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Terms in this set (104)

Pathogen-Associated Molecular Patterns (PAMPs)
Pathogens, especially bacteria, have molecular structures that

1. are not shared with their host;
2. are shared by many related pathogens;
3. are relatively invariant; that is, do not evolve rapidly (in contrast, for example, to such pathogen molecules as the hemaglutinin and neuraminidase of influenza viruses).


the flagellin of bacterial flagella;
the peptidoglycan of Gram-positive bacteria;
the lipopolysaccharide (LPS, also called endotoxin) of Gram-negative bacteria;
double-stranded RNA. (Some viruses of both plants and animals have a genome of dsRNA. And many other viruses of both plants and animals have an RNA genome that in the host cell is briefly converted into dsRNA [link to examples]).
unmethylated DNA (eukaryotes have many times more cytosines, in the dinucleotide CpG, with methyl groups attached — Link).

Pattern Recognition Receptors (PRRs)
There are three groups:

1. secreted molecules that circulate in blood and lymph;
2. surface receptors on phagocytic cells like macrophages that bind the pathogen for engulfment;
3. cell-surface receptors that bind the pathogen initiating a signal leading to the release of effector molecules (cytokines).

1. Secreted PRRs
Example: Circulating proteins (e.g., C-reactive protein) that bind to PAMPs on the surface of many pathogens. This interaction triggers the complement cascade leading to the opsonization of the pathogen and its speedy phagocytosis.
2. Phagocytosis Receptors
Macrophages have cell-surface receptors that recognize certain PAMPs, e.g., those containing mannose. When a pathogen covered with polysaccharide with mannose at its tips binds to these, it is engulfed into a phagosome.
3. Toll-Like Receptors (TLRs)

Macrophages, dendritic cells, and epithelial cells have a set of transmembrane receptors that recognize different types of PAMPs. These are called Toll-like receptors (TLRs) because of their homology to receptors first discovered and named in Drosophila.

Mammals have 12 different TLRs each of which specializes — often with the aid of accessory molecules — in a subset of PAMPs. In this way, the TLRs identify the nature of the pathogen and turn on an effector response appropriate for dealing with it. These signaling cascades lead to the expression of various cytokine genes.
T helper cells (Th cells) are a sub-group of lymphocytes, a type of white blood cell, that play an important role in the immune system, particularly in the adaptive immune system. These cells have no cytotoxic or phagocytic activity; they cannot kill infected host cells or pathogens. Rather, they help other immune cells -- they activate and direct other immune cells. They are essential in B cell antibody class switching, in the activation and growth of cytotoxic T cells, and in maximizing bactericidal activity of phagocytes such as macrophages.

Mature Th cells express the surface protein CD4 and are referred to as CD4+ T cells. CD4+ T cells are generally treated as having a pre-defined role as helper T cells within the immune system. For example, when an antigen presenting cell expresses an antigen on MHC class II, a CD4+ cell will aid those cells through a combination of cell to cell interactions (e.g. CD40 and CD40L) and through cytokines. Nevertheless, there are rare exceptions; for example, sub-groups of regulatory T cells, natural killer T cells, and cytotoxic T cells express CD4 (although cytotoxic examples have been observed in extremely low numbers in specific disease states, they are usually considered non-existent). All of the latter CD4+ T cell groups are not considered T helper cells.

The importance of helper T cells can be seen from HIV, a virus that infects cells that are CD4+ (including helper T cells). Towards the end of an HIV infection the number of functional CD4+ T cells falls, which leads to the symptomatic stage of infection known as the acquired immunodeficiency syndrome (AIDS). There are also some rare disorders that result in the absence or dysfunction of CD4+ T cells. These disorders produce similar symptoms, and many of these are fatal.
-Natural killer cells (or NK cells) are a type of cytotoxic lymphocyte that constitute a major component of the innate immune system. NK cells play a major role in the rejection of tumors and cells infected by viruses. They kill cells by releasing small cytoplasmic granules of proteins called perforin and granzyme that cause the target cell to die by apoptosis (programmed cell death).
NK cells are defined as large granular lymphocytes (LGL) and constitute the third kind of cells differentiated from the common lymphoid progenitor generating B and T lymphocytes.[1] They do not express T-cell antigen receptors (TCR) or Pan T marker CD3 or surface immunoglobulins (Ig) B cell receptors but they usually express the surface markers CD16 (FcγRIII) and CD56 in humans, NK1.1 or NK1.2 in C57BL/6 mice. Up to 80% of human NK cells also express CD8.
They were named "natural killers" because of the initial notion that they do not require activation in order to kill cells that are missing "self" markers of major histocompatibility complex (MHC) class I.
They are distinct from Natural Killer T cells.

