Messenger RNAs bearing tRNA-like features exemplified by interferon alfa 5 mRNA

Díaz-Toledano, Rosa; Gómez, Jordi

doi:10.1007/s00018-015-1908-0

Cited by 10 publications

(42 citation statements)

References 71 publications

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“…We first identified, for the key factor considered (e.g., RNase P), a set of substrate mRNA species. This was done by testing viral and cellular mRNAs that share a common origin and others that do not, but that are found in the same cell type, as well as those that have either common or antagonistic activities . Then, we tested whether the identified mRNAs could be substrates for other RNA structure−dependent factors, or could interact with a different factor (for instance, UVC light) .…”

Section: A Methods For Mrna Archaeologymentioning

confidence: 99%

“…RNase P is the only specific factor that has been used to identify sensitive sites in the entire mRNA population of human cells (hepatocytes) . A set of competition assays on the standard RNase P reaction suggested the presence of a massive number of RNA structures recognized by RNase P within this mRNA population.…”

Section: Review Of Identified Motifsmentioning

confidence: 99%

“…A set of competition assays on the standard RNase P reaction suggested the presence of a massive number of RNA structures recognized by RNase P within this mRNA population. Subsequent identification using DNA microarray screening of individual mRNA species within the bulk of liver mRNAs provided a list of over 100 different cellular mRNA−sensitive species . The RNase P−based screening method was very conservative, so that we believe that the potential number of mRNA carriers of signals recognized by this activity may actually be much higher.…”

Section: Review Of Identified Motifsmentioning

confidence: 99%

“…Three of these human liver mRNAs, likely representing different epochs of cellular life, were tested individually: the ribosomal protein RPS9, the histone H2AFJ, and a member of the interferon‐alpha subtype 5 (IFNA5). They were specifically cleaved by human RNase P and required a minimum RNA length of around 200 nucleotides . The particular case of IFNA5 was studied in depth because of its relationship with HCV infection .…”

Section: Review Of Identified Motifsmentioning

confidence: 99%

“…Therefore, the presence of cleavage sites may be a selective pressure to promote the interaction of sensitive mRNAs with a protecting factor. Such an interaction could have been hypothetically co‐opted for further functions, for example, the transport of mRNAs from the cell nucleus to the cytoplasm …”

Section: Review Of Identified Motifsmentioning

confidence: 99%

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The archaeology of coding RNA

Ariza-Mateos

Briones

Perales

et al. 2019

Annals of the New York Academy of Sciences

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Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto‐tRNA−like structures. Different biochemical and biophysical tools have been used to search for ancient‐like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as “archaeological,” and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA‐like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon‐alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA‐like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA‐like motif next to the tRNA‐like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny‐based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent “the losers” in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.

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Section: A Methods For Mrna Archaeologymentioning

confidence: 99%

Section: Review Of Identified Motifsmentioning

confidence: 99%

Section: Review Of Identified Motifsmentioning

confidence: 99%

Section: Review Of Identified Motifsmentioning

confidence: 99%

Section: Review Of Identified Motifsmentioning

confidence: 99%

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The archaeology of coding RNA

Ariza-Mateos

Briones

Perales

et al. 2019

Annals of the New York Academy of Sciences

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Virus is a Signal for the Host Cell

2015

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Currently, the concept of the cell as a society or an ecosystem of molecular elements is gaining increasing acceptance. The basic idea arose in the 19th century, from the surmise that there is not just a single unit underlying an individual’s appearance, but a plurality of entities with both collaborative and conflicting relationships. The following hypothesis is based around this model. The incompatible activities taking place between different original elements, which were subsumed into the first cell and could not be eliminated, had to be controlled very closely. Similarly, a strong level of control had to be developed over many cellular elements after the cell changed its genome to DNA. We assume that at least some of those original RNA agents and other biomolecules which carry incompatibilities and risks, are retained within current cells, although they are now under strict control. A virus functions as a signal informing these repressed cellular RNAs and other elements of ancient origin how to restore suppressed degrees of molecular freedom, favoring pre-existing molecular affinities and activities, re-establishing ancient molecular webs of interactions, and giving fragments of ancient coded information (mostly in the form of RNA structural motifs) the opportunity to be re-expressed. Collectively, these newly activated mechanisms lead to different possibilities for pathological cell states. All these processes are opposed by cell-control mechanisms. Thus, in this new scenario, the battle is considered intracellular rather than between the virus and the cell. And so the virus is treated as the signal that precipitates the cell’s change from a latent to an active pathological state.

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