Is the Evolution of Bacterial Resistance a Just-So Story? 09/12/2004
Evolutionists frequently point to the emergence of bacterial resistance to antibiotics as an example of Darwinian evolution occurring right under our noses. Bruce R. Levin of Emory University, writing in the Sept. 10 issue of Science,1 is not so sure about that. He points out that cells might just have a built-in mechanism to shut down growth and reproduction in times of stress (the SOS response), to minimize the damage from toxins in the environment. He points to two studies in the same issue that indicate how noninherited resistance to antibiotics can be generated without reference to Darwinian natural selection.
What’s more interesting in his report is his rebuke against fellow Darwinists who leap to unsubstantiated tales of evolution to explain how these mechanisms come about. His final paragraph states:
“It is easy to concoct just-so stories to explain the evolution of a mechanism that, like the SOS response, produces quiescent cells that are refractory to lethal agents. Yet it seems unlikely that ampicillin was the original selective force [sic] responsible for the evolution [sic] of the induction mechanism observed by Miller and colleagues. A bigger challenge to those in the evolution business is to account for the generation of lower fitness cell types when they do not provide an advantage to the collective, like the persisters of Balaban et al. in the absence of antibiotics. Then again, just like people, bacteria do some seemingly perverse things that are not easy to account for by simple stories of adaptive evolution.
--------------------------------------------------------------------------------
1Bruce R. Levin, “Microbiology: Noninherited Resistance to Antibiotics,” Science, Vol 305, Issue 5690, 1578-1579, 10 September 2004, [DOI: 10.1126/science.1103077].
Peering Into Paley’s Black Box: The Gears of the Biological Clock 09/15/2004
William Paley’s famous “watchmaker argument” for the existence of a Designer, though intuitively logical to many, has been criticized by naturalists on the grounds that one cannot compare mechanical devices to biological ones. Biological “contrivances” might operate on totally different principles than mechanical ones made by humans we know.
Michael Behe’s 1996 book Darwin’s Black Box was built on the theme that, until recently, the living cell was a “black box” to biologists: i.e., a system whose inner workings lay hidden from us. But now with the rapid advances in molecular biology, we are finding the cell to be a complex factory of molecular machines.
These themes of Paley and Behe seemingly converge in a commentary by Susan S. Golden (Texas A&M) in PNAS about biological clocks.1 Golden works at the Center for Research on Biological Clocks in the Texas A&M Biology Department, and was struck by recent findings in two other papers in PNAS on the circadian rhythms of “primitive” blue-green algae (cyanobacteria). To her, they suggested we are opening the black box of biological clocks, and finding treasures that look remarkably familiar to the clocks we know:
“A physiological black box is to a biologist what an ornately decorated package is to a small child: a mysterious treasure that promises delightful toys within. With fitting elan, a small community of scientists has ripped open the packaging of the cyanobacterial circadian clock, compiled the parts list, examined the gears, and begun to piece together the mechanism. Over the past 2 years, the 3D molecular structures have been solved for the core components of the cyanobacterial circadian clock: KaiA, KaiB, and KaiC. In a surprisingly literal analogy to mechanical timepieces, the protein that seems to be at the heart of the clock mechanism, KaiC, forms a hexameric ring that even looks like a cog: the escape wheel, perhaps. Previous work has shown that KaiC has an autophosphorylation activity, and that the presence of KaiA and KaiB modulates the extent to which KaiC is phosphorylated. In this issue of PNAS, Nishiwaki et al. biochemically identify two amino acid residues on KaiC to which phosphoryl groups covalently attach, and show the necessity in vivo of a phosphorylation-competent residue at these positions. By searching the crystal structure for evidence of phosphorylated sites, Xu et al. pinpoint a third residue that may “borrow” the phosphoryl group dynamically. Together, their work contributes richly to our understanding of what makes the gears mesh and turn to crank out a 24-h timing circuit....
Because each of these components (at minimum) is a dimer [composite of two molecular chains], KaiC is known to be a hexamer [composite of six chains], and other proteins may be present as well, the cyanobacterial clock can be thought of as an organelle unto itself: a “periodosome” that assembles and disassembles during the course of a day, defining the circadian period.”
The term “periodosome” means “time-keeping body” – i.e., clock. Her diagram shows KaiC as a six-sided carousel to which phosphate groups and other subunits attach and detach during the diurnal cycle. The feedback between the units provides the periodicity of the clock, similar to the back-and-forth pendulum in a grandfather clock or the escape wheel in a wristwatch. How is the clock tuned to the day-night cycle? Where do the parts come together, and how do the clock gears mesh with other cellular machines? We don’t know yet; the box has just been opened.
