Anti Microbes SIDMR6 1

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CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers

broad-spectrum disease resistance
Daniela Paula de Toledo Thomazella, Quinton Brail, Douglas Dahlbeck, Brian Staskawicz*
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA 94720
*corresponding author: [email protected]
Keywords: disease resistance, tomato, DMR6, CRISPR-Cas9 technology, crop engineering, food security
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bioRxiv preprint doi: https://doi.org/10.1101/064824; this version posted July 23, 2016. The copyright holder for this preprint (which was
Abstract
Pathogenic microbes are responsible for severe production losses in crops worldwide.
The use of disease resistant crop varieties can be a sustainable approach to meet the food demand
of the world’s growing population. However, classical plant breeding is usually laborious and
time-consuming, thus hampering efficient improvement of many crops. With the advent of
genome editing technologies, in particular the CRISPR-Cas9 (clustered regularly interspaced
short palindromic repeats-Cas9) system, we are now able to introduce improved crop traits in a
rapid and efficient manner. In this work, we genome edited durable disease resistance in tomato
by modifying a specific gene associated with disease resistance. Recently, it was demonstrated
that inactivation of a single gene called DMR6 (downy mildew resistance 6) confers resistance to
several pathogens in Arabidopsis thaliana. This gene is specifically up-regulated during
pathogen infection, and mutations in the dmr6 gene results in increased salicylic acid levels. The
tomato SlDMR6-1 orthologue Solyc03g080190 is also up-regulated during infection by
Pseudomonas syringae pv. tomato and Phytophthora capsici. Using the CRISPR-Cas9 system,
we generated tomato plants with small deletions in the SlDMR6-1 gene that result in frameshift
and premature truncation of the protein. Remarkably, these mutants do not have significant
detrimental effects in terms of growth and development under greenhouse conditions and show
disease resistance against different pathogens, including P. syringae, P. capsici and
Xanthomonas spp.
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Introduction
Tomato (Solanum lycopersicum) is one of the most important crops and the second most consumed
vegetable in the world. In particular, the United States is one of the world's leading producers of
tomatoes, accounting for a $2-billion-dollar annual market. Tomato is part of the Solanaceae family,
which also includes many other economically important crops, such as pepper, potato and eggplant.
Despite its great economic importance, plant pathogens (e.g. Pseudomonas syringae, Phytophthora spp.,
Xanthomonas spp.) are still a major limiting factor for tomato production around the world (Schwartz et
al., 2015). Plant breeding can be a sustainable and effective approach to obtain disease resistance in
tomato. However, the classical plant-breeding methods are in general slow, laborious and time-
consuming. Targeted genome editing has emerged as a promising alternative to classical breeding. This
strategy employs programmable nucleases that enable a broad range of genetic modifications by inducing
double-strand breaks in the DNA at specific genomic locations. These breaks stimulate error-prone non-
homologous end joining (NHEJ) or homology-directed repair (HR) machineries. NHEJ repair can cause
insertions or deletions (indels) around the DNA breaks, whereas HR can repair double-strand breaks
using a homologous repair template (Joung and Sander, 2013; Liu and Fan, 2014; Urnov et al., 2010).
Until recently, there were two types of programmable nucleases available for genome editing: the
ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator Like Effector Nucleases). These
chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a
non-specific DNA cleavage domain (Joung and Sander, 2013; Urnov et al., 2010). However, given the
complexity and high costs for designing these proteins, these technologies have not been widely adopted
by the plant research community. In the recent years, a novel precise tool for targeted genome editing was
developed. It is based on the bacterial CRISPR-associated protein-9 nuclease (Cas9) from Streptococcus
pyogenes (Liu and Fan, 2014). The CRISPR-Cas9 system is a bacterial immune system that has been
modified for genome engineering. It is based on the Cas9 nuclease and an engineered single guide RNA
(sgRNA) that specifies a targeted nucleic acid sequence. The target specificity relies on ribonucleotide-
protein complex formation and not on protein-DNA interaction and thus gRNAs can be designed easily
and economically to specifically target any sequence in the genome that is close to an NGG sequence
[protospacer adjacent motif (PAM)], required for Cas9 recognition (Liu and Fan, 2014). Since the first
application of the CRISPR-Cas9 system in mammalian cells (Cong et al., 2013), it has been extensively
used for genome editing in many organisms (Hwang et al., 2013; Dicarlo et al., 2013; Jiang et al., 2013;
Xie and Yang, 2013; Y., Wang et al., 2013; Friedland et al., 2013; Yu et al., 2013; Nakayama et al.,
2013; Editor, 2014; D., Li et al., 2013; Shen et al., 2013; H., Wang et al., 2013; W., Li et al., 2013). In
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plants, the first uses of the CRISPR system were reported in 2013, with successful application for both
transient expression and recovery of stable transgenic lines (J.,-F., Li et al., 2013; Nekrasov et al., 2013).
Over the last 25 years, the plant immune system has been extensively studied. These fundamental
discoveries have led to a mechanistic understanding of the molecular basis of plant disease resistance and
have enabled the identification of target host genes that can be altered by genome editing to produce
disease resistant plants. In a recent report by Zeilmaker et al. (2015), it has been shown that mutation of a
single gene associated with salicylic acid (SA) homeostasis results in the generation of Arabidopsis plants
that are resistant to different types of pathogens, including bacteria and oomycetes. This gene is called
DMR6 (downy mildew resistance 6), and was originally identified and characterized by van Damme et al.
(van Damme et al., 2005; van Damme et al., 2008). DMR6 belongs to the superfamily of 2-oxoglutarate
Fe(II) dependent oxygenases and is specifically up-regulated during pathogen infection. Interestingly,
dmr6 mutants have increased expression of defense genes and SA levels that correlate with enhanced
resistance to P. syringae, Hyaloperonospora arabidopsidis and Phytophthora capsici. A DMR6 paralog
(DLO1 or DMR6-like oxygenase), which is highly co-regulated with DMR6, was later identified in
Arabidopsis and showed synergic effects with DMR6 on plant resistance. dlo1 mutants showed a lower
level of resistance to H. arabidopsidis in relation to dmr6 mutants, whereas dmr6dlo1 double mutants
showed complete resistance. Moreover, it was verified that increased SA levels are the basis of resistance,
and these mutants require SA accumulation for the activation of plant immunity. Although the dmr6dlo1
double mutant shows strong impaired growth presumably due to constitutive activation of immunity, the
dmr6 single mutant only shows slight growth reduction, which is possibly a consequence of a lower
constitutive activation of plant defenses (Zeilmaker et al., 2015). Considering this minimal effect on plant
growth and the broad-spectrum resistance phenotype, generating dmr6 knockouts is a promising strategy
to control diseases in crop plants.
In this study, we identified a DMR6 orthologue in the tomato genome and employed the CRISPR-
Cas9 system to engineer disease resistance in this crop by inactivating this gene. We engineered tomato
plants containing frameshift deletions in the DMR6 gene that showed disease resistance against a wide
variety of pathogens, but no significant effect on plant growth and development. Currently, the
performance of these tomato varieties are being evaluated under conditions that are relevant to
agricultural practices.
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Materials and methods

