All processes related to the phage developmental cycles.
The set of processes by which a bacteriophage multiplies. Upon infection of a host bacterial cell, virulent phages replicate the viral genome and assemble progeny particles. Temperate phages can either follow that same route or establish as a prophage (lysogeny). Under some circumstances the prophage can be induced and complete a lytic cycle.
viral assembly, maturation, egress, and release
Any process by which a phage loosely binds to its host surface and scans it for receptors with its fibers, spikes or a baseplate component.
Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, recognizes and binds to its specific receptor on the host cell surface. This process can include enzymatic degradation of the surface polysaccharide of the bacterium.
Often defined by subtraction of the number of unadsorbed phages measured either as the number of plaque forming units (pfu) recovered following chloroform treatment of infected cells, or by co-sedimentation of pfu with cells (with or without dilution before centrifugation). These methods may give different values for the % adsorbed phage.
Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, initially recognizes and binds to its specific receptor on the host cell surface.
This process was historically defined by the release, by Waring blending or sonication, by dilution and centrifugation, or by filtration and washing, of infective virions from their complexes with cells, thus contrary to what is observed after irreversible adsorption.
The process by which conformational changes of virion proteins or injection of virion proteins into the infected cell initially commit infection. Disruption of the phage:cell complex at this step results in the loss of infective phage virions.
A set of processes by which temperate bacteriophages establish as a prophage either integrated in the host genome at a more or less specific or random location or as a linear or as a circular plasmid in the host cytoplasm. The lytic functions are repressed by a phage encoded lysogeny repressor. The lysogenic bacterium is immune to superinfection by phages related to the prophage and susceptible to that same repressor. Phages that are insensitive to that repressor are called heteroimmune.
Process by which a bacteriophage transfers its DNA in the host cell.
Processes leading to the building of a mature phage particle.
GO:0042963 definition is not appropriate: A late phase of bacteriophage replication during which all the components necessary for the formation of a mature virion collect at a particular site in the bacterial cell and the basic structure of the virus particle is formed.
Process by which phage heads/capsids are assembled.
Process by which phage tail fibers are assembled.
Process by which tailed phage heads and tails are put together.
Process of dissolution of cells by the action of specific phage encoded enzymes that causes cell rupture and release of the phage progeny.
Process of releasing mature phage particles from the host cell.
Process by which tailed phage tails are assembled.
Process used by some phages as part_of the host cell lysis process.
Process of building the precursor of the phage head/capsid, which shall later encapsidate the viral genome.
Process of incorporation of the phage genome into the phage head/capsid.
Processing of replicated DNA into a packageable structure, often a linear concatemer.
Mode of packaging of double stranded DNA phage genomes with terminally redundant and possibly circularly permuted ends. These are generated by the activity of the phage-encoded terminase, which as part_of the phage head specifically binds the pac site on tandem arrays of phage DNA copies and is triggered to cut the DNA when the phage head is full.
Generalized transducing phages usually use this mode of packaging. The prohead terminase binds pac-like sites on the host chromosome and processes it as if it was phage DNA.
Mode of packaging of double stranded DNA phage genomes with 3' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 3' protruding 'sticky' ends.
Mode of packaging of double stranded DNA phage genomes with 5' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 5' protruding 'sticky' ends.
Process of releasing mature enveloped phage particles (Plasmaviridae phages) by formation of a bulge.
Process of replicating the phage genome.
Process of replicating a phage RNA genome.
Process of replicating a phage DNA genome.
Any process that modulates the frequency, rate or extent of the phage genome replication.
Process of DNA-dependent DNA replication primed by a phage encoded protein bound at the ends of its linear genome to produce two linear daughter DNA molecules.
Process of DNA-dependent DNA replication proceeding by the rolling circle mode, i.e. on a circular DNA molecule to produce a concatemer.
Process of DNA replication proceeding uni or bidirectionally on a circular DNA template to produce two daughter circular DNA molecules .
Process of DNA-dependent DNA replication proceeding by successive rounds of replicative transposition.
This mode of replication is used by the transposable phages.
Process of DNA-dependent DNA replication intiated by homologous recombination.
Typically used by phages of the T4 family.
Cascade of transcription and translation of the phage genes.
Cascade of transcription of the phage genes.
The transcriptional period of the earliest expressed viral genes mainly encoding transcriptional regulators.
immediate early viral mRNA transcription
The second round of viral gene transcription, usually of replication genes.
(delayed) early viral mRNA transcription
The third round of phage transcription, usually of regulators involved in the progression of induction of the phage late gene expression.
The transcriptional period of the latest expressed viral genes mainly encoding phage capsid components, morphogenesis proteins and cell wall degradation enzymes.
Typically turned on by phage-encoded transcription factors.
Process by which phage gene transcription stops and RNA-polymerase is released from the DNA template.
Functions to prevent the termination of RNA synthesis. Acts as a regulatory device, e.g. in phage lambda, enabling a terminator to be masked from RNA polymerase so that distal genes can be expressed.
Any process that activates or represses phage gene expression.
