How Molecular Trucks Build Your Sensors
In the film Unlocking the Mystery of Life, biochemist Michael Behe, describing the intricacies of cells as we know them today, claimed that there are “little molecular trucks that carry supplies from one end of the cell to the other.” If that seems an overstatement, you should look at the illustration in Cell June 11 in a Minireview called “Cilia and flagella revealed” by Snell, Pan and Wang.1 They not only describe trucks, they’ve found a train of boxcars and a whole crew of engineers, conductors and brakemen.
Cilia are appendages in the cell membrane that wiggle. Everybody’s got them; they are ubiquitous in organisms, from bacteria to humans. They line our respiratory tract, cleaning debris from our lungs. They help our senses of smell and eyesight. They are important for kidney function. They may look simple, but only recently are scientists beginning to appreciate the complexity inside. The authors begin:
Our view of cilia has changed dramatically in the decade since Joel Rosenbaum and his colleagues discovered particles rapidly moving (2-4 micrometers/s) up and down within the flagella of the biflagellated green alga, Chlamydomonas (Kozminski et al., 1993). Once cell biologists identified the cellular machinery responsible for this intraflagellar transport (IFT), it became clear that IFT is essential for the assembly and maintenance of cilia and flagella in all eukaryotes (Rosenbaum and Witman, 2002). As we will outline in this brief review, the increased focus on these organelles has revealed that nearly all mammalian cells form a cilium, that the ciliary apparatus (a cilium plus its basal body) is somehow connected with cell proliferation, and that cilia play key (and as yet poorly understood) roles in development and homeostasis.
Michael Behe in his book Darwin’s Black Box had a whole chapter on how cilia move (see these illustrations). Recently, however, it has been appreciated that nonmotile cilia can also act as sensory probes. The authors explain:
Several properties of cilia recommend them for use as sensory transducers. They project a cell type-specific distance from the cell body, making them exquisitely designed probes of the external milieu; both their overlying membrane and their cytoplasmic contents are relatively well isolated from the cell body, thereby offering all of the advantages of compartmentalization; the machinery for their assembly makes possible rapid, regulated transport of proteins between the organelles and the cell body; and, the assembly machinery seems exploitable for use directly in signaling pathways.
Now that we know cilia are vital, it’s what goes on inside the narrow shafts during construction that is truly remarkable. The authors mentioned IFT, or intraflagellar transport, a class of proteins that operate the transportation system. During construction of a cilium or flagellum, parts need to be transported to the growing tip, or axoneme. The IFT particles move up and down the inside walls of the shaft. They describe how this works. Watch for the word trucks:
This flow of materials is driven by the IFT machinery. Flagellar proteins synthesized in the cell body are carried to the tip of the flagellum (the site of assembly of the axoneme) by IFT particles, which are composed of at least 17 highly conserved proteins that form A and B complexes. The plus end-directed microtubule motor protein kinesin II is essential for movement of particles and their cargo toward the tip (anterograde transport) of the flagellum, and a cytoplasmic dynein carries IFT particles back to the cell body (retrograde transport). Thus, IFT particles function as constantly moving molecular trucks on a closed loop. The tracks they travel on are the microtubule doublets of the ciliary/flagellar axoneme, microtubule motors power them, and the individual structural components (e.g., microtubule subunits, dynein arms, and radial spoke proteins) of the cilium/flagellum are their cargo.
The construction system they describe next is reminiscent of a gondola at a ski resort, a series of ore carts in a mine shaft, or a conveyor at a rock quarry. If you can picture architects building a tall structure like the Seattle Space Needle or the Eiffel Tower, imagine the engineers first devising a way to get the raw materials to the growing top. Suppose they design a double trackway that can be extended in length as the structure grows. Attached to this track are self-propelled dump trucks that can climb up the tracks, and another set of dump trucks that can climb down. Each truck can carry a load of cargo. New trucks are constantly added at the bottom, and old ones upon reaching the base are removed. A pool of trucks and drivers is always available to traverse this vertical highway. With this automated system running, workers at the top can take the cargo and build with it, and send waste products down the other side. This two-way transportation system works not only to build the tower, but to dismantle it.
Figure 2 presents a model for regulation of assembly, disassembly and for regulation of flagellar length. In this model, the rate of particle entry and the number of particles per unit length are independent of length, and cargo loading is regulated. Thus, in a rapidly growing flagellum (in the extreme case), every particle entering carries cargo, and every particle returning to the cell body is empty. Once the proper length is attained, length control mechanisms engage. At this steady-state length, the number of IFT particles entering and leaving per unit time is unchanged, but the proportion of cargo-loaded IFT particles that enters the flagella comes to equal the proportion of cargo-loaded IFT particles that leaves the flagellum. In a disassembling flagellum, the situation is reversed from that of a growing flagellum, and (in the extreme case) every particle that enters the flagellum is empty and every particle that leaves the tip is full. Thus, by regulating cargo binding to particles at both the base and the tip, and by controlling of assembly and disassembly of axonemal components at the tip (presumably driven by mass action and regulatory proteins), cells specify assembly/growth, steady-state length, or disassembly/resorption.
