Biochemistry Online: An Approach Based on Chemical Logic

CHAPTER 5 - BINDING

D: BINDING AND THE
CONTROL OF GENE TRANSCRIPTION

BIOCHEMISTRY - DR. JAKUBOWSKI

Last Updated: 03/30/16

Learning Goals/Objectives for Chapter 5D: After class and this reading, students will be able to

describe general mechanisms of how a gene for a given protein might be negatively and positively regulated at the level of gene transcription;
describe the structure/function/role of promoters, response elements, RNA polymerase, transcription factors, nucleosomes, histone proteins, epigenetic modifications of DNA in gene transcription;
explain the differences (structural, Kds) between specific and nonspecific binding of a ligand to a macromolecule, at the structural level;
describe the structural features of both proteins and DNA that result in specific and nonspecific binding;
describe and give examples of how post-translational modifications of proteins and epigenetic modifications of DNA can alter gene expression;
explain how the apparent Kd for a protein binding to DNA can be altered by the presence of another protein bound to DNA at a proximal site
describe the basis of RNA interference in gene expression

D14. Recognition of viral and bacterial DNA by the immune system

Before leaving the topic of RNA/proteins interactions, consider how a self cell would detect viruses and bacteria. It would be beneficial to the organism if the immune system could recognize and response to many types of bacteria, viruses, fungi, or protozoa by binding to common target on them. For example, it would be desirable to have a single cell type, such as a scavenging macrophage, have a recognition system that would recognize a common molecular pattern such as LPS found on gram negative bacteria. The part of the immune system that has this capability is called the innate immune system. The cells of the innate system (dendritic cells, macrophages, eosinophils, etc) have receptors (Toll-like Receptors 1-10 or TLRs) that recognize the common pathogen associated molecular patterns - PAMPs (sometimes called MAMP - microbe associated patterns), which leads to binding, engulfment, signal transduction, maturation (differentiation), antigen presentation, and cytokine/chemokine release from these cells. Take for example dendritic cells, which reside in the peripheral tissues and act as sentinels. They can bind PAMPs which include:

CHO/Lipids on bacteria surface (LPS)
mannose (CHO found in abundance on bacteria, yeast
dsRNA (from viruses)
nonmethylated CpG motiffs in bacterial DNA

TLR receptors are expressed on the cell surface for recognition of external PAMPS on foreign invaders. However, since bacterial and viral can be engulfed, it would be optimal to have intracellular recognition of viral and bacterial nucleic acids as well. These are recognized by intracellular TLRs in the cell after the they been taken up into the cells by endocytosis. The figure below shows how viral and bacterial nucleic acids found in endosomal vesicles, can be bound by endosomal membrane TLRs. A Jmol model of a recent structure of TLR3 and dsRNA is shown below.

Figure: Endosomal TLR3 Interaction with foreign RNA and DNA

Jmol: Updated TLR3:dsRNA complex Jmol14 (Java) | JSMol (HTML5) Needs updating

Inflammation can also arise when normal tissue is damaged due to injury, which exposes molecules usually located inside of the cell to the immune system. Such molecules include high mobility group proteins (associated with chromatin), proteoglycans and nucleic acids. These are referred to as damaged associated molecular pattern (DAMP) molecules. Intracellular proteins exists normally in a reducing environment so when they are exposed to the oxidizing conditions of the extracellular milieu, covalent and conformational changes may ensue that

Figure: Recognition of PAMPs by TLRs

TLR_PAMP Binding