The clocks examined in these papers are the “simple” clocks of blue-green algae, compared to the much more complex biological clocks in eukaryotes. Even about these relatively simple systems in cyanobacteria much remains to be understood, but our initial glimpses into the inner workings of a biological clock at the molecular level remind her of the delight of opening a chest of toys for the first time:
“Identification of other potential components of the periodosome, intracellular localization of the clock parts, and elucidation of other potential modifications all may yield gears that are required to smoothly tick away the time and ensure that daughter cells do not run fast or slow.
The cyanobacterial clock box, no longer black, is a chest filled with bioluminescence and attractive toys. Putting together the pieces to design a clock is a tedious task, but S. elongatus is a gracious host, and the guests at the party are hard at work.”
--------------------------------------------------------------------------------
1Susan S. Golden, “Meshing the gears of the cyanobacterial circadian clock,“ Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0405623101
Secrets of the Spliceosome Revealed 09/17/2004
A husband and wife team from Hebrew University has revealed the structure of the spliceosome, one of the most complex molecular machines in the cell (see 09/12/2002 headline), in more detail than ever before, says EurekAlert. The spliceosome is responsible for cutting out the introns in messenger RNA after it has transcribed DNA, and also for “alternative splicing” that rearranges the exons to produce a variety of proteins from the same DNA template: “Alternative splicing, which underlies the huge diversity of proteins in the body by allowing segments of the genetic code to be strung together in different ways, takes place in the spliceosome as well.”
The Sperlings found a tunnel between the two major subunits of the machine where they believe the cutting and splicing operations take place, and also a cavity that might provide a safe haven for the messenger RNA strand, like a waiting room, before its surgery. Also, they found that four spliceosomes are bound together into a “supraspliceosome” which is able to do “simultaneous multiple interactions, rather than by a stepwise assembly” as inferred from other experiments in vitro. Their investigation in vivo (within a functioning, living cell) revealed even more complexity in the composite machine than had been seen in the individual machines:
“Such a large number of interactions that the cell has to deal with can be regulated within the supraspliceosome. Having the native spliceosomes as the building blocks of this large macromolecular assembly, this large number of interactions can be compartmentalized into each intron that is being processed. At the same time, the whole supraspliceosome enables the communication between the native spliceosomes, which is needed for regulated splicing. The organization of the supraspliceosome, like other macromolecular assemblies that exist as preformed entities, avoids the necessity to recruit the multitude of splicing components each time the spliceosome turns over. In that sense, the overall coordination of the cellular interactions is reduced from the hard work of repeatedly placing each piece in the correct position of the puzzle to the relatively simpler work of coordinating the preformed puzzle.”
In short, “The supraspliceosome represents a stand-alone complete macromolecular machine capable of performing splicing of every pre-mRNA independent of its length or number of introns.” They found that the individual spliceosomes are joined with a flexible joint like a hinge to provide flexible interactions and communication. Their work was published in Molecular Cell Sept. 10.1
--------------------------------------------------------------------------------
1Sperling et al., “Three-Dimensional Structure of the Native Spliceosome by Cryo-Electron Microscopy,” Molecular Cell, Volume 15, Issue 5, 10 September 2004, Pages 833-839; doi:10.1016/j.molcel.2004.07.022.
Bacterial Flagellum Reveals New Structural Complexity 10/27/2004
The bacterial flagellum, the unofficial mascot of the Intelligent Design movement, got more praise from the evolutionary journal Nature this week: Samatey et al.1 analyzed the hook region in detail and found that it is composed of 120 copies of a specialized protein that “reveals the intricate molecular interactions and a plausible switching mechanism for the hook to be flexible in bending but rigid against twisting for its universal joint function.”
Christopher Surridge, commenting on this paper in the same issue,2 adds that this joint must be able to bend up to 90 degrees in a millisecond or less while rotating at up to 300 times per second. He says that the researchers describe “how they determined the atomic structure of this super-flexible universal joint, and thereby how it achieves such a feat of engineering.”
--------------------------------------------------------------------------------
1Samatey et al., “Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism,” Nature 431, 1062 - 1068 (28 October 2004); doi:10.1038/nature02997.
2Christopher Surridge, “Molecular motors: Smooth coupling in Salmonella,” Nature 431, 1047 (28 October 2004); doi:10.1038/4311047b.
“Crucial Evolutionary Link” Found for Eukaryotes 11/05/2004
Often the opening words of a news story are what stick in the memory: “crucial evolutionary link.” The corroborating evidence, however, is buried in technical details of the press release from Rockefeller University, posted on NewsWise. In short, the researchers claim:
“Scientists believe the emergence of organelles, compartments in the eukaryotic cell’s cytoplasm that perform such functions as energy production, waste removal and protein synthesis, and a nucleus evolved between 2 and 3 billion years ago.
