The nucleotide sequence of POX18, a gene encoding a small oleate-inducible peroxisomal protein from Candida tropicalis

Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae

BACKGROUND

Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood.

RESULTS

We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.

CONCLUSION

We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.

A yeast sterol carrier protein with fatty-acid and fatty-acyl-CoA binding activity

The 14-kDa sterol carrier protein 2 (SCP2) domain is present in Eukaria, Bacteria and Archaea, and has been implicated in the transport and metabolism of lipids. We report the cloning, expression, purification and physicochemical characterization of a SCP2 from the yeast Yarrowia lipolytica (YLSCP2). Analytical size-exclusion chromatography, circular dichroism and fluorescence spectra, indicate that recombinant YLSCP2 is a well-folded monomer. Thermal unfolding experiments show that SCP2 maximal stability is at pH 7.0-9.0. YLSCP2 binds cis-parinaric acid and palmitoyl-CoA with KD values of 81+/-40 nM and 73+/-33 nM, respectively, sustaining for the first time the binding of fatty acids and their CoA esters to a nonanimal SCP2. The role of yeast SCP2 and other lipid binding proteins in transport, storage and peroxisomal oxidation of fatty acids is discussed.

Fusion and fission, the evolution of sterol carrier protein-2

Sterol carrier protein-2 (SCP-2) is an intracellular, small, basic protein domain that in vitro enhances the transfer of lipids between membranes. It is expressed in bacteria, archaea, and eukaryotes. There are five human genes, HSD17B4, SCPX, HSDL2 STOML1, and C20orf79, which encode SCP-2. HSD17B4, SCPX, HSDL2, and STOML1 encode fusion proteins with SCP-2 downstream of another protein domain, whereas C20orf79 encodes an unfused SCP-2. We have extracted SCP-2 domains from databases and analyzed the evolution of the eukaryotic SCP-2. We show that SCPX and HSDL2 are present in most animals from Cnidaria to Chordata. STOML1 are present in nematodes and more advanced animals. HSD17B4 which encodes a D-bifunctional protein (DBP) with domains for D-3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase, and SCP-2 are found in animals from insects to mammals and also in fungi. Nematodes, amoebas, ciliates, apicomplexans, and oomycetes express an alternative DBP with the SCP-2 domain directly connected to the D-3-hydroxyacyl-CoA dehydrogenase. This fusion has not been retained in plant genomes, which solely express unfused SCP-2 domains. Proteins carrying unfused SCP-2 domains are also encoded in bacteria, archaea, ciliates, fungi, insects, nematodes, and vertebrates. Our results indicate that the fusion between D-3-hydroxyacyl-CoA dehydrogenase and SCP-2 was formed early during eukaryotic evolution. There have since been several gene fission events where genes encoding unfused SCP-2 domains have been formed, as well as gene fusion events placing the SCP-2 domain in novel protein domain contexts.

Addition of oleic acid increases expression of recombinant human serum albumin by the AOX2 promoter in Pichia pastoris

The addition of several kinds of fatty acid to the culture medium of a recombinant human serum albumin (rHSA)-producing yeast, Pichia pastoris, resulted in increased expression levels of the product. Among the fatty acids tested, a small amount of oleic acid (0.01% (w/v)) doubled the rHSA production level in a shake-flask culture when measured by the reversed passive hemagglutination assay method. To elucidate this phenomenon, studies were conducted using deletion mutants from the AOX2 promoter region. Deletion mutants, designed for a detailed evaluation of the methanol regulation elements (AOX2-UAS, AOX2-URS1, and AOX2-URS2) did not respond to the addition of oleic acid. However, a deletion mutant that was not lacking an upstream region from the AOX2 promoter showed a response to oleic acid. The results implied the presence of an oleic acid-responsive element between nucleotides (nt) -1529 and -803, and it may lie between nt -1411 and -1403 in the AOX2 promoter of P. pastoris. The response to oleic acid was shown to function even when the level of rHSA expression was increased by a mutation in the AOX2 promoter. Therefore addition of oleic acid to the medium is likely to play an important role, in cooperation with gene manipulation, in achieving high expression levels of rHSA for the purpose of commercial production.

