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138-431: Baltimore classification also closely corresponds to the manner of replicating the genome, so Baltimore classification is useful for grouping viruses together for both transcription and replication. Certain subjects pertaining to viruses are associated with multiple, specific Baltimore groups, such as specific forms of translation of mRNA and the host range of different types of viruses. Structural characteristics such as

276-489: A Nobel Prize -winning biologist, devised a system called the Baltimore Classification System to classify different viruses based on their unique replication strategy. There are seven different replication strategies based on this system (Baltimore Class I, II, III, IV, V, VI, VII). The seven classes of viruses are listed here briefly and in generalities. This type of virus usually must enter

414-428: A 5' to 3' direction. The phage polymerase also has an exonuclease activity that acts in a 3' to 5' direction, and this activity is employed in the proofreading and editing of newly inserted bases. A phage mutant with a temperature sensitive DNA polymerase , when grown at permissive temperatures, was observed to undergo recombination at frequencies that are about two-fold higher than that of wild-type phage. It

552-566: A DNA strand from the ssRNA strand, and the RNA strand is degraded and replaced with a DNA strand to create a dsDNA genome. The genome is then integrated into the DNA of the host cell, where it is now called a provirus . The host cell's RNA polymerase II then transcribes RNA in the nucleus from the proviral DNA. Some of this RNA may become mRNA whereas other strands will become copies of the viral genome for replication. ssRNA-RT viruses are all included in

690-432: A Family X polymerase, is also present in mitochondria. Any mutation that leads to limited or non-functioning Pol γ has a significant effect on mtDNA and is the most common cause of autosomal inherited mitochondrial disorders. Pol γ contains a C-terminus polymerase domain and an N-terminus 3'–5' exonuclease domain that are connected via the linker region, which binds the accessory subunit. The accessory subunit binds DNA and

828-581: A PCR. The main function of DNA polymerase is to synthesize DNA from deoxyribonucleotides , the building blocks of DNA. The DNA copies are created by the pairing of nucleotides to bases present on each strand of the original DNA molecule. This pairing always occurs in specific combinations, with cytosine along with guanine , and thymine along with adenine , forming two separate pairs, respectively. By contrast, RNA polymerases synthesize RNA from ribonucleotides from either RNA or DNA. When synthesizing new DNA, DNA polymerase can add free nucleotides only to

966-522: A complex with helicase . Plants use two Family A polymerases to copy both the mitochondrial and plastid genomes. They are more similar to bacterial Pol I than they are to mammalian Pol γ. Retroviruses encode an unusual DNA polymerase called reverse transcriptase , which is an RNA-dependent DNA polymerase (RdDp) that synthesizes DNA from a template of RNA. The reverse transcriptase family contain both DNA polymerase functionality and RNase H functionality, which degrades RNA base-paired to DNA. An example of

1104-480: A copy of the original DNA molecule can be passed to each daughter cell. In this way, genetic information is passed down from generation to generation. Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form, in the process breaking the hydrogen bonds between the nucleotide bases . This opens up or "unzips" the double-stranded DNA to give two single strands of DNA that can be used as templates for replication in

1242-413: A few exceptions and peculiarities exist. The family Anelloviridae is the only ssDNA family whose members have negative sense genomes, which are circular. Parvoviruses, as previously mentioned, may package either the positive or negative sense strand into virions. Lastly, bidnaviruses package both the positive and negative linear strands. In any case, the sense of ssDNA viruses, unlike for ssRNA viruses,

1380-436: A gap in one strand, which is repaired to create a complete dsDNA genome prior to transcription. dsDNA-RT viruses are transcribed in the same manner as dsDNA viruses, but make use of reverse transcription to replicate their circular genome while it is still in the capsid. The host cell's RNA polymerase II transcribes RNA strands from the genome in the cytoplasm, and the genome is replicated from these RNA strands. The dsDNA genome

1518-536: A heterodimer that interacts with UmuC, which in turn activates umuC's polymerase catalytic activity on damaged DNA. In E. coli , a polymerase "tool belt" model for switching pol III with pol IV at a stalled replication fork, where both polymerases bind simultaneously to the β-clamp, has been proposed. However, the involvement of more than one TLS polymerase working in succession to bypass a lesion has not yet been shown in E. coli . Moreover, Pol IV can catalyze both insertion and extension with high efficiency, whereas pol V

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1656-404: A high level of processivity. The main role of Pol II is thought to be the ability to direct polymerase activity at the replication fork and help stalled Pol III bypass terminal mismatches. Pfu DNA polymerase is a heat-stable enzyme of this family found in the hyperthermophilic archaeon Pyrococcus furiosus . Detailed classification divides family B in archaea into B1, B2, B3, in which B2

1794-429: A high rate of RF turnover when in excess, but remains stably associated with replication forks when concentration is limiting. Another single-molecule study showed that DnaB helicase activity and strand elongation can proceed with decoupled, stochastic kinetics. In E. coli , DNA polymerase IV (Pol IV) is an error-prone DNA polymerase involved in non-targeted mutagenesis. Pol IV is a Family Y polymerase expressed by

1932-434: A host cell and initiates replication by hijacking the host's cellular machinery to make new copies of the virus. In the lysogenic life cycle, the viral genome is incorporated into the host genome. The host genome will undergo its normal life cycle, replicating and dividing replicating the viral genome along with its own. The viral genome can be triggered to begin viral production via chemical and environmental stimulants. Once

2070-407: A loop around the circular genome is also common. Some dsDNA viruses use a strand displacement method whereby one strand is synthesized from a template strand, and a complementary strand is then synthesized from the prior synthesized strand, forming a dsDNA genome. Lastly, some dsDNA viruses are replicated as part of a process called replicative transposition whereby a viral genome in a host cell's DNA

2208-408: A lysogenic virus enters the lytic life cycle, it will continue in the viral production pathways and proceed with transcription / mRNA production. (ex: Cold sores, herpes simplex virus (HSV)-1, lysogenic bacteriophages, etc.) Assembly is when the newly manufactured viral proteins and genomes are gathered and put together to form immature viruses. Like the other steps, how a particular virus is assembled

2346-429: A molecule (in this case a virus) binds to receptor on the membrane of the cell. A series of chemical signals from this binding causes the cell to wrap the attached virus in the plasma membrane around it forming a virus-containing vesicle inside the cell. Viruses enter host cells using a variety of mechanisms, including the endocytic and non-endocytic routes. They can also fuse at the plasma membrane and can spread within

2484-405: A negative sense, single-stranded RNA (-ssRNA) genome. mRNA, which is positive sense, is transcribed directly from the negative sense genome. The first process for -ssRNA transcription involves RdRp binding to a leader sequence on the 3′ end of the genome, transcribing a 5′ triphosphate-leader RNA that is capped, then stopping and restarting on a transcription signal which is capped , continuing until

