Immunology II: Lymphoid Organs and Cells

As mentioned in the last post, several types of cells derive from lymphoid progenitor cells.  These cells are generated in the bone marrow in general, but only B cells mature there (hence the name B cells).  In contrast, T cells migrate to the thymus where they mature.  After full maturation of both B and T cells, they circulate in the blood system and then enter the peripheral lymphoid organs.  The central lymphoid organs are the bone marrow where the lymphocytes are generated, whereas the peripheral lymphoid organs are where T cells mature and where the adaptive immune responds to various stimuli.

The peripheral lymphoid organs

First, we will consider the components of the peripheral lymphoid system.  The lymph nodes are glands right near each armpit that is where fluid collects from the lymph system.  Lymph drains into the lymph nodes via lymphatic vessels and consists of the extracellular fluid filtered from the blood.  Thus, lymph is kind of a surveillance system for the body.  The afferent lymphatic vessels carry lymph and cells from infected tissues and drain into the lymph node.

The lymph node itself has a unique structure, illustrated to the right.  The follicles are where B lymphocytes set up shop, and T cells exist in paracortical areas (T-cell zones).  Germinal centers within the lymph node are where B cells proliferate after they have been stimulated by T cells.  Several additional tissues are organized similar to the lymph node drawn to the right, and this structure facilitates interaction between B and T cells.

The spleen is another peripheral lymphoid organ that mostly works to break down dead red blood cells.  This destruction occurs in the red pulp of the spleen, but the spleen also has white pulp where lymphocytes enter and exist within the spleen.  Within the white pulp is the periarteriolar lymphoid sheath (PALS) that contains T cells and a B-cell corona.

The digestive system is a major route for infection and has several gut-associated lymphoid tissues (GALT).  Some of these tissues include the tonsils, adenoids, and the appendix.  The intestine also has its own GALT, namely the Peyer's patches, which collect antigen directly from inside the intestine using multi-fenestrated (M) cells.

Similar to the digestive tract, the respiratory tract has its own lymphoid tissue, called the bronchial-associated lymphoid tissue (BALT).

The basics of immunology

Immunology scares me. I'm not ashamed to admit this fact. I find the topic intimidating and overwhelming, especially when I listen to talks given by prominent immunologists. The terminology is difficult, and the concepts seem very intertwined. I've always perceived that breaking into understanding immunology required a lot of work but that it would (and should) make sense... eventually.

 The next few blog posts are going to focus on immunology, not only because I need to learn this information, but also because it is fascinating and a challenging topic.

Components of the Immune System
All of the cells that comprise the immune system emerge from the bone marrow, where all of them originally come from and where some of them remain for maturation.  The cell type that gives rise to immune cells is the hematopoietic stem cell.  From this pluripotent state, the hematopoetic stem cell can then mature into a myeloid progenitor cell or a common lymphoid progenitor.  Myeloid progenitor cells can differentiate into several more cell types, including granulocyte and macrophage progenitors and megakaryocyte and erythrocyte progenitors.  The granulocyte and macrophage progenitors can then develop into neutrophils, eosinophils, basophils, mast cells, and macrophages.  Megakaryocyte and erythrocyte progenitors generate platelets upon maturation.

Hematopoietic stem cells can also develop into a common lymphoid progenitor, which consists of B cells, T cells, and NK cells.  These types of cells leave the bone marrow and migrate through the lymph nodes.  Dendritic cells also develop from lymphoid progenitor cells but mature in the bone marrow before entering the lymph node.