Identification of tomato orthologues of AtDMR6
To search for AtDMR6 homologous sequences in tomato, we performed a phylogenetic analysis

using the following plant species: Arabidopsis thaliana, Theobroma cacao, Manihot esculenta, Nicotiana
benthamiana and Solanum lycopersicum. Sequences were downloaded from the Phytozome database
(https://phytozome.jgi.doe.gov/pz/portal.html) and Sol Genomics databases (https://solgenomics.net/).
Proteins that contain the 2-oxoglutarate Fe(II) dependent oxygenase Pfam domain PF03171 were
selected. The alignment was performed using Clustal Omega, and the tree was calculated using the
neighbor-joining method. AtDMR6 homologues were defined as those tomato genes that formed a clade
along with AtDMR6 (TAIR ID At5g24530).
CRISPR-Cas9 construct design
Specific gRNAs were designed to generate mutations within the coding sequence of the tomato
DMR6 gene Solyc03g080190 (exons 2 and 3). The gRNA sequences were assembled alongside the Cas9
endonuclease gene in the entry vector pENTR/D-TOPO. To drive the expression of both CRISPR
components (gRNA and Cas9), we used the Arabidopsis U6-26 (AtU6-26) promoter and a 2 × 35S
promoter, respectively, as previously described (Hwang et al., 2013). gRNAs were assembled using the
Golden Gate cloning method (Weber et al., 2011). The insert containing the gRNA sequence and Cas9
gene is flanked by the attL1 and attL2 recombination sites and was gateway cloned into the binary
destination vector pPZP200 as described by Katzen (Katzen, 2007).
Transient assays in Nicotiana benthamiana for evaluation of gRNA efficiency
gRNA efficiency was first evaluated in transient expression assays using Nicotiana benthamiana.
To generate the tomato target template in the living N. benthamiana cells, a fragment of about 1000 bp of
SlDMR6 was cloned into the binary geminivirus vector pLSLR to generate several copies of the target
sequence. The gRNA/Cas9 pPZP200 and DMR6 template pLSL constructs were independently mobilized
into Agrobacterium tumefaciens strain GV3101 by the triparental mating method (Wise et al., 2006). The
transformed A. tumefaciens cells (OD600 0.15) were syringe-infiltrated into N. benthamiana leaves for
transient transformation. After four days, samples were collected for gDNA extraction, PCR analysis and
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amplicon sequencing with specific primers to detect mutations in the targeted regions of SlDMR6 exons 2
and 3.
Agrobacterium-mediated transformation of tomato
The binary vectors containing gRNAs 1 and 2 were mobilized into A. tumefaciens strain C58C1
by the triparental mating method (Wise et al., 2006). A. tumefaciens-mediated transformations of the S.
lycopersicum line FL8000 were performed according to Wang, 2015. In brief, cotyledon segments from
6- to 8-day-old seedlings were pre-cultured for one day followed by inoculation with A. tumefaciens strain
C58C1 containing the CRISPR-Cas9 constructs of interest. Following a 2-day co-cultivation, the
cotyledon segments were transferred to a selective regeneration medium containing 75 mg/l kanamycin.
When shoots were approximately 1.5 cm tall, they were transferred to a selective rooting medium that
also contained 75 mg/l kanamycin. Well-rooted plants were transferred to soil and grown for fruits
production.
Pathogen assays
FL8000 and dmr6-1 tomato seeds (T1 generation) were planted in Sunshine Aggregate Mix #4 in
3 L plastic pots. Seedlings were grown in a glass house at temperatures ranging from 25 to 35°C. In