2622-439: A nucleotide not included in the template strand. Editing of a genomic template would impair gene expression, so RNA editing is only done during and after transcription. For ebola viruses , RNA editing improves the ability to adapt to their hosts. Alternative splicing differs from RNA editing in that alternative splicing does not change the mRNA sequence like RNA editing but instead changes the coding capacity of an mRNA sequence as

2760-443: A portion of their genome transcribed. Typically, subgenomic RNA (sgRNA) strands are used for translation of structural and movement proteins needed during intermediate and late stages of infection. sgRNA transcription may occur by commencing RNA synthesis within the genome rather than from the 5′-end, by stopping RNA synthesis at specific sequences in the genome, or by, as a part of both prior methods, synthesizing leader sequences from

2898-419: A realm. The first Baltimore group contains viruses that have a double-stranded DNA (dsDNA) genome. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a transcription preinitiation complex binds to the DNA upstream of the site where transcription begins, allowing for the recruitment of a host RNA polymerase . Second, once the RNA polymerase is recruited, it uses the negative strand as

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3036-429: A realm. The realms Adnaviria and Duplodnaviria exclusively contains dsDNA viruses, Monodnaviria primarily contains ssDNA viruses but also contains dsDNA viruses, and Varidnaviria exclusively contains dsDNA viruses, although some proposed members of Varidnaviria , namely the family Finnlakeviridae , are ssDNA viruses. Viral replication Viral replication is the formation of biological viruses during

3174-451: A result of alternative splicing sites. The two mechanisms otherwise have the same result: multiple proteins are expressed from a single gene. Translation is the process by which proteins are synthesized from mRNA by ribosomes . Baltimore groups do not directly pertain to the translation of viral proteins, but various atypical types of translation used by viruses are usually found within specific Baltimore groups: Baltimore classification

3312-517: A retrovirus is HIV . Reverse transcriptase is commonly employed in amplification of RNA for research purposes. Using an RNA template, PCR can utilize reverse transcriptase, creating a DNA template. This new DNA template can then be used for typical PCR amplification. The products of such an experiment are thus amplified PCR products from RNA. Each HIV retrovirus particle contains two RNA genomes , but, after an infection, each virus generates only one provirus . After infection, reverse transcription

3450-411: A single original DNA duplex. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones. These enzymes catalyze the chemical reaction DNA polymerase adds nucleotides to the three prime (3') -end of a DNA strand, one nucleotide at a time. Every time a cell divides , DNA polymerases are required to duplicate the cell's DNA, so that

3588-496: A single pre-mRNA strand or for other specific purposes. For certain viruses, including the families Orthomyxoviridae and Papillomaviridae , alternative splicing acts as a way to regulate early and late gene expression during different stages of infection. Herpesviruses use it as a potential anti-host defense mechanism to prevent synthesis of specific antiviral proteins. Furthermore, in addition to alternative splicing, because cellular unspliced RNA cannot be transported out of

3726-495: A single virion so that the whole genome is in one virus particle, and the separate segments contain different genes. Monopartite viruses are found in all Baltimore groups, whereas multipartite viruses are usually RNA viruses. This is because most multipartite viruses infect plants or fungi, which are eukaryotes, and most eukaryotic viruses are RNA viruses. The family Pleolipoviridae varies as some viruses are monopartite ssDNA while others are bipartite with one segment being ssDNA and

3864-420: A single, long open reading frame (ORF), or translatable portion, and a site-specific nick in the 5′ region of the positive strand. dsRNA viruses are classified into two phyla within the kingdom Orthornavirae of the realm Riboviria : The fourth Baltimore group contains viruses that have a positive sense single-stranded RNA (+ssRNA) genome. For +ssRNA viruses, the genome functions as mRNA, so no transcription

4002-408: A stop signal is reached. The second manner is similar but instead of synthesizing a cap, RdRp may make use of cap snatching , whereby a short sequence of host cell mRNA is taken and used as the 5′ cap of the viral mRNA. Genomic -ssRNA is replicated from the positive sense antigenome in a similar manner as transcription, except in reverse using the antigenome as a template for the genome. RdRp moves from

4140-494: A template for production of viral mRNAs and a subgenomic RNA. The pregenome RNA serves as template for the viral reverse transcriptase and for production of the DNA genome. DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates , the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from

4278-476: A template for synthesizing mRNA strands. Third, the RNA polymerase terminates transcription upon reaching a specific signal, such as a polyadenylation site. dsDNA viruses make use of several mechanisms to replicate their genome. Bidirectional replication, in which two replication forks are established at a replication origin site and move in opposite directions of each other, is widely used. A rolling circle mechanism that produces linear strands while progressing in

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4416-463: Is ligated into a circular loop. The new ssDNA may be packaged into virions or replicated by a DNA polymerase to form a double-stranded form for transcription or continuation of the replication cycle. Parvoviruses contain linear ssDNA genomes that are replicated via rolling hairpin replication (RHR), which is similar to RCR. Parvovirus genomes have hairpin loops at each end of the genome that repeatedly unfold and refold during replication to change

4554-405: Is a group of pseudoenzymes . Pfu belongs to family B3. Others PolBs found in archaea are part of "Casposons", Cas1 -dependent transposons. Some viruses (including Φ29 DNA polymerase ) and mitochondrial plasmids carry polB as well. DNA polymerase III holoenzyme is the primary enzyme involved in DNA replication in E. coli and belongs to family C polymerases. It consists of three assemblies:

4692-503: Is a heat-stable enzyme of this family that lacks proofreading ability. DNA polymerase II is a family B polymerase encoded by the polB gene. Pol II has 3'–5' exonuclease activity and participates in DNA repair , replication restart to bypass lesions, and its cell presence can jump from ~30-50 copies per cell to ~200–300 during SOS induction. Pol II is also thought to be a backup to Pol III as it can interact with holoenzyme proteins and assume

4830-629: Is a heterodimer of two chains, each encoded by DP1 (small proofreading) and DP2 (large catalytic). Unlike other DNA polymerases, the structure and mechanism of the DP2 catalytic core resemble that of multi-subunit RNA polymerases . The DP1-DP2 interface resembles that of Eukaryotic Class B polymerase zinc finger and its small subunit. DP1, a Mre11 -like exonuclease, is likely the precursor of small subunit of Pol α and ε , providing proofreading capabilities now lost in Eukaryotes. Its N-terminal HSH domain

4968-399: Is a property of some, but not all DNA polymerases. This process corrects mistakes in newly synthesized DNA. When an incorrect base pair is recognized, DNA polymerase moves backwards by one base pair of DNA. The 3'–5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading ). Following base excision, the polymerase can re-insert

