l-Arginine influences the structure and function of arginase mRNA in Aspergillus nidulans

Borsuk, Piotr; Przykorska, Anna; Błachnio, Karina; Koper, Michał; Pawłowicz, Jerzy; Pękala, Małgorzata; Węgleński, Piotr

doi:10.1515/bc.2007.015

Cited by 23 publications

(17 citation statements)

References 37 publications

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“…A small number of examples of alternative splicing have been described in the Aspergilli [31–35]. Whole transcriptome analysis of A. oryzae (which was not strand specific and therefore could not account for the presence of antisense transcripts) reported 8.55% of genes displaying differential splicing with the majority of these events (91.56%) being due to intron retention [21].…”

Section: Resultsmentioning

confidence: 99%

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

Sibthorp

Cowley

et al. 2013

BMC Genomics

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BackgroundThe filamentous fungus Aspergillus nidulans has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 2005, including medically and industrially important species. In order to advance our knowledge of its biology and increase its utility as a genetic model by improving gene annotation we sequenced the transcriptome of A. nidulans with a focus on 5′ end analysis.ResultsStrand-specific whole transcriptome sequencing showed that 80-95% of annotated genes appear to be expressed across the conditions tested. We estimate that the total gene number should be increased by approximately 1000, to 11,800. With respect to splicing 8.3% of genes had multiple alternative transcripts, but alternative splicing by exon-skipping was very rare. 75% of annotated genes showed some level of antisense transcription and for one gene, meaB, we demonstrated the antisense transcript has a regulatory role. Specific sequencing of the 5’ ends of transcripts was used for genome wide mapping of transcription start sites, allowing us to interrogate over 7000 promoters and 5′ untranslated regions.ConclusionsOur data has revealed the complexity of the A. nidulans transcriptome and contributed to improved genome annotation. The data can be viewed on the AspGD genome browser.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-847) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

Sibthorp

Cowley

et al. 2013

BMC Genomics

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“…Specifically, a proposed riboswitch for aminoglycoside antibiotics (Jia et al 2013) is most likely a previously studied DNA element exclusively associated with integrons (Roth and Breaker 2013). A proposed arginine riboswitch in the fungal species Aspergillus nidulans lacks demonstration of a saturable binding site or evidence for sequence and structural conservation (Borsuk et al 2007). Similarly, a putative Mn 2+ riboswitch lacks sufficient genetic or biochemical evidence of ligand-induced function (Shi et al 2014).…”

Section: Orphan and Other Riboswitch Candidatesmentioning

confidence: 99%

Riboswitch diversity and distribution

McCown

Corbino

Stav

et al. 2017

RNA

392

516

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Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands. Some riboswitch classes are very common and are present in bacteria from nearly all lineages, whereas others are exceedingly rare and appear in only a few species whose DNA has been sequenced. Presented herein are the consensus sequences, structural models, and phylogenetic distributions for all validated riboswitch classes. Based on our findings, we predict that there are potentially many thousands of distinct bacterial riboswitch classes remaining to be discovered, but that the rarity of individual undiscovered classes will make it increasingly difficult to find additional examples of this RNA-based sensory and gene control mechanism.

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“…2C) (Kubodera et al 2003;Cheah et al 2007;Croft et al 2007;Bocobza et al 2007;Wachter et al 2007). Additional data is needed to validate the proposed existence of a eukaryotic riboswitch class responsive to arginine (Borsuk et al 2007), but it seems likely that more metabolite-binding riboswitches will be discovered in eukaryotes. Because eukaryotic TPP riboswitches appear to most commonly control splicing, introns may be excellent vehicles for riboswitch expression and regulatory function, and therefore may yield future riboswitch discoveries.…”

Section: Modern Mechanisms For Riboswitch-mediated Gene Controlmentioning

confidence: 99%

Riboswitches and the RNA World

Breaker

2010

Cold Spring Harbor Perspectives in Biology

564

522

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SUMMARYRiboswitches are structured noncoding RNA domains that selectively bind metabolites and control gene expression (Mandal and Breaker 2004a;Coppins et al. 2007;Roth and Breaker 2009). Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation. Newfound classes of riboswitches are being reported at a rate of about three per year (Ames and Breaker 2009), and these have been shown to selectively respond to fundamental metabolites including coenzymes, nucleobases or their derivatives, amino acids, and other small molecule ligands.The characteristics of some riboswitches suggest they could be modern descendents of an ancient sensory and regulatory system that likely functioned before the emergence of enzymes and genetic factors made of protein (Nahvi et al. 2002;Vitreschak et al. 2004;Breaker 2006). If true, then some of the riboswitch structures and functions that serve modern cells so well may accurately reflect the capabilities of RNA sensors and switches that existed in the RNAWorld. This article will address some of the characteristics of modern riboswitches that may be relevant to ancient versions of these metabolite-sensing RNAs.

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l-Arginine influences the structure and function of arginase mRNA in Aspergillus nidulans

Cited by 23 publications

References 37 publications

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

Riboswitch diversity and distribution

Riboswitches and the RNA World

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