Focus on Weed Control: A Novel Rice Cytochrome P450 Gene,CYP72A31, Confers Tolerance to Acetolactate Synthase-Inhibiting Herbicides in Rice and Arabidopsis

Target-site and non-target-site herbicide tolerance are caused by the prevention of herbicide binding to the target enzyme and the reduction to a nonlethal dose of herbicide reaching the target enzyme, respectively. There is little information on the molecular mechanisms involved in non-target-site herbicide tolerance, although it poses the greater threat in the evolution of herbicide-resistant weeds and could potentially be useful for the production of herbicide-tolerant crops because it is often involved in tolerance to multiherbicides. Bispyribac sodium (BS) is an herbicide that inhibits the activity of acetolactate synthase. Rice (Oryza sativa) of the indica variety show BS tolerance, while japonica rice varieties are BS sensitive. Map-based cloning and complementation tests revealed that a novel cytochrome P450 monooxygenase, CYP72A31, is involved in BS tolerance. Interestingly, BS tolerance was correlated with CYP72A31 messenger RNA levels in transgenic plants of rice and Arabidopsis (Arabidopsis thaliana). Moreover, Arabidopsis overexpressing CYP72A31 showed tolerance to bensulfuron-methyl (BSM), which belongs to a different class of acetolactate synthase-inhibiting herbicides, suggesting that CYP72A31 can metabolize BS and BSM to a compound with reduced phytotoxicity. On the other hand, we showed that the cytochrome P450 monooxygenase CYP81A6, which has been reported to confer BSM tolerance, is barely involved, if at all, in BS tolerance, suggesting that the CYP72A31 enzyme has different herbicide specificities compared with CYP81A6. Thus, the CYP72A31 gene is a potentially useful genetic resource in the fields of weed control, herbicide development, and molecular breeding in a broad range of crop species.The mechanism of herbicide tolerance can be classified roughly into two groups: target-site and non-target-site herbicide tolerance (Powles and Yu, 2010). Target-site herbicide tolerance is caused by the prevention of herbicide binding to the target enzyme, caused by point mutations occurring in the latter. It is relatively easy to elucidate the molecular mechanisms of target-site herbicide tolerance, because it is regulated mostly by a single gene encoding a target enzyme harboring point mutations. On the other hand, non-target-site herbicide tolerance is caused by reduction to a nonlethal dose of herbicide reaching the target enzyme, caused by mechanisms such as activation of herbicide detoxification, decrease of herbicide penetration, and herbicide compartmentation in plant cells (Yuan et al., 2007). Among these mechanisms, the oxidization of herbicides by endogenous cytochrome P450 monooxygenase is thought to be a major pathway in plants (Werck-Reichhart et al., 2000; Siminszky, 2006; Powles and Yu, 2010). From the point of view of weed control, non-target-site herbicide tolerance is a greater threat to crop production and in the evolution of herbicide-resistant weeds, because it is often involved in resistance to multiherbicides that inhibit different target proteins, including never-used and potential plant growth regulators (Yuan et al., 2007; Powles and Yu, 2010). Conversely, it is expected that multiherbicide-tolerant crops could be produced easily by the application of non-target-site herbicide tolerance. Moreover, information gained from study of the molecular mechanisms of non-target-site herbicide tolerance can be applied to the research and development of novel herbicides and plant growth regulators.Acetolactate synthase (ALS; also known as acetohydroxy acid synthase) plays a key role in the biosynthesis of branched-chain amino acids such as Val, Leu, and Ile in many organisms. ALS is the primary target site for at least four classes of herbicides: sulfonylurea, imidazolinone, pyrimidinyl carboxylates, and triazolopyrimidine herbicides (Shimizu et al., 2002, 2005). These herbicides can inhibit ALS activity, resulting in plant death caused by a deficiency of branched-chain amino acids. ALS-inhibiting herbicides control many weed species in addition to exhibiting high selectivity in major crops and low toxicity to mammals, which lack the branched-chain amino acid biosynthetic pathway. However, various mutations in ALS that confer ALS-inhibiting herbicide tolerance have been found in many weeds (Shimizu et al., 2005; Powles and Yu, 2010). Similar mutations in ALS have also been reported in crops (Shimizu et al., 2005). To date, crops that show tolerance to ALS-inhibiting herbicides have been produced by various approaches, such as conventional mutation breeding, conventional transformation, and pinpoint mutagenesis via gene targeting based on information obtained from analyses of ALS mutants (Shimizu et al., 2005; Endo and Toki, 2013). On the other hand, weeds that show tolerance to ALS-inhibiting herbicides by cytochrome P450-mediated detoxification have also been reported (Powles and Yu, 2010). However, compared with target-site herbicide tolerance, little is known of the molecular mechanism of herbicide metabolism mediated by cytochrome P450. In rice (Oryza sativa), an herbicide-sensitive mutant has been produced by γ-ray irradiation (Zhang et al., 2002). This mutant showed 60-fold higher sensitivity to bensulfuron-methyl (BSM), a sulfonylurea herbicide, compared with wild-type rice (Pan et al., 2006). Genetic mapping and complementation tests revealed that a cytochrome P450, CYP81A6, is involved in BSM tolerance (Pan et al., 2006). As far as we know, this is the only example of the isolation and characterization of a cytochrome P450 gene involved in nontarget herbicide tolerance in rice.Bispyribac sodium (BS), a pyrimidinyl carboxylate herbicide, is effective in controlling many annual and perennial weeds, with excellent selectivity on direct-seeded rice (Shimizu et al., 2002). Recently, it was reported that japonica rice varieties show higher sensitivity to BS compared with indica rice varieties at the early stages of plant growth (Ohno et al., 2008; Taniguchi et al., 2010). A mutated ALS gene confers BS tolerance in plants including rice (Shimizu et al., 2005; Endo and Toki, 2013). However, the deduced amino acid sequences were shown to be highly conserved among japonica and indica rice varieties, and ALS levels of sensitivity to BS were similar in japonica and indica rice varieties (Taniguchi et al., 2010). These results suggest the possibility that indica rice varieties might show higher tolerance to BS due to the acquisition of nontarget herbicide tolerance.In this study, we isolated and characterized a novel cytochrome P450 gene, CYP72A31, involved in BS tolerance in rice. We also demonstrated that overexpression of CYP72A31 confers tolerance to ALS-inhibiting herbicides, including BS and BSM, in Arabidopsis (Arabidopsis thaliana).     

Distinct Detoxification Mechanisms Confer Resistance to Mesotrione and Atrazine in a Population of Waterhemp

Previous research reported the first case of resistance to mesotrione and other 4-hydroxyphenylpyruvate dioxygenase (HPPD) herbicides in a waterhemp (Amaranthus tuberculatus) population designated MCR (for McLean County mesotrione- and atrazine-resistant). Herein, experiments were conducted to determine if target site or nontarget site mechanisms confer mesotrione resistance in MCR. Additionally, the basis for atrazine resistance was investigated in MCR and an atrazine-resistant but mesotrione-sensitive population (ACR for Adams County mesotrione-sensitive but atrazine-resistant). A standard sensitive population (WCS for Wayne County herbicide-sensitive) was also used for comparison. Mesotrione resistance was not due to an alteration in HPPD sequence, HPPD expression, or reduced herbicide absorption. Metabolism studies using whole plants and excised leaves revealed that the time for 50% of absorbed mesotrione to degrade in MCR was significantly shorter than in ACR and WCS, which correlated with previous phenotypic responses to mesotrione and the quantity of the metabolite 4-hydroxy-mesotrione in excised leaves. The cytochrome P450 monooxygenase inhibitors malathion and tetcyclacis significantly reduced mesotrione metabolism in MCR and corn (Zea mays) excised leaves but not in ACR. Furthermore, malathion increased mesotrione activity in MCR seedlings in greenhouse studies. These results indicate that enhanced oxidative metabolism contributes significantly to mesotrione resistance in MCR. Sequence analysis of atrazine-resistant (MCR and ACR) and atrazine-sensitive (WCS) waterhemp populations detected no differences in the psbA gene. The times for 50% of absorbed atrazine to degrade in corn, MCR, and ACR leaves were shorter than in WCS, and a polar metabolite of atrazine was detected in corn, MCR, and ACR that cochromatographed with a synthetic atrazine-glutathione conjugate. Thus, elevated rates of metabolism via distinct detoxification mechanisms contribute to mesotrione and atrazine resistance within the MCR population.Waterhemp (Amaranthus tuberculatus) is a troublesome annual weed species in midwestern U.S. corn (Zea mays) and soybean (Glycine max) production. The change to production systems with limited tillage has favored waterhemp germination and growth (Hager et al., 2002). Waterhemp seeds are small, and one female plant can produce up to one million seeds (Steckel et al., 2003), which endow waterhemp with an effective short-distance dispersal mechanism. In addition, multiple herbicide resistance mechanisms in waterhemp are facilitated by its dioecious biology and wind-pollinated flowers (Steckel, 2007). The long-distance flow of pollen may be one of the main reasons that multiple herbicide resistance in waterhemp has become widespread in the United States (Liu et al., 2012).Mesotrione (2-[4-(methylsulfonyl)-2-nitrobenzoyl]-1,3-cyclohexanedione) belongs to the triketone class of 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides (Beaudegnies et al., 2009). Molecular information regarding plant HPPD gene sequences and expression patterns is limited (for review, see Pallett, 2000; Kim and Petersen, 2002; Riechers and Stanford, 2002; Matringe et al., 2005), and only a single expressed HPPD gene was detected in waterhemp (Riggins et al., 2010). Herbicidal activity of mesotrione in sensitive plants is due to competitive inhibition of the HPPD enzyme, which is a key enzyme in the biosynthesis of tocopherols and plastoquinone. Plastoquinone is an electron acceptor for the phytoene desaturase reaction in the pathway of carotenoid biosynthesis and also serves as an electron acceptor in PSII (Hess, 2000). Tocopherols and carotenoids are responsible for the detoxification of reactive oxygen species and scavenging of free radicals in plant tissues (Maeda and DellaPenna, 2007; Triantaphylidès and Havaux, 2009; Mène-Saffrané and DellaPenna, 2010), and carotenoids also protect chlorophyll from photooxidation (Cazzonelli and Pogson, 2010). Following mesotrione treatment, carotenoid biosynthesis is inhibited in sensitive plants, resulting in bleaching and necrosis. In particular, new leaves and meristems are primarily affected due to the need for protective carotenoids and tocopherols in photosynthetic tissues (Triantaphylidès and Havaux, 2009) and the systemic nature of mesotrione, which is translocated in the phloem (Mitchell et al., 2001; Beaudegnies et al., 2009).There are two main mechanisms of herbicide resistance in plants: (1) target site alterations, such as mutations that affect herbicide-binding kinetics or amplification of the target site gene (Powles and Yu, 2010), and (2) nontarget site mechanisms, including metabolism, translocation, and sequestration (Yuan et al., 2007; Powles and Yu, 2010). Metabolic detoxification is a common nontarget-based mechanism for herbicide resistance, which typically may result from elevated levels of cytochrome P450 monooxygenase (P450) or glutathione S-transferase (GST) activity (Powles and Yu, 2010; Délye et al., 2011). In addition to conferring resistance in weeds, these enzymes also confer natural tolerance in crops (Kreuz et al., 1996; Riechers et al., 2010). Similar to tolerant sorghum (Sorghum bicolor) lines (Abit and Al-Khatib, 2009), corn is tolerant to mesotrione via rapid metabolism (i.e. ring hydroxylation catalyzed by P450 activity) in combination with slower uptake relative to sensitive weeds and a less sensitive form of the HPPD enzyme in grasses relative to dicots (Hawkes et al., 2001; Mitchell et al., 2001).Atrazine (2-chloro-4-(ethylamino)-6-(isopropylamino)-S-triazine) is a symmetrical triazine herbicide commonly used in corn to selectively control annual dicot weeds. Atrazine disrupts electron transport by competing with plastoquinone for the secondary electron-accepting plastoquinone-binding site on the D1 protein of PSII in chloroplasts (Hess, 2000). Atrazine resistance in weeds can be due to a mutation in the psbA gene that causes a Ser-Gly substitution at amino acid position 264 of the D1 protein (Hirschberg and McIntosh, 1983; Devine and Preston, 2000). Corn and grain sorghum are naturally tolerant to atrazine via the rapid metabolism of atrazine through conjugation with reduced glutathione (GSH; Frear and Swanson, 1970; Lamoureux et al., 1973), which is catalyzed by GST activities (Shimabukuro et al., 1971). Enhanced metabolism of atrazine and simazine in weedy species has been reported in Abutilon theophrasti, Lolium rigidum, and Alopecurus myosuroides due to either GST- or P450-mediated detoxification mechanisms (Burnet et al., 1993; Gray et al., 1996; Cummins et al., 1999; Délye et al., 2011).A population of waterhemp (designated MCR for McLean County mesotrione- and atrazine-resistant) from Illinois is resistant to HPPD inhibitors (Hausman et al., 2011) and atrazine as well as to acetolactate synthase (ALS)-inhibiting herbicides. A different population of waterhemp (designated ACR for Adams County mesotrione-sensitive but atrazine-resistant; Patzoldt et al., 2005) that is atrazine resistant but sensitive to mesotrione (Hausman et al., 2011) and a waterhemp population (designated WCS for Wayne County herbicide-sensitive; Patzoldt et al., 2005) that is sensitive to both mesotrione and atrazine (Hausman et al., 2011) were used in comparison with MCR in this research. MCR displayed 10- and 35-fold resistance to mesotrione in comparison with ACR and WCS, respectively, in greenhouse studies (Hausman et al., 2011). In addition, waterhemp populations with similar patterns of multiple resistance have recently been identified (Hausman et al., 2011; McMullan and Green, 2011; Heap, 2012). However, the mechanisms of resistance to mesotrione and atrazine in these waterhemp populations are currently unknown. Therefore, the objective of this study was to determine if the multiple-herbicide-resistant phenotype of MCR (in regard to mesotrione and atrazine resistance) is due to either target site or nontarget site mechanisms.     