5106-565: Is a seven-subunit (τ2γδδ ′ χψ) clamp loader complex. The old textbook "trombone model" depicts an elongation complex with two equivalents of the core enzyme at each replication fork (RF), one for each strand, the lagging and leading. However, recent evidence from single-molecule studies indicates an average of three stoichiometric equivalents of core enzyme at each RF for both Pol III and its counterpart in B. subtilis, PolC. In-cell fluorescent microscopy has revealed that leading strand synthesis may not be completely continuous, and Pol III* (i.e.,

5244-414: Is accompanied by template switching between the two genome copies (copy choice recombination). From 5 to 14 recombination events per genome occur at each replication cycle. Template switching (recombination) appears to be necessary for maintaining genome integrity and as a repair mechanism for salvaging damaged genomes. Bacteriophage (phage) T4 encodes a DNA polymerase that catalyzes DNA synthesis in

5382-654: Is also one of the most-studied types of viruses, alongside the double-stranded DNA viruses. The positive-sense RNA viruses and indeed all genes defined as positive-sense can be directly accessed by host ribosomes to immediately form proteins. These can be divided into two groups, both of which replicate in the cytoplasm: Examples of this class include the families Coronaviridae , Flaviviridae , and Picornaviridae . The negative-sense RNA viruses and indeed all genes defined as negative-sense cannot be directly accessed by host ribosomes to immediately form proteins. Instead, they must be transcribed by viral polymerases into

5520-408: Is an RNA-dependent DNA polymerase (RdDp). It polymerizes DNA from a template of RNA . Prokaryotic polymerases exist in two forms: core polymerase and holoenzyme. Core polymerase synthesizes DNA from the DNA template but it cannot initiate the synthesis alone or accurately. Holoenzyme accurately initiates synthesis. Prokaryotic family A polymerases include the DNA polymerase I (Pol I) enzyme, which

5658-420: Is chiefly based on the transcription of the viral genome, and viruses within each group typically share the manners by which the mRNA synthesis occurs. While not the direct focus of Baltimore classification, groups are organized in such a manner that viruses in each group also typically have the same mechanisms of replicating the viral genome. Because of this, Baltimore classification provides insights into both

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5796-478: Is considered the major SOS TLS polymerase. One example is the bypass of intra strand guanine thymine cross-link where it was shown on the basis of the difference in the mutational signatures of the two polymerases, that pol IV and pol V compete for TLS of the intra-strand crosslink. In 1998, the family D of DNA polymerase was discovered in Pyrococcus furiosus and Methanococcus jannaschii . The PolD complex

5934-530: Is dependent on what type of virus it is. Assembly can occur in the plasma membrane, cytosol, nucleus, golgi apparatus, and other locations within the host cell. Some viruses only insert their genome into a capsid once the capsid is completed, while in other viruses the will capsid will wrap around the genome as it is being copied. This is the final step before a competent virus is formed. This typically involves capsid modifications that are provided enzymes (host or virus-encoded). The final step in viral replication

6072-524: Is divided into two subphyla: Haploviricotina , whose members synthesize a cap structure on viral mRNA required for protein synthesis, and Polyploviricotina , whose members instead obtain caps on mRNA via cap snatching. Reverse transcribing (RT) viruses have genomes made of either DNA or RNA and replicate via reverse transcription. Two groups of reverse transcribing viruses exist: single-stranded RNA-RT (ssRNA-RT) viruses, and double-stranded DNA-RT (dsDNA-RT) viruses. Reverse transcribing viruses are classified in

6210-435: Is encoded by the polA gene and ubiquitous among prokaryotes . This repair polymerase is involved in excision repair with both 3'–5' and 5'–3' exonuclease activity and processing of Okazaki fragments generated during lagging strand synthesis. Pol I is the most abundant polymerase, accounting for >95% of polymerase activity in E. coli ; yet cells lacking Pol I have been found suggesting Pol I activity can be replaced by

6348-404: Is evidenced by the fact that gene encoding DNA polymerase η is referred as XPV, because loss of this gene results in the disease Xeroderma Pigmentosum Variant. Pol η is particularly important for allowing accurate translesion synthesis of DNA damage resulting from ultraviolet radiation . The functionality of Pol κ is not completely understood, but researchers have found two probable functions. Pol κ

6486-596: Is experienced. However, although the different mismatches result in different steric properties, DNA polymerase is still able to detect and differentiate them so uniformly and maintain fidelity in DNA replication. DNA polymerization is also critical for many mutagenesis processes and is widely employed in biotechnologies. The known DNA polymerases have highly conserved structure, which means that their overall catalytic subunits vary very little from species to species, independent of their domain structures. Conserved structures usually indicate important, irreplaceable functions of

6624-400: Is initiated by an endonuclease that bonds to and cleaves the positive strand, allowing a DNA polymerase to use the negative strand as a template for replication. Replication progresses in a loop around the genome by means of extending the 3′-end of the positive strand, displacing the prior positive strand, and the endonuclease cleaves the positive strand again to create a standalone genome that

6762-776: Is made of two subunits Rev3 , the catalytic subunit, and Rev7 ( MAD2L2 ), which increases the catalytic function of the polymerase, and is involved in translesion synthesis. Pol ζ lacks 3' to 5' exonuclease activity, is unique in that it can extend primers with terminal mismatches. Rev1 has three regions of interest in the BRCT domain , ubiquitin-binding domain , and C-terminal domain and has dCMP transferase ability, which adds deoxycytidine opposite lesions that would stall replicative polymerases Pol δ and Pol ε. These stalled polymerases activate ubiquitin complexes that in turn disassociate replication polymerases and recruit Pol ζ and Rev1. Together Pol ζ and Rev1 add deoxycytidine and Pol ζ extends past

6900-428: Is normally used to facilitate adhesion between other host cells. Entry, or penetration, is the second step in viral replication. This step is characterized by the virus passing through the plasma membrane of the host cell. The most common way a virus gains entry to the host cell is by receptor-mediated endocytosis , which comes at no energy cost to the virus, only the host cell. Receptor-mediated endocytosis occurs when

7038-556: Is not sufficient to separate ssDNA viruses into two groups since all ssDNA viral genomes are converted to dsDNA forms prior to transcription and replication. ssDNA viruses are classified into one of the four realms and include several families that are unassigned to a realm: RNA viruses have genomes made of ribonucleic acid (RNA) and comprise three groups: double-stranded RNA (dsRNA) viruses, positive sense single-stranded RNA (+ssRNA) viruses, and negative sense single-stranded RNA (-ssRNA) viruses. The majority of RNA viruses are classified in

