Most mammals, including 65% of humans, cannot digest lactose as adults. Lactase persistence, the opposite of lactose intolerance, is the result of an evolutionarily conserved mutation in the regulatory mechanisms of lactase-mRNA production. A SNP (single nucleotide polymorphism) in the binding site of one of lactase's transcription factors is associated with the continuation of lactase production into adulthood.
Biosynthesis of Lactase
The human lactase gene (LCT) is a 55 kilo-base pair segment of the second chromosome. It contains 17 exons. LCT is transcribed into Lactase-mRNA by RNA polymerase, and Lactase-mRNA is translated by a membrane-bound ribosome into a polypeptide called pre-pro-lactase. During translation, the 1,927 long amino acid sequence is fed into the ER (endoplasmic reticulum), but remains anchored in the lipid bilayer of the ER membrane. Several subunits of pre-pro-lactase are cleaved off as the enzyme is processed into its mature form. The immature protein is dimerized (attached to another copy of itself) within the ER. Then a transport vesicle containing pro-lactase blebs off the ER and travels to fuse with the Golgi Apparatus. Once within the Golgi Apparatus, the “pro” subunit prevents degradation and ensures proper folding of lactase into its mature quaternary structure before it is cleaved off. Finally, a vesicle containing mature lactase travels from the Golgi Apparatus to fuse with the external brush border membrane of epithelial cell. Here, the enzyme will carry out its function of breaking down dietary lactose.
Regulation of Lactase Synthesis
The regulation of lactase synthesis over developmental time is the factor that separates lactase persistent from non-persistent individuals. In most mammals, including 65% of humans, the level of lactase-mRNA found in the enterocytes is greatly decreased over the years after weaning. This is because mammals don't typically consume milk in adulthood, so the production of enzymes to help digest milk is unnecessary and therefore energetically wasteful at a cellular level. Age-dependent lactase regulation of this sort occurs at transcription.
A transcription factor (TF) is a protein that binds to a specific segment of DNA and influences a gene's transcription frequency. Once bound to DNA, a TF either attracts or repels the molecular machinery necessary for transcription. TFs can even attract other transcription factors to form large transcription complexes.
Special TFs called "activators" bind to specific enhancer sites on the DNA; these activators are helpful in initiating transcription by binding to RNA Polymerase and other enzymes used in transcription. This type of TF therefore increases the expression of a gene.
Other TFs influence the probability and frequency of transcription by binding to transcription factors at enhancer sites. Enhancer sites may be far away from the start of a gene, but the DNA loops around permitting the enhancers to come into contact with the transcription complex. This increases the frequency of transcription of the gene and, by extension, increases the expression of a gene.
A series of transcription factors have been identified that regulate the amount of lactase-mRNA an intestinal epithelial cell produces over the course of its life. These transcription factors bind to the DNA about 14,000 base pairs upstream of the lactase gene, within the introns (non-protein-coding regions) of an upstream gene, MCM6. Much of the research concerning the evolution of lactase persistence in humans focuses not on mutations in the lactase LCT gene, but rather on mutations in these enhancers within the introns of the MCM6 gene.
Single Nucleotide Polymorphism
If a nucleotide substitution mutation achieves a frequency of 1% in a population over time, it is considered a "single nucleotide polymorphism", or SNP.
The type of mutation that is studied in the context of lactase persistence evolution is a called a single nucleotide polymorphism, or SNP. A SNP is a mutation where only one nucleotide in a sequence is changed.
Several SNPs are associated with lactase persistence, all of which are thought to increase or decrease a transcription factor's ability to bind to DNA at that site. This binding affinity influences the likelihood that transcription factors will attach to the DNA and either repel or attract RNA polymerase.
In one well-studied SNP, 13910 bp upstream of the Lactase gene, a Thymine base has been substituted into the DNA sequence in the place of a Cytosine base. This mutation (T instead of C) increases the binding affinity of a transcription factor called Oct-1, which acts as an activator. It has been shown to increase transcription complex binding to the promoter, and therefore increase production of lactase-mRNA.