-A cytotoxic T cell (also known as TC, Cytotoxic T Lymphocyte, CTL, T-Killer cell, cytolytic T cell, CD8+ T-cells or killer T cell) belongs to a sub-group of T lymphocytes (a type of white blood cell) that are capable of inducing the death of infected somatic or tumor cells; they kill cells that are infected with viruses (or other pathogens), or are otherwise damaged or dysfunctional. Most cytotoxic T cells express T-cell receptors (TCRs) that can recognize a specific antigenic peptide bound to Class I MHC molecules, present on all nucleated cells, and a glycoprotein called CD8, which is attracted to non-variable portions of the Class I MHC molecule. The affinity between CD8 and the MHC molecule keeps the TC cell and the target cell bound closely together during antigen-specific activation. CD8+ T cells are recognized as TC cells once they become activated and are generally classified as having a pre-defined cytotoxic role within the immune system. However, CD8+ T cells also have the ability to make some cytokines.
The B-cell that recognized the foreign antigen clones itself to make many nearly identical copies of itself - with slight variations. Now, there are many B-cells that will recognize this particular foreign antigen. If infected again by an invader with this particular antigen, the immune system is ready and produces many more specific antibodies than before. This kills the invader much more quickly - making the body "immune" to this particular bug.
"The B-cells expressing low affinity antibody on their surface become progressively less able to bind and be stimulated by antigen; in the environment of the germinal center, these poorly stimulated B cells are programmed to die by a specific process known as "apoptosis" (Choe et al, J Immunol 157:1006,1996). In contrast, the cells with high affinity antibody continue to bind antigen, and thus continue be stimulated to proliferate and secrete antibody. As the antigen concentration progressively falls while mutation and selection continue, the intensity of the selective pressure for high affinity increases. Repeated cycles of mutation and selection can lead to affinity levels 100-fold higher than that of the original unmutated antibody. The 'competition' for efficient antigen binding has been shown to be the selective force driving the rise in antibody affinity, since if antigen is repeatedly administered to prevent the drop in antigen level and thereby eliminate the selective pressure for efficient antigen binding, antibody affinity does not rise (Eisen and Siskind, Biochemistry 3:996, 1964). Furthermore, when selection pressure has been experimentally removed by engineering mice with impaired capacity for programmed death by apoptosis, many B cells are found that make mutated antibodies with low affinity (Takahashi et al. J Exp Med. 190:39, 1999).
Late in the course of an immune response, as antigen becomes completely cleared from the bloodstream the amount of antibody secreted gradually falls and the immune response ends; but a subset of the last group of highly efficient cells persists as a quiescent population known as 'memory cells,' ready to respond with rapid secretion of high affinity antibody should they ever be triggered by another encounter with the same antigen in the future." 3
Live, Attenuated Vaccines

Live, attenuated vaccines contain a version of the living microbe that has been weakened in the lab so it can't cause disease. Because a live, attenuated vaccine is the closest thing to a natural infection, these vaccines are good "teachers" of the immune system: They elicit strong cellular and antibody responses and often confer lifelong immunity with only one or two doses.

Despite the advantages of live, attenuated vaccines, there are some downsides. It is the nature of living things to change, or mutate, and the organisms used in live, attenuated vaccines are no different. The remote possibility exists that an attenuated microbe in the vaccine could revert to a virulent form and cause disease. Also, not everyone can safely receive live, attenuated vaccines. For their own protection, people who have damaged or weakened immune systems— because they've undergone chemotherapy or have HIV, for example—cannot be given live vaccines.

Another limitation is that live, attenuated vaccines usually need to be refrigerated to stay potent. If the vaccine needs to be shipped overseas and stored by health care workers in developing countries that lack widespread refrigeration, a live vaccine may not be the best choice.

Live, attenuated vaccines are relatively easy to create for certain viruses. Vaccines against measles, mumps, and chickenpox, for example, are made by this method. Viruses are simple microbes containing a small number of genes, and scientists can therefore more readily control their characteristics. Viruses often are attenuated through a method of growing generations of them in cells in which they do not reproduce very well. This hostile environment takes the fight out of viruses: As they evolve to adapt to the new environment, they become weaker with respect to their natural host, human beings.

