ER, van Houte S (In Press). CRISPR-Cas antimicrobials: Challenges and future prospects. PLoS Pathog, 14(6). Author URL.
van Houte S, Buckling A, Westra ER (In Press). Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev, 80(3), 745-763. Abstract.  Author URL.  Full text.
Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL (In Press). Prophages mediate defense against phage infection through diverse mechanisms. ISME J, 10(12), 2854-2866. Abstract.  Author URL.
Landsberger M, Gandon S, Meaden S, Rollie C, Chevallereau A, Chabas H, Buckling A, Westra ER, van Houte S (2018). Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity. Cell, 174(4), 908-916.e12. Abstract.  Author URL.  Full text.
Morley D, Broniewski JM, Westra ER, Buckling A, van Houte S (2017). Host diversity limits the evolution of parasite local adaptation. Mol Ecol, 26(7), 1756-1763. Abstract.  Author URL.
Westra ER, Sünderhauf D, Landsberger M, Buckling A (2017). Mechanisms and consequences of diversity-generating immune strategies. Nat Rev Immunol, 17(11), 719-728. Abstract.  Author URL.  Full text.
Westra ER, Dowling AJ, Broniewski JM, Van Houte S (2016). Evolution and Ecology of CRISPR. Annual Review of Ecology, Evolution, and Systematics, 47, 307-331. Abstract.
Chabas H, van Houte S, Høyland-Kroghsbo NM, Buckling A, Westra ER (2016). Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies. Proc Biol Sci, 283(1837). Abstract.  Author URL.
Høyland-Kroghsbo NM, Paczkowski J, Mukherjee S, Broniewski J, Westra E, Bondy-Denomy J, Bassler BL (2016). Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proceedings of the National Academy of Sciences, 114(1), 131-135.
van Houte S, Ekroth AKE, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, et al (2016). The diversity-generating benefits of a prokaryotic adaptive immune system. Nature, 532(7599), 385-388. Abstract.  Author URL.  Full text.
Swarts DC, Koehorst JJ, Westra ER, Schaap PJ, van der Oost J (2015). Effects of Argonaute on Gene Expression in Thermus thermophilus. PLoS One, 10(4). Abstract.  Author URL.  Full text.
Künne T, Westra ER, Brouns SJJ (2015). Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes. Methods Mol Biol, 1311, 171-184. Abstract.  Author URL.
Westra ER, Van houte S, Oyesiku-Blakemore S, Makin B, Broniewski JM, Best A, Bondy-Denomy J, Davidson A, Boots M, Buckling A, et al (2015). Parasite exposure drives selective evolution of constitutive versus inducible defense. Current Biology, 25(8), 1043-1049. Abstract.
Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C (2015). Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol Cell, 58(1), 60-70. Abstract.  Author URL.
Westra ER, Buckling A, Fineran PC (2014). CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol, 12(5), 317-326. Abstract.  Author URL.
Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, et al (2014). DNA-guided DNA interference by a prokaryotic Argonaute. Nature, 507(7491), 258-261. Abstract.  Author URL.
Jackson RN, Golden SM, van Erp PBG, Carter J, Westra ER, Brouns SJJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B, et al (2014). Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science, 345(6203), 1473-1479. Abstract.  Author URL.
van der Oost J, Westra ER, Jackson RN, Wiedenheft B (2014). Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol, 12(7), 479-492. Abstract.  Author URL.
Ruigrok VJB, Westra ER, Brouns SJJ, Escudé C, Smidt H, van der Oost J (2013). A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide. Nucleic Acids Res, 41(10). Abstract.  Author URL.  Full text.
Westra ER, Staals RHJ, Gort G, Høgh S, Neumann S, de la Cruz F, Fineran PC, Brouns SJJ (2013). CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biol, 10(5), 749-761. Abstract.  Author URL.
Ruigrok VJB, Westra ER, Brouns SJJ, Escudé C, Smidt H, Van Der Oost J (2013). The role of DNA bending in type IIA topoisomerase function. Nucleic Acids Research, 41(10). Abstract.
Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJJ (2013). Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet, 9(9). Abstract.  Author URL.  Full text.
Westra ER, van Erp PBG, Künne T, Wong SP, Staals RHJ, Seegers CLC, Bollen S, Jore MM, Semenova E, Severinov K, et al (2012). CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell, 46(5), 595-605. Abstract.  Author URL.
Westra ER, Nilges B, van Erp PBG, van der Oost J, Dame RT, Brouns SJJ (2012). Cascade-mediated binding and bending of negatively supercoiled DNA. RNA Biol, 9(9), 1134-1138. Abstract.  Author URL.
van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJJ, Doudna JA, van der Oost J, et al (2012). 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, 11(11), 1430-1441. Abstract.  Author URL.
Westra ER, Swarts DC, Staals RHJ, Jore MM, Brouns SJJ, van der Oost J (2012). The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu Rev Genet, 46, 311-339. Abstract.  Author URL.
Westra ER, Brouns SJJ (2012). The rise and fall of CRISPRs--dynamics of spacer acquisition and loss. Mol Microbiol, 85(6), 1021-1025. Abstract.  Author URL.
Al-Attar S, Westra ER, van der Oost J, Brouns SJJ (2011). Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem, 392(4), 277-289. Abstract.  Author URL.
Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJJ, Severinov K (2011). Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A, 108(25), 10098-10103. Abstract.  Author URL.
Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, et al (2011). Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol, 18(5), 529-536. Abstract.  Author URL.
Abu-Dayyeh I, Hassani K, Westra ER, Mottram JC, Olivier M (2010). Comparative study of the ability of Leishmania mexicana promastigotes and amastigotes to alter macrophage signaling and functions. Infect Immun, 78(6), 2438-2445. Abstract.  Author URL.
Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, et al (2010). H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol, 77(6), 1380-1393. Abstract.  Author URL.
van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJJ (2009). CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci, 34(8), 401-407. Abstract.  Author URL.
Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, van der Oost J, et al (2008). Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 321(5891), 960-964. Abstract.  Author URL.

