The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

Boeke, Jef D.

doi:10.1101/gr.1392003

Cited by 55 publications

(55 citation statements)

References 68 publications

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“…Taking into account related nuclear introns and transposable LINE elements, as much as one third of the human DNA may have evolved from ancestral group II introns. [2] In addition, based on reaction pathway and sequence similarity, a common ancestry with the eukaryotic spliceosomal machinery has been proposed. [1] The spliceosome is a multicomponent RNA-protein complex that occurs in higher eukaryotes and consists of five highly structured snRNAs (U1, U2, U4, U5 and U6) and numerous proteins, the latter ones presumably having structural roles.…”

Section: Introductionmentioning

confidence: 99%

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg²⁺ Binding Site is Located Close to the Stacked Branch Adenosine

et al. 2007

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Group II intron self-splicing is essential for correct expression of organellar genes in plants, fungi, and yeast, as well as of bacterial genes. Self-excision of these autocatalytic introns from the primary RNA transcript is achieved in a two-step mechanism apparently analogous to the one of the eukaryotic spliceosome. The 2'-OH of a conserved adenosine (the branch point) located within domain 6 (D6) acts as the nucleophile in the first step of splicing. Despite the biological importance of group II introns, little is known about their structural organization and usage of metal ions in catalysis. Here we report the first solution structure of a catalytically active D6 construct encompassing the branch point and the neighboring helical regions from the mitochondrial yeast intron ai5 . The branch adenosine is the single unpaired nucleotide, and, in contrast to the spliceosomal branch site, resides within the helix being partially stacked between the two flanking GU wobble pairs. We identified a novel prominent Mg2+ binding site in the major groove of the branch site. Importantly, Mg2+ addition does not impair stacking of the branch-adenosine, but in contrast rather strengthens the interaction with the flanking uridines, as shown by NMR-and fluorescence studies. This means, that domain 6 presents the branch adenosine in a stacked fashion to the core of group II introns upon folding to the active conformation.

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Section: Introductionmentioning

confidence: 99%

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg²⁺ Binding Site is Located Close to the Stacked Branch Adenosine

et al. 2007

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“…The frequent partial replication of the 3Ј repeats in gecko elements (Table 2) also offers support for 3Ј tandem repeats such as the Drosophila I factor . Boeke (2003) further divides the slippage retrotransposition model. In the case of gecko, the slippage may provide a mechanism for the the later group into poly(dA)-related repeats such as…”

Section: Discussionmentioning

confidence: 99%

The Changing Tails of a Novel Short Interspersed Element in Aedes aegypti

Mao

2004

Genetics

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A novel family of tRNA-related SINEs named gecko was discovered in the yellow fever mosquito, Aedes aegypti. Approximately 7200 copies of gecko were distributed in the A. aegypti genome with a significant bias toward A ϩ T-rich regions. The 3Ј end of gecko is similar in sequence and identical in secondary structure to the 3Ј end of MosquI, a non-LTR retrotransposon in A. aegypti. Nine conserved substitutions and a deletion separate gecko into two groups. Group I includes all gecko that end with poly(dA) and a copy that ends with AGAT repeats. Group II comprises gecko elements that end with CCAA or CAAT repeats. Members within each group cannot be differentiated when the 3Ј repeats are excluded in phylogenetic and sequence analyses, suggesting that the alterations of 3Ј tails are recent. Imperfect poly(dA) tail was recorded in group I and partial replication of the 3Ј tandem repeats was frequently observed in group II. Genomic evidence underscores the importance of slippage retrotransposition in the alteration and expansion of the tandem repeat during the evolution of gecko sequences, although we do not rule out postinsertion mechanisms that were previously invoked to explain the evolution of Alu-associated microsatellites. We propose that the 3Ј tandem repeats and the poly(dA) tail may be generated by similar mechanisms during retrotransposition of both SINEs and non-LTR retrotransposons and thus the distinction between poly(dA) retrotransposons such as L1 and non-poly(dA) retrotransposons such as I factor may not be informative.

