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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Post-transcriptional capping generates coenzyme A-linked RNA.

Krishna Sapkota1, Jordyn K Lucas2,3, Jarrett W Faulkner1

  • 1Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA.

RNA Biology
|November 30, 2023
PubMed
Summary
This summary is machine-generated.

Researchers discovered that phosphopantetheine adenylyltransferase (PPAT) can post-transcriptionally cap RNA with 4-phosphopantetheine, forming CoA-RNA. This suggests a new pathway for CoA-RNA biogenesis in bacteria.

Keywords:
CoA-RNACoA-RNA CaptureSeqPPATcofactor-RNA conjugatespost-transcriptional CoA-capping

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA Biology

Background:

  • NAD can be incorporated into RNA co-transcriptionally.
  • CoA-linked RNA formation via this mechanism is unlikely due to low 3'-dephospho-CoA (dpCoA) levels.
  • A post-transcriptional mechanism for CoA-RNA biogenesis is needed.

Purpose of the Study:

  • Investigate if phosphopantetheine adenylyltransferase (PPAT) can form CoA-RNA.
  • Identify RNA features required for PPAT to act as a substrate.
  • Determine the mechanism and regulation of PPAT-mediated RNA capping.

Main Methods:

  • In vitro characterization of PPAT activity using synthetic RNAs.
  • Mutation analysis of RNA 5' termini and enzyme inhibitors.
  • CoA-RNA CaptureSeq following bacterial expression of candidate RNAs.

Main Results:

  • PPAT post-transcriptionally transfers 4'-phosphopantetheine to RNA 5' termini, forming CoA-RNA.
  • RNAs with 4-10 unpaired nucleotides at the 5' terminus are preferred substrates.
  • ATP inhibits PPAT activity, while PPAT binding is less dependent on specific 5' nucleotides.
  • In vivo experiments support PPAT-mediated CoA-capping of RNA transcripts.

Conclusions:

  • PPAT facilitates post-transcriptional RNA capping, yielding CoA-RNA.
  • This represents a novel mechanism for CoA-RNA biogenesis in bacteria.
  • RNA structure, specifically the 5' terminus, influences PPAT substrate recognition.