planta assays were conducted in controlled environmental growth chambers to compare the growth
curves of the Sldmr6-1 mutants with the wild type parent strain FL8000. Bacterial cultures for plant
inoculations were grown in NYGA media (peptone 5 g/L, yeast extract 3 g/L, agar 15 g/L, glycerol 20
ml/L) for 18 h at 28°C on a rotary shaker at 150 rpm. Cells were pelleted by centrifugation (4,000 × g, 15
min) and resuspended in sterile MgCl2 solution 10 mM. Bacterial suspensions were standardized to an
optical density at 600 nm of 0.1 and subsequently used to infect the plants. Plants were inoculated with
each species by being dipped into bacterial suspensions of X. gardneri (Xg153), X. perforans (Xp4b) and
P. syringae pv. tomato (Pst DC3000) amended with the surfactant Silwet L-77 at 0.02% for 30 s.
Following inoculation, plants were bagged and kept in a growth room on a 12-h photoperiod of
fluorescent light at 24 to 28°C. Three samples were taken from each treatment after 6 (Pst), 12 (Xg) and
14 days (Xp). Bacterial populations were quantified by macerating 1-cm2 leaf disks in 1 ml sterile MgCl2
solution 10 mM, running 10-fold serial dilutions in sterile MgCl2 solution 10 mM, and plating them onto
NYGA medium amended with rifampicin 100 µg/ml. After incubation at 28°C for 4 to 5 days, colonies
typical of Xanthomonas spp./P. syringae were observed and counted. Data were log10 transformed, and
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standard errors were determined. Bacterial growth in the infected leaves of each plant was determined at
days 6 post-inoculation (6 dpi), 12 post-inoculation (12 dpi) and 14 post-inoculation (14 dpi) for P.
syringae, X. gardneri and X. perforans, respectively, according to the method of (Katagiri et al., 2002).
For P. capsici pathogen assay, isolate LT1534 was grown on V8 agar 10% at 25°C for three days
in the dark and for additional two days under fluorescent light. For inoculation, a plate covered with
mycelium was flooded with cold water and the zoospore suspension was obtained after 30 minutes at
room temperature. Leaves were spot-inoculated by pipetting 10 µl droplets of the spore suspension (105
spores/ml) on the abaxial and adaxial sides.
Measurement of tomato growth
To better determine the effects of DMR6 impairment on plant growth, the height of 28 Sldmr6-1
mutants and 16 wild type plants was measured using a tape measure (Stanley FatMax 25’). The difference
between the means was tested using the t-test at the significance level of p≤0.05.
Results
Introduction of CRISPR-Cas9 mutations into the dmr6 gene of Solanum lycopersicum
DMR6 is part of the superfamily of 2-oxoglutarate Fe(II) dependent oxygenases. We performed a

phylogeny analysis of the family of 2-oxoglutarate oxygenases (Pfam domain PF03171) including five
different plant species: Arabidopsis thaliana (109 proteins), Theobroma cacao (109 proteins), Manihot
esculenta (136 proteins), Nicotiana benthamiana (110 proteins) and Solanum lycopersicum (142
proteins). We considered DMR6 homologues those genes that belong to the same clade of AtDMR6, and
two copies of the DMR6 gene were identified in tomato (SlDMR6-1: Solyc03g080190 and SlDMR6-2:
Solyc06g073080) (Figure 1).
Based on the inspection of public transcriptomic data (Yang et al., 2015; Jupe et al., 2013), we
verified that Solyc03g080190 is up-regulated by infection with P. syringae pv. tomato (DC3000) and P.
capsici, which suggests that Solyc03g080190 might have a similar function to the Arabidopsis DMR6
(Figure 2).
We designed specific gRNAs that target exons 2 (target region: 5’-

