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Eukaryotic Cell, December 2003, p. 1246-1252, Vol. 2, No. 6
1535-9778/03/$08.00+0 DOI: 10.1128/EC.2.6.1246-1252.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Departamento de Genética,1 Departamento de Microbiología, Universidad de Córdoba, Córdoba, Spain2
Received 15 July 2003/ Accepted 1 October 2003
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A key factor in fungal growth and development is ambient pH. Fungi grow over a wide range of pH conditions and must thus be able to tailor gene expression to the particular pH of their growth environment. A conserved signaling cascade integrated by the products of the pal genes, whose terminal component is the zinc-finger transcription factor PacC/Rim101p, regulates gene expression in response to ambient pH (18). Upon shift to alkaline pH, an inactive PacC precursor is posttranscriptionally activated by proteolytic processing into a shorter functional form that activates genes preferentially expressed at alkaline pH and represses genes expressed under acidic growth conditions (18). The pacC orthologue of F. oxysporum was recently cloned, and the encoded protein was shown to regulate pH-dependent gene expression and to function as a negative regulator of virulence on plants (11). Thus, pacC+/- loss-of-function mutants of F. oxysporum mimic growth at acidic ambient pH and exhibit increased virulence, whereas pacCc strains expressing a dominant activating pacC allele mimic growth at alkaline pH and show significantly reduced virulence. At present, the downstream effector genes regulated by PacC in F. oxysporum remain largely unknown.
Yet another hallmark of fungal versatility is the capacity to grow over a wide range of salt concentrations. Generally, salt tolerance in living cells is conditioned by the capacity to maintain intracellular ion homeostasis. Fungi have developed extrusion systems to keep levels of intracellular sodium below concentrations toxic to the cell (9). In the best-studied system, that of Saccharomyces cerevisiae, the main Na+ efflux system is encoded by the ENA genes, a tandem array of four to five genes encoding nearly identical proteins. ENA1, the most important and the best-studied component of this system, is essential for ion homeostasis and salt tolerance in yeast (15, 23). The ENA1 protein works as a P-type Na+-ATPase but can also mediate Li+ or K+ efflux (8, 14, 15, 23). Expression of ENA1 in S. cerevisiae is tightly regulated by Na+ but also depends on alkaline ambient pH (for a review, see reference 20). Recent studies suggest that full expression of ENA1 at alkaline pH requires RIM101, the S. cerevisiae orthologue of PacC, providing further evidence for a functional link between pH signaling and ENA1 (17, 25).
In the present study we have addressed the role of pacC in salt tolerance of F. oxysporum. We provide evidence for the presence of a sodium efflux system based on an orthologue of the S. cerevisiae ENA1 gene. We further show that full transcriptional activation of the ena1 gene requires PacC and that both PacC and Ena1 play a fundamental role in the salt stress response of F. oxysporum.
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For phenotypic analysis of colony growth, a 5-µl drop containing 2.5 x 105 freshly obtained microconidia was transferred on 1.5% (wt/vol) agar plates of synthetic medium (SM) (13) containing 1% (wt/vol) glucose, 0.1% NH4NO3, and different concentrations of NaCl or LiCl. Media were buffered with 100 mM Na2HPO4 at pH 4; 50 mM Na2HPO4, 50 mM NaH2PO4, and 50 mM NaCl at pH 6; and 100 mM NaH2PO4 and 100 mM NaCl at pH 8.
Determination of cation accumulation, influx, and efflux. For determination of intracellular cation accumulation, microconidia were germinated in SM containing 1% (wt/vol) glucose and 0.1% NH4NO3, supplemented with 0.05, 0.1, or 0.15 mM LiCl or 0.5, 1, or 1.5 M NaCl. After 12 h, samples were filtered and processed for determination of intracellular ion content as previously reported (10, 21). Briefly, samples of cells were filtered, washed with 0.02 M MgCl2, and treated with 0.2 M HCl, and the cations were analyzed by atomic absorption spectrophotometry.
For determination of lithium and rubidium influx (rubidium was used as a transport analog of potassium), microconidia were germinated in SM containing 1% (wt/vol) glucose and 0.1% NH4NO3 for 12 h. At time zero, 0.1 M LiCl or RbCl was added to the growth medium, and samples were taken at regular time intervals, filtered immediately, and processed for determination of intracellular ion content (21).
