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Antibiotics Cell Wall Inhibition
Two types of antimicrobial drugs work by inhibiting or interfering with cell wall synthesis of the target bacteria. Antibiotics commonly target bacterial cell wall formation (of which peptidoglycan is an important component) because animal cells do not have cell walls. The peptidoglycan layer is important for cell wall structural integrity, being the outermost and primary component of the wall.
The first class of antimicrobial drugs that interfere with cell wall synthesis are the β-Lactam antibiotics (beta-lactam antibiotics), consisting of all antibiotic agents that contains a β-lactam nucleus in their molecular structures. This includes penicillin derivatives (penams), cephalosporins (cephems), monobactams, and carbapenems. β-Lactam antibiotics are bacteriocidal and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls . The final step in the synthesis of the peptidoglycan is facilitated by penicillin-binding proteins (PBPs). PBPs vary in their affinity for binding penicillin or other β-lactam antibiotics.
Penicillin spheroplast generation
Bacteria often develop resistance to β-lactam antibiotics by synthesizing a β-lactamase, an enzyme that attacks the β-lactam ring. To overcome this resistance, β-lactam antibiotics are often given with β-lactamase inhibitors such as clavulanic acid.
The second class of antimicrobial drugs that interfere with cell wall synthesis are the glycopeptide antibiotics, which are composed of glycosylated cyclic or polycyclic nonribosomal peptides. Significant glycopeptide antibiotics include vancomycin, teicoplanin, telavancin, bleomycin, ramoplanin, and decaplanin. This class of drugs inhibit the synthesis of cell walls in susceptible microbes by inhibiting peptidoglycan synthesis. They bind to the amino acids within the cell wall preventing the addition of new units to the peptidoglycan .
Penicillin spheroplast generation
Catalysis
Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst. With a catalyst, reactions occur faster and with less energy. Because catalysts are not consumed, they are recycled. Often only tiny amounts are required.
Atomic Structure
The atom is the smallest unit that defines the chemical elements and their isotopes. Every substance, be it solid, liquid or gas is made up of atoms. The size of atoms is measured in picometers (trillionths of a meter). A single strand of human hair is about one million carbon atoms wide.
Every atom is composed of a nucleus made of protons and neutrons (hydrogen-1 has no neutrons). The nucleus is surrounded by a cloud of electrons. The electrons in an atom are bound to the atom by the electromagnetic force, and the protons and neutrons in the nucleus are bound to each other by the nuclear force. Over 99% of the atom's mass is in the nucleus. The protons have a positive electric charge, the electrons have a negative electric charge, and the neutrons have no electric charge. Normally, an atom's electrons balance out the positive charge of its protons to make it electrically neutral. If an atom has a surplus or deficit of electrons, then it will have an overall charge, and is called an ion.
The number of protons in the nucleus determines what chemical element the atom belongs to (e.g. all copper atoms contain 29 protons). The number of neutrons determines what isotope of the element it is.[2] The electron cloud of the atom determines the atom's chemical properties and strongly influences its magnetic properties.
Atoms can attach themselves to each other by chemical bonds to form molecules, network solids, metal alloys, crystals, and other solid solutions. The tendency for atoms to bond and break apart is responsible for most of the physical changes we observe in nature, and this is studied by the science of chemistry.
Atoms and sub-atomic particles behave in peculiar ways that cannot be explained through the classical laws of physics. The field of quantum mechanics was developed to explain the structure and behavior of atoms.
Not all matter is made up of atoms, but atoms do comprise all the types of matter than can be seen and touched. Astronomical observations indicate that most of the Universe's matter is "dark matter", composed of particles of a currently unknown type.
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CELL BIOLOGY,
Bacterial Locomotion
Bacterial locomotion
Locomotion or motility is important characteristic of bacteria. Bacterial locomotion is of three types: Flagellar, Spirochaetal and Gliding movement. The word motility, movement and locomotion are used synonymously.
Flagellar motility:
This type of motility is caused by flagella, cell surface appendages. Flagellum has typical structure; it is embedded in cell wall by S ring or stator (hook) and basal body or motor. M ring is attached to the flagellum and acts like a rotor (shaft). P and L are also present and work like bearings or bushers. Basal body is powered by proton energy, which is movement of ions between M and S rings. Transformation of proton energy into work operates flagella in clockwise and counterclockwise directions. Depending upon location of flagella, bacteria can swim smoothly, reverse the movement backward or forward or tumble. Peritrichously flagellated bacteria bear flagella all over the surface move by tumbling or anticlockwise swimming. Polar flagella (mono, bi or multipolar) are present at the ends of cell and bacteria move in one direction and as well as in reversal. Flagellar motility is present in Pseudomonas, Vibrio, Spirillum, Azospirillum, Klebsiella, Salmonella, Proteus and etc.