Evolution of a Double Amino Acid Substitution in the 5-Enolpyruvylshikimate-3-Phosphate Synthase in Eleusine indica Conferring High-Level Glyphosate Resistance

Glyphosate is the most important and widely used herbicide in world agriculture. Intensive glyphosate selection has resulted in the widespread evolution of glyphosate-resistant weed populations, threatening the sustainability of this valuable once-in-a-century agrochemical. Field-evolved glyphosate resistance due to known resistance mechanisms is generally low to modest. Here, working with a highly glyphosate-resistant Eleusine indica population, we identified a double amino acid substitution (T102I + P106S [TIPS]) in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene in glyphosate-resistant individuals. This TIPS mutation recreates the biotechnology-engineered commercial first generation glyphosate-tolerant EPSPS in corn (Zea mays) and now in other crops. In E. indica, the naturally evolved TIPS mutants are highly (more than 180-fold) resistant to glyphosate compared with the wild type and more resistant (more than 32-fold) than the previously known P106S mutants. The E. indica TIPS EPSPS showed very high-level (2,647-fold) in vitro resistance to glyphosate relative to the wild type and is more resistant (600-fold) than the P106S variant. The evolution of the TIPS mutation in crop fields under glyphosate selection is likely a sequential event, with the P106S mutation being selected first and fixed, followed by the T102I mutation to create the highly resistant TIPS EPSPS. The sequential evolution of the TIPS mutation endowing high-level glyphosate resistance is an important mechanism by which plants adapt to intense herbicide selection and a dramatic example of evolution in action.Modern herbicides make major contributions to global food production by easily removing weeds while maintaining sustainable soil conservation practices. However, persistent herbicide selection of huge weed numbers across vast areas has resulted in the widespread evolution of herbicide-resistant weed populations. Worldwide, there are currently more than 449 unique cases of herbicide resistance, with about 11 new cases reported annually, on average (Heap, 2015). Target site resistance due to target gene mutation is one of the major mechanisms enabling resistance evolution (Gressel, 2002; Powles and Yu, 2010).The most important and globally used herbicide in crop fields is glyphosate (Duke and Powles, 2008). Glyphosate disrupts the shikimate pathway by specifically inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; Steinrücken and Amrhein, 1980). Glyphosate resistance was initially considered to be unlikely to evolve in nature based on the facts that intentional selection for glyphosate tolerance using whole plants and cell/tissue culture was unsuccessful, and laboratory-generated highly resistant EPSPS mutants displayed undesirable enzyme kinetics (Bradshaw et al., 1997; for review, see Pline-Srnic, 2006). This seemed to be true, as resistance was not found during the first 15 years of glyphosate use, primarily as a nonselective herbicide. However, unprecedented intensive glyphosate use for controlling large numbers of weeds over massive areas, especially after the introduction of glyphosate-resistant transgenic crops, imposed high selection pressure on weeds, resulting in the evolution of glyphosate resistance in populations of 32 weed species (Heap, 2015). Since the first identification of a resistance-endowing EPSPS point mutation, P106S, in a glyphosate-resistant Eleusine indica population (Baerson et al., 2002), several other resistance-endowing single-amino acid substitutions at P106 (P106T, P106A, and P106L) have been reported in glyphosate-resistant weeds (e.g. Ng et al., 2004; Yu et al., 2007; Kaundun et al., 2011; for review, see Sammons and Gaines, 2014). These single-codon EPSPS resistance mutations only endow low-level glyphosate resistance (2- to 3-fold the recommended rates). This is not surprising, because glyphosate is a competitive inhibitor of the second substrate, phosphoenolpyruvate (PEP; Boocock and Coggins, 1983), and is considered a transition state mimic of the catalyzed reaction course (Schönbrunn et al., 2001). Indeed, highly glyphosate-resistant EPSPS variants (e.g. mutants at G101 or T102) have greatly increased K_m values (decreased affinity) for PEP when expressed in Escherichia coli (Eschenburg et al., 2002; Funke et al., 2009; for review, see Sammons and Gaines, 2014). In contrast, P106 substitutions confer weak glyphosate resistance but preserve adequate EPSPS functionality (Healy-Fried et al., 2007; for review, see Sammons and Gaines, 2014). Aside from P106 EPSPS gene mutations, there are other glyphosate resistance mechanisms, including EPSPS gene amplification and nontarget-site reduced glyphosate translocation/nontarget-site increased vacuole sequestration (Lorraine-Colwill et al., 2002; Gaines et al., 2010; Ge et al., 2010; for review, see Powles and Preston, 2006; Shaner, 2009; Powles and Yu, 2010; Sammons and Gaines, 2014). Generally, each of these mechanisms endows moderate-level (4- to 8-fold the recommended rates) glyphosate resistance.Low-level glyphosate resistance due to the EPSPS P106 mutations was reported in Malaysian E. indica (Baerson et al., 2002; Ng et al., 2004). Recently, we reported a highly (more than 10-fold the recommended rates) glyphosate-resistant Malaysian E. indica population (Jalaludin et al., 2015). This paper investigates the high-level glyphosate resistance in this population, and is, to our knowledge, the first to reveal the sequential evolution of a double amino acid substitution in EPSPS.     

