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Yarlett N, Jarroll EL, Morada M, Lloyd D. Protists: Eukaryotic single-celled organisms and the functioning of their organelles. Adv Microb Physiol 2024; 84:243-307. [PMID: 38821633 DOI: 10.1016/bs.ampbs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Organelles are membrane bound structures that compartmentalize biochemical and molecular functions. With improved molecular, biochemical and microscopy tools the diversity and function of protistan organelles has increased in recent years, providing a complex panoply of structure/function relationships. This is particularly noticeable with the description of hydrogenosomes, and the diverse array of structures that followed, having hybrid hydrogenosome/mitochondria attributes. These diverse organelles have lost the major, at one time, definitive components of the mitochondrion (tricarboxylic cycle enzymes and cytochromes), however they all contain the machinery for the assembly of Fe-S clusters, which is the single unifying feature they share. The plasticity of organelles, like the mitochondrion, is therefore evident from its ability to lose its identity as an aerobic energy generating powerhouse while retaining key ancestral functions common to both aerobes and anaerobes. It is interesting to note that the apicoplast, a non-photosynthetic plastid that is present in all apicomplexan protozoa, apart from Cryptosporidium and possibly the gregarines, is also the site of Fe-S cluster assembly proteins. It turns out that in Cryptosporidium proteins involved in Fe-S cluster biosynthesis are localized in the mitochondrial remnant organelle termed the mitosome. Hence, different organisms have solved the same problem of packaging a life-requiring set of reactions in different ways, using different ancestral organelles, discarding what is not needed and keeping what is essential. Don't judge an organelle by its cover, more by the things it does, and always be prepared for surprises.
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Affiliation(s)
- Nigel Yarlett
- Haskins Laboratories, Pace University, New York, NY, United States; The Department of Chemistry and Physical Sciences, Pace University, New York, NY, United States.
| | - Edward L Jarroll
- Department of Biological Sciences, CUNY-Lehman College, Bronx, NY, United States
| | - Mary Morada
- Haskins Laboratories, Pace University, New York, NY, United States
| | - David Lloyd
- Schools of Biosciences and Engineering, Cardiff University, Wales, United Kingdom
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2
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Shen S, Zhang C, Meng Y, Cui G, Wang Y, Liu X, He Q. Sensing of H2O2-induced oxidative stress by the UPF factor complex is crucial for activation of catalase-3 expression in Neurospora. PLoS Genet 2023; 19:e1010985. [PMID: 37844074 PMCID: PMC10578600 DOI: 10.1371/journal.pgen.1010985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
UPF-1-UPF-2-UPF-3 complex-orchestrated nonsense-mediated mRNA decay (NMD) is a well-characterized eukaryotic cellular surveillance mechanism that not only degrades aberrant transcripts to protect the integrity of the transcriptome but also eliminates normal transcripts to facilitate appropriate cellular responses to physiological and environmental changes. Here, we describe the multifaceted regulatory roles of the Neurospora crassa UPF complex in catalase-3 (cat-3) gene expression, which is essential for scavenging H2O2-induced oxidative stress. First, losing UPF proteins markedly slowed down the decay rate of cat-3 mRNA. Second, UPF proteins indirectly attenuated the transcriptional activity of cat-3 gene by boosting the decay of cpc-1 and ngf-1 mRNAs, which encode a well-studied transcription factor and a histone acetyltransferase, respectively. Further study showed that under oxidative stress condition, UPF proteins were degraded, followed by increased CPC-1 and NGF-1 activity, finally activating cat-3 expression to resist oxidative stress. Together, our data illustrate a sophisticated regulatory network of the cat-3 gene mediated by the UPF complex under physiological and H2O2-induced oxidative stress conditions.
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Affiliation(s)
- Shuangjie Shen
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chengcheng Zhang
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuanhao Meng
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guofei Cui
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Wang
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Qun He
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
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3
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HDA-2-Containing Complex Is Required for Activation of Catalase-3 Expression in Neurospora crassa. mBio 2022; 13:e0135122. [PMID: 35699373 PMCID: PMC9426557 DOI: 10.1128/mbio.01351-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is essential for aerobic organisms to maintain the homeostasis of intracellular reactive oxygen species (ROS) for survival and adaptation to the environment. In line with other eukaryotes, the catalase of Neurospora crassa is an important enzyme for clearing ROS, and its expression is tightly regulated by the growth phase and various oxidative stresses. Our study reveals that, in N. crassa, histone deacetylase 2 (HDA-2) and its catalytic activity positively regulate the expression of the catalase-3 (cat-3) gene. HDA-2, SIF-2, and SNT-1 may form a subcomplex with such a regulation role. As expected, deletion of HDA-2 or SIF-2 subunit increased acetylation levels of histone H4, indicating that loss of HDA-2 complex fails to deacetylate H4 at the cat-3 locus. Furthermore, loss of HDA-2 or its catalytic activity led to dramatic decreases of TFIIB and RNA polymerase II (RNAP II) recruitment at the cat-3 locus and also resulted in high deposition of H2A.Z at the promoter and transcription start site (TSS) regions of the cat-3 gene. Collectively, this study strongly demonstrates that the HDA-2-containing complex activates the transcription of the cat-3 gene by facilitating preinitiation complex (PIC) assembly and antagonizing the inhibition of H2A.Z at the cat-3 locus through H4 acetylation. IMPORTANCE Clearance of reactive oxygen species (ROS) is critical to the survival of aerobic organisms. In the model filamentous fungus Neurospora crassa, catalase-3 (cat-3) expression is activated in response to H2O2-induced ROS stress. We found that histone deacetylase 2 (HDA-2) positively regulates cat-3 transcription in N. crassa; this is widely divergent from the classical repressive role of most histone deacetylases. Like HDA-2, the SIF-2 or SNT-1 subunit of HDA-2-containing complex plays a positive role in cat-3 transcription. Furthermore, we also found that HDA-2-containing complex provides an appropriate chromatin environment to facilitate PIC assembly and to antagonize the inhibition role of H2A.Z at the cat-3 locus through H4 acetylation. Taken together, our results establish a mechanism for how the HDA-2-containing complex regulates transcription of the cat-3 gene in N. crassa.