TAGAGAAGTATGCTCCTGAA-3’) and 3 (target region: 5’-AGTTCTGGTTGTGGACAAGG-3’) of
the tomato DMR6 gene Solyc03g080190. As gRNA efficiency can vary according to the gRNA sequence,
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before proceeding to tomato transformation, we tested gRNA efficiency using transient expression assays
of the CRISPR constructs in Nicotiana benthamiana. We performed PCR analysis and amplicon
sequencing with specific primers (5’-ATGGTGTACCAAAGGAAGTTGTAGAGA-3’ and 5’-
TGCAACACTTCTCAGTTTGAGCCTCG-3’ for exon 2; 5’-
AGATATTGCAGGGAAATTCGTCAACTC-3’; 5’-GATGCCATACACTTCTGTACTTACCGTT-3’
for exon 3) and detected mutations in the targeted regions of both gRNAs (Figure 3).
Once we confirmed gRNA efficiencies, tomato plants (FL8000 line) were transformed via
Agrobacterium with the binary vector containing one of the two gRNAs and the Cas9 gene. After about 6
weeks, whole plants were successfully regenerated.
Molecular characterization of SlDMR6 mutations and transmission to F1 progeny
The CRISPR transformants were genotyped (PCR and sequencing of the target region) using the
primers described above for the N. benthamiana transient assays. Different mutations in the SlDMR6-1
gene were obtained, including frameshift deletions and insertions that truncate the protein and disrupt the
DMR6 active site. As previously discussed, DMR6 belongs to the superfamily of 2-oxoglutarate Fe(II)
dependent oxygenases. The active site of these enzymes is characterized by the conserved motif HxD/Ex
H (Clifton et al., 2006), and these amino acid residues are required for DMR6-dependent susceptibility
phenotype in A. thaliana (Zeilmaker et al., 2015). Remarkably, among the tomato mutant lines obtained,
homozygous Sldmr6-1 mutants were found in the primary transformants. Given that primary
transformants can show somaclonal variation, seeds of the tomato dmr6 mutants were obtained and the T1
plants were genotyped to be used in infection assays. In addition, we identified segregating progeny in the
T1 tomato plants that maintain mutations in the DMR6 gene and no longer contain the T-DNA with the
Cas9 gene. (Figure 4).
Characterization of growth traits and disease phenotypes of Sldmr6-1 mutants
T1 plants derived from a homozygous line with a 7 bp deletion in exon 3 of the DMR6 gene were
used in infection assays with Xanthomonas gardneri (Xg153), Xanthomonas perforans (Xp4b), and P.
syringae pv. tomato (DC3000). The bacterial growth assays were performed using the dip inoculation
method. Overall, the tomato dmr6 mutants were more resistant to all these pathogens, and the disease
symptoms were less severe in comparison to the wild type lines (Figure 5). In addition, the oomycete
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pathogen P. capsici has also been tested, and it was able to infect both wild type and dmr6 lines, but
symptoms developed earlier and were more severe in the wild type plants (Figure 6).
To better determine the effects of DMR6 impairment on plant growth, the height of 28 Sldmr6-1
mutants and 16 wild type plants was measured, and only a slight decrease in size, which was not
statistically significant, was verified for the Sldmr6-1 mutants (Figure 7).
Discussion
One of the current challenges for food security is to increase crop yields and support a sustainable
agriculture. Notably, pathogen infection is a major cause of crop yield losses around the world.
Introgression of resistance (R) genes is the classical approach to achieve disease resistance in crops. This
type of resistance leads to the development of the hypersensitive reaction (HR), which is a localized cell
death triggered by the interaction between a plant R gene and its respective pathogen avr (avirulence)
gene (Jones and Dangl, 2006). In addition to the use of plant R genes for resistance breeding, impairment
of some plant genes via loss-of-function mutations has been shown to confer broad-spectrum disease
resistance, as it is the case of the A. thaliana DMR6 gene. In this study, we show that inactivation of the
AtDMR6 homologue in tomato results in resistance to different pathogens, such as the bacterial pathogens
P. syringae and Xanthomonas spp. and the oomycete pathogen P. capsici.
DMR6 is part of the 2-oxoglutarate Fe(II)-dependent oxygenases superfamily, which is present in

