Naturally Occurring tRNAs With Non-canonical Structures

Krahn, Natalie; Fischer, J.P.; Söll, Dieter

doi:10.3389/fmicb.2020.596914

Cited by 35 publications

(29 citation statements)

References 115 publications

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“…We then analyzed other sncRNA categories where read lengths can be variable depending on how the RNA is processed. We found that reads aligned to tRNAs, which are ∼70 – 100 nt [37], had an average read length of 30 nt and a 90-precentile range of 28 – 31 nt ( Table 1 ). This result suggests that rat epididymosomes do not carry full length tRNAs, but rather carry either tRNA fragments (tRFs) or tRNA-halves, which are 14 – 30 nt and 30 – 40 nt in length respectively [38].…”

Section: Resultsmentioning

confidence: 99%

Small Noncoding Rna Contents of Rat Epididymal Extracellular Vesicles Including a Putative Novel Small Rna

Gillette

Waghwala

Gore

2022

Preprint

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Extracellular vesicles (EVs) released from the epididymal epithelium (epididymosomes) impart functional competence on sperm as they transit the epididymis by merging with sperm and releasing a complex repertoire of molecules. The cargo of epididymosomes includes small noncoding RNAs (sncRNAs) that are modified by external factors such as stress, nutrition, and drug use. If incorporated into sperm, the EV sncRNA cargo can affect offspring and lead to heritable phenotypes. In the current study we characterized the RNA contents of EVs collected from the caput epididymis of adult male rats in order to fill a gap in knowledge in this species and to establish a sncRNA profile. Small RNAs of EVs were isolated from the caput portion of the epididymis of adult male rats, and sequenced on a NovaSeq 6000 on a SP flow cell in a single-end 50 bp configuration. The resulting reads were checked for quality, trimmed for adapter sequences, aligned to the unmasked rat genome (Rnor 6), and assigned an annotation designation. The majority of RNA reads aligned to either tRNA fragments (79.1%) or piRNA (18.1%) loci. Micro RNAs (miRNAs) accounted for a surprisingly small proportion of reads (0.18%). The third largest category of aligned reads (1.5%) was in intergenic space and not strictly associated with canonical sncRNA loci. In-depth investigation determined these latter reads (~19 nt) aligned strictly within the boundaries of known CpG islands (CpGi), which have not previously been reported to express any form of sncRNA. These newly described CpGi sRNAs could not consistently be accounted for by overlaying features of any other annotation type (including rRNA and piRNA). The CpGi sRNAs have characteristics of RNA fragments that can associate with the Argonaute/PIWI family of proteins and therefore could have regulatory function via RNA induced silencing or de novo DNA methylation. We propose that CpGi sRNAs constitute a new family of sncRNA that may represent an important and unreported class of regulatory RNA in gametes.

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Section: Resultsmentioning

confidence: 99%

Small Noncoding Rna Contents of Rat Epididymal Extracellular Vesicles Including a Putative Novel Small Rna

Gillette

Waghwala

Gore

2022

Preprint

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“…Instead, in other bacteria, a deletion of a component of the transulfursome may lead many species of microorganisms to be auxotrophic for Cysteine due to their inability to synthesize it [ 28 , 29 ], resulting in a likely loss of information on specific tRNAs [ 26 ]. Recently, tRNA molecules with non-canonical structures have also been discovered [ 30 ]. These natural tRNA variants are, however, efficiently utilized during translation by the bacterial system and appear to be associated with functional interaction with enzymatic partners that is consistent with highly efficient evolutionary diversification of tRNAs.…”

Section: Discussionmentioning

confidence: 99%

Machine Learning Algorithms Highlight tRNA Information Content and Chargaff’s Second Parity Rule Score as Important Features in Discriminating Probiotics from Non-Probiotics

Bergamini

Bianchi

Giaccone

et al. 2022

Biology

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Probiotic bacteria are microorganisms with beneficial effects on human health and are currently used in numerous food supplements. However, no selection process is able to effectively distinguish probiotics from non-probiotic organisms on the basis of their genomic characteristics. In the current study, four Machine Learning algorithms were employed to accurately identify probiotic bacteria based on their DNA characteristics. Although the prediction accuracies of all algorithms were excellent, the Neural Network returned the highest scores in all the evaluation metrics, managing to discriminate probiotics from non-probiotics with an accuracy greater than 90%. Interestingly, our analysis also highlighted the information content of the tRNA sequences as the most important feature in distinguishing the two groups of organisms probably because tRNAs have regulatory functions and might have allowed probiotics to evolve faster in the human gut environment. Through the methodology presented here, it was also possible to identify seven promising new probiotics that have a higher information content in their tRNA sequences compared to non-probiotics. In conclusion, we prove for the first time that Machine Learning methods can discriminate human probiotic from non-probiotic organisms underlining information within tRNA sequences as the most important genomic feature in distinguishing them.

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“…A second hypothesis would be that the degenerated tRNA entirely missing the TV-loop, which was detected using ARWEN, could be functional. However, although non-standard forms of mitochondrial tRNA can be found among metazoans (Krahn et al, 2020), they are rather scarce among protists (Gray et al, 1998). A third hypothesis would be that a functional tRNA-Trp(uca) is imported from the cytosol.…”

Section: A Complex Mitogenomementioning

confidence: 99%

A New Insight Into Amicula, a Genus of Tiny Marine Benthic Diatoms With the Description of Two New Tropical Species and the Largest Mitogenome Known for a Stramenopile

Gastineau

Ashworth

et al. 2022

Front. Mar. Sci.

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The current article focuses on the morphological and molecular characterization of the often inconspicuous genus Amicula. This recently erected genus from brackish and marine sediments was monotypic but here we describe two new tropical species: Amicula micronesica sp. nov. and Amicula vermiculata sp. nov. Once considered an incertae sedis genus regarding its higher rank taxonomy, its position among the family Diploneidaceae is proposed here by molecular phylogenetics. The complete plastid and mitochondrial genomes of Amicula micronesica sp. nov. are also presented here. It appears that the 177614-bp long mitogenome is the biggest yet recorded among stramenopiles, due to its invasion by 57 introns. Moreover, it utilizes the genetic code 4 for translation instead of the code 1 usually found among diatoms.

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Naturally Occurring tRNAs With Non-canonical Structures

Cited by 35 publications

References 115 publications

Small Noncoding Rna Contents of Rat Epididymal Extracellular Vesicles Including a Putative Novel Small Rna

Small Noncoding Rna Contents of Rat Epididymal Extracellular Vesicles Including a Putative Novel Small Rna

Machine Learning Algorithms Highlight tRNA Information Content and Chargaff’s Second Parity Rule Score as Important Features in Discriminating Probiotics from Non-Probiotics

A New Insight Into Amicula, a Genus of Tiny Marine Benthic Diatoms With the Description of Two New Tropical Species and the Largest Mitogenome Known for a Stramenopile

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