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Carrillo AJ, Halilovic L, Hur M, Kirkwood JS, Borkovich KA. Targeted Metabolomics Using LC-MS in Neurospora crassa. Curr Protoc 2022; 2:e454. [PMID: 35616476 DOI: 10.1002/cpz1.454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The filamentous fungus Neurospora crassa has historically been a model for understanding the relationship between genes and metabolism-auxotrophic mutants of N. crassa were used by Beadle and Tatum to develop the one-gene-one-enzyme hypothesis for which they earned the Nobel Prize in 1958. In the ensuing decades, several techniques have been developed for the systematic analysis of metabolites in N. crassa and other fungi. Untargeted and targeted approaches have been used, with a focus on secondary metabolites over primary metabolism. Here, we describe a pipeline for sample preparation, metabolite extraction, Liquid Chromatography-Mass Spectrometry (LC-MS), and data analysis that can be used for targeted metabolomics of primary metabolites in N. crassa. Liquid cultures are grown with shaking in a defined minimal medium and then collected using filtration. Samples are lyophilized for 2 days at -80°C, pulverized, and mixed with a solution to extract polar metabolites. The metabolites are separated and identified using LC-MS, with downstream analysis using Skyline interpretive software. Relative levels of hundreds of metabolites can be detected and compared across strains. © 2022 Wiley Periodicals LLC. Basic Protocol: Metabolite extraction and detection from Neurospora crassa cell cultures using Liquid Chromatography-Mass Spectrometry.
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Affiliation(s)
- Alexander J Carrillo
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
| | - Manhoi Hur
- Institute for Integrative Genome Biology Metabolomics Core, University of California, Riverside, California
| | - Jay S Kirkwood
- Institute for Integrative Genome Biology Metabolomics Core, University of California, Riverside, California
| | - Katherine A Borkovich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
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Wu Y, Judge MT, Edison AS, Arnold J. Uncovering in vivo biochemical patterns from time-series metabolic dynamics. PLoS One 2022; 17:e0268394. [PMID: 35550643 PMCID: PMC9098013 DOI: 10.1371/journal.pone.0268394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/28/2022] [Indexed: 11/19/2022] Open
Abstract
System biology relies on holistic biomolecule measurements, and untangling biochemical networks requires time-series metabolomics profiling. With current metabolomic approaches, time-series measurements can be taken for hundreds of metabolic features, which decode underlying metabolic regulation. Such a metabolomic dataset is untargeted with most features unannotated and inaccessible to statistical analysis and computational modeling. The high dimensionality of the metabolic space also causes mechanistic modeling to be rather cumbersome computationally. We implemented a faster exploratory workflow to visualize and extract chemical and biochemical dependencies. Time-series metabolic features (about 300 for each dataset) were extracted by Ridge Tracking-based Extract (RTExtract) on measurements from continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) in Neurospora crassa under different conditions. The metabolic profiles were then smoothed and projected into lower dimensions, enabling a comparison of metabolic trends in the cultures. Next, we expanded incomplete metabolite annotation using a correlation network. Lastly, we uncovered meaningful metabolic clusters by estimating dependencies between smoothed metabolic profiles. We thus sidestepped the processes of time-consuming mechanistic modeling, difficult global optimization, and labor-intensive annotation. Multiple clusters guided insights into central energy metabolism and membrane synthesis. Dense connections with glucose 1-phosphate indicated its central position in metabolism in N. crassa. Our approach was benchmarked on simulated random network dynamics and provides a novel exploratory approach to analyzing high-dimensional metabolic dynamics.
