Gene expression on different carbon sources in response to hxt1 deletion in Ustilago maydis
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ABSTRACT:
ORGANISM(S): Ustilago maydis
PROVIDER: GSE16634 | GEO | 2009/09/30
SECONDARY ACCESSION(S): PRJNA117351
REPOSITORIES: GEO
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Project description:Plant pathogenic fungi cause massive crop losses and therefore, severe economic deficits. The smut Ustilago maydis, a ubiquitous pest of corn, is highly adapted to its host to parasitize on its organic carbon sources. Recently, we identified the U. maydis sucrose transporter Srt1 to be of crucial importance for biotrophic development. Here we report the identification of Hxt1, a further member of the U. maydis sugar transporter family, which is of importance for full fungal virulence. Hxt1 mainly utilizes the hexoses glucose, fructose and mannose, but with lower affinity also secondary carbon sources like galactose and xylose. Deletion of hxt1 in U. maydis reduces virulence and growth on hexoses, in contrast growth on the secondary carbon sources is enhanced. Expression analysis revealed that monosaccharide-dependent regulation of transcription is hampered in hxt1 deletion mutants, leading to the expression of genes involved in the metabolism of secondary sugars and in the initiation of pathogenicity. Thus, we propose that Hxt1 has a dual function as monosaccharide-transporter and -sensor. While Hxt1 aids the initiation of pathogenicity by sensing starvation conditions on the plant surface as a receptor, it feeds the fungus in planta as a transporter. To analyze expression changes of SG200 and SG200∆hxt1 both strains were grown in glutamine minimal array media supplemented with 1% glucose or 1 %xylose to an OD600 of 1.0 for 6 h, respectively. For each experiment two independent replicates were conducted.
2009-09-29 | E-GEOD-16634 | biostudies-arrayexpress
Project description:The basidiomycete Ustilago maydis is the causal agent of corn smut disease and induces tumor formation during biotrophic growth in its host plant maize. The Usilago maydis genome harbors a homolog to the GATA transcription factors Nit2 and AreA that act as global regulators of nitrogen catabolite repression in filamentous model fungi Neurospora crassa and Aspergillus nidulans, respectively. We aimed at resolving the role of the Ustilago maydis Nit2 homolog for the utilization of complex nitrogen sources and pathogenicity.
2012-01-01 | GSE28916 | GEO
Project description:Plant biomass is the most abundant and renewable carbon source for many fungal species. The composition of biomass consists of about 40-45% cellulose, 20-30% hemicellulose, and 15-25% lignin and varies among plant species. In the bio-based industry, Aspergillus species and other fungi are used for the production of lignocellulolytic enzymes to pretreat agricultural waste biomass (e.g. wheat bran). In this study, we aimed to evaluate if it would be possible to create an Aspergillus strain that releases but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were (partially) impaired in glycolysis, by deleting the hexokinase (hxkA) and glucokinase (glkA) genes. To prevent repression of enzyme production due to the accumulation of hexoses, strains were generated in which these mutations were combined with a mutation in creA, encoding the repressor involved in carbon catabolism. Phenotypic analysis revealed that growth of the ΔhxkAΔglkA mutant was reduced on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. Deletion of creA combined with blocking glycolysis resulted in an increased expression of pentose catabolic and phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources has resulted in a shift towards the pentose fraction of wheat bran as a major carbon source to support growth.
2018-02-26 | GSE94775 | GEO
Project description:RNA-binding proteins constitute key factors of the posttranscriptional machinery. These regulatory proteins recognise specific elements within target transcripts to promote e.g. maturation, translation or stability of mRNAs. In Ustilago maydis, evidence is accumulating that posttranscriptional processes are important to determine pathogenicity. Deletion of khd4, encoding a predicted RNA-binding protein with five K homology (KH) domains, causes aberrant cell morphology and reduced virulence. Here, we demonstrate that Khd4 recognises the sequence AUACCC in vivo via its tandem KH domains 3 and 4. This sequence functions most likely as regulatory RNA element in U. maydis, since it accumulates in 3â untranslated regions. Consistently, an independent transcriptional profiling approach revealed that the binding motif is significantly enriched in transcripts differentially regulated in khd4 strains. Since the vast majority of potential Khd4 target mRNAs exhibit increased expression in deletion mutants, Khd4 might promote mRNA instability. Mutants that fail to bind AUACCC resemble deletion mutants exhibiting altered cell morphology, disturbed filamentous growth and severely reduced virulence. Hence, RNA binding is essential for function of Khd4 stressing the importance of posttranscriptional control in regulating morphology and pathogenicity. keywords: gene deletion, RNA-binding protein, KH domain Strains FB2 (2 replicates, control) and FB2khd4Delta (2 individuals) were grown in minimal medium containing glucose and glutamine.