One hypothesis regarding the evolution of eukaryotic cells suggests that the endomembrane system developed because some ancient bacterial cells had the ability to sharply curve their membranes, allowing them to form internal membrane structures as well as to engulf other organisms. The findings reported by [Michael P.] Rout and colleagues [Rockefeller University] suggest that an ancestor of an NPC component, called the Nup84 complex, may have been a key molecular sculptor responsible for such a reshaping of the membrane.”
To find out what the Nup84 complex is, you have to wade through the boring body of the article. For one thing, Nup84 is complicated:
“...the scientists ... found that the Nup84 complex in yeast is composed of two types of protein structures, “alpha solenoids” and “beta propellers.” Two of the proteins are beta propellers, three are alpha solenoids and two are composed of beta propeller “heads” attached to alpha solenoid “tails.” The scientists showed that the architecture of the Nup84 complex also appears in the NPCs of human and plant cells and is therefore conserved throughout eukaryotes.”
As our regular readers know, any functional protein is composed of a chain of amino acids, all left-handed, assembled by a complex factory of molecular machines (see online book). The function of a protein is dependent on the precise sequence of the amino acids and the way the chain is folded with the help of other machines named chaperones. When you have a complex of proteins working together (and most proteins work in complexes), the requirements for specified complexity are even higher. The authors are assuming that this protein complex Nup84 emerged through a Darwinian process.
What’s the gist of the missing link claim? Basically, that Nup84 not only can curve a membrane, it is also involved in shuttling cargo around the cell. Since both prokaryotes and eukaryotes do that, but only eukaryotes curve their membranes to form organelles, they concluded that Nup84 is a missing link, a “crucial evolutionary link.”
Bacterial Hypodermic Needle Examined 11/10/2004
Those who have seen the film Unlocking the Mystery of Life might recall seeing the image of the “needle-nosed cellular pump” that some evolutionists claim was an intermediate for the bacterial flagellum. Those wishing to investigate this claim further might want to see the renditions that a Yale team produced of the pump, called a Type III Secretion System (TTSS), in the Nov. 5 issue of Science.1 Their introduction describes the machine:
“TTSSs are composed of more than 20 proteins, including a highly conserved group of integral membrane proteins, a family of customized cytoplasmic chaperones, and several accessory proteins, placing TTSSs among the most complex protein secretion systems known.”
Their images of the TTSS show parts resembling exquisitely crafted rings, gears, sockets, rods and tubes. The parts are flexible and undergo drastic conformational changes during assembly that amount to reprogramming of the parts. Here’s a small sample of what transpires during the assembly of this one molecular complex:
“Contoured longitudinal sections revealed conformational changes that occurred during the transition from the base to the fully assembled needle complex (Fig. 3, A and B). The cuplike protrusion that emerged from the basal plate of IR1 moved down, while an inward, clamping movement of IR2 redefined the shape of the cavity that is located below the basal plate of the base (movie S2). These conformational changes may provide the structural basis for the functional reprogramming of the TTSS machinery, which upon completion of needle assembly, switches from secreting the needle protein PrgI, the inner-rod protein PrgJ (see below), and the regulatory protein InvJ ... to secreting the effector proteins that are delivered into the host cell. On the opposite side of the basal plate, the socketlike structure underwent an outward movement, which created an attachment point for the inner rod (movie S2). A similar outward movement was observed for OR1, which created space for the needle to dock at the outermost perimeter of the base (movie S2). These changes were complemented by an outward movement of OR2 and a drastic remodeling that flattened the septum, sealing the apical side of the base, against OR2 during needle assembly (Fig. 3, A and B; movie S2). This rearrangement of the septum is essential for creation of the secretion channel and transformed part of InvG from being a barrier into forming two scaffolds that enable assembly of the needle and the inner rod. Like the socket structure at the basal end of the chamber, these new scaffolds likely serve as adaptors, accommodating the symmetry mismatches between the base, the needle, and the inner rod.”
Thus, the assembly of the TTSS involves not only parts coming together, but a coordinated series of shape changes of the parts relative to one another such that they fit together tightly, to enable the finished pumping action. We know the TTSS largely from “virulence of many Gramnegative bacteria pathogenic for animals and plants”.
--------------------------------------------------------------------------------
1Marlovits et al., “Structural Insights into the Assembly of the Type III Secretion Needle Complex,&148; Science, Vol 306, Issue 5698, 1040-1042, 5 November 2004, [DOI: 10.1126/science.1102610].
