Joined: May 2002
Some good stuff I found and posted in response to Nelson Alonzo here:
Or a pre-LCA ancestor got by with just a PPase, which is equally successful at generating proton energy gradients but is a heck of a lot simpler than the F1F0 ATPase (and shares some homology to boot).
What we see in nature is that B. subtilis, A. aeolicus, M.tuberculosis, M.
genitalium (the smallest genome) , and H. pylor have all 8 parts needed for the F-ATP synthase to function. If this system was truly designed, we would predict that we would find no such evolutionary history for the F-ATP synthase, and we find none. Because of IC, selection would have weeded out any broken ATP synthase, which is why we see it so conserved in all these organisms. Thus an obvious design hypothesis is that the LUCA of all bacteria contained an 8-part ATP synthase which was inteligently designed.
STRUCTURAL STUDIES OF PROTON TRANSLOCATING PYROPHOSPHATASE
Membrane-bound proton translocating pyrophosphatases (H+-PPase) use the energy of pyrophosphate (PPi) hydrolysis to drive proton transport across biological membranes. The formed proton gradient is subsequently used to energize many cellular processes e.g. solute transport and ATP synthesis. The active H+-PPase is a dimer of 60–82 kDa polypeptide monomers, which are predicted to contain 15 transmembrane a-helices. Transmembrane helices are connected by short extracellular turns and longer cytoplasmic loops, three of which are mainly thought to form the active site for PPi hydrolysis. Overall the predicted H+-PPase structure is pretty simple which makes it a good model system for structural and functional elucidation of the mechanism by which pyrophosphate hydrolysis is coupled to proton pumping.
Baltscheffsky is da guy to look at for beginning work on the origin of ATPases; brief online summary:
3.A.10 The H+-translocating Pyrophosphatase (H+-PPase) Family
Proteins of the H+-PPase family are found in the vacuolar (tonoplast) membrane of higher plants, algae, and protozoa, and in both bacteria and archaea. They are therefore ancient enzymes. The plant enzymes probably pump one H+ upon hydrolysis of pyrophosphate, thereby generating a proton motive force, postive and acidic in the tonoplast lumen. They establish a pmf of similar magnitude to that generated by the H+-translocating ATPases in the same vacuolar membrane . The bacterial and archaeal proteins may catalyze fully reversible reactions. The enzyme from R.rubrum contributes to the pmf when light intensity is insufficient to generate a pmf sufficient in magnitude to support rapid ATP synthesis.
Eukaryotic members of the H+-PPase family are large proteins of about 770 amino acyl residues with fifteen putative transmembrane a-helical spanners (TMSs). The N-termini are predicted to be in the vacuolar lumen while the C-termini are thought to be in the cytoplasm. These proteins exhibit a region that shows convincing sequence similarity to the regions surrounding the DCCD-sensitive glutamate in the C-terminal regions of the c-subunits of F-type ATPases (TC #3.A.2).
Note that pyrophosphate can be produced by common inorganic processes.
2. PPi and PPi synthase in the early evolution of biological energy conversion
After our discovery (with von Stedingk, Heldt and Klingenberg) of the first alternative biological electron transport phosphorylation system, leading in bacterial photophosphorylation to PPi rather than to ATP, we have sought evidence for or against the possibility that, in early biological evolution, PPi preceded ATP as the central energy carrier. At present we investigate active site motifs in the proton-pumping PPase family of enzymes (PPase = inorganic pyrophosphatase), to which also bacterial PPi synthase belongs. Of special significance may be certain recurring tetrapeptidyl motifs, which contain 75 - 100 % very early amino acids (Gly, Ala, Asp and Val). These motifs seem to play a central role in PPase function and may be particularly important for obtaining a first detailed picture of the molecular origin and early evolution of biological energy conversion with phosphate compounds. The motifs also show some similarity to corresponding, phosphate binding, regions in both ATP synthases and P-type ATPases.
Hmm, neither seems quite completely so true for the ATPase, because of the PPase. A simpler, partially sequence-similar system can perform the task. So even for a system older than the flagellum scientists are beginning to get hints indicating that ICness tain't all it's cracked up to be.
So lets review. A de-novo design hypothesis entails:
1. No evolutionary history
2. IC tied in with functional constraint (selection weeding out mutants because of ICness .
Well for starters, for the flagellum your reliance on Mike Gene has left you a bit out of date:
In the near future I want to bring Dembski into the mix. However, unless any relevant criticism of a specific system is brought up, I'm simply going to list them for now. And we can bring up another thread to discuss each system's history. For now, I'm just concerned with listing them.
