Crossover junction endodeoxyribonuclease

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Crossover junction endodeoxyribonuclease
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EC no. 3.1.22.4
CAS no. 99676-43-4
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Holliday junction resolvases
Identifiers
SymbolPDDEXK
Pfam clan CL0236
ECOD 2008.1.1

Crossover junction endodeoxyribonuclease, also known as Holliday junction resolvase, Holliday junction endonuclease, Holliday junction-cleaving endonuclease, Holliday junction-resolving endoribonuclease, crossover junction endoribonuclease, and cruciform-cutting endonuclease, is an enzyme involved in DNA repair and homologous recombination. Specifically, it performs endonucleolytic cleavage that results in single-stranded crossover between two homologous DNA molecules at the Holliday junction to produce recombinant DNA products for chromosomal segregation. This process is known as Holliday junction resolution.

Contents

Biological Function

The Holliday junction is a structure that forms during genetic recombination, and links two double-stranded DNA molecules with a single-stranded crossover, which form during mitotic and meiotic recombination. [1] Crossover junction endodeoxyribonucleases catalyze Holiday junction resolution, which is the formation of separate recombinant DNA molecules and chromosomal separation after the crossover event at the Holliday junction. [2] Crossover junction endodeoxyribonucleases with Holliday Junction resolution function have been identified in all three domains of life - bacteria, archaea, and eukarya. RuvC in bacteria, CCE1 in Saccharomyces cerevisiae, [1] and GEN1 in humans [3] are all crossover junction endodeoxyribonucleases that perform Holliday Junction resolution. Holliday junction resolution catalyzed by crossover junction endodeoxyribonuclease is shown in the figure below.

Holliday junction resolution catalyzed by crossover junction endodeoxyribonuclease. Left: First, four strands of DNA (two black and two white) combine to form two double stranded DNA molecules at a Holliday junction. Center: Next, substrate form a complex with crossover junction endodeoxyribonuclease complex for Holliday junction resolution. Right: Finally, completion of Holliday Junction Resolution results in recombinant DNA. Diagram generated based on Wyatt et al. Resolvase function.png
Holliday junction resolution catalyzed by crossover junction endodeoxyribonuclease. Left: First, four strands of DNA (two black and two white) combine to form two double stranded DNA molecules at a Holliday junction. Center: Next, substrate form a complex with crossover junction endodeoxyribonuclease complex for Holliday junction resolution. Right: Finally, completion of Holliday Junction Resolution results in recombinant DNA. Diagram generated based on Wyatt et al.

Crossover junction endodeoxyribonucleases also play key roles in DNA repair. During cell growth and meiosis, DNA double-strand breaks (DSBs) often occur, and are usually repaired by homologous recombination. [5] Because Crossover junction endodeoxyribonucleases perform Holliday Junction resolution, a crucial step of homologous recombination, they are therefore involved in repair of DSBs.

Structure

E. coli RuvC, a Crossover junction endodeoxyribonuclease, is a small protein of about 20 kD, and its active form is a dimer that requires and binds a magnesium ion [1]. RuvC is a 3-layer alpha-beta sandwich with a beta-sheet between 5 alpha-helices [6] . The enzyme contains two binding channels that contact the backbones of the Holliday junction over seven nucleotides. [7] A Holliday junction resolvase enzyme has also been identified in archaea in Pyrococcus furiosus cells - it is encoded by a gene called hjc and is composed of 123 amino acids [8] .

A figure of Thermus thermophilus RuvC in complex with a Holliday junction is shown below.

Archaea crossover junction endodeoxyribonuclease in complex with Holliday Junction DNA. Generated with 4LD0.pdb. 4LD0.png
Archaea crossover junction endodeoxyribonuclease in complex with Holliday Junction DNA. Generated with 4LD0.pdb.

Mechanism

These enzymes are highly selective for branched DNA, although induced fit occurs in the enzyme-substrate (resolvase-Holloday Junction) complex formation. [9] Much remains unknown about the exact mechanism of action, but it is known that bacteria, bacteriophages and archaea catalyze Holliday junction resolution by introducing symmetric nicks across the Holliday junction [10] . Analysis of crossover junction endodeoxyribonucleases from bacteriophages (T7 endonuclease I), bacteria (RuvC), fungi (GEN1) and humans (hMus81-Eme1) have revealed that the enzymes function in dimers, [11] and part of the resolution reaction takes place in a partially dissociated enzyme-substrate intermediate. [12]

