Gene Regulation III

Hemoglobin A1c: While this example of a protein that is modified after translation has nothing to do with the expression of the gene (that is, it is not related to whether or not the protein is active), it is a case of protein modification that is useful in disease diagnosis. Patients that develop diabetes 2 have traditionally been diagnosed by elevated blood glucose levels, but since these levels can vary with periods of fasting and carbohydrate consumption, an easier, more reliable test was needed. As it turns out, hemoglobin that has been exposed to high levels of glucose becomes chemically modified into Hb A1c. Since the half life of a red blood cell is about 3 months, the degree of modification (glycation) of hemoglobin can be used a an indicator of the average glucose level over the last three months. A level of Hb A1c ≥ 48 mmol/mol is an indication of diabetes (American Diabetes Association). The reaction in which a sugar is added to the N-terminus of the β-chain of hemoglobin is shown here (http://usmle.biochemistryformedics.com/hyperglycemia-induced-complications-in-diabetes-mellitus/).

While the main mechanism of turning genes on and off occurs at the level of transcription, the amount of active gene produced can also be regulated by events occurring after transcription. In fact, we have already covered (and you have been tested on) some of these processes under RNA processing on a previous outline. (I included the topics below in small type just as a reminder). By way of RNA processing, the ultimate expression of the gene is altered. However, there are also other post-transcriptional processes we have not yet covered (in normal size type below).
mRNA Processing 7-Methylguanosine Capping Polyadenylation Splicing The Process of Splicing Lariat Formation Splicing Alternate Splicing RNA Editing RNA Degradation
Translational Regulation of Gene Expression: The expression of a gene can also be regulated at the level of translation. mRNA Inactivation by Protein Binding: A protein can bind to a specific mRNA and thereby block its translation, as occurs in ferritin synthesis. This protein is an intracellular iron-storing molecule and therefore the higher the iron concentration in the cell, the more ferritin is needed. (Ferritin is also found in lower concentration in plasma.) Regulation is due to the binding of an iron regulatory protein (IRP)(IRP1 and IRP2) to the iron response element (IRE) of the ferritin mRNA. This site is in the 5' UTR (untranslated region) of the mRNA. This binding prevents the small ribosomal subunit from scanning for the AUG initiator codon, thereby turning off translation. In the presence of iron, IRP1 become inactive (does not bind to IRE) and IRP2 is degraded and translation can proceed. Other proteins bind to the 3' UTR and act as translation repressors.
Localization of mRNA in the Cytoplasm: Protein binding to the 3' UTR may affect the final destination of an mRNA in the cytoplasm, as is seen in early development.
Polyadenylation Changes: A protein binds to some oocyte mRNAs and shortens their 3' poly-A tails from about 200 nt to about 30-50 nt. This causes them to be inactive before fertilization. They become translationally active at the right stage of development due to re-polyadenylation.
miRNAs and siRNAs: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) can down-regulate the translation process. These RNAs may come from processing of intron RNA or from mRNA UTRs. Others are transcribed as a larger RNA that can be processed to produce more than one miRNA (or siRNA). An RNase called dicer converts larger molecules into a double stranded short RNA molecule. The final products (miRNAs and siRNAs) are about 20-26 nucleotides long and seem to be involved in the regulation of about one third of all human genes (over 1000 miRNAs have been discovered in humans and over 1.5 million in Arabidopsis!). One strand of the RNA then binds to a protein called Argonaut. This complex is called the RNA-induced silencing complex (RISC). This RISC complex then can bind to the 3' UTR of an mRNA. If this complementary base pairing is precise (siRNAs), it stimulates the cleavage of the mRNA. If it is not precise (miRNAs), it has the effect of inhibiting translation. (Small RNAs can also inhibit transcription.)(miRNAs and cancer and here)(miRNAs and immunity)(siRNA vs. miRNA) Hunting for miRNAs: Genes for these small, non-transcribed RNA are hard to find. One reason is that cells or organisms with a lack of an miRNA may not have a clear phenotype. Evidence from Caenorhabditis elegans indicate that there is miRNA redundancy and knocking out one miRNA may only produce a phenotype when the worm is under physical stress (Victor Ambros et al., GSA 2012)
Post-translational Regulation of Gene Expression: Even after the protein is produced, it effectiveness (expression of the gene) can be modulated. This process occurs by way of several process we will take up later as we study the cytoplasm in more detail (protein folding and chaperons, disulfide bridge formation, protein cleavage, protein glycosylation, allosteric regulation, protein phosphorylation, protein degradation and others). *Inteins:* These are amino acids sequences that have the ability to splice themselves out of a polypeptide. They have also been called protein introns. *Hemoglobin A1c:* While this example of a protein that is modified after translation has nothing to do with the expression of the gene (that is, it is not related to whether or not the protein is active), it is a case of protein modification that is useful in disease diagnosis. Patients that develop diabetes 2 have traditionally been diagnosed by elevated blood glucose levels, but since these levels can vary with periods of fasting and carbohydrate consumption, an easier, more reliable test was needed. As it turns out, hemoglobin that has been exposed to high levels of glucose becomes chemically modified into Hb A1c. Since the half life of a red blood cell is about 3 months, the degree of modification (glycation) of hemoglobin can be used a an indicator of the average glucose level over the last three months. A level of Hb A1c ≥ 48 mmol/mol is an indication of diabetes (American Diabetes Association). The reaction in which a sugar is added to the N-terminus of the β-chain of hemoglobin is shown here (http://usmle.biochemistryformedics.com/hyperglycemia-induced-complications-in-diabetes-mellitus/).