Sheffield's lab and others compared the sequences of human BBS genes to genome sequences from other organisms—from algae to higher plants, insects, fish, and mice—in search of similarities. They found that BBS genes are conserved in organisms with cilia but not in nonciliated organisms.

Charles S. Zuker, an HHMI investigator at the University of California, San Diego, was one of the first to carry out a whole-genome subtraction study. Zuker's postdoc, Tomer Avidor-Reis, crafted the analysis, which identified nearly 200 conserved ciliary genes encoding both known and candidate ciliary proteins. Using the fruit fly Drosophila as a model system, the lab then investigated the function of some of the candidate proteins, at least two of which were suspected to derive from BBS genes.

		View Image Inside cilia and flagella is a microtubule-based cytoskeleton called the axoneme. The axoneme of primary cilia typically has a ring of nine outer microtubule doublets (called a 9+0 axoneme), and the axoneme of a motile cilium has two central microtubule doublets in addition to the nine outer doublets (called a 9+2 axoneme). The axonemal cytoskeleton acts as scaffolding for various protein complexes and provides binding sites for molecular motor proteins, such as kinesin II, that help carry proteins up and down the microtubules. At the base of the cilium is the microtubule organizing center, also called a basal body, which is created as the centriole (a microtubular structure essential to cell division) migrates to the surface. The transition zone between basal body and axoneme serves as a docking station for intraflagellar transport and motor proteins. Cilia and basal bodies have been implicated directly in a number of developmental processes, including left-right asymmetry, heart development, maintenance of the renal epithelium, respiratory function, electrolyte balance in the cerebrospinal fluid, and reproductive fecundity. Image: A. Pasieka / Photo Researchers, Inc.

Another comparative study, this one led by Susan K. Dutcher, a researcher at Washington University School of Medicine, looked at the genes and proteins of humans, Chlamydomonas, and a weedy plant. The researchers subtracted all genes found in the weed from the combined genomes of humans and algae, leaving them with a set of 688 genes found exclusively in organisms with cilia or flagella. From this set, they identified a novel BBS gene, BBS5, and showed that the protein product from that gene localizes to the "basal body"—the point, underlying the cilium, from which its microtubule railways originate—in the mouse and in the worm Caenorhabditis elegans.

"Though none of the precise functions of the BBS gene products are known, it is clear that cilia dysfunction is involved in some of the phenotypic characteristics," says Sheffield. Male patients have infertility problems, for example, and in the BBS mouse model, sperm are missing flagella. Another phenotype of BBS, blindness, is also cilia-dependent. Humans and mice with BBS see fine at birth, but in time the photoreceptor cells within the retina degenerate. A key component of photoreceptors, it turns out, is a structure called a connecting cilium.

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