Spirochaetal movement:
Spirochaetal movement is seen in all genera of bacterial group (V), 'The Spirochetes' of Bergey's Manual of Determinative Bacteriology. Important genera include, Spirochaeta, Cristispira, Treponema, Borrelia and Leptospira. Spirochetes are helical bacteria. They have flagella like axial filament buried in space between inner and outer membranes of cell wall. Axial filament is composed of 2 or more fibrils which are embedded in inner membrane and acts like basal body or motor. Spirochetes can perform flexing, swimming, creeping or spinning types of movements. Imagination of motion of flexible helical rod in air will give you an exact idea about spirochetal movement.
Gliding movement:
Like spirochetes, gliding motility is represented by special bacteria, 'The Gliding Bacteria' group (II) of Bergey's Manual of Determinative Bacteriology. Bacteria move by gliding on the surface! They do not have flagellar structures either internally or externally but they secrete slimy substance like snails during locomotion. The exact mechanism of gliding locomotion is still unknown but some scientists have suggested presence of fimbriae like appendages at the poles of glider cell. The generation of contractile waves or surface tension or pushing by secreted slime was also proposed as possible mechanisms of gliding. Principle glider genera are Myxococcus, Archangium, Cystobacter, Melittangium, Stigmatella, Polyangium, Nannocystis, Chondromyces, Cytophaga, Flexithrix, Herpetosiphon, Beggiatoa, Saprospira, Thioplaca, Leucothrix, Alysiella, Achroonema and cyanobacterium Oscillatoria.
Laboratory detection and assay:
Motility can be directly observed under light microscope by hanging drop in cavity slide or wet mount preparation. It is important to determine true and false motility microscopically. Truly motile bacteria will show propelling action towards definite direction, as if they are pushing themselves with efforts! Nonmotile bacteria also appear to be motile because of bombardment of liquid medium particles or air currents. Motility of nonmotile bacteria is zigzag and directionless. This movement of nonmotile bacteria is actually a Brownian movement; even dead bacteria seem to be moving because of this movement. Craigie's tube or capillary tube can be used by placing them in broth culture for observation of directed movement of bacteria towards chemical or physical gradients with time. All motile bacteria show movement towards chemical or physical gradients. This phenomenon is known as tactic response. Chemical or physical gradient can be attractant or repellent and accordingly, tactic response would be positive or negative. Presence of gradients is sensed by special receptors of bacteria. Thus swimming towards certain glucose concentration present in the medium would be positive chemotactic or chemotaxis. Similarly, motile bacteria exhibit phytotaxis (light intensity) and magnetotaxis (magnetic particles) responses. Motile bacteria are assayed on semisolid agar or broth medium for chemotaxis and are very important in species identification and classification.
Importance of bacterial locomotion:
Chemotactic behavior and survival:
Motility confers bacteria an ability to change direction. This is important when bacteria require moving away or towards repellents or attractants respectively. It avoids unfavorable conditions of habitat and offers protection. It is thus important in the survival and offers to choose favorable environment containing positive stimuli, light, gravity or chemicals for bacteria.
Root colonization:
Root colonization is perquisite for establishment of bacteria in the rhizosphere region. Motile bacteria are effective root colonizers and can swim towards root exudates or other nutrient gradients earlier than nonmotile bacteria. Pseudomonads and Azospirilla are very efficient in attachment and subsequent root colonization of their host plants.
Pathogenesis: Most human pathogenic bacteria (Campylobacter, Salmonella and Vibrio) and saprophytes or opportunists (Escherichia) are motile and motility is important for attachment and colonization of cell wall of intestine and other vital organs.
Motile versus nonmotile:
Some bacteria like Acinetobacter spp. show twitching or jumping type of motility even though flagella are absent in them. These bacteria show the twitching particularly on semisolid media and also present chemotactic response. Twitching motility is thought to be because of piliated cell surface. It is the favorite topic of interest and research that why some bacteria are nonmotile? It has been found that in some bacterial genera that nonmotile species are equally efficient like their motile species. These nonmotile bacteria also possessed flagellar appendages; but basal body or motor function was found to be impaired or paralyzed. Reason for their efficiency even in absence of motility however could not be explained.
Covalent Bond
A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration.