For determination of the lithium efflux rate, microconidia germinated in SM were supplemented with 0.1 M LiCl (wild-type and pacC+/- strains) or 0.3 M LiCl (pacCc strain). After 12 h, microconidia were filtered, washed with sterile 0.02 M MgCl2, and resuspended in fresh SM buffered at pH 4.0 or 8.0 as described above. This medium was free of lithium and was supplemented with 0.05 M RbCl to trigger the efflux process. Samples were taken at regular time intervals, filtered, and processed for the determination of intracellular ion content (10, 21).
All experiments for determination of cation accumulation, influx, or efflux were performed at least three times with similar results (the maximum standard deviations were <10%).
Nucleic acid manipulations, cloning, and analysis of the ena1 gene. For Northern analysis, microconidia were germinated for 12 h in SM without added Na+ and then transferred for different periods of time to SM buffered at the indicated pH values, with or without 0.5 M Na+. Total RNA was extracted from mycelium as reported elsewhere (12), and Northern analysis and probe labeling was performed as described previously (13) by using the nonisotopic digoxigenin labeling kit (Roche Diagnostic S.L, Barcelona, Spain). Southern and Northern analyses were carried out as described above.
Genomic DNA of F. oxysporum isolate 4287 was extracted as previously reported (19) and used for PCR amplification on a Perkin-Elmer GeneAmp System 2400 with the primers ena3 (5'-TGACAAGCGACGATCTTTCTTCCG-3') and ena4 (5'-GGTGATGCCCTTGTGCTTGAAGAC-3') derived from an F. oxysporum expressed sequence tag clone. The following PCR conditions were used: 35 cycles with denaturation at 94°C for 30 s, annealing at 60°C for 30 s, and extension at 72°C for 30 s. An initial denaturation step of 5 min at 94°C and a final elongation step at 72°C for 7 min were also performed. The amplified 250-bp DNA fragment was cloned into pGEM-T (Promega, Madison, Wis.), sequenced, and used to screen a lambda EMBL3 genomic library of F. oxysporum f.sp. lycopersici isolate 4287. Library screening, subcloning, and other routine procedures were performed as described in standard protocols (24). Sequencing of both DNA strands was performed at the Servicio Centralizado de Apoyo a la Investigación, University of Córdoba, by using the Dyedeoxy terminator cycle sequencing kit (PE Biosystems, Foster City, Calif.) on an ABI Prism 377 genetic analyzer apparatus (Applied Biosystems, Foster City, Calif.). DNA and protein sequence databases were searched by using the basic local alignment search tool (BLAST) algorithm (2) at the National Center for Biotechnology Information (Bethesda, Md.).
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FIG. 1. F. oxysporum pacC mutants are affected in salt tolerance. (A) Wild-type strain 4287, loss-of-function mutant pacC+/-, and dominant activating mutant pacCc were grown for 3 days on plates with SM buffered at pH 6.0 and supplemented with the indicated compounds.
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FIG. 2. Mutations in pacC affect ion homeostasis. Intracellular accumulation of cations was determined in germlings of the F. oxysporum wild-type strain ( ), loss-of-function mutant pacC+/- ( ) grown for 12 h in the presence of the indicated concentrations of Li+ (A and C) or Na+ (B).
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FIG. 3. Mutations in pacC do not affect kinetics of cation import. Kinetics of cation import was determined in germlings of the F. oxysporum wild-type strain (), loss-of-function mutant pacC+/- strain ( ), or dominant activating mutant pacCc strain ( ). Samples were taken at the indicated times after the addition of 0.1 M LiCl (A) or 0.1 M RbCl (B).
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FIG. 4. Mutations in pacC affect cation efflux at alkaline but not at acidic ambient pH. Kinetics of cation export was determined in germlings of the F. oxysporum wild-type strain (), loss-of-function mutant pacC+/- strain ( ), or dominant activating mutant pacCc strain ( ). Microconidia were germinated for 12 h in SM containing 0.1 M Li+ (wild type and pacC+/- mutant) or 0.3 M Li+ (pacCc mutant), washed, and transferred to Li+-free medium buffered at pH 4.0 (A) or 8.0 (B), and samples were taken at the indicated times.
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EMBL3 genomic library of F. oxysporum isolate 4287. Sequencing of a hybridizing genomic clones revealed the presence of an open reading frame of 3,261 nucleotides encoding a predicted protein of 1,087 amino acids. Sequence alignment of F. oxysporum ena1 with fungal ena1 genes in the databases suggested the presence of three introns 215, 51, and 49 nucleotides in length, respectively. The 5'-flanking sequence of the ena1 gene contains four copies of the PacC consensus binding sequence 5'-GCCARG-3' (26) at positions -549, -474, -382, and -321. The sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession number AY345588. The deduced F. oxysporum Ena1 protein has 70 and 46% amino acid identity with the Ena1 proteins of N. crassa and S. cerevisiae, respectively, and contains nine putative transmembrane regions that are highly conserved between fungal P-type Na+-ATPases (Fig. 5). Southern analysis of genomic DNA digested with different restriction enzymes suggested that ena1 is present as a single copy in the F. oxysporum genome. Moreover, a BLAST search of the F. graminearum complete genome sequence with ena1 only produced one significant match (results not shown).
