Structure–function analysis of the yeast NAD<sup>+</sup>-dependent tRNA 2′-phosphotransferase Tpt1

Sawaya, Rana; Schwer, Beate; Shuman, Stewart

doi:10.1261/rna.7193705

Cited by 34 publications

(49 citation statements)

References 25 publications

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“…The genes of this cluster encode proteins with no defined function, the sole exception being orf35, possibly encoding a Tpt1/KptA family tRNA 2Ј-phosphotransferase. In Saccharomyces cerevisiae, Tpt1 is involved in the final step of tRNA splicing and catalyzes the transfer of the extra 2Ј-phosphate from the precursor-ligated tRNA to NAD (87). Our search for a S. pneumoniae Tpt1/KptA homolog yielded no results suggesting the absence of such function in this bacterium.…”

Section: Vol 193 2011 Genome and Interactome Of S Pneumoniae Phagementioning

confidence: 80%

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

et al. 2011

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Streptococcus pneumoniae causes several diseases, including pneumonia, septicemia, and meningitis. Phage Dp-1 is one of the very few isolated virulent S. pneumoniae bacteriophages, but only a partial characterization is currently available. Here, we confirmed that Dp-1 belongs to the family Siphoviridae. Then, we determined its complete genomic sequence of 56,506 bp. It encodes 72 open reading frames, of which 44 have been assigned a function. We have identified putative promoters, Rho-independent terminators, and several genomic clusters. We provide evidence that Dp-1 may be using a novel DNA replication system as well as redirecting host protein synthesis through queuosine-containing tRNAs. Liquid chromatography-mass spectrometry analysis of purified phage Dp-1 particles identified at least eight structural proteins. Finally, using comprehensive yeast two-hybrid screens, we identified 156 phage protein interactions, and this intraviral interactome was used to propose a structural model of Dp-1.Streptococcus pneumoniae (pneumococcus) is a low-GC-content, Gram-positive bacterium belonging to the mitis group of streptococci (40). It is a facultative human pathogen, colonizing the mucosal surface of the upper respiratory tract and causing invasive infections such as pneumonia, meningitis, and sepsis (97). S. pneumoniae diseases are associated with severe morbidity and a high rate of mortality, especially among young children and the elderly. Antibiotics are commonly used to control and cure the invasive pneumococcal diseases, but this high exposure to antibiotics has led to multiresistant S. pneumoniae strains worldwide (79). Vaccination is efficient in preventing invasive diseases (103), but pneumococcal clones expressing capsular polysaccharides with serotypes not included in the current vaccines' formulations exist, and the incidence of invasive diseases induced by these vaccine-escaping clones is increasing (34). Replacement of the vaccine-included clones by the vaccine-escaping ones is possible (91).The appearance of antibiotic-resistant and vaccine-escaping clones is partly due to the high genome plasticity of S. pneumoniae. This genome plasticity is supported by the ability of the pneumococcus to acquire DNA through natural competence and by genome rearrangements facilitated by the mobile elements present in its genome (15,43,93). S. pneumoniae is also able to colonize many sites inside the human host using phase variation of cell surface components such as polysaccharide capsule, lipoteichoic acid, and cell-surface expressed proteins (42,78,101). The complexity of physiology and genetics of S. pneumoniae complicates the search for novel therapeutic approaches needed to counter increasing antibiotic resistance and emergence of the vaccine-escaping clones.One of the novel therapeutic approaches toward antibioticresistant strains is the use of bacteriophage proteins to lyse pneumococcus cells. The feasibility of this approach was first demonstrated when bacteriophage endolysin enzymes were used successfully t...

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Section: Vol 193 2011 Genome and Interactome Of S Pneumoniae Phagementioning

confidence: 80%

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

et al. 2011

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“…KptA homolog has been identified that catalyzes the same reaction in vitro and can complement knockouts of the yeast counterpart [51,52] (Fig. 1).…”

Section: Nad-dependent Phosphotransferasementioning

confidence: 99%

NAD homeostasis in the bacterial response to DNA/RNA damage

2014

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“…1A). The deletion encompasses residues whose counterparts in yeast Tpt1p are essential for enzymatic activity (Sawaya et al 2005;Steiger et al 2005) and the mutant allele likely functions as a null. The mutation was transmitted through the germline of chimeric mice.…”

Section: Resultsmentioning

confidence: 99%

An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation

Harding¹,

Lackey²,

Hsu³

et al. 2007

RNA

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Unconventional mRNA splicing by an endoplasmic reticulum stress-inducible endoribonuclease, IRE1, is conserved in all known eukaryotes. It controls the expression of a transcription factor, Hac1p/XBP-1, that regulates gene expression in the unfolded protein response. In yeast, the RNA fragments generated by Ire1p are ligated by tRNA ligase (Trl1p) in a process that leaves a 29-PO 4 2À at the splice junction, which is subsequently removed by an essential 29-phosphotransferase, Tpt1p. However, animals, unlike yeast, have two RNA ligation/repair pathways that could potentially rejoin the cleaved Xbp-1 mRNA fragments. We report that inactivation of the Trpt1 gene, encoding the only known mammalian homolog of Tpt1p, eliminates all detectable 29-phosphotransferase activity from cultured mouse cells but has no measurable effect on spliced Xbp-1 translation. Furthermore, the relative translation rates of tyrosine-rich proteins is unaffected by the Trpt1 genotype, suggesting that the pool of (normally spliced) tRNATyr is fully functional in the Trpt1À/À mouse cells. These observations argue against the presence of a 29-PO 4 2À at the splice junction of ligated RNA molecules in Trpt1À/À cells, and suggest that Xbp-1 and tRNA ligation proceed by distinct pathways in yeast and mammals.

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Structure–function analysis of the yeast NAD⁺-dependent tRNA 2′-phosphotransferase Tpt1

Cited by 34 publications

References 25 publications

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

NAD homeostasis in the bacterial response to DNA/RNA damage

An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation

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Structure–function analysis of the yeast NAD+-dependent tRNA 2′-phosphotransferase Tpt1

Cited by 34 publications

References 25 publications

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

NAD homeostasis in the bacterial response to DNA/RNA damage

An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation

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Structure–function analysis of the yeast NAD⁺-dependent tRNA 2′-phosphotransferase Tpt1