Any process that stimulates the frequency, rate or extent of the phage genome replication.
positive regulation of viral genome replication
positive regulation of phage replication
Any process that decreases the frequency, rate or extent of the phage genome replication.
negative regulation of viral genome replication
negative regulation of phage replication
Any process that activates or represses the transcription of phage genes. Typically turned on by phage-encoded transcription factors.
transcriptional-regulation of phage gene expression
Any process that represses the expression of phage genes at the post-transcriptional level.
negative post transcriptional regulation of phage gene expression
Any process that activates the expression of phage genes at the post-transcriptional level.
positive post transcriptional regulation of phage gene expression
Any process that activates or represses the expression of phage genes at a post-trasncriptional level.
post-transcriptional regulation of phage gene expression
Any process that represses the expression of phage genes at the transcriptional level.
negative regulation of viral transcription
Typically turned off by phage-encoded transcription factors.
negative transcriptional regulation of phage gene expression
Any process that activates the expression of phage genes at the transcriptional level.
positive regulation of viral transcription
positive transcriptional regulation of phage gene expression
Any process that up or down-regulates protein activity or stability.
post-translational regulation of phage gene expression
A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a plasmid.
Process through which a prophage induces a hereditary change in the phenotype or fitness of the lysogen.
A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a linear plasmid.
establishment as a linear plasmid prophage
A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a circular plasmid.
establishment as a circular plasmid prophage
A process by which the phage integrates in the host genomes and establishes as a stable prophage.
Process by which the phage DNA integrates into the host genome by recombination. Integration usually proceeds via site-specific recombination into the host chromosome.
Process by which a latent prophage blocks the expression of its own lytic genes as well as expression of those genes by a related superinfecting phage with the same immunity. The host bacterium is thus "immune" to superinfection by such related phages.
Process of infection by a phage, which does not complete the lytic cycle and produces no viable phage burst. It may or may not provoke cell death.
Simulated lysogeny in a mixed population of phage-infected bacteria, non-infected phage-sensitive bacteria, and free phages.
All macromolecules, proteins, nucleic acids, sugars, lipids etc. that are part or participate in the assembly of the mature virion particle.
Process by which a prophage is made to switch from the latent/lysogenic state to the lytic cycle and production of phage progeny.
Process by which a prophage DNA is excised from the host genome.
Component of the closed shell (head or capsid) of the phage.
Transient internal component of the phage prohead, which allows for its assembly. It is degraded or leaves the prohead without being degraded and is replaced by the phage DNA upon maturation.
Abbreviated MHP, the major subunit component that forms the closed shell (capsid) of the phage head.
Also called gate keepers, these proteins close the head after packaging and maturation of the phage genome, are part of the completed head, allow for the binding of the tail and are part of the complete phage particle.
Protein component that forms the junction between the Caudovirales phage head and tail and serves as a gate through which DNA passes during packaging and translocation.
Component of the phage head/capsid. Located on the outer head surface they are involved in the stabilization of the head structure and, usually, are not essential.
Protein component of fiber structures, which decorate the head/capsid of some phages.
Protein covalently linked to the ends of dsDNA phages that use protein primed DNA replication.
The protein primes DNA replication and may have other functions including cell wall hydrolase.
A complex of large and small terminase subunits. It is responsible for binding to and thereby choosing the DNA that will be packaged; it also carries the ATPase motor (DNA translocase) that drives the DNA into the prohead during packaging and has the nuclease activity that cleaves virion-length DNA from overlength or circular replicating DNA. The name refers to the nuclease activity that creates the termini of the virion DNA. Some phage terminases exist as single polypeptides and some terminase complexes include an RNA component.
Phage component that forms a complex with the terminase small subunit at the base of the phage head.
Phage component that forms a complex with the terminase large subunit at the base of the phage head.
Protein component of fiber structures appended at the neck at the base of some phage heads.
Protein component of a phage, which is injected into the host cytoplasm upon phage infection.
Protein component of a phage, which is injected into the host cytoplasm upon phage infection prior to phage DNA translocation.
Protein component of a phage, which is injected into the host cytoplasm upon phage infection after phage DNA translocation.
Protein component of a phage, which is injected into the host membrane upon phage infection, creating a channel for phage DNA translocation.
Biochemical assembly that contains both proteins and lipids and is part_of some (Tectiviridae) phage capsids.
Protein component of the assembled tail of tailed phages (caudovirale).
Abbreviated MTP, the term refers to protein component found in large amount, easily detectable upon electrophoresis of tailed phage particles of the types Myoviridae and Siphoviridae.
Protein that forms the internal tube of the contractile tails of Myovirirdae phages. It is the channel for DNA ejection into the host cytoplasm.
Protein that forms the external contractile envelope of the tails of Myoviridae phages. Its contraction ensures ejection of the phage DNA into the host cytoplasm.
Protein that forms the tube of the non-contractile tails of Siphoviridae phages. It is the channel for DNA translocation into the host cytoplasm.
Protein TMP that controls the tail tube length in Myoviridae and tail shaft length in Siphoviridae. The protein is part of the finished tail. Some phages inject their TMP with their DNA in the host cytoplasm.
Protein structure that forms the basal tip of the phage tail and is used by the phage to adsorb to the host cell.
Multiprotein component at the head-distal end of the tail and to which fibers of tailed phages may be attached (Caudovirales). Sometimes referred to as the tail tip or tip structure in Siphoviridae.
