Monocot and dicot MLO powdery mildew susceptibility factors are functionally conserved in spite of the evolution of class-specific molecular features
© Appiano et al. 2015
Received: 11 June 2015
Accepted: 7 October 2015
Published: 26 October 2015
Specific members of the plant Mildew Locus O (MLO) protein family act as susceptibility factors towards powdery mildew (PM), a worldwide-spread fungal disease threatening many cultivated species. Previous studies indicated that monocot and dicot MLO susceptibility proteins are phylogenetically divergent.
A bioinformatic approach was followed to study the type of evolution of Angiosperm MLO susceptibility proteins. Transgenic complementation tests were performed for functional analysis.
Our results show that monocot and dicot MLO susceptibility proteins evolved class-specific conservation patterns. Many of them appear to be the result of negative selection and thus are likely to provide an adaptive value. We also tested whether different molecular features between monocot and dicot MLO proteins are specifically required by PM fungal species to cause pathogenesis. To this aim, we transformed a tomato mutant impaired for the endogenous SlMLO1 gene, and therefore resistant to the tomato PM species Oidium neolycopersici, with heterologous MLO susceptibility genes from the monocot barley and the dicot pea. In both cases, we observed restoration of PM symptoms. Finally, through histological observations, we demonstrate that both monocot and dicot susceptibility alleles of the MLO genes predispose to penetration of a non-adapted PM fungal species in plant epidermal cells.
With this study, we provide insights on the evolution and function of MLO genes involved in the interaction with PM fungi. With respect to breeding research, we show that transgenic complementation assays involving phylogenetically distant plant species can be used for the characterization of novel MLO susceptibility genes. Moreover, we provide an overview of MLO protein molecular features predicted to play a major role in PM susceptibility. These represent ideal targets for future approaches of reverse genetics, addressed to the selection of loss-of-function resistant mutants in cultivated species.
The plant Mildew Locus O (MLO) gene family codes for proteins harboring seven transmembrane domains and a calmodulin-binding site, topologically reminiscent of metazoan and fungal G-protein coupled receptors (GPCRs) . Following the completion of plant genome sequencing projects, a number of homologs varying from 12 to 19 has been identified in the MLO gene families of diploid species, namely Arabidopsis, rice, grapevine, cucumber, peach, woodland strawberry and sorghum [1–6].
Specific homologs of the MLO gene family act as susceptibility factors towards fungi causing the powdery mildew (PM) disease, worldwide spread and causing severe losses in agricultural settings. Inactivation of these genes, through loss-of function mutations or silencing, indeed results in resistance (referred to as mlo-based resistance) in several plant species . The first MLO gene described as required for PM pathogenesis was barley HvMLO [8, 9]. Since then, MLO susceptibility genes have been functionally characterized in rice (OsMLO3), wheat (TaMLO_A1 and TaMLO_B1), Arabidopsis (AtMLO2, AtMLO6 and AtMLO12), tomato (SlMLO1), pepper (CaMLO2), tobacco (NtMLO1), pea (PsMLO1), lotus (LjMLO1) and barrel clover (MtMLO1) [10–17].
Defense mechanisms involved in mlo-based resistance prevent fungal penetration in epidermal cells and are associated with the formation of cell wall appositions, referred to as papillae . Similar pre-penetration defense measures also take place in non-host resistance, following the interaction between PM fungal species and plant species beyond their host range. Consistent with the hypothesis of involvement of MLO genes in non-host resistance, loss of function of HvMLO in the interaction between barley and the wheat PM fungus Blumeria graminis f. sp. tritici is associated with decreased rate of penetration and lower incidence of epidermal cell death, the latter being a post-penetration defense mechanism [18, 19].
Several studies have been addressed to the characterization of regions of relevance for the functionality of MLO proteins. Multiple alignments have pointed out the occurrence of residues highly conserved within the whole MLO family, which were therefore predicted to provide a common protein structural scaffold [12, 20]. In addition, the occurrence of residues and motifs specifically conserved in putative orthologs of barley HvMLO has been reported . Finally, functionally important residues for MLO susceptibility proteins have been inferred by the association of naturally occurring and induced mutations with partial or complete PM resistance [11, 12, 21–25].
In our previous studies, we showed that phylogenetically related dicot MLO genes of the same botanic family are conserved for their function as a susceptibility gene to PM [6, 16]. Notably, monocot and dicot MLO proteins involved in PM susceptibility group in clearly separated phylogenetic clades (e.g. [2, 9]). Here, we show that the evolution of Angiosperm PM susceptibility genes led to the fixation of class-specific molecular traits. Many of them appear to be the result of negative selection. By means of transgenic complementation assays, we demonstrate that, despite having different conservation patterns, monocot and dicot MLO susceptibility genes are essentially conserved with respect to functional features having a role in interactions with PM fungi. Consequences of our findings for plant breeding research are discussed.