Basic functions of immune cells

• Macrophages are a common cell type that mature from monocytes (from the myeloid progenitor cells originally).  Monocytes circulate in the blood and continuously differentiate into macrophages when they enter the body's tissues.  Once in the tissues, macrophages can be considered the garge trucks of the body:  they engulf the environment as well as other cells in the process of phagocytosis.  Thus, macrophages can function to neutralize harmful elements within the body.
• Dendritic cells also mature from myeloid progenitor cells, and their main function is to process and display antigen that will then be readable by T lymphocytes.  This antigen display requires the presentation of co-stimulatory molecules, and when dendritic cells encounter a pathogen (or other foreign antigen), they mature and begin expressing these co-stimulatory molecules.
• Mast cells differentiate in body tissues and are involved in mediating mucosal immunity.  They are most well-known for their role in allergic reactions.
• Neutrophils are a type of granulocyte (so called because they have densely-staining and strange-shaped nuclei) that are involved in phagocytosis and increase in numbers upon an immune response.
• Eosinophils respond to parasites.
• Basophils may function similarly to mast cells.
• B cells differentiate into plasma cells and function to secrete antibodies.
• T cells destroy virus-infected cells and also function to activate other immune cells, such as B cells and macrophages.
• NK cells are involved in innate immunity and destroy "weird-looking" cells, such as tumor cells or cells infected with viruses.

References for the interested:

Immunobiology. Janeway, Travers, Walport, Shlomchik.
Basic Concepts of Immunology and Neuroimmunology: Basic Immunology

Basic Immunology: Nuts and Bolts of the Immune System

Introduction to the Immune System

Escaping Anergy

Cancer and Oncogenes

Cancer is a diverse group of diseases with one common characteristic: unchecked cellular replication.  Via several potential mechanisms, cancer cells are able to avoid all of the checkpoints involved in cell growth and division, thus enabling them to divide more frequently or indefinitely.  Many events can lead to the development of a cancer cell, including inheritance of mutated DNA or the activity of a carcinogen, or a chemical agent that leads to the development of cancer.

Gene expression is often deregulated in cancer cells such that some genes are overexpressed, while others are underexpressed.  Genes that can be mutated to lead to an upregulation of activity and lead to the development of a cancer cell are termed proto-oncogenes.  When these proto-oncogenes are actually mutated, they are considered oncogenes.

An oncogene is often a gene involved in regulating cell division and drive the cell cycle.  When they are overexpressed, such as during cancer, they can push the cell to divide more frequently and, with further mutations, transform the cell such that it divides without restriction.

Oncogenes were first discovered in viruses, specifically in Rous Sarcoma Virus (RSV), a retrovirus that encodes a homologue to cellular src kinase (the viral form called v-src).  Tumors in birds caused by RSV are the result of v-src causing unregulated cellular proliferation.  Large amounts of research into this area has identified cellular src kinase as a proto-oncogene that, when mutated to become constitutively active, becomes an oncogene and can drive cancer development.  Interestingly, viruses have highlighted a number of cellular oncogenes and pathways that are improperly regulated in cancer.  Over 20 viral oncogenes have been identified to date.

Cellular proto-oncogenes (the genes before they become oncogenes) can promote cellular proliferation and the development of cancer in several ways.  One of these ways is to be overexpressed and function when the gene product really shouldn't function.  This is the case with proteins such as myc and growth factor receptors.  With overexpression of these proteins, there is the potential for amplified signaling through these pathways that can push the cell to divide more than it normally does, leading to the development of cancer.  An additional mechanism whereby a proto-oncogene can become an oncogene is via mutation that leads to improper regulation, such as constitutive activity.  A classical example of this type of phenomenon is via Ras, which when mutated is constitutively active and cannot hydrolyze an attached GTP to inactivate.  Thus, Ras remains active and cannot be "turned off."  This constant activity of Ras results in  signal transduction to the nucleus of the cell and pushes the cell to divide through transcription of several genes involved in cell division.

The Trp Operon

The last post about an operon (the lac operon) is the most viewed post on this blog, so I thought that it might be helpful to follow this up with another operon, this time concentrating on the trp (tryptophan) operon.  This operon is another really elegant example of transcriptional regulation in E.coli and the mechanism is pretty cool.