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The Glyoxysomal Protease LON2 Is Involved in Fruiting-Body Development, Ascosporogenesis and Stress Resistance in Sordaria macrospora. J Fungi (Basel) 2021; 7:jof7020082. [PMID: 33530609 PMCID: PMC7911957 DOI: 10.3390/jof7020082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/05/2023] Open
Abstract
Microbodies, including peroxisomes, glyoxysomes and Woronin bodies, are ubiquitous dynamic organelles that play important roles in fungal development. The ATP-dependent chaperone and protease family Lon that maintain protein quality control within the organelle significantly regulate the functionality of microbodies. The filamentous ascomycete Sordaria macrospora is a model organism for studying fruiting-body development. The genome of S. macrospora encodes one Lon protease with the C-terminal peroxisomal targeting signal (PTS1) serine-arginine-leucine (SRL) for import into microbodies. Here, we investigated the function of the protease SmLON2 in sexual development and during growth under stress conditions. Localization studies revealed a predominant localization of SmLON2 in glyoxysomes. This localization depends on PTS1, since a variant without the C-terminal SRL motif was localized in the cytoplasm. A ΔSmlon2 mutant displayed a massive production of aerial hyphae, and produced a reduced number of fruiting bodies and ascospores. In addition, the growth of the ΔSmlon2 mutant was completely blocked under mild oxidative stress conditions. Most of the defects could be complemented with both variants of SmLON2, with and without PTS1, suggesting a dual function of SmLON2, not only in microbody, but also in cytosolic protein quality control.
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Duan J, Liu Q, Su S, Cha J, Zhou Y, Tang R, Liu X, Wang Y, Liu Y, He Q. The Neurospora RNA polymerase II kinase CTK negatively regulates catalase expression in a chromatin context-dependent manner. Environ Microbiol 2019; 22:76-90. [PMID: 31599077 DOI: 10.1111/1462-2920.14821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/25/2019] [Accepted: 10/02/2019] [Indexed: 01/15/2023]
Abstract
Clearance and adaptation to reactive oxygen species (ROS) are crucial for cell survival. As in other eukaryotes, the Neurospora catalases are the main enzymes responsible for ROS clearance and their expression are tightly regulated by the growth and environmental conditions. The RNA polymerase II carboxyl terminal domain (RNAPII CTD) kinase complex (CTK complex) is known as a positive elongation factor for many inducible genes by releasing paused RNAPII near the transcription start site and promoting transcription elongation. However, here we show that deletion of CTK complex components in Neurospora led to high CAT-3 expression level and resistance to H2 O2 -induced ROS stress. The catalytic activity of CTK-1 is required for such a response. On the other hand, CTK-1 overexpression led to decreased expression of CAT-3. ChIP assays shows that CTK-1 phosphorylates the RNAPII CTD at Ser2 residues in the cat-3 ORF region during transcription elongation and deletion of CTK-1 led to dramatic decreases of SET-2 recruitment and H3K36me3 modification. As a result, histones at the cat-3 locus become hyperacetylated to promote its transcription. Together, these results demonstrate that the CTK complex is negative regulator of cat-3 expression by affecting its chromatin structure.
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Affiliation(s)
- Jiabin Duan
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qingqing Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Sodgerel Su
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Joonseok Cha
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Yike Zhou
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ruiqi Tang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Wang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Sun X, Wang F, Lan N, Liu B, Hu C, Xue W, Zhang Z, Li S. The Zn(II)2Cys6-Type Transcription Factor ADA-6 Regulates Conidiation, Sexual Development, and Oxidative Stress Response in Neurospora crassa. Front Microbiol 2019; 10:750. [PMID: 31024511 PMCID: PMC6468284 DOI: 10.3389/fmicb.2019.00750] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/26/2019] [Indexed: 01/02/2023] Open
Abstract
Conidiation and sexual development are critical for reproduction, dispersal and better-adapted survival in many filamentous fungi. The Neurospora crassa gene ada-6 encodes a Zn(II)2Cys6-type transcription factor, whose deletion resulted in reduced conidial production and female sterility. In this study, we confirmed the positive contribution of ada-6 to conidiation and sexual development by detailed phenotypic characterization of its deletion mutant and the complemented mutant. To understand the regulatory mechanisms of ADA-6 in conidiation and sexual development, transcriptomic profiles generated by RNA-seq from the Δada-6 mutant and wild type during conidiation and sexual development were compared. During conidial development, differential expressed genes (DEGs) between the Δada-6 mutant and wild type are mainly involved in oxidation-reduction process and single-organism metabolic process. Several conidiation related genes are positively regulated by ADA-6, including genes that positively regulate conidiation (fluffy and acon-3), and genes preferentially expressed during conidial development (eas, con-6, con-8, con-10, con-13, pcp-1, and NCU9357), as the expression of these genes were lower in the Δada-6 mutant compared to wild type during conidial development. Phenotypic observation of deletion mutants for other genes with unknown function down-regulated by ada-6 deletion revealed that deletion mutants for four genes (NCU00929, NCU05260, NCU00116, and NCU04813) produced less conidia than wild type. Deletion of ada-6 resulted in female sterility, which might be due to that ADA-6 affects oxidation-reduction process and transmembrane transport process, and positively regulates the transcription of pre-2, poi-2, and NCU05832, three key genes participating in sexual development. In both conidiation and the sexual development process, ADA-6 regulates the transcription of cat-3 and other genes participating in reactive oxygen species production according to RNA-seq data, indicating a role of ADA-6 in oxidative stress response. This was further confirmed by the results that deletion of ada-6 led to hypersensitivity to oxidants H2O2 and menadione. Together, these results proved that ADA-6, as a global regulator, plays a crucial role in conidiation, sexual development, and oxidative stress response of N. crassa.