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7176-440: Is produced from pregenomic RNA strands via the same general mechanism as ssRNA-RT viruses, but with replication occurring in a loop around the circular genome. After replication, the dsDNA genome may be packed or sent to the nucleus for further rounds of transcription. dsDNA-RT viruses are, like ssRNA-RT, all included in the class Revtraviricetes . Two families of dsDNA-RT viruses are recognized: Caulimoviridae , which belongs to

7314-413: Is release, which is when the newly assembled and mature viruses leave the host cell. How a virus releases from the host cell is dependent on the type of virus it is. One common type of release is budding. This occurs when viruses that form their envelope from the host's plasma membrane bend the membrane around the capsid. As the virus bends the plasma membrane it begins to wrap around the whole capsid until

7452-462: Is replicated to another part of a host genome. dsDNA viruses can be subdivided between those that replicate in the nucleus, and as such are relatively dependent on host cell machinery for transcription and replication, and those that replicate in the cytoplasm, in which case they have evolved or acquired their own means of executing transcription and replication. dsDNA viruses are also commonly divided between tailed dsDNA viruses, referring to members of

7590-508: Is required for processivity of Pol γ. Point mutation A467T in the linker region is responsible for more than one-third of all Pol γ-associated mitochondrial disorders. While many homologs of Pol θ, encoded by the POLQ gene, are found in eukaryotes, its function is not clearly understood. The sequence of amino acids in the C-terminus is what classifies Pol θ as Family A polymerase, although

7728-431: Is required for translation. +ssRNA viruses will also, however, produce positive sense copies of the genome from negative sense strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. The 5′-end may be naked, capped, or covalently bound to a viral protein, and the 3′-end may be naked or polyadenylated. Many +ssRNA viruses are able to have only

7866-566: Is similar to AAA proteins , especially Pol III subunit δ and RuvB , in structure. DP2 has a Class II KH domain . Pyrococcus abyssi polD is more heat-stable and more accurate than Taq polymerase, but has not yet been commercialized. It has been proposed that family D DNA polymerase was the first to evolve in cellular organisms and that the replicative polymerase of the Last Universal Cellular Ancestor (LUCA) belonged to family D. Family X polymerases contain

8004-435: Is then transferred into the cytoplasm. Cell-to-cell fusion: Some viruses prompt specific protein expression on the surfaces of infected cells to attract uninfected cells. This interaction causes the uninfected cell to fuse with the infected cell at lower pH levels to form a multinuclear cell known as a syncytium. Endocytic routes: the process by which an intracellular vesicle is formed by membrane invagination, which results in

8142-437: Is thought to act as an extender or an inserter of a specific base at certain DNA lesions. All three translesion synthesis polymerases, along with Rev1, are recruited to damaged lesions via stalled replicative DNA polymerases. There are two pathways of damage repair leading researchers to conclude that the chosen pathway depends on which strand contains the damage, the leading or lagging strand. Pol ζ another B family polymerase,

8280-667: Is thought to provide a checkpoint before entering anaphase, provide stability to the holoenzyme, and add proteins to the holoenzyme necessary for initiation of replication. Pol ε has a larger "palm" domain that provides high processivity independently of PCNA. Compared to other Family B polymerases, the DEDD exonuclease family responsible for proofreading is inactivated in Pol α. Pol ε is unique in that it has two zinc finger domains and an inactive copy of another family B polymerase in its C-terminal. The presence of this zinc finger has implications in

8418-489: Is to perform translesion synthesis at the stalled replication fork like, for example, bypassing N2-deoxyguanine adducts at a faster rate than transversing undamaged DNA. Cells lacking the dinB gene have a higher rate of mutagenesis caused by DNA damaging agents. DNA polymerase V (Pol V) is a Y-family DNA polymerase that is involved in SOS response and translesion synthesis DNA repair mechanisms. Transcription of Pol V via

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8556-436: The 3' end of the newly forming strand. This results in elongation of the newly forming strand in a 5'–3' direction. It is important to note that the directionality of the newly forming strand (the daughter strand) is opposite to the direction in which DNA polymerase moves along the template strand. Since DNA polymerase requires a free 3' OH group for initiation of synthesis, it can synthesize in only one direction by extending

8694-691: The Circoviridae and Parvoviridae . They replicate within the nucleus, and form a double-stranded DNA intermediate during replication. A human Anellovirus called TTV is included within this classification and is found in almost all humans, infecting them asymptomatically in nearly every major organ . RNA viruses: The polymerase of RNA viruses lacks the proofreading functions found in the polymerase of DNA viruses. This contributed to RNA viruses having lower replicative fidelity compared to DNA viruses, causing RNA viruses to be highly mutagenic, which can increase their overall survival rate. RNA viruses lack

8832-518: The POLL and POLM genes respectively, are involved in non-homologous end-joining , a mechanism for rejoining DNA double-strand breaks due to hydrogen peroxide and ionizing radiation, respectively. TdT is expressed only in lymphoid tissue, and adds "n nucleotides" to double-strand breaks formed during V(D)J recombination to promote immunological diversity. Pol α (alpha) , Pol δ (delta) , and Pol ε (epsilon) are members of Family B Polymerases and are

8970-511: The Reoviridae and Birnaviridae . Replication is monocistronic and includes individual, segmented genomes, meaning that each of the genes codes for only one protein, unlike other viruses, which exhibit more complex translation. These viruses consist of two types, however both share the fact that replication is primarily in the cytoplasm, and that replication is not as dependent on the cell cycle as that of DNA viruses. This class of viruses

9108-415: The dinB gene that is switched on via SOS induction caused by stalled polymerases at the replication fork. During SOS induction, Pol IV production is increased tenfold and one of the functions during this time is to interfere with Pol III holoenzyme processivity. This creates a checkpoint, stops replication, and allows time to repair DNA lesions via the appropriate repair pathway. Another function of Pol IV

9246-442: The energy and synthetic machinery and the low-molecular-weight precursors for the synthesis of viral proteins and nucleic acids. Virus replication occurs in seven stages: It is the first step of viral replication. Some viruses attach to the cell membrane of the host cell and inject its DNA or RNA into the host to initiate infection. Attachment to a host cell is often achieved by a virus attachment protein that extends from

9384-427: The nucleoside triphosphates with the template base. The thumb domain plays a potential role n the processivity, translocation, and positioning of the DNA. DNA polymerase's rapid catalysis due to its processive nature. Processivity is a characteristic of enzymes that function on polymeric substrates. In the case of DNA polymerase, the degree of processivity refers to the average number of nucleotides added each time

9522-399: The replication fork . This increase is facilitated by the DNA polymerase's association with proteins known as the sliding DNA clamp . The clamps are multiple protein subunits associated in the shape of a ring. Using the hydrolysis of ATP, a class of proteins known as the sliding clamp loading proteins open up the ring structure of the sliding DNA clamps allowing binding to and release from

