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Guo Z, Wu H, Peng B, Kang B, Liu L, Luo C, Gu Q. Identifying pathogenicity-related genes in the pathogen Colletotrichum magnum causing watermelon anthracnose disease via T-DNA insertion mutagenesis. Front Microbiol 2023; 14:1220116. [PMID: 37547676 PMCID: PMC10399754 DOI: 10.3389/fmicb.2023.1220116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023] Open
Abstract
Fruit rot caused by Colletotrichum magnum is a crucial watermelon disease threatening the production and quality. To understand the pathogenic mechanism of C. magnum, we optimized the Agrobacterium tumefaciens-mediated transformation system (ATMT) for genetic transformation of C. magnum. The transformation efficiency of ATMT was an average of around 245 transformants per 100 million conidia. Southern blot analysis indicated that approximately 75% of the mutants contained a single copy of T-DNA. Pathogenicity test revealed that three mutants completely lost pathogenicity. The T-DNA integration sites (TISs) of three mutants were Identified. In mutant Cm699, the TISs were found in the intron region of the gene, which encoded a protein containing AP-2 complex subunit σ, and simultaneous gene deletions were observed. Two deleted genes encoded the transcription initiation protein SPT3 and a hypothetical protein, respectively. In mutant Cm854, the TISs were found in the 5'-flanking regions of a gene that was similar to the MYO5 encoding Myosin I of Pyricularia oryzae (78%). In mutant Cm1078, the T-DNA was integrated into the exon regions of two adjacent genes. One was 5'-3' exoribonuclease 1 encoding gene while the other encoded a WD-repeat protein retinoblastoma binding protein 4, the homolog of the MSl1 of Saccharomyces cerevisiae.
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Affiliation(s)
- Zhen Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Chaoxi Luo
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Witte CP. Urea metabolism in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:431-8. [PMID: 21421389 DOI: 10.1016/j.plantsci.2010.11.010] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/17/2010] [Accepted: 11/22/2010] [Indexed: 05/02/2023]
Abstract
Urea is a plant metabolite derived either from root uptake or from catabolism of arginine by arginase. In agriculture, urea is intensively used as a nitrogen fertilizer. Urea nitrogen enters the plant either directly, or in the form of ammonium or nitrate after urea degradation by soil microbes. In recent years various molecular players of plant urea metabolism have been investigated: active and passive urea transporters, the nickel metalloenzyme urease catalyzing the hydrolysis of urea, and three urease accessory proteins involved in the complex activation of urease. The degradation of ureides derived from purine breakdown has long been discussed as a possible additional metabolic source for urea, but an enzymatic route for the complete hydrolysis of ureides without a urea intermediate has recently been described for Arabidopsis thaliana. This review focuses on the proteins involved in plant urea metabolism and the metabolic sources of urea but also addresses open questions regarding plant urea metabolism in a physiological and agricultural context. The contribution of plant urea uptake and metabolism to fertilizer urea usage in crop production is still not investigated although globally more than half of all nitrogen fertilizer is applied to crops in the form of urea. Nitrogen use efficiency in crop production is generally well below 50% resulting in economical losses and creating ecological problems like groundwater pollution and emission of nitric oxides that can damage the ozone layer and function as greenhouse gasses. Biotechnological approaches to improve fertilizer urea usage bear the potential to increase crop nitrogen use efficiency.
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Affiliation(s)
- Claus-Peter Witte
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany.