Amino acids are essential for life (see the last post on their composition!) and cells synthesize amino acids using a variety of enzymes.  When nutrients are plentiful, such as E.coli would encounter in nutrient broth in the laboratory setting, cells no longer need to waste energy producing biosynthetic enzymes when they can utilize nutrients already in excess.  The trp operon contains several enzymes that are coordinately regulated and involved in the production of tryptophan.  When tryptophan is present in the cell's environment, it doesn't need to make any of these enzymes, but if the cell needs tryptophan, these enzymes are transcribed and shortly thereafter translated.  Control of this operon, thus, controls how much energy the cell is going to put into making tryptophan.

Similar to the lac operon, the trp operon contains an operator (O) sequence, within the promoter sequence, where an operator binds and prevents transcription.  In the presence of tryptophan, the operator binds the promoter and prevents RNA polymerase from transcribing genes.  In the absence of tryptophan, however, transcription occurs at a basal rate.  Sounds simple enough, right?  Let's take it a step further and consider...

Attenuation
An important concept in gene regulation is that of attenuation, which is fine-tuning of gene expression.  You might think that attenuation is mediated by protein factors that bind the DNA and affect gene expression; however, attenuation of the trp operon is a little different and, instead, depends on mRNA structure to modulate gene expression.

Before moving forward, let's look at the trp operon (diagrammed to the right).  Briefly,t here are four regions, and these four regions have differing levels of complementarity to each other.  Thus, when the DNA is transcribed into mRNA, the mRNA folds into all kinds of shapes and the regions of the trp operon fold on each other.

After transcription of the entire trp operon (we're dealing with mRNA from this point forward), the next event is translation of this mRNA into protein.  In bacteria, it's important to note that transcription and translation occur simultaneously, so as soon as we have a transcript in a bacterial cell, it's being translated.  The trp transcript contains two critical tryptophan codons immediately before region 1, so in order to synthesize the enzymatic machinery to make tryptophan, the cell must use a few residues to translate the protein.

In the presence of high amounts of tryptophan within the cell, the ribosome plows through these two tryptophan codons, adding in the appropriate amino acids, and continuing through region 1 of the mRNA.  This results in region 1 and 2 mRNA sequences binding together, and then regions 3 and 4 bind together as well.  This interaction between regions 3 and 4 results in the creation of a transcription-termination hairpin, basically a structure in the mRNA that kicks out RNA polymerase and prevents further transcription of the mRNA.  Thus, transcription (and then translation) are stopped because

In the absence of tryptophan, however, the ribosome cannot quickly add tryptophan during the translation process and it stalls before region 1.  This results in the folding of the mRNA such that regions 2 and 3 bind to each other.  When this structure forms, no transcriptional termination hairpin is formed, and mRNA synthesis continues.  Thus, the entire mRNA sequence for the trp operon is made and can be translated into enzymes that will synthesize tryptophan.

In summary:
Lots of tryptophan: Ribosome zooms through the mRNA, regions 1 & 2 and 3 & 4 bind (in pairs) and create a termination hairpin
End result: Transcription terminates and tryptophan synthetic enzymes not created (cell saves energy!)

Lack of tryptophan: Ribosome stalls immediately before region 1, regions 2 and 3 bind each other, no termination hairpin is formed
End result: Transcription continues and biosynthetic enzymes are eventually synthesized

This scheme is similar for other operons encoding amino acid biosynthetic enzymes (in bacteria, that is).  The trp operon is an elegant scheme to finely-tune transcription via mRNA structure to prevent the cell from wasting energy.

Amino Acids: The Building Blocks of Proteins

While I've written many posts describing signaling pathways and cellular phenomena of significant complexity, I'd like to use this post to take a step back and look at some fundamental building blocks, first turning to amino acids, the monomers that, when polymerized, make up polypeptides and proteins. At the most basic level, amino acids are really a rather simple chemical compound, consisting of a amino group, a carboxy group, a hydrogen, and a side chain, all sticking off a central carbon atom.  These amino acids are polymerized via their amino and carboxy chemical groups to create long, linear linkages.

