11.10

mRNA Stability and Gene Expression

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The extent and timing of gene expression is affected by mRNA stability.

Stable mRNAs can have half-lives of several hours and encode proteins that need to be continuously produced. Protein synthesis can continue long after transcription stops if an mRNA is not degraded.

In contrast, unstable mRNAs usually have short half-lives of less than 30 minutes and are rapidly degraded. Unless transcription of these genes is continuous, the mRNA can only be only translated for a short time. This helps an organism to quickly stop producing unnecessary proteins.

mRNAs are degraded by three different pathways.

The most common method is the deadenylation dependent pathway, where adenines are removed from the poly-A tail of an mRNA, triggering its degradation from both ends of the transcript.

The deadenylating nuclease complex degrades the poly-A tail in a 3’ to 5’ direction. After the adenines are removed, the mRNA is further degraded in the same direction by the cytoplasmic exosome complex.

The 5’ end of an mRNA has a cap to protect it from exonucleases. The mRNA often forms a loop where its 5’ cap and 3’ poly-A tail are held closely together by specific proteins.

When the poly-A tail gets reduced to less than 15 residues, many of these proteins cannot bind to the poly-A tail which exposes the 5’ cap to the decapping enzymes. This subsequently results in the decapping of the 5’ end.

This decapped mRNA is then degraded from 5’ to 3’ direction by another exonuclease.

The second type of degradation is a deadenylation independent pathway where decapping enzymes remove the 5’ caps. An exonuclease then degrades the unprotected mRNA from the 5’ to 3’ end.

The third and least frequent pathway involves the internal cleavage of an mRNA using specific endonucleases. The fragments of the mRNA have unprotected 5’ and 3’ ends. Specific exonucleases then can act on these unprotected ends and degrade the mRNA.

The degradation of mRNA occurs in aggregated protein bodies known as processing, or P bodies. These P bodies contain enzymes including those involved in decapping and the 5’ to 3’ degradation of the mRNA.

Overview

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The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.

Cis-acting Elements involved in mRNA stability

An mRNA sequence not only encodes proteins but also contains various cis-acting regions, which either alone or with the help of trans-acting proteins, regulate mRNA stability. The 5' end of an mRNA has a 7-methylguanylate (m⁷G) cap, and the 3' end has a poly-A tail, both of which protect mRNA from exonucleases. A poly-A tail shorter than 15-20 nucleotides can lead to decapping and subsequent degradation of the mRNA; therefore, the length of the poly-A tail is important for the stability of mRNA. The 5' and 3' untranslated regions (UTR) of mRNA contain various sequences that act as binding sites for proteins involved in mRNA degradation and stability. The 5' UTR contains binding regions for proteins that promote decapping or removal of the 5' m⁷G cap. The 3' UTR in some mRNAs, especially those with a half-life ofless than 30 minutes, carriesmultiple “AUUUA” repeats, known as AU-rich sequences. When mRNA-destabilizing proteins bind to these AU-rich sequences, they promote rapid deadenylation and degradation of the mRNA. On the other hand, when mRNA-stabilizing proteins are present, they compete with the destabilizing proteins for binding to the AU-rich sequences and decrease the degradation rate of the mRNA. Some other mRNAs also carry specific recognition sequences for endonucleases.

Major Pathways of m-RNA degradation

The most common mechanisms of mRNA degradation involve the removal of the 3' end poly-A tail and 5' m⁷G cap. Deadenylation, removal of adenines from the poly-A tail, can lead to degradation of mRNA by two different mechanisms. The first mechanism involves the shortening of the poly-A tail to less than 15-20 nucleotides, which destabilizes the association between the mRNA and its binding proteins. This exposes the 5' m⁷G cap to the decapping enzymes, DCP1 and DCP2. The decapped and unprotected 5' end of the mRNA then can be degraded with the help of the 5' to 3' exonuclease, XRN1. Another mechanism of degradation involves complete removal of the 3' poly-A tail by deadenylases and the subsequent degradation of the unprotected 3' end by the cytoplasmic exosome complex in the 3' to 5' direction. The 5' to 3' mRNA degradation is a major pathway in yeast, while the 3' to 5' mRNA degradation is a major one in mammalian cells; however, mRNA can also be degraded by both mechanisms at the same time. In some mRNAs, deadenylation is not a prerequisite for degradation. One mechanism involves the decapping of the 5' end followed by 5' to 3' mRNA degradation using exonuclease XRN1. The other less observed degradation pathway involves an internal cleavage of the mRNA using endonucleases. The nascent unprotected ends of the broken mRNA then can be easily degraded in 5' to 3' and 3' to 5' directions with the help of XRN1 and the exosome complex, respectively.

Transcript

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The extent and timing of gene expression is affected by mRNA stability.

Stable mRNAs can have half-lives of several hours and encode proteins that need to be continuously produced. Protein synthesis can continue long after transcription stops if an mRNA is not degraded.

In contrast, unstable mRNAs usually have short half-lives of less than 30 minutes and are rapidly degraded. Unless transcription of these genes is continuous, the mRNA can only be only translated for a short time. This helps an organism to quickly stop producing unnecessary proteins.

mRNAs are degraded by three different pathways.

The most common method is the deadenylation dependent pathway, where adenines are removed from the poly-A tail of an mRNA, triggering its degradation from both ends of the transcript.

The deadenylating nuclease complex degrades the poly-A tail in a 3’ to 5’ direction. After the adenines are removed, the mRNA is further degraded in the same direction by the cytoplasmic exosome complex.

The 5’ end of an mRNA has a cap to protect it from exonucleases. The mRNA often forms a loop where its 5’ cap and 3’ poly-A tail are held closely together by specific proteins.

When the poly-A tail gets reduced to less than 15 residues, many of these proteins cannot bind to the poly-A tail which exposes the 5’ cap to the decapping enzymes. This subsequently results in the decapping of the 5’ end.

This decapped mRNA is then degraded from 5’ to 3’ direction by another exonuclease.

The second type of degradation is a deadenylation independent pathway where decapping enzymes remove the 5’ caps. An exonuclease then degrades the unprotected mRNA from the 5’ to 3’ end.

The third and least frequent pathway involves the internal cleavage of an mRNA using specific endonucleases. The fragments of the mRNA have unprotected 5’ and 3’ ends. Specific exonucleases then can act on these unprotected ends and degrade the mRNA.

The degradation of mRNA occurs in aggregated protein bodies known as processing, or P bodies. These P bodies contain enzymes including those involved in decapping and the 5’ to 3’ degradation of the mRNA.

Key Terms and Definitions

Learning Objectives

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