Class-specific molecular features of Angiosperm MLO homologs required for PM susceptibility
Adaptive relevance of class-specific molecular features supported by evolutionary analysis
In order to make inference on the evolutionary events leading to the above mentioned class-specific molecular features, we performed a codon-based Single-Likelihood Ancestor Counting (SLAC) analysis on the difference of nonsynonymous to synonymous substitutions per nonsynonymous and synonymous sites (dN-dS). Tests were conducted to predict the evolution of each codon: neutral/dN = dS or negative (purifying)/dN < dS. We decided to restrict the analysis to a panel of nine dicot MLO susceptibility genes, as only four monocot MLO homologs have been so far associated with PM pathogenesis and the dN-dS analysis can provide significant results only when using a sequence dataset which is not too small. We found 130 codons under significant negative selection, coding for amino acids scattered throughout MLO protein domains. Among the 130 codons, 27 are translated into class-specific residues, which are therefore predicted to provide an adaptive value (Additional file 1).
Functional conservation of monocot and dicot MLO susceptibility genes
Functional conservation of monocot and dicot MLO susceptibility genes in non-host interactions
Amino acid residues in dicot AtMLO2 and monocot HvMLO whose mutation has been associated with PM resistance. For each amino-acid, localization in any of the MLO protein domains, including seven transmembrane (TM) regions, three extracellular loops (E), three intracellular (I) loops, the N-terminus and the C-terminus, is indicated
We cannot exclude that class-specific traits might have minor effects on interactions with PM fungi. Indeed, by comparing three independent T2 families for each construct, we found that that overexpression of PsMLO1 results in higher D.I. index scores than the one of HvMLO (Fig. 3 and Additional file 3). Clearly, complementation tests with several other monocot and dicot transgenes could help to answer this question.
Through the analysis of the dN-dS difference, we provide evidence for negative selection acting on several class-specific residues, which are thus likely to play a major adaptive role (Additional file 1). However, as mentioned before, transgenic complementation tests indicate that these class-specific residues are not crucial for the outcome of the interaction between plants and PM pathogens. Possibly, some of the class-specific residues identified in this study might underlie roles which are not related with the interaction with PM fungi. The implication of MLO susceptibility proteins in other physiological processes would explain why, in spite of being required for pathogenesis, they have been not excluded by evolution. With this respect, it is worth to mention that PM resistance in Arabidopsis and barley mlo mutants has been associated with the induction of leaf senescence, a pleiotropic phenotype .
We show that MLO homologs required for PM pathogenesis can complement a mlo mutant background in transgenic assays, irrespective of the phylogenetic distance between the donor and the recipient species (Fig. 3). This would be of great advantage in order to test the function of candidate MLO susceptibility genes which are currently being identified by several authors across cultivated species [4, 5]. Moreover, we provide an overview of MLO protein regions which are under negative selection and thus are expected to be of functional relevance. These regions represent ideal targets to select loss-of-function mutants resistant to the PM disease. With this respect, breeders may apply diverse tools, such as conventional targeted mutagenesis approaches of TILLING (targeted induced local lesions in genomes) or advanced technologies of genome editing, based on zinc finger nucleases (ZFNs), clustered regularly interspaced short palindromic repeat (CRISPR) and transcription activator-like effector nucleases (TALEN) [26–28].
This work provides insights on the evolution and function of Angiosperm MLO susceptibility genes. We show that complementation assays similar to those carried out in this study are suitable for future activities aimed at the characterization of novel PM susceptibility factors across cultivated species. Moreover, we indicate a series of gene targets for the selection of loss-of-function mlo resistant mutants.
The following MLO proteins, experimentally shown to be required for PM susceptibility, were used as dataset for CLUSTAL alignment using the CLC sequence viewer software (http://www.clcbio.com/products/clc-sequence-viewer/): Arabidopsis AtMLO2 [GenBank: NP172598], AtMLO6 [GeneBank: NP176350] and AtMLO12 [GeneBank: NP565902], tomato SlMLO1 [GeneBank: NP001234814], pea PsMLO1 [GeneBank: ACO07297], pepper CaMLO2 [GeneBank: AFH68055], lotus LjMLO1 [GeneBank: AAX77015], barrel clover MtMLO1 [GeneBank: ADV40949], barley HvMLO [GeneBank: P93766], rice OsMLO3 [GeneBank: AAK94907], wheat TaMLO_B1 [GeneBank: AAK94904] and TaMLO_A1b [GeneBank: AAK94905]. The alignment was given to Geneious v8 software (http://www.geneious.com,  ), to highlight amino acids with different polarity, and the online web service Phylogeny.fr (http://www.phylogeny.fr/) to construct an unrooted radial phylogenetic tree.
In order to make predictions on the type of evolution (negative or neutral) of class-specific molecular features, all the above mentioned dicot MLO susceptibility genes were used as dataset for a codon-based evolutionary analysis based on the difference of nonsynonymous-to-synonymous substitutions per nonsynonymous and synonymous sites (dN/dS). This was performed by using the Single-likelihood Ancestor Counting (SLAC) method implemented by the Datamonkey web server (www.datamonkey.org). The default p-value of 0.1 was taken as threshold to call codons under significant negative selection.