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Affiliation(s)
- Yue Wu
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Michael T. Judge
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Arthur S. Edison
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States of America
- * E-mail: (ASE); (JA)
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Department of Statistics, University of Georgia, Athens, GA, United States of America
- Department of Physics and Astronomy, University of Georgia, Athens, GA, United States of America
- * E-mail: (ASE); (JA)
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Che D, Nyingwa PS, Ralinala KM, Maswanganye GMT, Wu G. Amino Acids in the Nutrition, Metabolism, and Health of Domestic Cats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1285:217-231. [PMID: 33770409 DOI: 10.1007/978-3-030-54462-1_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Domestic cats (carnivores) require high amounts of dietary amino acids (AAs) for normal growth, development, and reproduction. Amino acids had been traditionally categorised as nutritionally essential (EAAs) or nonessential (NEAAs), depending on whether they are synthesized de novo in the body. This review will focus on AA nutrition and metabolism in cats. Like other mammals, cats do not synthesize the carbon skeletons of twelve proteinogenic AAs: Arg, Cys, His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Tyr, and Val. Like other feline carnivores but unlike many mammals, cats do not synthesize citrulline and have a very limited ability to produce taurine from Cys. Except for Leu and Lys that are strictly ketogenic AAs, most EAAs are both glucogenic and ketogenic AAs. All the EAAs (including taurine) must be provided in diets for cats. These animals are sensitive to dietary deficiencies of Arg and taurine, which rapidly result in life-threatening hyperammonemia and retinal damage, respectively. Although the National Research Council (NCR, Nutrient requirements of dogs and cats. National Academies Press, Washington, DC, 2006) does not recommend dietary requirements of cats for NEAAs, much attention should be directed to this critical issue of nutrition. Cats can synthesize de novo eight proteinogenic AAs: Ala, Asn, Asp, Gln, Glu, Gly, Pro, and Ser, as well as some nonproteinogenic AAs, such as γ-aminobutyrate, ornithine, and β-alanine with important physiological functions. Some of these AAs (e.g., Gln, Glu, Pro, and Gly) are crucial for intestinal integrity and health. Except for Gln, AAs in the arterial blood of cats may not be available to the mucosa of the small intestine. Plant-source foodstuffs lack taurine and generally contain inadequate Met and Cys and, therefore, should not be fed to cats in any age group. Besides meat, animal-source foodstuffs (including ruminant meat & bone meal, poultry by-product meal, porcine mucosal protein, and chicken visceral digest) are good sources of proteinogenic AAs and taurine for cats. Meeting dietary requirements for both EAAs and NEAAs in proper amounts and balances is crucial for improving the health, wellbeing, longevity, and reproduction of cats.
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Affiliation(s)
- Dongsheng Che
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, and Key Laboratory of Animal Production, Product Quality and Security of Ministry of Education, Jilin Agricultural University, Changchun, China
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Pakama S Nyingwa
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, and Key Laboratory of Animal Production, Product Quality and Security of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Khakhathi M Ralinala
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, and Key Laboratory of Animal Production, Product Quality and Security of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Gwen M T Maswanganye
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, and Key Laboratory of Animal Production, Product Quality and Security of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, TX, USA.
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Judge MT, Wu Y, Tayyari F, Hattori A, Glushka J, Ito T, Arnold J, Edison AS. Continuous in vivo Metabolism by NMR. Front Mol Biosci 2019; 6:26. [PMID: 31114791 PMCID: PMC6502900 DOI: 10.3389/fmolb.2019.00026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 04/04/2019] [Indexed: 01/10/2023] Open
Abstract
Dense time-series metabolomics data are essential for unraveling the underlying dynamic properties of metabolism. Here we extend high-resolution-magic angle spinning (HR-MAS) to enable continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) and provide analysis tools for these data. First, we reproduced a result in human chronic lymphoid leukemia cells by using isotope-edited CIVM-NMR to rapidly and unambiguously demonstrate unidirectional flux in branched-chain amino acid metabolism. We then collected untargeted CIVM-NMR datasets for Neurospora crassa, a classic multicellular model organism, and uncovered dynamics between central carbon metabolism, amino acid metabolism, energy storage molecules, and lipid and cell wall precursors. Virtually no sample preparation was required to yield a dynamic metabolic fingerprint over hours to days at ~4-min temporal resolution with little noise. CIVM-NMR is simple and readily adapted to different types of cells and microorganisms, offering an experimental complement to kinetic models of metabolism for diverse biological systems.
