Click here to see an animated pan-editing of L. tarentolae A6 mRNA (must use MIE ver 5; advance by clicking)

Purpose:

• This site is intended to act as a source of information on the U insertion/deletion type of RNA editing and to increase the interactions between researchers in this field. A list of all researchers and their email addresses and any available postdoctoral positions, literature references, sequence databases specific for this field, and upcoming scientific meetings will be presented. In addition, there will be a section with data taken from published and unpublished research to illustrate research problems and research directions.

Definition of U-insertion/deletion RNA editing:

• The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.

Definitions of Terms used in U-insertion/deletion RNA Editing.

Sequence Databases:

• KISS guide RNA relational database of Torsten Ochsenreiter

• Edited sequence database of Simpson et al.
  
  
• Minicircle sequence database of Barker, Brewster and Aslett

List of Literature References:

Click here for a list of literature references to the trypanosome type of RNA editing in journal format. Click here for the identical list in Medlar format for direct inclusion into bibliographic programs.

Sequence Maps, Diagrams and Some Interesting Recent Results (with my comments):

• Taxonomy of kinetoplastid protozoa
• Diagram of the single mitochondrion and the kDNA network in L. tarentolae stationary phase cell
• Electron micrograph of a fragment of a kDNA network from L. tarentolae
• Another electron micrograph of a fragment of a kDNA network from L. tarentolae
• Several micrographs of kDNA networks from L. tarentolae
• Map of maxicircle of L. tarentolae showing localization of genes, cryptogenes and gRNA genes
• Comparative maps of maxicircles of several species.
• The pan-edited NADH dehydrogenase 7 gene in T. brucei (Koslowsky et al., 1990) (This is the cover photo that got a lot of people interested in RNA editing!)
• Overlapping gRNAs for pan-edited RPS12 mRNA in L. tarentolae (Maslov and Simpson, 1992)(evidence for independent editing of three domains)
• Comparative genomic organization of gRNA genes in different kinetoplastids
• The enzyme cascade and transesterification models for RNA editing
• Modified enzyme cascade model for RNA editing (Byrne et al., 1996) (Development of a gRNA-medited in vitro U-insertion editing system from L. tarentolae. Intermediates were visualized by RT-PCR. The basic modification of the model is that U's are added in an untemplated manner to the 3' end of the 5' cleavage fragment and then deleted by an exonucleaase - in both deletion and insertion situations)
• A model for U-deletion (Seiwert et al., 1996)(A breakthrough in development of an in vitro gRNA-mediated U-deletion system in which A6 editing intermediates can be visualized on a gel. Provided evidence against the transesterification model and for the enzyme cascade model)
• A model for RNA editing in kinetoplastids (Kable et al., 1996)(Application of the A6 in vitro editing system from T. brucei for gRNA-mediated U-insertion editing)
• In vitro editing of site 1 of the A6 mRNA in T. brucei - evidence for involvement of gRNA-mediated endonuclease, 3' to 5' exonuclease and RNA ligase activities(an elegant analysis of the in vitro system developed by Seiwert et al.)
• Sterochemical evidence supporting the enzyme cascade model of U-insertion editing (Frech and Simpson, 1996)(Analyzed the gRNA-independent U-insertion editing reaction in L. tarentolae. The internal as well as the 3' incorporation of (SP)-alpha-S-UTP proceeds via inversion of the stereoconfiguration. Consistent with the enzyme cascade model and inconsistent with the transfer of U's from the 3' end of the gRNA).
• Secondary structure of a gRNA from T. brucei (Schmid et al., 1995)
• Tertiary structure of a gRNA from T. brucei (Hermann et al., 1997)
• RNA binding domain for the gRNA-binding protein from T. brucei, gBP21 (Hermann et al., 1997)
• Identification of three riboendonuclease activities in mitochondrial extract from T. brucei (Piller et al. 1997).(identification of gRNA-independent and gRNA-dependent cleavage activities)
• Disruption of a DEAD-Box gene in T. brucei affects RNA editing. (Missel et al., 1997)(first and yet the only demonstration that KO of a gene affects RNA editing)
• Purification of a functional enzymatic editing complex from T. brucei mitochondria (Rusche et al., 1997) (This 20S complex consists of only 8 polypeptides, including three that may represent RNA ligase components!)
• RNA editing occurs in the free-living bodonid, Bodo saltans (Blom et al., 1998)
• U-deletion editing differs enzymatically from U-insertion editing (Cruz-Reyes et al., 1998) (interesting observation that ATP and ADP stimulate U-deletion in vitro editing and inhibit U-insertion in vitro editing! But these two activities cosediment in the purified 20S editing complex (Cruz-Reyes et al., 1998))
• A book on modification and editing of RNA, edited by Grosjean and Benne.
• Trypanosoma brucei RBP16 Is a Mitochondrial Y-box Family Protein with Guide RNA Binding Activity (Hayman and Read, 1999)
