HERC2

HERC2, or HECT and RLD domain containing E3 ubiquitin protein ligase 2, is a giant E3 ubiquitin protein ligase, implicated in DNA repair regulation, pigmentation and neurological disorders. It is encoded by a gene of the same name belonging to the HERC family, which typically encodes large protein products with C-terminal HECT domains and one or more RCC1-like (RLD) domains.{{cite journal | vauthors = Sánchez-Tena S, Cubillos-Rojas M, Schneider T, Rosa JL | title = Functional and pathological relevance of HERC family proteins: a decade later | journal = Cellular and Molecular Life Sciences | volume = 73 | issue = 10 | pages = 1955–68 | date = May 2016 | pmid = 26801221 | doi = 10.1007/s00018-016-2139-8 | s2cid = 7457614 | pmc = 11108380 }}{{cite journal | vauthors = Hochrainer K, Mayer H, Baranyi U, Binder B, Lipp J, Kroismayr R | title = The human HERC family of ubiquitin ligases: novel members, genomic organization, expression profiling, and evolutionary aspects | journal = Genomics | volume = 85 | issue = 2 | pages = 153–64 | date = February 2005 | pmid = 15676274 | doi = 10.1016/j.ygeno.2004.10.006 }}

History

HERC2, previously referred to as the rjs gene locus, was first identified in 1990 as the gene responsible for two phenotypes in mice: the runty, jerky, sterile (rjs) phenotype and the juvenile development and fertility-2 (Jdf2) phenotype. Mutant alleles are known to cause hypo-pigmentation and pink eye phenotypes, as well reduced growth, jerky gait, male sterility, female semi-sterility, and maternal behaviour defects in mice.{{cite journal | vauthors = Lehman AL, Nakatsu Y, Ching A, Bronson RT, Oakey RJ, Keiper-Hrynko N, Finger JN, Durham-Pierre D, Horton DB, Newton JM, Lyon MF, Brilliant MH | title = A very large protein with diverse functional motifs is deficient in rjs (runty, jerky, sterile) mice | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 16 | pages = 9436–41 | date = August 1998 | pmid = 9689098 | pmc = 21356 | doi=10.1073/pnas.95.16.9436| bibcode = 1998PNAS...95.9436L | doi-access = free }}{{cite journal | vauthors = Ji Y, Walkowicz MJ, Buiting K, Johnson DK, Tarvin RE, Rinchik EM, Horsthemke B, Stubbs L, Nicholls RD | title = The ancestral gene for transcribed, low-copy repeats in the Prader-Willi/Angelman region encodes a large protein implicated in protein trafficking, which is deficient in mice with neuromuscular and spermiogenic abnormalities | journal = Human Molecular Genetics | volume = 8 | issue = 3 | pages = 533–42 | date = March 1999 | pmid = 9949213 | doi = 10.1093/hmg/8.3.533 | doi-access = free }}{{cite journal | vauthors = Brilliant MH | title = The mouse pink-eyed dilution locus: a model for aspects of Prader-Willi syndrome, Angelman syndrome, and a form of hypomelanosis of Ito | journal = Mammalian Genome | volume = 3 | issue = 4 | pages = 187–91 | date = 1992 | pmid = 1611213 | doi = 10.1007/bf00355717 | s2cid = 32406842 }}

Gene locus

The full HERC2 gene is located at 15q13, encoded by 93 exons and its transcription is under the control of a CpG rich promoter. This region on chromosome 15 is susceptible to breaks during chromosomal rearrangement and there are at least 12 partial duplicates of HERC2 between 15q11–15q13.{{cite journal | vauthors = Ji Y, Rebert NA, Joslin JM, Higgins MJ, Schultz RA, Nicholls RD | title = Structure of the highly conserved HERC2 gene and of multiple partially duplicated paralogs in human | journal = Genome Research | volume = 10 | issue = 3 | pages = 319–29 | date = March 2000 | pmid = 10720573 | pmc = 311424 | doi=10.1101/gr.10.3.319}}