Flagellar Oars Beat Like Galley Slaves In Synchronization 12/26/2004
The Dec. 14 issue of Current Biology1 investigated another mystery in the operation of eukaryotic flagella:
“Flagella are microtubule-based structures that propel cells through the surrounding fluid. The internal structure of a flagellum consists of nine parallel doublet microtubules arranged around a central pair of singlet microtubules (Figure 1). Force for propulsion is provided by thousands of dynein motors anchored in rows along one side of each doublet, which can walk along the microtubule of the adjacent doublet. In order to produce coordinated bending of the flagellum, these dynein motors — organized into multi-headed complexes called the inner and outer dynein arms — must produce their power strokes in synchrony, like the oarsmen on an ancient Mediterranean war-galley. But whereas oar-strokes were coordinated by a continuous drum-beat, it is much less clear how flagellar dynein motors are synchronized.”
The authors of the paper consider growing evidence that the central microtubule pair provides the drumbeat, with the aid of “a protein complex called the dynein regulatory complex, located between the spokes and the dynein arms.” However, “The molecular mechanism by which the central pair regulates dynein is not known.”
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1Kimberly A. Wemmer and Wallace F. Marshall, “Flagellar Motility: All Pull Together,” Current Biology Volume 14, Issue 23, 14 December 2004, Pages R992-R993, doi:10.1016/j.cub.2004.11.019.
Cells Find Signal in the Noise 12/20/2004
Parents at an amusement park know the challenge of picking out their child’s voice, or even hearing their own hollering, in the noise of the crowd. Yelling won’t help much if the rest of the crowd is yelling also. Acoustic engineers know that raising the volume while playing back a noisy tape amplifies the noise as well as the signal. Cells have a novel way of meeting this challenge, as two Japanese mathematical biologists discuss in PNAS.1 Cells are continuously sending and receiving chemical messages, a process called signal transduction. Treating the cell signal transduction network like a physical system of receivers and amplifiers, the researchers noted that a cell, like an amusement park, is an intrinsically noisy place, yet some of the reactions are very sensitive. “How cells respond properly to noisy signals by using noisy molecular networks is an important problem in elucidating the underlying ‘design principle’ of cellular systems,” they say in the introduction. How do the sensitive reactions get their messages through all that noise?
“Because intracellular processes are inherently noisy, stochastic reactions process noisy signals in cellular signal transduction. One essential feature of biological signal transduction systems is the amplification of small changes in input signals. However, small random changes in the input signals could also be amplified, and the transduction reaction can also generate noise. Here, we show theoretically how the abrupt response of ultrasensitive signal-transduction reactions results in the generation of large inherent noise and the high amplification of input noise. The inherently generated noise propagates with amplification through intracellular molecular network. We discuss how the contribution of such transmitted noise can be shown experimentally. Our results imply that the switch-like behavior of signal transduction could be limited by noise; however, high amplification reaction could be advantageous to generate large noise, which would be essential to maintain behavioral variability.”
They categorized the noise as intrinsic, coming from the reaction itself, to extrinsic, coming from other reactions. This is somewhat like hearing your own voice vs. the yelling of those around you. The intrinsic noise has higher frequency than the extrinsic noise. As one source of noise becomes dominant, it reaches a crossover point where the other source is less dominant. This provides a kind of signal, or switch, which the cell can use to advantage:
“From our result, it can be further suggested that if the extrinsic noise dominates, the upstream reactions affect the fluctuation of the most downstream reaction, which determines the cellular behavior. As a result, the behavioral fluctuations are made up of the contributions of the fluctuations of several upstream reactions. On the other hand, if the intrinsic noise dominates, only the intrinsic noise of the most downstream reaction determines the behavioral fluctuations. As a result, the behavior could be simpler than the case in which extrinsic noise is dominant....
....Consequently, the low-frequency modulations in the downstream reactions can be affected by the behaviors of upstream reactions, whereas the high-frequency modulations are expected to be independent of upstream reactions.”
As a result, a bacterium can respond to chemicals in the environment, the hemoglobin in your blood can respond to changing conditions in the capillaries, genes can respond correctly to requests for expression, and complex cascades of cellular reactions can respond to the signal from any reaction in the series, in the midst of all the noise. “Therefore,” they conclude, “the result implies that the extrinsic noise is essential to maintain the behavioral variability in wild-type bacteria.” Their experiments related to three relatively simple reactions, and their analysis considered primarily linear response. Many cellular reactions involve nonlinear behavior. “In these cases,” they admit, “the relation between the response and the fluctuations can be more complicated than the relations we studied.”
--------------------------------------------------------------------------------
1Tatsuo Shibata and Koichi Fujimoto, “Noisy signal amplification in ultrasensitive signal transduction,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0403350102, published online before print December 29, 2004.
