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Scientists discovered a new way cells make proteins using alternative open reading frames (Alt-ORFs). These novel alt-proteins have no sequence similarity to known proteins, expanding our understanding of the proteome.

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Area of Science:

  • Genomics
  • Proteomics
  • Molecular Biology

Background:

  • The proteome is diversified by transcriptional and post-transcriptional mechanisms that maintain sequence relationships between proteins.
  • A novel mechanism generates alternative proteins (alt-proteins) by translating alternative open reading frames (Alt-ORFs) within canonical host messenger RNAs (mRNAs).

Purpose of the Study:

  • To investigate the characteristics and origin of alt-proteins encoded by nested Alt-ORFs (nAlt-ORFs).
  • To establish a theoretical and conceptual framework for exploring these unannotated ORFs and their encoded proteins.

Main Methods:

  • Analysis of global amino acid frequencies and biochemical characteristics of nAlt-ORFs.
  • Theoretical prediction of nAlt-ORF characteristics based on encompassing host codon-pair frequencies.
  • Empirical analysis of 101 human nAlt-ORFs (length ≥150 codons).

Main Results:

  • nAlt-ORF biochemical characteristics are genetically driven and predictable from host codon-pair frequencies.
  • Human nAlt-ORF proteins exhibit a high median isoelectric point (pI) of 11.68 due to anomalous charged amino acid levels.
  • nAlt-ORF proteins show a preference for reading frame 2, predicted mitochondrial/nuclear localization, and elevated codon adaptation index.

Conclusions:

  • Alt-ORFs represent a significant, largely unannotated source of novel protein diversity.
  • The discovered mechanism challenges existing paradigms of proteome diversification.
  • Further exploration of nAlt-ORFs and their encoded proteins is warranted.