At least 15 SNPs in the HERC2 gene have been identified in introns and they are strongly associated with human iris colour variability, functioning to repress expression of the neighboring downstream gene OCA2.{{cite journal | vauthors = Kayser M, Liu F, Janssens AC, Rivadeneira F, Lao O, van Duijn K, Vermeulen M, Arp P, Jhamai MM, van Ijcken WF, den Dunnen JT, Heath S, Zelenika D, Despriet DD, Klaver CC, Vingerling JR, de Jong PT, Hofman A, Aulchenko YS, Uitterlinden AG, Oostra BA, van Duijn CM | title = Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene | journal = American Journal of Human Genetics | volume = 82 | issue = 2 | pages = 411–23 | date = February 2008 | pmid = 18252221 | pmc = 2427174 | doi = 10.1016/j.ajhg.2007.10.003 }}

Protein structure

HERC2 encodes a 4834-amino acid protein with a theoretical size of 528 kDa. While a full structure has not yet been elucidated, potentially due to its large size, partial structures of its domains have been captured.{{cite journal | vauthors = Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH | title = A novel strategy for NMR resonance assignment and protein structure determination | journal = Journal of Biomolecular NMR | volume = 49 | issue = 1 | pages = 27–38 | date = January 2011 | pmid = 21161328 | pmc = 3715383 | doi = 10.1007/s10858-010-9458-0 }}

It has an N-terminal bilobed HECT domain, conferring E3 ligase functionality, as well as 3 RLD domains with seven-bladed β-propeller folds. In addition to these HERC family hallmarks, it has several other motifs; a cytochrome-b5-like domain, several potential phosphorylation sites, and a ZZ-type zinc finger motif. This is likely involved in protein binding, and has recently been identified as a SUMOylation target following DNA damage.{{cite journal | vauthors = Danielsen JR, Povlsen LK, Villumsen BH, Streicher W, Nilsson J, Wikström M, Bekker-Jensen S, Mailand N | title = DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger | journal = The Journal of Cell Biology | volume = 197 | issue = 2 | pages = 179–87 | date = April 2012 | pmid = 22508508 | pmc = 3328386 | doi = 10.1083/jcb.201106152 }}

Expression of HERC2 is ubiquitous, though particularly high in the brain and testes. Cellular localisation is predominantly to the nucleus and cytoplasm.

File:3KCI The third RLD domain of HERC2.jpg]

File:2KEO cytochrome-b5-like domain.jpg]

File:4L1M Structure of the first RCC1-like domain of HERC2.jpg]