all angiosperms. Members of this superfamily are involved in secondary metabolism and biosynthesis of
plant hormones (Zeilmaker et al., 2015). The phylogenetic analysis of 2-oxoglutarate oxygenases showed
the presence of two AtDMR6 homologues in tomato, which grouped in the same clade of AtDMR6 and
were named SlDMR6-1 and SlDMR6-2 (Figure 1). These DMR6 homologues were analyzed in more
detail since they could play a similar role in defense as AtDMR6. To better characterize their participation
in plant defense, we first analyzed public transcriptomic data of tomato infected by P. syringae pv. tomato
(DC3000) and P. capsici. Only SlDMR6-1 was upregulated by pathogen attack (Figure 2), which suggests
that this paralogue is important for plant immunity. Therefore, we focused on mutating the SlDMR6-1
gene in tomato and verifying if impairment of this gene leads to broad spectrum disease resistance as it
has been described for A. thaliana.
Remarkably, tomato Sldmr6-1 mutants showed enhanced disease resistance to important bacterial
pathogens of tomato, such as P. syringae, X. gardneri and X. perforans as well as to the oomycete
pathogen P. capsici (Figures 5 and 6). These results indicate that the biological function of AtDMR6
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homologues might be conserved among different plant species. In particular, resistance to Xanthomonas
spp. is highly desired. X. gardneri and X. perforans belong to a complex of four Xanthomonas species (X.
euvesicatoria, X. vesicatoria, X. perforans and X. gardneri) that incite bacterial spot disease in tomato,
one of the most devastating and widespread diseases of this crop that can cause significant losses when
environmental conditions are suitable for the pathogen (i.e. moderate-to-high temperatures and high
humidity) (Schwartz et al., 2015). The use of chemicals for controlling bacterial spot disease have not
been effective due to the emergence of tolerant strains and the significant negative impact on the
environment (Abbasi et al., 2015). For this reason, resistance against bacterial spot has been a priority in
tomato breeding programs. The R protein Bs2 has been identified in pepper, and is able to recognize a
highly conserved Xanthomonas effector named AvrBs2, thus triggering HR. Field trials have shown that
transgenic tomato plants expressing the Bs2 gene show high disease resistance and significant increased
yield (Horvath et al., 2012). Although very promising, resistance based on the deployment of a single R
gene can be rapidly overcome by the pathogen due to the emergence of resistant strains (Dangl et al.,
2013). Moreover, Bs2 specifically recognizes a single effector in a specific species, limiting the use of
these resistant tomato lines. In this regard, to engineer long-lasting and broad-spectrum disease resistance
in tomato, the combination of Bs2 deployment with DMR6 inactivation is a very promising approach.
Preliminary data indicate that SA levels are increased in the Sldmr6-1 mutants (data not shown)
in comparison to the wild type tomato plants, suggesting that, resistance correlates with increased SA
levels. SA is a central phytohormone in defense responses against biotrophic and hemibiotrophic
pathogens. It induces plant production of secondary metabolites as well as expression of pathogenesis-
related protein genes. Also, SA-mediated responses often culminate with the onset of HR. Interestingly,
mutants displaying a broad-spectrum disease resistance phenotype derived from increased SA levels have
already been described. The cpr (constitutive expressor of PR genes) mutants exhibit increased
concentrations of SA, constitutive expression of PR genes, and enhanced resistance to different
pathogens. However, these mutants have a severe dwarf phenotype, which is a consequence of the high-
energy expenditure on keeping the defense responses active. Importantly, the tomato Sldmr6-1 mutants
did not show a significant detrimental effect on plant growth and development (Figure 7). This
characteristic definitely makes DMR6 a very promising target for resistance breeding in crops. Future
work will also evaluate the performance of these tomato Sldmr6-1 mutants in field conditions.
Although it is still unclear how impairment of DMR6 results in increased salicylic acid levels,
AtDMR6 activity has been recently demonstrated by Falcone Ferreyra et al. (2015). The authors showed
that AtDMR6 as well as its ortologue in maize have flavone synthase activity and catalyze the conversion