Live, attenuated vaccines are more difficult to create for bacteria. Bacteria have thousands of genes and thus are much harder to control. Scientists working on a live vaccine for a bacterium, however, might be able to use recombinant DNA technology to remove several key genes. This approach has been used to create a vaccine against the bacterium that causes cholera, Vibrio cholerae, although the live cholera vaccine has not been licensed in the United States.
Inactivated Vaccines

Scientists produce inactivated vaccines by killing the disease-causing microbe with chemicals, heat, or radiation. Such vaccines are more stable and safer than live vaccines: The dead microbes can't mutate back to their disease-causing state. Inactivated vaccines usually don't require refrigeration, and they can be easily stored and transported in a freeze-dried form, which makes them accessible to people in developing countries.

Most inactivated vaccines, however, stimulate a weaker immune system response than do live vaccines. So it would likely take several additional doses, or booster shots, to maintain a person's immunity. This could be a drawback in areas where people don't have regular access to health care and can't get booster shots on time.
Subunit Vaccines

Instead of the entire microbe, subunit vaccines include only the antigens that best stimulate the immune system. In some cases, these vaccines use epitopes—the very specific parts of the antigen that antibodies or T cells recognize and bind to. Because subunit vaccines contain only the essential antigens and not all the other molecules that make up the microbe, the chances of adverse reactions to the vaccine are lower.

Subunit vaccines can contain anywhere from 1 to 20 or more antigens. Of course, identifying which antigens best stimulate the immune system is a tricky, time-consuming process. Once scientists do that, however, they can make subunit vaccines in one of two ways:

They can grow the microbe in the laboratory and then use chemicals to break it apart and gather the important antigens.
They can manufacture the antigen molecules from the microbe using recombinant DNA technology. Vaccines produced this way are called "recombinant subunit vaccines."

A recombinant subunit vaccine has been made for the hepatitis B virus. Scientists inserted hepatitis B genes that code for important antigens into common baker's yeast. The yeast then produced the antigens, which the scientists collected and purified for use in the vaccine. Research is continuing on a recombinant subunit vaccine against hepatitis C virus.
Toxoid Vaccines

For bacteria that secrete toxins, or harmful chemicals, a toxoid vaccine might be the answer. These vaccines are used when a bacterial toxin is the main cause of illness. Scientists have found that they can inactivate toxins by treating them with formalin, a solution of formaldehyde and sterilized water. Such "detoxified" toxins, called toxoids, are safe for use in vaccines.

When the immune system receives a vaccine containing a harmless toxoid, it learns how to fight off the natural toxin. The immune system produces antibodies that lock onto and block the toxin. Vaccines against diphtheria and tetanus are examples of toxoid vaccines.
Conjugate Vaccines

If a bacterium possesses an outer coating of sugar molecules called polysaccharides, as many harmful bacteria do, researchers may try making a conjugate vaccine for it. Polysaccharide coatings disguise a bacterium's antigens so that the immature immune systems of infants and younger children can't recognize or respond to them. Conjugate vaccines, a special type of subunit vaccine, get around this problem.

When making a conjugate vaccine, scientists link antigens or toxoids from a microbe that an infant's immune system can recognize to the polysaccharides. The linkage helps the immature immune system react to polysaccharide coatings and defend against the disease-causing bacterium.

The vaccine that protects against Haemophilus influenzae type B (Hib) is a conjugate vaccine.
DNA Vaccines
Thumbnail of The Making of a DNA Vaccine Against West Nile Virus
The Making of a DNA Vaccine Against West Nile Virus. View the illustration.
Credit: NIAID

Once the genes from a microbe have been analyzed, scientists could attempt to create a DNA vaccine against it.

Still in the experimental stages, these vaccines show great promise, and several types are being tested in humans. DNA vaccines take immunization to a new technological level. These vaccines dispense with both the whole organism and its parts and get right down to the essentials: the microbe's genetic material. In particular, DNA vaccines use the genes that code for those all-important antigens.

Researchers have found that when the genes for a microbe's antigens are introduced into the body, some cells will take up that DNA. The DNA then instructs those cells to make the antigen molecules. The cells secrete the antigens and display them on their surfaces. In other words, the body's own cells become vaccine-making factories, creating the antigens necessary to stimulate the immune system.

A DNA vaccine against a microbe would evoke a strong antibody response to the free-floating antigen secreted by cells, and the vaccine also would stimulate a strong cellular response against the microbial antigens displayed on cell surfaces. The DNA vaccine couldn't cause the disease because it wouldn't contain the microbe, just copies of a few of its genes. In addition, DNA vaccines are relatively easy and inexpensive to design and produce.