Evolutionists frequently point to the emergence of bacterial resistance to antibiotics as an example of Darwinian evolution occurring right under our noses. Bruce R. Levin of Emory University, writing in the Sept. 10 issue of Science,1 is not so sure about that. He points out that cells might just have a built-in mechanism to shut down growth and reproduction in times of stress (the SOS response), to minimize the damage from toxins in the environment. He points to two studies in the same issue that indicate how noninherited resistance to antibiotics can be generated without reference to Darwinian natural selection.
What’s more interesting in his report is his rebuke against fellow Darwinists who leap to unsubstantiated tales of evolution to explain how these mechanisms come about. His final paragraph states:
“It is easy to concoct just-so stories to explain the evolution of a mechanism that, like the SOS response, produces quiescent cells that are refractory to lethal agents. Yet it seems unlikely that ampicillin was the original selective force [sic] responsible for the evolution [sic] of the induction mechanism observed by Miller and colleagues. A bigger challenge to those in the evolution business is to account for the generation of lower fitness cell types when they do not provide an advantage to the collective, like the persisters of Balaban et al. in the absence of antibiotics. Then again, just like people, bacteria do some seemingly perverse things that are not easy to account for by simple stories of adaptive evolution.
--------------------------------------------------------------------------------
1Bruce R. Levin, “Microbiology: Noninherited Resistance to Antibiotics,” Science, Vol 305, Issue 5690, 1578-1579, 10 September 2004, [DOI: 10.1126/science.1103077].
Peering Into Paley’s Black Box: The Gears of the Biological Clock 09/15/2004
William Paley’s famous “watchmaker argument” for the existence of a Designer, though intuitively logical to many, has been criticized by naturalists on the grounds that one cannot compare mechanical devices to biological ones. Biological “contrivances” might operate on totally different principles than mechanical ones made by humans we know.
Michael Behe’s 1996 book Darwin’s Black Box was built on the theme that, until recently, the living cell was a “black box” to biologists: i.e., a system whose inner workings lay hidden from us. But now with the rapid advances in molecular biology, we are finding the cell to be a complex factory of molecular machines.
These themes of Paley and Behe seemingly converge in a commentary by Susan S. Golden (Texas A&M) in PNAS about biological clocks.1 Golden works at the Center for Research on Biological Clocks in the Texas A&M Biology Department, and was struck by recent findings in two other papers in PNAS on the circadian rhythms of “primitive” blue-green algae (cyanobacteria). To her, they suggested we are opening the black box of biological clocks, and finding treasures that look remarkably familiar to the clocks we know:
“A physiological black box is to a biologist what an ornately decorated package is to a small child: a mysterious treasure that promises delightful toys within. With fitting elan, a small community of scientists has ripped open the packaging of the cyanobacterial circadian clock, compiled the parts list, examined the gears, and begun to piece together the mechanism. Over the past 2 years, the 3D molecular structures have been solved for the core components of the cyanobacterial circadian clock: KaiA, KaiB, and KaiC. In a surprisingly literal analogy to mechanical timepieces, the protein that seems to be at the heart of the clock mechanism, KaiC, forms a hexameric ring that even looks like a cog: the escape wheel, perhaps. Previous work has shown that KaiC has an autophosphorylation activity, and that the presence of KaiA and KaiB modulates the extent to which KaiC is phosphorylated. In this issue of PNAS, Nishiwaki et al. biochemically identify two amino acid residues on KaiC to which phosphoryl groups covalently attach, and show the necessity in vivo of a phosphorylation-competent residue at these positions. By searching the crystal structure for evidence of phosphorylated sites, Xu et al. pinpoint a third residue that may “borrow” the phosphoryl group dynamically. Together, their work contributes richly to our understanding of what makes the gears mesh and turn to crank out a 24-h timing circuit....
Because each of these components (at minimum) is a dimer [composite of two molecular chains], KaiC is known to be a hexamer [composite of six chains], and other proteins may be present as well, the cyanobacterial clock can be thought of as an organelle unto itself: a “periodosome” that assembles and disassembles during the course of a day, defining the circadian period.”
The term “periodosome” means “time-keeping body” – i.e., clock. Her diagram shows KaiC as a six-sided carousel to which phosphate groups and other subunits attach and detach during the diurnal cycle. The feedback between the units provides the periodicity of the clock, similar to the back-and-forth pendulum in a grandfather clock or the escape wheel in a wristwatch. How is the clock tuned to the day-night cycle? Where do the parts come together, and how do the clock gears mesh with other cellular machines? We don’t know yet; the box has just been opened.