Covalent bonding includes many kinds of interactions, including σ-bonding, π-bonding, metal-to-metal bonding, agostic interactions, and three-center two-electron bonds. The term covalent bond dates from 1939. The prefix co- means jointly, associated in action, partnered to a lesser degree, etc.; thus a "co-valent bond", in essence, means that the atoms share "valence", such as is discussed in valence bond theory.
In the molecule H
2, the hydrogen atoms share the two electrons via covalent bonding.Covalency is greatest between atoms of similar electronegativities. Thus, covalent bonding does not necessarily require that the two atoms be of the same elements, only that they be of comparable electronegativity. Covalent bonding that entails sharing of electrons over more than two atoms is said to be delocalized.
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CELL BIOLOGY,
Chemotaxis in E coli
Chemotaxis (from chemo- + taxis) is movement of an organism in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (e.g., glucose) by swimming toward the highest concentration of food molecules, or to flee from poisons (e.g., phenol). In multicellular organisms, chemotaxis is critical to early development (e.g., movement of sperm towards the egg during fertilization) and subsequent phases of development (e.g., migration of neurons or lymphocytes) as well as in normal function. In addition, it has been recognized that mechanisms that allow chemotaxis in animals can be subverted during cancer metastasis.
Positive chemotaxis occurs if the movement is toward a higher concentration of the chemical in question. However, negative chemotaxis occurs if the movement is in the opposite direction. Chemically prompted kinesis (randomly directed or nondirectional) can be called chemokinesis.
Ionic Bond
Ionic bonding is a type of chemical bond that involves the electrostatic attraction between oppositely charged ions. These ions represent atoms that have lost one or more electrons (known as cations) and atoms that have gained one or more electrons (known as an anions). In the simplest case, the cation is a metal atom and the anion is a nonmetal atom, but these ions can be of a more complex nature, e.g. molecular ions like NH4+ or SO42-
It is important to recognize that clean ionic bonding – in which one atom "steals" an electron from another – cannot exist: All ionic compounds have some degree of covalent bonding, or electron sharing. Thus, the term "ionic bonding" is given when the ionic character is greater than the covalent character—that is, a bond in which a large electronegativity difference exists between the two atoms, causing the bonding to be more polar (ionic) than in covalent bonding where electrons are shared more equally. Bonds with partially ionic and partially covalent character are called polar covalent bonds.
Ionic compounds conduct electricity when molten or in solution, but typically not as a solid. There are exceptions to this rule, such as rubidium silver iodide, where the silver ion can be quite mobile. Ionic compounds generally have a high melting point, depending on the charge of the ions they consist of. The higher the charges the stronger the cohesive forces and the higher the melting point. They also tend to be soluble in water. Here, the opposite trend roughly holds: The weaker the cohesive forces, the greater the solubility.
Formation
Ionic bonding can result from a redox reaction when atoms of an element (usually metal), whose ionization energy is low, release some of their electrons to achieve a stable electron configuration. In doing so, cations are formed. The atom of another element (usually nonmetal), whose electron affinity is positive, then accepts the electron(s), again to attain a stable electron configuration, and after accepting electron(s) the atom becomes an anion. Typically, the stable electron configuration is one of the noble gases for elements in the s-block and the p-block, and particular stable electron configurations for d-block and f-block elements. The electrostatic attraction between the anions and cations leads to the formation of a solid with a crystallographic lattice in which the ions are stacked in an alternating fashion. In such a lattice, it is usually not possible to distinguish discrete molecular units, so that the compounds formed are not molecular in nature. However, the ions themselves can be complex and form molecular ions like the acetate anion or the ammonium cation.
For example, common table salt is sodium chloride. When sodium (Na) and chlorine (Cl) are combined, the sodium atoms each lose an electron, forming cations (Na+), and the chlorine atoms each gain an electron to form anions (Cl−). These ions are then attracted to each other in a 1:1 ratio to form sodium chloride (NaCl).
Na + Cl → Na+ + Cl− → NaCl
However, to maintain charge neutrality, strict ratios between anions and cations are observed so that ionic compounds, in general, obey the rules of stoichiometry despite not being molecular compounds. For compounds that are transitional to the alloys and possess mixed ionic and metallic bonding, this may not be the case anymore. Many sulfides, e.g., do form non-stoichiometric compounds.
Many ionic compounds are referred to as salts as they can also be formed by the neutralization reaction of an Arrhenius base like NaOH with an Arrhenius acid like HCl
NaOH + HCl → NaCl + H2O
The salt NaCl is then said to consist of the acid rest Cl- and the base rest Na+.