Dehydroepiandrosterone (DHEA) metabolism in Saccharomyces cerevisiae expressing mammalian steroid hydroxylase CYP7B: Ayr1p and Fox2p display 17beta-hydroxysteroid dehydrogenase activity

We have engineered recombinant yeast to perform stereospecific hydroxylation of dehydroepiandrosterone (DHEA). This mammalian pro-hormone promotes brain and immune function; hydroxylation at the 7alpha position by P450 CYP7B is the major pathway of metabolic activation. We have sought to activate DHEA via yeast expression of rat CYP7B enzyme. Saccharomyces cerevisiae was found to metabolize DHEA by 3beta-acetylation; this was abolished by mutation at atf2. DHEA was also toxic, blocking tryptophan (trp) uptake: prototrophic strains were DHEA-resistant. In TRP(+) atf2 strains DHEA was then converted to androstene-3beta,17beta-diol (A/enediol) by an endogenous 17beta-hydroxysteroid dehydrogenase (17betaHSD). Seven yeast polypeptides similar to human 17betaHSDs were identified: when expressed in yeast, only AYR1 (1-acyl dihydroxyacetone phosphate reductase) increased A/enediol accumulation, while the hydroxyacyl-CoA dehydrogenase Fox2p, highly homologous to human 17betaHSD4, oxidized A/enediol to DHEA. The presence of endogenous yeast enzymes metabolizing steroids may relate to fungal pathogenesis. Disruption of AYR1 eliminated reductive 17betaHSD activity, and expression of CYP7B on the combination background (atf2, ayr1, TRP(+)) permitted efficient (>98%) bioconversion of DHEA to 7alpha-hydroxyDHEA, a product of potential medical utility.

An n-alkane-responsive promoter element found in the gene encoding the peroxisomal protein of Candida tropicalis does not contain a C(6) zinc cluster DNA-binding motif

When an asporogenic diploid yeast, Candida tropicalis, is cultivated on n-alkane, the expression of the genes encoding enzymes of the peroxisomal beta-oxidation pathway is highly induced. An upstream activation sequence (UAS) which can induce transcription in response to n-alkane (UAS(ALK)) was identified on the promoter region of the peroxisomal 3-ketoacyl coenzyme A (CoA) thiolase gene of C. tropicalis (CT-T3A). The 29-bp region (from -289 to -261) present upstream of the TATA sequence was sufficient to induce n-alkane-dependent expression of a reporter gene. Besides n-alkane, UAS(ALK)-dependent gene expression also occurred in the cells grown on oleic acid. Several kinds of mutant UAS(ALK) were constructed and tested for their UAS activity. It was clarified that the important nucleotides for UAS(ALK) activity were located within 10-bp region from -273 to -264 (5'-TCCTGCACAC-3'). This region did not contain a CGG triplet and therefore differed from the sequence of the oleate-response element (ORE), which is a UAS found on the promoter region of 3-ketoacyl-CoA thiolase gene of Saccharomyces cerevisiae. Similar sequences to UAS(ALK) were also found on several peroxisomal enzyme-encoding genes of C. tropicalis.

Peroxisome biogenesis in yeast

Eukaryotic cells have evolved a complex set of intracellular organelles, each of which possesses a specific complement of enzymes and performs unique metabolic functions. This compartmentalization of cellular functions provides a level of metabolic control not available to prokaryotes. However, it presents the eukaryotic cell with the problem of targeting proteins to their specific location(s). Proteins must be efficiently transported from their site of synthesis in the cytosol to their specific organelle(s). Such a process may require translocation across one or more hydrophobic membrane barriers and/or asymmetric integration into specific membranes. Proteins carry cis-acting amino acid sequences that serve to act as recognition motifs for protein sorting and for the cellular translocation machinery. Sequences that target proteins to the endoplasmic reticulum/secretory pathway, mitochondria, and chloroplasts are often present as cleavable amino-terminal extensions. In contrast, most peroxisomal proteins are synthesized at their mature size and are translocated to the organelle without any post-translational modification. This review will summarize what is known about how yeast solve the problem of specifically importing proteins into peroxisomes and will suggest future directions for investigations into peroxisome biogenesis in yeast.

