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Cell Machines: A Well-Designed DNA Pump

UMOL.jpgIn Unlocking the Mystery of Life, Jed Macosko commented that cells require a “host” of molecular machines. “There are as many machines in the human body as there are functions that the body has to do,” he said. Michael Behe mentioned a couple of them: “there are little molecular trucks that carry parts from one end of the cell to the other; machines that capture the energy of sunlight and turn it into usable energy.” The film highlighted one machine in particular, the bacterial flagellum, but animated several others too that are involved in DNA translation and protein synthesis.

Yet all that is only the tip of the iceberg. There are thousands of molecular machines. A living cell is a virtual factory of machines. Counting them and listing them, though, is only one way to showcase design. The power of intelligent design is best revealed by examining the details of specific machines. Here’s another one most non-specialists are not aware of: a DNA pump.

SpoIIIE: A Dramatic Example

Some bacteria have the ability to form spores. Like escape pods for a spaceship, these hardened bodies store the genetics of the organism to survive environmental stresses. Spores can survive for decades till conditions improve for them. They can even persist through efforts to sterilize surfaces or cook food.

But how does the DNA get into the escape pod? In Bacillus subtilis, there’s a machine called SpoIIIE, a multi-part motor that uses ATP to pump the 4,100 genes into the spore through a narrow opening called the septum. A member of the FtsK family of translocase motors, the machine was recently described in PLoS Biology by a team in France that used super-resolution microscopy to see how the machine parts are recruited and assembled. By the way, you probably have these motorized machines inside you right now. Bacillus subtilis is recognized as a part of commensal gut flora and can be added to your diet in some probiotics. Healthy digestion may depend on the little SpoIIIE pump.

Here’s a portion of the authors’ summary describing how it works:

Molecular motors are implicated in myriad cellular processes, notably in the transcription, replication, and segregation of DNA. Segregation or packaging of DNA is essential for production of viable viral particles, proper division of bacterial cells, and production of spores. A dramatic example of this process occurs during sporulation in Bacillus subtilis, in which a large proportion of the chromosome is actively transferred across a division septum by the SpoIIIE motor protein. Here, we use advanced microscopy methods to study the mechanism of recruitment and assembly of the SpoIIIE pump and the architecture of its complex with DNA. We found that SpoIIIE complexes are recruited before the beginning of cell division, and are subsequently escorted by the constriction machinery to the center of the septum. We show that the directionality of DNA transport by SpoIIIE results in the establishment of an asymmetric complex that exports DNA into the nascent spore. (Emphasis added.)

Notice that they improve on Macosko’s number of machines in the cell: it’s not just a “host” of machines; there are “myriad” cellular processes that use “molecular motors,” most notably those that process DNA. That comment is just a preface to what they called a “dramatic example of intercompartmental DNA transfer,” the “SpoIIIE DNA pump.”

In describing this marvel, the authors use the word “motor” 29 times, “machine” or “machinery” 24 times, and “mechanism” or “mechanical” 9 times -- but “evolution” or “evolved” (in the Darwinian sense) zero times. Contra Dobzhansky, it doesn’t appear that SpoIIIE makes sense in the light of evolution.

Irreducible Complexity

Like most other molecular machines, the SpoIIIE DNA pump appears to be irreducibly complex. The authors describe a sequence of events leading up to pumping that depends on timing and checkpoints. First, the “division apparatus” opens a pore between the bacterium and its spore, into which one fourth of the bacterium’s chromosome inserts before pumping begins. The timeline requires feedback between parts. They write,

DNA movement occurs through an open pore structurally maintained by the division apparatus, with SpoIIIE working as a checkpoint preventing membrane fusion until completion of chromosome segregation.

The SpoIIIE motor itself is composed of multiple components. It has three domains: a transmembrane-spanning portion, a linker, and a motor. There are also three subdomains, labeled alpha, beta and gamma. Alpha and beta subdomains combine into rings made up of six pairs encompassing a central pore into which the DNA is threaded. “SpoIIIE clusters contain ~50 molecules mostly in hexameric form,” they say.

SpoIIIE is non-specific, meaning that it can transport any DNA regardless of sequence. A special feature of SpoIIIE is its ability to translocate DNA unidirectionally, “a process that requires the recognition of highly skewed octameric chromosomal DNA sequence motifs,” called the SpoIIIE Recognition Sequence. The gamma domain has a special “winged helix” device connected to the alpha-beta pairs by flexible linkers that recognizes this sequence.

SpoIIIE is active in both normal cell division (symmetric division) and in spore formation (asymmetric), cooperating with the appropriate machinery for the two different processes:

Overall, our results suggest that SpoIIIE takes part in both sporulation and division machineries, and that the different functions of SpoIIIE in chromosome dynamics during division and sporulation may be regulated by alternative interactions with factors specific to asymmetric or symmetric septa or by factors that are specifically located in the terminus region of the chromosome.

Mode of Operation

SpoIIIE motors localize at points on the membrane where the division septum will form; the authors believe that assembly of the division machinery is their cue. Recruitment occurs before septum invagination begins. To the machine, the septum would look like a large circular door, somewhat like the iris of a camera, closing in upon the DNA. As the opening narrows, the SpoIIIE motors localize to the leading edge of the septum, preventing closure until the DNA makes it through the channel. These processes indicate sophisticated timing and checkpoint “quality control” throughout the process.

At first attachment to the DNA, the motors pull it toward the mother cell, until the linker domains are fully stretched. Then, they reverse gear and pump the DNA into the spore. Translocation continues till all the DNA is inside the spore.

Upon completion of DNA translocation, SpoIIIE motors disengage from DNA and the last segment of circular DNA is pulled into the forespore... After completion of DNA translocation, SpoIIIE or a protein interacting with it leads to membrane fission.

It’s remarkable that these motors won’t let the door close until the job is done. Here is a coordinated, time-dependent system that is vital to the survival of the bacterial cell when danger requires the escape pod.

Remember that this all takes place in a “simple” bacterium! The mechanisms of chromosome segregation for cell division in eukaryotes are even more astonishingly complex.

Design as Fertile Ground for Biological Understanding

As we look at their conclusion, ask whether evolutionary thinking or design thinking is the more productive way to evaluate evidence like this:

In brief, SpoIIIE/FtsK are extremely modular proteins, in which each domain encodes a separate function: SpoIIIEN/FtsKN is responsible for septal recruitment and interactions with downstream components of the divisome, SpoIIIEL/FtskL may act as a flexible linker communicating information between the motor domain and proteins composing the DNA-conducting pore, SpoIIIE?/Ftsk? is responsible for DNA translocation, SpoIIIE?/Ftsk? contains the ATPase motifs energizing the motor, and SpoIIIE?/Ftsk? provides motor directionality. Our model for the recruitment, assembly, and architecture of SpoIIIE provides a rationale for how the coordination and co-regulation of these specific activities could lead to the synchronization of DNA segregation and cell division. Our findings and proposed mechanism considerably advance our understanding of the function and mechanism of SpoIIIE, are relevant to further understand the coordination between chromosome segregation and cell division, and may illuminate the mechanisms of other complex machineries involved in DNA conjugation and protein transport across membranes.

Who would have thought in Darwin’s day that such machinery at this incredibly tiny scale was even possible? The biology of the 21st century leaves Darwinism in the dustbin of simplistic (and wrong) ideas. (See Casey Luskin's current cover story, "No, Scientists in Darwin's Day Did Not Grasp the Complexity of the Cell; Not Even Close.") Understanding information transfer via molecular machines requires a new biology for the information age: intelligent design.