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Münch S, Ludwig N, Floss DS, Sugui JA, Koszucka AM, Voll LM, Sonnewald U, Deising HB. Identification of virulence genes in the corn pathogen Colletotrichum graminicola by Agrobacterium tumefaciens-mediated transformation. MOLECULAR PLANT PATHOLOGY 2011; 12:43-55. [PMID: 21118348 PMCID: PMC6640349 DOI: 10.1111/j.1364-3703.2010.00651.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A previously developed Agrobacterium tumefaciens-mediated transformation (ATMT) protocol for the plant pathogenic fungus Colletotrichum graminicola led to high rates of tandem integration of the whole Ti-plasmid, and was therefore considered to be unsuitable for the identification of pathogenicity and virulence genes by insertional mutagenesis in this pathogen. We used a modified ATMT protocol with acetosyringone present only during the co-cultivation of C. graminicola and A. tumefaciens. Analysis of 105 single-spore isolates randomly chosen from a collection of approximately 2000 transformants, indicated that almost 70% of the transformants had single T-DNA integrations. Of 500 independent transformants tested, 10 exhibited attenuated virulence in infection assays on whole plants. Microscopic analyses primarily revealed defects at different pre-penetration stages of infection-related morphogenesis. Three transformants were characterized in detail. The identification of the T-DNA integration sites was performed by amplification of genomic DNA ends after endonuclease digestion and polynucleotide tailing. In one transformant, the T-DNA had integrated into the 5'-flank of a gene with similarity to allantoicase genes of other Ascomycota. In the second and third transformants, the T-DNA had integrated into an open reading frame (ORF) and into the 5'-flank of an ORF. In both cases, the ORFs have unknown function.
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Affiliation(s)
- Steffen Münch
- Martin-Luther-University Halle-Wittenberg, Faculty of Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Betty-Heimann-Str. 3, 06120 Halle (Saale), Germany
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5
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Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 2004; 68:1-108. [PMID: 15007097 PMCID: PMC362109 DOI: 10.1128/mmbr.68.1.1-108.2004] [Citation(s) in RCA: 434] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
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Affiliation(s)
- Katherine A Borkovich
- Department of Plant Pathology, University of California, Riverside, California 92521, USA. Katherine/
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6
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Leulliot N, Quevillon-Cheruel S, Sorel I, Graille M, Meyer P, Liger D, Blondeau K, Janin J, van Tilbeurgh H. Crystal Structure of Yeast Allantoicase Reveals a Repeated Jelly Roll Motif. J Biol Chem 2004; 279:23447-52. [PMID: 15020593 DOI: 10.1074/jbc.m401336200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allantoicase (EC 3.5.3.4) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 A by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-Unité Mixte de Recherche 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France
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7
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Franzen S. Use of Periodic Boundary Conditions To Calculate Accurate β-Sheet Frequencies Using Density Functional Theory. J Phys Chem A 2003. [DOI: 10.1021/jp035215k] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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8
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Nozawa SR, Ferreira-Nozawa MS, Martinez-Rossi NM, Rossi A. The pH-induced glycosylation of secreted phosphatases is mediated in Aspergillus nidulans by the regulatory gene pacC-dependent pathway. Fungal Genet Biol 2003; 39:286-95. [PMID: 12892641 DOI: 10.1016/s1087-1845(03)00051-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this communication, we show that the pacC(c)14 mutation drastically reduced the mannose and N-acetylglycosamine content of the pacA-encoded acid phosphatase secreted by the fungus Aspergillus nidulans when grown at 22 degrees C, pH 5.0, compared to a control strain. The staining after PAGE was not observed for the pacA-encoded acid phosphatase, while the palD-encoded Pi-repressible alkaline phosphatase had an altered electrophoretic mobility. In addition, the secreted acid phosphatase also had a reduced number of isoforms visualized by staining after IEF and glycosylation had a protective effect against its heat inactivation. We also show that a full-length version of gene pacC-1 cloned from Neurospora crassa complemented the pacC(c)14 mutation of A. nidulans, including the remediation of both the acid and alkaline Pi-repressible phosphatases secreted at pH 5.0, which indicates that glycosylation of secreted phosphatases is mediated in A. nidulans by the conserved PacC pathway that governs pH-responsive gene expression.