Human Relevance

After a 20-year search, in 2008, a human crossover junction endodeoxyribonuclease, GEN1, was finally identified [13] . GEN1 performs similar functions and operates by similar mechanisms as previously studied Crossover junction endodeoxyribonuclease in bacteria, archaea, and other eukarya. [13] The enzyme is thought to play a role in Bloom's syndrome. It has been proposed that Bloom's syndrome involves the induction of DSBs via an unidentified Holliday junction resolvase. [14] It has also been shown that overexpression of Holliday Junction resolvase function is correlated with RAD51-overexpressing cancers. [15]

Related Research Articles

<span class="mw-page-title-main">Chromosomal crossover</span> Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

<span class="mw-page-title-main">Genetic recombination</span> Production of offspring with combinations of traits that differ from those found in either parent

Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes ; & (2) intrachromosomal recombination, occurring through crossing over.

<span class="mw-page-title-main">Nuclease</span> Class of enzymes which cleave nucleic acids

In biochemistry, a nuclease is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleases variously effect single and double stranded breaks in their target molecules. In living organisms, they are essential machinery for many aspects of DNA repair. Defects in certain nucleases can cause genetic instability or immunodeficiency. Nucleases are also extensively used in molecular cloning.

<span class="mw-page-title-main">RecBCD</span> Family of protein complexes in bacteria

Exodeoxyribonuclease V is an enzyme of E. coli that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host of other factors. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. It catalyses exonucleolytic cleavage in either 5′- to 3′- or 3′- to 5′-direction to yield 5′-phosphooligonucleotides.

<span class="mw-page-title-main">RuvABC</span> Protein complex

RuvABC is a complex of three proteins that mediate branch migration and resolve the Holliday junction created during homologous recombination in bacteria. As such, RuvABC is critical to bacterial DNA repair.

<span class="mw-page-title-main">Heteroduplex</span>

A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms.

<span class="mw-page-title-main">Homologous recombination</span> Genetic recombination between identical or highly similar strands of genetic material

Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids.

<span class="mw-page-title-main">Holliday junction</span> Branched nucleic acid structure

A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after Robin Holliday, the molecular biologist who proposed its existence in 1964.

Chromosome segregation is the process in eukaryotes by which two sister chromatids formed as a consequence of DNA replication, or paired homologous chromosomes, separate from each other and migrate to opposite poles of the nucleus. This segregation process occurs during both mitosis and meiosis. Chromosome segregation also occurs in prokaryotes. However, in contrast to eukaryotic chromosome segregation, replication and segregation are not temporally separated. Instead segregation occurs progressively following replication.

<span class="mw-page-title-main">Exonuclease 1</span> Protein-coding gene in the species Homo sapiens

Exonuclease 1 is an enzyme that in humans is encoded by the EXO1 gene.

<span class="mw-page-title-main">MUS81</span> Protein-coding gene in the species Homo sapiens

Crossover junction endonuclease MUS81 is an enzyme that in humans is encoded by the MUS81 gene.

<span class="mw-page-title-main">MLH3</span> Protein-coding gene in the species Homo sapiens

DNA mismatch repair protein Mlh3 is a protein that in humans is encoded by the MLH3 gene.

<span class="mw-page-title-main">EME1</span> Protein-coding gene in the species Homo sapiens

Crossover junction endonuclease EME1 is an enzyme that in humans is encoded by the EME1 gene. It forms a complex with MUS81 which resolves Holliday junctions. In mammalian cells the EME1/MUS81 protein complex is redundant for DNA damage repair with GEN1 endonuclease. In mice, EME1/MUS81 and GEN1 redundantly contribute to Holliday junction processing. When homozygous mutations of Gen1 and Eme1 were combined in mice the result was synthetic lethality at an early embryonic stage. Homozygosity for Gen1 mutations did not cause a DNA repair deficiency in mice. But when mice were both homozygous mutant for Gen1 and also heterozyous for an Emc1 mutation, they showed increased sensitivity to DNA damaging agents. This finding, indicated a redundant role of GEN1 and EME1 in DNA repair. Gen1 and Emc1 were also shown to have redundant roles in meiotic recombination.

<span class="mw-page-title-main">Branch migration</span>

Branch migration is the process by which base pairs on homologous DNA strands are consecutively exchanged at a Holliday junction, moving the branch point up or down the DNA sequence. Branch migration is the second step of genetic recombination, following the exchange of two single strands of DNA between two homologous chromosomes. The process is random, and the branch point can be displaced in either direction on the strand, influencing the degree of which the genetic material is exchanged. Branch migration can also be seen in DNA repair and replication, when filling in gaps in the sequence. It can also be seen when a foreign piece of DNA invades the strand.

