Mechanisms Regulating Protein Translation

Protein synthesis is an essential function of unicellular and multicellular organisms alike. Enzymes, cell organelles, muscles, and bone matrix are all composed of proteins. For many years, biologists have known that proteins are composed of chains of amino acids linked together by peptide bonds. Prior to the 1960’s, however, almost nothing was known about the cellular mechanisms controlling protein synthesis. This article will explore some of the key discoveries that shed light on this fascinating realm of biology.

Cracking the Genetic Code

Watson and Crick’s discovery of the double helical structure of DNA in 1953 ushered in the era of modern genetics. It also sparked the quest to discover the connection between an organism’s DNA sequence and the amino acid sequence of its proteins. In other words, the time had come to crack the genetic code. To accomplish this, scientists synthesized strings of nucleotides, for example UUU or AAA, then incubated them with bacterial ribosomes, amino acids, and a high energy phosphate carrier (GTP). After some time elapsed, they sequenced the resulting peptide. In the case of UUU, the corresponding peptide was a string of phenylalanines. AAA coded for lysine, GGG for valine, CCC for proline, and so forth. Within a few years, all 64 codons had been matched to their corresponding amino acids. As it turned out, 61 nucleotide codons specified amino acids while three others (UAG, UGA, and UGG) served as stop codons to terminate protein synthesis.     

Prokaryotes vs. Eukaryotes

Most early studies of protein synthesis used bacteria because they are abundant and easy to grow in massive quantities. Scientists knew that bacteria could synthesize proteins rapidly. The reason turned out to be straightforward. As prokaryotes, bacteria lack a nuclear membrane surrounding their DNA. This means bacteria can transcribe their genes into messenger RNA (mRNA) and translate this mRNA into protein simultaneously.

In contrast to prokaryotes, eukaryotes (protozoa, fungi, plants, and animals) store their DNA inside a nuclear envelope. Consequently, in eukaryotic cells, DNA transcription and mRNA translation are separated in space and time. Although this lengthens the time required to synthesize proteins, it also presents multiple opportunities for fine tuning this process.

RNA Processing/RNA Turnover

By the late 1970’s, scientists learned that protein synthesis in eukaryotes was significantly more complicated than in bacteria. Not only must mRNA be transcribed and translated sequentially, mRNA must also be processed before leaving the nucleus. The key steps in mRNA processing are intron removal, exon selection, followed by the addition of a 5’ cap and a 3’ poly A tail. The 5’ cap is made of 7-methylguanosine while the 3’ tail consists of a long string of adenosines.

Once the mature mRNA enters the cytosol, several factors determine how many copies of a protein will be translated from that particular mRNA. First, the number of ribosomes in that cell sets a maximum limit on protein synthesis. Liver hepatocytes, skeletal muscle fibers, and B lymphocytes all have large numbers of ribosomes and can synthesize abundant amounts of protein. Conversely, adipocytes (fat storage cells) contain few ribosomes, while mature red blood cells and platelets lack ribosomes entirely.

A second factor regulating protein translation is the length of a given mRNA’s poly A tail. This determines mRNA stability, in essence acting as a built in time limit on protein translation. mRNAs with excessively long poly A tails (or lacking adenylation entirely) are degraded fairly rapidly by cytosolic nucleases. In contrast, stable mRNA can persist for hours or days, giving the cell’s ribosomes ample time to synthesize many copies of that particular protein.

A third mechanism involves specialized RNA sequences called response elements. Based upon their secondary structure and interactions with specific binding proteins, the mRNA is either protected or marked for rapid degradation. The best understood example of this phenomenon is the iron response element, which plays a pivotal role in the translation of two proteins involved in iron metabolism: ferritin and the transferrin receptor (TfR). Ferritin is abundant in the heart and liver and acts like a giant cage to trap iron atoms. On the other hand, the TfR extracts serum iron for use as an enzyme cofactor as well as in red blood cell production. Naturally, the question arises, how does the body know which protein to synthesize? 

The answer is that the iron level in a cell ultimately dictates which mRNA will be translated and which one degraded. A low iron level favors the translation of TfR because there is no point constructing ferritin for iron storage when iron is scarce. A shortage of iron means that the iron response element binding protein does not protect ferritin mRNA, which then gets degraded. Meanwhile, TfR mRNA is preferentially translated to maximize iron uptake by cells in the bone marrow. Conversely, when iron is abundant, it makes sense to store as much as possible. In this case, ferritin mRNA gets translated while the TfR mRNA gets degraded.

Finally, in humans and many other mammals, the availability of essential amino acids determines whether or not protein synthesis occurs at all. Children must obtain 10 out of the 20 naturally occurring amino acids in their diets to ensure proper growth. These are phenylalanine, valine, tryptophan, threonine, isoleucine, methionine, histidine, arginine, leucine, and lysine. One popular mnemonic to remember this is PVT. TIM HALL. Adults, who are not growing and have a slower metabolic rate, can scavenge enough arginine from the urea cycle to compensate for a dietary deficiency of this amino acid.