The number of parts in a flagellum that don't have homologs with different, non-flagellar functions is getting to be rather low; mostly they are filament and shaft proteins, which all may be homologous with each other, and of course nonmotile filaments are known to have a wide degree of uses in bacteria...
Biochemistry 2001 Oct 30;40(43):13041-50
Conformational change in the stator of the bacterial flagellar motor.
Kojima S, Blair DF.
Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA.
MotA and MotB are integral membrane proteins of Escherichia coli that form the stator of the proton-fueled flagellar rotary motor. The motor contains several MotA/MotB complexes, which function independently to conduct protons across the cytoplasmic membrane and couple proton flow to rotation. MotB contains a conserved aspartic acid residue, Asp32, that is critical for rotation. We have proposed that the protons energizing the motor interact with Asp32 of MotB to induce conformational changes in the stator that drive movement of the rotor. To test for conformational changes, we examined the protease susceptibility of MotA in membrane-bound complexes with either wild-type MotB or MotB mutated at residue 32. Small, uncharged replacements of Asp32 in MotB (D32N, D32A, D32G, D32S, or D32C) caused a significant change in the conformation of MotA, as evidenced by a change in the pattern of proteolytic fragments. The conformational change does not require any flagellar proteins besides MotA and MotB, as it was still seen in a strain that expresses no other flagellar genes. It affects a cytoplasmic domain of MotA that contains residues known to interact with the rotor, consistent with a role in the generation of torque. Influences of key residues of MotA on conformation were also examined. Pro173 of MotA, known to be important for rotation, is a significant determinant of conformation: Dominant Pro173 mutations, but not recessive ones, altered the proteolysis pattern of MotA and also prevented the conformational change induced by Asp32 replacements. Arg90 and Glu98, residues of MotA that engage in electrostatic interactions with the rotor, appear not to be strong determinants of conformation of the MotA/MotB complex in membranes. We note sequence similarity between MotA and ExbB, a cytoplasmic-membrane protein that energizes outer-membrane transport in Gram-negative bacteria. ExbB and associated proteins might also employ a mechanism involving proton-driven conformational change.
The occurrence of significant conformational change in the stator has implications not only for the present-day mechanism but also for the evolution of the flagellar motor. A membrane complex that undergoes proton-driven conformational changes could perform useful work in contexts other than (and simpler than) the flagellar motor, and ancestral forms of the MotA/MotB complex might have arisen independently of any part of the rotor. We queried the sequence database using the sequence of the best-conserved part of MotA (the segment containing membrane segments 3 and 4) from Aquifex aeolicus, a species whose lineage is deeply branched from other bacteria. In addition to the expected MotA homologues, the search returned a protein sequence from the archaeal species Methanobacterium thermoautotrophicum (protein MTH1022) that shows significant sequence similarity not only to MotA but also to the protein ExbB (Figure 9). ExbB is a cytoplasmic-membrane protein that functions in conjunction with ExbD, TonB, and outer-membrane receptors to drive active transport of certain essential nutrients across the outer membrane of Gram-negative bacteria. The energy for this transport comes from the proton gradient across the inner membrane. Thus, MotA and ExbB are both components of systems that tap the proton gradient to do work some distance away (at either the rotor-stator interface or the outer membrane; Figure 9).
Other features also point to a connection between the Mot and Exb systems. MotA functions in a complex with MotB, which as noted contains the critical residue Asp32 near the cytoplasmic end of its single membrane segment. ExbB functions in a complex with ExbD, which likewise has a single membrane segment with a critical Asp residue near its cytoplasmic end (Asp25 in ExbD of E. coli; ref 59). Although ExbB has only three membrane segments in contrast to the four in MotA, the membrane segments that show sequence similarity have the same topology. The protein TonB is also present in the complex with ExbB and ExbD (59, 60) and would provide an additional membrane segment to round out the topological correspondence (Figure 9). ExbB contains a well-conserved Pro residue (Pro141 in E. coli ExbB) that is the counterpart of Pro173 of MotA. Although MotB and ExbD do not share close sequence similarity apart from the critical Asp residue, in certain positions in the membrane segment the residues most common in MotB proteins are also common in ExbD proteins. Finally, like the MotA/MotB complex the ExbB/ExbD complex contains multiple copies of each protein (61). Together, these facts make a reasonable case for an evolutionary connection between the Mot proteins of the flagellar motor and the Exb proteins of outer-membrane transport (and by extension the TolQ/TolR proteins, which are related to ExbB/ExbD but whose functions are less understood).
So even for systems that are remote from us by 3 billion years there has been some recent progress.
What I'd really be interested in, Nelson, is your opinion on the vertebrate immune system. IC or not? Evolved or not? Behe says IC, and intelligently designed.