Sgs1, also known as slow growth suppressor 1, is a DNA helicase protein found in Saccharomyces cerevisiae. It is a homolog of the bacterial RecQ helicase. Like the other members of the RecQ helicase family, Sgs1 is important for DNA repair. In particular, Sgs1 collaborates with other proteins to repair double-strand breaks during homologous recombination in eukaryotes.

<span class="mw-page-title-main">Stephen C. West</span> British biochemist and molecular biologist

Stephen Craig West FRS is a British biochemist and molecular biologist specialising in research on DNA recombination and repair. He is known for pioneering studies on genome instability diseases including cancer. West obtained his BSc in 1974, and his PhD in 1977, both from Newcastle University. He is currently a Principal Group Leader at the Francis Crick Institute in London. He is an honorary Professor at University College London, and at Imperial College London. In recognition of his work he was awarded the Louis-Jeantet Prize for Medicine in 2007, is a fellow of the Royal Society, the Academy of Medical Sciences, an International Member of the National Academy of Sciences, and an International Honorary Member of the American Academy of Arts and Sciences. He received the 2022 Royal Medal for 'discovering and determining the functions of key enzymes that are essential for DNA recombination, repair and the maintenance of genomes'.

<span class="mw-page-title-main">Synthesis-dependent strand annealing</span>

Synthesis-dependent strand annealing (SDSA) is a major mechanism of homology-directed repair of DNA double-strand breaks (DSBs). Although many of the features of SDSA were first suggested in 1976, the double-Holliday junction model proposed in 1983 was favored by many researchers. In 1994, studies of double-strand gap repair in Drosophila were found to be incompatible with the double-Holliday junction model, leading researchers to propose a model they called synthesis-dependent strand annealing. Subsequent studies of meiotic recombination in S. cerevisiae found that non-crossover products appear earlier than double-Holliday junctions or crossover products, challenging the previous notion that both crossover and non-crossover products are produced by double-Holliday junctions and leading the authors to propose that non-crossover products are generated through SDSA.

Sulfolobus acidocaldarius is a thermoacidophilic archaeon that belongs to the phylum Thermoproteota. S. acidocaldarius was the first Sulfolobus species to be described, in 1972 by Thomas D. Brock and collaborators. This species was found to grow optimally between 75 and 80 °C, with pH optimum in the range of 2-3.

<span class="mw-page-title-main">GEN1, Holliday junction 5' flap endonuclease</span> Protein-coding gene in the species Homo sapiens

GEN1, Holliday junction 5' flap endonuclease is a protein that in humans is encoded by the GEN1 gene.

<span class="mw-page-title-main">Double-strand break repair model</span>

A double-strand break repair model refers to the various models of pathways that cells undertake to repair double strand-breaks (DSB). DSB repair is an important cellular process, as the accumulation of unrepaired DSB could lead to chromosomal rearrangements, tumorigenesis or even cell death. In human cells, there are two main DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR relies on undamaged template DNA as reference to repair the DSB, resulting in the restoration of the original sequence. NHEJ modifies and ligates the damaged ends regardless of homology. In terms of DSB repair pathway choice, most mammalian cells appear to favor NHEJ rather than HR. This is because the employment of HR may lead to gene deletion or amplification in cells which contains repetitive sequences. In terms of repair models in the cell cycle, HR is only possible during the S and G2 phases, while NHEJ can occur throughout whole process. These repair pathways are all regulated by the overarching DNA damage response mechanism. Besides HR and NHEJ, there are also other repair models which exists in cells. Some are categorized under HR, such as synthesis-dependent strain annealing, break-induced replication, and single-strand annealing; while others are an entirely alternate repair model, namely, the pathway microhomology-mediated end joining (MMEJ).