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FIG. 5. Amino acid sequence alignment of the predicted F. oxysporum ena1 gene product with fungal P-type Na+-ATPases. Deduced Ena1 proteins from F. oxysporum (EMBL accession no. AY345588), N. crassa (AJ243520), and S. cerevisiae (U24069) are shown. Identical amino acids are highlighted on a shaded background. Dashes indicate gaps in the alignments. Nine predicted transmembrane domains are indicated by solid bars.
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FIG. 6. Activation of ena1 transcription requires high salt concentrations, alkaline ambient pH, and PacC. Transcript levels of ena1 in the F. oxysporum wild-type strain, pacC+/- mutant, and pacCc mutant were analyzed by northern hybridization analysis. (A) Microconidia of the wild-type strain were germinated for 12 h in SM without added Na+ and then transferred for 2 h to SM buffered at the indicated pH values, with or without 0.5 M Na+. Total RNA was extracted, fractionated on an agarose gel, blotted onto a nylon membrane and hybridized with the ena1 probe. As a loading control, a probe corresponding to the F. oxysporum actin gene (act1) was hybridized to the same RNA samples. (B) Microconidia of the wild-type strain, the pacC+/- mutant and the pacCc mutant were germinated as in panel A and transferred to SM buffered at pH 8.0 and containing 0.5 M Na+. Total RNA was extracted from samples obtained at the indicated time points, fractionated, blotted, and hybridized with the ena1 or act1 probes.
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The changes in salt tolerance and intracellular Na+ and Li+ levels observed in the pacC mutants suggested a functional link between ambient pH, PacC, and ena1 expression in F. oxysporum. Our data support a positive role of PacC in the regulation of ena1, since pacC+/- loss-of-function mutants show strongly delayed and reduced expression of ena1, whereas pacCc strains expressing a dominant activating pacC allele induce ena1 expression more rapidly and to higher levels than did the wild type. Our results are similar to those reported in S. cerevisiae, where the pacC orthologue RIM101 was shown to control the expression of ENA1 (17, 25). Further supporting this view, we found that the 5'-flanking sequence of the ena1 gene of F. oxysporum contains four copies of the PacC consensus binding sequence 5'-GCCARG-3'. In Fig. 7 we present a model summarizing the regulation of ena1 expression by PacC in F. oxysporum. According to this model, PacC activates ena1 expression at alkaline ambient pH coordinately with a second factor that responds to high Na+ levels. Conversely, at an acidic ambient pH the Na+ efflux process would be mediated by a Na+/H+ antiporter acting independently of PacC. In S. cerevisiae, a Na+/H+ antiporter system encoded by the NHA1 gene mediates Na+ tolerance at acidic pH values (4, 5, 16). We have detected the existence in F. oxysporum of an orthologue of NHA, a plasma membrane Na+/H+ antiporter from fungi and plants (Z. Caracuel et al., unpublished data).
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FIG. 7. Model for the role of PacC in the control of ion homeostasis in F. oxysporum. High external concentrations of Na+ result in an increased influx of the cation, elevating intracellular Na+ levels beyond a threshold. This triggers transcriptional activation of the ena1 gene encoding a P-type Na+-ATPase via an unknown signaling mechanism. In addition, expression of ena1 also requires binding of the activated form of PacC transcription factor to its cognate binding sites in the promoter. Proteolytic activation of PacC occurs predominantly at alkaline ambient pH; therefore, both high Na+ concentrations and high pH are required for transcriptional activation of ena1. Conversely, at acidic pH an alternative, PacC-independent Na+ efflux system is active, possibly based on a Na+/H+ antiporter orthologous to Nha1 of S. cerevisiae. Besides activation of ena1, PacC may have additional regulatory effects on ion homeostasis.
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This research was supported by grants BIO2001-2601 to M.I.G.R. and BMC2002-04011-C05 to J.R. from the Spanish Ministerio de Ciencia y Tecnología. Z. C. has a Ph.D. fellowship from Ministerio de Ciencia y Tecnología. A.D.P. is the recipient of a Ramón y Cajal grant from Ministerio de Ciencia y Tecnología.
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