Reverse phosphorylation

By: James V. Kohl | Published on: March 9, 2015

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See for review: Let there be anti-entropic light (1)

Squid are hyper-editors when it comes to RNA

This is a great summary of what is currently known about anti-entropic light and nutrient-dependent RNA-mediated pheromone-controlled cell type differentiation.
Excerpt: “During RNA editing, specific enzymes alter nucleotides in mRNA transcripts so that the resulting protein differs in amino acid sequence from what was encoded by the original DNA. Such RNA editing is a means to generate greater protein diversity…”
The RNA-editing links specific enzymes to differences in the amino acid sequences of the bioluminescent bacteria in the light organ of the bobtail squid to its successful foraging and pheromone-controlled physiology of nutrient-dependent reproduction. An example of how quickly specific enzymes can cause reversible changes in phosphorylation linked to across-species changes in amino acid substitutions in the organized genomes of species from microbes to man was published as:
‘Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system‘
Excerpt: Table 1 Mutational trajectory toward slow- and fast-spreading phenotypes.

Mutations confirmed in slow-spreading motility variants are predicted to result in hyperphosphorylation of NtrC; mutations in fast-spreading variants lead to predicted switched specificity of NtrC-P toward FleQ targets. Slow- and fast-spreading variants share the same ancestry.”

