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Transcription Initiation01:47

Transcription Initiation

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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
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Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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Transfer RNA Synthesis02:36

Transfer RNA Synthesis

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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.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
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RNA Editing02:23

RNA Editing

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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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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
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Related Experiment Video

Updated: Jun 16, 2025

High-throughput Purification of Affinity-tagged Recombinant Proteins
07:44

High-throughput Purification of Affinity-tagged Recombinant Proteins

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Structural basis for substrate binding and selection by human mitochondrial RNA polymerase.

Karl Herbine1, Ashok R Nayak1, Dmitry Temiakov2

  • 1Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.

Nature Communications
|August 20, 2024
PubMed
Summary
This summary is machine-generated.

Human mitochondrial RNA polymerase (mtRNAP) selects substrates using structural mechanisms. Cryo-electron microscopy reveals how mtRNAP distinguishes between nucleotide types for accurate transcription.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Accurate transcription relies on RNA polymerase (RNAP) correctly selecting substrates and distinguishing between deoxyribonucleotides and ribonucleotides.
  • Understanding these selection mechanisms is crucial for maintaining genetic information fidelity during transcription.

Purpose of the Study:

  • To elucidate the structural basis of substrate selection and discrimination by human mitochondrial RNA polymerase (mtRNAP).
  • To investigate the mechanism of nucleotide triphosphate (NTP) binding and selection in transcription elongation complexes.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) was employed to determine high-resolution structures of human mtRNAP elongation complexes.
  • Analysis of substrate binding sites, including Entry and Insertion Sites, within the mtRNAP active site.

Main Results:

  • Cryo-EM structures revealed adenosine triphosphate (ATP) bound in both Entry and Insertion Sites of mtRNAP.
  • Interactions in the Entry Site discriminate against nucleosides and their phosphate derivatives, but not non-cognate rNTPs and dNTPs.
  • A distinct mtRNAP conformation was observed for rejecting non-cognate substrates from the active site.

Conclusions:

  • The study establishes a structural foundation for substrate binding and NTP selection in single-subunit RNAPs.
  • Findings suggest a unified mechanism for NTP selection employed by these enzymes.