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Affiliation(s)
- S R Nozawa
- Departamento de Genética, FMRP-USP, Ribeirão Preto, SP 14049-900, Brazil
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9
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Smith BM, Franzen S. Single-pass attenuated total reflection Fourier transform infrared spectroscopy for the analysis of proteins in H2O solution. Anal Chem 2002; 74:4076-80. [PMID: 12199577 DOI: 10.1021/ac020103v] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The application of single-pass attenuated total reflection Fourier transform infrared (ATR-FT-IR) microscopy was investigated for secondary structure analysis of 15 representative proteins in H2O solution. This is the first reported application of single-pass ATR-FT-IR for protein analysis; thus, the method was validated using transmission FT-IR and multipass ATR-FT-IR as referee methods. The single-pass ATR-FT-IR technique was advantageous since the single-pass geometry permits rapid secondary structure analysis on small volumes of protein in H2O solution without the use of demountable thin path length sample cells. Moreover, the fact that H2O backgrounds were small allowed the simultaneous observation of the amide I-III, A, and B regions without having to perform H2O subtraction. A comparison of replicate protein spectra indicated that the single-pass ATR-FT-IR method yields more reproducible data than those acquired by transmission FT-IR. The observed trends for the amide I-III and A bands obtained by single-pass ATR-FT-IR agreed with those in the literature for conventional transmission FT-IR.
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Affiliation(s)
- Brandye M Smith
- Department of Chemistry, North Carolina State University, Raleigh 27695-8204, USA
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10
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Smith BM, Oswald L, Franzen S. Single-pass attenuated total reflection Fourier transform infrared spectroscopy for the prediction of protein secondary structure. Anal Chem 2002; 74:3386-91. [PMID: 12139044 DOI: 10.1021/ac020104n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Principal component regression (PCR) was applied to a spectral library of proteins in H2O solution acquired by single-pass attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy. PCR was used to predict the secondary structure content, principally alpha-helical and the beta-sheet content, of proteins within a spectral library. Quantitation of protein secondary structure content was performed as a proof of principle that use of single-pass ATR-FT-IR is an appropriate method for protein secondary structure analysis. The ATR-FT-IR method permits acquisition of the entire spectral range from 700 to 3900 cm(-1) without significant interference from water bands. An "inside model space" bootstrap and a genetic algorithm (GA) were used to improve prediction results. Specifically, the bootstrap was utilized to increase the number of replicates for adequate training and validation of the PCR model. The GA was used to optimize PCR parameters, particularly wavenumber selection. The use of the bootstrap allowed for adequate representation of variability in the amide A, amide B, and C-H stretching regions due to differing levels of sample hydration. Implementation of the bootstrap improved the robustness of the PCR models significantly; however, the use of a GA only slightly improved prediction results. Two spectral libraries are presented where one was better suited for beta-sheet content prediction and the other for alpha-helix content prediction. The GA-optimized PCR method for alpha-helix content prediction utilized 120 wavenumbers within the amide I, II, A, B, and IV and the C-H stretching regions and 18 factors. For beta-sheet content predictions, 580 wavenumbers within the amide I, II, A, and B and the C-H stretching regions and 18 factors were used. The validation results using these two methods yielded an average absolute error of 1.7% for alpha-helix content prediction and an average absolute error of 2.3% for beta-sheet content prediction. After the PCR models were developed and validated, they were used to predict the alpha-helix and beta-sheet content of two unknowns, casein and immunoglobulin G.
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Affiliation(s)
- Brandye M Smith
- Department of Chemistry, North Carolina State University, Raleigh 27695-8204, USA
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11
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Vigetti D, Pollegioni L, Monetti C, Prati M, Bernardini G, Gornati R. Property comparison of recombinant amphibian and mammalian allantoicases. FEBS Lett 2002; 512:323-8. [PMID: 11852104 DOI: 10.1016/s0014-5793(02)02264-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allantoicase is an enzyme involved in uric acid degradation. Although it is commonly accepted that allantoicase is lost in mammals, birds and reptiles, we have recently identified its transcripts in mice and humans. The mouse mRNA seems capable of encoding a functional allantoicase, therefore we expressed the Xenopus and mouse allantoicases (MAlc and XAlc, respectively) in Escherichia coli and characterized the recombinant enzymes. The two recombinant allantoicases show a similar temperature and pH stability but, although XAlc and MAlc share a 54% amino acid identity, they differ in sensitivity to bivalent cations, in substrate affinity and in the level of expression in tissues (as revealed by means of Western blot analysis). We propose that the loss of allantoicase activity in mouse is due to a low substrate affinity and to a reduced expression level of the enzyme.