So-called naked DNA vaccines consist of DNA that is administered directly into the body. These vaccines can be administered with a needle and syringe or with a needle-less device that uses high-pressure gas to shoot microscopic gold particles coated with DNA directly into cells. Sometimes, the DNA is mixed with molecules that facilitate its uptake by the body's cells. Naked DNA vaccines being tested in humans include those against the viruses that cause influenza and herpes.
Recombinant Vector Vaccines

Recombinant vector vaccines are experimental vaccines similar to DNA vaccines, but they use an attenuated virus or bacterium to introduce microbial DNA to cells of the body. "Vector" refers to the virus or bacterium used as the carrier.

In nature, viruses latch on to cells and inject their genetic material into them. In the lab, scientists have taken advantage of this process. They have figured out how to take the roomy genomes of certain harmless or attenuated viruses and insert portions of the genetic material from other microbes into them. The carrier viruses then ferry that microbial DNA to cells. Recombinant vector vaccines closely mimic a natural infection and therefore do a good job of stimulating the immune system.

Attenuated bacteria also can be used as vectors. In this case, the inserted genetic material causes the bacteria to display the antigens of other microbes on its surface. In effect, the harmless bacterium mimics a harmful microbe, provoking an immune response.

Researchers are working on both bacterial and viral-based recombinant vector vaccines for HIV, rabies, and measles.
Consists of about 20 proteins
-Activate each other via proteolytic cleavage
•The alternative complement pathway begins with complement factor C3.
•C3 normally made and degraded quickly.
-Stabilized by Gram-negative LPS
-Inserts into bacterial outer membrane
-Reacts with other components
-Factor B, Factor D, properdin
-Cleaves C5 to C5b
•Complement C5b protein binds C6, C7.
-Form preporecomplex in target cell membrane
-C8, C9 proteins attach.
-Form membrane attack complex
-Lyses target membrane
•C3b is also a potent opsonin.
-Promotes phagocytosisof an organism
•C3a and C5a are anaphylatoxins.
-Trigger degranulationand chemotaxis

The complement system helps or "complements" the ability of antibodies and phagocytic cells to clear pathogens from an organism. It is part of the immune system called the innate immune system that is not adaptable and does not change over the course of an individual's lifetime. However, it can be recruited and brought into action by the adaptive immune system.

The complement system consists of a number of small proteins found in the blood, generally synthesized by the liver, and normally circulating as inactive precursors (pro-proteins). When stimulated by one of several triggers, proteases in the system cleave specific proteins to release cytokines and initiate an amplifying cascade of further cleavages. The end-result of this activation cascade is massive amplification of the response and activation of the cell-killing membrane attack complex. Over 25 proteins and protein fragments make up the complement system, including serum proteins, serosal proteins, and cell membrane receptors. They account for about 5% of the globulin fraction of blood serum.

Three biochemical pathways activate the complement system: the classical complement pathway, the alternative complement pathway, and the mannose-binding lectin pathway.
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA.[1] They are double-stranded and, in many cases, circular. Plasmids usually occur naturally in bacteria, but are sometimes found in eukaryotic organisms (e.g., the 2-micrometre ring in Saccharomyces cerevisiae).

Plasmid sizes vary from 1 to over 1,000 kbp. The number of identical plasmids in a single cell can range anywhere from one to even thousands under some circumstances. Plasmids can be considered part of the mobilome because they are often associated with conjugation, a mechanism of horizontal gene transfer.

The term plasmid was first introduced by the American molecular biologist Joshua Lederberg in 1952.[2]

Plasmids are considered "replicons", capable of autonomous replication within a suitable host. Plasmids can be found in all three major domains: Archaea, Bacteria, and Eukarya.[1] Similar to viruses, plasmids are not considered by some to be a form of "life".[3] Unlike viruses, plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host, though some classes of plasmids encode the sex pilus necessary for their own transfer. Plasmid host-to-host transfer requires direct, mechanical transfer by conjugation or changes in host gene expression allowing the intentional uptake of the genetic element by transformation.[1] Microbial transformation with plasmid DNA is neither parasitic nor symbiotic in nature, because each implies the presence of an independent species living in a commensal or detrimental state with the host organism. Rather, plasmids provide a mechanism for horizontal gene transfer within a population of microbes and typically provide a selective advantage under a given environmental state. Plasmids may carry genes that provide resistance to naturally occurring antibiotics in a competitive environmental niche, or the proteins produced may act as toxins under similar circumstances. Plasmids can also provide bacteria with the ability to fix elemental nitrogen or to degrade recalcitrant organic compounds that provide an advantage when nutrients are scarce.[1]
1. Physical requirements

a. Temperature

Bacteria have a minimum, optimum, and maximum temperature for growth and can be divided into 3 groups based on their optimum growth temperature:

1. Psychrophiles (def) are cold-loving bacteria. Their optimum growth temperature is between -5C and 15C. They are usually found in the Arctic and Antarctic regions and in streams fed by glaciers.