Protein component of the fiber, structure appended to the phage tail and used to scan, recognize and attach to the host cell.
Fibers typically bind to particular LPS, polysaccharide or protein receptors on the cell surface
A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated island.
Tandem array or branched complex of DNA bacteriophage genomes generated in the bacterial host cytoplasm during phage replication and which is the substrate for DNA packaging.
A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
A bacterial component to be added in GO that had to do with the phage life cycle.
A bacterial component located on the cell surface and which is specifically recognized and used by the phage for adsorption.
Minor protein component of the phage tail fiber.
Major protein component of the phage tail fiber.
Molecular functions of phage components.
Some anti-holins differ from their cognate holins by only a few terminal amino acids.
Catalysis of the temporally regulated formation of a transmembrane protein hole that directly or indirectly allows murein hydrolyases to access their cell wall substrate.
Inhibition, inactivation or degradation of a transcriptional repressor.
An activity as that of the lambda Cro repressor that has opposing effects on gene expression than another repressor, here lambda CI by operator binding is NOT considered an anti-repressor.
Catalysis of the reaction: ATP + H2O = ADP + phosphate. May or may not be coupled to another reaction.
Transcriptional repressor activity involved in switching between lytic and lysogenic transcription.
CI/Cro transcriptional repressor activity
Cell wall degradation enzyme synthesized by a phage during its lytic cycle and responsible for host cell lysis.
Cell wall hydrolase activity associated with phage structures (usually the tail or the base plate) and which helps DNA translocation by damaging the host cell envelope after adsorption.
Catalysis of the hydrolysis of peptide bonds.
Chaperon activity required for the assembly of the phage coat.
Chaperon activity required for the assembly of the phage tail.
Chaperon activity required for the assembly of the phage fibers.
Interacting selectively with DNA (deoxyribonucleic acid).
Interacting selectively with single stranded DNA (deoxyribonucleic acid).
Interacting selectively with double stranded DNA (deoxyribonucleic acid).
Catalysis of a topological transformation in double-stranded DNA by a covalent or non-covalent mechanism.
An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization.
DNA polymerase processivity factor activity
Catalysis of the hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from DNA replication.
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
Catalysis of the transfer of a methyl group to a DNA molecule.
Catalysis of the synthesis of short RNA primers for the Okazaki fragments on both DNA template strands at the replication fork. A DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase.
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
DNA-binding activity that activates excision by a serine or tyrosine based integrase, of a DNA segment from another, usually larger, DNA molecule such as a chromosome.
Protease activity involved in head maturation. Usually degrades the scaffolding or remove portions of coat or portal proteins in an assembly dependent manner. May be part_of the scaffolding protein or encoded by the same gene.
Protease activity involved in breaking down of the cell wall as part of the phage lysis process.
Catalysis of DNA cleavage involved in the packaging of DNA into phage heads.
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
Any transcription regulator activity that prevents or downregulates transcription.
Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
The processes by which a new genotype is formed by reassortment of genes resulting in gene combinations. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur between chromosome and plasmid or those and horizontally acquired DNA introduced in the cell via genetic transformation, conjugation or transduction.
This definition differs from that in GO.
The formation and repair of double strand breaks through a double Holliday junction intermediate that results in the equal exchange of genetic material between a pair of homologous DNA fragments (chromosome, plasmid, phage).
Recombination between two DNA sites begins by the recognition and binding of these sites by the recombinase protein. This is followed by the synapsis i.e. bringing the sites together to form the synaptic complex. It is within this synaptic complex that the strand exchange takes place, as the DNA is cleaved and rejoined by controlled transesterification reactions. During strand exchange, the DNA cut at fixed points within crossover region of the site releases a deoxyribose hydroxyl group, while recombinase protein forms a transient covalent bond to a DNA backbone phosphate. This phosphodiester bond between hydroxyl group of the nucleophilic, serine or tyrosine residue conserves the energy that was expended in cleaving the DNA. Energy stored in this bond is subsequently used for the rejoining of the DNA to the corresponding deoxyribose hydroxyl group on the other site. The entire process therefore goes through without the need for external energy rich cofactors such as ATP.
The process by which a segment of DNA is incorporated into another by a site-specific recombination event.
The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
The process by which a segment of DNA is separated from another by a site-specific recombination event. The process occurs during prophage excision, the resolution of a cointegrate DNA molecule resulting from a process of replicative transposition into finished transposition products, the resolution of multimeric plasmids into monomers and the separation of entangled circular bacterial chromosomes prior to cell division.
A process of transpositional recombination, which involves the replication of the transposed DNA segment.
replicative transpositional recombination
A process that moves a DNA region from one to another location in a genome via a DNA intermediate.
Synonyms recently associated with the GO term do not apply here. These are in fact much too specific.
A process of transpositional recombination, which does not involve the replication of the transposed DNA segment. This process can however lead to the duplication of the transposed DNA segment by recombinational repair.
conservative transpositional recombination
The repair of damaged DNA that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
A process involving DNA breakage and reunion that converts replicated telomeres into covalently closed hairpin telomeres on the ends of linear DNA molecules.
Activities related to bacteria, phage, plasmid and transposon recombination.
Processes related to bacteria, phage, plasmid and transposon recombination.
