The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development

. 2019 Jul ; 31 (7) : 1579-1597. [epub] 20190429

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid31036599

The maintenance of genome integrity over cell divisions is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is the STRUCTURAL MAINTENANCE OF CHROMOSOME5 (SMC5) and SMC6 (SMC5/6) complex, related to the cohesin and condensin complexes that control sister chromatid alignment and chromosome condensation, respectively. Here, we characterize NON-SMC ELEMENT4 (NSE4) paralogs of the SMC5/6 complex in Arabidopsis (Arabidopsis thaliana). NSE4A is expressed in meristems and accumulates during DNA damage repair. Partial loss-of-function nse4a mutants are viable but hypersensitive to DNA damage induced by zebularine. In addition, nse4a mutants produce abnormal seeds, with noncellularized endosperm and embryos that maximally develop to the heart or torpedo stage. This phenotype resembles the defects in cohesin and condensin mutants and suggests a role for all three SMC complexes in differentiation during seed development. By contrast, NSE4B is expressed in only a few cell types, and loss-of-function mutants do not have any obvious abnormal phenotype. In summary, our study shows that the NSE4A subunit of the SMC5-SMC6 complex is essential for DNA damage repair in somatic tissues and plays a role in plant reproduction.

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Abdelsamad A., Pecinka A. (2014). Pollen-specific activation of Arabidopsis retrogenes is associated with global transcriptional reprogramming. Plant Cell 26: 3299–3313. PubMed PMC

Alabert C., Groth A. (2012). Chromatin replication and epigenome maintenance. Nat. Rev. Mol. Cell Biol. 13: 153–167. PubMed

Anders S., Huber W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11: R106. PubMed PMC

Awasthi P., Foiani M., Kumar A. (2015). ATM and ATR signaling at a glance. J. Cell Sci. 128: 4255–4262. PubMed

Baroux C., Autran D. (2015). Chromatin dynamics during cellular differentiation in the female reproductive lineage of flowering plants. Plant J. 83: 160–176. PubMed PMC

Baroux C., Pecinka A., Fuchs J., Schubert I., Grossniklaus U. (2007). The triploid endosperm genome of Arabidopsis adopts a peculiar, parental-dosage-dependent chromatin organization. Plant Cell 19: 1782–1794. PubMed PMC

Bowman J.L., Mansfield S.G., Modrusan Z., Reiser L., Fischer R.L., Haughn G.W., Feldman K.A., Webb M.C. (1994). Ovules. In Arabidopsis, Bowman J., ed (New York: Springer; ), pp. 297–331.

Brudno M., Do C.B., Cooper G.M., Kim M.F., Davydov E., Green E.D., Sidow A., Batzoglou S., Batzoglou S.; NISC Comparative Sequencing Program (2003). LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721–731. PubMed PMC

Castresana J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17: 540–552. PubMed

Chiolo I., Minoda A., Colmenares S.U., Polyzos A., Costes S.V., Karpen G.H. (2011). Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 144: 732–744. PubMed PMC

Colón-Carmona A., You R., Haimovitch-Gal T., Doerner P. (1999). Technical advance: Spatio-temporal analysis of mitotic activity with a labile cyclin-GUS fusion protein. Plant J. 20: 503–508. PubMed

De Piccoli G., Torres-Rosell J., Aragón L. (2009). The unnamed complex: What do we know about Smc5-Smc6? Chromosome Res. 17: 251–263. PubMed

De Schutter K., Joubès J., Cools T., Verkest A., Corellou F., Babiychuk E., Van Der Schueren E., Beeckman T., Kushnir S., Inzé D., De Veylder L. (2007). Arabidopsis WEE1 kinase controls cell cycle arrest in response to activation of the DNA integrity checkpoint. Plant Cell 19: 211–225. PubMed PMC

Diaz M., Pecinka A. (2017). Seeds as emerging hotspot for maintenance of genome stability. Cytologia (Tokyo) 82: 467–480.