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Affiliation(s)
- Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Food Science and Engineering, Qilu University of Technology, Jinan, China
| | - Nan Lan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bo Liu
- College of Food Science and Engineering, Qilu University of Technology, Jinan, China
| | - Chengcheng Hu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Xue
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenying Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shaojie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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7
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Vega-García V, Díaz-Vilchis A, Saucedo-Vázquez JP, Solano-Peralta A, Rudiño-Piñera E, Hansberg W. Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase. Arch Biochem Biophys 2018; 640:17-26. [PMID: 29305053 DOI: 10.1016/j.abb.2017.12.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/24/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022]
Abstract
CAT-2, a cytosolic catalase-peroxidase (CP) from Neurospora crassa, which is induced during asexual spore formation, was heterologously expressed and characterized. CAT-2 had the Met-Tyr-Trp (M-Y-W) adduct required for catalase activity. Its KM for H2O2 was micromolar for peroxidase and millimolar for catalase activity. A Em = -158 mV reduction potential value was obtained and the Soret band shift suggested a mixture of low and high spin ferric iron. CAT-2 EPR spectrum at 10 K indicated an axial and a rhombic component. With peroxyacetic acid (PAA), formation of Compound I* was observed with EPR. CAT-2 homodimer crystallographic structure contained two K+ ions; Glu107 residues were displaced to bind them. CAT-2 showed the essential amino acid residues for activity in similar positions to other CPs. CAT-2 Arg426 is oriented towards the M-Y-W adduct, interacting with the deprotonated Tyr238 hydroxyl group. A perhydroxy modification of the indole nitrogen of Trp90 was oriented toward the catalytic His91. In contrast to cytochrome c peroxidase and ascorbate peroxidase, the catalase-peroxidase heme propionates are not exposed to the solvent. Together with other N. crassa enzymes that utilize H2O2 as a substrate, CAT-2 has many tryptophan and proline residues at its surface, probably related to H2O2 selection in water.
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Affiliation(s)
- Vanessa Vega-García
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Mexico
| | - Adelaida Díaz-Vilchis
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Mexico
| | - Juan Pablo Saucedo-Vázquez
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Mexico
| | - Alejandro Solano-Peralta
- Unidad de Servicios de Apoyo a la Investigación y a la Industria, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Mexico
| | - Wilhelm Hansberg
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Mexico.
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Abstract
Peroxisomes in fungi are involved in a huge number of different metabolic processes. In addition, non-metabolic functions have also been identified. The proteins that are present in a particular peroxisome determine its metabolic function, whether they are the matrix localized enzymes of the different metabolic pathways or the membrane proteins involved in transport of metabolites across the peroxisomal membrane. Other peroxisomal proteins play a role in organelle biogenesis and dynamics, such as fission, transport and inheritance. Hence, obtaining a complete overview of which proteins are present in peroxisomes at a given time or under a given growth condition provides invaluable insights into peroxisome biology. Bottom up approaches are ideal to follow one or a few proteins at a time but they are not able to give a global view of the content of peroxisomes. To gain such information, top down approaches are required and one that has provided valuable insights into peroxisome function is mass spectrometry based organellar proteomics. Here, we discuss the findings of several such studies in yeast and filamentous fungi and outline new insights into peroxisomal function that were gained from these studies.
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Affiliation(s)
- Xin Chen
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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Islinger M, Manner A, Völkl A. The Craft of Peroxisome Purification-A Technical Survey Through the Decades. Subcell Biochem 2018; 89:85-122. [PMID: 30378020 DOI: 10.1007/978-981-13-2233-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Purification technologies are one of the working horses in organelle proteomics studies as they guarantee the separation of organelle-specific proteins from the background contamination by other subcellular compartments. The development of methods for the separation of organelles was a major prerequisite for the initial detection and characterization of peroxisome as a discrete entity of the cell. Since then, isolated peroxisomes fractions have been used in numerous studies in order to characterize organelle-specific enzyme functions, to allocate the peroxisome-specific proteome or to unravel the organellar membrane composition. This review will give an overview of the fractionation methods used for the isolation of peroxisomes from animals, plants and fungi. In addition to "classic" centrifugation-based isolation methods, relying on the different densities of individual organelles, the review will also summarize work on alternative technologies like free-flow-electrophoresis or flow field fractionation which are based on distinct physicochemical parameters. A final chapter will further describe how different separation methods and quantitative mass spectrometry have been used in proteomics studies to assign the proteome of PO.
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Affiliation(s)
- Markus Islinger
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.
| | - Andreas Manner
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Alfred Völkl
- Department of Medical Cell Biology, Institute of Anatomy, University of Heidelberg, Heidelberg, Germany
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Sooch BS, Kauldhar BS, Puri M. Recent insights into microbial catalases: Isolation, production and purification. Biotechnol Adv 2014; 32:1429-47. [DOI: 10.1016/j.biotechadv.2014.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 09/10/2014] [Accepted: 09/18/2014] [Indexed: 01/08/2023]
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11
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Gyöngyösi N, Káldi K. Interconnections of reactive oxygen species homeostasis and circadian rhythm in Neurospora crassa. Antioxid Redox Signal 2014; 20:3007-23. [PMID: 23964982 DOI: 10.1089/ars.2013.5558] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
SIGNIFICANCE Both circadian rhythm and the production of reactive oxygen species (ROS) are fundamental features of aerobic eukaryotic cells. The circadian clock enhances the fitness of organisms by enabling them to anticipate cycling changes in the surroundings. ROS generation in the cell is often altered in response to environmental changes, but oscillations in ROS levels may also reflect endogenous metabolic fluctuations governed by the circadian clock. On the other hand, an effective regulation and timing of antioxidant mechanisms may be crucial in the defense of cellular integrity. Thus, an interaction between the circadian timekeeping machinery and ROS homeostasis or signaling in both directions may be of advantage at all phylogenetic levels. RECENT ADVANCES The Frequency-White Collar-1 and White Collar-2 oscillator (FWO) of the filamentous fungus Neurospora crassa is well characterized at the molecular level. Several members of the ROS homeostasis were found to be controlled by the circadian clock, and ROS levels display circadian rhythm in Neurospora. On the other hand, multiple data indicate that ROS affect the molecular oscillator. CRITICAL ISSUES Increasing evidence suggests the interplay between ROS homeostasis and oscillators that may be partially or fully independent of the FWO. In addition, ROS may be part of a complex cellular network synchronizing non-transcriptional oscillators with timekeeping machineries based on the classical transcription-translation feedback mechanism. FUTURE DIRECTIONS Further investigations are needed to clarify how the different layers of the bidirectional interactions between ROS homeostasis and circadian regulation are interconnected.