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Affiliation(s)
- Davide Vigetti
- Dipartimento di Biologia Strutturale e Funzionale, Universitá degli Studi dell'Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
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12
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Vigetti D, Monetti C, Bernardini G. Molecular cloning of mouse allantoicase cDNA. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1519:117-21. [PMID: 11406280 DOI: 10.1016/s0167-4781(01)00207-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The uric acid degradation pathway is progressively lost during vertebrate evolution. In mammals, the end product of this catabolic pathway is allantoin and, therefore, no allantoicase should be present in mouse tissues. Surprisingly, we have found an expressed sequence tag (EST) from mouse testis with high similarity to allantoicase. To characterize this transcript, we have completely sequenced the corresponding EST clone insert and found a 1495 bp long cDNA coding for a 414 amino acid long protein. Identities of mouse versus microorganism allantoicases range from 25 to 30%. Identity reaches 54% when compared to Xenopus allantoicase. Among the tested tissues, only testis possesses the allantoicase transcript. Although no deleterious mutations were found in the coding region, no allantoicase activity could be detected in mouse testis.
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Affiliation(s)
- D Vigetti
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi dell'Insubria, Via J.H. Dunant 3, I-21100 Varese, Italy
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13
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Metabolic Regulation in Fungi. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1874-5334(01)80005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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14
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Vigetti D, Monetti C, Acquati F, Taramelli R, Bernardini G. Human allantoicase gene: cDNA cloning, genomic organization and chromosome localization. Gene 2000; 256:253-60. [PMID: 11054555 DOI: 10.1016/s0378-1119(00)00342-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Uric-acid-degrading enzymes (uricase, allantoinase, allantoicase, ureidoglycolate lyase and urease) were lost during vertebrate evolution and the causes for this loss are still unclear. We have recently cloned the first vertebrate allantoicase cDNA from the amphibian Xenopus laevis. Surprisingly, we have found some mammalian expressed sequence tags (ESTs) that show high similarity with Xenopus allantoicase cDNA. From a human fetal spleen cDNA library and adult kidney EST clone, we have obtained a 1790 nucleotide long cDNA. The 3' end of this sequence reveals a substantial high identity with the corresponding portion of Xenopus allantoicase cDNA. In contrast, at the 5' end the human sequence diverges from that of Xenopus; since no continuous open reading frame can be found in this region, the hypothetical human protein appears truncated at its N-terminus. We proposed that such a transcript could be due to an incorrect splicing mechanism that introduces an intron portion at the 5' end of human cDNA. Allantoicase cDNA is expressed in adult testis, prostate, kidney and fetal spleen. By comparison with available genomic sequences deposited in database, we have determined that the human allantoicase gene consists of five exons and spans 8kb. We have also mapped the gene in chromosome 2.
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Affiliation(s)
- D Vigetti
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi dell'Insubria, Via J. H. Dunant 3, I-21100, Varese, Italy
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15
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Vigetti D, Monetti C, Pollegioni L, Taramelli R, Bernardini G. Xenopus allantoicase: molecular cloning, enzymatic activity and developmental expression. Arch Biochem Biophys 2000; 379:90-6. [PMID: 10864446 DOI: 10.1006/abbi.2000.1863] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Allantoicase is one of the enzymes of the purine degradation pathway and, interestingly, it appears to be lost, together with uricase and allantoinase, during mammalian evolution. Only allantoicases from the ascomycetes S. pombe, S. cerevisiae, and N. crassa have already been cloned, although the activity has been reported also in fishes and amphibians. By screening a cDNA expression library of Xenopus liver, we have cloned a 1491-bp-length cDNA coding for a 389 amino acid protein that shows an high similarity with the enzyme allantoicase. We have found that allantoicase mRNA is abundantly expressed in kidney and liver, but at much lower level is also present in brain, testis, intestine, and lung. We have detected enzymatic activity in crude extract from kidney, liver, and lung; we have also determined kinetic parameters (K(m) = 8.44 mM, V(max) = 6. 94 micromol min(-1) per mg protein) in kidney. During embryo development, we have detected allantoicase transcript and activity starting from 1 and 5 days after fertilization, respectively.