of the flavanone naringenin into the flavone apigenin (Falcone Ferreyra et al., 2015). Flavonoids and SA
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pathways share some precursors, thus the authors suggest that when DMR6 is inactivated, a minor flow
through the flavonoid pathway would lead to higher availability of substrates for SA biosynthesis, thus
increasing the levels of SA. Moreover, the authors speculate that this would be a strategy used by
pathogens to decrease SA levels and hence increase susceptibility (Falcone Ferreyra et al., 2015).
However, this hypothesis still needs to be confirmed.
Given the broad-spectrum disease resistance phenotype and the lack of significant detrimental
effects in the plant, impairment of some plant genes to obtain disease resistance has been considered a
promising strategy by many scientists in the field of plant pathology. Nevertheless, as the fitness costs of
DMR6 inactivation have not been clearly determined yet, more studies are still needed to evaluate the
performance of these mutant lines under conditions that are important to agricultural practices.
Acknowledgements
We thank the 2Blades Foundation for the financial support and the Tom Clemente Lab (Nebraska
University) for tomato transformation. DPTT is funded by the PEW Fellowship Program in the
Biomedical Sciences. We also thank Paulo José Teixeira for careful reading of the manuscript.
Author contribution
D.P.T.T. designed and performed experiments, analyzed data and wrote the manuscript; Q.B. and
D.D. performed experiments; and B.J.S. supervised the project, designed the study and the experiments
and analyzed data.
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References
Abbasi, P.A., Khabbaz, S.E., Weselowski, B. and Zhang, L. (2015) Occurrence of copper-resistant
strains and a shift in Xanthomonas spp. causing tomato bacterial spot in Ontario. Can. J. Microbiol.,
761, 1–9.
Clifton, I.J., McDonough, M.A., Ehrismann, D., Kershaw, N.J., Granatino, N. and Schofield, C.J.
(2006) Structural studies on 2-oxoglutarate oxygenases and related double-stranded ??-helix fold
proteins. J. Inorg. Biochem., 100, 644–669.
Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Hsu, P.D., Wu, X., Jiang, W. and Marraffini,
L.A. (2013) Multiplex Genome Engineering Using CRISPR/VCas Systems. Science (80-. )., 339,
819–823.
Damme, M. van, Andel, A., Huibers, R.P., Panstruga, R., Weisbeek, P.J. and Ackerveken, G. Van
den (2005) Identification of arabidopsis loci required for susceptibility to the downy mildew
pathogen Hyaloperonospora parasitica. Mol. Plant. Microbe. Interact., 18, 583–592.
Damme, M. van, Huibers, R.P., Elberse, J. and Ackerveken, G. Van Den (2008) Arabidopsis DMR6
encodes a putative 2OG-Fe(II) oxygenase that is defense-associated but required for susceptibility to
downy mildew. Plant J., 54, 785–793.
Dangl, J.L., Horvath, D.M. and Staskawicz, B.J. (2013) Pivoting the plant immune system from
dissection to deployment. Science, 341, 746–51. Available at:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3869199&tool=pmcentrez&rendertype=
abstract.
Dicarlo, J.E., Norville, J.E., Mali, P., Rios, X., Aach, J. and Church, G.M. (2013) Genome
engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res., 41, 4336–
4343.
Editor, D. (2014) Letter to the Editor Effective gene targeting in rabbits using RNA-guided Cas 9
nucleases. , 97–99.
Friedland, A.E., Tzur, Y.B., Esvelt, K.M., Colaiacovo, M.P., Church, G.M. and Calarco, J.A. (2013)
Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods, 10, 741–743.
Horvath, D.M., Stall, R.E., Jones, J.B., Pauly, M.H., Vallad, G.E., Dahlbeck, D., Staskawicz, B.J.
and Scott, J.W. (2012) Transgenic resistance confers effective field level control of bacterial spot
disease in tomato. PLoS One, 7.
Hwang, W.Y., Fu, Y., Reyon, D., Maeder, M.L., Tsai, S.Q., Sander, J.D., Peterson, R.T., Yeh, J.R.
and Joung, J.K. (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat
Biotechnol, 31, 227–229. Available at:
http://www.ncbi.nlm.nih.gov/pubmed/23360964\nhttp://www.nature.com/nbt/journal/v31/n3/pdf/nbt
.2501.pdf.
Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B. and Weeks, D.P. (2013) Demonstration of
CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and
rice. Nucleic Acids Res., 41, 1–12.
12
Jones, J.D.G. and Dangl, J.L. (2006) The plant immune system. Nature, 444, 323–329.
Joung, J.K. and Sander, J.D. (2013) TALENs: a widely applicable technology for targeted genome
editing. Nat Rev Mol Cell Biol, 14, 49–55. Available at:
http://www.ncbi.nlm.nih.gov/pubmed/23169466\nhttp://www.nature.com/nrm/journal/v14/n1/pdf/nr
