We saw in Chapter 6 that the 3ʹ end of a eukaryotic mRNA molecule is not formed by the termination of RNA synthesis by the RNA polymerase, as it is in bacteria. Instead, it results from an RNA cleavage reaction that is catalyzed by additional proteins while the transcript is elongating (see Figure 6–34). A cell can control the site of this cleavage so as to change the C-terminus of the resultant protein. In the simplest cases, one protein variant is simply a truncated version of the other; in many other cases, however, the alternative cleavage and polyadenylation sites lie within intron sequences and the pattern of splicing is thereby altered. This process can produce two closely related proteins differing only in the amino acid sequences at their C-terminal ends. Close analysis of RNAs produced from the human genome in a variety of cell types (see Figure 7–3) indicate that as many as 50% of human protein-coding genes produce mRNA species that differ at their site of polyadenylation.
A well-studied example of regulated polyadenylation is the switch from the synthesis of membrane-bound to secreted antibody molecules that occurs during the development of B lymphocytes (see Figure 24–22). Early in the life history of a B lymphocyte, the antibody it produces is anchored in the plasma membrane, where it serves as a receptor for antigen. Antigen stimulation causes B lymphocytes to multiply and to begin secreting their antibody. The secreted form of the antibody is identical to the membrane-bound form except at the extreme C-terminus. In this part of the protein, the membrane-bound form has a long string of hydrophobic amino acids that traverses the lipid bilayer of the membrane, whereas the secreted form has a much shorter string of hydrophilic amino acids. The switch from membrane-bound to secreted antibody is generated through a change in the site of RNA cleavage and polyadenylation, as shown in Figure 7–59.
The change is caused by an increase in the concentration of a subunit of a protein (CstF) that promotes RNA cleavage (see Figure 6–34). The first cleavage/ poly-A addition site that a transcribing RNA polymerase encounters is suboptimal and is usually skipped in unstimulated B lymphocytes, leading to production of the longer RNA transcript. When activated to produce antibodies, the B lymphocyte increases its CstF concentration; as a result, cleavage now occurs at the suboptimal site, and the shorter transcript is produced. In this way, a change in concentration of a general RNA-processing factor has a dramatic effect on the expression of a particular gene.
rnA editing Can Change the Meaning of the rnA Message
The molecular mechanisms used by cells are a continual source of surprises. An example is the process of RNA editing, which alters the nucleotide sequences of RNA transcripts once they are synthesized and thereby changes the coded message they carry. We saw in Chapter 6 that tRNA and rRNA molecules are chemically modified after they are synthesized: here we focus on changes to mRNAs.
In animals, two principal types of mRNA editing occur: the deamination of adenine to produce inosine (A-to-I editing) and, less frequently, the deamination of cytosine to produce uracil (C-to-U editing), as shown in Figure 5–43. Because these chemical modifications alter the pairing properties of the bases (I pairs with C, and U pairs with A), they can have profound effects on the meaning of the RNA. If the edit occurs in a coding region, it can change the amino acid sequence of the protein or produce a truncated protein by creating a premature stop codon. Edits that occur outside coding sequences can affect the pattern of pre-mRNA splicing, the transport of mRNA from the nucleus to the cytosol, the efficiency with which the RNA is translated, or the base-pairing between microRNAs (miRNAs) and their mRNA targets, a form of regulation that will be discussed later in the chapter.