9660-531: The umuDC genes is highly regulated to produce only Pol V when damaged DNA is present in the cell generating an SOS response. Stalled polymerases causes RecA to bind to the ssDNA, which causes the LexA protein to autodigest. LexA then loses its ability to repress the transcription of the umuDC operon. The same RecA-ssDNA nucleoprotein posttranslationally modifies the UmuD protein into UmuD' protein. UmuD and UmuD' form

9798-449: The "readable" complementary positive-sense. These can also be divided into two groups: Examples in this class include the families Orthomyxoviridae , Paramyxoviridae , Bunyaviridae , Filoviridae , and Rhabdoviridae (which includes rabies ). A well-studied family of this class of viruses include the retroviruses . One defining feature is the use of reverse transcriptase to convert the positive-sense RNA into DNA. Instead of using

9936-490: The 1990s to the 2010s, virus taxonomy used a 5-rank system ranging from order to species with Baltimore classification used in conjunction. Outside of the ICTV's official framework, various supergroups of viruses joining different families and orders were created over time based on increasing evidence of deeper evolutionary relations. Consequently, in 2016, the ICTV began to consider establishing ranks higher than order as well as how

10074-460: The 3' end of chromosome ends. The gradual decrease in size of telomeres as the result of many replications over a lifetime are thought to be associated with the effects of aging. Pol γ (gamma), Pol θ (theta), and Pol ν (nu) are Family A polymerases. Pol γ, encoded by the POLG gene, was long thought to be the only mitochondrial polymerase. However, recent research shows that at least Pol β (beta) ,

10212-467: The 3' end of the preexisting nucleotide chain. Hence, DNA polymerase moves along the template strand in a 3'–5' direction, and the daughter strand is formed in a 5'–3' direction. This difference enables the resultant double-strand DNA formed to be composed of two DNA strands that are antiparallel to each other. The function of DNA polymerase is not quite perfect, with the enzyme making about one mistake for every billion base pairs copied. Error correction

10350-414: The 3′-end of the mRNA. Additionally, some -ssRNA viruses are ambisense, as both the positive and negative strands separately encode viral proteins, and these viruses produce two separate mRNA strands: one directly from the genome and one from a complementary strand. -ssRNA viruses can be subdivided informally between those that have nonsegmented and segmented genomes. Nonsegmented -ssRNA viruses replicate in

10488-476: The 3′-end to the 5′-end of the antigenome and ignores all transcription signals when synthesizing genomic -ssRNA. Various -ssRNA viruses use special mechanisms for transcription. The manner of producing the polyA tail may be via polymerase stuttering , during which RdRp transcribes an adenine from uracil and then moves back in the RNA sequence with the mRNA to transcribe it again, continuing this process numerous times until hundreds of adenines have been added to

10626-505: The Baltimore groups would be treated among higher taxa. In two votes in 2018 and 2019, a 15-rank system ranging from realm to species was established by the ICTV. As part of this, the Baltimore groups for RNA viruses and RT viruses were incorporated into formal taxa. In 2018, the realm Riboviria was established and initially included the three RNA virus groups. A year later, Riboviria was expanded to also include both RT groups. Within

10764-418: The DNA strand. Protein–protein interaction with the clamp prevents DNA polymerase from diffusing from the DNA template, thereby ensuring that the enzyme binds the same primer/template junction and continues replication. DNA polymerase changes conformation, increasing affinity to the clamp when associated with it and decreasing affinity when it completes the replication of a stretch of DNA to allow release from

10902-475: The DNA-polymerase interactions. One motif is located in the 8 kDa domain that interacts with downstream DNA and one motif is located in the thumb domain that interacts with the primer strand. Pol β, encoded by POLB gene, is required for short-patch base excision repair , a DNA repair pathway that is essential for repairing alkylated or oxidized bases as well as abasic sites . Pol λ and Pol μ, encoded by

11040-463: The RNA for templates of proteins, they use DNA to create the templates, which is spliced into the host genome using integrase . Replication can then commence with the help of the host cell's polymerases. This small group of viruses, exemplified by the Hepatitis B virus, have a double-stranded, gapped genome that is subsequently filled in to form a covalently closed circle ( cccDNA ) that serves as

11178-659: The above reaction. In 1956, Arthur Kornberg and colleagues discovered DNA polymerase I (Pol I), in Escherichia coli . They described the DNA replication process by which DNA polymerase copies the base sequence of a template DNA strand. Kornberg was later awarded the Nobel Prize in Physiology or Medicine in 1959 for this work. DNA polymerase II was discovered by Thomas Kornberg (the son of Arthur Kornberg ) and Malcolm E. Gefter in 1970 while further elucidating

11316-423: The capacity to identify and repair mismatched or damaged nucleotides, and thus, RNA genomes are prone to mutations introduced by mechanisms intrinsic and extrinsic to viral replication. RNA viruses present a therapeutic double-edged sword: RNA viruses can withstand the challenge of antiviral drugs, cause epidemics, and infect multiple host species due to their mutagenic nature, making them difficult to treat. However,

11454-676: The cell to forcefully undergo cell division , which may lead to transformation of the cell and, ultimately, cancer . An example of a family within this classification is the Adenoviridae . There is only one well-studied example in which a class 1 family of viruses does not replicate within the nucleus. This is the Poxvirus family, which comprises highly pathogenic viruses that infect vertebrates . Viruses that fall under this category include ones that are not as well-studied, but still do pertain highly to vertebrates. Two examples include

11592-443: The cell, the maintenance of which provides evolutionary advantages. The shape can be described as resembling a right hand with thumb, finger, and palm domains. The palm domain appears to function in catalyzing the transfer of phosphoryl groups in the phosphoryl transfer reaction. DNA is bound to the palm when the enzyme is active. This reaction is believed to be catalyzed by a two-metal-ion mechanism. The finger domain functions to bind

11730-409: The clamp. DNA polymerase processivity has been studied with in vitro single-molecule experiments (namely, optical tweezers and magnetic tweezers ) have revealed the synergies between DNA polymerases and other molecules of the replisome ( helicases and SSBs ) and with the DNA replication fork. These results have led to the development of synergetic kinetic models for DNA replication describing

11868-479: The class Revtraviricetes , phylum Arterviricota , kingdom Pararnavirae of the realm Riboviria . Excluding Caulimoviridae , which belongs to Group VII, all members of the Revtraviricetes order Ortervirales are ssRNA-RT viruses. The seventh Baltimore group contains viruses that have a double-stranded DNA genome that has an RNA intermediate (dsDNA-RT) in its replication cycle. dsDNA-RT viruses have