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12
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The biogenesis protein PEX14 is an optimal marker for the identification and localization of peroxisomes in different cell types, tissues, and species in morphological studies. Histochem Cell Biol 2013; 140:423-42. [DOI: 10.1007/s00418-013-1133-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2013] [Indexed: 01/09/2023]
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13
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Mhamdi A, Noctor G, Baker A. Plant catalases: Peroxisomal redox guardians. Arch Biochem Biophys 2012; 525:181-94. [DOI: 10.1016/j.abb.2012.04.015] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 04/12/2012] [Accepted: 04/14/2012] [Indexed: 12/17/2022]
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14
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Hansberg W, Salas-Lizana R, Domínguez L. Fungal catalases: Function, phylogenetic origin and structure. Arch Biochem Biophys 2012; 525:170-80. [DOI: 10.1016/j.abb.2012.05.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/16/2022]
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15
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Wang ZL, Zhang LB, Ying SH, Feng MG. Catalases play differentiated roles in the adaptation of a fungal entomopathogen to environmental stresses. Environ Microbiol 2012; 15:409-18. [PMID: 22891860 DOI: 10.1111/j.1462-2920.2012.02848.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The catalase family of Beauveria bassiana (fungal entomopathogen) consists of catA (spore-specific), catB (secreted), catP (peroxisomal), catC (cytoplasmic) and catD (secreted peroxidase/catalase), which were distinguished in phylogeny and structure and functionally characterized by constructing single-gene disrupted and rescued mutants for enzymatic and multi-phenotypic analyses. Total catalase activity decreased 89% and 56% in ΔcatB and ΔcatP, corresponding to the losses of upper and lower active bands gel-profiled for all catalases respectively, but only 9-12% in other knockout mutants. Compared with wild type and complement mutants sharing similar enzymatic and phenotypic parameters, all knockout mutants showed significant (9-56%) decreases in the antioxidant capability of their conidia (active ingredients of mycoinsecticides), followed by remarkable phenotypic defects associated with the fungal biocontrol potential. These defects included mainly the losses of 40% thermotolerance (45°C) in ΔcatA, 46-48% UV-B resistance in ΔcatA and ΔcatD, and 33-47% virulence to Spodoptera litura larvae in ΔcatA, ΔcatP and ΔcatD respectively. Moreover, the drastic transcript upregulation of some other catalase genes observed in the normal culture of each knockout mutant revealed functionally complimentary effects among some of the catalase genes, particularly between catB and catC whose knockout mutants displayed little or minor phenotypic changes. However, the five catalase genes functioned redundantly in mediating the fungal tolerance to either hyperosmotic or fungicidal stress. The differentiated roles of five catalases in regulating the B. bassiana virulence and tolerances to oxidative stress, high temperature and UV-B irradiation provide new insights into fungal adaptation to stressful environment and host invasion.
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Affiliation(s)
- Zheng-Liang Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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16
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Bourdais A, Bidard F, Zickler D, Berteaux-Lecellier V, Silar P, Espagne E. Wood utilization is dependent on catalase activities in the filamentous fungus Podospora anserina. PLoS One 2012; 7:e29820. [PMID: 22558065 PMCID: PMC3338752 DOI: 10.1371/journal.pone.0029820] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 12/06/2011] [Indexed: 01/24/2023] Open
Abstract
Catalases are enzymes that play critical roles in protecting cells against the toxic effects of hydrogen peroxide. They are implicated in various physiological and pathological conditions but some of their functions remain unclear. In order to decipher the role(s) of catalases during the life cycle of Podospora anserina, we analyzed the role of the four monofunctional catalases and one bifunctional catalase-peroxidase genes present in its genome. The five genes were deleted and the phenotypes of each single and all multiple mutants were investigated. Intriguingly, although the genes are differently expressed during the life cycle, catalase activity is dispensable during both vegetative growth and sexual reproduction in laboratory conditions. Catalases are also not essential for cellulose or fatty acid assimilation. In contrast, they are strictly required for efficient utilization of more complex biomass like wood shavings by allowing growth in the presence of lignin. The secreted CATB and cytosolic CAT2 are the major catalases implicated in peroxide resistance, while CAT2 is the major player during complex biomass assimilation. Our results suggest that P. anserina produces external H2O2 to assimilate complex biomass and that catalases are necessary to protect the cells during this process. In addition, the phenotypes of strains lacking only one catalase gene suggest that a decrease of catalase activity improves the capacity of the fungus to degrade complex biomass.
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Affiliation(s)
- Anne Bourdais
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Institut Génétique et Développement de Rennes, CNRS, UMR 6061, Rennes, France
- UEB Université Rennes 1, IFR 140, Faculté de Médecine, Rennes, France
| | - Frederique Bidard
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Denise Zickler
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Veronique Berteaux-Lecellier
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Laboratoire d’Excellence « CORAIL », USR 3278 CNRS-EPHE, CRIOBE, BP 1013, Moorea, French Polynesia
| | - Philippe Silar
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Univ Paris Diderot, Sorbonne Paris Cité, UFR des Sciences du Vivant, Paris, France
| | - Eric Espagne
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- * E-mail:
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Yoshida Y, Iigusa H, Wang N, Hasunuma K. Cross-talk between the cellular redox state and the circadian system in Neurospora. PLoS One 2011; 6:e28227. [PMID: 22164247 PMCID: PMC3229512 DOI: 10.1371/journal.pone.0028227] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/03/2011] [Indexed: 01/03/2023] Open
Abstract
The circadian system is composed of a number of feedback loops, and multiple feedback loops in the form of oscillators help to maintain stable rhythms. The filamentous fungus Neurospora crassa exhibits a circadian rhythm during asexual spore formation (conidiation banding) and has a major feedback loop that includes the FREQUENCY (FRQ)/WHITE COLLAR (WC) -1 and -2 oscillator (FWO). A mutation in superoxide dismutase (sod)-1, an antioxidant gene, causes a robust and stable circadian rhythm compared with that of wild-type (Wt). However, the mechanisms underlying the functions of reactive oxygen species (ROS) remain unknown. Here, we show that cellular ROS concentrations change in a circadian manner (ROS oscillation), and the amplitudes of ROS oscillation increase with each cycle and then become steady (ROS homeostasis). The ROS oscillation and homeostasis are produced by the ROS-destroying catalases (CATs) and ROS-generating NADPH oxidase (NOX). cat-1 is also induced by illumination, and it reduces ROS levels. Although ROS oscillation persists in the absence of frq, wc-1 or wc-2, its homeostasis is altered. Furthermore, genetic and biochemical evidence reveals that ROS concentration regulates the transcriptional function of WCC and a higher ROS concentration enhances conidiation banding. These findings suggest that the circadian system engages in cross-talk with the cellular redox state via ROS-regulatory factors.