Diaz M., Pecinka A. (2018). Scaffolding for repair: Understanding molecular functions of the SMC5/6 complex. Genes (Basel) 9: 36. PubMed PMC

Duan X., Yang Y., Chen Y.-H., Arenz J., Rangi G.K., Zhao X., Ye H. (2009). Architecture of the Smc5/6 complex of Saccharomyces cerevisiae reveals a unique interaction between the Nse5–6 subcomplex and the hinge regions of Smc5 and Smc6. J. Biol. Chem. 284: 8507–8515. PubMed PMC

Edgar R.C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792–1797. PubMed PMC

Frazer K.A., Pachter L., Poliakov A., Rubin E.M., Dubchak I. (2004). VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 32: W273-279. PubMed PMC

Hanin M., Mengiste T., Bogucki A., Paszkowski J. (2000). Elevated levels of intrachromosomal homologous recombination in Arabidopsis overexpressing the MIM gene. Plant J. 24: 183–189. PubMed

Hirano T. (2006). At the heart of the chromosome: SMC proteins in action. Nat. Rev. Mol. Cell Biol. 7: 311–322. PubMed

Hirano T. (2012). Condensins: Universal organizers of chromosomes with diverse functions. Genes Dev. 26: 1659–1678. PubMed PMC

Huang L., Yang S., Zhang S., Liu M., Lai J., Qi Y., Shi S., Wang J., Wang Y., Xie Q., Yang C. (2009). The Arabidopsis SUMO E3 ligase AtMMS21, a homologue of NSE2/MMS21, regulates cell proliferation in the root. Plant J. 60: 666–678. PubMed

Hudson J.J.R., Bednarova K., Kozakova L., Liao C., Guerineau M., Colnaghi R., Vidot S., Marek J., Bathula S.R., Lehmann A.R., Palecek J. (2011). Interactions between the Nse3 and Nse4 components of the SMC5-6 complex identify evolutionarily conserved interactions between MAGE and EID Families. PLoS One 6: e17270. PubMed PMC

Ishida T., Fujiwara S., Miura K., Stacey N., Yoshimura M., Schneider K., Adachi S., Minamisawa K., Umeda M., Sugimoto K. (2009). SUMO E3 ligase HIGH PLOIDY2 regulates endocycle onset and meristem maintenance in Arabidopsis. Plant Cell 21: 2284–2297. PubMed PMC

Jeppsson K., Carlborg K.K., Nakato R., Berta D.G., Lilienthal I., Kanno T., Lindqvist A., Brink M.C., Dantuma N.P., Katou Y., Shirahige K., Sjögren C. (2014a). The chromosomal association of the Smc5/6 complex depends on cohesion and predicts the level of sister chromatid entanglement. PLoS Genet. 10: e1004680. PubMed PMC

Jeppsson K., Kanno T., Shirahige K., Sjögren C. (2014b). The maintenance of chromosome structure: Positioning and functioning of SMC complexes. Nat. Rev. Mol. Cell Biol. 15: 601–614. PubMed

Kagale S., Robinson S.J., Nixon J., Xiao R., Huebert T., Condie J., Kessler D., Clarke W.E., Edger P.P., Links M.G., Sharpe A.G., Parkin I.A.P. (2014). Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell 26: 2777–2791. PubMed PMC

Kanno T., Berta D.G., Sjögren C. (2015). The Smc5/6 complex is an ATP-dependent intermolecular DNA linker. Cell Reports 12: 1471–1482. PubMed

Kegel A., Sjögren C. (2010). The Smc5/6 complex: More than repair? Cold Spring Harb. Symp. Quant. Biol. 75: 179–187. PubMed

Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S.L. (2013). TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14: R36. PubMed PMC

Kozak J., West C.E., White C., da Costa-Nunes J.A., Angelis K.J. (2009). Rapid repair of DNA double strand breaks in Arabidopsis thaliana is dependent on proteins involved in chromosome structure maintenance. DNA Repair (Amst.) 8: 413–419. PubMed

Kwak J.S., Son G.H., Kim S.-I., Song J.T., Seo H.S. (2016). Arabidopsis HIGH PLOIDY2 sumoylates and stabilizes Flowering Locus C through its E3 ligase activity. Front. Plant Sci. 7: 530. PubMed PMC

Lampropoulos A., Sutikovic Z., Wenzl C., Maegele I., Lohmann J.U., Forner J. (2013). GreenGate---A novel, versatile, and efficient cloning system for plant transgenesis. PLoS One 8: e83043. PubMed PMC