12006-429: The correct base and replication can continue forwards. This preserves the integrity of the original DNA strand that is passed onto the daughter cells. Fidelity is very important in DNA replication. Mismatches in DNA base pairing can potentially result in dysfunctional proteins and could lead to cancer. Many DNA polymerases contain an exonuclease domain, which acts in detecting base pair mismatches and further performs in

12144-469: The cytoplasm, and segmented -ssRNA viruses replicate in the nucleus. During transcription, the RdRp produces one monocistronic mRNA strand from each segment of the genome. All -ssRNA viruses are classified in the phylum Negarnaviricota in the kingdom Orthornavirae in the realm Riboviria . Negarnaviricota only contains -ssRNA viruses, so "-ssRNA virus" is synonymous with Negarnaviricota . Negarnaviricota

12282-400: The direction of DNA synthesis to move back and forth along the genome, producing numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the viral endonuclease. For parvoviruses, either the positive or negative sense strand may be packaged into capsids, varying from virus to virus. Nearly all ssDNA viruses have positive sense genomes, but

12420-452: The dsDNA family Sphaerolipoviridae , and in the family Pleolipoviridae , viruses contain both linear and circular genomes, varying from genus to genus. RNA editing is used by various ssRNA viruses to produce different proteins from a single gene. This can be done via polymerase slippage during transcription or by post-transcriptional editing. In polymerase slippage, the RNA polymerase slips one nucleotide back during transcription, inserting

12558-433: The ends, or telomeres . The single-strand 3' overhang of the double-strand chromosome with the sequence 5'-TTAGGG-3' recruits telomerase. Telomerase acts like other DNA polymerases by extending the 3' end, but, unlike other DNA polymerases, telomerase does not require a template. The TERT subunit, an example of a reverse transcriptase , uses the RNA subunit to form the primer–template junction that allows telomerase to extend

12696-437: The engulfment of extracellular and membrane-bound components, in this context, a virus. Non-endocytic routes: the process by which viral particles are released into the cell by fusion of the extracellular viral envelope and the membrane of the host cell. Uncoating is the third step in viral replication. Uncoating is defined by the removal of the virion's protein "coat" and the release of its genetic material. This step occurs in

12834-419: The enzyme binds a template. The average DNA polymerase requires about one second locating and binding a primer/template junction. Once it is bound, a nonprocessive DNA polymerase adds nucleotides at a rate of one nucleotide per second. Processive DNA polymerases, however, add multiple nucleotides per second, drastically increasing the rate of DNA synthesis. The degree of processivity is directly proportional to

12972-521: The error rate for Pol θ is more closely related to Family Y polymerases. Pol θ extends mismatched primer termini and can bypass abasic sites by adding a nucleotide. It also has Deoxyribophosphodiesterase (dRPase) activity in the polymerase domain and can show ATPase activity in close proximity to ssDNA. Pol ν (nu) is considered to be the least effective of the polymerase enzymes. However, DNA polymerase nu plays an active role in homology repair during cellular responses to crosslinks, fulfilling its role in

13110-408: The function of Pol ε is to extend the leading strand during replication, while Pol δ primarily replicates the lagging strand; however, recent evidence suggested that Pol δ might have a role in replicating the leading strand of DNA as well. Pol ε's C-terminus "polymerase relic" region, despite being unnecessary for polymerase activity, is thought to be essential to cell vitality. The C-terminus region

13248-414: The genome is linear or circular, and different methods of translating viral mRNA. Alternative splicing is a mechanism by which different proteins can be produced from a single gene by means of using alternative splicing sites to produce different mRNAs. It is found in various DNA, -ssRNA, and reverse transcribing viruses. Viruses may make use of alternative splicing solely to produce multiple proteins from

13386-513: The genome is single-stranded, however, it is first made into a double-stranded form by a DNA polymerase upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome. Eukaryotic ssDNA viruses are replicated in the nucleus. Most ssDNA viruses contain circular genomes that are replicated via rolling circle replication (RCR). ssDNA RCR

13524-519: The holoenzyme α, ε, τ, δ and χ subunits without the ß2 sliding clamp) has a high frequency of dissociation from active RFs. In these studies, the replication fork turnover rate was about 10s for Pol III*, 47s for the ß2 sliding clamp, and 15m for the DnaB helicase. This suggests that the DnaB helicase may remain stably associated at RFs and serve as a nucleation point for the competent holoenzyme. In vitro single-molecule studies have shown that Pol III* has

13662-406: The host nucleus before it is able to replicate. Some of these viruses require host cell polymerases to replicate their genome , while others, such as adenoviruses or herpes viruses, encode their own replication factors. However, in either case, replication of the viral genome is highly dependent on a cellular state permissive to DNA replication and, thus, on the cell cycle . The virus may induce

13800-415: The host cell's cytoplasm. mRNA is forced out from the capsid in order to be translated or to be translocated from a mature capsid to a progeny capsid. While dsRNA viruses typically have capsids, viruses in the families Amalgaviridae and Endornaviridae have not been observed to form virions and as such apparently lack capsids. Endornaviruses are also unusual in that unlike other RNA viruses, they possess

13938-449: The host via fusion or cell-cell fusion. Viruses attach to proteins on the host cell surface known as cellular receptors or attachment factors to aid entry. Evidence shows that viruses utilize ion channels on the host cells during viral entry. Fusion: External viral proteins promote the fusion of the virion with the plasma membrane. This forms a pore in the host membrane, and after entry, the virion becomes uncoated, and its genomic material

14076-511: The infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome and packaging these copies, the virus continues infecting new hosts. Replication between viruses is greatly varied and depends on the type of genes involved in them. Most DNA viruses assemble in the nucleus while most RNA viruses develop solely in cytoplasm. Viruses multiply only in living cells. The host cell must provide

14214-399: The kingdom Orthornavirae in the realm Riboviria . The exceptions are generally viroids and other subviral agents . Some of the latter category, such as the hepatitis D virus , are classified in the realm Ribozyviria . The third Baltimore group contains viruses that have a double-stranded RNA (dsRNA) genome. After entering a host cell, the dsRNA genome is transcribed to mRNA from

14352-453: The kingdom Pararnavirae in the realm Riboviria . The sixth Baltimore group contains viruses that have a (positive-sense) single-stranded RNA genome that has a DNA intermediate ((+)ssRNA-RT) in its replication cycle. ssRNA-RT viruses are transcribed in the same manner as DNA viruses, but their linear genomes are first converted to a dsDNA form through a process called reverse transcription . The viral reverse transcriptase enzyme synthesizes