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Affiliation(s)
- Michael T. Judge
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Yue Wu
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Fariba Tayyari
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Ayuna Hattori
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - John Glushka
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Takahiro Ito
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Jonathan Arnold
- Department of Genetics, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Arthur S. Edison
- Department of Genetics, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
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Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. mBio 2019; 10:mBio.00192-19. [PMID: 30914504 PMCID: PMC6437048 DOI: 10.1128/mbio.00192-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Fungal spores germinate and undergo vegetative growth, leading to either asexual or sexual reproductive dispersal. Previous research has indicated that among developmental regulatory genes, expression is conserved across nutritional environments, whereas pathways for carbon and nitrogen metabolism appear highly responsive-perhaps to accommodate differential nutritive processing. To comprehensively investigate conidial germination and the adaptive life history decision-making underlying these two modes of reproduction, we profiled transcription of Neurospora crassa germinating on two media: synthetic Bird medium, designed to promote asexual reproduction; and a natural maple sap medium, on which both asexual reproduction and sexual reproduction manifest. A later start to germination but faster development was observed on synthetic medium. Metabolic genes exhibited altered expression in response to nutrients-at least 34% of the genes in the genome were significantly downregulated during the first two stages of conidial germination on synthetic medium. Knockouts of genes exhibiting differential expression across development altered germination and growth rates, as well as in one case causing abnormal germination. A consensus Bayesian network of these genes indicated especially tight integration of environmental sensing, asexual and sexual development, and nitrogen metabolism on a natural medium, suggesting that in natural environments, a more dynamic and tentative balance of asexual and sexual development may be typical of N. crassa colonies.IMPORTANCE One of the most remarkable successes of life is its ability to flourish in response to temporally and spatially varying environments. Fungi occupy diverse ecosystems, and their sensitivity to these environmental changes often drives major fungal life history decisions, including the major switch from vegetative growth to asexual or sexual reproduction. Spore germination comprises the first and simplest stage of vegetative growth. We examined the dependence of this early life history on the nutritional environment using genome-wide transcriptomics. We demonstrated that for developmental regulatory genes, expression was generally conserved across nutritional environments, whereas metabolic gene expression was highly labile. The level of activation of developmental genes did depend on current nutrient conditions, as did the modularity of metabolic and developmental response network interactions. This knowledge is critical to the development of future technologies that could manipulate fungal growth for medical, agricultural, or industrial purposes.
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Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant. PLoS One 2016; 11:e0165980. [PMID: 27870869 PMCID: PMC5117620 DOI: 10.1371/journal.pone.0165980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
A moderate heat shock induces Neurospora crassa to synthesize large quantities of heat shock proteins that are protective against higher, otherwise lethal temperatures. However, wild type cells do not survive when carbohydrate deprivation is added to heat shock. In contrast, a mutant strain defective in a stress-activated protein kinase does survive the combined stresses. In order to understand the basis for this difference in survival, we have determined the relative levels of detected proteins in the mutant and wild type strain during dual stress, and we have identified gene transcripts in both strains whose quantities change in response to heat shock or dual stress. These data and supportive experimental evidence point to reasons for survival of the mutant strain. By using alternative respiratory mechanisms, these cells experience less of the oxidative stress that proves damaging to wild type cells. Of central importance, mutant cells recycle limited resources during dual stress by undergoing autophagy, a process that we find utilized by both wild type and mutant cells during heat shock. Evidence points to inappropriate activation of TORC1, the central metabolic regulator, in wild type cells during dual stress, based upon behavior of an additional signaling mutant and inhibitor studies.
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Palma-Guerrero J, Hall CR, Kowbel D, Welch J, Taylor JW, Brem RB, Glass NL. Genome wide association identifies novel loci involved in fungal communication. PLoS Genet 2013; 9:e1003669. [PMID: 23935534 PMCID: PMC3731230 DOI: 10.1371/journal.pgen.1003669] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/10/2013] [Indexed: 01/25/2023] Open
Abstract
Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species. Many phenotypes of interest are controlled by multiple loci, and in biological systems identifying determinants of such complex traits is challenging. Here, we genotyped 112 wild isolates of Neurospora crassa and used this resource to identify genes that mediate a fundamental but poorly-understood attribute of this filamentous fungus: the ability of germinating spores to sense each other at a distance, extend projections toward one another, and fuse. Inheritance at a secretion gene, cse-1, was associated strongly with germling communication across wild strains; this association was validated in experiments showing reduced communication in a cse-1 deletion strain. By testing interacting partners of CSE1, and by assessing additional secretion and signaling factors whose inheritance associated more modestly with germling communication in wild strains, we identified eight other novel determinants of this phenotype. Our population of genotyped wild isolates provides a flexible and powerful community resource for the rapid identification of any varying, complex phenotype in N. crassa. The success of our approach, which used a phenotyping scheme far more tractable than would be required in a screen of the entire N. crassa gene deletion collection, serves as a proof of concept for association studies of wild populations for any organism.