Focus on Weed Control: In Vivo 31P-Nuclear Magnetic Resonance Studies of Glyphosate Uptake,Vacuolar Sequestration,and Tonoplast Pump Activity in Glyphosate-Resistant Horseweed

Horseweed (Conyza canadensis) is considered a significant glyphosate-resistant (GR) weed in agriculture, spreading to 21 states in the United States and now found globally on five continents. This laboratory previously reported rapid vacuolar sequestration of glyphosate as the mechanism of resistance in GR horseweed. The observation of vacuole sequestration is consistent with the existence of a tonoplast-bound transporter. ³¹P-Nuclear magnetic resonance experiments performed in vivo with GR horseweed leaf tissue show that glyphosate entry into the plant cell (cytosolic compartment) is (1) first order in extracellular glyphosate concentration, independent of pH and dependent upon ATP; (2) competitively inhibited by alternative substrates (aminomethyl phosphonate [AMPA] and N-methyl glyphosate [NMG]), which themselves enter the plant cell; and (3) blocked by vanadate, a known inhibitor/blocker of ATP-dependent transporters. Vacuole sequestration of glyphosate is (1) first order in cytosolic glyphosate concentration and dependent upon ATP; (2) competitively inhibited by alternative substrates (AMPA and NMG), which themselves enter the plant vacuole; and (3) saturable. ³¹P-Nuclear magnetic resonance findings with GR horseweed are consistent with the active transport of glyphosate and alternative substrates (AMPA and NMG) across the plasma membrane and tonoplast in a manner characteristic of ATP-binding cassette transporters, similar to those that have been identified in mammalian cells.Glyphosate is arguably the world’s most important herbicide (Duke and Powles, 2008). Environmental factors affecting its uptake and translocation in higher plants have been widely studied (Kells and Rieck, 1979; Coupland, 1983; Devine et al., 1983; Masiunas and Weller, 1988; Zhou et al., 2007). Notably, the role of light is important for effective uptake and translocation, suggesting that metabolic energy plays a role in this process (Simarmata et al., 2003; Shaner et al., 2005). Death of the whole plant requires effective glyphosate translocation from source to sink tissue, a process requiring ATP to maintain Suc gradients, which drive phloem movement (Bromilow et al., 1990; Dill et al., 2010).Weed species have developed glyphosate-resistant (GR) biotypes during the past decade (Heap, 2014). This has spurred interest in factors that may contribute to resistant attribute(s) as well as methods that can be used to screen plants for herbicide toxicity (Shaner, 2010). Resistance mechanisms have been reported for horseweed (Conyza canadensis; Feng et al., 2004; Zelaya et al., 2004; Ge et al., 2010, 2011), Palmer amaranth (Amaranthus palmeri; Gaines et al., 2010), and ryegrass (Lolium rigidum and Lolium multiflorum; Powles et al., 1998; Perez et al., 2004; Ge et al., 2012).Since glyphosate is foliar applied, glyphosate toxicity involves a multistep delivery process. Glyphosate must traverse the nonliving structures of the leaf cuticle and the cell walls of the epidermis, apoplast, and mesophyll prior to accessing the phloem for transport to sink tissues (Bromilow et al., 1990; Bromilow and Chamberlain, 2000). Indeed, restriction of glyphosate delivery to the plant cell cytoplasm (and chloroplast) by any means is, in itself, a resistance mechanism (Shaner, 2009; Ge et al., 2013). Elucidation of key factors governing delivery to the intracellular milieu of plant source leaves is critical for developing a complete understanding of the mechanism(s) of resistance to glyphosate.Glyphosate’s phosphono group offers the opportunity to employ in vivo ³¹P-NMR spectroscopy to track glyphosate movement and metabolism, additionally including monitoring of cellular pH, and gradients therein, and ATP levels, both indicators of tissue viability (Roberts, 1984). This laboratory has extended the ³¹P-NMR approach initially used by Gout et al. (1992) with suspension-cultured sycamore (Acer pseudoplatanus) cells. The initial findings, that source and sink leaf tissue from GR horseweed rapidly and avidly sequestered glyphosate within the vacuole compartment and that leaf tissue from glyphosate-sensitive (GS) horseweed did not, led to the hypothesis that vacuole sequestration was a key, perhaps the dominant, component of the resistance mechanism (Ge et al., 2010). It was then shown that GR horseweed acclimated and maintained at cold temperature (approximately 10°C–12°C) did not rapidly and avidly sequester glyphosate within the vacuole. Importantly, under such conditions, GR horseweed succumbed to the toxic effects of glyphosate. In short, by preventing glyphosate sequestration, GR horseweed became glyphosate sensitive, a laboratory finding confirmed in the field (Ge et al., 2011).The proposition that, by limiting the herbicide available for translocation, glyphosate vacuole sequestration could serve as an important if not dominant resistance mechanism was further strengthened by experiments that showed vacuolar glyphosate sequestration correlated with glyphosate resistance in ryegrass (Lolium spp.) from Australia, South America, and Europe (Ge et al., 2012). However, ³¹P-NMR studies of other weeds revealed that in some species, for example, Palmer amaranth, waterhemp (Amaranthus tuberculatus), and johnsongrass (Sorghum halepense), resistance correlated strongly with a lack of glyphosate uptake into the plant cell, a frontline resistance mechanism (Ge et al., 2013).Throughout these previous ³¹P-NMR studies, the finding that plants could regulate the compartmental access of glyphosate led us to speculate that the apoplast, tonoplast, and perhaps chloroplast possessed glyphosate-active transporters whose up-regulation or down-regulation and/or expression would confer resistance (Ge et al., 2010, 2011, 2012, 2013). This hypothesis motivated additional in vivo ³¹P-NMR experiments to further describe the determinants of glyphosate delivery in horseweed leaf tissue. Specifically, experiments with GR horseweed were designed with the goal of probing the transporter hypothesis.Findings from these experiments are reported herein and are consistent with the existence of a tonoplast transporter that is responsible for glyphosate resistance via vacuole sequestration. As described here, vacuole sequestration requires ATP, is active for multiple substrates, and shows substrate competition. Furthermore, glyphosate entry into the cell can be markedly inhibited by vanadate pretreatment. These characteristics are similar to those of ATP-binding cassette transporters in plants (Hetherington et al., 1998; Rea, 2007; Verrier et al., 2008; Prosecka et al., 2009; Conte and Lloyd, 2011) and mammalian cells (van de Ven et al., 2009; Ernst et al., 2010).     

Focus on Weed Control: Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia

Recent rapid evolution and spread of resistance to the most extensively used herbicide, glyphosate, is a major threat to global crop production. Genetic mechanisms by which weeds evolve resistance to herbicides largely determine the level of resistance and the rate of evolution of resistance. In a previous study, we determined that glyphosate resistance in Kochia scoparia is due to the amplification of the 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) gene, the enzyme target of glyphosate. Here, we investigated the genomic organization of the amplified EPSPS copies using fluorescence in situ hybridization (FISH) and extended DNA fiber (Fiber FISH) on K. scoparia chromosomes. In both glyphosate-resistant K. scoparia populations tested (GR1 and GR2), FISH results displayed a single and prominent hybridization site of the EPSPS gene localized on the distal end of one pair of homologous metaphase chromosomes compared with a faint hybridization site in glyphosate-susceptible samples (GS1 and GS2). Fiber FISH displayed 10 copies of the EPSPS gene (approximately 5 kb) arranged in tandem configuration approximately 40 to 70 kb apart, with one copy in an inverted orientation in GR2. In agreement with FISH results, segregation of EPSPS copies followed single-locus inheritance in GR1 population. This is the first report of tandem target gene amplification conferring field-evolved herbicide resistance in weed populations.Glyphosate [N-(phosphonomethyl) Gly] is the most widely used agricultural pesticide globally (Duke and Powles, 2008). Originally, being a nonselective herbicide, its use was limited to vegetation management in noncrop areas; however, introduction of glyphosate-resistant (GR) crops in the late 1990s, coupled with their exceptional adoption, led to accelerated use totaling approximately 128 million ha worldwide in 2012 (James, 2012). GR crop technology has made a significant contribution to global agriculture and the environment, as it not only increased farm income by $32.2 billion (Brookes and Barfoot, 2013), but also moderated the negative environmental impacts of mechanical weed management practices (Gardner and Nelson, 2008; Bonny, 2011). Glyphosate offers a simple, effective, and economic weed management option in GR crops. In addition, it provides immense value in no-till crop production systems by enabling soil and moisture conservation. However, due to intensive glyphosate selection pressure, several weed populations globally have evolved resistance through a variety of mechanisms. Globally, herbicide resistance, in particular the recent proliferation of glyphosate resistance in weed species, is a major crop protection threat; nearly two dozen GR weed species have been reported in the last 15 years (Heap, 2014).Glyphosate, an aminophosphonic analog of the natural amino acid Gly, nonselectively inhibits 5-Enolpyruvylshikimate-3-Phosphate synthase (EPSPS) in plants, preventing the biosynthesis of the aromatic amino acids Phe, Tyr, and Trp (Steinrücken and Amrhein, 1980), resulting in the death of glyphosate-sensitive individuals. In plants, EPSPS is one of the key enzymes in the shikimate pathway (Herrmann and Weaver, 1999), and glyphosate inhibits EPSPS by binding to EPSPS-shikimate-3-P binary complex forming an EPSPS-shikimate-3-P-glyphosate complex (Alibhai and Stallings, 2001). Bradshaw et al. (1997) hypothesized against the likelihood of weeds evolving resistance to glyphosate, primarily because of its complex biochemical interactions in the shikimate pathway and also due to the absence of known glyphosate metabolism in plants. Nonetheless, several cases of glyphosate resistance, as a result of difference in glyphosate translocation (Preston and Wakelin, 2008) or mutations in the EPSPS, were confirmed (Baerson et al., 2002). More importantly, duplication/amplification of the EPSPS appears to be the basis for glyphosate resistance in several weeds (Sammons and Gaines, 2014). Here, we use duplication to refer to the formation of first repetition of a chromosomal segment and amplification to refer to increase in number of the repetitions (more than two repetitions of a chromosomal segment) under positive selection. The first case of EPSPS amplification as a basis for glyphosate resistance was reported in an Amaranthus palmeri population from GA (Gaines et al., 2010). In this A. palmeri population, there is a massive increase (>100-fold relative to glyphosate-susceptible [GS] plants) in EPSPS copies, and these copies are dispersed throughout the genome (Gaines et al., 2010).Field-evolved GR Kochia scoparia populations were first reported in western Kansas in 2007 (Heap, 2014). We previously determined that evolution of GR populations of K. scoparia in the U.S. Great Plains is also due to amplification of the EPSPS (A. Wiersma and P. Westra, unpublished data). Unlike in GR A. palmeri, we found relative EPSPS:acetolactate synthase (ALS) copies ranging from three to nine in GR K. scoparia populations. While it quickly became widespread in the region, its presence was reported in another five Great Plains states by 2013 (Heap, 2014). GR K. scoparia populations we tested were 3- to 11-times resistant (population level) to glyphosate compared with a GS population (Godar, 2014), and EPSPS expression positively correlated with genomic EPSPS copy number (A. Wiersma and P. Westra, unpublished data). Here, we reveal the genomic organization of the amplified EPSPS copies in two GR K. scoparia populations, an alternative mechanism of gene amplification to that reported in GR A. palmeri.     

