Viruses in Bacteria, Plant and Fungi

Viruses in Bacteria, Plant and Fungi

Introduction to virus
Viruses are too small to be seen by the naked eye. They can't multiply on their own, so they have to invade a 'host' cell and take over its machinery in order to be able to make more virus particles.

Viruses consist of genetic materials (DNA or RNA) surrounded by a protective coat of protein. They are capable of latching onto cells and getting inside them.

The cells of the mucous membranes, such as those lining the respiratory passages that we breathe through, are particularly open to virus attacks because they are not covered by protective skin.

Viruses in bacteria
It's easy to mix these up since compared to us, both are very small.

Bacteria and viruses causes many of the diseases we're familiar with, people often confuse these two microbes. But viruses are as different from bacteria as they differ greatly in size. The biggest viruses are only as large as the tiniest bacteria. Another difference is their structure. Bacteria are complex compared to viruses.

A bacterium has a rigid cell wall and a thin, rubbery cell membrane surrounding the fluid, or cytoplasm, inside the cell. A bacterium contains all of the genetic information needed to make copies of itself—its DNA—in a structure called a chromosome. In addition, it may have extra loose bits of DNA called plasmids floating in the cytoplasm. Bacteria also have ribosomes, tools necessary for copying DNA so bacteria can reproduce. Some have threadlike structures called flagella that they use to move.

T4 bacteriophage is a virus that looks like an alien landing pod with 6 legs, the bacteria attatches to the surface of the much larger bacteria Escherichia coli (E.coli). once attatched, the bacteriophate injects DNA into the bacterium. DNA then instructs the produce masses of new viruses. And as many are produced, E.coli bursts.

Eschericia coli + coliphage T4

Viruses in plants

Plants are susceptible to viral diseases, just like any living systems. Plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without the host. Plant viruses are pathogenic to higher plants. Virus cause many plant diseases and are responsible for huge losses in crop production and quality in all parts of the world.

Classification of plant virus
There are 6 major groups, based on the nature of the genome:

• Double-stranded DNA (dsDNA): there are no plant viruses in this group, which is defined to include only those viruses that replicate without an RNA intermediate (see Reverse-transcribing viruses, below). It includes those viruses with the largest known genomes (up to about 400,000 base pairs) and there is only one genome component, which may be linear or circular. Well-known viruses in this group include the herpes and pox viruses.
• Single-stranded DNA (ssDNA): there are two families of plant viruses in this group and both of these have small circular genome components, often with two or more segments.
• Reverse-transcribing viruses: these have dsDNA or ssRNA genomes and their replication includes the synthesis of DNA from RNA by the enzyme reverse transcriptase; many integrate into their host genomes. The group includes the retroviruses, of which Human immunodeficiency virus (HIV), the cause of AIDS, is a member. There is a single family of plant viruses in this group and this is characterised by a single component of circular dsDNA, the replication of which is via an RNA intermediate.
• Double-stranded RNA (dsRNA): some plant viruses and many of the mycoviruses are included in this group.
• Negative sense single-stranded RNA (ssRNA-): in this group, some or all of the genes are translated into protein from an RNA strand complementary to that of the genome (as packaged in the virus particle). There are some plant viruses in this group and it also includes the viruses that cause measles, influenza and rabies.
• Positive sense single-stranded RNA (ssRNA+): the majority of plant viruses are included in this group. It also includes the SARS coronavirus and many other viruses that cause respiratory diseases (including the "common cold"), and the causal agents of polio and foot-and-mouth disease.

And within each of these groups, there are many different characteristics used to classify virus into families, genera and speces, by the combination of characters used. Some of them are:

• Particle morphology: the shape and size of particles as seen under the electron microscope.
• Genome properties: this includes the number of genome components and the translation strategy. Where genome sequences have been determined, the relatedness of different sequences is often an important factor in discriminating between species.
• Biological properties: this may include the type of host and also the mode of transmission.
• Serological properties: the relatedness (or otherwise) of the virion protein(s).

The particle morphology is one where amongst plant viruses, the most frequently encountered shapes are as follows:

Isometric: apparently spherical and (depending on the species) from about 18nm in diameter upwards. The example here shows Tobacco necrosis virus, genus Necrovirus with particles 26 nm in diameter.