Representation of ionic bonding between lithium and fluorine to form lithium fluoride. Lithium has a low ionization energy and readily gives up its lone valence electron to a fluorine atom, which has a positive electron affinity and accepts the electron that was donated by the lithium atom. The end-result is that lithium is isoelectronic with helium and fluorine is isoelectronic with neon. Electrostatic interaction occurs between the two resulting ions, but typically aggregation is not limited to two of them. Instead, aggregation into a whole lattice held together by ionic bonding is the result.
The removal of electrons from the cation is endothermic, raising the system's overall energy. There may also be energy changes associated with breaking of existing bonds or the addition of more than one electron to form anions. However, the action of the anion's accepting the cation's valence electrons and the subsequent attraction of the ions to each other releases (lattice) energy and, thus, lowers the overall energy of the system.
Ionic bonding will occur only if the overall energy change for the reaction is favorable. In general, the reaction is exothermic, but, e.g., the formation of mercuric oxide (HgO) is endothermic. The charge of the resulting ions is a major factor in the strength of ionic bonding, e.g. a salt C+A- is held together by electrostatic forces roughly four times weaker than C2+A2- according to Coulombs law, where C and A represent a generic cation and anion respectively. Of course the sizes of the ions and the particular packing of the lattice are ignored in this simple argument.
Bacterial Endospore Formation
An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. The name "endospore" is suggestive of a spore or seed-like form (endo means within), but it is not a true spore (i.e., not an offspring). It is a stripped-down, dormant form to which the bacterium can reduce itself. Endospore formation is usually triggered by a lack of nutrients, and usually occurs in Gram-positive bacteria. In endospore formation, the bacterium divides within its cell wall. One side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries. Revival of spores millions of years old has been claimed. When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state. Most types of bacteria cannot change to the endospore form. Examples of bacteria that can form endospores include Bacillus and Clostridium.
The endospore consists of the bacterium's DNA, ribosomes and large amounts of dipicolinic acid. Dipicolinic acid is a spore-specific chemical that appears to help in the ability for endospores to maintain dormancy. This chemical comprises up to 10% of the spore's dry weight.
Endospores can survive without nutrients. They are resistant to ultraviolet radiation, desiccation, high temperature, extreme freezing and chemical disinfectants. Thermo-resistant endospores were first hypothesized by Ferdinand Cohn after studying Bacillus subtilis (pictured to the right) growth on cheese after boiling the cheese. His notion of spores being the reproductive mechanism for the growth was a large blow to the previous suggestions of spontaneous generation. Astrophysicist Steinn Sigurdsson said "There are viable bacterial spores that have been found that are 40 million years old on Earth – and we know they're very hardened to radiation."Common anti-bacterial agents that work by destroying vegetative cell walls do not affect endospores. Endospores are commonly found in soil and water, where they may survive for long periods of time. A variety of different microorganisms form "spores" or "cysts," but the endospores of low G+C Gram-positive bacteria are by far the most resistant to harsh conditions. A low G+C Gram-positive bacteria is classified by the low number of guanine and cytosine pairs in comparison to the adenine and thymidine pairs. The G+C Gram-positive bacteria have no cell wall.
Some classes of bacteria can turn into exospores, also known as microbial cysts, instead of endospores. Exospores and endospores are two kinds of "hibernating" or dormant stages seen in some classes of microorganisms.
Binary Fission
In biology, fission occurs when a cell (or body, population, or species) divides into two or more parts and the regeneration of those parts into separate cells (bodies, populations, or species). Binary fission produces two separate cells, populations, species, etc., whereas multiple fission produces more than two cells, populations, species, etc.
Sodium Potassium Exchange Pump 2
Na+/K+-ATPase (sodium-potassium adenosine triphosphatase, also known as Na+/K+pump, sodium-potassium pump, or sodium pump) is an antiporter-like enzyme (an electrogenic transmembrane ATPase) located in the plasma membraneof all animal cells. The Na+/K+-ATPase enzyme pumps sodium out of cells, while pumping potassium into cells. It has antiporter-like activity but is not actually an anti-porter since both molecules are moving against their concentration gradient.
Bacterial chromosome compaction
DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo.Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems. Condensed DNA often has surprising properties, which one would not predict from classical concepts of dilute solutions. Therefore DNA condensation in vitro serves as a model system for many processes of physics, biochemistry and biology.In addition, DNA condensation has many potential applications in medicine and biotechnology.
