Codon usage bias in Archaea Laura R. Emery Ph.D. University of Edinburgh 2010 1 2 for Mom 3 ACKNOWLEDGEMENTS P.M. Sharp has provided me with this superb opportunity to pursue an area of research which has thoroughly intrigued me. I thank him for his experience, expertise and unsurpassed attention to detail. I thank the numerous members of I.E.B for their guidance and support throughout my time in Edinburgh. A particular thanks to B.C. and D.C. Charlesworth who have made me feel very welcome at their lab group, where I have learned a lot. The recent computational support from R.H.J. Perry has been invaluable and I thank P.R. Haddrill, J.J. Welsh, K. Zeng and S.J. Lycett for advice and/or discussion. I thank my school teachers for inspiration and C.M. Wade for the advice to embark upon this project in Edinburgh. The encouragement and endurance from my friends, J. Raghwani and M.J. Ward, has been greatly appreciated. I thank my family: B.A. Evans, S.C. Emery and M.W.H. Emery for their infallible support and tolerance. I would thank H.C. Emery if it were possible; she always insisted that I pursue my dreams, and yet ironically, has exemplified the roles of mutation and natural selection in bringing life in and out of existence. I DECLARATION The work of this thesis is my own unless stated otherwise. Laura R. Emery 2010 II PUBLICATIONS SHARP, P. M., L. R. EMERY and K. ZENG, 2010 Forces that influence the evolution of codon bias. Phil. Trans. R. Soc. 365: 1203-1212. EMERY, L. R., and P. M. SHARP, 2011 Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis. Biol. Lett. doi: 10.1098/rsbl.2010.0620. Published manuscripts have been reproduced here in accordance with the copyright guidelines of the publishers involved. III CONTENTS ABSTRACT............................................................................................................................. IX 1. INTRODUCTION 1.1 Codon usage bias in Bacteria....................................................................................................... 2 1.1.1 Mutational biases..................................................................................................................... 2 1.1.1.1 Variation in mutational patterns among bacterial genomes............................ 2 1.1.1.2 Selection upon base composition?............................................................................ 3 1.1.1.3 Variation in mutational patterns within bacterial genomes............................. 4 1.1.2 Natural selection...................................................................................................................... 6 1.1.2.1 Evidence for selected codon usage bias.................................................................. 6 1.1.2.2 Variation in translational selection among Bacteria............................................ 8 1.1.2.3 The benefit of translational selection....................................................................... 10 1.1.3 Other forms of selected codon bias.................................................................................. 13 1.2 Codon usage bias in Eukaryotes................................................................................................. 14 1.2.1 Codon usage bias in unicellular Eukaryotes................................................................... 14 1.2.2 Codon usage bias in multicellular Eukaryotes.............................................................. 16 1.3 Codon usage bias in Archaea....................................................................................................... 17 1.4 Aims....................................................................................................................................................... 19 2. METHODS 2.1 Indices of codon usage bias......................................................................................................... 21 2.1.1 G+C content at synonymously variable third codon positions (GC3s)................ 21 2.1.2 Additional base composition indices of synonymously variable third codon positions (N3s)........................................................................................................................ 22 2.1.3 Base composition skew indices.......................................................................................... 22 2.1.4 Relative synonymous codon usage (RSCU).................................................................... 23 2.1.5 The effective number of codons (Nc)................................................................................. 23 2.1.6 The frequency of optimal codons (Fop)............................................................................ 25 2.1.7 The codon adaptation index (CAI).................................................................................... 25 2.2 Within-group correspondence analysis.................................................................................. 26 2.3 Identifying optimal codons......................................................................................................... 27 2.4 Estimating the strength of selected codon usage bias (S)................................................ 27 2.5 Accounting for phylogenetic non-independence............................................................... 28 IV 3. THE STRENGTH AND PATTERN OF SELECTED CODON USAGE BIAS IN METHANOCOCCUS MARIPALUDIS 3.1 Introduction...................................................................................................................................... 30 3.2 Methods.............................................................................................................................................. 30 3.2.1 Data sources.............................................................................................................................. 30 3.2.2 Exploring variation among genes...................................................................................... 31 3.2.3 Indices of selected codon usage bias.............................................................................. 31 3.3 Results................................................................................................................................................. 34 3.3.1 Variation in codon usage among genes in M. maripaludis...................................... 34 3.3.2 The strength of selected codon usage bias in M. maripaludis................................ 39 3.4 Discussion.......................................................................................................................................... 40 4. TRENDS IN CODON USAGE BIAS WITHIN ARCHAEAL GENOMES 4.1 Introduction...................................................................................................................................... 43 4.2 Methods............................................................................................................................................. 43 4.2.1 Data sources............................................................................................................................. 43 4.2.2 Multivariate analyses............................................................................................................ 44 4.2.3 Exploring variation among genes.................................................................................... 45 4.3 Results................................................................................................................................................ 45 4.3.1 Trends in codon usage within archaeal genomes..................................................... 45 4.3.2 Comparing trends among Archaea and Bacteria....................................................... 48 4.3.3 Trends in strand skew within the genomes of Archaea........................................... 49 4.3.4 Trends in GC3s within the genomes of Archaea........................................................ 50 4.4 Discussion......................................................................................................................................... 52 4.4.1 The causes of strand skew in Archaea........................................................................... 53 4.4.2 The causes of variation in GC3s among genes in Archaea..................................... 54 4.4.3 Conclusions............................................................................................................................. 55 V 5. THE STRENGTH OF SELECTED CODON USAGE BIAS IN ARCHAEA 5.1 Introduction...................................................................................................................................... 56 5.2 Methods............................................................................................................................................. 57 5.2.1 Data sources............................................................................................................................. 57 5.2.2 Estimating S.............................................................................................................................. 57 5.2.3 Phylogenetic analyses.......................................................................................................... 58 5.3 Results................................................................................................................................................. 59 5.3.1 The strength of selected codon usage