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Toledo Arana, Alejandro

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https://academica-e.unavarra.es/handle/2454/50078

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Toledo Arana

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Alejandro

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Instituto de AgrobiotecnologĆ­a (IdAB)

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0000-0001-8148-6281

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5497

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2011 - 20193
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Subject: Overlapping transcription Ɨ

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Now showing 1 - 3 of 3
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    PublicationOpen Access
    An effort to make sense of antisense transcription in bacteria
    (Taylor & Francis, 2012) Lasa Uzcudun, ĆĆ±igo; Toledo Arana, Alejandro; Gingeras, Thomas R.; IdAB. Instituto de AgrobiotecnologĆ­a / Agrobioteknologiako Institutua
    Analysis of bacterial transcriptomes have shown the existence of a genome-wide process of overlapping transcription due to the presence of antisense RNAs, as well as mRNAs that overlapped in their entire length or in some portion of the 5ā€²- and 3ā€²-UTR regions. The biological advantages of such overlapping transcription are unclear but may play important regulatory roles at the level of transcription, RNA stability and translation. In a recent report, the human pathogen Staphylococcus aureus is observed to generate genome-wide overlapping transcription in the same bacterial cells leading to a collection of short RNA fragments generated by the endoribonuclease III, RNase III. This processing appears most prominently in Gram-positive bacteria. The implications of both the use of pervasive overlapping transcription and the processing of these double stranded templates into short RNAs are explored and the consequences discussed.
  • Thumbnail Image
    PublicationOpen Access
    Genome-wide antisense transcription drives mRNA processing in bacteria
    (National Academy of Sciences, 2011) Lasa Uzcudun, ĆĆ±igo; Toledo Arana, Alejandro; Dobin, Alexander; Villanueva San MartĆ­n, Maite; Ruiz de los Mozos Aliaga, Igor; Vergara Irigaray, Marta; Segura, VĆ­ctor; Fagegaltier, Delphine; PenadĆ©s, JosĆ© R.; Valle Turrillas, Jaione; Solano GoƱi, Cristina; Gingeras, Thomas R.; IdAB. Instituto de AgrobiotecnologĆ­a / Agrobioteknologiako Institutua
    RNA deep sequencing technologies are revealing unexpected levels of complexity in bacterial transcriptomes with the discovery of abundant noncoding RNAs, antisense RNAs, long 5ā€² and 3ā€² untranslated regions, and alternative operon structures. Here, by applying deep RNA sequencing to both the long and short RNA fractions (<50 nucleotides) obtained from the major human pathogen Staphylococcus aureus, we have detected a collection of short RNAs that is generated genome-wide through the digestion of overlapping sense/antisense transcripts by RNase III endoribonuclease. At least 75% of sense RNAs from annotated genes are subject to this mechanism of antisense processing. Removal of RNase III activity reduces the amount of short RNAs and is accompanied by the accumulation of discrete antisense transcripts. These results suggest the production of pervasive but hidden antisense transcription used to process sense transcripts by means of creating double-stranded substrates. This process of RNase III-mediated digestion of overlapping transcripts can be observed in several evolutionarily diverse Gram-positive bacteria and is capable of providing a unique genome-wide posttranscriptional mechanism to adjust mRNA levels.
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    PublicationOpen Access
    Noncontiguous operon is a genetic organization for coordinating bacterial gene expression
    (National Academy of Sciences, 2019) SĆ”enz Lahoya, S.; Bitarte Manzanal, Nerea; GarcĆ­a, BeƱat; Burgui Erice, Saioa; Vergara Irigaray, Marta; Valle Turrillas, Jaione; Solano GoƱi, Cristina; Toledo Arana, Alejandro; Lasa Uzcudun, ĆĆ±igo; IdAB. Instituto de AgrobiotecnologĆ­a / Agrobioteknologiako Institutua
    Bacterial genes are typically grouped into operons defined as clusters of adjacent genes encoding for proteins that fill related roles and are transcribed into a single polycistronic mRNA molecule. This simple organization provides an efficient mechanism to coordinate the expression of neighboring genes and is at the basis of gene regulation in bacteria. Here, we report the existence of a higher level of organization in operon structure that we named noncontiguous operon and consists in an operon containing a gene(s) that is transcribed in the opposite direction to the rest of the operon. This transcriptional architecture is exemplified by the genes menE-menC-MW1733-ytkD-MW1731 involved in menaquinone synthesis in the major human pathogen Staphylococcus aureus. We show that menE-menC-ytkD-MW1731 genes are transcribed as a single transcription unit, whereas the MW1733 gene, located between menC and ytkD, is transcribed in the opposite direction. This genomic organization generates overlapping transcripts whose expression is mutually regulated by transcriptional interference and RNase III processing at the overlapping region. In light of our results, the canonical view of operon structure should be revisited by including this operon arrangement in which cotranscription and overlapping transcription are combined to coordinate functionally related gene expression.