Serpin genes AtSRP2 and AtSRP3 are required for normal growth sensitivity to a DNA alkylating agent in Arabidopsis
© Ahn et al; licensee BioMed Central Ltd. 2009
Received: 15 December 2008
Accepted: 11 May 2009
Published: 11 May 2009
The complex responses of plants to DNA damage are incompletely understood and the role of members of the serpin protein family has not been investigated. Serpins are functionally diverse but structurally conserved proteins found in all three domains of life. In animals, most serpins have regulatory functions through potent, irreversible inhibition of specific serine or cysteine proteinases via a unique suicide-substrate mechanism. Plant serpins are also potent proteinase inhibitors, but their physiological roles are largely unknown.
Six Arabidopsis genes encoding full-length serpins were differentially expressed in developing seedlings and mature tissues. Basal levels of AtSRP2 (At2g14540) and AtSRP3 (At1g64030) transcripts were highest in reproductive tissues. AtSRP2 was induced 5-fold and AtSRP3 100-fold after exposure of seedlings to low concentrations of methyl methanesulfonate (MMS), a model alkylating reagent that causes DNA damage. Homozygous T-DNA insertion mutants atsrp2 and atsrp3 exhibited no differential growth when mutant and wild-type plants were left untreated or exposed to γ-radiation or ultraviolet light. In contrast, atsrp2 and atsrp3 plants exhibited greater root length, leaf number and overall size than wild-type plants when exposed to MMS. Neither of the two serpins was required for meiosis. GFP-AtSRP2 was localized to the nucleus, whereas GFP-AtSRP3 was cytosolic, suggesting that they target different proteinases. Induction of cell cycle- and DNA damage-related genes AtBRCA1, AtBARD1, AtRAD51, AtCYCB1;1 and AtCYCD1;1, but not AtATM, was reduced relative to wild-type in atsrp2 and atsrp3 mutants exposed to MMS.
Expression of specific serpin genes (AtSRP2 and AtSRP3 in Arabidopsis) is required for normal responses of plants following exposure to alkylating genotoxins such as MMS.
DNA damage results from exposure to specific chemicals in the environment, UV light, ionizing radiation and errors in DNA replication and proofreading. Plants utilize several pathways for DNA repair, including photoreactivation, nucleotide excision repair, base excision repair, mismatch repair and double-stranded break repair . Methyl methanesulfonate (MMS) is a simple, direct alkylating agent recognized as a standard for genotoxicity assays of environmental pollutants . MMS has been widely utilized as a γ-radiation mimic in the belief it causes double-stranded breaks (DSBs). A recent report found, however, that no MMS-mediated DSBs could be detected in vivo in yeast or mammalian cells, and those reported previously were almost certainly artefacts . Molecular responses of organisms to alkylating phytotoxins are likely to be distinct from those to ionizing radiation.
Many intra- and extracellular processes in plant growth, development and responses to stress involve specific proteolytic enzyme activities. The Arabidopsis genome contains 656 known and putative peptidases  but the functions of only a tiny minority are known. Furthermore, little is known of the control of proteolytic activity in planta by endogenous peptidase inhibitors, including the serpins [5, 6], which are one of seven families of peptidase inhibitors in Arabidopsis . Serpins are metastable inhibitors with a unique, irreversible mechanism of action .
Almost all plant serpins studied are potent inhibitors of mammalian proteinases of the chymotrypsin family in vitro [8–12]. An Arabidopsis serpin, AtSerpin1 (At1g47710), was shown to inhibit the endogenous cysteine proteinase Metacaspase 9 (AtMC9) in vitro  but no other putative endogenous targets for plant serpins have been identified. Plant serpins are likely to function in direct defence against proteinases from pests and pathogens and in the regulation of endogenous proteolytic events, but no functions have been demonstrated [5, 6].
Here we report the differential basal expression of six Arabidopsis serpin genes and the effect of MMS exposure of seedlings on the activity of AtSRP2 (At2g14540) and AtSRP3 (At1g64030), both specifically expressed in reproductive tissues. We determine the subcellular localizations of AtSRP2 and AtSRP3 and examine the growth responses of atsrp2 and atsrp3 mutants (vs wild-type) to MMS, γ-radiation and UV light treatments. Finally we compare the induction levels of cell cycle-related genes in the atsrp2 and atsrp3 plants compared to wild-type after exposure to MMS.
