Alternative Splicing

Alternative Splicing Definition

Alternative splicing is a method cells use to create many proteins from the same strand of DNA. It is also called alternative RNA splicing. In regular DNA translation, specialized proteins create messenger RNA (mRNA) from the DNA template. This mRNA then finds its way to a ribosome, where the RNA code is translated into the structure of a new protein. In alternative splicing, interactions between different proteins, the cell, and the environment can cause different segments of the original DNA to be omitted from the mRNA. When this happens, the alternate mRNA is translated into an entirely different protein.

Proteins differ only in the basic arrangement of their amino acids, which is dictated by the mRNA. Once that is changed, the function of the protein changes. Using the method of alternative splicing, organisms can produce many more proteins than their DNA might indicate. For instance, humans have around 20,000 genes which code for a protein. However, there are thought to be over 100,000 different proteins in the human body. Alternative splicing creates these different forms.

How Does Alternative Splicing Work?

Alternative splicing occurs after a primary mRNA is created from the DNA. This process is called transcription, as the languages of RNA and DNA are basically the same. They both rely on 4 nucleotide bases. When a ribosome reads this language, it translates the message into the language of proteins, which consists of around 21 amino acids.

Therefore, before a primary mRNA is translated into a protein, it must first be modified and edited. In normal splicing, a special protein and RNA complex called the spliceosome attaches itself to the primary mRNA. The primary mRNA has various regions, called introns and exons. These regions are mixed together, and the introns must be removed to create a functional protein.

The spliceosome is specially equipped to remove the introns. Spliceosomes consist of four different subunits, called small nuclear ribonucleoproteins (snRNP or “snurp”). Each “snurp” has two small nuclear RNAs (snRNAs). These special strands of RNA contain sequences of nucleotides which match specific locations in the exons and bind to them. The protein portion of the spliceosome then acts as an enzyme, removing the introns and binding the exons together. This spliced mRNA is now ready to be translated into a protein.

However, alternate splicing can also take place. While the entire mechanism is not well understood, it is known that certain chemical factors can stimulate the spliceosome to operate in different ways. A signal may be given to exclude an exon, or even multiple exons from the final mRNA. Other signals and pathways can cause the spliceosome to leave introns intact or skip large sections of the protein. Our bodies have many different uses for proteins, and can often use the same DNA blueprint to make many of these proteins. See the examples section for specific examples. Below is a generalize chart showing the different ways a spliceosome can alternatively splice a primary RNA.

There is another form of alternative splicing, known as trans splicing, in which exons from two different genes get assembled together by a spliceosome. This genetic process has only been observed in a few single-celled organisms, but could help explain their genetic diversity without sexual reproduction. While sexual reproducing organisms must breed to mix their genetics and produce new varieties, these organisms can do it much faster. This form of alternative splicing can easily create entirely new functions in these organisms, which may prove to be beneficial.

Examples of Alternative Splicing

Neurexin Genes

Humans have 3 genes which code for a family of proteins known as neurexins. These proteins are incorporated into the plasma membrane. They extend out of the plasma membrane and into the space between nerves. Here, they bind to a protein from the other nerve cell. This protein complex holds the cells in place. While there are only 3 different genes which code for neurexins, there are over 3,000 different proteins in the neurexin family.

This is possible through alternative splicing. As the spliceosome processes the primary mRNA molecules from these genes, it is influenced by a number of promoter genes, molecules in the cell, and other signals. These influence which exons get included into the final mRNA. The alternate splicing can make the proteins larger or smaller, or with regions missing, but it generally still produces a working protein. In this way, each variation of cellular environment or extracellular signal creates a different protein with a slightly different function.

While all the neurexin proteins will function in holding together the synapse between two nerves, the variation produced is theorized to do a number of things. First, it may alter the signal traveling between the two neurons. This could produce a necessary effect for the brain to process the signal. Different proteins may be employed at different times, in different cells, in the same animal. This might be necessary to accommodate the many different environments within an organism, and ensure the neurons are working properly.

When scientist observed the same genes in fish, they found something interesting. While fish also have these genes, they cannot splice the genes into nearly as many alternatives. This lead scientists to hypothesize that alternative splicing might be used to modify these genes in a way which makes them specific to certain parts of the brain. In this way, alternative splicing may be providing a kind of “indexing system” for the brain. This might be the reason humans can store so much extra information and has such efficient long term memory.

Making Antibodies

In a similar process, the human body makes antibodies to fight bacteria, viruses, and foreign bodies which infect the tissues. To do this, the body must make an antibody, or protein which is specifically designed to stick to the invader. These proteins are manufactured by B lymphocytes, which contain the DNA and machinery to create these complex proteins. However, there is a problem.

The B lymphocytes need to attach the protein to themselves, and they need to release the antibody into the bloodstream. The antibody in the bloodstream will bind to invaders, allowing immune cells to target them. By attaching antibodies directly to the B lymphocytes, these cells can easily swallow up the invaders as they encounter them. To do this with minimal energy and by using the same DNA, these immune cells use alternative splicing.

The last two exons in the genetic code for antibodies are special. These two exons encode for a region of protein which is hydrophobic, or resists water. These regions attach themselves within the hydrophobic core of the phospholipid bilayer. This effectively locks them into the cell membrane. Alternative splicing simply removes these two exons. Now, the protein will serve the same purpose, but it is water soluble and can travel through the blood and fluids.

Upon receiving a signal to create antibodies, the B lymphocyte must create many at once for both itself and to be release into the body. To do this, it actively transcribes the gene for the antibody quickly, to create as many primary transcripts as possible. Some of these will be processed to retain the hydrophobic region, and some spliceosomes will cut that out. Thus, proteins for both uses are created from the same signal to create antibodies. Alternative splicing makes it possible to initiate many different processes from the same DNA transcription signal.

Quiz

1. What is the main purpose of alternative splicing?
A. To create variants of proteins
B. To assist with the metabolism
C. To speed the process of creating proteins

Answer to Question #1

A is correct. Alternative splicing allows organisms to store the information for an entire family of genes in the same place. Because the genes can be edited, spliced differently, and modified, they can create many more actual proteins than number of genes they have.

2. Why do organisms need so many versions of the same protein?
A. They don’t, it’s just extra genetic variation
B. For the thousands of different functions their cells complete
C. Scientists don’t know the answer

Answer to Question #2

C is correct. Scientists have yet to fully determine the function of alternative splicing. All of the above may be correct, or none of them. It does seem to be related to increased complexity. However, the common fruit fly is one of the organism with the most complex alternative splicing schemes we have studied.

3. How might alternative splicing help create intelligence?
A. By producing different proteins, it can create advanced neural connections
B. The more protein you have, the smarter you are
C. It is unlikely alternative splicing creates intelligence

Answer to Question #3

A is correct. Alternative splicing can essentially allow the brain to map the connections between different nerves, and designate specific nerves for certain tasks. This is the basis of intelligence and memory. The more specialized connections the brain has, the more an organism can remember and process.

References

• GeneCardsSuite. (2018, February 28). NRXN1 Gene (Protein Coding). Retrieved from Genecards.org: http://www.genecards.org/cgi-bin/carddisp.pl?gene=NRXN1


• Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., & Silver, L. M. (2011). Genetics: From Genes to Genomes. Boston: McGraw Hill.


• Nelson, D. L., & Cox, M. M. (2008). Principles of Biochemistry. New York: W.H. Freeman and Company.

Alternative Splicing