The clocks examined in these papers are the “simple” clocks of blue-green algae, compared to the much more complex biological clocks in eukaryotes. Even about these relatively simple systems in cyanobacteria much remains to be understood, but our initial glimpses into the inner workings of a biological clock at the molecular level remind her of the delight of opening a chest of toys for the first time:
“Identification of other potential components of the periodosome, intracellular localization of the clock parts, and elucidation of other potential modifications all may yield gears that are required to smoothly tick away the time and ensure that daughter cells do not run fast or slow.
The cyanobacterial clock box, no longer black, is a chest filled with bioluminescence and attractive toys. Putting together the pieces to design a clock is a tedious task, but S. elongatus is a gracious host, and the guests at the party are hard at work.”
--------------------------------------------------------------------------------
1Susan S. Golden, “Meshing the gears of the cyanobacterial circadian clock,“ Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0405623101
Secrets of the Spliceosome Revealed 09/17/2004
A husband and wife team from Hebrew University has revealed the structure of the spliceosome, one of the most complex molecular machines in the cell (see 09/12/2002 headline), in more detail than ever before, says EurekAlert. The spliceosome is responsible for cutting out the introns in messenger RNA after it has transcribed DNA, and also for “alternative splicing” that rearranges the exons to produce a variety of proteins from the same DNA template: “Alternative splicing, which underlies the huge diversity of proteins in the body by allowing segments of the genetic code to be strung together in different ways, takes place in the spliceosome as well.”
The Sperlings found a tunnel between the two major subunits of the machine where they believe the cutting and splicing operations take place, and also a cavity that might provide a safe haven for the messenger RNA strand, like a waiting room, before its surgery. Also, they found that four spliceosomes are bound together into a “supraspliceosome” which is able to do “simultaneous multiple interactions, rather than by a stepwise assembly” as inferred from other experiments in vitro. Their investigation in vivo (within a functioning, living cell) revealed even more complexity in the composite machine than had been seen in the individual machines:
“Such a large number of interactions that the cell has to deal with can be regulated within the supraspliceosome. Having the native spliceosomes as the building blocks of this large macromolecular assembly, this large number of interactions can be compartmentalized into each intron that is being processed. At the same time, the whole supraspliceosome enables the communication between the native spliceosomes, which is needed for regulated splicing. The organization of the supraspliceosome, like other macromolecular assemblies that exist as preformed entities, avoids the necessity to recruit the multitude of splicing components each time the spliceosome turns over. In that sense, the overall coordination of the cellular interactions is reduced from the hard work of repeatedly placing each piece in the correct position of the puzzle to the relatively simpler work of coordinating the preformed puzzle.”
In short, “The supraspliceosome represents a stand-alone complete macromolecular machine capable of performing splicing of every pre-mRNA independent of its length or number of introns.” They found that the individual spliceosomes are joined with a flexible joint like a hinge to provide flexible interactions and communication. Their work was published in Molecular Cell Sept. 10.1
--------------------------------------------------------------------------------
1Sperling et al., “Three-Dimensional Structure of the Native Spliceosome by Cryo-Electron Microscopy,” Molecular Cell, Volume 15, Issue 5, 10 September 2004, Pages 833-839; doi:10.1016/j.molcel.2004.07.022.
Bacterial Flagellum Reveals New Structural Complexity 10/27/2004
The bacterial flagellum, the unofficial mascot of the Intelligent Design movement, got more praise from the evolutionary journal Nature this week: Samatey et al.1 analyzed the hook region in detail and found that it is composed of 120 copies of a specialized protein that “reveals the intricate molecular interactions and a plausible switching mechanism for the hook to be flexible in bending but rigid against twisting for its universal joint function.”
Christopher Surridge, commenting on this paper in the same issue,2 adds that this joint must be able to bend up to 90 degrees in a millisecond or less while rotating at up to 300 times per second. He says that the researchers describe “how they determined the atomic structure of this super-flexible universal joint, and thereby how it achieves such a feat of engineering.”
--------------------------------------------------------------------------------
1Samatey et al., “Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism,” Nature 431, 1062 - 1068 (28 October 2004); doi:10.1038/nature02997.
2Christopher Surridge, “Molecular motors: Smooth coupling in Salmonella,” Nature 431, 1047 (28 October 2004); doi:10.1038/4311047b.
“Crucial Evolutionary Link” Found for Eukaryotes 11/05/2004
Often the opening words of a news story are what stick in the memory: “crucial evolutionary link.” The corroborating evidence, however, is buried in technical details of the press release from Rockefeller University, posted on NewsWise. In short, the researchers claim:
“Scientists believe the emergence of organelles, compartments in the eukaryotic cell’s cytoplasm that perform such functions as energy production, waste removal and protein synthesis, and a nucleus evolved between 2 and 3 billion years ago.