Catalysis of cleavage and formation of new phosphodiester bonds between a pair of DNA target sequences.
Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequence by cleavage of one DNA strand and formation of a covalent phosphotyrosyl enzyme intermediate. Depending on the enzyme families, this bond can be a 3' or 5',phosphotyrosyl, liberating a 5' or a 3'OH nucleophile involved in the reunion part of the reaction.
Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a 5-prime phosphoseryl enzyme intermediate in which the target sequence is first cleaved by nucleophilic attack by a serine in the active site.
Tyrosine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another.
Tyrosine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two.
Catalysis of a topological transformation in DNA through the cleavage of one DNA strand and formation of a covalent 3-prime-phosphotyrosyl enzyme intermediate to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
tyrosine based topoisomerase IB activity
Catalysis of a site-specific breakage and reunion reaction that generates two hairpin telomeres from a replicated telomere substrate. Occurs via a two-step transesterification with a protein-DNA intermediate similar to that used by topoisomerases and site-specific recombinases.
Tyrosine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome.
Serine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another.
Serine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two.
Serine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome.
Recomoinases with aDDE transposase have a related amino-acid motif (the DDE motif), which forms the active site of the transposase and is responsible for coordinating the cleavage and joining steps of transposition. Breakage of the DNA occurs at the end of the element (usually a hydrolysis) and is followed by breakage and integration at the target site (a transesterification reaction).
Any multiprotein recombinogenic complex containing DNA, recombinase and accessory proteins.
Any multiprotein recombinogenic complex containing DNA, site-specific tyrosine or serine based integrase and accessory proteins and involved in the intgeration or ecision of DNA fragments.
A multi-component enzymatic machine including a relaxase, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition.
A multi-component enzymatic machine, which mediates DNA transposition; it Includes the DDE (DDD?) transposase and accessory proteins including nucleoid associated proteins such as HU or IHF.
A multi-component enzymatic machine including a tyrosine or serine based resolvase, which mediates resolution of chromosome dimers and replicon fusions.
Y2-transposases catalyze the rolling circle transposition. They contain several conserved motifs including a pair of tyrosine residues, that are conserved among plasmid and phage rolling-circle replication proteins, which are important for DNA binding, breakage and reunion.
Movement of a DNA segment form one to another location in a genome by a mechanism that resembles rolling-circle replication carried out by many bacterial plasmids and phage.
The protein coat that surrounds the infective nucleic acid in phage particles. It comprises numerous regularly arranged subunits.
Activity that represses RNA polymerase activity.
Typically expressed by phages to turn off host egne expression.
Activity that inhibits DNA degradation by the phage host protein complex RecBCD.
Any process that modulates host gene expression as a result of phage gene expression.
plasmid mediated regulation of host gene expression
Any process that up-regulates host gene expression as a result of phage gene expression.
plasmid mediated positive regulation of host gene expression
Any process that down-regulates host gene expression as a result of phage gene expression.
plasmid mediated negative regulation of host gene expression
Activity that inhibits protein breakdown by the phage host protease FtsH.
Activity that modulates the nucleoid associated protein/DNA chaperon HNS.
modulator of nucleoid associated protein HNS
Activity that decreases deoxyguanosine triphospho-hydrolase activity.
inhibitor-of deoxyguanosine triphospho hydrolase
Any process that activates or represses the activity of a host protein.
plasmid mediated modulation of host protein activity
Activity that provokes host cell kiling independently of any other phage lytic or plasmid activity.
Protein that is a major component of the phage particle.
Component of the tailed phages i.e. the Caudovirales, which have a double stranded DNA genome. The tail can be short (Podoviridae), long and non-contractile (Siphoviridae) or long and contractile (Myoviridae). The tail is the channel through which the phage genome is injected into the host bacterial cell.
Tail fibers are appended at the phage tail tip and serve to scan, recognize and attach to the cognate receptor on bacterial host cell surface. Tail fibers typically bind to particular LPS, polysaccharide, protein or other components of the cell surface.
Fiber structures, which decorate the head of some phages.
The precursor protein complex that will evolve into the coat that surrounds the infective nucleic acid in phage particles. It builds up around the scaffolding, which assembles on top of the portal complex and is later degraded or leaves the prohead without degradation to be replaced by DNA.
Protein component found in low number of copies in the tail of phage particles of the types myoviridae and siphoviridae.
Phage head/capsid protein component located inside the finished head.
Activity that inhibits the protease activity of the host RecA protein.
Chaperon activity required for the assembly of phage components.
The process by which a segment of DNA is separated from another, usually larger, DNA molecule such as a chromosome.
Catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
Protein component found in low number of copies in the shell/head/capsid of phage particles.
Protein that is a minor component of the phage particle.
Usually taken in with food or water contaminated with bacteria that express it, the Shiga toxin is composed of two subunits, A and B. It acts on the lining of the blood vessels, the vascular endothelium. After it enters the cell, the toxin inhibits the ribosomes, leading to cell death.
One of the two subunits. The A subunit of the Shiga toxin is an N-glycosidase that modifies the RNA component of the ribosome to inactivate it and so brings a halt to protein synthesis leading to cell death.
Shiga toxin subunit B binds to a component of the cell membrane known as Gb3 allowing the complex AB toxin to enter the cell.
