Prokaryotes and Viruses
The prokaryotes are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles. The word prokaryote comes from the Greek πρό- (pro-) "before" + καρυόν (karyon) "nut or kernel", referring to the cell nucleus, + suffix -ώτης (-ōtēs) (pl. -ώτες (-ōtes)). It is also spelled "procaryote".
The prokaryotes are divided into two domains: the bacteria and the archaea. Archaea were recognized as a domain of life in 1990. These organisms were originally thought to live only in inhospitable conditions such as extremes of temperature, pH, and radiation but have since been found in all types of habitats.
Cell structure of a bacterium, one of the two domains of prokaryotic life.
Relationship to eukaryotes
A distinction between prokaryotes and eukaryotes (meaning true kernel, also spelled "eucaryotes") is that eukaryotes do have "true" nuclei containing their DNA, whereas the genetic material in prokaryotes is not membrane-bound. Eukaryotic organisms may be unicellular, as in amoebae, or multicellular, as in plants and animals. The difference between the structure of prokaryotes and eukaryotes is so great that it is sometimes considered to be the most important distinction among groups of organisms. However, a criticism of this classification is that the word "prokaryote" is based on what these organisms are not (they are not eukaryotic), rather than what they are (either archaea or bacteria). In 1977, Carl Woese proposed dividing prokaryotes into the Bacteria and Archaea (originally Eubacteria and Archaebacteria) because of the major differences in the structure and genetics between the two groups of organisms. This arrangement of Eukaryota (also called "Eukarya"), Bacteria, and Archaea is called the three-domain system replacing the traditional two-empire system.
The cell structure of prokaryotes differs greatly from that of eukaryotes. The defining characteristic is the absence of a nucleus. The genomes of prokaryotes are held within an irregular DNA/protein complex in the cytosol called the nucleoid, which lacks a nuclear envelope. Prokaryotes generally lack membrane-bound cell compartments: such as mitochondria and chloroplasts. Instead processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic plasma membrane. However, prokaryotes do possess some internal structures, such as cytoskeletons, and the bacterial order Planctomycetes have a membrane around their nucleoid and contain other membrane-bound cellular structures. Both eukaryotes and prokaryotes contain large RNA/protein structures called ribosomes, which produce protein. Prokaryotes are usually much smaller than eukaryotic cells.
Prokaryotes also differ from eukaryotes in that they contain only a single loop of stable chromosomal DNA stored in an area named the nucleoid, while eukaryote DNA is found on tightly bound and organized chromosomes. Although some eukaryotes have satellite DNA structures called plasmids, these are generally regarded as a prokaryote feature, and many important genes in prokaryotes are stored on plasmids.
Prokaryotes have a larger surface-area-to-volume ratio giving them a higher metabolic rate, a higher growth rate and consequently a shorter generation time compared to Eukaryotes.
While prokaryotes are still commonly imagined to be strictly unicellular, most are capable of forming stable aggregate communities. When such communities are encased in a stabilizing polymer matrix (“slime”), they may be called “biofilms”. Cells in biofilms often show distinct patterns of gene expression (phenotypic differentiation) in time and space. Also, like multicellular eukaryotes, these changes in expression appear to often result from cell-to-cell signaling, a phenomenon known as quorum sensing.
Biofilms may be highly heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces, or potentially even liquid-liquid interfaces. Bacterial biofilms are often made up of microcolonies (approximately dome-shaped masses of bacteria and matrix) separated by “voids” through which the medium (e.g. water) may flow relatively uninhibited. The microcolonies may join together above the substratum to form a continuous layer, closing the network of channels separating microcolonies. This structural complexity—combined with observations that oxygen limitation (a ubiquitous challenge for anything growing in size beyond the scale of diffusion) is at least partially eased by movement of medium throughout the biofilm—has led some to speculate that this may constitute a circulatory system many researchers have started calling prokaryotic communities multicellular. Differential cell expression, collective behavior, signaling, programmed cell death, and (in some cases) discrete biological dispersal events all seem to point in this direction. However, these colonies are seldom if ever founded by a single founder (in the way that animals and plants are founded by single cells), which presents a number of theoretical issues. Most explanations of co-operation and the evolution of multicellularity have focused on high relatedness between members of a group (or colony, or whole organism). If a copy of a gene is present in all members of a group, behaviors that promote cooperation between members may permit those members to have (on average) greater fitness than a similar group of selfish individuals . What to make of prokaryotic communities clearly founded by many (most likely unrelated) individuals, yet defined by (apparently) high levels of cooperation, communication, and coordinated behavior?
