Editing Point mutation (section)

==Repeat-induced point mutation==
In [[molecular biology]], '''repeat-induced point mutation''' or '''RIP''' is a process by which [[DNA]] accumulates [[Guanine|G]]:[[Cytosine|C]] to [[Adenine|A]]:[[Thymine|T]] [[Transition (genetics)|transition]] mutations. Genomic evidence indicates that RIP occurs or has occurred in a variety of fungi<ref name="pmid20854921">{{cite journal| author=Clutterbuck AJ| title=Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes. | journal=Fungal Genet Biol | year= 2011 | volume= 48 | issue= 3 | pages= 306–26 | pmid=20854921 | doi=10.1016/j.fgb.2010.09.002}}</ref> while experimental evidence indicates that RIP is active in ''[[Neurospora crassa]]'',<ref name="pmid2960455">{{cite journal |vauthors=Selker EU, Cambareri EB, Jensen BC, Haack KR |title=Rearrangement of duplicated DNA in specialized cells of Neurospora |journal=Cell |volume=51 |issue=5 |pages=741–752 |date=December 1987 |pmid=2960455 |doi=10.1016/0092-8674(87)90097-3|s2cid=23036409 }}</ref> ''[[Podospora anserina]]'',<ref name="pmid11359565">{{cite journal |vauthors=Graïa F, Lespinet O, Rimbault B, Dequard-Chablat M, Coppin E, Picard M |title=Genome quality control: RIP (repeat-induced point mutation) comes to Podospora |journal=Mol Microbiol |volume=40 |issue=3 |pages=586–595 |date=May 2001 |pmid=11359565 |doi=10.1046/j.1365-2958.2001.02367.x|s2cid=25096512 |doi-access=free }}</ref> ''[[Magnaporthe grisea]]'',<ref name="pmid12207702">{{cite journal |vauthors=Ikeda K, Nakayashiki H, Kataoka T, Tamba H, Hashimoto Y, Tosa Y, Mayama S |title=Repeat-induced point mutation (RIP) in ''Magnaporthe grisea'': implications for its sexual cycle in the natural field context |journal=Mol Microbiol |volume=45 |issue=5 |pages=1355–1364 |date=September 2002 |pmid=12207702 |doi=10.1046/j.1365-2958.2002.03101.x|doi-access=free }}</ref> ''[[Leptosphaeria maculans]]'',<ref name="pmid12742061">{{cite journal |vauthors=Idnurm A, Howlett BJ |title=Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete ''Leptosphaeria maculans'' |journal=Fungal Genet Biol |volume=39 |issue=1 |pages=31–37 |date=June 2003 |pmid=12742061 |doi=10.1016/S1087-1845(02)00588-1}}</ref> ''[[Gibberella zeae]]'',<ref name="pmid17823352">{{cite journal  |vauthors=Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma LJ, etal |title=The ''Fusarium graminearum'' genome reveals a link between localized polymorphism and pathogen specialization |journal=Science |volume=317 |issue=5843 |pages=1400–2 |date=September 2007 |pmid=17823352 |doi=10.1126/science.1143708|bibcode=2007Sci...317.1400C |s2cid=11080216 }}</ref> ''[[Nectria haematococca]]''<ref name="pmid19714214">{{cite journal  |vauthors=Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, etal |title=The genome of ''Nectria haematococca'': contribution of supernumerary chromosomes to gene expansion |journal=PLOS Genet |volume=5 |issue=8 |date=August 2009 |pmid=19714214 |doi=10.1371/journal.pgen.1000618 |pmc=2725324 |pages=e1000618 |doi-access=free }}</ref> and ''[[Paecilomyces variotii]]''.<ref>{{Cite journal |last1=Urquhart |first1=Andrew S. |last2=Mondo |first2=Stephen J. |last3=Mäkelä |first3=Miia R. |last4=Hane |first4=James K. |last5=Wiebenga |first5=Ad |last6=He |first6=Guifen |last7=Mihaltcheva |first7=Sirma |last8=Pangilinan |first8=Jasmyn |last9=Lipzen |first9=Anna |last10=Barry |first10=Kerrie |last11=de Vries |first11=Ronald P. |last12=Grigoriev |first12=Igor V. |last13=Idnurm |first13=Alexander |date=2018-12-13 |title=Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales) |journal=Frontiers in Microbiology |language=English |volume=9 |page=3058 |doi=10.3389/fmicb.2018.03058 |doi-access=free |pmid=30619145 |pmc=6300479 |issn=1664-302X|hdl=20.500.11937/74553 |hdl-access=free }}</ref> In ''[[Neurospora crassa]]'', sequences mutated by RIP are often [[DNA methylation|methylated]] ''de novo''.<ref name="pmid2960455" />

RIP occurs during the sexual stage in [[Haploid cell#Haploid and monoploid|haploid nuclei]] after fertilization but prior to [[meiosis|meiotic]] [[DNA replication]].<ref name="pmid2960455" /> In ''[[Neurospora crassa]]'', [[Repeated sequence (DNA)|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 mutation]]s.