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Affiliation(s)
- Javier Palma-Guerrero
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Charles R. Hall
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Juliet Welch
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Rachel B. Brem
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RBB); (NLG)
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RBB); (NLG)
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Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol 2013; 9:e1003126. [PMID: 23935467 PMCID: PMC3730674 DOI: 10.1371/journal.pcbi.1003126] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/20/2013] [Indexed: 11/18/2022] Open
Abstract
The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. Here, we have reconstructed a genome-scale model of its metabolism. This model consists of 836 metabolic genes, 257 pathways, 6 cellular compartments, and is supported by extensive manual curation of 491 literature citations. To aid our reconstruction, we developed three optimization-based algorithms, which together comprise Fast Automated Reconstruction of Metabolism (FARM). These algorithms are: LInear MEtabolite Dilution Flux Balance Analysis (limed-FBA), which predicts flux while linearly accounting for metabolite dilution; One-step functional Pruning (OnePrune), which removes blocked reactions with a single compact linear program; and Consistent Reproduction Of growth/no-growth Phenotype (CROP), which reconciles differences between in silico and experimental gene essentiality faster than previous approaches. Against an independent test set of more than 300 essential/non-essential genes that were not used to train the model, the model displays 93% sensitivity and specificity. We also used the model to simulate the biochemical genetics experiments originally performed on Neurospora by comprehensively predicting nutrient rescue of essential genes and synthetic lethal interactions, and we provide detailed pathway-based mechanistic explanations of our predictions. Our model provides a reliable computational framework for the integration and interpretation of ongoing experimental efforts in Neurospora, and we anticipate that our methods will substantially reduce the manual effort required to develop high-quality genome-scale metabolic models for other organisms. Few organisms have been as foundational to the development of modern genetics and cellular metabolism as Neurospora crassa. Given the wealth of knowledge available for this filamentous fungus, the effort required to manually curate a high-quality genome-scale metabolic reconstruction would be daunting. To aid the reconstruction process, we developed three optimization-based algorithms. The first algorithm predicts flux while linearly accounting for metabolite dilution; the second algorithm removes blocked reactions with one compact linear program; and the third algorithm reconciles differences between in silico predictions and experimental observations of mutant viability. We have used these algorithms to develop the first genome-scale metabolic model for Neurospora. We have validated the accuracy of our model against an independent test set of more than 300 growth/no-growth phenotypes, and our model displays 93% sensitivity and specificity. Simulating the biochemical genetics experiments originally performed on Neurospora, we comprehensively predicted essential genes, nutrient rescues of auxotroph mutants and synthetic lethal interactions. With these predictions, we provide potential mechanistic insight into known mutant phenotypes, and testable hypotheses for novel mutant phenotypes. The model, the algorithms and the testable hypotheses provide a computational foundation for the study of Neurospora crassa metabolism.
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Affiliation(s)
- Jonathan M. Dreyfuss
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
| | - Jeremy D. Zucker
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Tardigrade Biotechnologies, Jamaica Plain, Massachusetts, United States of America
| | - Heather M. Hood
- Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Linda R. Ocasio
- Tardigrade Biotechnologies, Jamaica Plain, Massachusetts, United States of America
| | - Matthew S. Sachs
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - James E. Galagan
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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Use of 1H nuclear magnetic resonance to measure intracellular metabolite levels during growth and asexual sporulation in Neurospora crassa. EUKARYOTIC CELL 2011; 10:820-31. [PMID: 21460191 DOI: 10.1128/ec.00231-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Conidiation is an asexual sporulation pathway that is a response to adverse conditions and is the main mode of dispersal utilized by filamentous fungal pathogens for reestablishment in a more favorable environment. Heterotrimeric G proteins (consisting of α, β, and γ subunits) have been shown to regulate conidiation in diverse fungi. Previous work has demonstrated that all three of the Gα subunits in the filamentous fungus Neurospora crassa affect the accumulation of mass on poor carbon sources and that loss of gna-3 leads to the most dramatic effects on conidiation. In this study, we used (1)H nuclear magnetic resonance (NMR) to profile the metabolome of N. crassa in extracts isolated from vegetative hyphae and conidia from cultures grown under conditions of high or low sucrose. We compared wild-type and Δgna-3 strains to determine whether lack of gna-3 causes a significant difference in the global metabolite profile. The results demonstrate that the global metabolome of wild-type hyphae is influenced by carbon availability. The metabolome of the Δgna-3 strain cultured on both high and low sucrose is similar to that of the wild type grown on high sucrose, suggesting an overall defect in nutrient sensing in the mutant. However, analysis of individual metabolites revealed differences in wild-type and Δgna-3 strains cultured under conditions of low and high sucrose.