Rod-shaped: about 20-25 nm in diameter and from about 100 to 300 nm long. These appear rigid and often have a clear central canal (depending on the staining method used). Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Tobacco mosaic virus, genus Tobamovirus with particles 300 nm long.

Filamentous: usually about 12 nm in diameter and more flexuous than the rod-shaped particles. They can be up to 1000 nm long, or even longer in some instances. Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Potato virus Y, genus Potyvirus with particles 740 nm long.

Geminate: twinned isometric particles about 30 x 18 nm. These particles are diagnostic for viruses in the family Geminiviridae which are widespread in many crops especially in tropical regions. The example here shows Maize streak virus, genus Mastrevirus.

Bacilliform: Short round-ended rods. These come in various forms up to about 30 nm wide and 300 nm long. The example here shows Cocoa swollen shoot virus, genus Badnavirus with particles 28 x 130 nm.

Genome properties of plant virus

• Nature of the genome: circular, as in all known plant DNA viruses, or linear.
• Number of genome components: This varies from a single component, example in the genera Potyvirus and Tobamovirus, to 11, in some members of the genus Nanovirus. Individual components vary in size from about 1kb Nanovirus components to about 20 kb in the genus Closterovirus.
• Number of genes: These might vary considerably. Most plant viruses have at least 3 genes: 1, or more, concerned with replication of the nucleic acid, 1, or more, concerned with cell-to-cell movement of the virus and 1, or more, encoding a structural protein that is assembled into the virus particle usually called the "coat" or "capsid" protein. There may also be additional genes that have a regulatory function or which are required for transmission between plants association with a vector.
• Translation strategy: A variety of strategies are employed to translate the genes from the genome components either directly or via mRNA intermediates and, in some cases, to permit different amounts of protein to be produced from the different genes. These are summarised for each genus in the genus description pages but 3 examples here serve to illustrate some of the variety:
  - Genus Potyvirus: in this very large genus, there is one ssRNA component that encodes one large (c. 350 kDa) polyprotein. This is cleaved by 3 different proteases (all encoded by the virus itself) into 10 different mature proteins. The two proteins at the C-terminus of the polyprotein are respectively an RNA-dependent RNA polymerase (Nib) involved in replication of the virus and the single coat protein (CP). Many of the proteins have multiple functions. The genome organisation of a typical member is shown here, indicating the 10 mature proteins and the nine cleavage sites (arrowed).

• - Genus Furovirus: in this genus there are two ssRNA components. The 5'-proximal gene on each RNA is translated directly from the genomic RNA: on RNA1 (the larger RNA component) this gene encodes a replication protein and on RNA2 it is the coat protein. The stop codons of both of these genes are "leaky" and in a small percentage of cases, translation continues to produce a larger ("readthrough") protein. On RNA1, the replication protein is extended to include an RNA-dependent RNA polymerase (RdRp) while the readthrough region of the coat protein is probably required for particle assembly and for transmission by the plasmodiophorid vector. There is a further (3'-proximal) gene on each of the RNAs and these are translated from shorter RNA molecules transcribed from the 3'-end of the genomic RNA ("subgenomic" mRNAs). That from RNA1 is a cell-to-cell movement protein (MP) that enables the virus to move between adjacent plant cells via the plasmodesmata while the function of the product from RNA2 is uncertain but may involve supression of the host plant defence reaction. The genome organisation of a typical member is shown here:

• - Genus Fijivirus: in this genus there are 10 components of dsRNA. Most of the components encode a single protein and at least 3 of these are structural proteins assembled into the complex virion.
• Genome relatedness: the degree of nucleotide identity (or amino acid identity in the protein sequence) between sequences is often used to examine the relationship between different viruses or isolates. For example, recent studies in the genus Carlavirus show that when different species are compared, they have less than 73% nucleotide identity (or 80% amino acid identity) in their coat proteins.

