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Eisosome disruption by noncoding RNA deletion increases protein secretion in yeast.

Matthew Wenjie Feng1, Daniela Delneri1,2, Catherine B Millar1

  • 1Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK.

PNAS Nexus
|January 30, 2023
PubMed
Summary

Deleting specific noncoding RNAs (ncRNAs) and disrupting yeast eisosomes enhances protein secretion. This discovery offers a new strategy for improving biopharmaceutical production through engineered yeast.

Keywords:
PIL1Saccharomyces cerevisiaeeisosome membrane compartment (EMC)noncoding RNAprotein secretion

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Yeast Genetics

Background:

  • Noncoding RNAs (ncRNAs) play crucial roles in regulating gene expression.
  • Efficient protein secretion in yeast is vital for biotechnology and biopharmaceutical production.
  • Eisosomes, plasma membrane invaginations, are involved in cellular organization and transport.

Purpose of the Study:

  • To investigate the impact of ncRNA deletions on endogenous invertase secretion in yeast.
  • To identify specific ncRNAs that, when deleted, enhance protein secretion.
  • To explore the potential of eisosome disruption as a strategy for improving protein secretion.

Main Methods:

  • Large-scale screening of ncRNA deletion strains (SUTs, CUTs, tRNAs, snRNAs) for improved invertase secretion.
  • Quantification of adjacent gene transcription in ncRNA deletion strains.
  • Analysis of protein secretion (invertase, GFP, monoclonal antibody peptide) in knockout strains and upon eisosome disruption.

Main Results:

  • Deletion of SUT418, SUT390, and SUT125 significantly improved invertase secretion.
  • PIL1 gene down-regulation in the SUT125 deletion strain led to increased invertase secretion, further enhanced by combined deletions of eisosome components.
  • Eisosome disruption increased secretion of various proteins, including heterologous proteins and a monoclonal antibody peptide, linked to sphingolipid metabolism alterations.

Conclusions:

  • Specific ncRNAs, such as SUT125, can be deleted to enhance protein secretion.
  • Disruption of eisosomes, particularly through PIL1 deletion, represents a novel pathway to improve both endogenous and heterologous protein secretion in yeast.
  • This strategy holds potential for enhancing biopharmaceutical production using engineered yeast systems.