14490-474: The leading and lagging strand synthesis from Pol α. Pol δ is expressed by genes POLD1 , creating the catalytic subunit, POLD2 , POLD3 , and POLD4 creating the other subunits that interact with Proliferating Cell Nuclear Antigen (PCNA), which is a DNA clamp that allows Pol δ to possess processivity. Pol ε is encoded by the POLE1 , the catalytic subunit, POLE2 , and POLE3 gene. It has been reported that

14628-500: The lesion. Through a yet undetermined process, Pol ζ disassociates and replication polymerases reassociate and continue replication. Pol ζ and Rev1 are not required for replication, but loss of REV3 gene in budding yeast can cause increased sensitivity to DNA-damaging agents due to collapse of replication forks where replication polymerases have stalled. Telomerase is a ribonucleoprotein which functions to replicate ends of linear chromosomes since normal DNA polymerase cannot replicate

14766-447: The main cytoplasmic area of the cell. +ssRNA viruses can be subdivided between those that have polycistronic mRNA, which encodes a polyprotein that is cleaved to form multiple mature proteins, and those that produce subgenomic mRNAs and therefore undergo two or more rounds of translation. +ssRNA viruses are included in three phyla in the kingdom Orthornavirae in the realm Riboviria : The fifth Baltimore group contains viruses that have

14904-429: The main polymerases involved with nuclear DNA replication. Pol α complex (pol α-DNA primase complex) consists of four subunits: the catalytic subunit POLA1 , the regulatory subunit POLA2 , and the small and the large primase subunits PRIM1 and PRIM2 respectively. Once primase has created the RNA primer, Pol α starts replication elongating the primer with ~20 nucleotides. Due to its high processivity, Pol δ takes over

15042-441: The major groove and the purine towards the minor groove. Relative to the shape of DNA polymerase's binding pocket, steric clashes occur between the purine and residues in the minor groove, and important van der Waals and electrostatic interactions are lost by the pyrimidine. Pyrimidine:pyrimidine and purine:purine mismatches present less notable changes since the bases are displaced towards the major groove, and less steric hindrance

15180-507: The negative strand by the viral RNA-dependent RNA polymerase (RdRp). The mRNA may be used for translation or replication. Single-stranded mRNA is replicated to form the dsRNA genome. The 5′-end of the genome may be naked, capped, or covalently bound to a viral protein. dsRNA is not a molecule made by cells, so cellular life has evolved antiviral systems to detect and inactivate viral dsRNA. To counteract this, many dsRNA genomes are constructed inside of capsids, thereby avoiding detection inside of

15318-406: The nucleus, hepadnaviruses and retroviruses contain their own proteins for exporting their unspliced genomic RNA out of the nucleus. Viral genomes can exist in a single, or monopartite, segment, or they may be split into more than one molecule, called multipartite . For monopartite viruses, all genes are on the single segment of the genome. Multipartite viruses typically package their genomes into

15456-409: The order Ortervirales , and Hepadnaviridae , which is the sole family in the order Blubervirales . A number of characteristics of viruses are not directly associated with Baltimore classification but nonetheless closely correspond to multiple, specific Baltimore groups. This includes alternative splicing during transcription, whether the viral genome is segmented, the host range of viruses, whether

15594-469: The origins of Eukaryota, which in this case is placed into the Asgard group with archaeal B3 polymerase. Pol η (eta) , Pol ι (iota), and Pol κ (kappa), are Family Y DNA polymerases involved in the DNA repair by translation synthesis and encoded by genes POLH, POLI , and POLK respectively. Members of Family Y have five common motifs to aid in binding the substrate and primer terminus and they all include

15732-533: The other dsDNA. Viruses in the ssDNA plant virus family Geminiviridae likewise vary between being monopartite and bipartite. Different Baltimore groups tend to be found within different branches of cellular life. In prokaryotes, the large majority of viruses are dsDNA viruses, and a significant minority are ssDNA viruses. Prokaryotic RNA viruses, in contrast, are relatively rare. Most eukaryotic viruses, including most animal and plant viruses, are RNA viruses, although eukaryotic DNA viruses are also common. By group,

15870-454: The other four polymerases. Pol I adds ~15-20 nucleotides per second, thus showing poor processivity. Instead, Pol I starts adding nucleotides at the RNA primer:template junction known as the origin of replication (ori). Approximately 400 bp downstream from the origin, the Pol III holoenzyme is assembled and takes over replication at a highly processive speed and nature. Taq polymerase

16008-420: The pol III core, the beta sliding clamp processivity factor, and the clamp-loading complex. The core consists of three subunits: α, the polymerase activity hub, ɛ, exonucleolytic proofreader, and θ, which may act as a stabilizer for ɛ. The beta sliding clamp processivity factor is also present in duplicate, one for each core, to create a clamp that encloses DNA allowing for high processivity. The third assembly

16146-402: The polymerase, to the exonuclease domain. In addition, an incorporation of a wrong nucleotide causes a retard in DNA polymerization. This delay gives time for the DNA to be switched from the polymerase site to the exonuclease site. Different conformational changes and loss of interaction occur at different mismatches. In a purine:pyrimidine mismatch there is a displacement of the pyrimidine towards

16284-424: The protein shell ( capsid ), of a virus. This protein is responsible for binding to a surface receptor on the plasma membrane (or membrane carbohydrates) of a host cell. Viruses can exploit normal cell receptor functions to allow attachment to occur by mimicking molecules that bind to host cell receptors. For example, the rhinovirus uses their virus attachment protein to bind to the receptor ICAM-1 on host cells that

16422-400: The rate of DNA synthesis. The rate of DNA synthesis in a living cell was first determined as the rate of phage T4 DNA elongation in phage infected E. coli . During the period of exponential DNA increase at 37 °C, the rate was 749 nucleotides per second. DNA polymerase's ability to slide along the DNA template allows increased processivity. There is a dramatic increase in processivity at

16560-446: The realm Duplodnaviria , usually the tailed bacteriophages of the order Caudovirales , and tailless or non-tailed dsDNA viruses of the realm Varidnaviria . dsDNA viruses are classified into three of the four realms and include many taxa that are unassigned to a realm: The second Baltimore group contains viruses that have a single-stranded DNA (ssDNA) genome. ssDNA viruses have the same manner of transcription as dsDNA viruses. Because

16698-478: The realm, RT viruses are included in the kingdom Pararnavirae and RNA viruses in the kingdom Orthornavirae . Furthermore, the three Baltimore groups for RNA viruses are used as defining characteristics of the phyla in Orthornavirae . Unlike RNA viruses and RT viruses, DNA viruses have not been united under a single realm but are instead dispersed across four realms and various taxa that are not assigned to