m3486.pdf.
Jupe, J., Stam, R., Howden, A.J.M., Morris, J. a, Zhang, R., Hedley, P.E. and Huitema, E. (2013)
Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with
a hemi-biotrophic lifestyle. Genome Biol., 14, R63.
Katagiri, F., Thilmony, R. and He, S.Y. (2002) The Arabidopsis Thaliana-Pseudomonas Syringae
Interaction. Arab. B., 1, e0039. Available at: http://www.bioone.org/doi/abs/10.1199/tab.0039.
Katzen, F. (2007) Recombinational Cloning: a Biological Operating System. Expert Opin. Drug Discov.,
2, 571–589.
Li, D., Qiu, Z., Shao, Y., et al. (2013) Heritable gene targeting in the mouse and rat using a CRISPR-Cas
system. Nat. Biotechnol., 31, 681–683.
Li, J.-F., Norville, J.E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G.M. and Sheen, J.
(2013) Multiplex and homologous recombination–mediated genome editing in Arabidopsis and
Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol., 31, 688–691. Available at:
http://dx.doi.org/10.1038/nbt.2650\npapers2://publication/doi/10.1038/nbt.2650\nhttp://www.nature.
com/doifinder/10.1038/nbt.2654.
Li, W., Teng, F., Li, T. and Zhou, Q. (2013) Simultaneous generation and germline transmission of
multiple gene mutations in rat using CRISPR-Cas systems. Nat. Biotechnol., 31, 684–686.
Liu, L. and Fan, X.-D. (2014) CRISPR--Cas system: a powerful tool for genome engineering. Plant Mol.
Biol., 85, 209–218. Available at: http://dx.doi.org/10.1007/s11103-014-0188-7.
Nakayama, T., Fish, M.B., Fisher, M., Oomen-Hajagos, J., Thomsen, G.H. and Grainger, R.M.
(2013) Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis.
Genesis, 51, 835–843.
Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J.D.G. and Kamoun, S. (2013) Targeted mutagenesis
in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotech, 31,
691–693. Available at: http://dx.doi.org/10.1038/nbt.2655.
Schwartz, A.R., Potnis, N., Timilsina, S., et al. (2015) Phylogenomics of Xanthomonas field strains
infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of
host specificity. Front. Microbiol., 6. Available at:
http://journal.frontiersin.org/Article/10.3389/fmicb.2015.00535/abstract [Accessed July 12, 2016].
Shen, B., Zhang, J., Wu, H., Wang, J., Ma, K., Li, Z., Zhang, X., Zhang, P. and Huang, X. (2013)
Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res., 23, 720–3.
Urnov, F.D., Rebar, E.J., Holmes, M.C., Zhang, H.S. and Gregory, P.D. (2010) Genome editing with
engineered zinc finger nucleases. Nat Rev Genet, 11, 636–646. Available at:
http://www.ncbi.nlm.nih.gov/pubmed/20717154\nhttp://www.nature.com/nrg/journal/v11/n9/pdf/nr
g2842.pdf.
13
Wang, H., Yang, H., Shivalila, C.S., Dawlaty, M.M., Cheng, A.W., Zhang, F. and Jaenisch, R.
(2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/cas-mediated
genome engineering. Cell, 153, 910–918.
Wang, K. (2015) Methods in Molecular Biology, vol 343: Agrobacterium protocols-vol I, Available at:
www.humanapress.com.
Wang, Y., Li, Z., Xu, J., Zeng, B., Ling, L., You, L., Chen, Y., Huang, Y. and Tan, A. (2013) The
CRISPR/Cas system mediates efficient genome engineering in Bombyx mori. Cell Res., 23, 1414–
1416.
Weber, E., Engler, C., Gruetzner, R., Werner, S. and Marillonnet, S. (2011) A modular cloning
system for standardized assembly of multigene constructs. PLoS One, 6.
Wise, A. a, Liu, Z. and Binns, A.N. (2006) Three methods for the introduction of foreign DNA into
Agrobacterium. Methods Mol. Biol., 343, 43–53. Available at:
http://www.ncbi.nlm.nih.gov/pubmed/16988332.
Xie, K. and Yang, Y. (2013) RNA-Guided genome editing in plants using a CRISPR-Cas system. Mol.
Plant, 6, 1975–1983.
Yang, Y.-X., Wang, M.-M., Yin, Y.-L., et al. (2015) RNA-seq analysis reveals the role of red light in
resistance against Pseudomonas syringae pv. tomato DC3000 in tomato plants. BMC Genomics, 16,
120. Available at:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4349473&tool=pmcentrez&rendertype=
abstract.
Yu, Z., Ren, M., Wang, Z., Zhang, B., Rong, Y.S., Jiao, R. and Gao, G. (2013) Highly efficient
genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics, 195, 289–291.
Zeilmaker, T., Ludwig, N.R., Elberse, J., Seidl, M.F., Berke, L., Doorn, A. Van, Schuurink, R.C.,
Snel, B. and Ackerveken, G. Van Den (2015) DOWNY MILDEW RESISTANT 6 and DMR6-
LIKE OXYGENASE 1 are partially redundant but distinct suppressors of immunity in Arabidopsis.
, 210–222.
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Figure Legends
Figure 1: Phylogenetic tree of 2-oxoglutarate oxygenase proteins from Arabidopsis thaliana and four