DNA diameter is about 2 nm, while the length of a stretched single molecule may be up to several dozens of centimetres depending on the organism. Many features of the DNA double helix contribute to its large stiffness, including the mechanical properties of the sugar-phosphate backbone, electrostatic repulsion between phosphates (DNA bears on average one elementary negative charge per each 0.17 nm of the double helix), stacking interactions between the bases of each individual strand, and strand-strand interactions. DNA is one of the stiffest natural polymers, yet it is also one of the longest molecules. This means that at large distances DNA can be considered as a flexible rope, and on a short scale as a stiff rod. Like a garden hose, unpacked DNA would randomly occupy a much larger volume than when it is orderly packed. Mathematically, for a non-interacting flexible chain randomly diffusing in 3D, the end-to-end distance would scale as a square root of the polymer length. For real polymers such as DNA this gives only very rough estimate; what is important, is that the space available for the DNA in vivo is much smaller than the space that it would occupy in the case of a free diffusion in the solution. In order to cope with the volume constraints, DNA has a striking property to pack itself in the appropriate solution conditions with the help of ions and other molecules. Usually, DNA condensation is defined as "the collapse of extended DNA chains into compact, orderly particles containing only one or a few molecules". This definition applies to many situations in vitro and is also close to the definition of DNA condensation in bacteria as "adoption of relatively concentrated, compact state occupying a fraction of the volume available".In eukaryotes, the DNA size and the number of other participating players are much larger, and a DNA molecule forms millions of ordered nucleoprotein particles, the nucleosomes, which is just the first of many levels of DNA packing.
Second Messenger cAMP
Earl Wilbur Sutherland, Jr., discovered second messengers, for which he won the 1971 Nobel Prize in Physiology or Medicine. Sutherland saw that epinephrine would stimulate the liver to convert glycogen to glucose (sugar) in liver cells, but epinephrine alone would not convert glycogen to glucose. He found that epinephrine had to trigger a second messenger, cyclic AMP, for the liver to convert glycogen to glucose.The mechanisms were worked out in detail by Martin Rodbell and Alfred G. Gilman, who won the 1994 Nobel prize.
Secondary messenger systems can be synthesized and activated by enzymes, like the cyclases that synthesize cyclic nucleotides, or by opening of ion channels to allow influx of metal ions, like Ca2+ signaling. These small molecules bind and activate protein kinases, ion channels, and other proteins, thus continuing the signaling cascade.
Treatment of HIV
The aim of antiretroviral treatment is to keep the amount of HIV in the body at a low level. This stops any weakening of the immune system and allows it to recover from any damage that HIV might have caused already. The drugs are often referred to as: antiretrovirals, ARVs, anti-HIV or anti-AIDS drugs.
Overview of the Fungal Cell Structure
Fungi are unicellular or multicellular thick-cell-walled heterotroph decomposers that eat decaying matter and make tangles of filaments.
KEY POINTS
Fungal cell walls are rigid and contain complex polysaccharides called chitin (adds structural strength) and glucans.
Ergosterol is the steroid molecule in the cell membranes that replaces the cholesterol found in animal cell membranes.
Fungi can be unicellular, multicellular, or dimorphic, which is when the fungi is unicellular or multicellular depending on environmental conditions.
Fungi in the morphological vegetative stage consist of a tangle of slender, thread-like hyphae, whereas the reproductive stage is usually more obvious.
Fungi like to be in a moist and slightly acidic environment; they can grow with or without light or oxygen.
Fungi are saprophyte heterotrophs in that they use dead or decomposing organic matter as a source of carbon.
TERMS
chitin
a complex polysaccharide, a polymer of N-acetylglucosamine, found in the exoskeletons of arthropods and in the cell walls of fungi; thought to be responsible for some forms of asthma in humans
glucan
any polysaccharide that is a polymer of glucose
ergosterol
the functional equivalent of cholesterol found in cell membranes of fungi and some protists, as well as, the steroid precursor of vitamin D2
septum
cell wall division between hyphae of a fungus
mycelium
the vegetative part of any fungus, consisting of a mass of branching, threadlike hyphae, often underground
hypha
a long, branching, filamentous structure of a fungus that is the main mode of vegetative growth
thallus
vegetative body of a fungus
saprophyte
any organism that lives on dead organic matter, as certain fungi and bacteria
A B Exotoxins Diphtheria Exotoxin
The AB toxins are two-component protein complexes secreted by a number of pathogenic bacteria. They can be classified as Type III toxins because they interfere with internal cell function They are named AB toxins due to their components: the "A" component is usually the "active" portion, and the "B" component is usually the "binding" portion. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit.Among the toxins produced by certain Clostridium spp. are the binary exotoxins. These proteins consist of two independent polypeptides, which correspond to the A/B subunit moieties. The enzyme component (A) enters the cell through endosomes produced by the oligomeric binding/translocation protein (B), and prevents actin polymerisation through ADP-ribosylation of monomeric G-actin.