Thioredoxins are proteins that act as antioxidants by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange. Thioredoxins are found in nearly all known organisms and are essential for life in mammals. Thioredoxin is a co-factor of some phage DNA-polymerases.
thiol-disulfide exchange intermediate activity
Any process that results into the inhibition of a host restriction.
The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
Phage encoded protein that antagonizes ribosome-mediated translation of mRNA into a polypeptide.
Any process that controls the number of copies of a plasmid per host cell.
Phage which upon infection has no other choice than entering the lytic cycle.
Phage which upon infection has the choice between going lytic or lysogenic.
Activity resulting in the degradation of hyaluronic acid.
Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes, and macrophages.
Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes and macrophages.
Family of potent immunostimulators able to simultaneously bind to the MHC class 2 molecules and the T cell receptor bacterial, resulting in alpha-beta T cell activation.
Staphylokinases (SAK) are enzymes, which activate plasminogen, which in turn can degrade various host proteins during infection.
Streptodornases are DNases secreted by S. pyogenes and which protect the bacteria from being trapped in neutrophil extracellular traps (NETs) by digesting the NET's web of DNA, to which are bound neutrophil serine proteases that can kill the bacteria.
Exfoliative toxin A is a Staphylococcus aureus protease activity, which causes peeling of the skin observed in staphylococcal scalded-skin syndrome.
Protein component of a constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae).
Protein component of a small disk located below some phage heads.
Protein component of the fibers attached to the collar structure of some phages.
Short stuctures (generally 30 nm long) at the tail tip of some phages and used for attachment.
Genomic island which carries genes encoding proteins related to pathogenicity such as attachment, invasion of the host, other virulence factors, toxins, etc.
SO definition: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
Number of triangles into which an icosahedral virus capsid can be subdivided.
Short DNA sequence, which is a target region for site-specific integration and/or excision and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
site specific recombination target region
Integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
Attachment site located on the on the phage genome.
Attachment site located on the bacterial chromosome at the left of a prophage region and which is used for prophage site-specific excision.
A region that results from recombination between attP site and attB site, composed of the 5' portion of attP site and the 3' portion of attB site.
An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
Attachment site located on a gene cassette (sensu integron) and used for site-specific integration in an integron.
Exists in SO but I prefer my definition, because SO's does not mention the cassette.
Target region for site-specific recombination leading to the resolution of a chromosome or plasmid dimer or a cointegrate resulting from replicative transposition.
Region located at either end of an integrated transposon; it includes binding sites for the cognate transposase enzyme, which nicks the transposon at its last base pair.
The left transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence.
The left end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRR.
In the case of transposable (pro)phages it is called attL and includes several subsites, attL1, attL2 and attL3.
The right end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRL.
In the case of transposable (pro)phages it is called attR and includes several subsites, attR1, attR2 and attR3.
The left transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence.
The right transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence.
The right transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence.
type I secretion membrane fusion protein activity
A region specifically recognized by a recombinase, which inverts the region flanked by a pair of sites.
Component of the inversion site located at the left of a region susceptible to site-specific inversion.
Component of the inversion site located at the right of a region susceptible to site-specific inversion.
DNA region recognized by the terminase small subunit as the first step in synapsis of the double stranded DNA phage full head packaging complex.
DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates double stranded DNA phage genomes with sticky ends.
DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates phage genomes with 3'-extended protruding sticky ends.
DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex, which generates phage genomes with 5'-extended protruding sticky ends.
Chromosomal DNA region that has features suggesting a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
A DNA region encoding an integrase, which acts at an adjacent attI site to insert a gene cassette with an attC site through attI-attC recombination. The integron also carries a promoter that controls expression of the gene on the cassette.
A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. DEF in SO not really complete.
DNA region that contains a tyrosine based recombinase gene, a primary recombination site attI and a strong outward promoter Pc.
Discrete DNA region which can exist either as discrete circular region with an attC site, or integrated after attI by attC recombination, downstream of the integron Pc promoter, which controls the expression of its usually single encoded gene.
Transposable DNA region that encodes mobility and its regulatory functions and other phenotypic traits such as antibiotic resistance, catabolic enzymes etc.
SO definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequence.
Transposon in which mobility genes and phenotypic genes are surrounded by imperfect inverted repeats.
Transposon composed of two identical IS sequences in the same or opposite orientation flanking a region containing the phenotypic genes.
A genomic island which contains genes for integration/excision and intercellular transfer by conjugation.
Diiferes fro OS def (A transposon that encodes function required for conjugation).
A genomic island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
DNA region that contains genes for phage head and tail formation but no replication genes. The produced heads only encapsidate host DNA, generating defective generalized transducing particles.
DNA region flanked by inverted repeats and containing genes coding for transposition enzymes and regulators of transposition.
A DNA region consisting of two fused replicons/plasmids resulting from a replicative transposition event.
SO definition for cointegrate replicon: A MGE region consisting of two fused replicons/plasmids resulting from a replicative transposition event.