My comment: Nutrient-dependent phosphorylation and the pheromone-controlled fixation of amino acid substitutions appears to be the most obvious difference between bacteria that “re-evolved” their functional flagella over-the-weekend and those that did not. However, the nutrient-dependent phosphorylation was reported in the context of mutations in the slow-spreading and in the fast-spreading variants that shared the same ancestry. Results were reported in the context of mutations and evolution in Bacteria ‘hotwire their genes’ to fix a faulty motor.
Excerpt: “Amazingly, we found that just a single tiny change to one of these genetic switches was enough to convert it from being a switch that would normally turn on the genes for using nitrogen into a switch that now turns on the genes to build the flagella. The result is that the bacterium had, in effect, evolved a way to hotwire its motor practically overnight.”
My comment: This does not seem to me to exemplify mutation-driven evolution of microbial flagella or their re-evolution, which occurs “practically overnight.” Instead, it places both outcomes into the same process of what must involve the biophysically constrained chemistry of protein folding and RNA-directed DNA methylation that appears to leads to the RNA-mediated amino acid substitutions via reversible phosphorylation.
If flagella are required to find food, the mutations that caused their loss and loss of function can be repaired if the right nutrients are within their reach.
“Nutrients within reach” is one of the basic principles of DNA repair. In the context of viral microRNAs and genetic entropy, nutrients lead to anti-entropic epigenetic effects on the pheromone-controlled physiology of reproduction. If they did not, organisms could not ecologically adapt. They would be forced to mutate and become another species, which is only possible in the context of ridiculous theories about evolution and some science fiction novels.
The tractable model of fixed amino acid substitutions that they presented was extended across species to primates brain development in 1973, when Dobzhansky wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” Links from nutrient-dependent energy to cell type differentiation via amino acid substitutions were addressed, in theory, in Metabolic theory predicts whole-ecosystem properties. However, the intimate relationships among carbon and energy budgets are not just theoretical.
Excerpt: Carbon dioxide, water, and solar energy are incorporated into the high-energy bonds of organic compounds of plant producers during photosynthesis. When the organic bonds are broken during respiration, plants, animal consumers, and microbial decomposers obtain usable energy in the form of ATP.
My comment: If the authors had simply explained that all biological energy comes from the sun, the link from light-induced amino acid substitutions and photosynthesis to nutrient-dependent pheromone-controlled fixation of amino acid substitutions liked to expansion of the human neocortex compared to other primates might have been clearer. The link is clear in Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion.
Journal Excerpt: “This indicates that the C-terminal 47 amino-acids of ARHGAP11B (after lysine-220) constitute not only a unique sequence, resulting from a frameshifting deletion (fig. S10), but also are functionally distinct from their counterpart in ARHGAP11A.”
My comment: The unique sequence of amino-acids that differentiate the cell types in primate brains was reported as A gene for brain size only found in humans.
Excerpt: “ARHGAP11B is the first human-specific gene where we could show that it contributes to the pool of basal brain stem cells and can trigger a folding of the neocortex. In that way, we managed to take the next step in tracing evolution”, summarizes Wieland Huttner.
My comment: The article about mutations and the evolution of the flagellum and its re-evolution over the weekend, can now be placed into the context of an evolved human-specific gene that might otherwise link mutations to developmental difference in primate brains. However, mutations perturb protein folding, which means they cannot possibly lead to increasing organismal complexity manifested in the structure and function of the flagellum or the structure and function of cell types in primate brains. Simply put, despite the claims of theorists, there is no such thing as a beneficial mutation that could lead to the creation or evolution of a new structure or function.
Note, however, that the co-author of the article on the human-specific gene and neocortex is Svante Paabo, who is considered one of the world’s foremost experts on the evolution of different species. He is frequently involved in reporting on the fossil record and many other aspects of evolution. Most researchers have recently quit reporting evolution as if it occurred via natural selection. See for example: The Surprising Origins of Evolutionary Complexity.
Excerpt: “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.
My comment: Evolution also seems to “just happen” in the context of constraint-breaking mutation. See for example: Mutation-Driven Evolution.
Conclusion: “In other words, genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.” (p. 199)
The problem with reporting evolution in the context of mutations and natural selection is tractable to the senior author, Svante Paabo, of Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
Conclusion (2003): “We find evidence for natural selection acting on OR genes in both human and chimpanzee. The data are consistent with purifying selection acting on intact OR genes in chimpanzee and positive selection acting on at least some of the intact OR genes in humans. We suggest that, whereas most human OR genes are under no or little evolutionary constraint, others have important functions shared with the apes and that a subset have evolved under positive selection in humans. Further studies of specific OR gene clusters in humans may identify the selected changes and shed light on what olfactory stimuli have exercised selective pressures on the human OR gene repertoire.”
My comment: The de novo creation of olfactory receptor genes is biophysically constrained by the nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation. The protein biosynthesis and degradation is perturbed by mutations, for example in the female mosquitoes of some species. See: orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET. The protein biosynthesis and degradation is nutrient-dependent and pheromone-controlled, which enables fixation of the amino acid substitutions linked to the de novo creation of olfactory receptor genes in species from insects to humans. See: Evolution of mosquito preference for humans linked to an odorant receptor and also see: Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex. (March 5, 2012)
I don’t think the link from the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man will become much clearer, which is why I wrote this:
My March 15, 2012 conclusion: “Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000). — Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
My 2013 conclusion: “Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.” — Nutrient-dependent/pheromone-controlled adaptive evolution: a model
My comment: Experts still make claims about mutations that lead to the re-evolution of the flagellum in microbes within days and they make claims about evolution of the human brain that supposedly somehow occurred during millions of years linked to natural selection on olfactory receptor genes. Serious scientists have realized that mutations perturb protein folding, which is stabilized by nutrient-dependent amino acid substitutions. Unfortunately, some scientists appear to be unable to coordinate the reporting of their results. On February 27, 2015 in “Science” ‘Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system‘ was linked to mutations and Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion was reported as if it “just happens.”
Excerpt: “ARHGAP11B arose on the human evolutionary lineage after the divergence from the chimpanzee lineage by partial duplication of ARHGAP11A (25, 26), which is found throughout the animal kingdom…”
My comment: The flagellum did not automagically arise in the microbial lineage. It arose in the context of nutrient uptake and pheromone-controlled fixation of amino-substitutions that differentiated the cell types of the same lineage, virtually overnight. The expansion of the human neocortex did not occur virtually overnight, but it clearly was nutrient-dependent and clearly involves RNA-directed DNA methylation and the RNA-mediated amino acid substitutions that link the de novo creation of structures and functions to difference in morphological and behavioral phenotypes in species from microbes to man via the biophysically constrained chemistry of protein folding. Clearly, serious scientists must view biologically-based cause and effect in the context of physical constraints and chemical constraints. For example, see: Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Excerpt: “…alternative splicing is used to alter protein phosphorylation, which can alter protein stability, subcellular localization, activity, and other properties [45].
My comment: Without alternative splicings, nutrient-dependent pheromone-controlled cell type differentiation could not be linked from RNA-directed DNA methylation to RNA-mediated amino acid substitutions that stabilize the DNA in the organized genomes of species from microbes to man.