Peroxisome biogenesis in Saccharomyces cerevisiae

The observation that peroxisomes of Saccharomyces cerevisiae can be induced by oleic acid has opened the possibility to investigate the biogenesis of these organelles in a biochemically and genetically well characterized organism. Only few enzymes have been identified as peroxisomal proteins in Saccharomyces cerevisiae so far; the three enzymes involved in beta-oxidation of fatty acids, enzymes of the glyoxylate cycle, catalase A and the PAS3 gene product have been unequivocally assigned to the peroxisomal compartment. However, more proteins are expected to be constituents of the peroxisomes in Saccharomyces cerevisiae. Mutagenesis of Saccharomyces cerevisiae cells gave rise to mutants unable to use oleic acid as sole carbon source. These mutants could be divided in two groups: those with defects in structural genes of beta-oxidation enzymes (fox-mutants) and those with defects in peroxisomal assembly (pas-mutants). All fox-mutants possess morphologically normal peroxisomes and can be assigned to one of three complementation groups (FOX1, 2, 3). All three FOX genes have been cloned and characterized. The pas-mutants isolated are distributed among 13 complementation groups and represent 3 different classes: peroxisomes are either morphologically not detectable (type I) or present but non-proliferating (type II). Mislocalization concerns all peroxisomal proteins in cells of these two classes. The third class of mutants contains peroxisomes normal in size and number, however, distinct peroxisomal matrix proteins are mislocalized (type III). Five additional complementation groups were found in the laboratory of H.F. Tabak. Not all PAS genes have been cloned and characterized so far, and only for few of them the function could be deduced from sequence comparisons. Proliferation of microbodies is repressed by glucose, derepressed by non-fermentable carbon sources and fully induced by oleic acid. The regulation of four genes encoding peroxisomal proteins (PAS1, CTA1, FOX2, FOX3) occurs on the transcriptional level and reflects the morphological observations: repression by glucose and induction by oleic acid. Moreover, trans-acting factors like ADR1, SNF1 and SNF4, all involved in derepression of various cellular processes, have been demonstrated to affect transcriptional regulation of genes encoding peroxisomal proteins. The peroxisomal import machinery seems to be conserved between different organisms as indicated by import of heterologous proteins into microbodies of different host cells. In addition, many peroxisomal proteins contain C-terminal targeting signals. However, more than one import route into peroxisomes does exist.(ABSTRACT TRUNCATED AT 400 WORDS)

Sequences of two tandem genes regulated by carbon sources, one being essential for n-alkane assimilation in Candida maltosa

Several n-alkane-inducible clones were isolated from the genomic library of an n-alkane-assimilation yeast, Candida maltosa, by the differential hybridization method. Among these, one of the most predominantly expressed clones was analyzed. The nucleotide sequence of the cloned DNA fragment showed that it contained two open reading frames, one encoding a protein of 127 amino acids (aa) and the other a protein of 276 aa. The former was named POX18Cm, because the sequence was highly homologous to that of the Candida tropicalis gene, POX18, which already had been identified as encoding a small oleate-inducible peroxisomal protein. The latter, named ALI1, had no homologous sequences in the EMBL database (1990 release). Northern-blot hybridization indicated that the expression of these two genes was regulated by carbon sources in the media. From gene-disruption experiments, it was concluded that ALI1 was essential for assimilation of n-alkane by C. maltosa.

