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Wang ZD, Wang BT, Jin L, Ruan HH, Jin FJ. Implications of carbon catabolite repression for Aspergillus-based cell factories: A review. Biotechnol J 2024; 19:e2300551. [PMID: 38403447 DOI: 10.1002/biot.202300551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 02/27/2024]
Abstract
Carbon catabolite repression (CCR) is a global regulatory mechanism that allows organisms to preferentially utilize a preferred carbon source (usually glucose) by suppressing the expression of genes associated with the utilization of nonpreferred carbon sources. Aspergillus is a large genus of filamentous fungi, some species of which have been used as microbial cell factories for the production of organic acids, industrial enzymes, pharmaceuticals, and other fermented products due to their safety, substrate convenience, and well-established post-translational modifications. Many recent studies have verified that CCR-related genetic alterations can boost the yield of various carbohydrate-active enzymes (CAZymes), even under CCR conditions. Based on these findings, we emphasize that appropriate regulation of the CCR pathway, especially the expression of the key transcription factor CreA gene, has great potential for further expanding the application of Aspergillus cell factories to develop strains for industrial CAZymes production. Further, the genetically modified CCR strains (chassis hosts) can also be used for the production of other useful natural products and recombinant proteins, among others. We here review the regulatory mechanisms of CCR in Aspergillus and its direct application in enzyme production, as well as its potential application in organic acid and pharmaceutical production to illustrate the effects of CCR on Aspergillus cell factories.
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Affiliation(s)
- Zhen-Dong Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Bao-Teng Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Long Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Hua Ruan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
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2
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Green VE, Klancher CA, Yamamoto S, Dalia AB. The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae. PLoS Genet 2023; 19:e1010767. [PMID: 37172034 PMCID: PMC10208484 DOI: 10.1371/journal.pgen.1010767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 05/24/2023] [Accepted: 04/30/2023] [Indexed: 05/14/2023] Open
Abstract
Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. In this niche, V. cholerae commonly interacts with the chitinous shells of crustacean zooplankton. As a chitinolytic microbe, V. cholerae degrades insoluble chitin into soluble oligosaccharides. Chitin oligosaccharides serve as both a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae. Namely, these oligosaccharides induce the chitin sensor, ChiS, to activate the genes required for chitin utilization and horizontal gene transfer by natural transformation. Thus, interactions with chitin impact the survival of V. cholerae in marine environments. Chitin is a complex carbon source for V. cholerae to degrade and consume, and the presence of more energetically favorable carbon sources can inhibit chitin utilization. This phenomenon, known as carbon catabolite repression (CCR), is mediated by the glucose-specific Enzyme IIA (EIIAGlc) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). In the presence of glucose, EIIAGlc becomes dephosphorylated, which inhibits ChiS transcriptional activity by an unknown mechanism. Here, we show that dephosphorylated EIIAGlc interacts with ChiS. We also isolate ChiS suppressor mutants that evade EIIAGlc-dependent repression and demonstrate that these alleles no longer interact with EIIAGlc. These findings suggest that EIIAGlc must interact with ChiS to exert its repressive effect. Importantly, the ChiS suppressor mutations we isolated also relieve repression of chitin utilization and natural transformation by EIIAGlc, suggesting that CCR of these behaviors is primarily regulated through ChiS. Together, our results reveal how nutrient conditions impact the fitness of an important human pathogen in its environmental reservoir.
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Affiliation(s)
- Virginia E. Green
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Catherine A. Klancher
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Shouji Yamamoto
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ankur B. Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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3
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Li S, Tang Y, Tang L, Yan X, Xiao J, Xiang H, Wu Q, Yu R, Jin Y, Yu J, Xu N, Wu C, Wang S, Wang C, Chen Q. Preliminary study on the effect of catabolite repression gene knockout on p-nitrophenol degradation in Pseudomonas putida DLL-E4. PLoS One 2022; 17:e0278503. [PMID: 36459525 PMCID: PMC9718395 DOI: 10.1371/journal.pone.0278503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Abstract
P-nitrophenol (PNP) is a carcinogenic, teratogenic, and mutagenic compound that can cause serious harm to the environment. A strain of Pseudomonas putida DLL-E4, can efficiently degrade PNP in a complex process that is influenced by many factors. Previous studies showed that the expression level of pnpA, a key gene involved in PNP degradation, was upregulated significantly and the degradation of PNP was obviously accelerated in the presence of glucose. In addition, the expression of crc, crcY, and crcZ, key genes involved in catabolite repression, was downregulated, upregulated, and upregulated, respectively. To investigate the effect of the carbon catabolite repression (CCR) system on PNP degradation, the crc, crcY, and crcZ genes were successfully knocked out by conjugation experiments. Our results showed that the knockout of crc accelerated PNP degradation but slowed down the cell growth. However, the knockout of crcY or crcZ alone accelerated PNP degradation when PNP as the sole carbon source, but that knockout slowed down PNP degradation when glucose was added. The results indicate that the CCR system is involved in the regulation of PNP degradation, and further work is required to determine the details of the specific regulatory mechanism.