Biological properties

• In some families, the type of host is a useful feature for classification. For example, in the family Reoviridae, there are currently 3 genera with plant-infecting members (Fijivirus, Oryzavirus, Phytoreovirus), 1 genus of mycoviruses (Mycoreovirus), 1 genus containing viruses of fish and cephalopods (Aquareovirus), two genera that are restricted to insects (Cypovirus and Entomoreovirus) and 5 genera of vertebrate viruses that sometimes also infect insects.
• The mode of transmission is also a useful characteristic of some groups of plant viruses. For example in the family Potyviridae, members of the largest genus (Potyvirus) are transmitted by aphids, while viruses in the genera Rymovirus and Tritimovirus are transmitted by mites of the genus Abacarus or Aceria respectively, those in the genus Ipomovirus are transmitted by whiteflies and those in the genus Bymovirus by plasmodiphorids (root-infecting parasites once considered to be fungi but probably more closely related to protists).

Serological properties
Many viruses are good antigens (elicit strong antibody production when purified preparations are injected into a mammal) and this property has been widely exploited to produce specific antibodies that can be used for virus detection and for examining relationships between viruses. Earlier studies used agar diffusion plates but in the last 20 years these have been largely superseded by ELISA (enzyme-linked immunosorbent assay) procedures. Although serological properties are still important, their significance in taxonomy has declined to some extent now that nucleotide sequence data are available.

Symptoms of plant virus
There are a range of symptoms depending on the disease but often there is leaf yellowing, either of the whole leaf or in a pattern of stripes or blotches, leaf distortion, example curling, and other growth distortions like for example stunting of the whole plant, abnormalities in flower or fruit formation.

Below are some of the examples of viruses in plants:

Pepper mild mottle virus

Yellow mosaic symptoms on lettuce caused by Lettuce mosaic virus

Yellow vein-banding symptoms on grapevine caused by Grapevine fanleaf virus

Fruit distortion on eggplant fruit caused by Tomato bushy stunt virus.
(A healthy fruit is shown on the left.)

Bark scaling caused by Citrus psorosis virus.

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Sometimes the virus is restricted to certain parts of the plant, example the vascular system, the discrete spots on the leaf, but in others it spreads throughout the whole plant causing a systemic infection. Infection does not always result in visible symptoms, as witnessed by names such as Carnation latent virus and Lily symptomless virus, both members of the genus Carlavirus. Occasionally, virus infection can result in symptoms of ornamental value, such as 'breaking' of tulips or variegation of Abutilon.

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Causes of plant viruses
Some animal and human viruses are spread through aerosols as they have the ‘machiney’ to enter the animal cells directly by fusing with the cell membrane, like those in the lining or gut.

In contrast, plant cells have a robust cell wall and viruses cannot penetrate them unaided. Most plant viruses are therefore transmitted by a vector organism that feeds on the plant or, in some diseases, are introduced through wounds made, for example, during cultural operations, take pruning for example. A small number of viruses can be transmitted through pollen to the seed (e.g. Barley stripe mosaic virus, genus Hordeivirus) while many that cause systemic infections accumulate in vegetatively-propagated crops. The major vectors of plant viruses are:

• Insects, this forms the largest and most significant vector group and particularly includes:
  # Aphids: transmit viruses from many different genera, including Potyvirus, Cucumovirus and Luteovirus.The picture shows the green peach aphid Myzus persicae, the vector of many plant viruses, including Potato virus Y.

• # Whiteflies: transmit viruses from several genera but particularly those in the genus Begomovirus. The picture shows Bemisia tabaci, the vector of many viruses including Tomato yellow leaf curl virus and Lettuce infectious yellows virus.

• # Hoppers: transmit viruses from several genera, including those in the families Rhabdoviridae and Reoviridae. The picture shows Micrutalis malleifera, the treehopper vector of Tomato pseudo-curly top virus.
  
  
  
  
  # Thrips: transmit viruses in the genus Tospovirus. The picture shows Frankinella occidentalis, the western flower thrips that is a major vector of Tomato spotted wilt virus.
  