Glucose-responsive and oleic acid-responsive elements in the gene encoding the peroxisomal trifunctional enzyme of Candida tropicalis

We have investigated the regulation of expression of the gene (HDE), encoding the peroxisomal trifunctional enzyme hydratase-dehydrogenase-epimerase (HDE), of the diploid yeast Candida tropicalis. Heterologous expression in Saccharomyces cerevisiae of constructs containing deletions in the upstream region of the HDE gene has allowed for determination of regions responsible for the control of expression of the HDE gene. Expression was monitored by immunoblot analysis of yeast lysates with anti-HDE serum. Regions have been identified that are responsible for both repression by glucose and induction by oleic acid. A glucose-responsive region lies between nucleotides (nt) -526 and -393. An oleic acid-responsive region lies between nt -393 and -341. An additional region controlling derepression by nonfermentable carbon sources is located downstream from nt -341. Comparison of the nt sequences of these regions to upstream regions of other oleic acid-responsive genes of C. tropicalis has identified possible consensus nt sequences for glucose- and oleic acid-responsive upstream elements in these genes. The regulation of the HDE gene in S. cerevisiae closely resembles that found in C. tropicalis, suggesting that similar mechanisms of transcriptional control operate in both yeasts.

Cloning, sequencing and chromosomal assignment of a gene from Saccharomyces cerevisiae which is negatively regulated by glucose and positively by lipids

We report the molecular cloning, nucleotide (nt) sequence and chromosomal assignment of the Saccharomyces cerevisiae gene GLP1. This gene encoded a 15-kDa protein that was synthesized at a low level during growth on glucose and was induced ninefold upon glucose deprivation. When glucose withdrawal was accompanied by the addition of fatty acids the induction was enhanced an additional two- to threefold. The GLP1 gene product was identified as a soluble protein and purified using a combination of gel permeation and ion exchange chromatography. Using oligodeoxyribonucleotides as hybridization probes we have isolated the GLP1 gene and sequenced the single, long open reading frame which is 351 nt in length and is not interrupted by introns. The GLP1 gene directed the transcription of a 700-nt mRNA in response to glucose deprivation. The accumulation of the mRNA was further enhanced twofold by the addition of oleate. We have localized the GLP1 gene to S. cerevisiae chromosome VI.

Genetics of Candida albicans

Candida albicans is among the most common fungal pathogens. Infections caused by C. albicans and other Candida species can be life threatening in individuals with impaired immune function. Genetic analysis of C. albicans pathogenesis is complicated by the diploid nature of the species and the absence of a known sexual cycle. Through a combination of parasexual techniques and molecular approaches, an effective genetic system has been developed. The close relationship of C. albicans to the more extensively studied Saccharomyces cerevisiae has been of great utility in the isolation of Candida genes and development of the C. albicans DNA transformation system. Molecular methods have been used for clarification of taxonomic relationships and more precise epidemiologic investigations. Analysis of the physical and genetic maps of C. albicans and the closely related Candida stellatoidea has provided much information on the highly fluid nature of the Candida genome. The genetic system is seeing increased application to biological questions such as drug resistance, virulence determinants, and the phenomenon of phenotypic variation. Although most molecular analysis to data has been with C. albicans, the same methodologies are proving highly effective with other Candida species.

A novel peroxisomal nonspecific lipid-transfer protein from Candida tropicalis. Gene structure, purification and possible role in beta-oxidation

We have sequenced the nucleotides of the gene POX18 that encodes PXP-18, a major peroxisomal polypeptide inducible by oleic acid in the yeast Candida tropicalis. POX18 had a single open reading frame of 127 amino acids. Some 33% of the amino acid sequence of the predicted basic polypeptide (13,805 Da), was identical to that of the nonspecific lipid-transfer protein (sterol carrier protein 2) from rat liver. PXP-18, purified to near homogeneity from isolated peroxisomes, had an amino-terminal sequence identical to that of the predicted polypeptide except for the initiator methionine, and had nonspecific lipid-transfer activity comparable to that of its mammalian equivalents. Unexpectedly, PXP-18 lacked the cysteine residue thought to be essential for the activity of this protein in mammals. RNA blot analysis showed that the POX18 gene was expressed exclusively in cells grown on oleic acid, suggesting that PXP-18 has a role in the beta-oxidation of long-chain fatty acids. PXP-18 modulated acyl-coenzyme A oxidase activity at low pH.