2. Mesophiles (def) are bacteria that grow best at moderate temperatures. Their optimum growth temperature is between 25C and 45C. Most bacteria are mesophilic and include common soil bacteria and bacteria that live in and on the body.

3. Thermophiles (def) are heat-loving bacteria. Their optimum growth temperature is between 45C and 70C and are comonly found in hot springs and in compost heaps.

4. Hyperthermophiles (def) are bacteria that grow at very high temperatures. Their optimum growth temperature is between 70C and 110C. They are usually members of the Archae and are found growing near hydrothermal vents at great depths in the ocean.

b. Oxygen requirements

Microorganisms show a great deal of variation in their requirements for gaseous oxygen. Most can be placed in one of the following groups:

1. Obligate aerobes (def) are organisms that grow only in the presence of oxygen. They obtain their energy through aerobic respiration (def).

2. Microaerophiles (def) are organisms that require a low concentration of oxygen (2% to 10%) for growth, but higher concentrations are inhibitory. They obtain their energy through aerobic respiration (def).

3. Obligate anaerobes (def) are organisms that grow only in the absense of oxygen and, in fact, are often inhibited or killed by its presense. They obtain their energy through anaerobic respiration (def) or fermentation (def).

4. Aerotolerant anaerobes (def), like obligate anaerobes, cannot use oxygen to transform energy but can grow in its presence. They obtain energy only by fermentation (def) and are known as obligate fermenters.

5. Facultative anaerobes (def) are organisms that grow with or without oxygen, but generally better with oxygen. They obtain their energy through aerobic respiration (def) if oxygen is present, but use fermentation (def) or anaerobic respiration (def) if it is absent. Most bacteria are facultative anaerobes.

c. pH

Microorganisms can be placed in one of the following groups based on their optimum pH (def) requirements:

1. Neutrophiles (def) grow best at a pH range of 5 to 8.

2. Acidophiles (def) grow best at a pH below 5.5.

3. Allaliphiles (def) grow best at a pH above 8.5.

d. Osmosis

Osmosis (def) is the diffusion of water across a membrane from an area of higher water concentration (lower solute concentration) to lower water concentration (higher solute concentration). Osmosis is powered by the potential energy of a concentration gradient and does not require the expenditure of metabolic energy. While water molecules are small enough to pass between the phospholipids in the cytoplasmic membrane, their transport can be enhanced by water transporting transport proteins known as aquaporins (def). The aquaporins form channels that span the cytoplasmic membrane and transport water in and out of the cytoplasm (see channel proteins below).

To understand osmosis, one must understand what is meant by a solution (def). A solution consists of a solute (def) dissolved in a solvent (def). In terms of osmosis, solute refers to all the molecules or ions dissolved in the water (the solvent). When a solute such as sugar dissolves in water, it forms weak hydrogen bonds with water molecules. While free, unbound water molecules are small enough to pass through membrane pores, water molecules bound to solute are not (see Fig. 4C and Fig. 4D).Therefore, the higher the solute concentration, the lower the concentration of free water molecules capable of passing through the membrane.

A cell can find itself in one of three environments: isotonic (def), hypertonic (def), or hypotonic (def). (The prefixes iso-, hyper-, and hypo- refer to the solute concentration).

In an isotonic environment (see Fig. 5A), both the water and solute concentration are the same inside and outside the cell and water goes into and out of the cell at an equal rate.

Flash animation showing osmosis in an isotonic environment.

If the environment is hypertonic (see Fig. 5B), the water concentration is greater inside the cell while the solute concentration is higher outside (the interior of the cell is hypotonic to the surrounding hypertonic environment). Water goes out of the cell.

Flash animation showing osmosis in a hypertonic environment.

In an environment that is hypotonic (see Fig. 5C), the water concentration is greater outside the cell and the solute concentration is higher inside (the interior of the cell is hypertonic to the hypotonic surroundings). Water goes into the cell.

Flash animation showing osmosis in a hypotonic environment.

Most bacteria require an isotonic environment (def) or a hypotonic environment (def) for optimum growth. Organisms that can grow at relatively high salt concentration (up tp 10%) are said to be osmotolerant (def). Those that require relatively high salt concentrations for growth, like some of the Archea that require sodium chloride concentrations of 20 % or higher halophiles (def).