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Affiliation(s)
- D Vigetti
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi dell'Insubria, Via J. H. Dunant 3, Varese, I-21100, Italy
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Abstract
In the fungi, nitrogen metabolism is controlled by a complex genetic regulatory circuit which ensures the preferential use of primary nitrogen sources and also confers the ability to use many different secondary nitrogen sources when appropriate. Most structural genes encoding nitrogen catabolic enzymes are subject to nitrogen catabolite repression, mediated by positive-acting transcription factors of the GATA family of proteins. However, certain GATA family members, such as the yeast DAL80 factor, act negatively to repress gene expression. Selective expression of the genes which encode enzymes for the metabolism of secondary nitrogen sources is often achieved by induction, mediated by pathway-specific factors, many of which have a GAL4-like C6/Zn2 DNA binding domain. Regulation within the nitrogen circuit also involves specific protein-protein interactions, as exemplified by the specific binding of the negative-acting NMR protein with the positive-acting NIT2 protein of Neurospora crassa. Nitrogen metabolic regulation appears to play a significant role in the pathogenicity of certain animal and plant fungal pathogens.
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Affiliation(s)
- G A Marzluf
- Department of Biochemistry, Ohio State University, Columbus 43210, USA.
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Chiang TY, Marzluf GA. Binding affinity and functional significance of NIT2 and NIT4 binding sites in the promoter of the highly regulated nit-3 gene, which encodes nitrate reductase in Neurospora crassa. J Bacteriol 1995; 177:6093-9. [PMID: 7592372 PMCID: PMC177447 DOI: 10.1128/jb.177.21.6093-6099.1995] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In the filamentous fungus Neurospora crassa, both the global-acting regulatory protein NIT2 and the pathway-specific regulatory protein NIT4 are required to turn on the expression of the nit-3 gene, which encodes nitrate reductase, the first enzyme in the nitrate assimilatory pathway. Three NIT2 binding sites and two NIT4 binding sites have been identified in the 1.3-kb nit-3 promoter region via mobility shift and footprinting experiments with NIT2-beta-galactosidase and NIT4-beta-Gactosidase fusion proteins. Quantitative mobility shift assays were used to examine the affinity of individual NIT2 binding sites for the native NIT2 protein present in N. crassa nuclear extracts. In vivo analysis of nit-3 promoter 5' deletion constructs and individual NIT2 and NIT4 binding-site deletions or mutations revealed that all of the NIT2 and NIT4 binding sites are required for the full level of expression of the nit-3 gene. A cluster of two NIT2 and two NIT4 binding sites located more than 1 kb upstream of the translational start site is required for nit-3 expression, and one NIT2 binding site and one NIT4 site, which are immediately adjacent to each other, are of particular functional importance. A significant NIT2-NIT4 protein-protein interaction might occur upon their binding to nearby sites.