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.<ref>{{cite journal  |vauthors=Van de Wouw AP, Cozijnsen AJ, Hane JK, etal |title=Evolution of linked avirulence effectors in ''Leptosphaeria maculans'' is affected by genomic environment and exposure to resistance genes in host plants |journal=PLOS Pathog. |volume=6 |issue=11 |pages=e1001180 |year=2010 |pmid=21079787 |pmc=2973834 |doi=10.1371/journal.ppat.1001180 |doi-access=free }}</ref>

Rep and Kistler have speculated that the presence of highly repetitive regions containing transposons, may promote mutation of resident effector genes.<ref>{{cite journal |vauthors=Rep M, Kistler HC |title=The genomic organization of plant pathogenicity in Fusarium species |journal=Curr. Opin. Plant Biol. |volume=13 |issue=4 |pages=420–6 |date=August 2010 |pmid=20471307 |doi=10.1016/j.pbi.2010.04.004 |bibcode=2010COPB...13..420R |url=https://naldc-legacy.nal.usda.gov/naldc/download.xhtml?id=45784&content=PDF |access-date=29 December 2018 |archive-date=2 June 2020 |archive-url=https://web.archive.org/web/20200602073324/https://naldc-legacy.nal.usda.gov/naldc/download.xhtml?id=45784&content=PDF |url-status=dead |url-access=subscription }}</ref> So the presence of effector genes within such regions is suggested to promote their adaptation and diversification when exposed to strong selection pressure.<ref>{{cite journal |author=Farman ML |title=Telomeres in the rice blast fungus ''Magnaporthe oryzae'': the world of the end as we know it |journal=FEMS Microbiol. Lett. |volume=273 |issue=2 |pages=125–32 |date=August 2007 |pmid=17610516 |doi=10.1111/j.1574-6968.2007.00812.x |doi-access=free }}</ref>

As RIP mutation is traditionally observed to be restricted to repetitive regions and not single copy regions, Fudal ''et al.''<ref>{{cite journal  |vauthors=Fudal I, Ross S, Brun H, etal |title=Repeat-induced point mutation (RIP) as an alternative mechanism of evolution toward virulence in ''Leptosphaeria maculans'' |journal=Mol. Plant Microbe Interact. |volume=22 |issue=8 |pages=932–41 |date=August 2009 |pmid=19589069 |doi=10.1094/MPMI-22-8-0932 |doi-access=free |bibcode=2009MPMI...22..932F }}</ref>  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.<ref>{{cite journal |vauthors=Irelan JT, Hagemann AT, Selker EU |title=High frequency repeat-induced point mutation (RIP) is not associated with efficient recombination in Neurospora |journal=Genetics |volume=138 |issue=4 |pages=1093–103 |date=December 1994 |doi=10.1093/genetics/138.4.1093 |pmid=7896093 |pmc=1206250 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=7896093}}</ref>
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 [[Guanine|G]]:[[Cytosine|C]] to [[Adenine|A]]:[[Thymine|T]] [[Transition (genetics)|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.<ref name="pmid12072568">{{cite journal|vauthors=Freitag M, Williams RL, Kothe GO, Selker EU | title=A cytosine methyltransferase homologue is essential for repeat-induced point mutation in ''Neurospora crassa'' | journal=Proc Natl Acad Sci U S A | year= 2002 | volume= 99 | issue= 13 | pages= 8802–7 | pmid=12072568 | doi=10.1073/pnas.132212899 | pmc=124379| bibcode=2002PNAS...99.8802F | doi-access=free }}</ref> Deletion of the ''rid'' homolog in ''[[Aspergillus nidulans]]'', ''dmtA'', results in loss of fertility<ref name="pmid18575630">{{cite journal|vauthors=Lee DW, Freitag M, Selker EU, Aramayo R | title=A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. | journal=PLOS ONE | year= 2008 | volume= 3 | issue= 6 | pages= e2531 | pmid=18575630 | doi=10.1371/journal.pone.0002531 | pmc=2432034| bibcode=2008PLoSO...3.2531L | doi-access=free }}</ref> while deletion of the ''rid'' homolog in ''[[Ascobolus immersens]]'', ''masc1'', results in fertility defects and loss of [[methylation induced premeiotically|methylation induced premeiotically (MIP)]].<ref name="pmid9346245">{{cite journal |vauthors=Malagnac F, Wendel B, Goyon C, Faugeron G, Zickler D, Rossignol JL, etal | title=A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure. | journal=Cell | year= 1997 | volume= 91 | issue= 2 | pages= 281–90 | pmid=9346245 | doi= 10.1016/S0092-8674(00)80410-9 | s2cid=14143830 | doi-access=free }}</ref>

===Consequences===

RIP is believed to have evolved as a defense mechanism against [[Transposon|transposable elements]], which resemble [[Parasitism|parasites]] by invading and multiplying within the genome.
RIP creates multiple [[Missense mutation|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 [[Methylation|methylated]], thus decreasing transcription.

===Use in molecular biology===

Because RIP is so efficient at detecting and mutating repeats, biologists working on ''[[Neurospora crassa]]'' have used it as a tool for [[mutagenesis]]. A second copy of a single-copy [[gene]] is first [[Transformation (genetics)|transformed]] into the [[genome]]. The fungus must then [[mating|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.<ref name="pmid2150906">{{cite journal| author=Selker EU| title=Premeiotic instability of repeated sequences in Neurospora crassa. | journal=Annu Rev Genet | year= 1990 | volume= 24 | pages= 579–613 | pmid=2150906 | doi=10.1146/annurev.ge.24.120190.003051 }}</ref>