Rodent malaria parasites : genome organization & comparative genomics

Rodent malaria parasites : genome organization & comparative

genomics

Kooij, Taco W.A.

Citation

Kooij, T. W. A. (2006, March 9). Rodent malaria parasites : genome organization &

comparative genomics. Retrieved from https://hdl.handle.net/1887/4326

Version:

Corrected Publisher’s Version

License:

Licence agreement concerning inclusion of doctoral thesis in the

_{Institutional Repository of the University of Leiden}

Downloaded from:

https://hdl.handle.net/1887/4326

Rodent Malaria Parasites:

Genom e Organization & Com parative Genom ics

Rodent Malaria Parasites: Genome Organization & Comparative Genomics Kooij, Taco W ilhelmus Antonius

Thesis Leiden University, with summary in Dutch

ISBN-10: 90-9020399-0 ISBN-13: 978-90-9020399-7

Rodent Malaria Parasites:

Genome Organization & Comparative Genomics

Proefschrift

ter verkrijging van

de graad van Doctor aan de Universiteit Leiden,

op gezag van de Rector Magnificus Dr. D.D. Breimer,

hoogleraar in de faculteit der W iskunde en

Natuurwetenschappen en die der Geneeskunde,

volgens besluit van het College voor Promoties

te verdedigen op donderdag 9 maart 2006

klokke 15.15 uur

door

Taco Wilhelmus Antonius Kooij

Promotiecommissie

Promotor: Prof. dr. A.P. Waters

Referent: Prof. dr. J.H. Adams

University of Notre Dame, IN, USA

Overige Leden: Prof. dr. P. ten Dijke Prof. dr. M.A. Huynen

Radboud Universiteit Nijmegen Prof. dr. H.P. Spaink

Prof. dr. H.G. Stunnenberg

Radboud Universiteit Nijmegen Dr. A.W. Thomas

Biomedical Primate Research Centre, Rijswijk

The printing of this thesis was financially supported by: J.E. Jurriaanse Stichting

You sleep in the light

Yet the night and the silent water Still so dark…

Opeth

So much has been done, exclaimed the soul of Frankenstein - more, far more, will I achieve: treading in the steps already marked, I will pioneer a new way, explore unknown powers, and unfold to the world the deepest mysteries of creation.

Contents

Abbreviations 9

Chapter 1 Introduction 11

Chapter 2 Plasmodium post-genomics - better the bug you know? 23

Chapter 3 Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

43

Chapter 4 A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses

63

Chapter 5 A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes

79

Chapter 6 Plasmodium berghei Į-tubulin II: a role in both male gamete formation and asexual blood stages

97

Chapter 7 General discussion 113

9

Abbreviations

ACP = acyl-CoA binding protein ACS = acyl-CoA synthetase AMA1 = apical membrane antigen 1 CAT = centrally located AT-rich chr = chromosome CLAG = cytoadherence-linked asexual gene CS = circumsporozoite protein CTRP = circumsporozoite TRAP-related protein DHFR-TS = dihydrofolate reductase- thymidilate synthetase EMP = erythrocyte membrane protein EST = expressed sequence tag ETRAMP = early transcribed

membrane protein ETS = external transcribed spacer indel = insertions and deletions GBP = glycophorin-binding protein GFP = green fluorescent protein GLURP = glutamate-rich protein GPI-AP = glycosylphosphatidyl inositol-

anchored protein GSS = genome-survey sequence HMM = hidden Markov model ITS = internal transcribed spacer LSA = liver-stage antigen LSU = large subunit

MRCA = most recent common ancestor mRNA = messenger RNA

MSP = merozoite surface protein My = million years

OMP-DC = orotidine 5’-monophosphate decarboxylase

ORF = open reading frame (RT-)PCR = (reverse transcription-)

polymerase chain reaction PEXEL = Plasmodium export element PFGE = pulsed-field gel electrophoresis PIR = Plasmodium interspersed repeat PUF = RNA-binding proteins

of the pumilio family RAP = rhoptry-associated protein (c)RMP = (composite)

rodent malaria parasite rRNA = ribosomal RNA SB = synteny block SBP = synteny breakpoint SERA = serine-repeat antigen SOM = supporting online material SP = signal peptide

SSU = small subunit STS = sequence tagged site TAP = tandem affinity purification TGF-ȕ = transforming growth factor ȕ TM = transmembrane

TR = translational repression TRAP = thrombospondin-related

adhesive protein tRNA = transfer RNA TSTK = TGF-ȕ receptor-like

serine/threonine protein kinase UTR = untranslated region