Alarmones as Vestiges of a Bygone RNA World

Hernández-Morales, Ricardo; Becerra, Arturo; Lazcano, Antonio

doi:10.1007/s00239-018-9883-3

Cited by 18 publications

(16 citation statements)

References 118 publications

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“…Besides its role in protein biosynthesis, plant lysyl-tRNA synthetases may be involved in the synthesis of adenylated 5 -nucleosidyl tetraphosphates (AP4Ns), analogously to what described in Escherichia coli [42]. AP4Ns were shown to accumulate in stressed prokaryotic and eukaryotic cells [43,44] and their production in stressed plant cells suggests that they may function as "alarmones" [41,45] (i.e., intracellular signals affecting duplication and gene expression under harsh environmental conditions [46]).…”

Section: Gene Ontology Categories Characterizing Callogenesis At Different Time Points In Nettlementioning

confidence: 91%

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Xuan

Legay

Berni

et al. 2021

IJMS

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Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a trans-differentiation step characterized by the proliferation of a mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. Therefore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals for pharmacological, nutraceutical and cosmeceutical use. Thus, it is of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, a time point at which a well-visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies characterizing each of the four time points investigated (0, 1, 10 and 34 days). The results show that, while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to the immune response and cell wall loosening, respectively.

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Section: Gene Ontology Categories Characterizing Callogenesis At Different Time Points In Nettlementioning

confidence: 91%

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Xuan

Legay

Berni

et al. 2021

IJMS

View full text Add to dashboard Cite

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“…A focus of our research team in recent years has been the discovery of riboswitches that sense specific metabolites or inorganic ions to regulate the expression of genes whose protein products synthesize, transport, utilize, or respond to the ligands being monitored. Over 50 distinct classes of riboswitches have been experimentally validated to date [11][12][13][14][15][16][17][18][19][20][21][22][23], and many of these sense nucleotide-derived compounds proposed to have been present during an era of biology before the evolutionary emergence of proteins [24][25][26][27][28]. Thus, uncovering additional classes of riboswitches promises to reveal more about how modern cells regulate critical biochemical processes, and perhaps also to provide insight into the functions of ancient RNA-based regulatory systems [29,30].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes

et al. 2021

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Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel riboswitch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.

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“…This is significant because the ribosome is arguably an evolutionary anachronism from a period where RNA polymers acted as both enzymes (protein) and information storage (DNA) (Petrov et al., 2015). Additional discoveries of structural and regulatory RNA molecules (Breaker, 2012) suggest that life may have emerged from an earlier RNA world dominated by ribozymes (e.g., the ribosome) (Gilbert, 1986) and ribonucleotide‐containing molecules (e.g., adenosine triphosphate—ATP) (Hernández‐Morales et al., 2019) catalyzing reactions and mediating a protometabolism.…”

Section: Introductionmentioning

confidence: 99%

In search of the RNA world on Mars

et al. 2021

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The origins of life can best be understood as a series of plausible steps culminating in the emergence of a "self-sustaining chemical system capable of Darwinian evolution" (NASA Astrobiology). However, life as we know it is a highly complex collection of molecular machinery and genetic information. The central dogma of molecular biology stipulates that deoxyribonucleic acid (DNA) makes ribonucleic acid (RNA) via transcription, RNA makes protein via translation, and information cannot be transferred backwards from proteins to nucleic acids

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Alarmones as Vestiges of a Bygone RNA World

Cited by 18 publications

References 118 publications

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes

In search of the RNA world on Mars

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