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Affiliation(s)
- T Y Chiang
- Department of Biochemistry, Ohio State University, Columbus 43210, USA
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18
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Haas H, Marzluf GA. NRE, the major nitrogen regulatory protein of Penicillium chrysogenum, binds specifically to elements in the intergenic promoter regions of nitrate assimilation and penicillin biosynthetic gene clusters. Curr Genet 1995; 28:177-83. [PMID: 8590470 DOI: 10.1007/bf00315785] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NRE, the nitrogen regulatory protein of Penicillium chrysogenum, contains a single Cys2/Cys2-type zinc-finger motif followed immediately by a highly basic region. The zinc-finger domain was expressed to Escherichia coli as a fusion protein with beta-galactosidase. In order to test the putative DNA-binding ability of NRE, the intergenic promoter region of the nitrate reductase/nitrite reductase gene cluster (niiA-niaD) of Penicillium was sequenced. Our results show that NRE is a DNA-binding protein and binds to the intergenic promoter regions of the P. chrysogenum niiA-niaD and acvA-pcbC gene cluster, encoding the first two enzymes in penicillin biosynthesis. Three of the four high-affinity NRE-binding sites contained two GATA core elements. In one of the recognition sites for NRE, one GATA motif was replaced by GATT. The two GATA elements showed all possible orientations, head-to-head, head-to-tail and tail-to-tail, and were separated by between 4 and 27 bp. Missing-contact analysis showed that all three purines in both of the GATA core sequences and the single adenine residue in each of the complementary TATC sequences were involved in the binding of NRE. Moreover, loss of purines in the flanking regions of the GATA elements also affect binding of NRE, as their loss causes reduced affinity.
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Affiliation(s)
- H Haas
- Department of Biochemistry, Ohio State University, Columbus 43210, USA
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19
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Fu YH, Feng B, Evans S, Marzluf GA. Sequence-specific DNA binding by NIT4, the pathway-specific regulatory protein that mediates nitrate induction in Neurospora. Mol Microbiol 1995; 15:935-42. [PMID: 7596294 DOI: 10.1111/j.1365-2958.1995.tb02362.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The expression of the structural genes nit-3 and nit-6, which encode the nitrate assimilatory enzymes nitrate reductase and nitrite reductase, respectively, is highly regulated by the global-acting NIT2 regulatory protein. These structural genes are also controlled by nitrogen catabolite repression and by specific induction via nitrate. A pathway-specific regulatory protein, NIT4, appears to mediate nitrate induction of nit-3 and of nit-6. The NIT4 protein, composed of 1090 amino acids, contains a putative GAL4-like Cys-6 zinc cluster DNA-binding motif, which is joined by a short segment to a stretch of amino acids that appear to constitute a coiled-coil dimerization domain. Chemical crosslinking studies demonstrated that a truncated form of NIT4 forms homodimers. Mobility-shift and DNA-footprinting experiments have identified two NIT4-binding sites of significantly different strengths in the promoter region of the nit-3 gene. The stronger binding site contains a symmetrical octameric sequence, TCCGCGGA, whereas the weaker site has a related sequence. Sequences related to this palindromic element can be found upstream of the nit-6 gene.
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Affiliation(s)
- Y H Fu
- Department of Biochemistry, Ohio State University, Columbus 43210, USA
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20
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Haas H, Bauer B, Redl B, Stöffler G, Marzluf GA. Molecular cloning and analysis of nre, the major nitrogen regulatory gene of Penicillium chrysogenum. Curr Genet 1995; 27:150-8. [PMID: 7788718 DOI: 10.1007/bf00313429] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have isolated the Penicillium chrysogenum nre gene which is homologous to the major nitrogen regulatory genes areA from Aspergillus nidulans and nit-2 from Neurospora crassa. Overall, nre shows 60% identity to areA and 30% identity to nit-2 at the amino-acid level. The gene encodes a protein of 835 amino-acid residues and contains a single Cys2/Cys2-type zinc finger with an adjacent basic region and a putative acidic activation region. In the DNA-binding domain, 98% of the amino-acid residues are identical in nre, areA and nit-2. The nre gene has been shown to be functional in N. crassa by heterologous complementation of a nit-2 mutant. Growth tests indicated that transformants could utilize nitrate, amino-acids, purines and amides as sole nitrogen sources. Nitrate reductase activity assays performed with transformants demonstrated that nitrogen control was completely normal. Complementation of N. crassa nit-2 mutants with 5'-deletion clones of nre suggests the possible presence of an internal promoter within the coding region. Northern analysis and ribonuclease protection assays of total cellular RNA indicated that nre encodes a 3.2-kb transcript which is reduced in content under conditions of nitrogen repression.
