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Diversity and roles of (t)RNA ligases.

Popow J, Schleiffer A, Martinez J - Cell. Mol. Life Sci. (2012)

Bottom Line: As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins.Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing.In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria.

ABSTRACT
The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.

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Domain and polypeptide organization of archetypical RNA ligase systems from bacteriophage T4 (T4 Pnkp, T4 Rnl2, and T4 Rnl1) [70, 77, 79, 80], S. cerevisiae (ScTRL1) [74], A. thaliana (AtRNL) [52, 75], and B. floridae (BfRNL and BfKinase/CPD) [87]. Nucleotidyl transferase domains are depicted in light blue, kinase domains in green, the DxDxT Pase (aspartic acid-based phosphatase) domain in white and 2H-CPD (two conserved histidine based phosphoesterase) domains in yellow. No published domain boundaries are currently available for the A. thaliana and B. floridae Kinase/CPD modules, which is indicated by a gradual transition between the two respective colors. The positions of key motifs are drawn to scale. Pnkp polynucleotide kinase/phosphatase; Pase phosphatase; CPD cyclic phosphodiesterase
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Fig3: Domain and polypeptide organization of archetypical RNA ligase systems from bacteriophage T4 (T4 Pnkp, T4 Rnl2, and T4 Rnl1) [70, 77, 79, 80], S. cerevisiae (ScTRL1) [74], A. thaliana (AtRNL) [52, 75], and B. floridae (BfRNL and BfKinase/CPD) [87]. Nucleotidyl transferase domains are depicted in light blue, kinase domains in green, the DxDxT Pase (aspartic acid-based phosphatase) domain in white and 2H-CPD (two conserved histidine based phosphoesterase) domains in yellow. No published domain boundaries are currently available for the A. thaliana and B. floridae Kinase/CPD modules, which is indicated by a gradual transition between the two respective colors. The positions of key motifs are drawn to scale. Pnkp polynucleotide kinase/phosphatase; Pase phosphatase; CPD cyclic phosphodiesterase

Mentions: In addition to T4 Rnl1, another RNA ligase, T4 Rnl2, has been identified in the genome of bacteriophage T4 [66]. T4 Rnl1 and T4 Rnl2 constitute distinct and only distantly related protein families sharing characteristic features (Fig. 3). Members of the Rnl2 family have been detected and examined in viral, bacterial, and archaeal genomes, suggesting a common phylogenetic origin and possibly a function in RNA repair [66–70]. Potentially, this type of ligases might also be involved in archaeal tRNA splicing. In trypanosomatids, 5′–3′ RNA ligases of the Rnl2 type are involved in RNA-guided editing of mitochondrial pre-mRNAs by nucleolytic cleavage and ligation [71].Fig. 3


Diversity and roles of (t)RNA ligases.

Popow J, Schleiffer A, Martinez J - Cell. Mol. Life Sci. (2012)

Domain and polypeptide organization of archetypical RNA ligase systems from bacteriophage T4 (T4 Pnkp, T4 Rnl2, and T4 Rnl1) [70, 77, 79, 80], S. cerevisiae (ScTRL1) [74], A. thaliana (AtRNL) [52, 75], and B. floridae (BfRNL and BfKinase/CPD) [87]. Nucleotidyl transferase domains are depicted in light blue, kinase domains in green, the DxDxT Pase (aspartic acid-based phosphatase) domain in white and 2H-CPD (two conserved histidine based phosphoesterase) domains in yellow. No published domain boundaries are currently available for the A. thaliana and B. floridae Kinase/CPD modules, which is indicated by a gradual transition between the two respective colors. The positions of key motifs are drawn to scale. Pnkp polynucleotide kinase/phosphatase; Pase phosphatase; CPD cyclic phosphodiesterase
© Copyright Policy
Related In: Results  -  Collection

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Fig3: Domain and polypeptide organization of archetypical RNA ligase systems from bacteriophage T4 (T4 Pnkp, T4 Rnl2, and T4 Rnl1) [70, 77, 79, 80], S. cerevisiae (ScTRL1) [74], A. thaliana (AtRNL) [52, 75], and B. floridae (BfRNL and BfKinase/CPD) [87]. Nucleotidyl transferase domains are depicted in light blue, kinase domains in green, the DxDxT Pase (aspartic acid-based phosphatase) domain in white and 2H-CPD (two conserved histidine based phosphoesterase) domains in yellow. No published domain boundaries are currently available for the A. thaliana and B. floridae Kinase/CPD modules, which is indicated by a gradual transition between the two respective colors. The positions of key motifs are drawn to scale. Pnkp polynucleotide kinase/phosphatase; Pase phosphatase; CPD cyclic phosphodiesterase
Mentions: In addition to T4 Rnl1, another RNA ligase, T4 Rnl2, has been identified in the genome of bacteriophage T4 [66]. T4 Rnl1 and T4 Rnl2 constitute distinct and only distantly related protein families sharing characteristic features (Fig. 3). Members of the Rnl2 family have been detected and examined in viral, bacterial, and archaeal genomes, suggesting a common phylogenetic origin and possibly a function in RNA repair [66–70]. Potentially, this type of ligases might also be involved in archaeal tRNA splicing. In trypanosomatids, 5′–3′ RNA ligases of the Rnl2 type are involved in RNA-guided editing of mitochondrial pre-mRNAs by nucleolytic cleavage and ligation [71].Fig. 3

Bottom Line: As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins.Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing.In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria.

ABSTRACT
The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.

Show MeSH