References

  1. 1 2 Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H (December 1991). "Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure". The EMBO Journal. 10 (13): 4381–9. doi:10.1002/j.1460-2075.1991.tb05016.x. PMC   453191 . PMID   1661673.
  2. Cañas C, Suzuki Y, Marchisone C, Carrasco B, Freire-Benéitez V, Takeyasu K, Alonso JC, Ayora S (June 2014). "Interaction of branch migration translocases with the Holliday junction-resolving enzyme and their implications in Holliday junction resolution". The Journal of Biological Chemistry. 289 (25): 17634–46. doi: 10.1074/jbc.M114.552794 . PMC   4067198 . PMID   24770420.
  3. Ip SC, Rass U, Blanco MG, Flynn HR, Skehel JM, West SC (November 2008). "Identification of Holliday junction resolvases from humans and yeast". Nature. 456 (7220): 357–61. Bibcode:2008Natur.456..357I. doi:10.1038/nature07470. PMID   19020614. S2CID   4362699.
  4. Wyatt HD, West SC (September 2014). "Holliday junction resolvases". Cold Spring Harbor Perspectives in Biology. 6 (9): a023192. doi:10.1101/cshperspect.a023192. PMC   4142969 . PMID   25183833.
  5. Agmon N, Yovel M, Harari Y, Liefshitz B, Kupiec M (September 2011). "The role of Holliday junction resolvases in the repair of spontaneous and induced DNA damage". Nucleic Acids Research. 39 (16): 7009–19. doi:10.1093/nar/gkr277. PMC   3167605 . PMID   21609961.
  6. 1 2 Górecka KM, Komorowska W, Nowotny M (November 2013). "Crystal structure of RuvC resolvase in complex with Holliday junction substrate". Nucleic Acids Research. 41 (21): 9945–55. doi:10.1093/nar/gkt769. PMC   3834835 . PMID   23980027.
  7. Lilley DM (April 2017). "Holliday junction-resolving enzymes-structures and mechanisms" (PDF). FEBS Letters. 591 (8): 1073–1082. doi: 10.1002/1873-3468.12529 . PMID   27990631.
  8. Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y (August 1999). "A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea". Proceedings of the National Academy of Sciences of the United States of America. 96 (16): 8873–8. Bibcode:1999PNAS...96.8873K. doi: 10.1073/pnas.96.16.8873 . PMC   17700 . PMID   10430863.
  9. Rass U, Compton SA, Matos J, Singleton MR, Ip SC, Blanco MG, Griffith JD, West SC (July 2010). "Mechanism of Holliday junction resolution by the human GEN1 protein". Genes & Development. 24 (14): 1559–69. doi:10.1101/gad.585310. PMC   2904945 . PMID   20634321.
  10. Hadden JM, Déclais AC, Carr SB, Lilley DM, Phillips SE (October 2007). "The structural basis of Holliday junction resolution by T7 endonuclease I". Nature. 449 (7162): 621–4. Bibcode:2007Natur.449..621H. doi:10.1038/nature06158. PMID   17873858. S2CID   4403846.
  11. Shah Punatar R, Martin MJ, Wyatt HD, Chan YW, West SC (January 2017). "Resolution of single and double Holliday junction recombination intermediates by GEN1". Proceedings of the National Academy of Sciences of the United States of America. 114 (3): 443–450. doi: 10.1073/pnas.1619790114 . PMC   5255610 . PMID   28049850.
  12. Zhou R, Yang O, Déclais AC, Jin H, Gwon GH, Freeman AD, Cho Y, Lilley DM, Ha T (March 2019). "Junction resolving enzymes use multivalency to keep the Holliday junction dynamic". Nature Chemical Biology. 15 (3): 269–275. doi:10.1038/s41589-018-0209-y. PMC   6377835 . PMID   30664685.
  13. 1 2 West SC (June 2009). "The search for a human Holliday junction resolvase". Biochemical Society Transactions. 37 (Pt 3): 519–26. doi:10.1042/BST0370519. PMC   4120095 . PMID   19442245.
  14. Karow JK, Constantinou A, Li JL, West SC, Hickson ID (June 2000). "The Bloom's syndrome gene product promotes branch migration of holliday junctions". Proceedings of the National Academy of Sciences of the United States of America. 97 (12): 6504–8. Bibcode:2000PNAS...97.6504K. doi: 10.1073/pnas.100448097 . PMC   18638 . PMID   10823897.
  15. Xia J, Chen LT, Mei Q, Ma CH, Halliday JA, Lin HY, Magnan D, Pribis JP, Fitzgerald DM, Hamilton HM, Richters M, Nehring RB, Shen X, Li L, Bates D, Hastings PJ, Herman C, Jayaram M, Rosenberg SM (November 2016). "Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase". Science Advances. 2 (11): e1601605. Bibcode:2016SciA....2E1605X. doi:10.1126/sciadv.1601605. PMC   5222578 . PMID   28090586.