Evolution of neuronal signalling: Transmitters and receptors

Hoyle, Charles H.V.

doi:10.1016/j.autneu.2010.05.007

Cited by 27 publications

(15 citation statements)

References 306 publications

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“…This suggests that a number of genes, which were duplicated early in the vertebrate lineage, took on specialized functions in the brain, and were subsequently fixed in expression patterns, whereas we did not observe this consistently in the other tissues for which sequence was available. The pattern we see would fit with the theory that the complexity of the vertebrate brain and nervous system can in part be contributed to the redundancy of genes following the two whole genome duplications early in vertebrate evolution [36,37]. Moreover, in three primates we found overlap of un-annotated transcribed regions, likely non-coding RNAs, with transcription levels most highly correlated across species in testis.…”

Section: Discussionsupporting

confidence: 82%

A universal genomic coordinate translator for comparative genomics

et al. 2014

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BackgroundGenomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N.ResultsHere, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species.ConclusionsKraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.

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Section: Discussionsupporting

confidence: 82%

A universal genomic coordinate translator for comparative genomics

et al. 2014

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“…28,29 One native opioid peptide, MENK, has emerged as a modulator on several immunological functions both in vitro and in vivo such as enhancing the proliferation of peripheral blood lymphocytes and splenocytes. 30 MENK possesses bilateral regulation on immune cells, which means that MENK at higher concentrations such as 10 -6 M or lower concentrations such as 10 -18 M will delay immune cell growth and the possible mechanism is MENK can interact with OGFr to upregulate cyclin-dependent kinase inhibitory (CKI) pathways and markedly delay the G 1 /S phase of the cell cycle.…”

Section: Discussionmentioning

confidence: 99%

Synergistic effect of methionine encephalin (MENK) combined with pidotimod(PTD) on the maturation of murine dendritic cells (DCs)

Meng

wang²,

Zhang³

et al. 2013

Human Vaccines & Immunotherapeutics

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“…The most evolutionarily ancient adenosine receptors were identified in the sea anemone Nematostella vectensis, and they are abundant in insects, in bivalves (mussels) and in echinoderms [212]. The P2Y metabotropic receptors seem to emerge in vertebrates: the earliest homologues have been found in sharks and skate, Raja erinacea [213]. The evolutionary roots of P0 adenine receptors are unknown; these have been cloned only from mouse and hamster [205].…”

Section: Ca 2þ As a Regulator Of Programmed Cell Deathmentioning

confidence: 99%

Inseparable tandem: evolution chooses ATP and Ca²⁺to control life, death and cellular signalling

Plattner

Verkhratsky

2016

Phil. Trans. R. Soc. B

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From the very dawn of biological evolution, ATP was selected as a multipurpose energy-storing molecule. Metabolism of ATP required intracellular free Ca 2þ to be set at exceedingly low concentrations, which in turn provided the background for the role of Ca 2þ as a universal signalling molecule. The early-eukaryote life forms also evolved functional compartmentalization and vesicle trafficking, which used Ca 2þ as a universal signalling ion; similarly, Ca 2þ is needed for regulation of ciliary and flagellar beat, amoeboid movement, intracellular transport, as well as of numerous metabolic processes. Thus, during evolution, exploitation of atmospheric oxygen and increasingly efficient ATP production via oxidative phosphorylation by bacterial endosymbionts were a first step for the emergence of complex eukaryotic cells. Simultaneously, Ca 2þ started to be exploited for shortrange signalling, despite restrictions by the preset phosphate-based energy metabolism, when both phosphates and Ca 2þ interfere with each other because of the low solubility of calcium phosphates. The need to keep cytosolic Ca 2þ low forced cells to restrict Ca 2þ signals in space and time and to develop energetically favourable Ca 2þ signalling and Ca 2þ microdomains. These steps in tandem dominated further evolution. The ATP molecule (often released by Ca 2þ -regulated exocytosis) rapidly grew to be the universal chemical messenger for intercellular communication; ATP effects are mediated by an extended family of purinoceptors often linked to Ca 2þ signalling. Similar to atmospheric oxygen, Ca 2þ must have been reverted from a deleterious agent to a most useful (intra-and extracellular) signalling molecule. Invention of intracellular trafficking further increased the role for Ca 2þ homeostasis that became critical for regulation of cell survival and cell death. Several mutually interdependent effects of Ca 2þ and ATP have been exploited in evolution, thus turning an originally unholy alliance into a fascinating success story.This article is part of the themed issue 'Evolution brings Ca 2þ and ATP together to control life and death'.

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Evolution of neuronal signalling: Transmitters and receptors

Cited by 27 publications

References 306 publications

A universal genomic coordinate translator for comparative genomics

A universal genomic coordinate translator for comparative genomics

Synergistic effect of methionine encephalin (MENK) combined with pidotimod(PTD) on the maturation of murine dendritic cells (DCs)

Inseparable tandem: evolution chooses ATP and Ca²⁺to control life, death and cellular signalling

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Evolution of neuronal signalling: Transmitters and receptors

Cited by 27 publications

References 306 publications

A universal genomic coordinate translator for comparative genomics

A universal genomic coordinate translator for comparative genomics

Synergistic effect of methionine encephalin (MENK) combined with pidotimod(PTD) on the maturation of murine dendritic cells (DCs)

Inseparable tandem: evolution chooses ATP and Ca2+to control life, death and cellular signalling

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Inseparable tandem: evolution chooses ATP and Ca²⁺to control life, death and cellular signalling