Arabidopsisserpin genes are differentially expressed
AtSRP2 and AtSRP3are upregulated following MMS treatment of seedlings
Wild-type (5-d) seedlings were transplanted to liquid media containing 200 ppm MMS and transcript levels of AtSRP2 and AtSRP3 determined by quantitative RT-PCR. AtSRP2 and AtSRP3 were induced ~5-fold and ~100-fold, respectively, after 2 d (Figure 2C). In a separate experiment, wild-type seedlings (5-d) were exposed to MMS for 1 and 3 h but no induction was detected. In untreated seedlings (5-d) and in seedlings 1 and 3 h after exposure to γ-radiation (125 Gy) no AtSRP2 and AtSRP3 transcripts were detected using semiquantitative RT-PCR (data not shown).
Subcellular localization of AtSRP2 and AtSRP3
GFP-AtSRP2 was localized to the nucleus whereas GFP-AtSRP3 was localized to the cytosol (as was GFP alone, as expected) (Figure 2D). DAPI staining confirmed the identity of the nucleus.
Identification of T-DNA insertion mutants
atsrp2 and atsrp3mutants grow faster than wild-type plants when exposed to MMS but not to γ-radiation or UV-C
Induction of DNA repair- and cell cycle-related genes is reduced in atsrp2 and atsrp3mutants exposed to MMS
Diversity of Arabidopsisserpin reactive centres and differential expression
The reactive centres of the Arabidopsis serpins are highly diverse (Figure 1), suggesting a range of target proteinases and therefore distinct biochemical pathways in which the serpins might participate. The only specific target proteinase suggested for a plant serpin to date is the cysteine proteinase Metacaspase 9 (AtMC9) for AtSerpin1 . Differential expression of the serpin genes (Figure 2A and 2B) is corroborated by AtProteome data  and provides more evidence for functional diversity. The nuclear localization of AtSRP2 is consistent with predictions  based on WoLF PSORT and contrasts with the cytosolic localization of AtSRP3 (Figure 2D). AtSRP2 contains the nuclear localization signal PKKK at the distal end of the RCL (Figure 1); the one-residue difference between this and the corresponding sequence in AtSRP3, PPKK, appears sufficient to retain the latter serpin in the cytosol.
Responses of AtSRP2 and AtSRP3are specific to MMS-induced DNA damage
A test of cross-sensitivity of a collection of MMS-sensitive yeast mutants to hydroxyurea, UV light and γ-radiation found only 41 of 103 mutants showed cross-sensitivity to all three treatments . Deficiency in ATM (ataxia telangiectasia mutated gene) in plants and mammals confers hypersensitivity to γ-radiation and MMS but not to UV light [16, 17]. These and other studies show different sources of DNA damage cause distinct types of lesions and forms of cell cycle arrest. This is consistent with the differential responses of our serpin mutants (vs. wild-type) to MMS but not to UV-C or γ-radiation.
Knockouts of AtSRP2 and AtSRP3transiently reduce responses to MMS exposure
Mutants atsrp2 and atsrp3 exposed to MMS displayed lower levels of induction of AtBRCA1, AtBARD1, AtRAD51 and AtCYCB1;1, as well as a downregulation of AtCYCD1;1, after 1 d compared to wild-type. Expression levels returned to wild-type levels 2 d after MMS exposure (Figure 6A–C). Thus AtSRP2 and AtSRP3 may be required for relatively early responses to alkylation damage. In humans, BRCA1 appears to be involved in all phases of the cell cycle  and BRCA1 deficiency causes abnormalities in the S-phase and G2/M checkpoint . RAD51 is involved in homologous DNA repair and interacts with BRCA1 ; moreover, transcription of RAD51 (and AtRAD51) is highest in S-phase . Yeast is most sensitive to MMS during S-phase . Thus down-regulation of AtBRCA1 and AtRAD51 in the atsrp2 and atsrp3 mutants may be associated with abnormal S-phase and a defective G2/M checkpoint.
Transcripts of mitotic cyclin AtCYCB1;1 are reported to accumulate around the G2/M transition , whereas AtCYCD1;1 promotes not only transition through G0/G1/S but also S/G2/M . Cyclins (type D) are expressed throughout the cell cycle in proliferating plant tissues . The CYCD1 interaction with cyclin-dependent protein kinase A (CDKA) acts at the G1/S and the G2/M boundaries in Arabidopsis . These results suggest AtSRP2 and AtSRP3 may be involved in the regulation of different cell-cycle checkpoints in response to MMS-induced DNA damage. Interestingly, we detected no difference in AtATM expression between mutants and wild-type (Figure 6A–C). The Arabidopsis atm mutant is hypersensitive to γ-radiation and MMS but not to UV light . The functions of AtSRP2 and AtSRP3 may be overlapping, as is found for AtATM and AtATR , and they may be independent of AtATM in a DNA damage-response pathway; alternatively, both serpins may act downstream of AtATM.