2010-05-06 | E-GEOD-17956 | biostudies-arrayexpress
Project description:The basidiomycete Ustilago maydis is the causal agent of corn smut disease and induces tumor formation during biotrophic growth in its host plant maize. The Usilago maydis genome harbors a homolog to the GATA transcription factors Nit2 and AreA that act as global regulators of nitrogen catabolite repression in filamentous model fungi Neurospora crassa and Aspergillus nidulans. We aimed at resolving the role of the Ustilago maydis homolog Ncr1 for the utilization of complex nitrogen sources and pathogenicity. Sporidia of the indicated Ustilago maydis strains were grown overnight in ammonium minimal medium (Holliday, 1976) and samples for total RNA extraction were taken 2h after transfer to minimal medium lacking any nitrogen source (-N) during the exponential growth phase to assess those genes that are regulated in response to nitrogen starvation. The solopathogenic strain SG200 (control) and deletion mutants of (Nitrogen catabolite repression1) Ncr1 and (Target of Ncr1) Ton1, both being in the SG200 background, were studied in two independent experiments (one experiment for Ton1). Per strain and experiment, three biological replicate samples were analyzed (except for only biological replicates for Ncr1 in the second experiment).
2012-01-01 | E-GEOD-28916 | biostudies-arrayexpress
Project description:RNA-binding proteins constitute key factors of the posttranscriptional machinery. These regulatory proteins recognise specific elements within target transcripts to promote e.g. maturation, translation or stability of mRNAs. In Ustilago maydis, evidence is accumulating that posttranscriptional processes are important to determine pathogenicity. Deletion of khd4, encoding a predicted RNA-binding protein with five K homology (KH) domains, causes aberrant cell morphology and reduced virulence. Here, we demonstrate that Khd4 recognises the sequence AUACCC in vivo via its tandem KH domains 3 and 4. This sequence functions most likely as regulatory RNA element in U. maydis, since it accumulates in 3’ untranslated regions. Consistently, an independent transcriptional profiling approach revealed that the binding motif is significantly enriched in transcripts differentially regulated in khd4 strains. Since the vast majority of potential Khd4 target mRNAs exhibit increased expression in deletion mutants, Khd4 might promote mRNA instability. Mutants that fail to bind AUACCC resemble deletion mutants exhibiting altered cell morphology, disturbed filamentous growth and severely reduced virulence. Hence, RNA binding is essential for function of Khd4 stressing the importance of posttranscriptional control in regulating morphology and pathogenicity. keywords: gene deletion, RNA-binding protein, KH domain
2009-09-04 | GSE17956 | GEO
Project description:Carbon catabolite repression (CCR) is a gene regulation process that allows bacteria to use carbon-energy sources in a hierarchical manner. Thus, the presence of a preferred sugar, usually D-glucose, results in downregulation of genes participating in the transport and catabolic pathways of secondary carbon sources. Further, CCR controls the expression of global regulators that control expression of many genes involved in multiple aspects of bacterial physiology such as stress response proteins and virulence factors. The human-restricted pathogen Neisseria gonorrhoeae can rely upon a limited number of carbon-energy sources, including glucose and lactate and both are available within its infection niches. We recently reported that expression of the L-lactate permease-encoding gene lctP is subjected to glucose repression within physiological concentrations. However, the transducing mechanism or the gene that connect glucose with lctP promoter repression remained unknown. To address this issue, we performed an RNA-Seq analysis to determine the transcriptional landscape of gonococci due to changes in glucose or lactate concentrations in the growth media. Glucose was found to regulate 144 genes (5.5% of total genes in the genome) while lactate influenced the expression of 434 (16.5%) genes with an overlap of 97 genes between the two sugars. Both, glucose and lactate were found to upregulate genes involved in protein translation, a high energy consumption cellular function. Individually, glucose enhanced genes participating in glycolysis and repressed genes in the tricarboxylic acid (TCA) cycle, while lactate enhanced genes encoding respiratory enzymes and ATP synthase. Interestingly, lactate was found to repress expression of several genes encoding known gonococcal virulence factors such as tbpAB encoding the transferrin-binding proteins; the tonB and exbBD genes encoding the membrane energy transfer complex TonB-ExbB-ExbD required for many outer membrane transport systems; katA encoding an important H2O2-inducible catalase and to upregulate mtrR encoding the master repressor of the mtrCDE antimicrobial efflux pump genes. Moreover, glucose repressed mntC encoding a Zn/Mn ABC transporter and lctP, both required for resistance to killing by H2O2. These results set the framework to determine important gonococci virulent factor genes whose expression can be modulated by CCR as well as to discover the corresponding CCR regulators that control such genes.
