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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Translation in Prokaryotes01:29

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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
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Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling
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Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes.

Mengshi Zhang1,2, Changyi Zhang3, Anayancy Ramos1

  • 1School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA.

Mbio
|July 24, 2025
PubMed
Summary

Scientists developed RNA-to-protein conversion factors to better predict protein levels from gene expression data in microbes. This method improves functional insights from transcriptomics across diverse species, reducing the need for protein data.

Keywords:
Pseudomonas aeruginosaRNA-to-protein conversioncross-domain predictionmicrobiome functional inferenceproteometranscriptomicstranslation

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Area of Science:

  • Microbial ecology
  • Systems biology
  • Genomics

Background:

  • Microbial community function is often inferred from gene expression (mRNA) data, but mRNA levels do not reliably predict protein abundance.
  • Accurate protein abundance is crucial for understanding microbial function, yet obtaining proteomic data is resource-intensive.

Purpose of the Study:

  • To develop a strategy for improving protein abundance prediction from transcriptomic data by deriving gene-specific RNA-to-protein (RTP) conversion factors.
  • To assess the cross-species and cross-domain utility of these RTP conversion factors.

Main Methods:

  • Generated paired mRNA and protein abundance data from seven bacterial and one archaeal species.
  • Identified orthologous genes with conserved protein-to-RNA (ptr) ratios across species.
  • Calculated RTP conversion factors based on conserved ptr ratios.

Main Results:

  • RTP conversion factors significantly improved protein abundance predictions from mRNA levels.
  • Conversion factors derived from one species accurately predicted protein levels in distantly related species and even across domains (bacteria to archaea).
  • Conserved ptr ratios were observed across diverse microbial taxa, highlighting a fundamental biological principle.

Conclusions:

  • A broadly applicable framework was established to enhance functional prediction in microbiomes using only transcriptomic data.
  • This approach reduces the reliance on organism-specific proteomic data, offering a powerful tool for microbial research.
  • The findings reveal significant cross-domain conservation in RNA-to-protein relationships, advancing our understanding of microbial systems.