Regulation of the cell cycle includes mechanisms for cell cycle arrest following DNA damage to allow time for repair of the DNA . Failure of these checkpoint responses leads to a build up of harmful mutations. Cell cycle arrest results in reduced rates of growth and a delay in the development of tissues. Lesions such as specific gene knockouts can interfere with the signal transduction required for the detection of DNA damage and responses including cell cycle arrest. We observed greater rates of growth of our atsrp2 and atsrp3 mutant plants exposed to MMS than that of wild-type plants given the same treatment. Thus we speculate that knockouts of these serpin genes result in de-repression of cell division following MMS treatment, thereby implicating AtSRP2 and AtSRP3 in the normal signal transduction required for the relevant checkpoint responses. It is important to note that Hefner et al. (2006) found that plant cell-cycle responses to ionizing radiation that were observed in meristematic tissues did not occur in strictly somatic tissues .
Serpin-mediated control of proteolysis and its links to DNA damage responses
Sequence analysis strongly suggests AtSRP2 and AtSRP3 are inhibitory serpins [5, 6]. AtSerpin1 can inhibit AtMC9, which is Arg/Lys specific . In contrast, we predict AtSRP2 and AtSRP3 inhibit proteinases that cleave at small residues (Figure 1). Since AtSRP2 is localized to the nucleus, its candidate targets are different than those for AtSRP3, which was localized to the cytosol (Figure 2D). Seventeen expressed genes encoding serpins with either P1 Gly or P1 Cys were recently identified from several monocots and eudicots . Thus it is likely that serpins in other plant species are functional homologues of AtSRP2 and AtSRP3.
The inhibitory serpins encoded in the Arabidopsis genome display a variety of reactive centres, suggesting a range of target proteinases, and are differentially expressed, indicating a diversity of functions. Our results strongly suggest a new role for plant serpins, which is likely to involve inhibition of specific endogenous proteinases that target Gly and Cys residues to regulate plant responses to alkylating DNA damage. AtSRP2 and AtSRP3 are found in the cytosol and nucleus, respectively, and thus may perform distinct tasks in the signalling required for these responses. The requirement for AtSRP2 and AtSRP3 in responses to exposure to alkylating genotoxins but not to UV-C or γ-radiation provides support for distinct biochemical pathways associated with these stresses. We suggest our data have potential importance for development of crops with greater resistance to alkylating genotoxins.
Plant materials and treatments with MMS, UV-C and γ-radiation
Seeds of Arabidopsis thaliana (Col-0) were sterilized in 4% sodium hypochlorite for 5 min and rinsed five times with sterilized water. Plants were grown in a chamber at 24°C (16 h light/8 h dark). For MMS treatment, B5 medium (Gamborg's B5 medium ; Gibco) containing 2% sucrose and 1/2 MS medium (half-strength Murashige & Skoog medium ; Sigma) containing 0.5% sucrose were used. Seedlings (5-d) on sterile media (both types) were transplanted into 5 ml of each liquid medium containing zero to 100 ppm MMS (Sigma). Samples were incubated for 15 d on an orbital shaker with constant light. For measurement of root lengths, seedlings (5-d) were transplanted into each solid medium containing MMS and measurements made 15 d later. Seedlings (2 weeks old) were transplanted to media containing MMS for measurements of plant size and leaf number made 4 weeks later. Seedlings (5-d) were exposed to UV-C light (1 and 10 J cm-1) in open Petri dishes using a Stratalinker 2400 (Stratagene). For γ-radiation treatment, seedlings (5-d) were irradiated with zero to 200 Gy using a 60Co source and then placed into a growth chamber at 24°C for 3 weeks.
RNA isolation and RT-PCR
Total RNA from Arabidopsis tissues was extracted using the RNeasy Plant Mini kit (Qiagen) with 1 U RNase-free DNase (Qiagen). Reverse transcription was performed using 5 μg total RNA as described . cDNAs were used as templates for semi-quantitative RT-PCR and real-time RT-PCR. Primer sequences for all experiments are given in Additional File 1 (Tables one-five). RT-PCR products were cloned and sequences confirmed.
Isolation of knockout mutants
Seeds from atsrp2 and atsrp3 T-DNA insertion mutants were obtained from the Salk Institute Genomic Analysis Laboratory. For selection of lines homozygous for the T-DNA insertion, primers a-f and LB were used to amplify left border-flanking and serpin DNA from genomic DNA. For confirmation of knockouts of AtSRP2 and AtSRP3 expression in atsrp2 and atsrp3 mutants, semi-quantitative RT-PCR was performed using total RNA from developing siliques.