2. Nutritional requirements

In addition to a proper physical environment, microorgaisms also depend on an available source of chemical nutrients. Microorganisms are often grouped according to their energy source and their source of carbon.

a. Energy source

1. Phototrophs (def) use radiant energy (light) as their primary energy source.

2. Chemotrophs (def) use the oxidation (def) and reduction (def) of chemical compounds as their primary energy source.

b. Carbon source

Carbon is the structural backbone of the organic compounds that make up a living cell. Based on their source of carbon bacteria can be classified as autotrophs or heterotrophs.

1. Autotrophs (def): require only carbon dioxide as a carbon source. An autotroph can synthesize organic molecules from inorganic nutrients.

2. Heterotrophs (def): require organic forms of carbon. A Heterotroph cannot synthesize organic molecules from inorganic nutrients.

Combining their nutritional patterns, all organisms in nature can be placed into one of four separate groups: photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs.

1. Photoautotrophs (def) use light as an energy source and carbon dioxide as their main carbon source. They include photosynthetic bacteria (green sulfur bacteria, purple sulfur bacteria, and cyanobacteria), algae, and green plants. Photoautotrophs transform carbon dioxide and water into carbohydrates and oxygen gas through photosynthesis (def).

Cyanobacteria, as well as algae and green plants, use hydrogen atoms from water to reduce carbon dioxide to form carbohydrates, and during this process oxygen gas is given off (an oxygenic process). Other photosynthetic bacteria (the green sulfur bacteria and purple sulfur bacteria) carry out an anoxygenic process, using sulfur, sulfur compounds or hydrogen gas to reduce carbon dioxide and form organic compounds.

2. Photoheterotrophs (def) use light as an energy source but cannot convert carbon dioxide into energy. Instead they use organic compounds (def) as a carbon source. They include the green nonsulfur bacteria and the purple nonsulfur bacteria.

3. Chemolithoautotrophs (def) use inorganic compounds such as hydrogen sulfide, sulfur, ammonia, nitrites, hydrogen gas, or iron as an energy source and carbon dioxide as their main carbon source.

4. Chemooganoheterotrophs (def) use organic compounds (def) as both an energy source and a carbon source. Saprophytes (def) live on dead organic matter while parasites (def) get their nutrients from a living host. Most bacteria, and all protozoans, fungi, and animals are chemoorganoheterotrophs.

c. Nitrogen source

Nitrogen is needed for the synthesis of such molecules as amino acids, DNA, RNA and ATP (def). Depending on the organism, nitrogen, nitrates, ammonia, or organic nitrogen compounds may be used as a nitrogen source.

d. Minerals

1. sulfur

Sulfur is needed to synthesisize sulfur-containing amino acids and certain vitamins. Depending on the organism, sulfates, hydrogen sulfide, or sulfur-containing amino acids may be used as a sulfur sorce.

2. phosphorus

Phosphorus is needed to synthesize phospholipids (def), DNA, RNA, and ATP (def). Phosphate ions are the primary source of phosphorus.

3. potassium, magnesium, and calcium

These are required for certain enzymes to function as well as additional functions.

4. iron

Iron is a part of certain enzymes.

5. trace elements

Trace elements are elements required in very minute amounts, and like potassium, magnesium, calcium, and iron, they usually function as cofactors (def) in enzyme reactions. They include sodium, zinc, copper,molybdenum, manganese, and cobalt ions. Cofactors usually function as electron donors or electron acceptors during enzyme reactions.

e. Water

f. Growth factors

Growth factors are organic compounds such as amino acids (def), purines (def), pyrimidines (def), and vitamins (def) that a cell must have for growth but cannot synthesize itself. Organisms having complex nutritional requirements and needing many growth factors are said to be fastidious (def).

Some pathogenic bacteria are inherently able to resist the bactericidal components of host tissues. For example, the poly-D-glutamate capsule of Bacillus anthracis protects the organisms against cell lysis by cationic proteins in sera or in phagocytes. The outer membrane of Gram-negative bacteria is a formidable permeability barrier that is not easily penetrated by hydrophobic compounds such as bile salts which are harmful to the bacteria. Pathogenic mycobacteria have a waxy cell wall that resists attack or digestion by most tissue bactericides. And intact lipopolysaccharides (LPS) of Gram-negative pathogens may protect the cells from complement-mediated lysis or the action of lysozyme.

Most successful pathogens, however, possess additional structural or biochemical features which allow them to resist the main lines of host internal defense against them, i.e., the phagocytic and immune responses of the host.

