Abstract 309 14.1 Introduction 310 14.2 The Endomembrane System 311

14.2.1 Evolution of an Endomembrane System: An Important Transition 311 14.2.2 Organelles of the Endomembrane System 311 14.2.3 Steps in the Transport Reaction 313 14.2.4 Vesicular Transport in Non-Opisthokont Lineages 316

14.3 Mining the Databases 319 14.3.1 Candidate Proteins To Be Used as Representative Queries 319 14.3.2 Search Methods 319

14.4 Endomembrane System Component Homologues in Diverse Genomes 320 14.4.1 Bottom Up: Prokaryotic Homologues of Endomembrane

System Components 320 14.4.2 Top Down: Reconstructing the Vesicular Transport

Machinery of the Last Common Eukaryotic Ancestor 323 14.5 Beyond BLAST: Examples from Functional Studies 326

14.5.1 Genomics and Phylogeny 326 14.5.2 Genomics and Cell Biology 327

14.6 Conclusions 327 14.7 Materials and Methods 328

14.7.1 Search Queries 328 14.7.2 Search Methods 328 14.7.3 Databases 328

Acknowledgments 329 References 329

Comparative genomics provides a powerful tool for both evolutionary and cellular biology. As an example of how comparative genomics can be used in these fields, we examine how

cell biological studies in model systems, together with the rapidly accumulating genomic data from diverse taxa, can be applied to reconstruct complex aspects of the biosyntheticsecretory and endocytic pathways in eukaryotes. The near-universal presence within eukaryotes of the core features of an intracellular transport system serves to highlight the vital role that this elaborate system must play in cell function. The evolution of this system is nonobvious, as prokaryotes have been generally considered to lack primitive or precursor structures that could have given rise to an endomembrane system. We consider, in detail, the proteins involved in vesicular transport, emphasizing a number of insights from selected divergent systems and comparing these with crown eukaryotes. We highlight possible prokaryotic precursors, survey the eukaryotic diversity of vesicular transport machinery and discuss how genomics initiatives have helped push forward cell biological studies of the endomembrane system in diverse organisms. Importantly, the mechanistic details of the transport systems are essentially conserved, indicating an ancient origin for these processes. All the while, increasing complexity in the sense of pathway multiplicity is observed in the vesicular transport system when comparing unicellular eukaryotes to more complex multicellular organisms.