AtSRP2 and AtSRP3 full-length cDNAs were amplified by PCR and cloned into a 326-GFP plasmid such that GFP was joined to the N-terminus of the serpins. Fusion constructs expressed under control of the cauliflower mosaic virus 35S promoter were introduced into Arabidopsis protoplasts isolated from seedlings (10-d) by polyethylene glycol-mediated transformation. The protoplasts were incubated at 24°C for 24 h. Expression of fusion proteins was observed using a Leica TCS SP2 confocal system.
reactive centre loop
We thank the following people from Macquarie University, Sydney: Debra Birch, Nicole Vella, Krystyna Tomsia and Hermant Bhatta for assistance with microscopy; Yu-Kyung Kim for technical assistance; Roger Hiller for advice on molecular biology; and Tom Joss for helpful discussions. We thank Anne Britt (University of California, Davis, USA) for helpful comments on the manuscript. Joon-Woo Ahn is supported by a Macquarie University Research Excellence Scholarship. Funding was through a Macquarie University Research and Development Grant.
- Kimura S, Sakaguchi K: DNA repair in plants. Chem Rev. 2006, 106: 753-766. 10.1021/cr040482n.PubMedView ArticleGoogle Scholar
- Knight AW, Keenan PO, Goddard NJ, Fielden PR, Walmsley RM: A yeast-based cytotoxicity and genotoxicity assay for environmental monitoring using novel portable instrumentation. J Environ Monit. 2004, 6: 71-79. 10.1039/b310206h.PubMedView ArticleGoogle Scholar
- Lundin C, North M, Erixon K, Walters K, Jenssen D, Goldman AS, Helleday T: Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks. Nucl Acids Res. 2005, 33: 3799-3811. 10.1093/nar/gki681.PubMedPubMed CentralView ArticleGoogle Scholar
- Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ: MEROPS: the peptidase database. Nucl Acids Res. 2008, 36: D320-325. 10.1093/nar/gkm954.PubMedPubMed CentralView ArticleGoogle Scholar
- Roberts TH, Hejgaard J: Serpins in plants and green algae. Funct Integr Genomics. 2008, 8: 1-27. 10.1007/s10142-007-0059-2.PubMedView ArticleGoogle Scholar
- Hejgaard J, Roberts TH: Plant serpins. Molecular and Cellular Aspects of the Serpinopathies and Disorders in Serpin Activity. Edited by: Silverman GA, Lomas DA. New Jersey: World Scientific; 2007:279-300.View ArticleGoogle Scholar
- Huntington JA, Read RJ, Carrell RW: Structure of a serpin-protease complex shows inhibition by deformation. Nature. 2000, 407: 923-926. 10.1038/35038119.PubMedView ArticleGoogle Scholar
- Ostergaard H, Rasmussen SK, Roberts TH, Hejgaard J: Inhibitory serpins from wheat grain with reactive centers resembling glutamine-rich repeats of prolamin storage proteins – Cloning and characterization of five major molecular forms. J Biol Chem. 2000, 275: 33272-33279. 10.1074/jbc.M004633200.PubMedView ArticleGoogle Scholar
- Hejgaard J: Inhibitory serpins from rye grain with glutamine as P-1 and P-2 residues in the reactive center. FEBS Lett. 2001, 488: 149-153. 10.1016/S0014-5793(00)02425-X.PubMedView ArticleGoogle Scholar
- Hejgaard J, Laing WA, Marttila S, Gleave AP, Roberts TH: Serpins in fruit and vegetative tissues of apple (Malus domestica): expression of four serpins with distinct reactive centres and characterisation of a major inhibitory seed form, MdZ1b. Funct Plant Biol. 2005, 32: 517-527. 10.1071/FP04220.View ArticleGoogle Scholar
- Vercammen D, Belenghi B, Cotte van de B, Beunens T, Gavigan JA, De Rycke R, Brackenier A, Inze D, Harris JL, Van Breusegem F: Serpin1 of Arabidopsis thaliana is a suicide inhibitor for Metacaspase 9. J Mol Biol. 2006, 364: 625-636. 10.1016/j.jmb.2006.09.010.PubMedView ArticleGoogle Scholar
- Yoo BC, Aoki K, Xiang Y, Campbell LR, Hull RJ, Xoconostle-Cazares B, Monzer J, Lee JY, Ullman DE, Lucas WJ: Characterization of Cucurbita maxima phloem serpin-1 (CmPS-1) – A developmentally regulated elastase inhibitor. J Biol Chem. 2000, 275: 35122-35128. 10.1074/jbc.M006060200.PubMedView ArticleGoogle Scholar