  
  
  
  # Beetles: transmit viruses from several genera, including Comovirus and Sobemovirus
• Virus-vector relationships are of several types:
  - The association occurs within the feeding apparatus of the insect, where the virus can be rapidly adsorbed and then released into a different plant cell. The feeding insect looses the virus rapidly when feeding on a non-infected plant. Such a relationship is termed "non-persistent". The best studied examples are of potyvirus transmission by aphids.
  - On the other hand, the virus is taken up into the vector, circulates within the vector body and is released through the salivary glands. The vector needs to feed on an infected plant for much longer and there is an interval (perhaps several hours) before it can transmit. Once it becomes viruliferous, the vector will remain so for many days and such a relationship is therefore termed "persistent" or "circulative". The best studied examples are of luteovirus transmission by aphids. In some examples of this type like some hoppers and thrips, the virus multiplies within the vector and this is termed "propagative".
  
• # Nematodes: these are root-feeding parasites, some of which transmit viruses in the genera Nepovirus and Tobravirus. The picture shows an adult female of Paratrichodorus pachydermus, the vector of Tobacco rattle virus.
  




# Plasmodiophorids: these are root-infecting obligate parasites traditionally regarded as fungi but now known to be more closely related to protists. They transmit viruses in the genera Benyvirus, Bymovirus, Furovirus, Pecluvirus and Pomovirus. The picture shows Polymyxa graminis, the vector of several cereal viruses including Barley yellow mosaic virus, growing within a barley root cell.



# Mites: these transmit viruses in the genera Rymovirus and Tritimovirus. The picture shows Aceria tosichella, the vector of Wheat streak mosaic virus.

Prevention of plant virus
Plants virus cannot only be directly controlled by chemical application, in fact, a major means of control is needed, depending on the disease, and they includes:

• Chemical or biological control of the vector (the organism transmitting the disease, often an insect): this can be very effective where the vectors need to feed for some time on a crop before the virus is transmitted but are of much less value where transmission occurs very rapidly and may already have taken place before the vector succumbs to the pesticide.
• Growing resistant crop varieties: in some crops and for some viruses there are highly effective sources of resistance that plant breeders have been using for many years. However, no such "natural" resistance has been identified for many others. Transgenic resistance has shown considerable promise for many plant-virus combinations following the discovery that the incorporation of part of the virus genome into the host plant may confer a substantial degree of resistance. For example, the use of this approach in Hawaii to control Papaya ringspot virus has been credited with saving the local papaya industry. However, this technology is controversial, particularly in Europe, and the extent to which it will be used commercially is currently uncertain.
• Use of virus-free planting material: in vegetatively propagated crops (e.g. potatoes, many fruit crops) and where viruses are transmitted through seed major efforts are made through breeding, certification schemes etc., to ensure that the planting material is virus-free.
• Exclusion: the prevention of disease establishment in areas where it does not yet occur. This is a major objective of plant quarantine procedures throughout the world as well as more local schemes.

Virus in fungi

Introduction to bacteria in fungi
Viruses and other genetic elements are common inhabitants of fungi. As viruses have a small genome, increased virulence resulting from a chance mutation is likely. Some of the principles of this page apply to all microbes associated with the host, and some are specific to viruses.

The viruses that have been detected in fungi are all thought to be double stranded RNA. A protein coat may envelope the virion (nucleic acid). Further, some encapsulated virions are wrapped in a membrane of host origin. The observation of a single structural type, must be viewed in recognition that current searches for viruses in fungi assume a structure consisting of double stranded RNA. Other forms may be ignored. Further, some potential viruses might also be considered as transmissible genetic elements, and given a different name. Care must be taken when reading the literature on fungal viruses.

Viruses are thought to be ubiquitous in fungi. Estimates of their presence suggest that 30% of species may be colonised. Most viruses have not been associated with any form of noticeable pathology, or expression of phenotypic change, and are thought to be benign (see below for some exceptions). All viruses have been found within fungi and their existence outside the fungal host is unknown. The lack of an extracellular phase has implications for transmission.

Transmission
In those few associations where transmission has been studied, the virus is transmitted vertically or horizontally, or both

Vertical transmission refers to the movement of virions into the reproductive units of the fungus, to then be expressed in the next generation. The virions may be carried in the spores. Following germination of the spore, the virus appears in the next generation.

Horizontal transmission is where fusion between compatible hyphae results in the movement of cytoplasm containing the virions to the uninfested mycelium. The importance of vegetative compatibility cannot be overemphasised. Compatibility determines the potential for transmission, and is thus enormously important in the ecology of the virus, especially when infection is associated with disease.