Protein function

= Pigmentation =

SNPs found within the HERC2 gene are strongly associated with iris colour variability in humans, through effects on the expression of the downstream gene OCA2. In particular, two intronic SNPs, rs916977 and rs12913832, have been reported as good predictors of this trait, and the latter is also significantly associated with skin and hair colour. Nonetheless, the ancestral allele is associated with darker pigmentation and dominant over the lighter pigment recessive allele.{{cite journal | vauthors = Branicki W, Brudnik U, Wojas-Pelc A | title = Interactions between HERC2, OCA2 and MC1R may influence human pigmentation phenotype | journal = Annals of Human Genetics | volume = 73 | issue = 2 | pages = 160–70 | date = March 2009 | pmid = 19208107 | doi = 10.1111/j.1469-1809.2009.00504.x | s2cid = 5233533 }}{{cite journal | vauthors = Eiberg H, Troelsen J, Nielsen M, Mikkelsen A, Mengel-From J, Kjaer KW, Hansen L | title = Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression | journal = Human Genetics | volume = 123 | issue = 2 | pages = 177–87 | date = March 2008 | pmid = 18172690 | doi = 10.1007/s00439-007-0460-x | s2cid = 9886658 }} The rs12913832 SNP, located in intron 86 of the HERC2 gene contains a silencing sequence that can inhibit the expression of OCA2 and, if two copies of the recessive allele are present, can result in blue eyes.{{cite journal | vauthors = Sturm RA, Larsson M | title = Genetics of human iris colour and patterns | journal = Pigment Cell & Melanoma Research | volume = 22 | issue = 5 | pages = 544–62 | date = October 2009 | pmid = 19619260 | doi = 10.1111/j.1755-148X.2009.00606.x | s2cid = 893259 | url = http://www.bashaar.org.il/files/4150.pdf }} This genotype is present in almost all people with blue eyes and is hypothesised as being the founder mutation of blue eyes in humans.{{cite web|url=http://www.nbcnews.com/id/22934464|title=Here's what made those brown eyes blue|author=Bryner J|date=2008-01-31|work=Health News|publisher=NBC News|access-date=2008-11-06|quote=}}; {{cite web|url=http://www.livescience.com/health/080131-blue-eyes.html|title=One Common Ancestor Behind Blue Eyes|author=Bryner J|date=2008-01-31|work=LiveScience|publisher=Imaginova Corp.|access-date=2008-11-06|quote=}}; {{cite web|url=http://www.ku.dk/english/news/?content=http://www.ku.dk/english/news/blue-eyes.htm|title=Blue-eyed humans have a single, common ancestor|date=2008-01-30|work=News|publisher=University of Copenhagen|access-date=2008-11-06|archive-date=2008-11-08|archive-url=https://web.archive.org/web/20081108022318/http://www.ku.dk/english/news/?content=http://www.ku.dk/english/news/blue-eyes.htm|url-status=dead}}{{cite journal | vauthors = Sturm RA, Duffy DL, Zhao ZZ, Leite FP, Stark MS, Hayward NK, Martin NG, Montgomery GW | title = A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color | journal = American Journal of Human Genetics | volume = 82 | issue = 2 | pages = 424–31 | date = February 2008 | pmid = 18252222 | pmc = 2427173 | doi = 10.1016/j.ajhg.2007.11.005 }}{{cite journal | vauthors = Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Barta C, Lu RB, Zhukova OV, Kim JJ, Siniscalco M, New M, Li H, Kajuna SL, Manolopoulos VG, Speed WC, Pakstis AJ, Kidd JR, Kidd KK | title = A global view of the OCA2-HERC2 region and pigmentation | journal = Human Genetics | volume = 131 | issue = 5 | pages = 683–96 | date = May 2012 | pmid = 22065085 | pmc = 3325407 | doi = 10.1007/s00439-011-1110-x }}

The rs916977 SNP is most common in Europe; particularly in the north and east, where it nears fixation. The variant is also found at high frequencies in North Africa, the Near East, Oceania and the Americas.{{cite web|url=https://alfred.med.yale.edu/alfred/SiteTable1A_working.asp?siteuid=SI663423Y|title=Allele Frequency For Polymorphic Site: rs916977|publisher=ALFRED|access-date=22 June 2016}}

= DNA repair pathways =

HERC2 is a component of the replication fork and essential for DNA damage repair pathways. Regulating DNA repair pathways is necessary, as unchecked they can target and excise undamaged DNA, potentially leading to mutation.{{cite journal | vauthors = Branum ME, Reardon JT, Sancar A | title = DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations | journal = The Journal of Biological Chemistry | volume = 276 | issue = 27 | pages = 25421–6 | date = July 2001 | pmid = 11353769 | doi = 10.1074/jbc.M101032200 | doi-access = free }}