16836-474: The removal of the incorrect nucleotide to be replaced by the correct one. The shape and the interactions accommodating the Watson and Crick base pair are what primarily contribute to the detection or error. Hydrogen bonds play a key role in base pair binding and interaction. The loss of an interaction, which occurs at a mismatch, is said to trigger a shift in the balance, for the binding of the template-primer, from

16974-401: The replication enzymes in the host cell nucleus to replicate the viral genome. Many RNA viruses typically replicate in the cytosol , and can directly access the host cell's ribosomes to manufacture viral proteins once the RNA is in a replicative form. Viruses may undergo two types of life cycles: the lytic cycle and the lysogenic cycle. In the lytic cycle, the virus introduces its genome into

17112-440: The resulting DNA polymerase processivity increase. Based on sequence homology, DNA polymerases can be further subdivided into seven different families: A, B, C, D, X, Y, and RT. Some viruses also encode special DNA polymerases, such as Hepatitis B virus DNA polymerase . These may selectively replicate viral DNA through a variety of mechanisms. Retroviruses encode an unusual DNA polymerase called reverse transcriptase , which

17250-510: The reverse transcriptase protein that often comes with the RNA virus can be used as an indirect target for RNA viruses, preventing transcription and synthesis of viral particles. (This is the basis for anti-AIDs and anti-HIV drugs ) Like most viruses with RNA genomes, double-stranded RNA viruses do not rely on host polymerases for replication to the extent that viruses with DNA genomes do. Double-stranded RNA viruses are not as well-studied as other classes. This class includes two major families,

17388-419: The role of Pol I in E. coli DNA replication. Three more DNA polymerases have been found in E. coli , including DNA polymerase III (discovered in the 1970s) and DNA polymerases IV and V (discovered in 1999). From 1983 on, DNA polymerases have been used in the polymerase chain reaction (PCR), and from 1988 thermostable DNA polymerases were used instead, as they do not need to be added in every cycle of

17526-501: The same area that viral transcription occurs. Different viruses have various mechanisms for uncoating. Some RNA viruses such as Rhinoviruses use the low pH in a host cell's endosomes to activate their uncoating mechanism. This involves the rhinovirus releasing a protein that creates holes in the endosome, and allows the virus to release its genome through the holes. Many DNA viruses travel to the host cells nucleus and release their genetic material through nuclear pores. The fourth step in

17664-433: The shape of the viral capsid , which stores the viral genome, and the evolutionary history of viruses are not necessarily related to Baltimore groups. Baltimore classification was created in 1971 by virologist David Baltimore . Since then, it has become common among virologists to use Baltimore classification alongside standard virus taxonomy, which is based on evolutionary history. In 2018 and 2019, Baltimore classification

17802-472: The strandedness of the genome, which can be either single- or double-stranded, and the sense of a single-stranded genome, which is either positive or negative. The primary advantage of Baltimore classification is that by classifying viruses according to the aforementioned characteristics, viruses that behave in the same manner can be studied as distinct groups. There are seven Baltimore groups numbered with Roman numerals, listed hereafter. Baltimore classification

17940-708: The transcription and replication parts of the viral life cycle . Structural characteristics of a virus particle, called a virion, such as the shape of the viral capsid and the presence of a viral envelope , a lipid membrane that surrounds the capsid, have no direct relation to Baltimore groups, nor do the groups necessarily show genetic relation based on evolutionary history. DNA viruses have genomes made of deoxyribonucleic acid (DNA) and are organized into two groups: double-stranded DNA (dsDNA) viruses, and single-stranded DNA (ssDNA) viruses. They are assigned to four separate realms: Adnaviria , Duplodnaviria , Monodnaviria , and Varidnaviria . Many have yet to be assigned to

18078-568: The typical right hand thumb, palm and finger domains with added domains like little finger (LF), polymerase-associated domain (PAD), or wrist. The active site, however, differs between family members due to the different lesions being repaired. Polymerases in Family Y are low-fidelity polymerases, but have been proven to do more good than harm as mutations that affect the polymerase can cause various diseases, such as skin cancer and Xeroderma Pigmentosum Variant (XPS). The importance of these polymerases

18216-602: The vast majority of dsDNA viruses infect prokaryotes, ssDNA viruses are found in all three domains of life, dsRNA and +ssRNA viruses are primarily found in eukaryotes but also in bacteria, and -ssRNA and reverse transcribing viruses are only found in eukaryotes. Viral genomes may be either linear with ends or circular in a loop. Whether a virus has a linear or circular genome varies from group to group. A significant percentage of dsDNA viruses are both, ssDNA viruses are primarily circular, RNA viruses and ssRNA-RT viruses are typically linear, and dsDNA-RT viruses are typically circular. In

18354-472: The viral RNA that are then attached to sgRNA strands. Because replication is required for sgRNA synthesis, RdRp is always translated first. Because the process of replicating the viral genome produces intermediate dsRNA molecules, +ssRNA viruses can be targeted by the host cell's immune system. To avoid detection, +ssRNA viruses replicate in membrane-associated vesicles that are used as replication factories. From there, only viral +ssRNA, which may be mRNA, enters

18492-433: The viral cycle is replication, which is defined by the rapid production of the viral genome. How a virus undergoes replication relies on the type of genetic material the virus possesses. Based on their genetic material, viruses will hijack the corresponding cellular machinery for said genetic material. Viruses that contain double-stranded DNA (dsDNA) share the same kind of genetic material as all organisms, and can therefore use

18630-477: The virus is no longer attached to the host cell. Another common way viruses leave the host cell is through cell lysis , where the viruses lyse the cell causing it to burst which releases mature viruses that were in the host cell. Viruses are split into seven classes, according to the type of genetic material and method of mRNA production, each of which has its own families of viruses, which in turn have differing replication strategies themselves. David Baltimore ,

18768-410: The well-known eukaryotic polymerase pol β (beta) , as well as other eukaryotic polymerases such as Pol σ (sigma), Pol λ (lambda) , Pol μ (mu) , and Terminal deoxynucleotidyl transferase (TdT) . Family X polymerases are found mainly in vertebrates, and a few are found in plants and fungi. These polymerases have highly conserved regions that include two helix-hairpin-helix motifs that are imperative in

18906-431: Was partially integrated into virus taxonomy based on evidence that certain groups were descended from common ancestors. Various realms, kingdoms, and phyla now correspond to specific Baltimore groups. Baltimore classification groups viruses together based on their manner of mRNA synthesis. Characteristics directly related to this include whether the genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA),

19044-511: Was proposed in 1971 by virologist David Baltimore in a paper titled Expression of Animal Virus Genomes . It initially contained the first six groups but was later expanded to include group VII. Because of the utility of Baltimore classification, it has come to be used alongside standard virus taxonomy, which is based on evolutionary relationships and governed by the International Committee on Taxonomy of Viruses (ICTV). From

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