Is SUMOylation RNA-directed DNA methylation? (revisited)

By: James V. Kohl | Published on: July 3, 2015

See: Is SUMOylation RNA-directed DNA methylation? posted here on 6/16/15
See also:
1) The Persistence of Hippocampal-Based Memory Requires Protein Synthesis Mediated by the Prion-like Protein CPEB3 (subscription required 6/17/15)
2) SUMOylation Is an Inhibitory Constraint that Regulates the Prion-like Aggregation and Activity of CPEB3 (open access 6/23/15)
3) The CPEB3 Protein Is a Functional Prion that Interacts with the Actin Cytoskeleton (open access 6/23/15)
4) MicroRNA-22 Gates Long-Term Heterosynaptic Plasticity in Aplysia through Presynaptic Regulation of CPEB and Downstream Targets (open access 6/30/15)
The journal articles linked above were collectively reported on 7/2/15 in the context of:

Long-term memories are maintained by prion-like proteins

On the same day, this free on demand webinar from Beckman Coulter became available.

Exosome Biogenesis and the Budding of Proteins and Viruses

Exosomes are small secreted vesicles that have a diameter of ~50-200 nm. Exosomes are enriched for a specific subset of host-derived proteins, nucleic acids, lipids and carbohydrates, though they also incorporate most host cell molecules at baseline levels. Various models of exosome biogenesis have been proposed, but the field lacks the robust mechanistic studies that are needed to obtain a molecular understanding of vesicle secretion. To shed light on this process, our laboratory has taken a cargo-based approach in which we focus on the cis-acting signals that are necessary and sufficient for the budding of specific proteins. These studies have revealed that exosomal proteins are targeted to sites of vesicle budding by a combination of (1) high-order oligomerization and (2) binding to the plasma membrane. In addition, our work supports the hypothesis that the plasma membrane is a major site of exosome budding. Interestingly, HIV and other retroviruses have the same topology, size, and array of host cell molecules as exosomes, raising the possibility that retroviruses bud from infected cells by an exosomal pathway. This hypothesis is supported by the fact that retroviral Gag proteins, their main structural protein, are targeted to sites of exosome budding, bud from cells in association with exosomal cargo proteins, form high-order oligomeric complexes that bind the plasma membrane, and require plasma membrane binding in order to bud from cells. Modeling HIV budding as an exosomal process has led to new lines of experimentation, new sets of data, and new interpretations of decades-old observations, all of which provide increasing support for the hypothesis that HIV and other retroviruses exploit the exosomal machinery to generate infectious viral particles.
The talk is presented by Stephen J. Gould, Ph.D.
Exosomes and human endogenous retroviruses share similar properties. Their propertiest link viral microRNAs that contribute to entropic elasticity and the anti-entropic epigenetic effects of nutrient-dependent microRNAs from the epigenetic landscape to the physical landscape of DNA via the conserved molecular mechanisms of nutrient-dependent RNA-mediated protein folding. The protein folding is perturbed by viruses, which is how prions and viruses are linked to learning and memory pathologies.
@ 27:52 A 10-amino acid decapeptide appears to link glycine to the stability of the genome.
This question arises: Is the light-induced de novo creation of achiral glycine also the link to the stability of all organized genomes via the ability of nutrient uptake to epigenetically effect cell type differentiation?
That question arises because we all have the human endogenous retrovirus (HERV)-K in our organized genomes. The answer to the question about achiral glycine may link the organized genomes of microbes, such as yeasts, to learning and memory in humans via the decapeptide hormone, GnRH, which links odors and pheromones to feedback loops and the physiology of reproduction in mammals. See: Feedback loops link odor and pheromone signaling with reproduction
See also: The Darwin Code by Greg Bear

In fact, even in 1983, when I was preparing my novel Blood Music, I asked myself–what do viruses do ¬for us

Greg Bear’s interest in HERVs was piqued by what was known about HIV in the mid-1980s.
@ 34:01 minutes what was known in the 1980s about  retrovirus “evolution” is placed into the context of a “selective advantage.” Is only the nutrient-dependent RNA-mediated glycine substitution required for the selective advantage to be manifested?
We may never know. The Gly2 substitution is referred to as a single-point mutation. Also, NIH doesn’t like the idea of a “Trojan Exosome.” Is that because it links virus-perturbed protein folding to pathology and nutrient-dependent RNA-mediated amino acid substitutions to health and longevity via the biophysically constrained chemistry of protein folding?
We may never get the answer to that question.  But, here’s a clue.
See also: Chapter 1: How Genes Work

Over time, mutations supply the raw material from which new life forms evolve (see Chapter 3, “Life’s Genetic Tree”).

The idea that mutation can be linked, over time, to the evolution of new life forms, has not been supported by experimental evidence of biologically-based cause and effect, which links RNA-mediated cell type differentiation to learning and memory via the honeybee model organism.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

That fact can be understood and compared in the context of a stated opinion about mutations and evolution that is a misrepresentation of what is known to serious scientists about the biophysically constrained chemistry of protein folding. However, the facts about RNA-mediated protein folding challenge the position on mutations and evolution that the NIH has typically defended. The director of the NIH is a theistic evolutionist who wrote The Language of God: A Scientist Presents Evidence for Belief. The challenge to his misrepresentation of DNA as the “language of God” has been placed into the context of biologically-based cause and effect that clearly links nutritional epigenetics to the pharmacogenomic testing that was touted in the President’s  2015 “State of the Union” address.
In the presentation by Stephen J. Gould, the SP2 substitution appears to inhibit viral replication and budding is restored with via mutations, which appear to be amino acid substitutions.
If the substitution of achiral glycine inhibits viral replication in species from microbes to humans, it could be the key to RNA-mediated cell type differentiation in all genera. However, making synthetic exosomes seems to be a primary concern of drug manufacturers who make no money by teaching people how to control the nutrient-dependent RNA-mediated cell type differentiation that links perturbed protein folding to pathology and proper protein folding to healthy longevity.

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