Brief aside: In my chemistry class in undergrad, my TA helped us remember the order of the chemical bonds following polymerization by saying N-H, C-H, C-O, N-H, C-H, C-O, ...


You may remember briefly from any stint in chemistry class that a carbon atom that is covalently bound to four different chemical entities (in this case, a side chain, a hydrogen atom, a carboxyl group, and an amino group) can take two different conformations, depending on how these bonds are spatially oriented.  In the case of amino acids, the vast majority of amino acids found in our bodies and used to generate proteins are L stereoisomers.  This is a result of the amino acid synthesis machinery structure exclusively generating L amino acids.  There are exceptions, but we won't get into that.

As I mentioned, amino acids have a side chain: the part of the amino acid that endows it with its identity.  These side chains can be broken into a few groups that we will explore now:

The first set of side chains is the nonpolar, hydrophobic side chains.  The amino acids in this group include alanine, valine, leucine, isoleucine, glycine, methionine, and proline (structures shown to the right).  What you'll immediately notice is that these amino acid side chains are composed mostly of hydrogens and carbons.  Thus, these side chains do not contain polar covalent bonds and do not interact as readily with water (thus the term hydrophobic - they're "afraid" of water.  Some amino acids of note in this group are proline, which contains a ring structure that creates a "kink" in the amino acid, and methionine, which contains a sulfur atom.

The next set is composed of the aromatic side chains, which includes phenylalanine, tyrosine, and tryptophan.  These amino acids all contain an aromatic ring, which makes them relatively nonpolar; thus, they do not interact favorably with water.  These amino acids are involved in mediating protein protein interactions and are frequently found at the active sites of enzymes.

Next up: polar, uncharged side chains: asparagine, cysteine, glutamine, serine, and threonine.  These amino acids contain hydroxyl, sulfhydryl, or amide groups that mediate interactions with water, but they carry no net charge.  An amino acid of note in this family is cysteine, which can react with itself to form cystine, which is important in mediating the formation of disulfide bonds in protein structures.

We'll consider basic side chains next.  These amino acids consist of arginine, histidine, and lysine, which all carry a net positive charge in solution.  Of note, histidine is commonly found at the active site of enzymes to serve as a protein donor or acceptor.

Finally, we find acidic side chains: aspartate and glutamate.  In solution, these amino acids carry a negative charge and are considered acidic.

In the diagram at right, I've drawn up each of the amino acids along with their three-letter and one-letter codes.  These codes are frequently used to abbreviate long lists of amino acids.

Another brief aside:  Did you know that a single woman designated the amino acid abbreviations?  She chose letters that made sense for most amino acids (as you can see above).  For tryptophan, for example, she chose W because she envisioned saying tryptophan as twyptophan.  Kind of cool, huh?


As a summary, here are the amino acid abbreviations:

• A, ala, alanine
• C, cys, cysteine
• D, asp, aspartate
• E, glu, glutamate
• F, phe, phenylalanine
• G, gly, glycine
• H, his, histidine
• I, ile, isoleucine
• K, lys, lysine
• L, leu, leucine
• M, met, methionine
• N, asn, asparagine
• P, pro, proline
• Q, gln, glutamine
• R, arg, arginine (think aRRRRginine)
• S, ser, serine
• T, thr, threonine
• V, val, valine
• W, trp, tryptophan (tWWWyptophan)
• Y, tyr, tyrosine

So there you have it: 20 amino acids.  In addition to these amino acids, our bodies contain several more, including selenocysteine (identical to cysteine but containing selenium rather than sulfur) and ornithine (remember this from glycolysis?).  Amino acids can also undergo modifications: for instance, lysine residues can be acetylated.  More amino acids and their variants are always being discovered as well.

Now that we have the building blocks of proteins established, the next blog post will focus on how these amino acids can be combined (polymerized) into long structures that make up polypeptides and proteins.