Rhamnolipids Elicit Defense Responses and Induce Disease Resistance against Biotrophic, Hemibiotrophic, and Necrotrophic Pathogens That Require Different Signaling Pathways in Arabidopsis and Highlight a Central Role for Salicylic Acid

Plant resistance to phytopathogenic microorganisms mainly relies on the activation of an innate immune response usually launched after recognition by the plant cells of microbe-associated molecular patterns. The plant hormones, salicylic acid (SA), jasmonic acid, and ethylene have emerged as key players in the signaling networks involved in plant immunity. Rhamnolipids (RLs) are glycolipids produced by bacteria and are involved in surface motility and biofilm development. Here we report that RLs trigger an immune response in Arabidopsis (Arabidopsis thaliana) characterized by signaling molecules accumulation and defense gene activation. This immune response participates to resistance against the hemibiotrophic bacterium Pseudomonas syringae pv tomato, the biotrophic oomycete Hyaloperonospora arabidopsidis, and the necrotrophic fungus Botrytis cinerea. We show that RL-mediated resistance involves different signaling pathways that depend on the type of pathogen. Ethylene is involved in RL-induced resistance to H. arabidopsidis and to P. syringae pv tomato whereas jasmonic acid is essential for the resistance to B. cinerea. SA participates to the restriction of all pathogens. We also show evidence that SA-dependent plant defenses are potentiated by RLs following challenge by B. cinerea or P. syringae pv tomato. These results highlight a central role for SA in RL-mediated resistance. In addition to the activation of plant defense responses, antimicrobial properties of RLs are thought to participate in the protection against the fungus and the oomycete. Our data highlight the intricate mechanisms involved in plant protection triggered by a new type of molecule that can be perceived by plant cells and that can also act directly onto pathogens.In their environment, plants are challenged by potentially pathogenic microorganisms. In response, they express a set of defense mechanisms including preformed structural and chemical barriers, as well as an innate immune response quickly activated after microorganism perception (Boller and Felix, 2009). Plant innate immunity is triggered after recognition by pattern recognition receptors of conserved pathogen- or microbe-associated molecular patterns (PAMPs or MAMPs, respectively) or by plant endogenous molecules released by pathogen invasion and called danger-associated molecular patterns (Boller and Felix, 2009; Dodds and Rathjen, 2010). This first step of recognition leads to the activation of MAMP-triggered immunity (MTI). Successful pathogens can secrete effectors that interfere or suppress MTI, resulting in effector-triggered susceptibility. A second level of perception involves the direct or indirect recognition by specific receptors of pathogen effectors leading to effector-triggered immunity (ETI; Boller and Felix, 2009; Dodds and Rathjen, 2010). Whereas MTI and ETI are thought to involve common signaling network, ETI is usually quantitatively stronger than MTI and associated with more sustained and robust immune responses (Katagiri and Tsuda, 2010; Tsuda and Katagiri, 2010).The plant hormones, salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) have emerged as key players in the signaling networks involved in MTI and ETI (Robert-Seilaniantz et al., 2007; Tsuda et al., 2009; Katagiri and Tsuda, 2010; Mersmann et al., 2010; Tsuda and Katagiri, 2010; Robert-Seilaniantz et al., 2011). Interactions between these signal molecules allow the plant to activate and/or modulate an appropriate spectrum of responses, depending on the pathogen lifestyle, necrotroph or biotroph (Glazebrook, 2005; Koornneef and Pieterse, 2008). It is assumed that JA and ET signaling pathways are important for resistance to necrotrophic fungi including Botrytis cinerea and Alternaria brassicicola (Thomma et al., 2001; Ferrari et al., 2003; Glazebrook, 2005). Infection of Arabidopsis (Arabidopsis thaliana) with B. cinerea causes the induction of the JA/ET responsive gene PLANT DEFENSIN1.2 (PDF1.2; Penninckx et al., 1996; Zimmerli et al., 2001). Induction of PDF1.2 by B. cinerea is blocked in ethylene-insensitive2 (ein2) and coronatine-insensitive1 (coi1) mutants that are respectively defective in ET and JA signal transduction pathways. Moreover, ein2 and coi1 plants are highly susceptible to B. cinerea infection (Thomma et al., 1998; Thomma et al., 1999). JA/ET-dependent responses do not seem to be usually induced during resistance to biotrophs, but they can be effective if they are stimulated prior to pathogen challenge (Glazebrook, 2005). Plants impaired in SA signaling are highly susceptible to biotrophic and hemibiotrophic pathogens. Following pathogen infection, SA hydroxylase (NahG), enhanced disease susceptibility5 (eds5), or SA induction-deficient2 (sid2) plants are unable to accumulate high SA levels and they display heightened susceptibility to Pseudomonas syringae pv tomato (Pst), Hyaloperonospora arabidopsidis, or Erysiphe orontii (Delaney et al., 1994; Lawton et al., 1995; Wildermuth et al., 2001; Nawrath et al., 2002; Vlot et al., 2009). Mutants that are insensitive to SA, such as nonexpressor of PATHOGENESIS-RELATED (PR) genes1 (npr1), have enhanced susceptibility to these pathogens (Cao et al., 1994; Glazebrook et al., 1996; Shah et al., 1997; Dong, 2004). According to some reports, plant defense against necrotrophs also involves SA. Arabidopsis plants expressing the nahG gene and infected with B. cinerea show larger lesions compared with wild-type plants (Govrin and Levine, 2002). In tobacco (Nicotiana tabacum), acidic isoforms of PR3 and PR5 gene that are specifically induced by SA (Ménard et al., 2004) are up-regulated after challenge by B. cinerea (El Oirdi et al., 2010). Resistance to some necrotrophs like Fusarium graminearum involves both SA and JA signaling pathways (Makandar et al., 2010). It is assumed that SA and JA signaling can be antagonistic (Bostock, 2005; Koornneef and Pieterse, 2008; Pieterse et al., 2009; Thaler et al., 2012). In Arabidopsis, SA inhibits JA-dependent resistance against A. brassicicola or B. cinerea (Spoel et al., 2007; Koornneef et al., 2008). Recent studies demonstrated that ET modulates the NPR1-mediated antagonism between SA and JA (Leon-Reyes et al., 2009; Leon-Reyes et al., 2010a) and suppression by SA of JA-responsive gene expression is targeted at a position downstream of the JA biosynthesis pathway (Leon-Reyes et al., 2010b). Synergistic effects of SA- and JA-dependent signaling are also well documented (Schenk et al., 2000; van Wees et al., 2000; Mur et al., 2006) and induction of some defense responses after pathogen challenge requires intact JA, ET, and SA signaling pathways (Campbell et al., 2003).Isolated MAMPs trigger defense responses that also require the activation of SA, JA, and ET signaling pathways (Tsuda et al., 2009; Katagiri and Tsuda, 2010). For instance, treatment with the flagellin peptide flg22 induces many SA-related genes including SID2, EDS5, NPR1, and PR1 (Ferrari et al., 2007; Denoux et al., 2008), causes SA accumulation (Tsuda et al., 2008; Wang et al., 2009), and activates ET signaling (Bethke et al., 2009; Mersmann et al., 2010). Local application of lipopolysaccharides elevates the level of SA (Mishina and Zeier, 2007). The oomycete Pep13 peptide induces defense responses in potato (Solanum tuberosum) that require both SA and JA (Halim et al., 2009). Although signaling networks induced by isolated MAMPs are well documented, the contribution of SA, JA, and ET in MAMP- or PAMP-induced resistance to biotrophs and necrotrophs is poorly understood.Rhamnolipids (RLs) are glycolipids produced by various bacteria species including some Pseudomonas and Burkholderia species. They are essential for bacterial surface motility and biofilm development (Vatsa et al., 2010; Chrzanowski et al., 2012). RLs are potent stimulators of animal immunity (Vatsa et al., 2010). They have recently been shown to elicit plant defense responses and to induce resistance against B. cinerea in grapevine (Vitis vinifera; Varnier et al., 2009). They also participate to biocontrol activity of the plant beneficial bacteria Pseudomonas aeruginosa PNA1 against oomycetes (Perneel et al., 2008). However, the signaling pathways used by RLs to stimulate plant innate immunity are not known. To gain more insights into RL-induced MTI, we investigated RL-triggered defense responses and resistance to the necrotrophic fungus B. cinerea, the biotroph oomycete H. arabidopsidis, and the hemibiotroph bacterium Pst in Arabidopsis. Our results show that RLs trigger an innate immune response in Arabidopsis that protects the plant against these different lifestyle pathogens. We demonstrate that RL-mediated resistance involves separated signaling sectors that depend on the type of pathogen. In plants challenged by RLs, SA has a central role and participates to the restriction of the three pathogens. ET is fully involved in RL-induced resistance to the biotrophic oomycete and to the hemibiotrophic bacterium whereas JA is essential for the resistance to the necrotrophic fungus.     

The Rubisco Small Subunit Is Involved in Tobamovirus Movement and Tm-22-Mediated Extreme Resistance