Isolation and cloning of full-length PsMLO1 and HvMLO
Total RNAs from pea (cultivar Sprinter) and barley (cultivar Maythorpe) were isolated by using the RNeasy plant mini kit (Qiagen), and corresponding cDNAs were synthesized by using the SuperScript III first-strand synthesis kit (Invitrogen) and the oligo(dT)20 primer. Specific primer pairs, named PsMLO1-Fw/PsMLO1-Rev and HvMLO-Fw/HvMLO-Rev (Additional file 4: Table S2) were manually designed in order to amplify the PsMLO1 and HvMLO full-length coding sequences, respectively. PCR reactions were performed by using the high-fidelity Phusion DNA polymerase (New England Biolabs) and an annealing temperature of 55 °C. Amplicons were ligated into the Gateway-compatible vector pENTR D-TOPO (Invitrogen) and cloned into the E. coli One Shot® TOP10 cells (Invitrogen), according to the manufacturer’s instructions. After selecting positive colonies by colony PCR, using the two gene-specific primer pairs above mentioned, recombinant plasmids were extracted and their inserts were sequenced. A single colony for each construct was selected, in which the inserts resulted to have sequences identical to those of HvMLO and PsMLO1 deposited in the NCBI database.
Generation and functional characterization of transgenic SlMLO1 mutant tomato plants expressing PsMLO1 and HvMLO
Following the manufacturer instructions (Invitrogen), cloned HvMLO and PsMLO1 gene sequences were inserted by LR recombination into the binary plasmid vector pK7WG2, which harbors the 35S Cauliflower Mosaic Virus (CaMV) promoter and the marker gene nptII for kanamycin resistance selection. Plasmids were then transferred to E. coli and positive colonies were screened by colony PCR and sequencing, as previously mentioned. Finally, recombinant vectors were extracted and transferred to the AGL1-virG strain of A. tumefaciens by electroporation.
The transformation of the tomato ol-2 mutant line, carrying a loss-of-function mutation of the PM susceptibility gene SlMLO1, was performed according to the methods described by  and . The evaluation of the expression levels of PsMLO1 and HvMLO in T1 plants was carried out by real-time qPCR using the primer pairs qPsMLO1-Fw/qPsMLO1-Rev and qHvMLO-Fw/qHvMLO-Rev (Additional file 4). A primer pair designed on the elongation factor 1α gene (qEF-Fw/qEF-Rev) was used for relative quantification (Additional file 4).
Functional characterization of host and non-host interactions
For each of the two transgenes above mentioned, three T1 individuals showing the highest expression levels were allowed to self-pollinate, resulting in a total of six T2 families. Individuals of each family were assayed for the presence/absence of the overexpression construct by means of PCR, using the primer pairs NPTII_Fw/ NPTII_Rev and 35S-Fw/35S-Rev designed on the nptII marker gene and the 35S promoter, respectively (Additional file 4). Ten resistant Slmlo1 plants carrying the loss-of-function SlMLO1 allele and ten individuals of each family were challenged with an isolate of the tomato PM fungus O. neolycopersici maintained at the Plant Breeding Department of the University of Wageningen, The Netherlands. Inoculation was performed as described by , spraying 4 weeks-old plants with a suspension of conidiospores obtained from freshly sporulating leaves of heavily infected plants and adjusted to a final concentration of 4 × 104 spores/ml. Inoculated plants were grown in a greenhouse compartment at 20 ± 2 °C with 70 ± 15 % relative humidity. Disease evaluation was visually carried out 15 days after inoculation, based on the presence of disease signs on the third and fourth leaf, according to the scale from 0 to 3 reported by .
For the functional characterization of a non-host interaction, seeds from one of the three 35S::HvMLO T2 families previously tested were surface-sterilized and sown on half-strength Murashige and Skoog (MS) agar supplemented with 50 mg/ml kanamycin for selection of transgenic plants. Seeds were left for 2 days at 4 °C and then transferred to a growing chamber for 10 days. Five transgenic seedlings were transplanted in pots and transferred to a greenhouse compartment. Three barley plants of the PM susceptible cultivar Manchuria, five Slmlo1 plants and five MoneyMaker plants were used as controls. An isolate of B. graminis f. sp. hordei (Bgh) collected in Wageningen (Wag.04) was used for the inoculation. This was performed by rubbing Manchuria leaves heavily infected with Bgh on the third tomato leaf. After 72 h, in which inoculated plants were kept in a climate chamber at 20 °C, 16 h of light/day and 70 % RH, a 4 cm2 segment was cut from the inoculated leaves (third leaf). Three samples were taken from 3 plants of each genotype.
Each leaf segment was bleached is a 1:3 (v/v) acetic-acid/ethanol solution and 48 h later stained in 0.005 % Trypan Blue as described by . The rate of fungal penetration was estimated by the frequency of infection units showing epidermal cell death. For each genotype, three biological replicates were considered, considering at least 100 infection units.
We acknowledge Dr. Henk Schouten, Dr. Anne-Marie Wolters and Dr. Rients Niks for critical reading and valuable suggestions during the preparation of the manuscript. We also acknowledge Romero Cynara for her help for inoculation with Blumeria graminis f.sp. hordei. The work of MA, CL, LR and SP were supported by the Italian Ministry of University and Research through the GenHort PON R&C project.
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