It is likely that these instances of prokaryotic sociality are the rule rather than the exception, which would have serious implications for the way we view prokaryotes in general and the way we deal with them in medicine. Bacterial biofilms may be 100x more resistant to antibiotics than free-living unicells and may be nearly impossible to remove from surfaces once they have colonized them. Other aspects of bacterial cooperation—such as bacterial conjugation and quorum-sensing mediated pathogenicity—present additional challenges to researchers and medical professionals seeking to treat the associated diseases.
Bacteria and archaea reproduce through asexual reproduction, usually by binary fission or budding. Genetic exchange and recombination still occur, but this is a form of horizontal gene transfer and is not a replicative process, simply involving DNA being transferred between two cells, as in bacterial conjugation.
Recent research indicates that all prokaryotes actually do have cytoskeletons, albeit more primitive than those of eukaryotes. Besides homologues of actin and tubulin the helically arranged building block of the flagellum, flagellin, is one of the most significant cytoskeletal proteins of bacteria as it provides structural backgrounds of chemotaxis, the basic cell physiological response of bacteria. At least some prokaryotes also contain intracellular structures which can be seen as primitive organelles. Membranous organelles (a.k.a. intracellular membranes) are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, e.g. photosynthesis or chemolithotrophy. Additionally, some species also contain protein-enclosed microcompartments, which have distinct physiological roles (e.g. carboxysomes or gas vacuoles).
Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm to 750 µm.
Morphology of prokaryotic cells
Prokaryotic cells have various shapes; the four basic shapes are:Cocci - spherical
Bacilli - rod shaped
Spirochaete - spiral shaped
Vibrio - comma shaped
Prokaryotes live in nearly all environments on earth where there is liquid water. Some archaea and bacteria thrive in harsh conditions, such as high temperatures (thermophiles) or high salinity (halophiles). Organisms such as these are referred to as extremophiles. Many archaea grow as plankton in the oceans. Symbiotic prokaryotes live in or on the bodies of other organisms, including humans.
Evolution of prokaryotes
Phylogenetic tree showing the diversity of prokaryotes, compared to eukaryotes.
The current model of the evolution of the first living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. The eukaryotes are generally thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single a gene pool. This controversy was summarized in 2005:
There is no consensus among biologists concerning the position of the eukaryotes in the overall scheme of cell evolution. Current opinions on the origin and position of eukaryotes span a broad spectrum including the views that eukaryotes arose first in evolution and that prokaryotes descend from them, that eukaryotes arose contemporaneously with eubacteria and archeabacteria and hence represent a primary line of descent of equal age and rank as the prokaryotes, that eukaryotes arose through a symbiotic event entailing an endosymbiotic origin of the nucleus, that eukaryotes arose without endosymbiosis, and that eukaryotes arose through a symbiotic event entailing a simultaneous endosymbiotic origin of the flagellum and the nucleus, in addition to many other models, which have been reviewed and summarized elsewhere.
The oldest known fossilized prokaryotes were laid down approximately 3.5 billion years ago, only about 1 billion years after the formation of the Earth's crust. Even today, prokaryotes are perhaps the most successful and abundant life forms. Eukaryotes only appear in the fossil record later, and may have formed from endosymbiosis of multiple prokaryote ancestors. The oldest known fossil eukaryotes are about 1.7 billion years old. However, some genetic evidence suggests eukaryotes appeared as early as 3 billion years ago.