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Affiliation(s)
- Yusuke Yoshida
- Kihara Institute for Biological Research, Graduate School of Integrated Science, Yokohama City University, Totsuka-ku, Yokohama, Japan.
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18
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Managadze D, Würtz C, Wiese S, Meyer HE, Niehaus G, Erdmann R, Warscheid B, Rottensteiner H. A proteomic approach towards the identification of the matrix protein content of the two types of microbodies in Neurospora crassa. Proteomics 2011; 10:3222-34. [PMID: 20707002 DOI: 10.1002/pmic.201000095] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Microbodies (peroxisomes) comprise a class of organelles with a similar biogenesis but remarkable biochemical heterogeneity. Here, we purified the two distinct microbody family members of filamentous fungi, glyoxysomes and Woronin bodies, from Neurospora crassa and analyzed their protein content by HPLC/ESI-MS/MS. In the purified Woronin bodies, we unambiguously identified only hexagonal 1 (HEX1), suggesting that the matrix is probably exclusively filled with the HEX1 hexagonal crystal. The proteomic analysis of highly purified glyoxysomes allowed the identification of 191 proteins. Among them were 16 proteins with a peroxisomal targeting signal type 1 (PTS1) and three with a PTS2. The collection also contained the previously described N. crassa glyoxysomal matrix proteins FOX2 and ICL1 that lack a typical PTS. Three PTS1 proteins were identified that likely represent the long sought glyoxysomal acyl-CoA dehydrogenases of filamentous fungi. Two of them were demonstrated by subcellular localization studies to be indeed glyoxysomal. Furthermore, two PTS proteins were identified that are suggested to be involved in the detoxification of nitroalkanes. Since the glyoxysomal localization was experimentally demonstrated for one of these enzymes, a new biochemical reaction is expected to be associated with microbody function.
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Affiliation(s)
- David Managadze
- Department of Systems Biochemistry, Institute of Physiological Chemistry, Ruhr-University of Bochum, Bochum, Germany
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Watters MK, Boersma M, Johnson M, Reyes C, Westrick E, Lindamood E. A screen for Neurospora knockout mutants displaying growth rate dependent branch density. Fungal Biol 2011; 115:296-301. [PMID: 21354536 DOI: 10.1016/j.funbio.2010.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 12/21/2010] [Accepted: 12/27/2010] [Indexed: 11/18/2022]
Abstract
Branch density (the spatial distribution of branch initiation points along a growing hypha) in wild-type Neurospora has been shown to remain constant at different growth rates due to a hypothesized system which compensates for hyphal growth rate. Here we report the results of a survey of the Neurospora knockout library for mutants affecting this proposed growth rate compensation system. The mutants identified fail to maintain branching homeostasis at different growth rates, thus showing growth rate-dependent branch density. The gene functions highlighted by this screen are diverse with several emerging themes including: ubiquitin-binding proteins, kinases, metal binding/metal metabolism proteins, reactive oxygen species (ROS) control proteins, and clock-associated/clock-controlled proteins. Other than their common influence on branch density homeostasis, the relationships between these gene functions and how they interact to influence branching are unclear.
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Affiliation(s)
- Michael K Watters
- Department of Biology, Neils Science Centre, Valparaiso University, 1610 Campus Drive East, Valparaiso, IN 46383, USA.
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20
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Managadze D, Würtz C, Wiese S, Schneider M, Girzalsky W, Meyer HE, Erdmann R, Warscheid B, Rottensteiner H. Identification of PEX33, a novel component of the peroxisomal docking complex in the filamentous fungus Neurospora crassa. Eur J Cell Biol 2010; 89:955-64. [DOI: 10.1016/j.ejcb.2010.07.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Catalase overexpression reduces the germination time and increases the pathogenicity of the fungus Metarhizium anisopliae. Appl Microbiol Biotechnol 2010; 87:1033-44. [DOI: 10.1007/s00253-010-2517-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
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Abstract
Fungi are amongst the most industrially important microorganisms in current use within the biotechnology industry. Most such fungal cultures are highly aerobic in nature, a character that has been frequently referred to in both reactor design and fungal physiology. The most fundamentally significant outcome of the highly aerobic growth environment in fermenter vessels is the need for the fungal culture to effectively combat in the intracellular environment the negative consequences of high oxygen transfer rates. The use of oxygen as the respiratory substrate is frequently reported to lead to the development of oxidative stress, mainly due to oxygen-derived free radicals, which are collectively termed as reactive oxygen species (ROS). Recently, there has been extensive research on the occurrence, extent, and consequences of oxidative stress in microorganisms, and the underlying mechanisms through which cells prevent and repair the damage caused by ROS. In the present study, we critically review the current understanding of oxidative stress events in industrially relevant fungi. The review first describes the current state of knowledge of ROS concisely, and then the various antioxidant strategies employed by fungal cells to counteract the deleterious effects, together with their implications in fungal bioprocessing are also discussed. Finally, some recommendations for further research are made.
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Affiliation(s)
- Qiang Li
- Strathclyde Fermentation Centre, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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23
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Hutchison E, Brown S, Tian C, Glass NL. Transcriptional profiling and functional analysis of heterokaryon incompatibility in Neurospora crassa reveals that reactive oxygen species, but not metacaspases, are associated with programmed cell death. MICROBIOLOGY-SGM 2009; 155:3957-3970. [PMID: 19696111 DOI: 10.1099/mic.0.032284-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heterokaryon incompatibility (HI) is a nonself recognition phenomenon occurring in filamentous fungi that is important for limiting resource plundering and restricting viral transfer between strains. Nonself recognition and HI occurs during hyphal fusion between strains that differ at het loci. If two strains undergo hyphal fusion, but differ in allelic specificity at a het locus, the fusion cell is compartmentalized and undergoes a rapid programmed cell death (PCD). Incompatible heterokaryons show a macroscopic phenotype of slow growth and diminished conidiation, and a microscopic phenotype of hyphal compartmentation and cell death. To understand processes associated with HI and PCD, we used whole-genome microarrays for Neurospora crassa to assess transcriptional differences associated with induction of HI mediated by differences in het-c pin-c haplotype. Our data show that HI is a dynamic and transcriptionally active process. The production of reactive oxygen species is implicated in the execution of HI and PCD in N. crassa, as are several genes involved in phosphatidylinositol and calcium signalling pathways. However, genes encoding mammalian homologues of caspases or apoptosis-inducing factor (AIF) are not required for HI or programmed cell death. These data indicate that PCD during HI occurs via a novel and possibly fungal-specific mechanism, making this pathway an attractive drug target for control of fungal infections.
