Base pairs, olfaction and RNA thermometers

By: James V. Kohl | Published on: September 22, 2016

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RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae (2014)

Excerpt:

The stem-loop can be stabilized by strengthening the base pairing between the fourU element and SD sequence through the substitution of G-C base pairs, and this results in an elevated melting temperature (10).

Conclusion:

RNA thermometers represent a simple yet elegant mechanism for controlling temperature-dependent gene expression and may be more widespread among pathogenic bacteria that interact with mammalian hosts than is currently known.

Excerpt:

GC-poor miRNAs (GC<40%) were shown to be more degraded than GC-rich miRNAs. Although miRNAs are more robust than mRNAs, the deep sequencing data obtained using FFPE samples cannot be directly compared with the data obtained using fresh frozen tissue samples. The miRNA read counts in FFPE specimens are comparable only if the samples are prepared under the constant fixation conditions, and using the same sequencing protocol.

My comment: Energy-dependent changes link thermodynamic cycles of protein biosynthesis and degradation via the microRNA/messenger RNA balance. The balance links hydrogen-atom transfer in DNA base pairs in solution to microRNA flanking sequences, which have been linked from the de novo creation of olfactory receptor genes and other G protein-coupled receptors (GPCRs). The GPCRs are linked to all healthy longevity in all living genera. Loss of the GPCRs links virus-driven energy theft to all pathology via loss of functional structures in the olfactory glomeruli in the Drosophila antennal lobe.

See for instance: Elucidating the Neuronal Architecture of Olfactory Glomeruli in the Drosophila Antennal Lobe
Conclusion:

… our study demonstrates that each glomerulus is a unique morphological and functional unit whose significance regarding odor detection and odor-guided behavior can be predicted. Future studies dedicated to elucidating the synaptic connectivity in more detail will reveal whether ultrastructural characteristics of individual glomeruli are also correlated with functional properties.

Reported as: The basic units of the olfactory system in the fly brain provide references to their function and ecological relevance
Excerpt:

Because these new insights are not limited to the vinegar fly, and may also apply to other animals or even humans, they have far-reaching significance.

My comment: Anna Di Cosmo’s group has linked the far-reaching significance from all invertebrates to all vertebrates via the conserved molecular epigenetics of biophysically constrained energy-dependent cell type differentiation in species from microbes to humans.

See: Role of olfaction in Octopus vulgaris reproduction

Excerpt:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Excerpt:

Olfactory sensory cells in all vertebrates are characterized by cycles of birth, maturation, and death (Graziadei and Monti Graziadei, 1978). This proliferation is remarkable given that the olfactory receptor cells are neurons, cells that are not generally considered to undergo neurogenesis in adults. The same labeling technique used to document turnover in vertebrates shows that OSNs in the anterior tentacles (olfactory organs) of snails also turn over (Chase and Rieling, 1986). Functional constancy in diverse groups of animals argues that turnover is a common adaptive property of OSNs. We verify the presence of OSNs proliferation in O. vulgaris based on the presence and distribution of PCNA immunoreactivity.

My comment: Thermodynamic cycles of RNA-directed DNA methylation link energy-dependent amino acid substitutions to cell type stability in all cell types of all individuals of all living genera via the physiology of reproduction.

See: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

Excerpt:

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, and diseases of the X chromosome (Honeybee Genome Sequencing Consortium, 2006). Included among these different aspects of eusocial species survival are learning and memory, as well as conditioned responses to sensory stimuli (Maleszka, 2008; Menzel, 1983).

Following olfactory reward conditioning proteins catalyzing DNA methylation (i.e., DNA methyltransferases, Dnmts) and demethylation (i.e., ten–eleven translocation methylcytosine dioxygenase, Tet) are upregulated and DNA methylation levels change in memory-associated genes (Biergans et al., 2015).

My comment to the “Frontiers site”

Re: …that epigenetic regulation of memory specificity might be conserved across animals.

Anna Di Cosmo’s group addressed that fact in the context of the Octopus model organism.

See: Role of olfaction in Octopus vulgaris reproduction https://www.ncbi.nlm.nih.gov/pubmed/25449183

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

See also: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization https://bio.biologists.org/content/early/2016/04/06/bio.017764

See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

My comment: All conditioning paradigms are energy-dependent and they link the energy from the innate immune system to learning and memory. RNA methylation is linked from RNA-directed DNA methylation and energy-dependent fixation of RNA-mediated amino acid substitutions. Transgenerational epigenetic inheritance of biologically-based cause and effect links the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.

See also: The Buzz about Honey Bee Viruses

See my attempt to discuss this on the Neuroscience FB group.

Scientists at the Max Planck Institute for Chemical Ecology in Jena, Germany, have now quantified and mapped the functional units of the olfactory center in the brains of vinegar flies responsible for the perception of odors.