The multifunctional movement protein (MP) of Tomato mosaic tobamovirus (ToMV) is involved in viral cell-to-cell movement, symptom development, and resistance gene recognition. However, it remains to be elucidated how ToMV MP plays such diverse roles in plants. Here, we show that ToMV MP interacts with the Rubisco small subunit (RbCS) of Nicotiana benthamiana in vitro and in vivo. In susceptible N. benthamiana plants, silencing of NbRbCS enabled ToMV to induce necrosis in inoculated leaves, thus enhancing virus local infectivity. However, the development of systemic viral symptoms was delayed. In transgenic N. benthamiana plants harboring Tobacco mosaic virus resistance-2² (Tm-2²), which mediates extreme resistance to ToMV, silencing of NbRbCS compromised Tm-2²-dependent resistance. ToMV was able to establish efficient local infection but was not able to move systemically. These findings suggest that NbRbCS plays a vital role in tobamovirus movement and plant antiviral defenses.Plant viruses use at least one movement protein (MP) to facilitate viral spread between plant cells via plasmodesmata (PD; Lucas and Gilbertson, 1994; Ghoshroy et al., 1997). Among viral MPs, the MP of tobamoviruses, such as Tobacco mosaic virus (TMV) and its close relative Tomato mosaic virus (ToMV), is the best characterized. TMV MP specifically accumulates in PD and modifies the plasmodesmatal size exclusion limit in mature source leaves or tissues (Wolf et al., 1989; Deom et al., 1990; Ding et al., 1992). TMV MP and viral genomic RNA form a mobile ribonucleoprotein complex that is essential for cell-to-cell movement of viral infection (Watanabe et al., 1984; Deom et al., 1987; Citovsky et al., 1990, 1992; Kiselyova et al., 2001; Kawakami et al., 2004; Waigmann et al., 2007). TMV MP also enhances intercellular RNA silencing (Vogler et al., 2008) and affects viral symptom development, host range, and host susceptibility to virus (Dardick et al., 2000; Bazzini et al., 2007). Furthermore, ToMV MP is identified as an avirulence factor that is recognized by tomato (Solanum lycopersicum) resistance proteins Tobacco mosaic virus resistance-2 (Tm-2) and Tm-2² (Meshi et al., 1989; Lanfermeijer et al., 2004). Indeed, tomato Tm-2² confers extreme resistance against TMV and ToMV in tomato plants and even in heterologous tobacco (Nicotiana tabacum) plants (Lanfermeijer et al., 2003, 2004).To date, several host factors that interact with TMV MP have been identified. These TMV MP-binding host factors include cell wall-associated proteins such as pectin methylesterase (Chen et al., 2000), calreticulin (Meshi et al., 1989), ANK1 (Ueki et al., 2010), and the cellular DnaJ-like protein MPIP1 (Shimizu et al., 2009). Many cytoskeletal components such as actin filaments (McLean et al., 1995), microtubules (Heinlein et al., 1995), and the microtubule-associated proteins MPB2C (Kragler et al., 2003) and EB1a (Brandner et al., 2008) also interact with TMV MP. Most of these factors are involved in TMV cell-to-cell movement.Rubisco catalyzes the first step of CO₂ assimilation in photosynthesis and photorespiration. The Rubisco holoenzyme is a heteropolymer consisting of eight large subunits (RbCLs) and eight small subunits (RbCSs). RbCL was reported to interact with the coat protein of Potato virus Y (Feki et al., 2005). Both RbCS and RbCL were reported to interact with the P3 proteins encoded by several potyviruses, including Shallot yellow stripe virus, Onion yellow dwarf virus, Soybean mosaic virus, and Turnip mosaic virus (Lin et al., 2011). Proteomic analysis of the plant-virus interactome revealed that RbCS participates in the formation of virus complexes of Rice yellow mottle virus (Brizard et al., 2006). However, the biological function of Rubisco in viral infection remains unknown.In this study, we show that RbCS plays an essential role in virus movement, host susceptibility, and Tm-2²-mediated extreme resistance in the ToMV-host plant interaction.     

Spore Density Determines Infection Strategy by the Plant Pathogenic Fungus Plectosphaerella cucumerina

Necrotrophic and biotrophic pathogens are resisted by different plant defenses. While necrotrophic pathogens are sensitive to jasmonic acid (JA)-dependent resistance, biotrophic pathogens are resisted by salicylic acid (SA)- and reactive oxygen species (ROS)-dependent resistance. Although many pathogens switch from biotrophy to necrotrophy during infection, little is known about the signals triggering this transition. This study is based on the observation that the early colonization pattern and symptom development by the ascomycete pathogen Plectosphaerella cucumerina (P. cucumerina) vary between inoculation methods. Using the Arabidopsis (Arabidopsis thaliana) defense response as a proxy for infection strategy, we examined whether P. cucumerina alternates between hemibiotrophic and necrotrophic lifestyles, depending on initial spore density and distribution on the leaf surface. Untargeted metabolome analysis revealed profound differences in metabolic defense signatures upon different inoculation methods. Quantification of JA and SA, marker gene expression, and cell death confirmed that infection from high spore densities activates JA-dependent defenses with excessive cell death, while infection from low spore densities induces SA-dependent defenses with lower levels of cell death. Phenotyping of Arabidopsis mutants in JA, SA, and ROS signaling confirmed that P. cucumerina is differentially resisted by JA- and SA/ROS-dependent defenses, depending on initial spore density and distribution on the leaf. Furthermore, in situ staining for early callose deposition at the infection sites revealed that necrotrophy by P. cucumerina is associated with elevated host defense. We conclude that P. cucumerina adapts to early-acting plant defenses by switching from a hemibiotrophic to a necrotrophic infection program, thereby gaining an advantage of immunity-related cell death in the host.Plant pathogens are often classified as necrotrophic or biotrophic, depending on their infection strategy (Glazebrook, 2005; Nishimura and Dangl, 2010). Necrotrophic pathogens kill living host cells and use the decayed plant tissue as a substrate to colonize the plant, whereas biotrophic pathogens parasitize living plant cells by employing effector molecules that suppress the host immune system (Pel and Pieterse, 2013). Despite this binary classification, the majority of pathogenic microbes employ a hemibiotrophic infection strategy, which is characterized by an initial biotrophic phase followed by a necrotrophic infection strategy at later stages of infection (Perfect and Green, 2001). The pathogenic fungi Magnaporthe grisea, Sclerotinia sclerotiorum, and Mycosphaerella graminicola, the oomycete Phytophthora infestans, and the bacterial pathogen Pseudomonas syringae are examples of hemibiotrophic plant pathogens (Perfect and Green, 2001; Koeck et al., 2011; van Kan et al., 2014; Kabbage et al., 2015).Despite considerable progress in our understanding of plant resistance to necrotrophic and biotrophic pathogens (Glazebrook, 2005; Mengiste, 2012; Lai and Mengiste, 2013), recent debate highlights the dynamic and complex interplay between plant-pathogenic microbes and their hosts, which is raising concerns about the use of infection strategies as a static tool to classify plant pathogens. For instance, the fungal genus Botrytis is often labeled as an archetypal necrotroph, even though there is evidence that it can behave as an endophytic fungus with a biotrophic lifestyle (van Kan et al., 2014). The rice blast fungus Magnaporthe oryzae, which is often classified as a hemibiotrophic leaf pathogen (Perfect and Green, 2001; Koeck et al., 2011), can adopt a purely biotrophic lifestyle when infecting root tissues (Marcel et al., 2010). It remains unclear which signals are responsible for the switch from biotrophy to necrotrophy and whether these signals rely solely on the physiological state of the pathogen, or whether host-derived signals play a role as well (Kabbage et al., 2015).The plant hormones salicylic acid (SA) and jasmonic acid (JA) play a central role in the activation of plant defenses (Glazebrook, 2005; Pieterse et al., 2009, 2012). The first evidence that biotrophic and necrotrophic pathogens are resisted by different immune responses came from Thomma et al. (1998), who demonstrated that Arabidopsis (Arabidopsis thaliana) genotypes impaired in SA signaling show enhanced susceptibility to the biotrophic pathogen Hyaloperonospora arabidopsidis (formerly known as Peronospora parastitica), while JA-insensitive genotypes were more susceptible to the necrotrophic fungus Alternaria brassicicola. In subsequent years, the differential effectiveness of SA- and JA-dependent defense mechanisms has been confirmed in different plant-pathogen interactions, while additional plant hormones, such as ethylene, abscisic acid (ABA), auxins, and cytokinins, have emerged as regulators of SA- and JA-dependent defenses (Bari and Jones, 2009; Cao et al., 2011; Pieterse et al., 2012). Moreover, SA- and JA-dependent defense pathways have been shown to act antagonistically on each other, which allows plants to prioritize an appropriate defense response to attack by biotrophic pathogens, necrotrophic pathogens, or herbivores (Koornneef and Pieterse, 2008; Pieterse et al., 2009; Verhage et al., 2010).In addition to plant hormones, reactive oxygen species (ROS) play an important regulatory role in plant defenses (Torres et al., 2006; Lehmann et al., 2015). Within minutes after the perception of pathogen-associated molecular patterns, NADPH oxidases and apoplastic peroxidases generate early ROS bursts (Torres et al., 2002; Daudi et al., 2012; O’Brien et al., 2012), which activate downstream defense signaling cascades (Apel and Hirt, 2004; Torres et al., 2006; Miller et al., 2009; Mittler et al., 2011; Lehmann et al., 2015). ROS play an important regulatory role in the deposition of callose (Luna et al., 2011; Pastor et al., 2013) and can also stimulate SA-dependent defenses (Chaouch et al., 2010; Yun and Chen, 2011; Wang et al., 2014; Mammarella et al., 2015). However, the spread of SA-induced apoptosis during hyperstimulation of the plant immune system is contained by the ROS-generating NADPH oxidase RBOHD (Torres et al., 2005), presumably to allow for the sufficient generation of SA-dependent defense signals from living cells that are adjacent to apoptotic cells. Nitric oxide (NO) plays an additional role in the regulation of SA/ROS-dependent defense (Trapet et al., 2015). This gaseous molecule can stimulate ROS production and cell death in the absence of SA while preventing excessive ROS production at high cellular SA levels via S-nitrosylation of RBOHD (Yun et al., 2011). Recently, it was shown that pathogen-induced accumulation of NO and ROS promotes the production of azelaic acid, a lipid derivative that primes distal plants for SA-dependent defenses (Wang et al., 2014). Hence, NO, ROS, and SA are intertwined in a complex regulatory network to mount local and systemic resistance against biotrophic pathogens. Interestingly, pathogens with a necrotrophic lifestyle can benefit from ROS/SA-dependent defenses and associated cell death (Govrin and Levine, 2000). For instance, Kabbage et al. (2013) demonstrated that S. sclerotiorum utilizes oxalic acid to repress oxidative defense signaling during initial biotrophic colonization, but it stimulates apoptosis at later stages to advance necrotrophic colonization. Moreover, SA-induced repression of JA-dependent resistance not only benefits necrotrophic pathogens but also hemibiotrophic pathogens after having switched from biotrophy to necrotrophy (Glazebrook, 2005; Pieterse et al., 2009, 2012).Plectosphaerella cucumerina ((P. cucumerina, anamorph Plectosporum tabacinum) anamorph Plectosporum tabacinum) is a filamentous ascomycete fungus that can survive saprophytically in soil by decomposing plant material (Palm et al., 1995). The fungus can cause sudden death and blight disease in a variety of crops (Chen et al., 1999; Harrington et al., 2000). Because P. cucumerina can infect Arabidopsis leaves, the P. cucumerina-Arabidopsis interaction has emerged as a popular model system in which to study plant defense reactions to necrotrophic fungi (Berrocal-Lobo et al., 2002; Ton and Mauch-Mani, 2004; Carlucci et al., 2012; Ramos et al., 2013). Various studies have shown that Arabidopsis deploys a wide range of inducible defense strategies against P. cucumerina, including JA-, SA-, ABA-, and auxin-dependent defenses, glucosinolates (Tierens et al., 2001; Sánchez-Vallet et al., 2010; Gamir et al., 2014; Pastor et al., 2014), callose deposition (García-Andrade et al., 2011; Gamir et al., 2012, 2014; Sánchez-Vallet et al., 2012), and ROS (Tierens et al., 2002; Sánchez-Vallet et al., 2010; Barna et al., 2012; Gamir et al., 2012, 2014; Pastor et al., 2014). Recent metabolomics studies have revealed large-scale metabolic changes in P. cucumerina-infected Arabidopsis, presumably to mobilize chemical defenses (Sánchez-Vallet et al., 2010; Gamir et al., 2014; Pastor et al., 2014). Furthermore, various chemical agents have been reported to induce resistance against P. cucumerina. These chemicals include β-amino-butyric acid, which primes callose deposition and SA-dependent defenses, benzothiadiazole (BTH or Bion; Görlach et al., 1996; Ton and Mauch-Mani, 2004), which activates SA-related defenses (Lawton et al., 1996; Ton and Mauch-Mani, 2004; Gamir et al., 2014; Luna et al., 2014), JA (Ton and Mauch-Mani, 2004), and ABA, which primes ROS and callose deposition (Ton and Mauch-Mani, 2004; Pastor et al., 2013). However, among all these studies, there is increasing controversy about the exact signaling pathways and defense responses contributing to plant resistance against P. cucumerina. While it is clear that JA and ethylene contribute to basal resistance against the fungus, the exact roles of SA, ABA, and ROS in P. cucumerina resistance vary between studies (Thomma et al., 1998; Ton and Mauch-Mani, 2004; Sánchez-Vallet et al., 2012; Gamir et al., 2014).This study is based on the observation that the disease phenotype during P. cucumerina infection differs according to the inoculation method used. We provide evidence that the fungus follows a hemibiotrophic infection strategy when infecting from relatively low spore densities on the leaf surface. By contrast, when challenged by localized host defense to relatively high spore densities, the fungus switches to a necrotrophic infection program. Our study has uncovered a novel strategy by which plant-pathogenic fungi can take advantage of the early immune response in the host plant.     