Chapters

Arslan Z, Westra ER, Wagner R, Pul Ü (2013). Regulation of CRISPR-based immune responses. In  (Ed) CRISPR-Cas Systems: RNA-Mediated Adaptive Immunity in Bacteria and Archaea, 93-113.  Abstract.

Conferences

Blosser TR, Westra ER, van der Oost J, Dekker C, Brouns SJJ, Joo C (2013). Defense against viral attack: single-molecule view on a bacterial adaptive immune system.  Author URL.

Publications by year


In Press

Pursey E, Sünderhauf D, Gaze WH, Westra ER, van Houte S (In Press). CRISPR-Cas antimicrobials: Challenges and future prospects. PLoS Pathog, 14(6). Author URL.
van Houte S, Buckling A, Westra ER (In Press). Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev, 80(3), 745-763. Abstract.  Author URL.  Full text.
Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL (In Press). Prophages mediate defense against phage infection through diverse mechanisms. ISME J, 10(12), 2854-2866. Abstract.  Author URL.

2018

Landsberger M, Gandon S, Meaden S, Rollie C, Chevallereau A, Chabas H, Buckling A, Westra ER, van Houte S (2018). Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity. Cell, 174(4), 908-916.e12. Abstract.  Author URL.  Full text.

2017

Morley D, Broniewski JM, Westra ER, Buckling A, van Houte S (2017). Host diversity limits the evolution of parasite local adaptation. Mol Ecol, 26(7), 1756-1763. Abstract.  Author URL.
Westra ER, Sünderhauf D, Landsberger M, Buckling A (2017). Mechanisms and consequences of diversity-generating immune strategies. Nat Rev Immunol, 17(11), 719-728. Abstract.  Author URL.  Full text.

2016

Westra ER, Dowling AJ, Broniewski JM, Van Houte S (2016). Evolution and Ecology of CRISPR. Annual Review of Ecology, Evolution, and Systematics, 47, 307-331. Abstract.
Chabas H, van Houte S, Høyland-Kroghsbo NM, Buckling A, Westra ER (2016). Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies. Proc Biol Sci, 283(1837). Abstract.  Author URL.
Høyland-Kroghsbo NM, Paczkowski J, Mukherjee S, Broniewski J, Westra E, Bondy-Denomy J, Bassler BL (2016). Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proceedings of the National Academy of Sciences, 114(1), 131-135.
van Houte S, Ekroth AKE, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, et al (2016). The diversity-generating benefits of a prokaryotic adaptive immune system. Nature, 532(7599), 385-388. Abstract.  Author URL.  Full text.