Disease of mushrooms
Cultivated mushrooms have been examined for viruses especially after reductions in productivity. Although several different viruses appear to be pathogens, La France disease has been most widely studied.

The presence of an isometric particle has been consistently associated with the disease. Infected cultures grow more slowly. Basidiocarps of infected tissue appear earlier, they are smaller and commonly deformed. Total spore production is reduced though spores appear sooner. The disease is highly infectious, and rapid spread through a production system, and between adjacent farms, is possible.

The virus can be spread vertically and horizontally. Vertical spread is associated with the early appearance and release of spores from infected mushrooms. These spores anastomose with uncontaminated hyphae and transfer the virus. The virus multiplies rapidly and spreads through the contiguous mycelia.

Horizontal transmission means that only a small amount of contaminated mycelia mixed in with spawn may result in the entire bed becoming infected rapidly. Hyphae grow rapidly and establish anastomoses with compatible hyphae (most likely all the bed).

Transmission between farms is possible if they are using fungi with compatible hyphae. This is the case when farmers are using a single variety. Use of different varieties reduces the chance of transmission. However, even unrelated varieties may have a low level of compatibility, thereby enabling the occasional anastomosis and transmission of the virus. Complete incompatibility is uncommon, so virus transmission remains a potential problem for all mushroom farms.

Killer yeast
Killer Yeasts are strains that are infected with one of a group of viruses that produce a toxic protein that kills closely related but uninfected yeasts. The yeasts belong to a wide diversity of fungi, including the bread-making and alcohol-producing Saccharomyces cereviseae and the maize smut Ustilago maydis. Killer yeasts are tolerant of the toxins they produce, but may be susceptible to toxins of different Killer yeasts. The genes that confer immunity and toxin production appear to be on the virus genome. However, replication and other functional genes of the virus may be on the host nucleus.

The fitness of Killer yeasts in natural habitats is partly attributed to their toxin production. The toxin apparently regulates competition and enables the host cell to proliferate.

Killer yeasts are commonly found on fruits and flowers. They are commonly found widely on grapes. They are important for fermentation of grapes, because they may slow fermentation and leave undesirable flavours in the wine. Killer yeasts can take over fermentation by killing the inoculated yeasts, even when the concentration of killer cells is low at the beginning of the process. The potential of Killer yeasts is being examined for commercial exploitation. The capacity to add desirable fermentation characters to strains that already reduce competitors in the must is a valuable attribute. Use of killer strains may reduce the need to sterilise must at the beginning of fermentation. The sterilant, sulphur dioxide, induces asthma and allergic sinus conditions in some individuals, and is therefore seen as an undesirable though necessary additive to wine.

Pathogenesis of virus in fungi
Pathogenic viruses are only found in a few situations where the fungal population is held at artificially high levels by human intervention. This has led to the suggestion that most viruses are naturally benign. Viruses have become pathogens because chance mutations in the small genome occur at a much faster rate than in the host, and selection is for pathogens when host populations are held at high densities. In other words, disease is a function of the attempts by humans to manipulate the environment. However, the presence of Killer yeasts indicates that the interaction between virus and fungus may be more complex. Where the virus provides a beneficial function for the host, then the virus may become incorporated into the host genome. Competitors may be almost entirely replaced in a population. Thus viruses are not one functional grouping. They have attributes determined by their genome, and we will no doubt find further variants as fungi are used more extensively and intensively.

The vast majority of viruses of fungi have no noticeable effect on host phenotype. In those that modify host function, some are deleterious and others beneficial. Because viruses can be transmitted following compatible anastomoses, single genotypes remain potentially at risk of rapid spread of disease (in industry). Lack of transmission across incompatible strains limits their use in biological control of problem fungi.

Reference
http://www.microbeworld.org/microbes/virus_bacterium.aspx
http://www.cellsalive.com/phage.htm
http://en.wikipedia.org/wiki/Plant_virus
http://www.ext.colostate.edu/Ptlk/1443.html
http://www.dpvweb.net/intro/index.php
http://bugs.bio.usyd.edu.au/Mycology/UsesOf_Fungi/primaryProduction/fungiDiseases.shtml