Disease relevance of RNT1

• RNase III-deficient cells are hypersensitive to high iron concentrations, suggesting that Rnt1p-mediated RNA surveillance is required to prevent iron toxicity [1].
• E. coli RNase III recognized RNA duplexes longer than 11 bp with little specificity, and no specific features were required for cleavage [2].
• In bacteria, RNase III contributes to the processing of many noncoding RNAs and directly cleaves several cellular and phage mRNAs [3].
• In addition, perturbation of the expression level of yeast RNase III alters meiosis and causes sterility [4].

High impact information on RNT1

• A yeast gene homologous to bacterial RNase III (RNT1) encodes a double-strand-specific endoribonuclease essential for ribosome synthesis [5].
• Consistent with this substrate specificity, the isolated Rnt1p dsRBD and the 30-40 amino acids that follow bind to AGNN-containing stem-loops preferentially in vitro [6].
• While bacterial RNAse III enzymes cleave double-stranded RNA, Rnt1p specifically cleaves RNAs that possess short irregular stem-loops containing 12-14 base pairs interrupted by internal loops and bulges and capped by conserved AGNN tetraloops [6].
• Correct cleavage of intron-encoded U18 and snR38 snoRNAs can be reproduced in vitro by incubating together purified Nop1p and Rnt1p [7].
• The dsRNA substrates of Saccharomyces cerevisiae RNase III (Rnt1p) are capped by tetraloops with the consensus sequence AGNN, which act as the primary docking site for the RNase [8].

Biological context of RNT1

• These results demonstrate that the majority of independently transcribed box C/D snoRNAs from the yeast genome undergo 5'-end processing and that the Rnt1p endonuclease and the Xrn1p and Rat1p 5' --> 3'exonucleases have partially redundant functions in the 5'-end processing of these snoRNAs [9].
• Interestingly, two of the newly identified Rnt1p-dependent snoRNAs, snR39 and snR59, are located in the introns of the ribosomal protein genes RPL7A and RPL7B [10].
• Most Rnt1 cleavage sites fall within potentially double-stranded regions closed by tetraloops with a novel consensus sequence AGNN [11].
• In cell extracts, the native enzyme effectively cleaved the DNA/RNA hybrid, indicating much broader Rnt1p substrate specificity than previously thought [12].
• Moreover, we show that 2'-hydroxyl groups of nucleotides of the tetraloop or adjacent base pairs predicted to interact with residues of alpha-helix 1 are important for Rnt1p cleavage in vitro [13].

Anatomical context of RNT1

• Members of the RNase III family of double-stranded RNA (dsRNA) endonucleases are important enzymes of RNA metabolism in eukaryotic cells [13].

Associations of RNT1 with chemical compounds

• Hydroxyl radical footprints indicate that Rnt1p specifically interacts with the NGNN tetraloop and its surrounding nucleotides [2].
• Characterization of the Reactivity Determinants of a Novel Hairpin Substrate of Yeast RNase III [14].
• Mutations of the invariant guanosine stringently inhibit binding and cleavage of all known Rnt1p substrates [14].
• Mig2p mRNA became more stable upon the deletion of Rnt1p and resisted glucose-dependent degradation [3].
• Expression of a yeast RNase III gene in transgenic tobacco silences host nitrite reductase genes [15].

Physical interactions of RNT1

• In vitro, Rnt1p binding to Gar1p is mutually exclusive of its RNA binding and cleavage activities [16].
• We report the solution structure of Rnt1p dsRBD complexed to the 5' terminal hairpin of one of its small nucleolar RNA substrates, the snR47 precursor [17].

Regulatory relationships of RNT1

• We show that the ADI1 mRNA is up-regulated under heat shock conditions in a Rnt1p-independent manner [18].

Other interactions of RNT1

• We propose that Rnt1p cleavage targets degradation of the ADI1 mRNA to prevent its expression prior to heat shock conditions and that RNA surveillance by multiple ribonucleases helps prevent accumulation of aberrant 3'-extended forms of this mRNA that arise from intrinsically inefficient 3'-processing signals [18].
• Moreover, inactivation of the DBR1 gene in rrp2-1, or the RNT1 gene in rrp5-Delta3 mutant cells also negates the effects of the original mutation on pre-rRNA processing [19].
• These data link a total of three RNA catabolic enzymes, Rex4p, Rnt1p, and Dbr1p, to ITS1 processing and the relative production of 5.8SS and 5.8SL rRNA [19].
• In contrast, snR59 is produced by a direct cleavage of the RPL7B pre-mRNA, indicating that a single pre-mRNA transcript cannot be spliced to produce a mature RPL7B mRNA and processed by Rnt1p to produce a mature snR59 simultaneously [10].
• However, deletion mutants for the 3' end-processing enzyme Rnt1p or the Rpa12p subunit of Pol I both show Pol I transcription in the spacer [20].

Analytical, diagnostic and therapeutic context of RNT1

• In order to understand how Rnt1p recognizes its cognate processing sites, we have defined its minimal RNA-binding domain and determined its structure by solution NMR spectroscopy and X-ray crystallography [6].
• The presence of AGNN tetraloops also enhances Rnt1p binding, as shown by surface plasmon resonance monitoring and modification interference studies [21].
• Comparative sequence analyses have revealed an additional N-terminal domain unique to the eukaryotic homologues of RNase III [22].
• Size exclusion chromatography and cross-linking assays indicated that the N-terminal domain and the dsRBD self-interact to stabilize the Rnt1 homodimer [22].
• Rnt1p was found associated with the endogenous rDNA by chromatin immunoprecipitation [23].

References