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Affiliation(s)
- Elizabeth Hutchison
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720-3102, USA
| | - Sarah Brown
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720-3102, USA
| | - Chaoguang Tian
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720-3102, USA
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720-3102, USA
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Intracellular catalase/peroxidase from the phytopathogenic rice blast fungus Magnaporthe grisea: expression analysis and biochemical characterization of the recombinant protein. Biochem J 2009; 418:443-51. [DOI: 10.1042/bj20081478] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Phytopathogenic fungi such as the rice blast fungus Magnaporthe grisea are unique in having two catalase/peroxidase (KatG) paralogues located either intracellularly (KatG1) or extracellularly (KatG2). The coding genes have recently been shown to derive from a lateral gene transfer from a (proteo)bacterial genome followed by gene duplication and diversification. Here we demonstrate that KatG1 is expressed constitutively in M. grisea. It is the first eukaryotic catalase/peroxidase to be expressed heterologously in Escherichia coli in high amounts, with high purity and with almost 100% haem occupancy. Recombinant MagKatG1 is an acidic, mainly homodimeric, oxidoreductase with a predominant five-co-ordinated high-spin haem b. At 25 °C and pH 7.0, the E0′ (standard reduction potential) of the Fe(III)/Fe(II) couple was found to be −186±10 mV. It bound cyanide monophasically with an apparent bimolecular rate constant of (9.0±0.4)×105 M−1·s−1 at pH 7.0 and at 25 °C and with a Kd value of 1.5 μM. Its predominantly catalase activity was characterized by a pH optimum at 6.0 and kcat and Km values of 7010 s−1 and 4.8 mM respectively. In addition, it acts as a versatile peroxidase with a pH optimum in the range 5.0–5.5 using both one-electron [2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) o-dianisidine, pyrogallol or guaiacol] and two-electron (Br−, I− or ethanol) donors. Structure–function relationships are discussed with respect to data reported for prokaryotic KatGs, as is the physiological role of MagKatG1. Phylogenetic analysis suggests that (intracellular) MagKatG1 can be regarded as a typical representative for catalase/peroxidase of both phytopathogenic and saprotrophic fungi.
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Kiel JAKW, van den Berg MA, Fusetti F, Poolman B, Bovenberg RAL, Veenhuis M, van der Klei IJ. Matching the proteome to the genome: the microbody of penicillin-producing Penicillium chrysogenum cells. Funct Integr Genomics 2009; 9:167-84. [PMID: 19156454 DOI: 10.1007/s10142-009-0110-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 01/05/2009] [Accepted: 01/05/2009] [Indexed: 10/21/2022]
Abstract
In the filamentous fungus Penicillium chrysogenum, microbodies are essential for penicillin biosynthesis. To better understand the role of these organelles in antibiotics production, we determined the matrix enzyme contents of P. chrysogenum microbodies. Using a novel in silico approach, we first obtained a catalogue of 200 P. chrysogenum proteins with putative microbody targeting signals (PTSs). This included two orthologs of proteins involved in cephalosporin biosynthesis, which we demonstrate to be bona fide microbody matrix constituents. Subsequently, we performed a proteomics based inventory of P. chrysogenum microbody matrix proteins using nano-LC-MS/MS analysis. We identified 89 microbody proteins, 79 with a PTS, including the two known microbody-borne penicillin biosynthesis enzymes, isopenicillin N:acyl CoA acyltransferase and phenylacetyl-CoA ligase. Comparative analysis revealed that 69 out of 79 PTS proteins identified experimentally were in the reference list. A prominent microbody protein was identified as a novel fumarate reductase-cytochrome b5 fusion protein, which contains an internal PTS2 between the two functional domains. We show that this protein indeed localizes to P. chrysogenum microbodies.
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Affiliation(s)
- Jan A K W Kiel
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, AA Haren, The Netherlands.
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ATF-1 transcription factor regulates the expression of ccg-1 and cat-1 genes in response to fludioxonil under OS-2 MAP kinase in Neurospora crassa. Fungal Genet Biol 2008; 45:1562-9. [DOI: 10.1016/j.fgb.2008.09.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2008] [Revised: 09/12/2008] [Accepted: 09/24/2008] [Indexed: 11/16/2022]
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27
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Chagas RF, Bailão AM, Pereira M, Winters MS, Smullian AG, Deepe GS, de Almeida Soares CM. The catalases of Paracoccidioides brasiliensis are differentially regulated: protein activity and transcript analysis. Fungal Genet Biol 2008; 45:1470-8. [PMID: 18799136 DOI: 10.1016/j.fgb.2008.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 08/21/2008] [Accepted: 08/22/2008] [Indexed: 11/29/2022]
Abstract
Paracoccidioides brasiliensis is a fungal pathogen of humans. The P. brasiliensis response to oxidative stress is largely unexplored. We report the analysis of three catalases, PbCatA, PbCatP and PbCatC. The former are monofunctional catalases and the latter is a catalase-peroxidase. Differential expression of catalases as measured by activity and by quantitative analysis of transcripts was observed in the morphological conversion and in response to different stress conditions. PbCatA manifested higher activity in the mycelial phase, showed increased activity during transition from mycelium to yeast and during conditions of endogenous oxidative stress. Consistent with our previous studies, PbCatP manifested higher activity in yeast cells since it is putatively involved in the control of exogenous reactive oxygen species. P. brasiliensis displays an oxidative stress response following phagocytosis by macrophages, inducing the expression of catalase A and P transcripts. PbCatC displayed a relatively constant pattern of expression, being modestly induced in cells exposed to osmotic and heat stress.