One hypothesis regarding the evolution of eukaryotic cells suggests that the endomembrane system developed because some ancient bacterial cells had the ability to sharply curve their membranes, allowing them to form internal membrane structures as well as to engulf other organisms. The findings reported by [Michael P.] Rout and colleagues [Rockefeller University] suggest that an ancestor of an NPC component, called the Nup84 complex, may have been a key molecular sculptor responsible for such a reshaping of the membrane.”
To find out what the Nup84 complex is, you have to wade through the boring body of the article. For one thing, Nup84 is complicated:
“...the scientists ... found that the Nup84 complex in yeast is composed of two types of protein structures, “alpha solenoids” and “beta propellers.” Two of the proteins are beta propellers, three are alpha solenoids and two are composed of beta propeller “heads” attached to alpha solenoid “tails.” The scientists showed that the architecture of the Nup84 complex also appears in the NPCs of human and plant cells and is therefore conserved throughout eukaryotes.”
As our regular readers know, any functional protein is composed of a chain of amino acids, all left-handed, assembled by a complex factory of molecular machines (see online book). The function of a protein is dependent on the precise sequence of the amino acids and the way the chain is folded with the help of other machines named chaperones. When you have a complex of proteins working together (and most proteins work in complexes), the requirements for specified complexity are even higher. The authors are assuming that this protein complex Nup84 emerged through a Darwinian process.
What’s the gist of the missing link claim? Basically, that Nup84 not only can curve a membrane, it is also involved in shuttling cargo around the cell. Since both prokaryotes and eukaryotes do that, but only eukaryotes curve their membranes to form organelles, they concluded that Nup84 is a missing link, a “crucial evolutionary link.”
Bacterial Hypodermic Needle Examined 11/10/2004
Those who have seen the film Unlocking the Mystery of Life might recall seeing the image of the “needle-nosed cellular pump” that some evolutionists claim was an intermediate for the bacterial flagellum. Those wishing to investigate this claim further might want to see the renditions that a Yale team produced of the pump, called a Type III Secretion System (TTSS), in the Nov. 5 issue of Science.1 Their introduction describes the machine:
“TTSSs are composed of more than 20 proteins, including a highly conserved group of integral membrane proteins, a family of customized cytoplasmic chaperones, and several accessory proteins, placing TTSSs among the most complex protein secretion systems known.”
Their images of the TTSS show parts resembling exquisitely crafted rings, gears, sockets, rods and tubes. The parts are flexible and undergo drastic conformational changes during assembly that amount to reprogramming of the parts. Here’s a small sample of what transpires during the assembly of this one molecular complex:
“Contoured longitudinal sections revealed conformational changes that occurred during the transition from the base to the fully assembled needle complex (Fig. 3, A and B). The cuplike protrusion that emerged from the basal plate of IR1 moved down, while an inward, clamping movement of IR2 redefined the shape of the cavity that is located below the basal plate of the base (movie S2). These conformational changes may provide the structural basis for the functional reprogramming of the TTSS machinery, which upon completion of needle assembly, switches from secreting the needle protein PrgI, the inner-rod protein PrgJ (see below), and the regulatory protein InvJ ... to secreting the effector proteins that are delivered into the host cell. On the opposite side of the basal plate, the socketlike structure underwent an outward movement, which created an attachment point for the inner rod (movie S2). A similar outward movement was observed for OR1, which created space for the needle to dock at the outermost perimeter of the base (movie S2). These changes were complemented by an outward movement of OR2 and a drastic remodeling that flattened the septum, sealing the apical side of the base, against OR2 during needle assembly (Fig. 3, A and B; movie S2). This rearrangement of the septum is essential for creation of the secretion channel and transformed part of InvG from being a barrier into forming two scaffolds that enable assembly of the needle and the inner rod. Like the socket structure at the basal end of the chamber, these new scaffolds likely serve as adaptors, accommodating the symmetry mismatches between the base, the needle, and the inner rod.”
Thus, the assembly of the TTSS involves not only parts coming together, but a coordinated series of shape changes of the parts relative to one another such that they fit together tightly, to enable the finished pumping action. We know the TTSS largely from “virulence of many Gramnegative bacteria pathogenic for animals and plants”.
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1Marlovits et al., “Structural Insights into the Assembly of the Type III Secretion Needle Complex,&148; Science, Vol 306, Issue 5698, 1040-1042, 5 November 2004, [DOI: 10.1126/science.1102610].