Long-Term Evolution of Nucleotide-Binding Site-Leucine-Rich Repeat Genes: Understanding Gained from and beyond the Legume Family

Proper utilization of plant disease resistance genes requires a good understanding of their short- and long-term evolution. Here we present a comprehensive study of the long-term evolutionary history of nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes within and beyond the legume family. The small group of NBS-LRR genes with an amino-terminal RESISTANCE TO POWDERY MILDEW8 (RPW8)-like domain (referred to as RNL) was first revealed as a basal clade sister to both coiled-coil-NBS-LRR (CNL) and Toll/Interleukin1 receptor-NBS-LRR (TNL) clades. Using Arabidopsis (Arabidopsis thaliana) as an outgroup, this study explicitly recovered 31 ancestral NBS lineages (two RNL, 21 CNL, and eight TNL) that had existed in the rosid common ancestor and 119 ancestral lineages (nine RNL, 55 CNL, and 55 TNL) that had diverged in the legume common ancestor. It was shown that, during their evolution in the past 54 million years, approximately 94% (112 of 119) of the ancestral legume NBS lineages experienced deletions or significant expansions, while seven original lineages were maintained in a conservative manner. The NBS gene duplication pattern was further examined. The local tandem duplications dominated NBS gene gains in the total number of genes (more than 75%), which was not surprising. However, it was interesting from our study that ectopic duplications had created many novel NBS gene loci in individual legume genomes, which occurred at a significant frequency of 8% to 20% in different legume lineages. Finally, by surveying the legume microRNAs that can potentially regulate NBS genes, we found that the microRNA-NBS gene interaction also exhibited a gain-and-loss pattern during the legume evolution.To combat the constant challenges by pathogens, plants have evolved a sophisticated two-layered defense system, in which proteins encoded by disease RESISTANCE (R) genes serve to sense pathogen invasion signals and to elicit defense responses (Jones and Dangl, 2006; McDowell and Simon, 2006; Bent and Mackey, 2007). Over 140 R genes have been characterized from different flowering plants, which confer resistance to a large array of pathogens, including bacteria, fungi, oomycetes, viruses, and nematodes (Liu et al., 2007; Yang et al., 2013). Among these, about 80% belong to the NBS-LRR class, which encodes a central nucleotide-binding site (NBS) domain and a C-terminal leucine-rich repeat (LRR) domain. Based on whether their N termini are homologous to the Toll/Interleukin1 receptor (TIR), the angiosperm NBS-LRR genes are further divided into the TIR-NBS-LRR (TNL) subclass and the non-TIR-NBS-LRR (nTNL) subclass (Meyers et al., 1999; Bai et al., 2002; Cannon et al., 2002). The latter has been also called CC-NBS-LRR (CNL) subclass, since a coiled-coil (CC) structure is often detected at the N terminus (Meyers et al., 2003). Interestingly, a small group of nTNL genes have an N-terminal RPW8-like domain with a transmembrane region before the CC structure (Xiao et al., 2001). This group of RPW8-NBS-LRR (RNL) genes has been usually viewed as a specific lineage of CNLs (Bonardi et al., 2011; Collier et al., 2011); however, its real phylogenetic relationship with CNLs and TNLs requires further investigation.NBS-LRR genes have been surveyed in many sequenced genomes of flowering plants, including four monocots: rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), and Brachypodium distachyon; one basal eudicot: Nelumbo nucifera; two asterid species: potato (Solanum tuberosum) and tomato (Solanum lycopersicum); and 14 rosids: Vitis vinifera, Populus trichocarpa, Ricinus communis, Medicago truncatula, soybean (Glycine max), Lotus japonicus, Cucumis sativus, Cucumis melo, Citrullus lanatus, Gossypium raimondii, Carica papaya, Arabidopsis (Arabidopsis thaliana), Arabidopsis lyrata, and Brassica rapa (Bai et al., 2002; Meyers et al., 2003; Monosi et al., 2004; Zhou et al., 2004; Yang et al., 2006, 2008b; Ameline-Torregrosa et al., 2008; Mun et al., 2009; Porter et al., 2009; Chen et al., 2010; Li et al., 2010a, 2010b; Guo et al., 2011; Zhang et al., 2011; Jupe et al., 2012; Lozano et al., 2012; Luo et al., 2012; Tan and Wu, 2012; Andolfo et al., 2013; Jia et al., 2013; Lin et al., 2013; Wan et al., 2013; Wei et al., 2013; Wu et al., 2014). Variable numbers (from dozens to hundreds) of NBS-LRR genes were reported from these genomes, making one wonder: how did these genes evolve so variably during flowering plant speciation?Comparative genomic studies conducted in the available genome sequences of closely related species or subspecies revealed that a significant proportion of NBS-LRR genes are not shared. For example, 70 NBS-LRR genes between Arabidopsis and A. lyrata show the presence/absence of polymorphisms (Chen et al., 2010; Guo et al., 2011). Moreover, synteny analysis revealed that, among 363 NBS-LRR gene loci in indica (cv 93-11) and japonica (cv Nipponbare) rice, 124 loci exist in only one genome (Luo et al., 2012). Unequal crossover, homologous repair, and nonhomologous repair are the three ways that NBS-LRR gene deletions are caused in rice genomes (Luo et al., 2012).In many surveyed genomes, the majority of NBS-LRR genes are found in a clustered organization (physically close to each other), with the rest exhibited as singletons. Many clusters are homogenous, with only duplicated members occupying the same phylogenetic lineage, whereas heterogenous clusters comprise members from distantly related clades (Meyers et al., 2003). Leister (2004) defined three types of NBS gene duplications: local tandem, ectopic, and segmental duplications. Although a general agreement on the widespread occurrence of local tandem duplications can be reached by various genome survey studies, the relative importance of ectopic and segmental duplications has been seldom investigated since the earliest surveys of the Arabidopsis genome (Richly et al., 2002; Baumgarten et al., 2003; Meyers et al., 2003; McDowell and Simon, 2006).With more genomic data available in certain angiosperm families, NBS-LRR genes should be further investigated among phylogenetically distant species to fill the gaps in the understanding of their long-term evolutionary patterns. The legume family contains many economically important crop species, such as clover (Trifolium spp.), soybean, peanut (Arachis hypogaea), and common bean (Phaseolus vulgaris). Although these legumes are constantly threatened by various pathogens, only a few functional legume R genes have been characterized, and all of them belong to the NBS-LRR class (Ashfield et al., 2004; Hayes et al., 2004; Gao et al., 2005; Seo et al., 2006; Yang et al., 2008a; Meyer et al., 2009). Therefore, it would be interesting to investigate the NBS-LRR gene repertoire among different legume species. Here, we carried out a comprehensive analysis of NBS-LRR genes in four divergent legume genomes, M. truncatula, pigeon pea (Cajanus cajan), common bean, and soybean, which shared a common ancestor approximately 54 million years ago (MYA; Fig. 1; Lavin et al., 2005). Approximately 1,000 nTNL and 667 TNL subclass NBS-encoding genes were identified in our study. Their genomic distribution, organization modes, phylogenetic relationships, and syntenic patterns were examined to obtain insight into the long-term evolutionary patterns of NBS-LRR genes.Open in a separate windowFigure 1.The phylogenetic tree of four investigated legume species (M. truncatula, pigeon pea, common bean, and soybean). Two WGD events are indicated with triangles: one occurred approximately 59 MYA in the common ancestor of the four investigated legumes, and the other occurred approximately 13 MYA in the Glycine spp. lineage alone (Schmutz et al., 2010). The numbers at the branch nodes indicate divergence times (Lavin et al., 2005; Stefanovic et al., 2009). [See online article for color version of this figure.]     