While Earth is the only place in the universe where life is known to exist, some have suggested that there is evidence on Mars of fossil or living prokaryotes; but this possibility remains the subject of considerable debate and skepticism.
Prokaryotes have diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct prokaryotic types. For example, in addition to using photosynthesis or organic compounds for energy, as eukaryotes do, prokaryotes may obtain energy from inorganic compounds such as hydrogen sulfide. This enables prokaryotes to thrive in harsh environments as cold as the snow surface of Antarctica, and as hot as undersea hydrothermal vents and land-based hot springs.
virus (from the Latin virus meaning toxin or poison) is a small infectious agent that can replicate only inside the living cells of other organisms. Most viruses are too small to be seen directly with a light microscope. Viruses infect all types of organisms, from animals and plants to bacteria and archaea.< Since the initial discovery of tobacco mosaic virus by Martinus Beijerinck in 1898, about 5,000 viruses have been described in detail, although there are millions of different types. Viruses are found in almost every ecosystem on Earth and these minute structures are the most abundant type of biological entity. The study of viruses is known as virology, a sub-specialty of microbiology.
Unlike prions and viroids, viruses consist of two or three parts: all viruses have genes made from either DNA or RNA, long molecules that carry genetic information; all have a protein coat that protects these genes; and some have an envelope of lipids that surrounds them when they are outside a cell. (Viroids do not have a protein coat and prions contain no RNA or DNA.) Viruses vary from simple helical and icosahedral shapes to more complex structures. Most viruses are about one hundred times smaller than an average bacterium. The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity.
Viruses spread in many ways; plant viruses are often transmitted from plant to plant by insects that feed on sap, such as aphids, while animal viruses can be carried by blood-sucking insects. These disease-bearing organisms are known as vectors. Influenza viruses are spread by coughing and sneezing. The norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal-oral route and are passed from person to person by contact, entering the body in food or water. HIV is one of several viruses transmitted through sexual contact and by exposure to infected blood. Viruses can infect only a limited range of host cells called the "host range". This can be broad as when a virus is capable of infecting many species or narrow.
Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection. However, some viruses including those causing HIV and viral hepatitis evade these immune responses and result in chronic infections. Microorganisms also have defenses against viral infection, such as restriction modification systems which restrict the growth of viruses. Antibiotics have no effect on viruses, but several antiviral drugs have been developed.
Viruses are found wherever there is life and have probably existed since living cells first evolved. The origin of viruses is unclear because they do not form fossils, so molecular techniques have been the most useful means of investigating how they arose. These techniques rely on the availability of ancient viral DNA or RNA, but, unfortunately, most of the viruses that have been preserved and stored in laboratories are less than 90 years old. There are three main hypotheses that try to explain the origins of viruses:
Prions are infectious protein molecules that do not contain DNA or RNA. They cause an infection in sheep called scrapie and cattle bovine spongiform encephalopathy ("mad cow" disease). In humans they cause kuru and Creutzfeldt-Jakob disease. They are able to replicate because some proteins can exist in two different shapes and the prion changes the normal shape of a host protein into the prion shape. This starts a chain reaction where each prion protein converts many host proteins into more prions, and these new prions then go on to convert even more protein into prions. Although they are fundamentally different from viruses and viroids, their discovery gives credence to the idea that viruses could have evolved from self-replicating molecules Computer analysis of viral and host DNA sequences is giving a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modern viruses. To date, such analyses have not helped to decide on which of these hypotheses are correct. However, it seems unlikely that all currently known viruses have a common ancestor and viruses have probably arisen numerous times in the past by one or more mechanisms.
Are viruses alive ?
Opinions differ on whether viruses are a form of life, or organic structures that interact with living organisms. They have been described as "organisms at the edge of life", since they resemble organisms in that they possess genes and evolve by natural selection, and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism, and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell although bacterial species such as rickettsia and chlamydia are considered living organisms despite the same limitation. Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.