Li G., Zou W., Jian L., Qian J., Deng Y., Zhao J. (2017). Non-SMC elements 1 and 3 are required for early embryo and seedling development in Arabidopsis. J. Exp. Bot. 68: 1039–1054. PubMed PMC

Li X., Zhang Y., Clarke J.D., Li Y., Dong X. (1999). Identification and cloning of a negative regulator of systemic acquired resistance, SNI1, through a screen for suppressors of npr1-1. Cell 98: 329–339. PubMed

Liu C.-M., Meinke D.W. (1998). The titan mutants of Arabidopsis are disrupted in mitosis and cell cycle control during seed development. Plant J. 16: 21–31. PubMed

Liu C.M., McElver J., Tzafrir I., Joosen R., Wittich P., Patton D., Van Lammeren A.A.M., Meinke D. (2002). Condensin and cohesin knockouts in Arabidopsis exhibit a titan seed phenotype. Plant J. 29: 405–415. PubMed

Liu C.-H., Finke A., Díaz M., Rozhon W., Poppenberger B., Baubec T., Pecinka A. (2015). Repair of DNA damage induced by the cytidine analog zebularine requires ATR and ATM in Arabidopsis. Plant Cell 27: 1788–1800. PubMed PMC

Liu M., Shi S., Zhang S., Xu P., Lai J., Liu Y., Yuan D., Wang Y., Du J., Yang C. (2014). SUMO E3 ligase AtMMS21 is required for normal meiosis and gametophyte development in Arabidopsis. BMC Plant Biol. 14: 153. PubMed PMC

Lu Q., Tang X., Tian G., Wang F., Liu K., Nguyen V., Kohalmi S.E., Keller W.A., Tsang E.W.T., Harada J.J., Rothstein S.J., Cui Y. (2010). Arabidopsis homolog of the yeast TREX-2 mRNA export complex: Components and anchoring nucleoporin. Plant J. 61: 259–270. PubMed

Mengiste T., Revenkova E., Bechtold N., Paszkowski J. (1999). An SMC-like protein is required for efficient homologous recombination in Arabidopsis. EMBO J. 18: 4505–4512. PubMed PMC

Menolfi D., Delamarre A., Lengronne A., Pasero P., Branzei D. (2015). Essential roles of the Smc5/6 complex in replication through natural pausing sites and endogenous DNA damage tolerance. Mol. Cell 60: 835–846. PubMed PMC

Mosher R.A., Durrant W.E., Wang D., Song J., Dong X. (2006). A comprehensive structure-function analysis of Arabidopsis SNI1 defines essential regions and transcriptional repressor activity. Plant Cell 18: 1750–1765. PubMed PMC

Mozgova I., Hennig L. (2015). The polycomb group protein regulatory network. Annu. Rev. Plant Biol. 66: 269–296. PubMed

Nagai T., Ibata K., Park E.S., Kubota M., Mikoshiba K., Miyawaki A. (2002). A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 20: 87–90. PubMed

Palecek J.J., Gruber S. (2015). Kite proteins: A superfamily of SMC/kleisin partners conserved across bacteria, archaea, and eukaryotes. Structure 23: 2183–2190. PubMed

Palecek J., Vidot S., Feng M., Doherty A.J., Lehmann A.R. (2006). The Smc5-Smc6 DNA repair complex. bridging of the Smc5-Smc6 heads by the KLEISIN, Nse4, and non-Kleisin subunits. J. Biol. Chem. 281: 36952–36959. PubMed

Paterson A.H., et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556. PubMed

Pebernard S., Wohlschlegel J., McDonald W.H., Yates J.R. III, Boddy M.N. (2006). The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex. Mol. Cell. Biol. 26: 1617–1630. PubMed PMC

Potts P.R., Yu H. (2007). The SMC5/6 complex maintains telomere length in ALT cancer cells through SUMOylation of telomere-binding proteins. Nat. Struct. Mol. Biol. 14: 581–590. PubMed

Puchta H., Swoboda P., Hohn B. (1995). Induction of intrachromosomal homologous recombination in whole plants. Plant J. 7: 203–210.