Flagellar Oars Beat Like Galley Slaves In Synchronization 12/26/2004
The Dec. 14 issue of Current Biology1 investigated another mystery in the operation of eukaryotic flagella:
“Flagella are microtubule-based structures that propel cells through the surrounding fluid. The internal structure of a flagellum consists of nine parallel doublet microtubules arranged around a central pair of singlet microtubules (Figure 1). Force for propulsion is provided by thousands of dynein motors anchored in rows along one side of each doublet, which can walk along the microtubule of the adjacent doublet. In order to produce coordinated bending of the flagellum, these dynein motors — organized into multi-headed complexes called the inner and outer dynein arms — must produce their power strokes in synchrony, like the oarsmen on an ancient Mediterranean war-galley. But whereas oar-strokes were coordinated by a continuous drum-beat, it is much less clear how flagellar dynein motors are synchronized.”
The authors of the paper consider growing evidence that the central microtubule pair provides the drumbeat, with the aid of “a protein complex called the dynein regulatory complex, located between the spokes and the dynein arms.” However, “The molecular mechanism by which the central pair regulates dynein is not known.”
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1Kimberly A. Wemmer and Wallace F. Marshall, “Flagellar Motility: All Pull Together,” Current Biology Volume 14, Issue 23, 14 December 2004, Pages R992-R993, doi:10.1016/j.cub.2004.11.019.
Cells Find Signal in the Noise 12/20/2004
Parents at an amusement park know the challenge of picking out their child’s voice, or even hearing their own hollering, in the noise of the crowd. Yelling won’t help much if the rest of the crowd is yelling also. Acoustic engineers know that raising the volume while playing back a noisy tape amplifies the noise as well as the signal. Cells have a novel way of meeting this challenge, as two Japanese mathematical biologists discuss in PNAS.1 Cells are continuously sending and receiving chemical messages, a process called signal transduction. Treating the cell signal transduction network like a physical system of receivers and amplifiers, the researchers noted that a cell, like an amusement park, is an intrinsically noisy place, yet some of the reactions are very sensitive. “How cells respond properly to noisy signals by using noisy molecular networks is an important problem in elucidating the underlying ‘design principle’ of cellular systems,” they say in the introduction. How do the sensitive reactions get their messages through all that noise?
“Because intracellular processes are inherently noisy, stochastic reactions process noisy signals in cellular signal transduction. One essential feature of biological signal transduction systems is the amplification of small changes in input signals. However, small random changes in the input signals could also be amplified, and the transduction reaction can also generate noise. Here, we show theoretically how the abrupt response of ultrasensitive signal-transduction reactions results in the generation of large inherent noise and the high amplification of input noise. The inherently generated noise propagates with amplification through intracellular molecular network. We discuss how the contribution of such transmitted noise can be shown experimentally. Our results imply that the switch-like behavior of signal transduction could be limited by noise; however, high amplification reaction could be advantageous to generate large noise, which would be essential to maintain behavioral variability.”
They categorized the noise as intrinsic, coming from the reaction itself, to extrinsic, coming from other reactions. This is somewhat like hearing your own voice vs. the yelling of those around you. The intrinsic noise has higher frequency than the extrinsic noise. As one source of noise becomes dominant, it reaches a crossover point where the other source is less dominant. This provides a kind of signal, or switch, which the cell can use to advantage:
“From our result, it can be further suggested that if the extrinsic noise dominates, the upstream reactions affect the fluctuation of the most downstream reaction, which determines the cellular behavior. As a result, the behavioral fluctuations are made up of the contributions of the fluctuations of several upstream reactions. On the other hand, if the intrinsic noise dominates, only the intrinsic noise of the most downstream reaction determines the behavioral fluctuations. As a result, the behavior could be simpler than the case in which extrinsic noise is dominant....
....Consequently, the low-frequency modulations in the downstream reactions can be affected by the behaviors of upstream reactions, whereas the high-frequency modulations are expected to be independent of upstream reactions.”
As a result, a bacterium can respond to chemicals in the environment, the hemoglobin in your blood can respond to changing conditions in the capillaries, genes can respond correctly to requests for expression, and complex cascades of cellular reactions can respond to the signal from any reaction in the series, in the midst of all the noise. “Therefore,” they conclude, “the result implies that the extrinsic noise is essential to maintain the behavioral variability in wild-type bacteria.” Their experiments related to three relatively simple reactions, and their analysis considered primarily linear response. Many cellular reactions involve nonlinear behavior. “In these cases,” they admit, “the relation between the response and the fluctuations can be more complicated than the relations we studied.”
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1Tatsuo Shibata and Koichi Fujimoto, “Noisy signal amplification in ultrasensitive signal transduction,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0403350102, published online before print December 29, 2004.