A group II intron has invaded the genus <i>Azotobacter</i> and is inserted within the termination codon of the essential <i>groEL</i> gene

Ferat, Jean-Luc; Gouar, Martine Le; Michel, François

doi:10.1046/j.1365-2958.2003.03649.x

Cited by 33 publications

(32 citation statements)

References 61 publications

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“…The capability of selfsplicing and ligation was demonstrated for several bacterial introns (37)(38)(39)(40) and was tested accordingly on the introns investigated here ( Fig. 3 A and B).…”

Section: Resultsmentioning

confidence: 99%

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Salman

Amann

Shub³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The gene encoding the small subunit rRNA serves as a prominent tool for the phylogenetic analysis and classification of Bacteria and Archaea owing to its high degree of conservation and its fundamental function in living organisms. Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis , regularly contain numerous self-splicing introns of variable length. The 16S rRNA genes can thus be enlarged to up to 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although they are the most frequently sequenced genes today. This may be caused in part by a bias during the PCR amplification step that discriminates against longer homologs, as we show experimentally. Such length heterogeneity of 16S rRNA genes has so far never been considered when constructing 16S rRNA-based clone libraries, even though an elongation of rRNA genes due to intervening sequences has been reported previously. The detection of elongated 16S rRNA genes has profound implications for common methods in molecular ecology and may cause systematic biases in several techniques. In this study, catalyzed reporter deposition–fluorescence in situ hybridization on both ribosomes and rRNA precursor molecules as well as in vitro splicing experiments were performed and confirmed self-splicing of the introns. Accordingly, the introns do not inhibit the formation of functional ribosomes.

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“…The capability of selfsplicing and ligation was demonstrated for several bacterial introns (37)(38)(39)(40) and was tested accordingly on the introns investigated here ( Fig. 3 A and B).…”

Section: Resultsmentioning

confidence: 99%

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Salman

Amann

Shub³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Notably, some bacteria contain natural group II introns inserted into essential genes (e.g., groEL in Azotobacter) (Ferat et al 2003). It will be of interest to determine whether these and other group II introns display temperature-sensitive splicing similar to that of the Ll.LtrB intron.…”

Section: Discussionmentioning

confidence: 99%

Use of targetrons to disrupt essential and nonessential genes in Staphylococcus aureus reveals temperature sensitivity of Ll.LtrB group II intron splicing

Yao¹,

Zhong²,

Fang³

et al. 2006

RNA

105

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We show that a targetron based on the Lactococcus lactis Ll.LtrB group II intron can be used for efficient chromosomal gene disruption in the human pathogen Staphylococcus aureus. Targetrons expressed from derivatives of vector pCN37, which uses a cadmium-inducible promoter, or pCN39, a derivative of pCN37 with a temperature-sensitive replicon, gave site-specific disruptants of the hsa and seb genes in 37%-100% of plated colonies without selection. To disrupt hsa, an essential gene, we used a group II intron that integrates in the sense orientation relative to target gene transcription and thus could be removed by RNA splicing, enabling the production of functional HSa protein. We show that because splicing of the Ll.LtrB intron by the intron-encoded protein is temperature-sensitive, this method yields a conditional hsa disruptant that grows at 32°C but not 43°C. The temperature sensitivity of the splicing reaction suggests a general means of obtaining one-step conditional disruptions in any organism. In nature, temperature sensitivity of group II intron splicing could limit the temperature range of an organism containing a group II intron inserted in an essential gene.

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“…How important are these ribozymes for the regulation of gene expression? Selfsplicing introns can interrupt genes, but the ability of introns to self-excise from mRNA potentially renders them neutral to the host 91 . Nevertheless, in the roaA gene of the Euglena gracilis chloroplast, self-splicing introns cause alternative splicing of pre-mRNAs to produce two distinct transcripts 92 , highlighting one way in which these RNAs can affect gene expression.…”

Section: The Role Of Ribozymes In Gene Expressionmentioning

confidence: 99%

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

2007

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Although various functions of RNA are carried out in conjunction with proteins, some catalytic RNAs, or ribozymes, which contribute to a range of cellular processes, require little or no assistance from proteins. Furthermore, the discovery of metabolite-sensing riboswitches and other types of RNA sensors has revealed RNA-based mechanisms that cells use to regulate gene expression in response to internal and external changes. Structural studies have shown how these RNAs can carry out a range of functions. In addition, the contribution of ribozymes and riboswitches to gene expression is being revealed as far more widespread than was previously appreciated. These findings have implications for understanding how cellular functions might have evolved from RNA-based origins.More than 40 years of extensive research has revealed that RNAs participate in a range of cellular functions. Some RNAs, despite being composed of only four chemically similar nucleotides, can fold into distinct three-dimensional architectures. In many cases, these constitute simple scaffolds that provide binding sites for proteins that function together with the RNAs. However, the discovery of the first catalytic RNAs -later named RNA enzymes, or ribozymes -in the 1980s demonstrated that RNAs can also have important functional roles in their own right 1,2 . The list of naturally occuring ribozymes is short, and additions over the years have been rare, with each new discovery eliciting considerable excitement in the field.Studies of molecular evolution suggest that RNA molecules significantly influenced the development of modern organisms by mediating the genetic flow from DNA to proteins, as well as through their own contribution to catalytic functions. The 'RNA world' hypothesis implies that RNA molecules appeared before DNA and proteins 3 . Nevertheless, even with a head start, RNA catalysts do not prevail in the modern world. Moreover, most ubiquitous ribozymes require proteins for efficient catalysis in vivo, and most true protein-devoid catalytic RNAs have been found in only a few viral-like sources, suggesting that the contribution of protein-free RNAs to the functions of modern cells has been limited.Correspondence to A.S. or D.J.P. serganoa@mskcc.org; pateld@mskcc.org. Competing interests statementThe authors declare no competing financial interests. HHS Public AccessAuthor manuscript Nat Rev Genet. Author manuscript; available in PMC 2015 December 23. Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptThe discovery of riboswitches 4-6 and other RNA-based sensors reignited interest in the roles of protein-devoid RNA-based elements. These RNA sensors can be broadly defined as mRNA regions that are capable of modulating gene expression in response to internal and external inputs, without the initial participation of proteins. Unlike ribozymes, many of these sensors direct gene expression purely through changes in RNA conformation. For instance, riboswitches alter their conformations in response to small metabolite...

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A group II intron has invaded the genus Azotobacter and is inserted within the termination codon of the essential groEL gene

Cited by 33 publications

References 61 publications

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Use of targetrons to disrupt essential and nonessential genes in Staphylococcus aureus reveals temperature sensitivity of Ll.LtrB group II intron splicing

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

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