Members of the "A" binary toxin family include C. perfringens iota toxin Ia, C. botulinum C2 toxin CI, and Clostridium difficile ADP-ribosyltransferase . Other homologous proteins have been found in Clostridium spiroforme.
Members of the "B" binary toxin family include the Bacillus anthracis protective antigen (PA) protein,[3] most likely due to a common evolutionary ancestor. B. anthracis, a large Gram-positive spore-forming rod, is the causative agent of anthrax. Its two virulence factors are the poly-D-glutamate polypeptide capsule, and the actual anthrax exotoxin. The toxin comprises three factors: the protective antigen (PA); the oedema factor (EF); and the lethal factor (LF). Each is a thermolabile protein of ~80kDa. PA forms the "B" part of the exotoxin and allows passage of the "A" moiety (consisting of EF and LF) into target cells. PA protein forms the central part of the complete anthrax toxin, and translocates the B moiety into host cells after assembling as a heptamer in the membrane.
The AB5 toxins are usually considered a type of AB toxin, characterized by B pentamers. Less commonly, the term "AB toxin" is used to emphasize the monomeric character of the B component.
Steps in Replication of T4 Phage in E coli
The Bacteriophages
Viruses that attack bacteria were observed by Twort and d'Herelle in 1915 and 1917. They observed that broth cultures of certain intestinal bacteria could be dissolved by addition of a bacteria-free filtrate obtained from sewage. The lysis of the bacterial cells was said to be brought about by a virus which meant a "filterable poison" ("virus" is Latin for "poison").
Probably every known bacterium is subject to infection by one or more viruses or "bacteriophages" as they are known ("phage" for short, from Gr. "phagein" meaning "to eat" or "to nibble"). Most research has been done on the phages that attack E. coli, especially the T-phages and phage lambda.
Like most viruses, bacteriophages typically carry only the genetic information needed for replication of their nucleic acid and synthesis of their protein coats. When phages infect their host cell, the order of business is to replicate their nucleic acid and to produce the protective protein coat. But they cannot do this alone. They require precursors, energy generation and ribosomes supplied by their bacterial host cell.
Bacterial cells can undergo one of two types of infections by viruses termed lytic infections andlysogenic (temperate) infections. In E. coli, lytic infections are caused by a group seven phages known as the T-phages, while lysogenic infections are caused by the phage lambda.
Lytic Infections
The T-phages, T1 through T7, are referred to as lytic phages because they always bring about the lysis and death of their host cell, the bacterium E. coli. T-phages contain double-stranded DNA as their genetic material. In addition to their protein coat or capsid (also referred to as the "head"), T-phages also possess a tail and some related structures. A diagram and electron micrograph of bacteriophage T4 is shown below. The tail includes a core, a tail sheath, base plate, tail pins, and tail fibers, all of which are composed of different proteins. The tail and related structures of bacteriophages are generally involved in attachment of the phage and securing the entry of the viral nucleic acid into the host cell.
Left. Electron Micrograph of bacteriophage T4. Right. Model of phage T4. The phage possesses a genome of linear ds DNA contained within an icosahedral head. The tail consists of a hollow core through which the DNA is injected into the host cell. The tail fibers are involved with recognition of specific viral "receptors" on the bacterial cell surface.
Before viral infection, the cell is involved in replication of its own DNA and transcription and translation of its own genetic information to carry out biosynthesis, growth and cell division. After infection, the viral DNA takes over the machinery of the host cell and uses it to produce the nucleic acids and proteins needed for production of new virus particles. Viral DNA replaces the host cell DNA as a template for both replication (to produce more viral DNA) and transcription (to produce viral mRNA). Viral mRNAs are then translated, using host cell ribosomes, tRNAs and amino acids, into viral proteins such as the coat or tail proteins. The process of DNA replication, synthesis of proteins, and viral assembly is a carefully coordinated and timed event. The overall process of lytic infection is diagrammed in the figure below. Discussion of the specific steps follows.
The lytic cycle of a bacterial virus, e.g. bacteriophage T4.
The first step in the replication of the phage in its host cell is called adsorption. The phage particle undergoes a chance collision at a chemically complementary site on the bacterial surface, then adheres to that site by means of its tail fibers.