2022-12-31 | GSE148774 | GEO
Project description:The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), and set2 knockout strain (Δset2) in different carbon sources. The deletion of set2 upregulated genes involved in oxidation- reduction process, extracellular region, and plasma membrane ATP synthesis coupled proton transport both with 2% glucose or 1% cellulose and 1% wheat bran as carbon sources. We find the expression levels of 20 secondary metabolism gene clusters were upregulated or downregulated under different carbon sources in Δset2. This study provides the information that SET2 function are required in conidiation and hydrolase activity of P. oxalicum.
2017-11-07 | GSE106558 | GEO
Project description:Background The catabolite control protein A (CcpA) is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in S. aureus wild type and ccpA-deleted mutant, focussing on short-time effects of glucose under stable pH conditions. Results The addition of glucose to exponentially growing S. aureus increased enzymes of glycolytic pathway, indicating a higher glycolytic activity, while proteins required for the complete oxidation in the TCA cycle were repressed via CcpA. Phosphotransacetylase and acetate kinase, converting acetylCoA to acetate with a concomitant substrate-level phosphorylation were neither regulated by glucose nor by CcpA. Most CcpA directly repressed genes were involved in utilization of amino acids as secondary carbon sources. More genes were found to be differentially expressed by CcpA in a glucose-independent manner than in the classical, glucose dependent way, suggesting that glucose-independent regulation by CcpA may be of particular importance in S. aureus. In the presence of glucose, CcpA was found to regulate expression of genes involved in metabolism, but that of genes coding for virulence determinants. Conclusions This study identified the CcpA regulon of exponentially growing S. aureus, for the first time. As in other bacteria, the CcpA-regulon of S. aureus comprised a large amount of metabolic genes but also some 50 genes associated with virulence. CcpA seemed to work in a glucose- as well as glucose-independent way.
2008-12-20 | GSE12614 | GEO
Project description:Alternaria brassicicola is a successful saprophyte and necrotrophic pathogen with a broad host range. It produces secondary metabolites that marginally affect virulence, in contrast to many A. alternata strains that produce secondary metabolites as host-specific pathogenicity factors. Cell wall-degrading enzymes (CWDEs) have been considered important for pathogenesis, but no CWDEs have been identified as significant virulence factors in A. brassicicola. In this study, we discovered mutants of a gene, AbVf19, which consistently produced smaller lesions than the wild type. The mutants grew slower than the wild type on an axenic medium with pectin as a major carbon source. Gene expression comparisons identified several hydrolytic enzyme-coding genes being down-regulated in the mutant during a late stage of infection. These down-regulated genes comprised a small fraction of genes within each family. Three of these genes had mutants that showed no or little change in virulence. This suggested that each down regulated gene only made a small contribution to virulence, or that their functions were redundant. This study demonstrated the existence and importance of a transcription factor that regulates a suite of genes that are probably important for decomposing and utilizing plant material during the late stage of plant infection. gene expression profile comparisons between wild type and a transcription factor mutant during host infection
2012-05-03 | E-GEOD-33148 | biostudies-arrayexpress