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Affiliation(s)
- H Haas
- Department of Biochemistry, Ohio State University, Columbus 43210, USA
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21
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Chiang TY, Rai R, Cooper TG, Marzluf GA. DNA binding site specificity of the Neurospora global nitrogen regulatory protein NIT2: analysis with mutated binding sites. MOLECULAR & GENERAL GENETICS : MGG 1994; 245:512-6. [PMID: 7808401 DOI: 10.1007/bf00302264] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
NIT2, a positive-acting regulatory protein in Neurospora crassa, activates the expression of a series of unlinked structural genes that encode nitrogen catabolic enzymes. NIT2 binding sites in the promoter regions of nit3, alc and lao have at least two GATA sequence elements. We have examined the binding affinity of the NIT2 protein for the yeast DAL5 wild-type upstream activation sequence UASNTR, which contains two GATA elements, and for a series of mutated binding sites, each differing from the wild-type site by a single base. Substitution for individual nucleotides within 5' or 3' sequences that flank the GATA elements had only modest effects upon NIT2 binding. In contrast, nearly all substitutions within the GATA elements almost completely eliminated NIT2 binding, demonstrating the importance of the GATA sequence for NIT2 binding. Four high-affinity binding sites for the NIT2 protein were found within a central region of the nit-2 gene itself.
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Affiliation(s)
- T Y Chiang
- Department of Biochemistry, Ohio State University, Columbus 43210
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22
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Li Q, Jarai G, Yaghmai B, Marzluf GA. The leu-1 gene of Neurospora crassa: nucleotide and deduced amino acid sequence comparisons. Gene 1993; 136:301-5. [PMID: 8294021 DOI: 10.1016/0378-1119(93)90484-k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Neurospora crassa leu-1 gene encodes beta-isopropylmalate dehydrogenase (IPMDH; EC 1.1.1.85), an enzyme in the leucine biosynthetic pathway. We determined the nucleotide sequence of the entire leu-1 gene and of four independent cDNA clones. By comparing the genomic and cDNA sequences, four introns were identified in the 5' portion of the gene and a single open reading frame was established. One of the introns is located within the 5'-noncoding region of the transcript. The deduced amino acid sequence encoded by leu-1 was aligned with that of the homologous yeast enzyme and extensive sequence identity was uncovered. The lesion present in a conventional leu-1 mutant was identified as the insertion of a single base pair.
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Affiliation(s)
- Q Li
- Department of Biochemistry, Ohio State University, Columbus 43210
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23
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Xiao XD, Marzluf GA. Amino-acid substitutions in the zinc finger of NIT2, the nitrogen regulatory protein of Neurospora crassa, alter promoter element recognition. Curr Genet 1993; 24:212-8. [PMID: 8221929 DOI: 10.1007/bf00351794] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
NIT2, the major nitrogen regulatory protein of Neurospora crassa mediates nitrogen catabolite derepression of the structural genes which specify enzymes of nitrogen catabolism. The promoter of the structural gene for L-amino acid oxidase, a nitrogen-regulated enzyme, was found to contain two NIT2 binding sites, each with two copies of a GATA core consensus sequence. Site-directed mutagenesis was employed to create amino-acid substitutions within the single zinc-finger region of NIT2, which serves as the DNA-binding domain. The affect of those mutations upon NIT2 function in vivo in the activation of three separate structural genes was examined by transformation assays and relevant enzyme activities, and DNA-binding activity in vitro was determined by gel band mobility-shift assays. It was shown that specific amino-acid residues within the zinc-finger loop region of NIT2 are important for DNA-binding activity, whereas other residues influence the specificity of DNA binding. Mutant NIT2 proteins were obtained which retain DNA-binding activity and alter the specificity of DNA recognition, thus allowing a distinction between related DNA elements.