Following adsorption, the phage injects its DNA into the bacterial cell. The tail sheath contracts and the core is driven through the wall to the membrane. This process is called penetration and it may be both mechanical and enzymatic. Phage T4 packages a bit of lysozyme in the base of its tail from a previous infection and then uses the lysozyme to degrade a portion of the bacterial cell wall for insertion of the tail core. The DNA is injected into the periplasm of the bacterium, and generally it is not known how the DNA penetrates the membrane. The adsorption and penetration processes are illustrated below.
Adsorption, penetration and injection of bacteriophage T4 DNA into an E. coli cell. T4 attaches to an outer membrane porin protein, ompC.
Immediately after injection of the viral DNA there is a process initiated called synthesis of early proteins. This refers to the transcription and translation of a section of the phage DNA to make a set of proteins that are needed to replicate the phage DNA. Among the early proteins produced are a repair enzyme to repair the hole in the bacterial cell wall, a DNAase enzyme that degrades the host DNA into precursors of phage DNA, and a virus specific DNA polymerase that will copy and replicate phage DNA. During this period the cell's energy-generating and protein-synthesizing abilities are maintained, but they have been subverted by the virus. The result is the synthesis of several copies of the phage DNA.
The next step is the synthesis of late proteins. Each of the several replicated copies of the phage DNA can now be used for transcription and translation of a second set of proteins called the late proteins. The late proteins are mainly structural proteins that make up the capsomeres and the various components of the tail assembly. Lysozyme is also a late protein that will be packaged in the tail of the phage and be used to escape from the host cell during the last step of the replication process.
Having replicated all of their parts, there follows an assembly process. The proteins that make up the capsomeres assemble themselves into the heads and "reel in" a copy of the phage DNA. The tail and accessory structures assemble and incorporate a bit of lysozyme in the tail plate. The viruses arrange their escape from the host cell during the assembly process.
While the viruses are assembling, lysozyme is being produced as a late viral protein. Part of this lysozome is used to escape from the host cell by lysing the cell wall peptiodglycan from the inside. This accomplishes the lysis of the host cell and the release of the mature viruses, which spread to nearby cells, infect them, and complete the cycle. The life cycle of a T-phage takes about 25-35 minutes to complete. Because the host cells are ultimately killed by lysis, this type of viral infection is referred to as lytic infection.
Lysogenic Infections
Bacteriophage Lambda, the lysogenic phage that infects E. coli. Bock laboratories. University of Wisconsin-Madison.
Lysogenic or temperate infection rarely results in lysis of the bacterial host cell. Lysogenic viruses, such as lambda which infects E. coli, have a different strategy than lytic viruses for their replication. After penetration, the virus DNA integrates into the bacterial chromosome and it becomes replicated every time the cell duplicates its chromosomal DNA during normal cell division. The life cycle of a lysogenic bacteriophage is illustrated below.
The lysogenic cycle of a temperate bacteriophage such as lambda.
Temperate viruses usually do not kill the host bacterial cells they infect. Their chromosome becomes integrated into a specific section of the host cell chromosome. Such phage DNA is called prophage and the host bacteria are said to be lysogenized. In the prophage state all the phage genes except one are repressed. None of the usual early proteins or structural proteins are formed.
The phage gene that is expressed is an important one because it codes for the synthesis of a repressor molecule that prevents the synthesis of phage enzymes and proteins required for the lytic cycle. If the synthesis of the repressor molecule stops or if the repressor becomes inactivated, an enzyme encoded by the prophage is synthesized which excises the viral DNA from the bacterial chromosome. This excised DNA (the phage genome) can now behave like a lytic virus, that is to produce new viral particles and eventually lyse the host cell (see diagram above). This spontaneous derepression is a rare event occurring about one in 10,000 divisions of a lysogenic bacterium., but it assures that new phage are formed which can proceed to infect other cells.
Usually it is difficult to recognize lysogenic bacteria because lysogenic and nonlysogenic cells appear identical. But in a few situations, the prophage supplies genetic information such that the lysogenic bacteria exhibit a new characteristic (new phenotype), not displayed by the nonlysogenic cell, a phenomenon called lysogenic conversion. Lysogenic conversion has some interesting manifestations in pathogenic bacteria that only exert certain determinants of virulence when they are in a lysogenized state. Hence, Corynebacterium diphtheriae can only produce the toxin responsible for the disease if it carries a temperate virus called phage beta. Only lysogenized streptococci produce the erythrogenic toxin (pyrogenic exotoxin) which causes the skin rash of scarlet fever; and some botulinum toxins are synthesized only by lysogenized strains of C. botulinum.