When bacteriophages complete their lytic cycle, random bacterial chromosomal DNA segments or plasmid DNA instead of viral DNA may be inserted into the viral capsid. The phage particle loaded with a piece of bacterial DNA may infect another bacterial cell. This newly acquired DNA can fall to one of three fates. It can be recycled. If the DNA was originally a plasmid, it can recircularize inside the new cell and become a plasmid again. If the new DNA matches with a homologous region of the recipient chromosome, it will recombine so that part or most of that DNA material is incorporated into the new host chromosome.
This definition differs from that in GO:0009293.
While excising from the chromosome incorrectly, a prophage can leave part of its DNA in the chromosome and pick up adjacent bacterial DNA. This DNA may be packaged into a mature phage particle, which can be released and infect a new host. Depending on which part of the phage DNA has been lost, this new genome may or not be able to complete a lytic cycle. If its bacterial DNA moiety is homologous to the recipient cell chromosome, integration can occur by homologous recombination. If the integrase and attachment site components of the phage are still present, integration can also occur by site-specific recombination. In both cases the recipient chromosome will contain two copies of the bacterial DNA segment carried by the transducing genome. The genes most susceptible to transfer by this mechanism are those in the direct vicinity of the original prophage.
Transfer of a DNA segment from one to another cell by a virus (usually a bacteriophage).
Process of releasing mature phage particles (filamentous phages) by passing through bacterial membranes.
Genomic island which carries genes encoding proteins involved in catabolism, usually of man-made toxic compounds (chlorinated aromatic and aliphatic compounds for instance).
Genomic island that carries genes encoding proteins involved in symbiosis, usually with plants.
SO definition: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
Genomic island whose presence increases the fitness of the host.
Genomic island that carries determinants for integration and excision of the host genome and for inter-cellular transfer by conjugation. The former include an integrase of the tyrosine or serine base integrase and cognate att sites. The latter can or not be related to plasmid encoded conjugation machinery.
The nucleotide sequence of a virus that infects bacteria.
A DS DNA phage that integrates and replicates by transpositional recombination.
Any process that changes the level of transcription of plasmid genes.
Genome of a DS DNA phage that integrates and replicates by transpositional recombination.
A complex of proteins that permits the transfer of proteins into the extracellular milieu or directly into host cells via the type V secretion system.
Poisonous activity, especially of proteins or conjugated proteins produced by certain animals, higher plants, and pathogenic bacteria.
A complex of proteins that permits the transfer of nucleoprotein DNA conjugation intermediates or proteins directly into host cells or into the extracellular milieu In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s).
Term and definition differ from those in GO.
type IV protein secretion/mating pair formation system complex
Protein associated with the bacterial nucleoid.
A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space.
A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of secreted proteins from the cytoplasm into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane.
type II protein secretion system complex
A complex nanomachine of approximately 20 proteins that carries out protein secretion in the type III secretion system. It contains an ATPase, spans the inner membrane, the peptidoglycan layer and the outer membrane and secretes a stiff needle like structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In some T3S the needle is not complete and the structure serves as the conduit for protein secretion.
type III protein secretion system complex
Process of bidirectional (theta) vegetative replication of a plasmid DNA genome.
Process of sigma-type replication of a plasmid DNA genome from the origin of transfer oriT, during conjugation.
A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell (donor) is then transferred into the other cell (recipient) unidirectional conjugation occurs between cells of different mating types.
It is essential NOT to use 'male' and female' because any bacterium can be donor and recipient even at the same time.
Inner membrane ATPase (TraG/VirD4) that recruits the DNA substrate including the conjugative relaxase to the T4SS and powers the intercellular transfer of DNA by conjugation.
type IV secretion system coupling protein
Alpha-beta fibrous proteins found in pilus structures in bacteria. Bacterial pili are used in partner recognition and exchange of genetic material during bacterial conjugation. Pili are more common in gram-negative bacteria, where, individual pilin molecules are linked by noncovalent protein-protein interactions. Gram-positive bacteria often have polymerized pilin.
Several terms associated to pilus and flagllum as components and their biogenesis are in GO.
A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter.
Structural subunit of the T4SS Secretion pilus of the T4SS formed or VirB2/TrbC/TraA/TraX structural subunits, some of which when mature assumes a circular configuration. The pilus is involved in mating pair formation prior to unidirectional conjugation.
Outer membrane component (TrbD/TraL) of the T4SS also involved in mating pair formation prior to unidirectional conjugation. VirB3 interacts with T4SS VirB6 and VirB4 related proteins.
Heart of the T4SS, this complex consists of a Walker A- Walker B hexameric ATPase (VirB4/TrwK/TrbE/TraC/TraU), possibly cytosolic and anchored to the inner membrane through interaction with the integral inner membrane protein (VirB3/TrwM/?), an hexameric ATP dependent chaperon (VirB11/TrwD/?) and a third ATPase devoted to DNA trasnfer (TraG/VirD4) also called coupling protein. VirB4 and alike are supposed to power transfer of the pilin protein, VirB11 and alike to power unfolding of the secreted pilin, and TraG and alike to power DNA transfer.
Component (TrbJ/TraE) of the T4SS pilus that may be involved in adhesion.
type IV secretion system minor pilus component
Protein of the T4SS, also involved in mating pair formation prior to unidirectional conjugation and that perforates the peptidoglycan cell wall.
VirB1 related cell wall hydrolase activity
Polytopic inner membrane protein (VirB6/TrbL/TraG/), which is part of the lumen of the T4SS-Mating pair formation channel.