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Affiliation(s)
- X D Xiao
- Department of Biochemistry, Ohio State University, Columbus 43210
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24
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Jarai G, Truong HN, Daniel-Vedele F, Marzluf GA. NIT2, the nitrogen regulatory protein of Neurospora crassa, binds upstream of nia, the tomato nitrate reductase gene, in vitro. Curr Genet 1992; 21:37-41. [PMID: 1531184 DOI: 10.1007/bf00318652] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nit-2 gene of Neurospora crassa encodes a trans-acting regulatory protein that activates the expression of a number of structural genes which code for nitrogen catabolic enzymes, including nitrate reductase. The NIT2 protein contains a Cys2/Cys2-type zinc-finger DNA-binding domain that recognizes promoter regions of the Neurospora nitrogen-related genes. The NIT2 zinc-finger domain/beta-Gal fusion protein was shown to recognize and bind in a specific manner to two upstream fragments of the nia gene of Lycopersicon esculentum (tomato) in vitro, whereas two mutant NIT2 proteins failed to bind to the same fragments. The dissociation kinetics of the complexes formed between the NIT2 protein and the Neurospora nit-3 and the tomato nia gene promoters were examined; NIT2 binds more strongly to the nit-3 promoter DNA fragment than it does to fragments derived from the plant nitrate reductase gene itself. The observed specificity of the binding suggests the existence of a NIT2-like homolog which regulates the expression of the nitrate assimilation pathway of higher plants.
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Affiliation(s)
- G Jarai
- Department of Biochemistry, Ohio State University, Columbus 43210
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25
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Lee FJ, Moss J. Cloning of a Saccharomyces cerevisiae gene encoding a protein homologous to allantoicase of Neurospora crassa. Yeast 1991; 7:993-5. [PMID: 1839481 DOI: 10.1002/yea.320070912] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- F J Lee
- Laboratory of Cellular Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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26
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Yoo HS, Cooper TG. Sequences of two adjacent genes, one (DAL2) encoding allantoicase and another (DCG1) sensitive to nitrogen-catabolite repression in Saccharomyces cerevisiae. Gene 1991; 104:55-62. [PMID: 1916277 DOI: 10.1016/0378-1119(91)90464-m] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Reported are the nucleotide sequences of the yeast allantoicase-encoding gene (DAL2) and that of an unknown gene adjacent to it. Expression of the unidentified gene is sensitive to nitrogen catabolite repression (NCR) and regulated by the DAL80 product, a previously documented control element regulating allantoin pathway gene expression. Both genes possess multiple upstream activation sequences (UAS) homologous to the UASNTR element shown to be required for sensitivity to NCR. Also present upstream from DAL2 is a mutant form of the upstream induction sequence required for response of DAL7 to induction. Its occurrence in mutant form is consistent with the poor induction of DAL2 expression observed in vivo.
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Affiliation(s)
- H S Yoo
- Department of Microbiology and Immunology, University of Tennessee, Memphis 38163
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27
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Okamoto PM, Fu YH, Marzluf GA. Nit-3, the structural gene of nitrate reductase in Neurospora crassa: nucleotide sequence and regulation of mRNA synthesis and turnover. MOLECULAR & GENERAL GENETICS : MGG 1991; 227:213-23. [PMID: 1829499 DOI: 10.1007/bf00259673] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The nit-3 gene of the filamentous fungus Neurospora crassa encodes the enzyme nitrate reductase, which catalyzes the first reductive step in the highly regulated nitrate assimilatory pathway. The nucleotide sequence of nit-3 was determined and translates to a protein of 982 amino acid residues with a molecular weight of approximately 108 kDa. Comparison of the deduced nit-3 protein sequence with the nitrate reductase protein sequences of other fungi and higher plants revealed that a significant amount of homology exists, particularly within the three cofactor-binding domains for molybdenum, heme and FAD. The synthesis and turnover of the nit-3 mRNA were also examined and found to occur rapidly and efficiently under changing metabolic conditions.
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Affiliation(s)
- P M Okamoto
- Department of Biochemistry, Ohio State University, Columbus 43210
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