Overcoming Host Phagocytic Defenses

Microorganisms invading tissues are first and foremost exposed to phagocytes. Bacteria that readily attract phagocytes, and that are easily ingested and killed, are generally unsuccessful as parasites. In contrast, most bacteria that are successful as parasites interfere to some extent with the activities of phagocytes or in some way avoid their attention.

Microbial strategies to avoid phagocytic killing are numerous and diverse, but are usually aimed at blocking one or of more steps in the phagocytic process. Recall the steps in phagocytosis:

1. Contact between phagocyte and microbial cell

2. Engulfment

3. Phagosome formation

4. Phagosome-lysosome fusion

5. Killing and digestion

Avoiding Contact with Phagocytes

Bacteria can avoid the attention of phagocytes in a number of ways.

1. Invade or remain confined in regions inaccessible to phagocytes. Certain internal tissues (e.g. the lumen of glands) and surface tissues (e.g. the skin) are not patrolled by phagocytes.

2. Avoid provoking an overwhelming inflammatory response. Some pathogens induce minimal or no inflammation required to focus the phagocytic defenses.

3. Inhibit phagocyte chemotaxis. e.g. Streptococcal streptolysin (which also kills phagocytes) suppresses neutrophil chemotaxis, even in very low concentrations. Fractions of Mycobacterium tuberculosis are known to inhibit leukocyte migration. Clostridium ø toxin inhibits neutrophil chemotaxis.

4. Hide the antigenic surface of the bacterial cell. Some pathogens can cover the surface of the bacterial cell with a component which is seen as "self" by the host phagocytes and immune system. Phagocytes cannot recognize bacteria upon contact and the possibility of opsonization by antibodies to enhance phagocytosis is minimized. For example, pathogenic Staphylococcus aureus produces cell-bound coagulase which clots fibrin on the bacterial surface. Treponema pallidum binds fibronectin to its surface. Group A streptococci are able to synthesize a capsule composed of hyaluronic acid.

Inhibition of Phagocytic Engulfment

Some bacteria employ strategies to avoid engulfment (ingestion) if phagocytes do make contact with them. Many important pathogenic bacteria bear on their surfaces substances that inhibit phagocytic adsorption or engulfment. Clearly it is the bacterial surface that matters. Resistance to phagocytic ingestion is usually due to a component of the bacterial cell wall, or fimbriae, or a capsule enclosing the bacterial wall. Classical examples of antiphagocytic substances on the bacterial surface include:

Polysaccharide capsules of S. pneumoniae, Haemophilus influenzae, Treponema pallidum and Klebsiella pneumoniae

M protein and fimbriae of Group A streptococci

Surface slime (polysaccharide) produced by Pseudomonas aeruginosa

O antigen associated with LPS of E. coli

K antigen of E. coli or the analogous Vi antigen of Salmonella typhi

Cell-bound or soluble Protein A produced by Staphylococcus aureus
Survival Inside of Phagocytes

Some bacteria survive inside of phagocytic cells, in either neutrophils or macrophages. Bacteria that can resist killing and survive or multiply inside of phagocytes are considered intracellular parasites. The environment of the phagocyte may be a protective one, protecting the bacteria during the early stages of infection or until they develop a full complement of virulence factors. The intracellular environment guards the bacteria against the activities of extracellular bactericides, antibodies, drugs, etc.

Most intracellular parasites have special (genetically-encoded) mechanisms to get themselves into their host cell as well as special mechanisms to survive once they are inside. Intracellular parasites usually survive by virtue of mechanisms which interfere with the bactericidal activities of the host cell. Some of these bacterial mechanisms include:

1. Inhibition of phagosome-lysosome fusion. The bacteria survive inside of phagosomes because they prevent the discharge of lysosomal contents into the phagosome environment. Specifically phagolysosome formation is inhibited in the phagocyte. This is the strategy employed by Salmonella, M. tuberculosis, Legionella and the Chlamydiae.

2. Survival inside the phagolysosome. With some intracellular parasites, phagosome-lysosome fusion occurs but the bacteria are resistant to inhibition and killing by the lysosomal constituents. Also, some extracellular pathogens can resist killing in phagocytes utilizing similar resistance mechanisms. Little is known of how bacteria can resist phagocytic killing within the phagocytic vacuole, but it may be due to the surface components of the bacteria or due to extracellular substances that they produce which interfere with the mechanisms of phagocytic killing. Bacillus anthracis, Mycobacterium tuberculosis and Staphylococcus aureus all possess mechanisms to survive intracellular killing in macrophages.

3. Escape from the phagosome. Early escape from the phagosome vacuole is essential for growth and virulence of some intracellular pathogens. This is a very clever strategy employed by the Rickettsias which produce a phospholipase enzyme that lyses the phagosome membrane within thirty seconds of after ingestion.