Corynebacterium diphtheriae only produces diphtheria toxin when lysogenized by beta phage.C. diphtheriae strains that lack the prophage do not produce diphtheria toxin and do not cause the disease diphtheria. Surprisingly, the genetic information for production of the toxin is found to be on the phage chromosome, rather than the bacterial chromosome.
A similar phenomenon to lysogenic conversion exists in the relationship between an animal tumor virus and its host cell. In both instances, viral DNA is incorporated into the host cell genome, and there is a coincidental change in the phenotype of the cell. Some human cancers may be caused by viruses which establish a state in human cells analogous to lysogeny in bacteria.
Phage Therapy
Phage therapy is the therapeutic use of lytic bacteriophages to treat pathogenic bacterial infections. Phage therapy is an alternative to antibiotics being developed for clinical use by research groups in Eastern Europe and the U.S. After having been extensively used and developed mainly in former Soviet Union countries for about 90 years, phage therapies for a variety of bacterial and poly microbial infections are now becoming available on an experimental basis in other countries, including the U.S. The principles of phage therapy have potential applications not only in human medicine, but also in dentistry, veterinary science, food science and agriculture.
An important benefit of phage therapy is derived from the observation that bacteriophages are much more specific than most antibiotics that are in clinical use. Theoretically, phage therapy is harmless to the eucaryotic host undergoing therapy, and it should not affect the beneficial normal flora of the host. Phage therapy also has few, if any, side effects, as opposed to drugs, and does not stress the liver. Since phages are self-replicating in their target bacterial cell, a single, small dose is theoretically efficacious. On the other hand, this specificity may also be disadvantageous because a specific phage will only kill a bacterium if it is a match to the specific subspecies. Thus, phage mixtures may be applied to improve the chances of success, or clinical samples can be taken and an appropriate phage identified and grown.
Phages are currently being used therapeutically to treat bacterial infections that do not respond to conventional antibiotics, particularly in the country of Georgia. They are reported to be especially successful where bacteria have constructed a biofilm composed of a polysaccharide matrix that antibiotics cannot penetrate.
Lamda Phage Replication Cycle
Enterobacteria phage λ (lambda phage, coliphage λ) is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli (E. coli). It was discovered by Esther Lederberg in 1950 when she noticed that streaks of mixtures of two E. coli strains, one of which treated with ultraviolet light, was "nibbled and plaqued". This virus has a temperate lifecycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase (during which it kills and lyses the cell to produce offspring).
The phage particle consists of a head (also known as a capsid), a tail, and tail fibers (see image of virus below). The head contains the phage's double-strand linear DNA genome. During infection, the phage particle recognizes and binds to its host, E. coli, causing DNA in the head of the phage to be ejected through the tail into the cytoplasm of the bacterial cell. Usually, a "lytic cycle" ensues, where the lambda DNA is replicated and new phage particles produced within the cell. This is followed by cell lysis, releasing the cell contents, including virions that have been assembled, into the environment. However, under certain conditions, the phage DNA may integrate itself into the host cell chromosome in the lysogenic pathway. In this state, the λ DNA is called a prophage and stays resident within the host's genome without apparent harm to the host. The host is termed a lysogen when a prophage is present. This prophage may enter the lytic cycle when the lysogen enters a stressed condition.
Entry of Virus into Host Cell
Viral entry is the earliest stage of infection in the viral life cycle, as the virus comes into contact with the host cell and introduces viral material into the cell. The major steps involved in viral entry are shown below.[1] Despite the variation among viruses, the generalities are quite similar. However, the specifics are varied.
Mechanism for Releasing Enveloped Viruses
Abstract
Many enveloped viruses complete their replication cycle by forming vesicles that bud from the plasma membrane. Some viruses encode “late” (L) domain motifs that are able to hijack host proteins involved in the vacuolar protein sorting (VPS) pathway, a cellular budding process that gives rise to multivesicular bodies and that is topologically equivalent to virus budding. Although many enveloped viruses share this mechanism, examples of viruses that require additional viral factors and viruses that appear to be independent of the VPS pathway have been identified. Alternative mechanisms for virus budding could involve other topologically similar process such as cell abscission, which occurs following cytokinesis, or virus budding could proceed spontaneously as a result of lipid microdomain accumulation of viral proteins. Further examination of novel virus–host protein interactions and characterization of other enveloped viruses for which budding requirements are currently unknown will lead to a better understanding of the cellular processes involved in virus assembly and budding.