Lipoprotein component (VirB7/TrbH/TraV/TraI) that connects the pilus to the core of the T4SS-Mating pair formation complex.
type IV secretion system pilus associated lipoprotein
Protein that forms a bridge over the periplasm connecting the inner membrane and outer membrane components of the T4SS-Mating pair formation complex. Interacts with VirB1, VirB3, VirB4, VirB9 and VirB10.
VirB8 related inner-outer membrane bridging protein
Periplasm spanning and outer membrane component of T4SS formed of the VirB9/TrbG/TraK/TraN subunit.
A nodal point connecting the inner and outer membrane components of the T4SS formed of VirB10/TrbI/TraB/TraO subunits.
type IV secretion system bridging component
Hexameric ring shaped NTPase similar to the F1-ATPase molecular motors and that fuels the T4SS and TIISS.
VirB11 typeII/IV secretion NTPase activity
Protein involved in the determination of the length of the needle from the injectisome. This protein (YscP, Spa32, InvJ) is thought to operate as a molecular ruler coupled to a substrate-specificity switch.
Located in the outer membrane of the bacterial cell this part of the injectisome contains the pilotin (YscW, MxiA), a lipoprotein ancillary to the secretin (YscW) and the secretin ( YscC ) .
Needle component of the TIIISS system, which is formed of YscF (MxiH, EscF) proteins and protrudes outside from the bacterial surface by about 60 nm.
type III secretion system extracellular needle
Terminal structure of the needle made of protein LcrV (PcrV, AcrV, IpaD) serving as a scaffold for the translocation pore YopBD.
Component of the injectisome that spans the outer membrane and contains YscC subunits.
A set of two hydrophobic (YopB/YopD in Yersinia, PopB/PopD in Pseudomonas aeruginosa) and one hydrophilic (LcrV in Yersinia, PcrV in P.aeruginosa) proteins, exported by the injectisome and which form a pore in the host cell membrane to allow effector translocation.
Peptidase component of the TIISS system.
type II secretion system outer membrane component
Envelope protein component of TIISS. PulD, Out? etc.
Inner membrane ring component of the type III secretion machine, which includes lipoprotein YscJ (PrgK, EscJ), YscS, T, U and V and probably the YscR and D subunits.
Cytoplasmic ring component of the type III secretion machine, which includes YscQ subunits and probably YScK and YscL and the YscN ATpase.
type III secretion system cytoplasmic ring component
An origin of vegetative replication in plasmids and phages.
A self-replicating linear or circular DNA molecule that is distinct from a chromosome in the organism.
"Plasmid" in SO. Add "linear" in SO definition as it is.
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
An MGE that is integrated into the host chromosome.
A transposon where the mechanism of transposition is via a DNA intermediate.
The sequence is complementary and repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
Any process by which plasmids are segregated or distributed into daughter cells upon cell division. As in, but not restricted to, the taxon Bacteria.
Should be connected to chromsome segregation? GO:0007059?
The recombination process that separates plasmid dimers or higher multimers into monomers.
Any process that controls the initiation of bidirectional (theta) vegetative replication of a plasmid DNA genome.
regulation of vegetative plasmid DNA replication
Any process that controls plasmid DNA conjugation.
Fiber attached to the collar structure of some phages.
Small disk located below some phage heads.
A constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae).
Fiber appended at the neck at the base of some phage heads.
Integrated genome of a transposable phage.
Internal activating sequence for transposition in transposable phages. It transiently binds transposase to stimulate transpososome synapsis.
Process that during assembly of the T4SS removes the C-terminal aa from the pilin and generates the final cyclic pilin product by introducing a new peptide bond. This process requires the TraF/TrhI component of the T4SS.
type IV secretion system pilin maturation
Ontology for non-phage prokaryotic mobile genetic elements.
The regulated release of proteins from a cell or group of cells.
Relaxase is an enzyme in prokaryotes that is involved bacterial conjugation. It forms part of the relaxosome multi protein complex and nicks double-stranded DNA at the OriT origin of transfer on a bacterial plasmid forming a covalent 5'phosphotyrosyl bond.
Any step required for the synthesis of an autoinducer (AI) molecule, otherwise called a pheromone, a signaling molecule used by bacteria participating in quorum sensing. One common type of autoinducer is an acyl homoserine lactone (AHL).
Lantibiotics are a class of peptide antibiotics that contain polycyclic thioether amino acids as well as the unsaturated amino acids dehydroalanine and 2-aminoisobutyric acid. These characteristic cyclic thioether amino acids are composed of either lanthionine or methyllanthionine. Lantibiotics are produced by a large number of Gram positive bacteria such as Streptococcus and Streptomyces to attack other gram positive bacteria and as such they are considered a member of the bacteriocins. They are synthesised with a leader polypeptide sequence that is only removed during the transport of the molecule out of the synthesizing cell.
Toxin that exerts its activity within the target eukaryotic cell. The B subunit attaches to target regions on cell membranes, the A subunit enters through the membrane and possesses enzymatic function that affects internal cellular bio-mechanisms.
Plasmid-sensu, process of increased plasmid prevalence (number of plasmid-containing cells/total number of cells) in growing bacterial populations by selective elimination of daughter cells that did not inherit a plasmid copy at cell division.