Räschle M., et al. (2015). DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. Science 348: 1253671. PubMed PMC

Schoft V.K., Chumak N., Mosiolek M., Slusarz L., Komnenovic V., Brownfield L., Twell D., Kakutani T., Tamaru H. (2009). Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep. 10: 1015–1021. PubMed PMC

Schubert V. (2009). SMC proteins and their multiple functions in higher plants. Cytogenet. Genome Res. 124: 202–214. PubMed

Slotkin R.K., Vaughn M., Borges F., Tanurdzić M., Becker J.D., Feijó J.A., Martienssen R.A. (2009). Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461–472. PubMed PMC

Stangeland B., Salehian Z. (2002). An improved clearing method for GUS assay in Arabidopsis endosperm and seeds. Plant Mol. Biol. Report. 20: 107–114.

Stingele J., Jentsch S. (2015). DNA-protein crosslink repair. Nat. Rev. Mol. Cell Biol. 16: 455–460. PubMed

Tian G., Lu Q., Zhang L., Kohalmi S.E., Cui Y. (2011). Detection of protein interactions in plant using a gateway compatible bimolecular fluorescence complementation (BiFC) system. J. Vis. Exp. 55: 3473. PubMed PMC

Torres-Rosell J., Sunjevaric I., De Piccoli G., Sacher M., Eckert-Boulet N., Reid R., Jentsch S., Rothstein R., Aragón L., Lisby M. (2007). The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus. Nat. Cell Biol. 9: 923–931. PubMed

Tretyakova N.Y., Groehler A. IV, Ji S. (2015). DNA-protein cross-links: Formation, structural identities, and biological outcomes. Acc. Chem. Res. 48: 1631–1644. PubMed PMC

Tzafrir I., McElver J.A., Liu Cm C.M., Yang L.J., Wu J.Q., Martinez A., Patton D.A., Meinke D.W. (2002). Diversity of TITAN functions in Arabidopsis seed development. Plant Physiol. 128: 38–51. PubMed PMC

Uhlmann F. (2016). SMC complexes: From DNA to chromosomes. Nat. Rev. Mol. Cell Biol. 17: 399–412. PubMed

Vielle-Calzada J.-P., Baskar R., Grossniklaus U. (2000). Delayed activation of the paternal genome during seed development. Nature 404: 91–94. PubMed

Watanabe K., Pacher M., Dukowic S., Schubert V., Puchta H., Schubert I. (2009). The STRUCTURAL MAINTENANCE OF CHROMOSOMES 5/6 complex promotes sister chromatid alignment and homologous recombination after DNA damage in Arabidopsis thaliana. Plant Cell 21: 2688–2699. PubMed PMC

Wu N., Yu H. (2012). The Smc complexes in DNA damage response. Cell Biosci. 2: 5. PubMed PMC

Xu P., Yuan D., Liu M., Li C., Liu Y., Zhang S., Yao N., Yang C. (2013). AtMMS21, an SMC5/6 complex subunit, is involved in stem cell niche maintenance and DNA damage responses in Arabidopsis roots. Plant Physiol. 161: 1755–1768. PubMed PMC

Yan S., Wang W., Marqués J., Mohan R., Saleh A., Durrant W.E., Song J., Dong X. (2013). Salicylic acid activates DNA damage responses to potentiate plant immunity. Mol. Cell 52: 602–610. PubMed PMC

Yuan D., Lai J., Xu P., Zhang S., Zhang J., Li C., Wang Y., Du J., Liu Y., Yang C. (2014). AtMMS21 regulates DNA damage response and homologous recombination repair in Arabidopsis. DNA Repair (Amst.) 21: 140–147. PubMed

Zabrady K., Adamus M., Vondrova L., Liao C., Skoupilova H., Novakova M., Jurcisinova L., Alt A., Oliver A.W., Lehmann A.R., Palecek J.J. (2016). Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA. Nucleic Acids Res. 44: 1064–1079. PubMed PMC

Zhang S., Qi Y., Liu M., Yang C. (2013). SUMO E3 ligase AtMMS21 regulates drought tolerance in Arabidopsis thaliana(F). J. Integr. Plant Biol. 55: 83–95. PubMed

Zhang X., Henriques R., Lin S.-S., Niu Q.-W., Chua N.-H. (2006). Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat. Protoc. 1: 641–646. PubMed

Zhao X., Blobel G. (2005). A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. Proc. Natl. Acad. Sci. USA 102: 4777–4782. PubMed PMC

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