It is involved in coordinating the Chk1-directed DNA damage/cell cycle checkpoint response by regulating the stability of the deubiquitination enzyme USP20. Under normal conditions HERC2 associates with USP20 and ubiquitinates it for degradation. Under replication stress, for example a DNA polymerase mismatch error, USP20 disassociates from HERC2 and deubiquitinates claspin, stabilising it to then bind and activate Chk1. This allows for DNA replication to be paused and the error corrected.{{cite journal | vauthors = Zhu M, Zhao H, Liao J, Xu X | title = HERC2/USP20 coordinates CHK1 activation by modulating CLASPIN stability | journal = Nucleic Acids Research | volume = 42 | issue = 21 | pages = 13074–81 | date = December 2014 | pmid = 25326330 | pmc = 4245974 | doi = 10.1093/nar/gku978 }}{{cite journal | vauthors = Yuan J, Luo K, Deng M, Li Y, Yin P, Gao B, Fang Y, Wu P, Liu T, Lou Z | title = HERC2-USP20 axis regulates DNA damage checkpoint through Claspin | journal = Nucleic Acids Research | volume = 42 | issue = 21 | pages = 13110–21 | date = December 2014 | pmid = 25355518 | pmc = 4245938 | doi = 10.1093/nar/gku1034 }}{{cite journal | vauthors = Izawa N, Wu W, Sato K, Nishikawa H, Kato A, Boku N, Itoh F, Ohta T | title = HERC2 Interacts with Claspin and regulates DNA origin firing and replication fork progression | journal = Cancer Research | volume = 71 | issue = 17 | pages = 5621–5 | date = September 2011 | pmid = 21775519 | doi = 10.1158/0008-5472.CAN-11-0385 | doi-access = free }}

At the site of doubles stranded breaks, HERC2 facilitates the binding of RNF8, a RING finger ubiquitin ligase to the E2 ubiquitin-conjugating enzyme UBC13. This association is required for RNF8 mediated Lys-63 poly-ubiquitination signalling, which both recruits and retains repair factors at the site of DNA damage to commence homologous recombination repair.{{cite journal | vauthors = Bekker-Jensen S, Rendtlew Danielsen J, Fugger K, Gromova I, Nerstedt A, Lukas C, Bartek J, Lukas J, Mailand N | title = HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes | language = En | journal = Nature Cell Biology | volume = 12 | issue = 1 | pages = 80–6; sup pp 1–12 | date = January 2010 | pmid = 20023648 | doi = 10.1038/ncb2008 | s2cid = 9996031 }}

HERC2 is also involved in regulating nucleotide excision repair by ubiquitinating the XPA repair protein for proteolysis. XPA is involved in recognising DNA damage and provides a scaffold for other repair factors to bind at the damage site.{{cite journal | vauthors = Lee TH, Park JM, Leem SH, Kang TH | title = Coordinated regulation of XPA stability by ATR and HERC2 during nucleotide excision repair | language = En | journal = Oncogene | volume = 33 | issue = 1 | pages = 19–25 | date = January 2014 | pmid = 23178497 | doi = 10.1038/onc.2012.539 | doi-access = free }}{{cite journal | vauthors = Kang TH, Lindsey-Boltz LA, Reardon JT, Sancar A | title = Circadian control of XPA and excision repair of cisplatin-DNA damage by cryptochrome and HERC2 ubiquitin ligase | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 11 | pages = 4890–5 | date = March 2010 | pmid = 20304803 | pmc = 2841896 | doi = 10.1073/pnas.0915085107 | bibcode = 2010PNAS..107.4890K | doi-access = free }}

= Centrosome assembly =

HERC2 has been implicated in regulating stable centrosome architecture in conjunction with NEURL4 other ubiquitinated binding partners. Its absence is associated with aberrant centrosome morphology.{{cite journal | vauthors = Al-Hakim AK, Bashkurov M, Gingras AC, Durocher D, Pelletier L | title = Interaction proteomics identify NEURL4 and the HECT E3 ligase HERC2 as novel modulators of centrosome architecture | journal = Molecular & Cellular Proteomics | volume = 11 | issue = 6 | pages = M111.014233 | date = June 2012 | pmid = 22261722 | pmc = 3433907 | doi = 10.1074/mcp.M111.014233 | doi-access = free }}

= Iron metabolism =

HERC2 has recently been associated with regulating iron metabolism through ubiquitinating the F-box and leucine-rich repeat protein 5 (FBXL5) for proteasomal degradation. FBXL5 regulates the stability of the iron regulatory protein (IR2), which in turn controls the stability of proteins overlooking cellular iron homeostasis. Depletion of HERC2 results in decreased cellular iron levels. Iron is an essential nutrient in cells, but high levels can be cytotoxic, so maintaining cellular levels is important.