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Spevak CC, Ivanov IP, Sachs MS. Sequence requirements for ribosome stalling by the arginine attenuator peptide. J Biol Chem 2010; 285:40933-42. [PMID: 20884617 DOI: 10.1074/jbc.m110.164152] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5' regions of eukaryotic mRNAs often contain upstream open reading frames (uORFs). The Neurospora crassa arg-2 uORF encodes the 24-residue arginine attenuator peptide (AAP). This regulatory uORF-encoded peptide, which is evolutionarily conserved in fungal transcripts specifying an arginine biosynthetic enzyme, functions as a nascent peptide within the ribosomal tunnel and negatively regulates gene expression. The nascent AAP causes ribosomes to stall at the uORF stop codon in response to arginine, thus, blocking ribosomes from reaching the ARG-2 initiation codon. Here scanning mutagenesis with alanine and proline was performed to systematically determine which AAP residues were important for conferring regulation. Changing many of the most highly conserved residues (Asp-12, Tyr-13, Lys-14, and Trp-19) abolished regulatory function. The minimal functional domain of the AAP was determined by positioning AAP sequences internally within a large polypeptide. Pulse-chase analyses revealed that residues 9-20 of the AAP composed the minimal domain that was sufficient to confer regulatory function. An extensive analysis of predicted fungal AAPs revealed that the minimal functional domain of the N. crassa AAP corresponded closely to the region that was most highly conserved among the fungi. We also observed that the tripeptide RGD could function similarly to arginine in triggering AAP-mediated ribosome stalling. These studies provide a better understanding of the elements required for a nascent peptide and a small regulatory molecule to control translational processes.
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Affiliation(s)
- Christina C Spevak
- Department of Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA
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Elleuche S, Pöggeler S. A cyanase is transcriptionally regulated by arginine and involved in cyanate decomposition in Sordaria macrospora. Fungal Genet Biol 2008; 45:1458-69. [PMID: 18796334 DOI: 10.1016/j.fgb.2008.08.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 08/04/2008] [Accepted: 08/15/2008] [Indexed: 10/21/2022]
Abstract
Cyanase degrades toxic cyanate to NH3 and CO2 in a bicarbonate-dependent reaction. High concentrations of cyanate are fairly toxic to organisms. Here, we characterize a eukaryotic cyanase for the first time. We have isolated the cyn1 gene encoding a cyanase from the filamentous ascomycete Sordaria macrospora and functionally characterized the cyn1 product after heterologous expression in Escherichia coli. Site-directed mutagenesis confirmed a predicted catalytic centre of three conserved amino-acids. A Deltacyn1 knockout in S. macrospora was totally devoid of cyanase activity and showed an increased sensitivity to exogenously supplied cyanate in an arginine-depleted medium, defects in ascospore germination, but no other obvious morphological phenotype. By means of real-time PCR we have demonstrated that the transcriptional level of cyn1 is markedly elevated in the presence of cyanate and down-regulated by addition of arginine. The putative functions of cyanase in fungi are discussed.
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Affiliation(s)
- Skander Elleuche
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
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Hood HM, Spevak CC, Sachs MS. Evolutionary changes in the fungal carbamoyl-phosphate synthetase small subunit gene and its associated upstream open reading frame. Fungal Genet Biol 2006; 44:93-104. [PMID: 16979358 DOI: 10.1016/j.fgb.2006.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Revised: 07/11/2006] [Accepted: 07/19/2006] [Indexed: 11/28/2022]
Abstract
The Neurospora crassa arg-2 and the Saccharomyces cerevisiae ortholog CPA1 encode the arginine-specific carbamoyl-phosphate synthetase (CPS-A) small subunit. Arginine decreases synthesis of this subunit through the action of a 5' upstream open reading frame in the mRNA that encodes a cis-regulatory element, the arginine attenuator peptide (AAP), which stalls ribosomes in response to arginine. We performed a comparative analysis of the genomic structure and predicted peptide sequence of the AAP and CPS-A small subunit across many fungi. Differences at the genomic level included variation in intron number and position within the AAP and CPS-A coding regions and differences in known regulatory motifs. Although differences exist in AAP sequence, there were three absolutely conserved amino acid residues in the predicted peptide, including an aspartic acid crucial for arginine-dependent regulation of arg-2 and CPA1. A diverged Basidiomycete AAP was shown to retain function as an Arg-specific negative regulator of translation.
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Affiliation(s)
- Heather M Hood
- Department of Environmental and Biomolecular Systems, Oregon Health & Science University, Beaverton, OR 97006-8921, USA
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