Repeat induced point-mutation
Encyclopedia
In molecular biology
, repeat induced point-mutation or RIP is a process by which DNA
accumulates G
:C
to A
:T
transition
mutations. Genomic evidence indicates that RIP occurs or has occurred in a variety of fungi while experimental evidence indicates that RIP is active in Neurospora crassa
, Podospora anserina, Magnaporthe grisea
, Leptosphaeria maculans
, Gibberella zeae
and Nectria haematococca. In Neurospora crassa
, sequences mutated by RIP are often methylated
de novo.
RIP occurs during the sexual stage in haploid nuclei after fertilization but prior to meiotic
DNA replication
. In Neurospora crassa
, repeat sequences
of at least 400 base pair
s in length are vulnerable to RIP. Repeats with as low as 80% nucleotide
identity may also be subject to RIP. Though the exact mechanism of repeat recognition and mutagenesis are poorly understood, RIP results in repeated sequences undergoing multiple transition mutations.
The RIP mutations do not seem to be limited to repeated sequences. Indeed, for example, in the phytopathogenic fungus L. maculans, RIP mutations are found in single copy regions, adjacent to the repeated elements. These regions are either non-coding regions, or genes encoding small secreted proteins including avirulence genes.
The degree of RIP within these single copy regions was proportional to their proximity to repetitive elements .
Rep and Kistler have speculated that the presence of highly repetitive regions containing transposons, may promote mutation of resident effector genes . So the presence of effector genes within such regions is suggested to promote their adaptation and diversification when exposed to strong selection pressure .
As RIP mutation is traditionally observed to be restricted to repetitive regions and not single copy regions, Fudal et al suggested that leakage of RIP mutation might occur within a relatively short distance of a RIP-affected repeat. Indeed, this has been reported in N. crassa whereby leakage of RIP was detected in single copy sequences at least 930 bp from the boundary of neighbouring duplicated sequences .
To elucidate the mechanism of detection of repeated sequences leading to RIP may allow to understand how the flanking sequences may also be affected.
:C
to A
:T
transition
mutations within repeats, however, the mechanism that detects the repeated sequences is unknown. RID is the only known protein essential for RIP. It is a DNA methyltransferease-like protein, that when mutated or knocked out results in loss of RIP. Deletion of the rid homolog in Aspergillus nidulans
, dmtA, results in loss of fertility while deletion of the rid homolog in Ascobolus immersens, masc1, results in fertility defects and loss of methylation induced premeiotically (MIP)
.
, which resemble parasites
by invading and multiplying within the genome.
RIP creates multiple missense
and nonsense mutation
s in the coding sequence. This hypermutation of G-C to A-T in repetitive sequences eliminates functional gene product
s of the sequence (if there were any to begin with). In addition, many of the C-bearing nucleotides become methylated
, thus decreasing transcription.
. A second copy of a single-copy gene
is first transformed
into the genome
. The fungus must then mate
and go through its sexual cycle to activate the RIP machinery. Many different mutations within the duplicated gene are obtained from even a single fertilization event so that inactivated alleles, usually due to nonsense mutations, as well as alleles containing missense mutations can be obtained.
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, repeat induced point-mutation or RIP is a process by which DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
accumulates G
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
:C
Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...
to A
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
:T
Thymine
Thymine is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by methylation of uracil at...
transition
Transition (genetics)
In genetics, a transition is a point mutation that changes a purine nucleotide to another purine or a pyrimidine nucleotide to another pyrimidine . Approximately two out of three single nucleotide polymorphisms are transitions....
mutations. Genomic evidence indicates that RIP occurs or has occurred in a variety of fungi while experimental evidence indicates that RIP is active in Neurospora crassa
Neurospora crassa
Neurospora crassa is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" refers to the characteristic striations on the spores. The first published account of this fungus was from an infestation of French bakeries in 1843. N...
, Podospora anserina, Magnaporthe grisea
Magnaporthe grisea
Magnaporthe grisea, also known as rice blast fungus, rice rotten neck, rice seedling blight, blast of rice, oval leaf spot of graminea, pitting disease, ryegrass blast, and Johnson spot, is a plant-pathogenic fungus that causes an important disease affecting rice. It is now known that M...
, Leptosphaeria maculans
Leptosphaeria maculans
Leptosphaeria maculans is a fungal pathogen that is the causal agent of blackleg disease on Brassica crops. The major yield loss is due to stem canker....
, Gibberella zeae
Gibberella zeae
Gibberella zeae, also known by the name of its anamorph Fusarium graminearum, is a plant pathogen which causes the wheat headblight disease. Fusarium head blight is a devastating disease on wheat and barley. The pathogen is responsible for billions of dollars in economic losses worldwide each year...
and Nectria haematococca. In Neurospora crassa
Neurospora crassa
Neurospora crassa is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" refers to the characteristic striations on the spores. The first published account of this fungus was from an infestation of French bakeries in 1843. N...
, sequences mutated by RIP are often methylated
DNA methylation
DNA methylation is a biochemical process that is important for normal development in higher organisms. It involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring...
de novo.
