Subcytoplasmic location of translation controls protein output
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Abstract
The cytoplasm is highly compartmentalized, but the extent and consequences of subcytopIasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endopIasmic reticuIum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on non-membrane protein-encoding mRNAs, we observed that 52% have a biased transcript distribution across these compartments. Compartment enrichment is determined by a combinatorial code based on mRNA length, exon length, and 3′UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentaIized by local translation environments.
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Review coordinated by Life Science Editors Foundation
Reviewed by: Dr. Angela Andersen
Potential Conflicts of Interest: None
Background:
- mRNAs in polarized cells often have a distinct spatial localization patterns that enable localized protein production
- In non-polarized cells, mRNAs encoding membrane and secretory proteins are predominantly translated on the endoplasmic reticulum (ER), some mRNAs are enriched on the mitochondrial surface, some mRNAs are bound to the RNA-binding protein (RBP) TIS11B at the surface of the rough ER in "TIS granules".
- The translation of specific mRNAs in TIS granules allows assembly of protein complexes that cannot be established when the mRNAs are translated on the ER but outside of TIS granules (physiological relevance).
- The canonical rough ER (CRER) is distinct from the TIS granule ER (TGER), and both are …
Review coordinated by Life Science Editors Foundation
Reviewed by: Dr. Angela Andersen
Potential Conflicts of Interest: None
Background:
- mRNAs in polarized cells often have a distinct spatial localization patterns that enable localized protein production
- In non-polarized cells, mRNAs encoding membrane and secretory proteins are predominantly translated on the endoplasmic reticulum (ER), some mRNAs are enriched on the mitochondrial surface, some mRNAs are bound to the RNA-binding protein (RBP) TIS11B at the surface of the rough ER in "TIS granules".
- The translation of specific mRNAs in TIS granules allows assembly of protein complexes that cannot be established when the mRNAs are translated on the ER but outside of TIS granules (physiological relevance).
- The canonical rough ER (CRER) is distinct from the TIS granule ER (TGER), and both are distinct from the cytosol.
Questions:
- Do mRNAs that encode non-membrane proteins differentially localize to the ER or the cytosol? (in steady state)
- Does the amount of protein synthesis differ depending on the subcytoplasmic location of an mRNA?
Summary:
- A third of mRNAs that encode non-membrane proteins have a biased localization to TGER or CRER, indicating that the ER membrane is a general site of translation for both membrane and non-membrane proteins.
- 52% of mRNAs that encode non-membrane proteins have a biased mRNA transcript localization pattern towards a single cytoplasmic compartment. the TGER, CRER or cytosol.
- The localization at the TGER or CRER was largely controlled by a combinatorial code of AU-RBPs at the 3'UTR. TIS11B promotes mRNA localization to TGER and TIA1/L1 to CRER.
- LARP4B bound to the 3'UTR promotes cytosolic localization.
- The location of translation has an independent effect on protein levels independent of the RBPs/3'UTR: redirecting cytosolic mRNAs to the rough ER membrane increased their steady-state protein levels by two-fold, indicating that the ER environment promotes protein expression.
- Compartment-enriched mRNAs differed in their mRNA production and degradation rates, as well as functional classes and levels of their encoded proteins. Therefore the cytoplasm is partitioned into different functional and regulatory compartments that are not enclosed by membranes.
- low-abundance proteins are translated in the TGER region. mRNAs encoding zinc finger proteins and transcription factors were substantially enriched at the TGER. These gene classes are usually expressed at lower levels than others.. This localization may regulate protein complex assembly (membrane proteins that are translated in the TGER domain establish protein complexes that cannot be formed when the proteins are translated on the CRER). The TGER may ensure that low-abundance mRNAs are effectively translated into low-abundance proteins.
- mRNAs that are the most stable and encode the most highly expressed proteins are enriched on the CRER and include helicases, cytoskeleton-bound proteins, and chromatin regulators, overturning the idea that most non-membrane protein-encoding mRNAs are translated in the cytosol.
- mRNAs overrepresented in the cytosol had the highest production and degradation rates and were enriched in proteins involved in mRNA processing and translation factors, whose abundance levels require tight control.
Advance: Evidence for functional compartmentalization of non-membrane mRNA protein expression in the cytosol vs ER. In steady state, general localization of mRNAs to the ER promotes high protein levels.
Significance: Engineered 3'UTR sequences could potentially boost protein expression by localizing mRNAs to the ER in experimental settings, for vaccines etc.
Remaining questions/points:
- How does the rough ER stimulate protein expression?
- Does the mRNA localization affect complex formation and/or function of non-membrane proteins?
- Does this occur in cells other than HEK293T?
- Is this regulated?
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