= Other functions =

HERC2 helps to regulate p53 signalling by facilitating the oligomerization of p53, which is necessary for its transcriptional activity. Silencing of HERC2 reportedly inhibits the expression of genes regulated by p53 and also results in increased cellular growth.{{cite journal | vauthors = Cubillos-Rojas M, Amair-Pinedo F, Peiró-Jordán R, Bartrons R, Ventura F, Rosa JL | title = The E3 ubiquitin protein ligase HERC2 modulates the activity of tumor protein p53 by regulating its oligomerization | journal = The Journal of Biological Chemistry | volume = 289 | issue = 21 | pages = 14782–95 | date = May 2014 | pmid = 24722987 | pmc = 4031533 | doi = 10.1074/jbc.M113.527978 | doi-access = free }}

Clinical significance

The 15q11-q13 locus of HERC2 is also associated with Angelman syndrome (AS), specifically when a region of this locus is deleted. Similar to the rjs phenotype attributed to HERC2 in mice, AS is associated with seizures, developmental delay, intellectual disability and jerky movements. While a variety of disturbances to this locus can cause AS, all known mechanisms affect the functioning and expression of the E6AP E3 ligase, which also sits at this locus. HER2 is an allosteric activator of E6AP, and lies at the most commonly deleted region in AS.{{cite journal | vauthors = Kühnle S, Kogel U, Glockzin S, Marquardt A, Ciechanover A, Matentzoglu K, Scheffner M | title = Physical and functional interaction of the HECT ubiquitin-protein ligases E6AP and HERC2 | journal = The Journal of Biological Chemistry | volume = 286 | issue = 22 | pages = 19410–6 | date = June 2011 | pmid = 21493713 | pmc = 3103319 | doi = 10.1074/jbc.M110.205211 | doi-access = free }} Its deletion could result in the inactivation of E6AP and consequently the development of AS.{{cite journal | vauthors = Harlalka GV, Baple EL, Cross H, Kühnle S, Cubillos-Rojas M, Matentzoglu K, Patton MA, Wagner K, Coblentz R, Ford DL, Mackay DJ, Chioza BA, Scheffner M, Rosa JL, Crosby AH | title = Mutation of HERC2 causes developmental delay with Angelman-like features | journal = Journal of Medical Genetics | volume = 50 | issue = 2 | pages = 65–73 | date = February 2013 | pmid = 23243086 | doi = 10.1136/jmedgenet-2012-101367 | s2cid = 206997462 | url = https://kops.uni-konstanz.de/bitstream/123456789/21937/2/Harlalka_219370.pdf }}

In Old Order Amish families, a homozygous proline to leucine missense mutation within the first RLD domain has been implicated in a neurodevelopmental disorder with autism and features resembling AS.{{cite journal | vauthors = Puffenberger EG, Jinks RN, Wang H, Xin B, Fiorentini C, Sherman EA, Degrazio D, Shaw C, Sougnez C, Cibulskis K, Gabriel S, Kelley RI, Morton DH, Strauss KA | title = A homozygous missense mutation in HERC2 associated with global developmental delay and autism spectrum disorder | journal = Human Mutation | volume = 33 | issue = 12 | pages = 1639–46 | date = December 2012 | pmid = 23065719 | doi = 10.1002/humu.22237 | s2cid = 10372349 | doi-access = free }} In addition, a homozygous deletion of both OCA2 and HERC2 genes was recently reported as presenting with severe developmental abnormalities.{{cite journal | vauthors = Morice-Picard F, Benard G, Rezvani HR, Lasseaux E, Simon D, Moutton S, Rooryck C, Lacombe D, Baumann C, Arveiler B | title = Complete loss of function of the ubiquitin ligase HERC2 causes a severe neurodevelopmental phenotype | language = En | journal = European Journal of Human Genetics | volume = 25 | issue = 1 | pages = 52–58 | date = January 2016 | pmid = 27759030 | pmc = 5159772 | doi = 10.1038/ejhg.2016.139 }} These phenotypes are suggestive of a role for HERC2 in normal neurodevelopment.