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“…They bind small metabolites like FMN, SAM, TPP, guanine, adenine, and coenzyme B 12 with a high degree of affinity and specificity [6] [7]. Upon binding of the corresponding metabolite, the riboswitch sequence presumably undergoes structural changes [8] and in some cases even cleavage of the RNA strand occurs [4].…”

Section: Riboswitchesmentioning

confidence: 99%

“…In our group, we work with the so-called B 12 riboswitch. This riboswitch consists of an about 200 nt long and highly conserved sequence located in the 5ʹ-UTR of mRNAs associated with the metabolism and transport of coenzyme B 12 and vitamin B 12 , respectively [9].…”

Section: Riboswitchesmentioning

confidence: 99%

Structure Determination of Catalytic RNAs and Investigations of Their Metal Ion-Binding Properties

Erat¹,

Sigel²

2005

Chimia

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Naturally occurring RNA molecules exhibit many unexpected and fascinating properties in living cells like protein synthesis and transport, regulation of metabolic functions, and catalytic cleavage reactions. To understand this functional diversity, a detailed knowledge of RNA structure and metal ion-binding properties is crucial. In our research group, we address these problems by combining various biochemical, analytical and spectroscopic techniques. A large part of our work is devoted to the structure determination of catalytic RNA molecules, i.e. ribozymes, by NMR. Based on the three-dimensional structure, further experiments are carried out to understand in detail the effects of different metal ions on the local and global structure, as well as catalysis itself. Our research concentrates on two classes of the naturally occurring RNAs: (i) riboswitches and (ii) group II intron ribozymes. The emphasis of this short review is on our structural and analytical NMR studies on group II intron ribozymes; our riboswitch work is only briefly indicated in the following Section. RiboswitchesRiboswitches are highly conserved RNA sequences occurring for example in the 5ʹ-UTR (see Abbreviations) of certain mRNAs. They bind small metabolites like FMN, SAM, TPP, guanine, adenine, and coenzyme B 12 with a high degree of affinity and specificity [6] [7]. Upon binding of the corresponding metabolite, the riboswitch sequence presumably undergoes structural changes [8] and in some cases even cleavage of the RNA strand occurs [4]. Both cleavage and structural changes inhibit binding of the 5ʹ-UTR to the ribosome, and thus prohibit translation to the corresponding protein. As the protein(s) expressed by a mRNA is always involved in either biosynthesis or transport of the metabolite that binds to the riboswitch, this new class of RNA molecules constitutes an elegant way of feedback control within living cells.In our group, we work with the so-called B 12 riboswitch. This riboswitch consists of an about 200 nt long and highly conserved sequence located in the 5ʹ-UTR of mRNAs associated with the metabolism and transport of coenzyme B 12 and vitamin B 12 , respectively [9]. Our investigations encompass structural studies as well as binding studies of coenzyme B 12 and its derivatives to this riboswitch sequence in the presence of different metal ions. Group II Intron RibozymesThe main efforts of our research are presently devoted to group II intron ribozymes. These large molecular machines are self-splicing introns, i.e. capable of cutting themselves out of the precursor RNA and in a second step joining the adjacent exons to yield the final mRNA -all without the aid of proteins (Fig. 1). In addition, these amazing molecules can insert themselves again into RNA and even DNA. The occurrence, reaction mechanisms, and the different aspects of metal ion binding to group II introns have lately been reviewed [10][11], thus only a few important points are summarized below:

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The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

Cited by 55 publications

References 68 publications

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg²⁺ Binding Site is Located Close to the Stacked Branch Adenosine

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg²⁺ Binding Site is Located Close to the Stacked Branch Adenosine

The Changing Tails of a Novel Short Interspersed Element in Aedes aegypti

Structure Determination of Catalytic RNAs and Investigations of Their Metal Ion-Binding Properties

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The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

Cited by 55 publications

References 68 publications

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg2+ Binding Site is Located Close to the Stacked Branch Adenosine

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg2+ Binding Site is Located Close to the Stacked Branch Adenosine

The Changing Tails of a Novel Short Interspersed Element in Aedes aegypti

Structure Determination of Catalytic RNAs and Investigations of Their Metal Ion-Binding Properties

Contact Info

Product

Resources

About

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg²⁺ Binding Site is Located Close to the Stacked Branch Adenosine

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg²⁺ Binding Site is Located Close to the Stacked Branch Adenosine