other plants (left panel), including the Solanaceae model Nicotiana benthamiana and three crops
(Solanum lycopersicum, Manihot esculenta and Theobroma cacao). The DMR6-clade of 2-oxoglutarate
oxygenases is highlighted on the right. Bootstrap values are shown in the tree.
Figure 2: Expression of the tomato DMR6 gene obtained from public transcriptomic data (Jupe et al.,
2013, Yang et al., 2015) in response to pathogen infection. (A) Tomato DMR6 is upregulated at 19hpi by
the bacteria Pseudomonas syringae pv. tomato (DC3000). NI= non-inoculated; hpi= hours after infection.
(B) Tomato DMR6 is also upregulated by infection with the oomycete Phytophthora capsici.
Figure 3: Mutagenesis of the tomato DMR6 gene using the CRISPR-Cas9 system. (A) Specific gRNAs
were designed to generate mutations within the coding sequence of the tomato DMR6 gene
Solyc03g080190 (exons 2 and 3). The gRNA target sequence is represented by a red bar over the gene
sequence. Frameshift mutations (5 bp deletion in exon 2 and 7 bp deletion in exon 3) generated by these
gRNAs are shown in details. These sequences are from homozygous mutants obtained in the T0 tomato
plants. (B) Clustal alignment of the SLDMR6-1 amino acid sequences that correspond to the wild type
line, the 5bp-deletion mutant (generated with gRNA1) and the 7bp-deletion mutant (generated with
gRNA2) lines. The region highlighted in blue are the amino acids present in all three lines, and the amino
acid residues highlighted in red are the conserved amino acids HxD/H that form the protein active site.
These amino acids are essential for the protein enzymatic activity and are not present in the mutant lines
described above.
Figure 4: PCR with Cas9 gene specific primers using gDNA extracted from dmr6 tomato mutants (T1).
In this case, the Cas9 gene probably integrated in a single locus in the tomato genome and, as a
consequence, the gene segregated out in about 20% of the T1 plants. The mutation in the DMR6 gene is a
7 nucleotide deletion in exon 3 that disrupts the protein active site. + Cas9 is present; - Cas9 is absent.
Figure 5: Wild type and dmr6 mutant lines infected with Xanthomonas gardneri (Xg153), Xanthomonas
15
perforans (Xp4B) and Pseudomonas syringae pv. tomato (DC3000). On the left, bacterial counts for X.
gardneri (A), X. perforans (B) and P. syringae (C) are shown in the wild type and in the dmr6 mutant
lines at 0 dai (days after infection) and 12 dai, 14 dai and 6 dai, respectively. Inactivation of DMR6
results in lower bacterial numbers for all three species. Bars represent standard error of three replicates.
On the right, lesions (black dots) in the leaf correspond to the disease symptoms, which are more severe
in the wild type plants.
Figure 6: Wild type and dmr6 mutant lines infected with Phytophthora capsici at 10 days after infection
(dai). The necrosis in the leaf corresponds to the disease symptom, which is considerably more severe in
the wild type plant. Inoculation was performed using droplets of a suspension of P. capsici zoospores at
105 zoospores/ml.
Figure 7. Height growth of tomato plants (Sldmr6-1 and wild type lines). Height was measured along the
length of the stem starting on the stem aboveground to the apex. Twenty-eight Sldmr6-1 mutants and 18
wild type plants were used. The difference between the means was tested using the t-test at the
significance level of p≤0.05.
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Anti Microbes SIDMR6 1

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Anti Microbes SIDMR6 1

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bioRxiv preprint doi: https://doi.org/10.1101/064824; this version posted July 23, 2016.

The copyright holder for this preprint (which was

CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers

*corresponding author: [email protected]

Materials and methods

To search for AtDMR6 homologous sequences in tomato, we performed a phylogenetic analysis

CRISPR-Cas9 construct design

Transient assays in Nicotiana benthamiana for evaluation of gRNA efficiency

Agrobacterium-mediated transformation of tomato

Measurement of tomato growth

DMR6 is part of the superfamily of 2-oxoglutarate Fe(II) dependent oxygenases. We performed a

We designed specific gRNAs that target exons 2 (target region: 5’-

Molecular characterization of SlDMR6 mutations and transmission to F1 progeny

Characterization of growth traits and disease phenotypes of Sldmr6-1 mutants

DMR6 is part of the 2-oxoglutarate Fe(II)-dependent oxygenases superfamily, which is present in

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