Products of Bacteria that Kill or Damage Phagocytes

One obvious strategy in defense against phagocytosis is direct attack by the bacteria upon the professional phagocytes. Any of the substances that pathogens produce that cause damage to phagocytes have been referred to as "aggressins". Most of these are actually extracellular enzymes or toxins that kill phagocytes. Phagocytes may be killed by a pathogen before or after ingestion.

Killing phagocytes before ingestion. Many Gram-positive pathogens, particularly the pyogenic cocci, secrete extracellular enzymes which kill phagocytes. Many of these enzymes are called "hemolysins" because their activity in the presence of red blood cells results in the lysis of the rbcs.

Pathogenic streptococci produce streptolysin. Streptolysin O binds to cholesterol in membranes. The effect on neutrophils is to cause lysosomal granules to explode, releasing their contents into the cell cytoplasm.

Pathogenic staphylococci produce leukocidin, which also acts on the neutrophil membrane and causes discharge of lysosomal granules.

Other examples of bacterial extracellular proteins that inhibit phagocytosis include the Exotoxin A of Pseudomonas aeruginosa which kills macrophages, and the bacterial exotoxins that are adenylate cyclases (e.g. anthrax toxin EF and pertussis AC) which decrease phagocytic activity.
Killing phagocytes after ingestion. Some bacteria exert their toxic action on the phagocyte after ingestion has taken place. They may grow in the phagosome and release substances which can pass through the phagosome membrane and cause discharge of lysosomal granules, or they may grow in the phagolysosome and release toxic substances which pass through the phagolysosome membrane to other target sites in the cell. Many bacteria which are the intracellular parasites of macrophages (e.g. Mycobacteria, Brucella, Listeria) usually destroy macrophages in the end, but the mechanisms are not understood.

Evading Complement

Antibodies that are bound to bacterial surfaces will activate complement by the classical pathway and bacterial polysaccharides activate complement by the alternative pathway. Bacteria in serum and other tissues, especially Gram-negative bacteria, need protection from the antimicrobial effects of complement before and during an immunological response.

One role of capsules in bacterial virulence is to protect the bacteria from complement activation and the ensuing inflammatory response. Polysaccharide capsules can hide bacterial components such as LPS or peptidoglycan which can induce the alternate complement pathway. Some bacterial capsules are able to inhibit formation of the C3b complex on their surfaces, thus avoiding C3b opsonization and subsequent formation of C5b and the membrane attack complex (MAC) on the bacterial cell surface. Capsules that contain sialic acid (a common component of host cell glycoproteins), such as found in Neisseria meningitidis, have this effect.

One of the principal targets of complement on Gram-negative bacteria is LPS. It serves as the attachment site for C3b and triggers the alternative pathway of activation. It also binds C5b.

LPS can be modified by pathogens in two ways that affects its interaction with complement. First, by attachment of sialic acid residues to the LPS O antigen, a bacterium can prevent the formation of C3 convertase just as capsules that contain sialic acid can do so. Both Neisseria meningitidis and Haemophilus influenzae, which cause bacterial meningitis, are able to covalently attach sialic acid residues to their O antigens resulting in resistance to MAC. Second, LPS with long, intact O antigen side-chains can prevent effective MAC killing. Apparently the MAC complex is held too far from the vulnerable outer membrane to be effective.

Bacteria that are not killed and lysed in serum by the complement MAC are said to be serum resistant. As might be expected many of the Gram-negative bacteria that cause systemic infections, (bacteremia or septicemia) are serum resistant. Gram-positive bacteria are naturally serum-resistant since their cells are not enclosed in an outer membrane.

Other ways that pathogens are able to inhibit the activity of complement is to destroy one or more of the components of complement. Pseudomonas aeruginosa produces an extracellular elastase enzyme that inactivates components of complement.

Avoiding Host Immunological Responses

On epithelial surfaces the main antibacterial immune defense of the host is the protection afforded by secretory antibody (IgA). Once the epithelial surfaces have been penetrated, however, the major host defenses of inflammation, complement, phagocytosis, Antibody-mediated Immunity (AMI), and Cell-mediated Immunity (CMI) are encountered. If there is a way for a pathogen to successfully bypass or overcome these host defenses, then some bacterial pathogen has probably discovered it. Bacteria evolve very rapidly in relation to their host, so that most of the feasible anti-host strategies are likely to have been tried out and exploited. Ability to defeat the immune defenses may play a major role in the virulence of a bacterium and in the pathology of disease. Several strategic bacterial defenses are described below.