Focus Issue on Roots: Duplicate and Conquer: Multiple Homologs of PHOSPHORUS-STARVATION TOLERANCE1 Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.Increasing food production is one of the major global challenges in dealing with continuously growing population and food consumption (Godfray et al., 2010). One of the major obstacles to improve crop production in tropical regions is phosphorus (P) deficiency caused by P fixation in the soil clays. P is one of the most important plant nutrients, contributing approximately 0.2% of a plant’s dry weight, and is a component of key organic molecules such as nucleic acids, phospholipids, and ATP (Schachtman et al., 1998). On tropical soils, even when the total amount of soil P is high, its bioavailability is low due to P fixation by aluminum and iron oxides in clay minerals (Marschner, 1995) and immobilization into organic forms (Schachtman et al., 1998). Approximately half of the world’s agricultural lands occurs on low-P soils (Lynch, 2011); hence, crop adaptation to P insufficiency should be a major breeding target to enable sustainable agricultural production worldwide. In addition, because phosphate rock fertilizer is a nonrenewable resource that is being depleted by agricultural demands, increasing fertilizer prices negatively impact agriculture, particularly for small-holder farmers in developing countries in the tropics and subtropics (Cordell et al., 2009; Sattari et al., 2012). In sorghum (Sorghum bicolor), breeding strategies for low-P adaptation have been developed based on multienvironment trials in West Africa, indicating the importance of undertaking selection in low-P soil conditions (Leiser et al., 2012a, 2012b). Therefore, developing crops with greater ability to grow and maintain satisfactory yields on soils with reduced P availability is expected to substantially improve food security worldwide.Tolerance to P deficiency in plants can be achieved by mechanisms underlying both P acquisition and P internal utilization efficiency (Parentoni and Souza Junior, 2008). One of the major mechanisms that plants have evolved to overcome low-P availability is to maximize the ability of the roots to acquire and absorb P from the soil. Plants can mobilize P through the exudation of organic acids, acid phosphatases, and ribonucleases, resulting in enhanced P availability and uptake (Hinsinger, 2001; Ryan et al., 2001; Dakora and Phillips, 2002; Hammond and White, 2008; Ma et al., 2009; Pang et al., 2009). Another strategy to cope with low-P availability is to increase the soil volume accessed by root systems by forming mycorrhizal symbioses (Li et al., 2012; Smith and Smith, 2012; Rai et al., 2013). Due to low-P mobility on tropical soils, changes in root architecture and morphology enhance P uptake by facilitating soil exploration (Williamson et al., 2001; Ho et al., 2005; Walk et al., 2006; Svistoonoff et al., 2007; Lynch, 2011; Ingram et al., 2012; Niu et al., 2013). Root structural changes leading to higher P uptake include increased root hair growth (Yan et al., 2004; Haling et al., 2013; Lan et al., 2013) and length and enhancing lateral root over primary root growth (Williamson et al., 2001; Wang et al., 2013). In addition, increased root surface area is achieved by a combination of reduced root diameter and enhanced elongation of relatively thinner roots (Fitter et al., 2002). There is both intraspecific and interspecific genetic variation for P deficiency tolerance in crop species (Lynch and Brown, 2001, 2012; Mudge et al., 2002; Paszkowski et al., 2002; Rausch and Bucher, 2002; Huang et al., 2011; Zhang et al., 2011; Leiser et al., 2014a) that can be explored to develop P-efficient cultivars.In rice (Oryza sativa), Phosphorus uptake1 (Pup1), a major quantitative trait locus (QTL) for P deficiency tolerance donated by an aus-type Indian variety, Kasalath, was mapped to the long arm of chromosome 12 (Ni et al., 1998; Wissuwa et al., 1998, 2002; Heuer et al., 2009). Near-isogenic lines bearing the Kasalath allele at Pup1 showed 3-fold higher P uptake and grain yield in low-P trials compared with the recurrent parent, cv Nipponbare, which is intolerant to P starvation (Wissuwa and Ae, 2001). Following high-resolution mapping of Pup1, comparative sequence analyses of homologous bacterial artificial chromosomes showed that a Kasalath genomic fragment contained several genes not present in cv Nipponbare, highlighting an approximately 90-kb deletion in the cv Nipponbare reference genome that encompassed the Pup1 locus (Heuer et al., 2009). Within this insertion/deletion, OsPupK46-2, a gene encoding a Ser/Thr kinase of the Receptor-like Protein Kinase LRK10L-2 subfamily, was found to enhance grain yield and P uptake in rice lines overexpressing this gene, indicating that this protein kinase underlies the Pup1 locus (Gamuyao et al., 2012). OsPupK46-2, which is now designated PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was found to be up-regulated in the root tissues of tolerant near-isogenic lines under P-deficient conditions and was shown to increase P uptake by a physiological mechanism based on the enhancement of early root growth and development. Furthermore, lines overexpressing OsPupK46-2 showed an approximately 30% grain yield increase in comparison with the null lines, suggesting that PSTOL1 has potential for molecular breeding applications to improve crop performance under low-P conditions. Consistent with the proposed physiological mechanism underlying OsPSTOL1, the superior performance of the transgenic lines was related to enhanced root dry weight, root length, and root surface area (Gamuyao et al., 2012).Sorghum is the world’s fifth most important cereal crop and is a staple food for more than half a billion people. It is widely adapted to harsh environmental conditions, and more specifically, to arid and semiarid regions of the world (Doumbia et al., 1993, 1998). It has been estimated that rice diverged from its most recent common ancestor with sorghum and maize (Zea mays) approximately 50 million years ago (Kellogg, 1998; Paterson et al., 2000, 2004; Paterson, 2008). About 60% of the genes in the sorghum genome are located in syntenic regions to rice (Paterson et al., 2009), emphasizing the potential for using comparative genomics for cross-species identification of genes underlying abiotic stress tolerance in the grass family. Here, we applied association analysis to specifically study the role of sorghum homologs of rice OsPSTOL1 in tolerance to P starvation in sorghum. Single-nucleotide polymorphisms (SNPs) within PSTOL1 homologs in sorghum, collectively designated SbPSTOL1, were significantly associated with grain yield under low-P conditions and also root morphology and root system architecture (RSA) traits phenotyped from hydroponically grown plants. Under low P, SbPSTOL1 genes increased biomass accumulation and P content in the African landrace panel and grain yield in the sorghum association panel phenotyped in a low-P Brazilian soil. This suggests a stable effect across environments and sorghum genotypes that potentially can be used for molecular breeding applications. QTL mapping with a large sorghum recombinant inbred line population was used to validate the association results, indicating that SbPSTOL1 homologs colocalize with QTLs related to root morphology and performance under low P. Our results indicate that SbPSTOL1 homologs have the ability to enhance P uptake and sorghum performance in low-P soils by a mechanism related not only to early root growth enhancement, as was the case for rice OsPSTOL1, but also by modulating RSA.     

The Role of a Potassium Transporter OsHAK5 in Potassium Acquisition and Transport from Roots to Shoots in Rice at Low Potassium Supply Levels