Viral populations do not grow through cell division, because they are acellular; instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.
The life cycle of viruses differs greatly between species but there are six basic stages in the life cycle of viruses:
Effects on the host cell
The range of structural and biochemical effects that viruses have on the host cell is extensive. These are called cytopathic effects. Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis. Often cell death is caused by cessation of its normal activities because of suppression by virus-specific proteins, not all of which are components of the virus particle.
Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally. This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses. Some viruses, such as Epstein-Barr virus, can cause cells to proliferate without causing malignancy, while others, such as papillomaviruses, are established causes of cancer.
Viruses are by far the most abundant parasites on earth and they have been found to infect all types of cellular life including animals, plants and bacteria. However, different types of viruses can only infect a limited range of hosts and many are species-specific. Some, such as smallpox virus for example, can only infect one species—in this case humans, and is said to have a narrow host range. Other viruses, such as rabies virus, can infect different species of mammals and is said to have a broad range. The viruses that infect plants are harmless to animals and most viruses that infect other animals are harmless to humans. The host range of some Bacteriophages is limited to a single strain of bacteria and they can be used to trace the source of outbreaks of infections by a method called phage typing.
Examples of common human diseases caused by viruses include the common cold, influenza, chickenpox and cold sores. Many serious diseases such as Ebola, AIDS, avian influenza and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation as to whether they too have a virus as the causative agent, such as the possible connection between human herpes virus six (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome. There is controversy over whether the borna virus, previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans.
Viruses have different mechanisms by which they produce disease in an organism, which largely depends on the viral species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die the whole organism will start to suffer the effects. Although viruses cause disruption of healthy homeostasis, resulting in disease, they may exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which causes cold sores, to remain in a dormant state within the human body. This is called latency and is a characteristic of the herpes viruses including Epstein-Barr virus, which causes glandular fever, and varicella zoster virus, which causes chickenpox. Most people have been infected with at least one of these types of herpes virus. However, these latent viruses might sometimes be beneficial, as the presence of the virus can increase immunity against bacterial pathogens, such as Yersinia pestis. On the other hand, latent chickenpox infections return in later life as the disease called shingles.
Some viruses can cause life-long or chronic infections, where the viruses continue to replicate in the body despite the host's defense mechanisms. This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus. In populations with a high proportion of carriers, the disease is said to be endemic. In contrast to acute lytic viral infections this persistence implies compatible interactions with the host organism. Persistent viruses may even broaden the evolutionary potential of host species.
Epidemics and pandemics
Native American populations were devastated by contagious diseases, particularly smallpox, brought to the Americas by European colonists. It is unclear how many Native Americans were killed by foreign diseases after the arrival of Columbus in the Americas, but the numbers have been estimated to be close to 70% of the indigenous population. The damage done by this disease significantly aided European attempts to displace and conquer the native population.
A pandemic is a worldwide epidemic. The 1918 flu pandemic, commonly referred to as the Spanish flu, was a category 5 influenza pandemic caused by an unusually severe and deadly influenza A virus. The victims were often healthy young adults, in contrast to most influenza outbreaks, which predominantly affect juvenile, elderly, or otherwise weakened patients.
The Spanish flu pandemic lasted from 1918 to 1919. Older estimates say it killed 40–50 million people, while more recent research suggests that it may have killed as many as 100 million people, or 5% of the world's population in 1918.Most researchers believe that HIV originated in sub-Saharan Africa during the twentieth century; it is now a pandemic, with an estimated 38.6 million people now living with the disease worldwide. The Joint United Nations Programme on HIV/AIDS (UNAIDS) and the World Health Organization (WHO) estimate that AIDS has killed more than 25 million people since it was first recognized on June 5, 1981, making it one of the most destructive epidemics in recorded history. In 2007 there were 2.7 million new HIV infections and 2 million HIV-related deaths.