RIP occurs during the sexual stage in haploid nuclei after fertilization but prior to meiotic
Meiosis
Meiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....
DNA replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
. In Neurospora crassa
Neurospora crassa
Neurospora crassa is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" refers to the characteristic striations on the spores. The first published account of this fungus was from an infestation of French bakeries in 1843. N...
, repeat sequences
Repeated sequence (DNA)
In the study of DNA sequences, one can distinguish two main types of repeated sequence:*Tandem repeats:**Satellite DNA**Minisatellite**Microsatellite*Interspersed repeats:**SINEs...
of at least 400 base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
s in length are vulnerable to RIP. Repeats with as low as 80% nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
identity may also be subject to RIP. Though the exact mechanism of repeat recognition and mutagenesis are poorly understood, RIP results in repeated sequences undergoing multiple transition mutations.
The RIP mutations do not seem to be limited to repeated sequences. Indeed, for example, in the phytopathogenic fungus L. maculans, RIP mutations are found in single copy regions, adjacent to the repeated elements. These regions are either non-coding regions, or genes encoding small secreted proteins including avirulence genes.
The degree of RIP within these single copy regions was proportional to their proximity to repetitive elements .
Rep and Kistler have speculated that the presence of highly repetitive regions containing transposons, may promote mutation of resident effector genes . So the presence of effector genes within such regions is suggested to promote their adaptation and diversification when exposed to strong selection pressure .
As RIP mutation is traditionally observed to be restricted to repetitive regions and not single copy regions, Fudal et al suggested that leakage of RIP mutation might occur within a relatively short distance of a RIP-affected repeat. Indeed, this has been reported in N. crassa whereby leakage of RIP was detected in single copy sequences at least 930 bp from the boundary of neighbouring duplicated sequences .
To elucidate the mechanism of detection of repeated sequences leading to RIP may allow to understand how the flanking sequences may also be affected.
mechanism
RIP causes GGuanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
:C
Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...
to A
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
:T
Thymine
Thymine is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by methylation of uracil at...
transition
Transition (genetics)
In genetics, a transition is a point mutation that changes a purine nucleotide to another purine or a pyrimidine nucleotide to another pyrimidine . Approximately two out of three single nucleotide polymorphisms are transitions....
mutations within repeats, however, the mechanism that detects the repeated sequences is unknown. RID is the only known protein essential for RIP. It is a DNA methyltransferease-like protein, that when mutated or knocked out results in loss of RIP. Deletion of the rid homolog in Aspergillus nidulans
Aspergillus nidulans
Aspergillus nidulans is one of many species of filamentous fungi in the phylum Ascomycota...
, dmtA, results in loss of fertility while deletion of the rid homolog in Ascobolus immersens, masc1, results in fertility defects and loss of methylation induced premeiotically (MIP)
Methylation induced premeiotically
In molecular biology, methylation induced premeiotically is a process by which cytosines within repeated DNA sequences are de novo methylated prior to the sexual cycle. This process was first described in the ascomycete Ascobolus immersens...
.
consequences
RIP is believed to have evolved as a defense mechanism against Transposable ElementsTransposon
Transposable elements are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's...
, which resemble parasites
Parasitism
Parasitism is a type of symbiotic relationship between organisms of different species where one organism, the parasite, benefits at the expense of the other, the host. Traditionally parasite referred to organisms with lifestages that needed more than one host . These are now called macroparasites...
by invading and multiplying within the genome.
RIP creates multiple missense
Missense mutation
In genetics, a missense mutation is a point mutation in which a single nucleotide is changed, resulting in a codon that codes for a different amino acid . This can render the resulting protein nonfunctional...
and nonsense mutation
Nonsense mutation
In genetics, a nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product. It differs from a missense mutation, which is a point mutation...
s in the coding sequence. This hypermutation of G-C to A-T in repetitive sequences eliminates functional gene product
Gene product
A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the...
s of the sequence (if there were any to begin with). In addition, many of the C-bearing nucleotides become methylated
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
, thus decreasing transcription.
use in molecular biology
Because RIP is so efficient at detecting and mutating repeats, fungal biologists often use it as a tool for mutagenesisMutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...
. A second copy of a single-copy gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
is first transformed
Transformation (genetics)
In molecular biology transformation is the genetic alteration of a cell resulting from the direct uptake, incorporation and expression of exogenous genetic material from its surroundings and taken up through the cell membrane. Transformation occurs naturally in some species of bacteria, but it can...
into the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
. The fungus must then mate
Mating
In biology, mating is the pairing of opposite-sex or hermaphroditic organisms for copulation. In social animals, it also includes the raising of their offspring. Copulation is the union of the sex organs of two sexually reproducing animals for insemination and subsequent internal fertilization...
and go through its sexual cycle to activate the RIP machinery. Many different mutations within the duplicated gene are obtained from even a single fertilization event so that inactivated alleles, usually due to nonsense mutations, as well as alleles containing missense mutations can be obtained.