A molecular entity with a toxin disposition\, the realization of which damages host cells.
Molecular functions associated with plasmids.
No process, component or activity can yet be assigned to this phage function.
Process by which tailed phage base plates are assembled.
The process by which a segment of DNA is inverted from its original orientation.
The process by which a segment of DNA is inverted from its original orientation through the action of a site-specific recombinase.
The process that converts a linear double stranded DNA phage genome into the circular form, either by homologous recombination between redundant ends or by association of complementary single stranded ends (sticky ends). The circular form is the template for genome replication and for most temperate phages it is also necessary for lysogenisation, either as a circular plasmid or as an integrated prophage.
Any process through which a prophage inhibits the development of an unrelated, usually virulent superinfecting phage.
No process, component or activity can yet be assigned to this plasmid function.
Any process through which a plasmid inhibits the development of an infecting phage.
Any process by which a phage activates or represses the expression or the activity of one or more of its host proteins.
regulation of host mRNA translation by virus
modification by virus of host cellular process
modulation by virus of host transcription
phage mediated modulation of host functions
Any process by which a plasmid activates or represses the expression or the activity of one or more of its host proteins.
plasmid mediated modulation of host functions
Any process that results in preventing or decreasing the SOS response of the bacterial host.
plasmid mediated inhibition of host SOS repsonse
A protein activity necessary for the correct non-covalent folding or unfolding of another protein.
Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
Cell wall amidase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
Cell wall endopeptidase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
cell wall degrading endopeptidase activity
Nearly ubiquitous among phages of Gram-negative hosts, these proteins are predicted to span the bacterial host periplasm providing a physical connection between the inner and outer membranes. They are required for phage release by lysis.
Rz/Rz1 type spanins are two component spanins. The Rz protein has a predicted N-terminal transmembrane domain that spans the bacterial host inner membrane. The Rz1 protein is tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moeities of the N-terminal cysteine.
T1 type spanins are one component spanins tethered to the bacterial host outer membrane by the fatty acid and lipid moieties of the N-terminal cysteine and to the host inner membrane by a predicted C-terminal transmembrane domain.
The Rz proteins have a predicted N-terminal transmembrane domain, which spans the bacterial host inner membrane. There C-terminal domain interact with the C-terminal domain of cognate Rz1 spanin components.
Rz1-like proteins are tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moieties of their N-terminal cysteine and interact with the Rz-like C-terminal domains through their C-terminal domain. The Rz1 coding sequence is either embedded within or adjacent to the Rz gene.
Tail fiber component, which during infection is injected into the host, likely piercing a hole in the host cell envelope.
cell wall degrading transglycosylase activity
Component of the transpososme, this protein contributes to target site selction. Some proteins in the family select specific sites (as the Tn7 TnsE protein) others more or less random sites (as the Tn7 TnsD protein).
Any process that controls the process of DNA transposition.
Any process that stimulates the process of DNA transposition.
positive regulation of DNA transposition
Any process that inhibits the process of DNA transposition.
negative regulation of DNA transposition
Any phage activity that provokes the disruption of the host bacterial nuceloid.
The process by which genetic material is organized and physically separated and apportioned to two daughter bacterial cells.
A phage or plasmid-mediated process that prevents entry of an infecting phage into the host cell.
This process differs from immunity established by a prophage through the synthesis of a repressor protein that blocks gene expression by a superinfecting phage with the same immunity region.
Structure found in many T3S nanomachines that possess a stiff needlelike structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In other T3S the needle is not complete and the structure serves as the conduit for protein secretion.
Is a synonym of type III secretion complex
The process that leads to the assembly of the relaxosome, a multi-component enzymatic machine, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition.
This is a temporary term: parent to all functions related to plasmid processes, components and molecular activities.
Any process that inhibits the process of transcription of plasmid genes.
negative regulation of plasmid gene expression
Any process that stimulates the process of transcription of plasmid genes.
positive regulation of plasmid gene expression
Any process that influences the level of plasmid gene transcription.
Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s).
Any step required for the synthesis of cobalamin, a term that may refer to several substances depending on the upper axial ligand of the cobalt ion.
Process by which a phage genome reaches a latent state, becoming a component of its host genome.
Any process by which a host bacterium stops, prevents or reduces the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template.
negative regulation by host of viral transcription
negative regulation by host of phage transcription
Any process by which a host bacterium activates the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template.
positive regulation by host of viral transcription
positive regulation by host of phage transcription
The process by which a capsid acquires a membrane envelope.
Lysis inhibition (LIN) refers to a highly adaptive attribute of the T4-related phages, which delay lysis for several hours in response to sensing the presence of external related phages attacking the cell. A block in expressing LIN results in large-plaque morphology.
A resistance to drug that mitigates the damaging effects of an antibiotic.
The set of processes by which a bacteriophage produces infectious progeny.
A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
A toxin excreted by a microorganism, including bacteria, fungi, algae, and protozoa. Exotoxins can cause damage by destroying host cells or disrupting normal host cellular metabolism. Exotoxins are either secreted, or, similar to endotoxins, released during lysis of the cell.
No process, component or activity can yet be assigned to this predicted prophage function.