Several highly lethal viral pathogens are members of the Filoviridae. Filoviruses are filament-like viruses that cause viral hemorrhagic fever, and include the Ebola and Marburg viruses. The Marburg virus attracted widespread press attention in April 2005 for an outbreak in Angola. Beginning in October 2004 and continuing into 2005, the outbreak was the world's worst epidemic of any kind of viral hemorrhagic fever.
Vaccination is a cheap and effective way of preventing infections by viruses. Vaccines were used to prevent viral infections long before the discovery of the actual viruses. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps and rubella. Smallpox infections have been eradicated. Vaccines are available to prevent over thirteen viral infections of humans, and more are used to prevent viral infections of animals. Vaccines can consist of live-attenuated or killed viruses, or viral proteins (antigens). Live vaccines contain weakened forms of the virus, which do not cause the disease but nonetheless confer immunity. Such viruses are called attenuated. Live vaccines can be dangerous when given to people with a weak immunity, (who are described as immuno-compromised), because in these people, the weakened virus can cause the original disease. Biotechnology and genetic engineering techniques are used to produce subunit vaccines. These vaccines use only the capsid proteins of the virus. Hepatitis B vaccine is an example of this type of vaccine. Subunit vaccines are safe for immuno-compromised patients because they cannot cause the disease. The yellow fever virus vaccine, a live-attenuated strain called 17D, is probably the safest and most effective vaccine ever generated.
Over the past twenty years, the development of antiviral drugs has increased rapidly. This has been driven by the AIDS pandemic. Antiviral drugs are often nucleoside analogues, (fake DNA building blocks), which viruses incorporate into their genomes during replication. The life-cycle of the virus is then halted because the newly synthesized DNA is inactive. This is because these analogues lack the hydroxyl groups, which, along with phosphorus atoms, link together to form the strong "backbone" of the DNA molecule. This is called DNA chain termination. Examples of nucleoside analogues are aciclovir for Herpes simplex virus infections and lamivudine for HIV and Hepatitis B virus infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs. Other antiviral drugs in use target different stages of the viral life cycle. HIV is dependent on a proteolytic enzyme called the HIV-1 protease for it to become fully infectious. There is a large class of drugs called protease inhibitors that inactivate this enzyme.
Hepatitis C is caused by an RNA virus. In 80% of people infected, the disease is chronic, and without treatment, they are infected for the remainder of their lives. However, there is now an effective treatment that uses the nucleoside analogue drug ribavirin combined with interferon. The treatment of chronic carriers of the hepatitis B virus by using a similar strategy using lamivudine has been developed.
Infection in other species
Viruses infect all cellular life and, although viruses occur universally, each cellular species has its own specific range that often infect only that species. Some viruses, called satellites, can only replicate within cells that have already been infected by another virus. Viruses are important pathogens of livestock. Diseases such as Foot and Mouth Disease and bluetongue are caused by viruses. Companion animals such as cats, dogs, and horses, if not vaccinated, are susceptible to serious viral infections. Canine parvovirus is caused by a small DNA virus and infections are often fatal in pups. Like all invertebrates, the honey bee is susceptible to many viral infections. Fortunately, most viruses co-exist harmlessly in their host and cause no signs or symptoms of disease.
Role in evolution
Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. It is thought that viruses played a central role in the early evolution, before the diversification of bacteria, archaea and eucaryotes and at the time of the last universal common ancestor of life on Earth. Viruses are still one of the largest reservoirs of unexplored genetic diversity on the Earth.
The ability of viruses to cause devastating epidemics in human societies has led to the concern that viruses could be weaponised for biological warfare. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory. The smallpox virus devastated numerous societies throughout history before its eradication. There are officially only two centers in the world which keep stocks of smallpox virus—the Russian Vector laboratory, and the United States Centers for Disease Control. But fears that it may be used as a weapon are not totally unfounded; the vaccine for smallpox is not safe—during the years before the eradication of smallpox disease more people became seriously ill as a result of vaccination than did people from smallpox — and smallpox vaccination is no longer universally practiced. Thus, much of the modern human population has almost no established resistance to smallpox.