In plants, K transporter (KT)/high affinity K transporter (HAK)/K uptake permease (KUP) is the largest potassium (K) transporter family; however, few of the members have had their physiological functions characterized in planta. Here, we studied OsHAK5 of the KT/HAK/KUP family in rice (Oryza sativa). We determined its cellular and tissue localization and analyzed its functions in rice using both OsHAK5 knockout mutants and overexpression lines in three genetic backgrounds. A β-glucuronidase reporter driven by the OsHAK5 native promoter indicated OsHAK5 expression in various tissue organs from root to seed, abundantly in root epidermis and stele, the vascular tissues, and mesophyll cells. Net K influx rate in roots and K transport from roots to aerial parts were severely impaired by OsHAK5 knockout but increased by OsHAK5 overexpression in 0.1 and 0.3 mm K external solution. The contribution of OsHAK5 to K mobilization within the rice plant was confirmed further by the change of K concentration in the xylem sap and K distribution in the transgenic lines when K was removed completely from the external solution. Overexpression of OsHAK5 increased the K-sodium concentration ratio in the shoots and salt stress tolerance (shoot growth), while knockout of OsHAK5 decreased the K-sodium concentration ratio in the shoots, resulting in sensitivity to salt stress. Taken together, these results demonstrate that OsHAK5 plays a major role in K acquisition by roots faced with low external K and in K upward transport from roots to shoots in K-deficient rice plants.Potassium (K) is one of the three most important macronutrients and the most abundant cation in plants. As a major osmoticum in the vacuole, K drives the generation of turgor pressure, enabling cell expansion. In the vascular tissue, K is an important participant in the generation of root pressure (for review, see Wegner, 2014 [including his new hypothesis]). In the phloem, K is critical for the transport of photoassimilates from source to sink (Marschner, 1996; Deeken et al., 2002; Gajdanowicz et al., 2011). In addition, enhancing K absorption and decreasing sodium (Na) accumulation is a major strategy of glycophytes in salt stress tolerance (Maathuis and Amtmann, 1999; Munns and Tester, 2008; Shabala and Cuin, 2008).Plants acquire K through K-permeable proteins at the root surface. Since available K concentration in the soil may vary by 100-fold, plants have developed multiple K uptake systems for adapting to this variability (Epstein et al., 1963; Grabov, 2007; Maathuis, 2009). In a classic K uptake experiment in barley (Hordeum vulgare), root K absorption has been described as a high-affinity and low-affinity biphasic transport process (Epstein et al., 1963). It is generally assumed that the low-affinity transport system (LATS) in the roots mediates K uptake in the millimolar range and that the activity of this system is insensitive to external K concentration (Maathuis and Sanders, 1997; Chérel et al., 2014). In contrast, the high-affinity transport system (HATS) was rapidly up-regulated when the supply of exogenous K was halted (Glass, 1976; Glass and Dunlop, 1978).The membrane transporters for K flux identified in plants are generally classified into three channels and three transporter families based on phylogenetic analysis (Mäser et al., 2001; Véry and Sentenac, 2003; Lebaudy et al., 2007; Alemán et al., 2011). For K uptake, it was predicted that, under most circumstances, K transporters function as HATS, while K-permeable channels mediate LATS (Maathuis and Sanders, 1997). However, a root-expressed K channel in Arabidopsis (Arabidopsis thaliana), Arabidopsis K Transporter1 (AKT1), mediates K absorption over a wide range of external K concentrations (Sentenac et al., 1992; Lagarde et al., 1996; Hirsch et al., 1998; Spalding et al., 1999), while evidence is accumulating that many K transporters, including members of the K transporter (KT)/high affinity K transporter (HAK)/K uptake permease (KUP) family, are low-affinity K transporters (Quintero and Blatt, 1997; Senn et al., 2001), implying that functions of plant K channels and transporters overlap at different K concentration ranges.Out of the three families of K transporters, cation proton antiporter (CPA), high affinity K/Na transporter (HKT), and KT/HAK/KUP, CPA was characterized as a K⁺(Na⁺)/H⁺ antiporter, HKT may cotransport Na and K or transport Na only (Rubio et al., 1995; Uozumi et al., 2000), while KT/HAK/KUP were predicted to be H⁺-coupled K⁺ symporters (Mäser et al., 2001; Lebaudy et al., 2007). KT/HAK/KUP were named by different researchers who first identified and cloned them (Quintero and Blatt, 1997; Santa-María et al., 1997). In plants, the KT/HAK/KUP family is the largest K transporter family, including 13 members in Arabidopsis and 27 members in the rice (Oryza sativa) genome (Rubio et al., 2000; Mäser et al., 2001; Bañuelos et al., 2002; Gupta et al., 2008). Sequence alignments show that genes of this family share relatively low homology to each other. The KT/HAK/KUP family was divided into four major clusters (Rubio et al., 2000; Gupta et al., 2008), and in cluster I and II, they were further separated into A and B groups. Genes of cluster I or II likely exist in all plants, cluster III is composed of genes from both Arabidopsis and rice, while cluster IV includes only four rice genes (Grabov, 2007; Gupta et al., 2008).The functions of KT/HAK/KUP were studied mostly in heterologous expression systems. Transporters of cluster I, such as AtHAK5, HvHAK1, OsHAK1, and OsHAK5, are localized in the plasma membrane (Kim et al., 1998; Bañuelos et al., 2002; Gierth et al., 2005) and exhibit high-affinity K uptake in the yeast Saccharomyces cerevisiae (Santa-María et al., 1997; Fu and Luan, 1998; Rubio et al., 2000) and in Escherichia coli (Horie et al., 2011). Transporters of cluster II, like AtKUP4 (TINY ROOT HAIRS1, TRH1), HvHAK2, OsHAK2, OsHAK7, and OsHAK10, could not complement the K uptake-deficient yeast (Saccharomyces cerevisiae) but were able to mediate K fluxes in a bacterial mutant; they might be tonoplast transporters (Senn et al., 2001; Bañuelos et al., 2002; Rodríguez-Navarro and Rubio, 2006). The function of transporters in clusters III and IV is even less known (Grabov, 2007).Existing data suggest that some KT/HAK/KUP transporters also may respond to salinity stress (Maathuis, 2009). The cluster I transporters of HvHAK1 mediate Na influx (Santa-María et al., 1997), while AtHAK5 expression is inhibited by Na (Rubio et al., 2000; Nieves-Cordones et al., 2010). Expression of OsHAK5 in tobacco (Nicotiana tabacum) BY2 cells enhanced the salt tolerance of these cells by accumulating more K without affecting their Na content (Horie et al., 2011).There are only scarce reports on the physiological function of KT/HAK/KUP in planta. In Arabidopsis, mutation of AtKUP2 (SHORT HYPOCOTYL3) resulted in a short hypocotyl, small leaves, and a short flowering stem (Elumalai et al., 2002), while a loss-of-function mutation of AtKUP4 (TRH1) resulted in short root hairs and a loss of gravity response in the root (Rigas et al., 2001; Desbrosses et al., 2003; Ahn et al., 2004). AtHAK5 is the only system currently known to mediate K uptake at concentrations below 0.01 mm (Rubio et al., 2010) and provides a cesium uptake pathway (Qi et al., 2008). AtHAK5 and AtAKT1 are the two major physiologically relevant molecular entities mediating K uptake into roots in the range between 0.01 and 0.05 mm (Pyo et al., 2010; Rubio et al., 2010). AtAKT1 may contribute to K uptake within the K concentrations that belong to the high-affinity system described by Epstein et al. (1963).Among all 27 members of the KT/HAK/KUP family in rice, OsHAK1, OsHAK5, OsHAK19, and OsHAK20 were grouped in cluster IB (Gupta et al., 2008). These four rice HAK members share 50.9% to 53.4% amino acid identity with AtHAK5. OsHAK1 was expressed in the whole plant, with maximum expression in roots, and was up-regulated by K deficiency; it mediated high-affinity K uptake in yeast (Bañuelos et al., 2002). In this study, we examined the tissue-specific localization and the physiological functions of OsHAK5 in response to variation in K supply and to salt stress in rice. By comparing K uptake and translocation in OsHAK5 knockout (KO) mutants and in OsHAK5-overexpressing lines with those in their respective wild-type lines supplied with different K concentrations, we found that OsHAK5 not only mediates high-affinity K acquisition but also participates in root-to-shoot K transport as well as in K-regulated salt tolerance.     

Evolution of Conifer Diterpene Synthases: Diterpene Resin Acid Biosynthesis in Lodgepole Pine and Jack Pine Involves Monofunctional and Bifunctional Diterpene Synthases

Abscisic acid (ABA) induces stomatal closure and inhibits light-induced stomatal opening. The mechanisms in these two processes are not necessarily the same. It has been postulated that the ABA receptors involved in opening inhibition are different from those involved in closure induction. Here, we provide evidence that four recently identified ABA receptors (PYRABACTIN RESISTANCE1 [PYR1], PYRABACTIN RESISTANCE-LIKE1 [PYL1], PYL2, and PYL4) are not sufficient for opening inhibition in Arabidopsis (Arabidopsis thaliana). ABA-induced stomatal closure was impaired in the pyr1/pyl1/pyl2/pyl4 quadruple ABA receptor mutant. ABA inhibition of the opening of the mutant’s stomata remained intact. ABA did not induce either the production of reactive oxygen species and nitric oxide or the alkalization of the cytosol in the quadruple mutant, in accordance with the closure phenotype. Whole cell patch-clamp analysis of inward-rectifying K⁺ current in guard cells showed a partial inhibition by ABA, indicating that the ABA sensitivity of the mutant was not fully impaired. ABA substantially inhibited blue light-induced phosphorylation of H⁺-ATPase in guard cells in both the mutant and the wild type. On the other hand, in a knockout mutant of the SNF1-related protein kinase, srk2e, stomatal opening and closure, reactive oxygen species and nitric oxide production, cytosolic alkalization, inward-rectifying K⁺ current inactivation, and H⁺-ATPase phosphorylation were not sensitive to ABA.The phytohormone abscisic acid (ABA), which is synthesized in response to abiotic stresses, plays a key role in the drought hardiness of plants. Reducing transpirational water loss through stomatal pores is a major ABA response (Schroeder et al., 2001). ABA promotes the closure of open stomata and inhibits the opening of closed stomata. These effects are not simply the reverse of one another (Allen et al., 1999; Wang et al., 2001; Mishra et al., 2006).A class of receptors of ABA was identified (Ma et al., 2009; Park et al., 2009; Santiago et al., 2009; Nishimura et al., 2010). The sensitivity of stomata to ABA was strongly decreased in quadruple and sextuple mutants of the ABA receptor genes PYRABACTIN RESISTANCE/PYRABACTIN RESISTANCE-LIKE/REGULATORY COMPONENT OF ABSCISIC ACID RECEPTOR (PYR/PYL/RCAR; Nishimura et al., 2010; Gonzalez-Guzman et al., 2012). The PYR/PYL/RCAR receptors are involved in the early ABA signaling events, in which a sequence of interactions of the receptors with PROTEIN PHOSPHATASE 2Cs (PP2Cs) and subfamily 2 SNF1-RELATED PROTEIN KINASES (SnRK2s) leads to the activation of downstream ABA signaling targets in guard cells (Cutler et al., 2010; Kim et al., 2010; Weiner et al., 2010). Studies of Commelina communis and Vicia faba suggested that the ABA receptors involved in stomatal opening are not the same as the ABA receptors involved in stomatal closure (Allan et al., 1994; Anderson et al., 1994; Assmann, 1994; Schwartz et al., 1994). The roles of PYR/PYL/RCAR in either stomatal opening or closure remained to be elucidated.Blue light induces stomatal opening through the activation of plasma membrane H⁺-ATPase in guard cells that generates an inside-negative electrochemical gradient across the plasma membrane and drives K⁺ uptake through voltage-dependent inward-rectifying K⁺ channels (Assmann et al., 1985; Shimazaki et al., 1986; Blatt, 1987; Schroeder et al., 1987; Thiel et al., 1992). Phosphorylation of the penultimate Thr of the plasma membrane H⁺-ATPase is a prerequisite for blue light-induced activation of the H⁺-ATPase (Kinoshita and Shimazaki, 1999, 2002). ABA inhibits H⁺-ATPase activity through dephosphorylation of the penultimate Thr in the C terminus of the H⁺-ATPase in guard cells, resulting in prevention of the opening (Goh et al., 1996; Zhang et al., 2004; Hayashi et al., 2011). Inward-rectifying K⁺ currents (I_Kin) of guard cells are negatively regulated by ABA in addition to through the decline of the H⁺ pump-driven membrane potential difference (Schroeder and Hagiwara, 1989; Blatt, 1990; McAinsh et al., 1990; Schwartz et al., 1994; Grabov and Blatt, 1999; Saito et al., 2008). This down-regulation of ion transporters by ABA is essential for the inhibition of stomatal opening.A series of second messengers has been shown to mediate ABA-induced stomatal closure. Reactive oxygen species (ROS) produced by NADPH oxidases play a crucial role in ABA signaling in guard cells (Pei et al., 2000; Zhang et al., 2001; Kwak et al., 2003; Sirichandra et al., 2009; Jannat et al., 2011). Nitric oxide (NO) is an essential signaling component in ABA-induced stomatal closure (Desikan et al., 2002; Guo et al., 2003; Garcia-Mata and Lamattina, 2007; Neill et al., 2008). Alkalization of cytosolic pH in guard cells is postulated to mediate ABA-induced stomatal closure in Arabidopsis (Arabidopsis thaliana) and Pisum sativum and Paphiopedilum species (Irving et al., 1992; Gehring et al., 1997; Grabov and Blatt, 1997; Suhita et al., 2004; Gonugunta et al., 2008). These second messengers transduce environmental signals to ion channels and ion transporters that create the driving force for stomatal movements (Ward et al., 1995; MacRobbie, 1998; Garcia-Mata et al., 2003).In this study, we examined the mobilization of second messengers, the inactivation of I_Kin, and the suppression of H⁺-ATPase phosphorylation evoked by ABA in Arabidopsis mutants to clarify the downstream signaling events of ABA signaling in guard cells. The mutants included a quadruple mutant of PYR/PYL/RCARs, pyr1/pyl1/pyl2/pyl4, and a mutant of a SnRK2 kinase, srk2e.