Certain alleles of HERC2 has recently been implicated in increasing the risk of iris cancer. Due its role in pigment determination, three HERC2 SNPs have been highlighted as associated with uveal melanoma.{{cite journal | vauthors = Ferguson R, Vogelsang M, Ucisik-Akkaya E, Rai K, Pilarski R, Martinez CN, Rendleman J, Kazlow E, Nagdimov K, Osman I, Klein RJ, Davidorf FH, Cebulla CM, Abdel-Rahman MH, Kirchhoff T | title = Genetic markers of pigmentation are novel risk loci for uveal melanoma | journal = Scientific Reports | volume = 6 | issue = 1 | pages = 31191 | date = August 2016 | pmid = 27499155 | pmc = 4976361 | doi = 10.1038/srep31191 | bibcode = 2016NatSR...631191F }} HERC2 frameshift mutations have also been described in colorectal cancers.{{cite journal | vauthors = Yoo NJ, Park SW, Lee SH | title = Frameshift mutations of ubiquitination-related genes HERC2, HERC3, TRIP12, UBE2Q1 and UBE4B in gastric and colorectal carcinomas with microsatellite instability | journal = Pathology | volume = 43 | issue = 7 | pages = 753–5 | date = December 2011 | pmid = 22124266 | doi = 10.1097/pat.0b013e32834c7e78 }}

In accordance to its role in facilitating p53 oligomerization, HERC2 may be causally related to Li-Fraumeni syndrome and Li-Fraumeni-like syndromes, which occur in the absence of sufficient p53 oligomerization.

Interactions

HERC2 is known to interact with the following:

RNF8
FBXL5{{cite journal | vauthors = Moroishi T, Yamauchi T, Nishiyama M, Nakayama KI | title = HERC2 targets the iron regulator FBXL5 for degradation and modulates iron metabolism | journal = The Journal of Biological Chemistry | volume = 289 | issue = 23 | pages = 16430–41 | date = June 2014 | pmid = 24778179 | pmc = 4047410 | doi = 10.1074/jbc.M113.541490 | doi-access = free }}
OCA2
UBC13
USP20
XPA
Claspin
E6AP
NEURL4
RNF168
BRCA1{{cite journal | vauthors = Wu W, Sato K, Koike A, Nishikawa H, Koizumi H, Venkitaraman AR, Ohta T | title = HERC2 is an E3 ligase that targets BRCA1 for degradation | journal = Cancer Research | volume = 70 | issue = 15 | pages = 6384–92 | date = August 2010 | pmid = 20631078 | doi = 10.1158/0008-5472.CAN-10-1304 | doi-access = free }}
p53
LRRK2{{cite journal | vauthors = Imai Y, Kobayashi Y, Inoshita T, Meng H, Arano T, Uemura K, Asano T, Yoshimi K, Zhang CL, Matsumoto G, Ohtsuka T, Kageyama R, Kiyonari H, Shioi G, Nukina N, Hattori N, Takahashi R | title = The Parkinson's Disease-Associated Protein Kinase LRRK2 Modulates Notch Signaling through the Endosomal Pathway | journal = PLOS Genetics | volume = 11 | issue = 9 | pages = e1005503 | date = September 2015 | pmid = 26355680 | pmc = 4565672 | doi = 10.1371/journal.pgen.1005503 | doi-access = free }}

Evolution

The HERC2 variation for blue eyes first appears around 14,000 years ago in Italy and the Caucasus.{{cite journal|last1=Fu|first1=Qiaomei|last2=Posth|first2=Cosimo|title=The genetic history of Ice Age Europe|journal=Nature|volume=534|issue=7606|pages=200–205|date=May 2, 2016|doi=10.1038/nature17993|pmid=27135931 |pmc=4943878|bibcode=2016Natur.534..200F|hdl=10211.3/198594}}