2015

Swarts DC, Koehorst JJ, Westra ER, Schaap PJ, van der Oost J (2015). Effects of Argonaute on Gene Expression in Thermus thermophilus. PLoS One, 10(4). Abstract.  Author URL.  Full text.
Künne T, Westra ER, Brouns SJJ (2015). Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes. Methods Mol Biol, 1311, 171-184. Abstract.  Author URL.
Westra ER, Van houte S, Oyesiku-Blakemore S, Makin B, Broniewski JM, Best A, Bondy-Denomy J, Davidson A, Boots M, Buckling A, et al (2015). Parasite exposure drives selective evolution of constitutive versus inducible defense. Current Biology, 25(8), 1043-1049. Abstract.
Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C (2015). Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol Cell, 58(1), 60-70. Abstract.  Author URL.

2014

Westra ER, Buckling A, Fineran PC (2014). CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol, 12(5), 317-326. Abstract.  Author URL.
Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, et al (2014). DNA-guided DNA interference by a prokaryotic Argonaute. Nature, 507(7491), 258-261. Abstract.  Author URL.
Jackson RN, Golden SM, van Erp PBG, Carter J, Westra ER, Brouns SJJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B, et al (2014). Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science, 345(6203), 1473-1479. Abstract.  Author URL.
van der Oost J, Westra ER, Jackson RN, Wiedenheft B (2014). Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol, 12(7), 479-492. Abstract.  Author URL.

2013

Ruigrok VJB, Westra ER, Brouns SJJ, Escudé C, Smidt H, van der Oost J (2013). A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide. Nucleic Acids Res, 41(10). Abstract.  Author URL.  Full text.
Westra ER, Staals RHJ, Gort G, Høgh S, Neumann S, de la Cruz F, Fineran PC, Brouns SJJ (2013). CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biol, 10(5), 749-761. Abstract.  Author URL.
Blosser TR, Westra ER, van der Oost J, Dekker C, Brouns SJJ, Joo C (2013). Defense against viral attack: single-molecule view on a bacterial adaptive immune system.  Author URL.
Arslan Z, Westra ER, Wagner R, Pul Ü (2013). Regulation of CRISPR-based immune responses. In  (Ed) CRISPR-Cas Systems: RNA-Mediated Adaptive Immunity in Bacteria and Archaea, 93-113.  Abstract.
Ruigrok VJB, Westra ER, Brouns SJJ, Escudé C, Smidt H, Van Der Oost J (2013). The role of DNA bending in type IIA topoisomerase function. Nucleic Acids Research, 41(10). Abstract.
Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJJ (2013). Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet, 9(9). Abstract.  Author URL.  Full text.

2012

Westra ER, van Erp PBG, Künne T, Wong SP, Staals RHJ, Seegers CLC, Bollen S, Jore MM, Semenova E, Severinov K, et al (2012). CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell, 46(5), 595-605. Abstract.  Author URL.
Westra ER, Nilges B, van Erp PBG, van der Oost J, Dame RT, Brouns SJJ (2012). Cascade-mediated binding and bending of negatively supercoiled DNA. RNA Biol, 9(9), 1134-1138. Abstract.  Author URL.
van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJJ, Doudna JA, van der Oost J, et al (2012). 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, 11(11), 1430-1441. Abstract.  Author URL.
Westra ER, Swarts DC, Staals RHJ, Jore MM, Brouns SJJ, van der Oost J (2012). The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu Rev Genet, 46, 311-339. Abstract.  Author URL.
Westra ER, Brouns SJJ (2012). The rise and fall of CRISPRs--dynamics of spacer acquisition and loss. Mol Microbiol, 85(6), 1021-1025. Abstract.  Author URL.

2011

Al-Attar S, Westra ER, van der Oost J, Brouns SJJ (2011). Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem, 392(4), 277-289. Abstract.  Author URL.
Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJJ, Severinov K (2011). Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A, 108(25), 10098-10103. Abstract.  Author URL.
Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, et al (2011). Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol, 18(5), 529-536. Abstract.  Author URL.

2010

Abu-Dayyeh I, Hassani K, Westra ER, Mottram JC, Olivier M (2010). Comparative study of the ability of Leishmania mexicana promastigotes and amastigotes to alter macrophage signaling and functions. Infect Immun, 78(6), 2438-2445. Abstract.  Author URL.
Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, et al (2010). H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol, 77(6), 1380-1393. Abstract.  Author URL.

2009

van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJJ (2009). CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci, 34(8), 401-407. Abstract.  Author URL.

2008

Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, van der Oost J, et al (2008). Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 321(5891), 960-964. Abstract.  Author URL.

Edze_Westra Details from cache as at 2018-12-14 04:20:39

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