- Schechter I, Berger A: On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun. 1967, 27: 157-162. 10.1016/S0006-291X(67)80055-X.PubMedView ArticleGoogle Scholar
- Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S: Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science. 2008, 320: 938-941. 10.1126/science.1157956.PubMedView ArticleGoogle Scholar
- Chang M, Bellaoui M, Boone C, Brown GW: A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci USA. 2002, 99: 16934-16939. 10.1073/pnas.262669299.PubMedPubMed CentralView ArticleGoogle Scholar
- Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell. 2001, 12: 2987-3003.PubMedPubMed CentralView ArticleGoogle Scholar
- Garcia V, Bruchet H, Camescasse D, Granier F, Bouchez D, Tissier A: AtATM is essential for meiosis and the somatic response to DNA damage in plants. Plant Cell. 2003, 15: 119-132. 10.1105/tpc.006577.PubMedPubMed CentralView ArticleGoogle Scholar
- Deng CX: BRCA1: cell cycle checkpoint, genetic instability, DNA damage response and cancer evolution. Nucl Acids Res. 2006, 34: 1416-1426. 10.1093/nar/gkl010.PubMedPubMed CentralView ArticleGoogle Scholar
- Xu X, Weaver Z, Linke SP, Li C, Gotay J, Wang XW, Harris CC, Ried T, Deng CX: Centrosome amplification and a defective G2-M cell cycle checkpoint induce genetic instability in BRCA1 exon 11 isoform-deficient cells. Mol Cell. 1999, 3: 389-395. 10.1016/S1097-2765(00)80466-9.PubMedView ArticleGoogle Scholar
- Pellegrini L, Yu DS, Lo T, Anand S, Lee M, Blundell TL, Venkitaraman AR: Insights into DNA recombination from the structure of a RAD51-BRCA2 complex. Nature. 2002, 420: 287-293. 10.1038/nature01230.PubMedView ArticleGoogle Scholar
- Doutriaux MP, Couteau F, Bergounioux C, White C: Isolation and characterisation of the RAD51 and DMC1 homologs from Arabidopsis thaliana. Mol Gen Genet. 1998, 257: 283-291. 10.1007/s004380050649.PubMedView ArticleGoogle Scholar
- Tercero JA, Diffley JF: Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature. 2001, 412: 553-557. 10.1038/35087607.PubMedView ArticleGoogle Scholar
- Doerner P, Jorgensen JE, You R, Steppuhn J, Lamb C: Control of root growth and development by cyclin expression. Nature. 1996, 380: 520-523. 10.1038/380520a0.PubMedView ArticleGoogle Scholar
- Koroleva OA, Tomlinson M, Parinyapong P, Sakvarelidze L, Leader D, Shaw P, Doonan JH: CycD1, a putative G1 cyclin from Antirrhinum majus, accelerates the cell cycle in cultured tobacco BY-2 cells by enhancing both G1/S entry and progression through S and G2 phases. Plant Cell. 2004, 16: 2364-2379. 10.1105/tpc.104.023754.PubMedPubMed CentralView ArticleGoogle Scholar
- Sorrell DA, Combettes B, Chaubet-Gigot N, Gigot C, Murray JA: Distinct cyclin D genes show mitotic accumulation or constant levels of transcripts in tobacco bright yellow-2 cells. Plant Physiol. 1999, 119: 343-352. 10.1104/pp.119.1.343.PubMedPubMed CentralView ArticleGoogle Scholar
- Culligan KM, Robertson CE, Foreman J, Doerner P, Britt AB: ATR and ATM play both distinct and additive roles in response to ionizing radiation. Plant J. 2006, 48: 947-961. 10.1111/j.1365-313X.2006.02931.x.PubMedView ArticleGoogle Scholar
- Hefner E, Huefner N, Britt AB: Tissue-specific regulation of cell-cycle responses to DNA damage in Arabidopsis seedlings. DNA Repair. 2006, 5: 102-110. 10.1016/j.dnarep.2005.08.013.PubMedView ArticleGoogle Scholar
- Gamborg OL, Miller RA, Ojima K: Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res. 1968, 50: 151-158. 10.1016/0014-4827(68)90403-5.PubMedView ArticleGoogle Scholar
- Murashige T, Skoog F: A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant. 1962, 15: 473-497. 10.1111/j.1399-3054.1962.tb08052.x.View ArticleGoogle Scholar
- Kim M, Ahn JW, Jin UH, Choi D, Paek KH, Pai HS: Activation of the programmed cell death pathway by inhibition of proteasome function in plants. J Biol Chem. 2003, 278: 19406-19415. 10.1074/jbc.M210539200.PubMedView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.