A basic guide to Gene Expression
A few important definitions
Gene - The basic unit of inheritance, a region of DNA made up of a sequence of nucleotides (“A, T, G, C”). This sequence forms a code that can code for a protein that has a particular function, or can be “non-coding” and serve other purposes.
DNA - Deoxyribonucleic Acid. A double helix structure that contains two complementary strands and is made up of nucleic acids, deoxyribose, and Hydrogen bonds. The organized storage of DNA forms Chromosomes and is located in the nucleus of eukaryotic cells.
mRNA - messenger Ribonucleic Acid. A short, single-stranded complimentary copy of a region of DNA that codes for a gene. RNA is mobile and can leave the cell nucleus where it can be “read” and its coded protein formed.
Protein - a three-dimensional structure made up of a strand of amino acids that bind together, much like when you twist a rubber band between your fingers. The structure of the protein dictates the function and is the basis for how most cellular functions are performed.
Nucleus - The central organelle in eukaryotic cells that houses DNA and has pores for selective entry/exit.
Transcription - The process of copying DNA to RNA.
Translation - The process of reading the mRNA code and making its perspective protein based on the sequence of amino acids the RNA codes for.
RNA Polymerase - The enzyme that synthesizes RNA from the DNA source code.
Up/Down-regulated - A way of describing if a gene is expressed more or less in a treatment sample compared to a control sample.
Complimentary - Certain nucleotides will only pair in double strands with other specific nucleotides. The “partner” nucleotides are considered complementary base pairs. Adenosine (“A”) only binds with Thymine (“T”) in DNA and Uracil (“U”) in RNA, and Guanine (“G”) only binds with Cytosine (“C”).
Codon - A sequence of three base pairs that codes for an amino acid.
Basic rendering of DNA being transcribed into RNA in the cell nucleus and then translated into Protein outside the nucleus
How does it work?
Whenever a gene is expressed, the region of the DNA that codes for that gene is unzipped. RNA polymerase copies the code by combining “complementary” nucleotide base pairs and forming a single-stranded mRNA. Once the complete mRNA strand is formed and edited by other enzymes to remove non-coding sequences (called “introns”), the mRNA is ready to leave the cell nucleus and be transported to wherever it needs to go within the cell to be translated. To be translated, ribosomes read the codons within the mRNA strand and piece together amino acids based on the required sequence. The strand of amino acids has certain chemical properties and polarities (like positive and negative sides of a magnet that either attract or repel one another). These polarities cause the strand of amino acids to twist up on itself in a specific three-dimensional shape, thus forming a protein.
What does it mean?
For most genes (though there are exceptions), the more copies of mRNA that are made, the more of that protein that will be made, and thus an increased function of whatever the protein does. Techniques like mRNA sequencing and Real Time quantitative PCR (RT-qPCR), allow us to measure the amount of mRNA copies present for each gene. When more copies of a gene’s mRNA are present in a treatment sample, compared to the amount present in a control sample, then we say that this gene’s expression level is up-regulated in the treatment sample. Similarly, if there are fewer copies in the treatment compared to the control sample, then this gene’s expression level is down-regulated.
Why does it matter?
A gene being expressed is not the beginning of the signal transduction chain. Something must occur to trigger the mechanisms to express the gene. Genes are expressed as a response to something. That stimulus might not be something external, it could be internal developmental triggers, hormone signals, or other genes. Then a gene’s expression can affect how a plant grows, develops, or responds to its environment. Multiple levels of regulation make sure that a gene is accurately copied, is expressed only when and where it should be, and is translated correctly. There are also regulatory mechanisms that keep the proteins that are made in check.
Countless projects over the last decade have identified many of the genes and gene pathways that control how plants grow, develop, reproduce, and senesce. There’s still much work to be done, but most crop species have “annotated genomes,” or genomes with many of the genes identified. Because annotated genomes are available for all major crops, we can use transcriptomic analyses like mRNA sequencing or RT-qPCR to see how treatments or environments affect how a plant’s genes are expressed. We can use this information to optimize how we apply products, develop new products, and better understand the nutritional and biochemical needs of the plants due to the genes being expressed.
Additional Resources
The website for the National Human Genome Institute has many great explanations, illustrations, and videos.