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Affiliation(s)
- Ronney Fernandes Chagas
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
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28
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Würtz C, Schliebs W, Erdmann R, Rottensteiner H. Dynamin-like protein-dependent formation of Woronin bodies in Saccharomyces cerevisiae upon heterologous expression of a single protein. FEBS J 2008; 275:2932-41. [PMID: 18435762 DOI: 10.1111/j.1742-4658.2008.06430.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Filamentous ascomycetes harbor Woronin bodies and glyoxysomes, two types of microbodies, within one cell at the same time. The dominant protein of the Neurospora crassa Woronin body, HEX1, forms a hexagonal core crystal via oligomerization and evidence has accumulated that Woronin bodies bud off from glyoxysomes. We analyzed whether HEX1 is sufficient to induce Woronin body formation upon heterologous expression in Saccharomyces cerevisiae, an organism devoid of this specialized organelle. In wild-type strain BY4742, initial import of HEX1 into existing peroxisomes enabled the formation of organelles with a hexagonal crystal. The observed structures mimicked the shape of genuine Woronin bodies, but exhibited a lower density and were significantly larger. Double-immunofluorescence analysis revealed that hexagonal HEX1 structures only occasionally co-localized with peroxisomal marker proteins, indicating that the Woronin-body-like structures are well separated from peroxisomes. In cells lacking Vps1p and Dnm1p, dynamin-like proteins required for the division of peroxisomes, the Woronin-body-like organelles remained attached to peroxisomes. The data indicate that Woronin bodies emerge after the formation of a HEX1 core crystal within peroxisomes followed by Vps1p- and Dnm1p-mediated fission.
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Affiliation(s)
- Christian Würtz
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, Germany
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29
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Genetic analysis of the role of peroxisomes in the utilization of acetate and fatty acids in Aspergillus nidulans. Genetics 2008; 178:1355-69. [PMID: 18245820 DOI: 10.1534/genetics.107.085795] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peroxisomes are organelles containing a diverse array of enzymes. In fungi they are important for carbon source utilization, pathogenesis, development, and secondary metabolism. We have studied Aspergillus nidulans peroxin (pex) mutants isolated by virtue of their inability to grow on butyrate or by the inactivation of specific pex genes. While all pex mutants are able to form colonies, those unable to import PTS1 proteins are partially defective in asexual and sexual development. The pex mutants are able to grow on acetate but are affected in growth on fatty acids, indicating a requirement for the peroxisomal localization of beta-oxidation enzymes. However, mislocalization of malate synthase does not prevent growth on either fatty acids or acetate, showing that the glyoxylate cycle does not require peroxisomal localization. Proliferation of peroxisomes is dependent on fatty acids, but not on acetate, and on PexK (Pex11), expression of which is activated by the FarA transcription factor. Proliferation was greatly reduced in a farADelta strain. A mutation affecting a mitochodrial ketoacyl-CoA thiolase and disruption of a mitochondrial hydroxy-acyl-CoA dehydrogenase gene prevented growth on short-chain but not long-chain fatty acids. Together with previous results, this is consistent with growth on even-numbered short-chain fatty acids requiring a mitochondrial as well as a peroxisomal beta-oxidation pathway. The mitochondrial pathway is not required for growth on valerate or for long-chain fatty acid utilization.
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Yamashita K, Shiozawa A, Banno S, Fukumori F, Ichiishi A, Kimura M, Fujimura M. Involvement of OS-2 MAP kinase in regulation of the large-subunit catalases CAT-1 and CAT-3 in Neurospora crassa. Genes Genet Syst 2008; 82:301-10. [PMID: 17895581 DOI: 10.1266/ggs.82.301] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Neurospora crassa has four catalase genes--cat-1, cat-2, cat-3, and ctt-1/cat-4. cat-1 and cat-3 encode two fungal-specific large-subunit catalases CAT-1 and CAT-3 normally produced in conidia and growing hyphae, respectively. cat-2 encodes CAT-2 catalase-peroxidase normally produced in conidia. ctt-1 (or cat-4), of which expression was controlled by OS-2 MAP kinase (Noguchi et al., Fungal Genet. Biol. 44, 208-218), encodes a small-subunit catalase with unknown function. To clarify the contribution of OS-2 on the regulation of CAT-1, CAT-2, and CAT-3, we performed quantitative RT-PCR and in-gel catalase activity analyses. When the hyphae were treated with a fungicide (1 mug/ml fludioxonil) or subjected to an osmotic stress (1 M sorbitol), cat-1 was strongly upregulated and CAT-1 was reasonably induced in the wild-type strain. Interestingly, fludioxonil caused not only the CAT-1 induction but also a remarkable CAT-3 decrease in the wild-type hyphae, implying of an abnormal stimulation of asexual differentiation. These responses were not observed in an os-2 mutant hyphae, indicating an involvement of OS-2 in the cat-1 expression; however, os-2 was dispensable for the production of CAT-1 in conidia. In contrast, the expression of cat-2 was significantly induced by heat shock (45 degrees C) and that of cat-3 was moderately stimulated by an oxidative stress (50 microg/ml methyl viologen) in both the wild-type strain and the os-2 mutant, and corresponding enzyme activities were detected after the treatments. Although basal levels of transcription of cat-1 and cat-3 in an os-2 mutant hyphae were a few-fold lower than in the wild-type hyphae, the os-2 mutant exhibited a considerably lower levels of CAT-3 activity than the wild-type strain. These findings suggest that OS-2 MAP kinase regulated the expression of cat-1 and cat-3 transcriptionally, and probably that of cat-3 posttranscriptionally, even though the presence of another regulatory system for each of these two genes is evident.
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Cornell MJ, Alam I, Soanes DM, Wong HM, Hedeler C, Paton NW, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG. Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. Genes Dev 2007; 17:1809-22. [PMID: 17984228 PMCID: PMC2099590 DOI: 10.1101/gr.6531807] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 09/17/2007] [Indexed: 11/24/2022]
Abstract
The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions-empirically determined in Saccharomyces cerevisiae-among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi.