The diagram in their figure shows what look like little ore-carts climbing up to the tip and back. The authors describe next how these tall structures function not only as oars and outboard motors, but as chemical antennae. Experiments have “called to the attention of cell biologists the under-appreciated but hardly insignificant role of cilia in sensory transduction.” Here are some of your body parts that depend on these miniature probes that extend out from the cell into the surrounding environment, sensing what’s out there:
Humans experience the environment through cilia in major sensory organs. The outer segments of retinal rod cells are modified, nonmotile cilia, replete with photoreceptors for interacting with light; and the odorant receptors in the olfactory epithelium are peppered over the surface of the cilia of olfactory neurons. Moreover, almost every mammalian cell contains a solitary cilium, called a primary cilium, whose most likely function is in signaling (Pazour and Witman, 2003). For example, many of the neurons in brain contain primary cilia, some of which express receptors for somatostatin and serotonin (Pazour and Witman, 2003). Perhaps the most striking example of the importance of primary cilia in homeostasis [i.e., dynamic equilibrium] comes from work on the epithelial cells of the collecting tubules in the kidney. The primary cilium on each renal tubule cell functions as a flow sensor both in vivo and in MDCK cells in vitro. Bending the cilium causes a large, transient increase in intracellular calcium concentration and a consequent alteration in potassium conductance (references in Boletta and Germino [2003]).
Each of these cilia, and many more, are constructed by this molecular transportation system. How many parts are involved in building a cilium? If this system were magnified a hundred million times, children might find this the ultimate Lego toy:
New proteomic and genomic studies may finally provide a platform for discovery of most of the as yet unidentified genes that encode ciliary/flagellar proteins. A proteomic analysis of the axoneme of human cilia identified over 200 potentially axonemal proteins (Ostrowski et al., 2002). Several of the proteins were previously identified as being in the axoneme, but many have no homologs or are of unknown function.
(That would be over 200 different kinds of pieces, kids, and a lot of each.) From genomic studies, they estimate it would require at least 362 genes to build a motionless cilium, and “more than 400-500 genes that are predicted to be needed for forming and regulating the ciliary apparatus” One team measured the proteome (set of proteins) required to build the basal body (the bottom foundation of the structure) and flagellum to consist of 688 genes. “There is no doubt,” they say, “that the FABB [flagellar and basal body] proteome represents an incredibly rich resource.”
Failure of cilia and flagella to develop properly are implicated in many diseases (see “Don’t mutate this gene, or else” in the 10/01/2003 headline). Even some human obesity disorders might be traced to ciliary breakdown, as well as hypertension, diabetes and other “seemingly unrelated clinical problems”.
The authors do not speculate on how such a complex system with so many parts might have evolved, other than to assume that it did: for instance, “Paralogs of other mitotic proteins have also evolved to play roles in cilia.” They also claim that plants unevolved them: they seem to have lost the 400-500 genes needed for building cilia or flagella, if they ever had them. The authors examine studies in comparative genomics to determine how many of the cilia/flagella genes are ancestral, going back to the original machinery in the simplest alga or bacterium. One study compared the IFT genes in several organisms with those in fruit flies:
Using a large number of genomes provided stringent criteria and identified 187 candidate ancestral ciliary genes. Sixteen are conserved in all ciliated organisms examined and absent in all nonciliated organisms; 18 are present only in organisms with motile cilia; 103 are common to organisms that utilize only conventional ciliogenesis; and 50 are shared only by organisms that form motile cilia in the ciliary compartment.
Other studies are cited; 67% of the basal body genes in green algae and 90% of their flagellar and IFT genes were present in the full FABB proteome. It appears, therefore, that this transportation system evolved early on, if it did, and has not changed much since.
1William J. Snell, Junmin Pan, and Qian Wang, “Minireview: Cilia and Flagella Revealed: From Flagellar Assembly in Chlamydomonas to Human Obesity Disorders,” Cell, Vol 117, 693-697, 11 June 2004.
Although this is a headlines service, sometimes we need to give enough detail to show just what the Darwinians are up against in the age of molecular biology. As Michael Behe said in the film, scientists in Darwin’s day thought the cell was just a blob of protoplasm, not much different than a piece of jello. Now, here is just one example of hundreds of complex systems in the cell that could drive the point home that a cell is a sophisticated factory of molecular machines running off self-correcting programmed instructions (and that is a simplistic understatement). These authors admit that the intraflagellar transport system was already functional in green alga and bacteria, with no precursors. The genes for the most part have changed little or none all the way to humans. Even taking their most optimistic claim that 18 genes for motile cilia might be ancestral, when you consider that getting just one of them by chance is astronomically improbable in the best of all possible worlds (see online book), an honest evolutionist must surely throw up his hands in utter despair to believe that time and chance could produce such wonders.
Wouldn’t it be fun to take this knowledge in a time machine back to 1859 and show it to Charlie and his bulldog? Actually, it would be cruel. Chuck was already plagued by an upset stomach, and this would be like giving him a gallon of ipecac with free lifetime refills.