Intraflagellar transport (IFT) involves the transport of ciliary precursors onoligomeric protein complexes (A, B) attached to microtubule motors (kinesin-2 andcytoplasmic dynein-1b) for ciliary assembly and maintenance. The assembly of the threeaxonemal segments (proximal, middle, distal) and the regulation of the differentcomponents of the IFT pathway are poorly understood. Moreover, the form in whichtubulin is transported into cilia is not known. This work explores the mechanism of IFT,with respect to its regulation and assembly of distinct axonemal segments.I studied the mechanism of suppression in a suppressor of IFT52, a complex Bprotein. Partial suppressors (IFT52sm) are conditional and assemble cilia under: eitherlower temperature or hypoxia. I showed a novel intragenic mechanism of suppressionthat occurs in two steps. First by native RNAi-mediated genome rearrangements fordeleting micronucleus-specific sequences during conjugation of two heterokaryonscarrying micronuclear copies of neo2-disrupted IFT52. Next the flanking sequencescontrolling neo expression are processed as multiple artificial introns, thereby restoringthe translational frame. Chlamydomonas mutants of IFT46 (a complex B protein) arepartially suppressed under hypoxia, suggesting a conserved link between oxygen andIFT-regulation.The detergent-soluble fraction of cilia from IFT52sm cells was analyzed by twodimensionalgels, which showed an increase in the concentration of a single protein spot,identified as tubulin folding cofactor B (TCB). TCB is one of the five cofactors in thetubulin folding pathway that generates -tubulin dimers from monomers. The presenceof TCB in the cilium indicated a potential ciliary role of the components of tubulinfolding factors in ciliogenesis, such as the transport of tubulin. We show that a knockoutof TCB1 in Tetrahymena produces a lethal phenotype associated with a general loss ofmicrotubules. Folding -tubulin by Tcb1p is its primary role.I explored the functions of DYF-1 (an IFT-associated protein), in axonemeassembly. In C. elegans, Osm-3 kinesin-2 assembles the distal-most segment of theaxoneme (with outer singlets). DYF-1 is required for Osm-3 function and was proposedas a motor activator or adaptor. Tetrahymena cells lacking DYF-1 have non-functionalcilia with a variety of axonemal defects. Zebrafish dyf-1 mutants assemble non-functionalcilia lacking polyglutamylation, an important post-translational tubulin modification.Tetrahymena cells lacking Dyf1p have hyperglutamylated short axonemes. Thus, DYF-1functions in axoneme assembly and/or stability but the phenotypes from loss of DYF-1are organism-specific.