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Affiliation(s)
- Michael J. Cornell
- School of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Intikhab Alam
- School of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Darren M. Soanes
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Han Min Wong
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Cornelia Hedeler
- School of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Norman W. Paton
- School of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Magnus Rattray
- School of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Simon J. Hubbard
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Nicholas J. Talbot
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Stephen G. Oliver
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1 GA, United Kingdom
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32
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Gessler NN, Aver’yanov AA, Belozerskaya TA. Reactive oxygen species in regulation of fungal development. BIOCHEMISTRY (MOSCOW) 2007; 72:1091-109. [DOI: 10.1134/s0006297907100070] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Wang N, Yoshida Y, Hasunuma K. Catalase-1 (CAT-1) and nucleoside diphosphate kinase-1 (NDK-1) play an important role in protecting conidial viability under light stress in Neurospora crassa. Mol Genet Genomics 2007; 278:235-42. [PMID: 17636331 DOI: 10.1007/s00438-007-0244-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Accepted: 04/26/2007] [Indexed: 10/23/2022]
Abstract
Recently we reported that Catalase-1 (CAT-1) played an important role in protecting conidial viability in Neurospora crassa, and interacted with a light signal transducer, nucleoside diphosphate kinase-1 (NDK-1). To disclose the functional interaction between CAT-1 and NDK-1 at the genetic level, we created CAT-1 and NDK-1 double mutants, cat-1;ndk-1-1 and cat-1;ndk-1-2, by crossing single mutants of cat-1 ( RIP ) and ndk-1 ( P72H ) previously isolated in our laboratory. The double mutant strains grew normally, but showed increased CAT-2 activity. In cat-1 ( RIP ), NDK activity was increased when dCDP was used as a substrate. ndk-1 ( P72H ), cat-1;ndk-1-1, and cat-1;ndk-1-2 were more sensitive to riboflavin than the wild type and cat-1 ( RIP ) under strong light (100 microE m(-2) s(-1)). The pull-down experiment suggests that His-tagged NDK-1 is bound to [(32)P]NADH. However, his-tagged NDK-1(P72H) was not bound to [(32)P]NADH. The double mutants showed much lower conidial viability and lost all conidial germination ability much more rapidly than cat-1 ( RIP ), when they were cultured under continuous light for more than 2 weeks. These results indicate that the interaction of CAT-1 with NDK-1 plays an important role in supporting the survival of conidia under oxidative and light-induced stress including singlet oxygen, and confirm our former conclusion that reactive oxygen species play an important role in light signal transduction via NDK-1 at the genetic level.
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Affiliation(s)
- Niyan Wang
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama 244-0813, Japan
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Engh I, Würtz C, Witzel-Schlömp K, Zhang HY, Hoff B, Nowrousian M, Rottensteiner H, Kück U. The WW domain protein PRO40 is required for fungal fertility and associates with Woronin bodies. EUKARYOTIC CELL 2007; 6:831-43. [PMID: 17351077 PMCID: PMC1899833 DOI: 10.1128/ec.00269-06] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fruiting body formation in ascomycetes is a highly complex process that is under polygenic control and is a fundamental part of the fungal sexual life cycle. However, the molecular determinants regulating this cellular process are largely unknown. Here we show that the sterile pro40 mutant is defective in a 120-kDa WW domain protein that plays a pivotal role in fruiting body maturation of the homothallic ascomycete Sordaria macrospora. Although WW domains occur in many eukaryotic proteins, homologs of PRO40 are present only in filamentous ascomycetes. Complementation analysis with different pro40 mutant strains, using full-sized or truncated versions of the wild-type pro40 gene, revealed that the C terminus of PRO40 is crucial for restoring the fertile phenotype. Using differential centrifugation and protease protection assays, we determined that a PRO40-FLAG fusion protein is located within organelles. Further microscopic investigations of fusion proteins with DsRed or green fluorescent protein polypeptides showed a colocalization of PRO40 with HEX-1, a Woronin body-specific protein. However, the integrity of Woronin bodies is not affected in mutant strains of S. macrospora and Neurospora crassa, as shown by fluorescence microscopy, sedimentation, and immunoblot analyses. We discuss the function of PRO40 in fruiting body formation.
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Affiliation(s)
- Ines Engh
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstrasse 150, 44780 Bochum, Germany
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Idnurm A, Giles SS, Perfect JR, Heitman J. Peroxisome function regulates growth on glucose in the basidiomycete fungus Cryptococcus neoformans. EUKARYOTIC CELL 2006; 6:60-72. [PMID: 17041184 PMCID: PMC1800366 DOI: 10.1128/ec.00214-06] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The function of the peroxisomes was examined in the pathogenic basidiomycete Cryptococcus neoformans. Recent studies reveal the glyoxylate pathway is required for virulence of diverse microbial pathogens of plants and animals. One exception is C. neoformans, in which isocitrate lyase (encoded by ICL1) was previously shown not to be required for virulence, and here this was extended to exclude also a role for malate synthase (encoded by MLS1). The role of peroxisomes, in which the glyoxylate pathway enzymes are localized in many organisms, was examined by mutation of two genes (PEX1 and PEX6) encoding AAA (ATPases associated with various cellular activities)-type proteins required for peroxisome formation. The pex1 and pex6 deletion mutants were unable to localize the fluorescent DsRED-SKL protein to peroxisomal punctate structures, in contrast to wild-type cells. pex1 and pex6 single mutants and a pex1 pex6 double mutant exhibit identical phenotypes, including abolished growth on fatty acids but no growth difference on acetate. Because both icl1 and mls1 mutants are unable to grow on acetate as the sole carbon source, these findings demonstrate that the glyoxylate pathway can function efficiently outside the peroxisome in C. neoformans. The pex1 mutant exhibits wild-type virulence in a murine inhalation model and in an insect host, demonstrating that peroxisomes are not required for virulence under these conditions. An unusual phenotype of the pex1 and pex6 mutants was that they grew poorly with glucose as the carbon source, but nearly wild type with galactose, which suggested impaired hexokinase function and that C. neoformans peroxisomes might function analogously to the glycosomes of the trypanosomid parasites. Deletion of the hexokinase HXK2 gene reduced growth in the presence of glucose and suppressed the growth defect of the pex1 mutant on glucose. The hexokinase 2 protein of C. neoformans contains a predicted peroxisome targeting signal (type 2) motif; however, Hxk2 fused to fluorescent proteins was not localized to peroxisomes. Thus, we hypothesize that glucose or glycolytic metabolites are utilized in the peroxisome by an as yet unidentified enzyme or regulate a pathway required by the fungus in the absence of peroxisomes.
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Affiliation(s)
- Alexander Idnurm
- Room 322 CARL Building, Box 3546, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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