• The involvement of gRNA-binding protein gBP21 in RNA editing- an in vitro and in vivo analysis (Lambert et al.,1999)
• A cis-acting A-U sequence element induces kinetoplastid U-insertions (Brown et al., 1999)(uses a novel assay for in vitro U-insertion editing)
• Mapping contacts between gRNA and mRNA in trypanosome RNA editing (Leung and Koslowsky, 1999) (evidence that the 3' oligo[U] tail interacts with the preedited region of the mRNA)
• Large minicircles in kDNA from Trypanosoma avium (journal cover photo) (Yurchenko et al., 1999)
• In vitro U-insertion using a L. tarentolae mitochondrial extract mediated by cis-acting guide RNAs (Kapuchoc and Simpson, 1999)
• Computer simulations of random segregation of kDNA minicircles in trypanosomatids (Savill and Higgs, 1999) (The random segregation hypothesis was shown by computer simulations to successfully explain the presence of a few major and many minor minicircle sequence classes, the long survival time of a few of these classes, and the fluctuations of sequence class copy numbers over time!)
• A 'Constructive Neutral Evolution' theory for the evolution of U-insertion editing (Stoltzfus, 1999)(see also Simpson and Maslov, 1999, and Simpson, RNA Editing - An Evolutionary Perspective, in The RNA World Second Edition, Cold Spring harbor Laboratory Press, p 585-608, 1999, for other speculations on the origin of RNA editing)
• Kinetoplastid RNA editing does not require the terminal 3' hydroxyl of guide RNA but modifications to the gRNA terminus can inhibit U-insertion (Burgess et al., 1999)
• mRNA editing and localization of gRNA genes in mitochondria of Phytomonas serpens (Maslov et al., 1998)
• Deletions of the COIII and Cyb genes in the maxicircle DNA of the respiratory deficient Phytomonas serpens (Maslov et al., 1999) (Phytomonas could yet become a model system for respiratory-deficient trypanosomes; they are certainly easier to work with than bloodstream T. brucei!)
• The ATPase 6 cryptogene from human-infecting Leishmania is very similar to that from the lizard-infecting L. tarentolae (Brewster and Barker, 1999) (more evidence that lizard Leishmania and mammalian Leishmania are closely related and that the separate genus, Sauroleishmania, should be discarded. See also Croan and Ellis, 1996; Croan et al., 1997; Noyes et al., Parasitol. Today 14, 167, 1998)
• Knockout of the glutamate dehydrogenase gene from bloodstream T. brucei has no effect on RNA editing (Estevez et al., 1999)(another good theory destroyed (possibly) by a hard fact!)
• Characterization of a partially purified mitochondrial RNA ligase from Leishmania tarentolae. The ligase can preferentially join RNA molecules bridged by a complementary RNA, and the ligation is negatively affected by a gap between the donor and acceptor nucleotides. (Blanc et al., 1999).
• Phytomonas serpens maxicircle sequences - unedited and edited - were added to the Edited Sequences Database on Nov. 26, 1999.
• I have created a Parasite Genomes Web Site which has links to parasite genome projects and Blast servers.
• First direct evidence for the translation of unedited and edited mRNAs in the mitochondrion of a trypanosomatid (Horvath et al.a, 2000); (Horvath et al.b, 2000). (It is nice to actually see evidence for something we all felt was the case. A real breakthrough!)
• Mitochondrial minicircles in the free-living bodonid Bodo saltans contain two gRNA gene cassettes and are not found in large networks (Blom et al., 2000). (The first example of a kinetoplastid species with noncatenated, gRNA gene-containing minicircles, which implies that the creation of minicircles and minicircle networks are separate evolutionary events).
• RNA-binding properties of the mitochondrial Y-box protein RBP16 (Pelletier et al., 2000). (another in the growing list of gRNA-binding proteins, the genetic function of which is still uncertain).
• Trypanosoma brucei guide RNA poly(U) tail formation is stabilized by cognate mRNA (McManus et al., 2000). (A model is proposed in which the purine-rich region of the cognate mRNA protects the uridine tail from a uridine exonuclease activity that is present within the complex. Two chromatographically distinct TUTase activities were detected in mitochondrial extract.)
• A specific C to U nucleotide modification in the first position of the anticodon of the nuclear-encoded and mitochondrial-imported tryptophan tRNA in Leishmania tarentolae allows the decoding the the mitochondrial UGA tryptophan codon (Alfonzo et al., 1999). (the first evidence for C to U editing in the mitochondrion of trypanosomatids).

Scientific Meetings:

2005 RNA Editing Gordon Conference, January 21-28, 2005, Ventura Beach Marriott, Ventura, CA.

List of Researchers in U-insertion/deletion editing
(in no particular order!):

• Ken Stuart (URL, email)

• Uli Goringer (Email)

• Barbara Sollner-Webb (Email)

• Dmitri Maslov (URL, Email)

• Greg Connell (URL, Email)

• Steve Hajduk (URL, Email)

• Paul Sloof (Email)

• Rob Benne (Email)

• Donna Koslowsky (Email)

• Julius Lukes (URL, Email)

• Laurie Read (Email)

• Larry Simpson (URL, Email)

• Juan Alfonzo (Email)

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