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Affiliation(s)
- Shuang Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Yichao Tang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Lingran Tang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Xuanyu Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Jiali Xiao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Huijun Xiang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Qing Wu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Ruqi Yu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Yushi Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Jingyu Yu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Nuo Xu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Chu Wu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Shengqin Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Chuanhua Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
| | - Qiongzhen Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People’s Republic of China
- National and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, Wenzhou University, Wenzhou, People’s Republic of China
- * E-mail:
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4
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. Plant Commun 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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5
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Huberman LB, Wu VW, Kowbel DJ, Lee J, Daum C, Grigoriev IV, O'Malley RC, Glass NL. DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus. Proc Natl Acad Sci U S A 2021; 118:e2009501118. [PMID: 33753477 PMCID: PMC8020665 DOI: 10.1073/pnas.2009501118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors that activate genes necessary to utilize specific nitrogen sources in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of the nonpreferred nitrogen sources proline, branched-chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources, which require metabolic processing before being used as a nitrogen source, is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and the pathway-specific transcription factors NIT-4 and AMN-1 in directly regulating genes involved in nitrogen utilization. Although previous studies suggested promoter binding by both a pathway-specific transcription factor and NIT-2 may be necessary for activation of nitrogen-responsive genes, our data show that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization.
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Affiliation(s)
- Lori B Huberman
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720;
- Energy Biosciences Institute, University of California, Berkeley, CA 94720
| | - Vincent W Wu
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720
- Energy Biosciences Institute, University of California, Berkeley, CA 94720
| | - David J Kowbel
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Igor V Grigoriev
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Ronan C O'Malley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720;
- Energy Biosciences Institute, University of California, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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6
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de Assis LJ, Silva LP, Liu L, Schmitt K, Valerius O, Braus GH, Ries LNA, Goldman GH. The High Osmolarity Glycerol Mitogen-Activated Protein Kinase regulates glucose catabolite repression in filamentous fungi. PLoS Genet 2020; 16:e1008996. [PMID: 32841242 PMCID: PMC7473523 DOI: 10.1371/journal.pgen.1008996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/04/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
The utilization of different carbon sources in filamentous fungi underlies a complex regulatory network governed by signaling events of different protein kinase pathways, including the high osmolarity glycerol (HOG) and protein kinase A (PKA) pathways. This work unraveled cross-talk events between these pathways in governing the utilization of preferred (glucose) and non-preferred (xylan, xylose) carbon sources in the reference fungus Aspergillus nidulans. An initial screening of a library of 103 non-essential protein kinase (NPK) deletion strains identified several mitogen-activated protein kinases (MAPKs) to be important for carbon catabolite repression (CCR). We selected the MAPKs Ste7, MpkB, and PbsA for further characterization and show that they are pivotal for HOG pathway activation, PKA activity, CCR via regulation of CreA cellular localization and protein accumulation, as well as for hydrolytic enzyme secretion. Protein-protein interaction studies show that Ste7, MpkB, and PbsA are part of the same protein complex that regulates CreA cellular localization in the presence of xylan and that this complex dissociates upon the addition of glucose, thus allowing CCR to proceed. Glycogen synthase kinase (GSK) A was also identified as part of this protein complex and shown to potentially phosphorylate two serine residues of the HOG MAPKK PbsA. This work shows that carbon source utilization is subject to cross-talk regulation by protein kinases of different signaling pathways. Furthermore, this study provides a model where the correct integration of PKA, HOG, and GSK signaling events are required for the utilization of different carbon sources. Filamentous fungi secrete an array of biotechnologically valuable enzymes, with enzyme production being inhibited in the presence of preferred carbon sources, such as glucose, in a process known as carbon catabolite repression (CCR). This work unravels upstream signalling events that regulate CCR in Aspergillus nidulans. Different mitogen-activated protein kinases (MAPKs) were identified and shown to be crucial for CCR and protein kinase A (PKA) activity, which is essential for carbon source utilisation in filamentous fungi. Furthermore, the MAPKs formed a protein complex with additional protein kinases, such as glycogen synthase kinase (GSK), which is important for glucose metabolism; resulting in the inhibition of CCR in the presence of non-preferred carbon sources. GSK was shown to potentially phosphorylate the MAPK PbsA of the high osmolarity glycerol (HOG) pathway. This study thus unravels the cross-talk between protein kinases from different signalling pathways that regulate carbon source utilisation in filamentous fungi.
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Affiliation(s)
- Leandro José de Assis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Bloco Q, Universidade de São Paulo, Brazil
| | - Lilian Pereira Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Bloco Q, Universidade de São Paulo, Brazil
| | - Li Liu
- Department of Molecular Microbiology and Genetics and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- * E-mail: (GHB); (LNAR); (GHG)
| | - Laure Nicolas Annick Ries
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
- * E-mail: (GHB); (LNAR); (GHG)
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Bloco Q, Universidade de São Paulo, Brazil
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
- * E-mail: (GHB); (LNAR); (GHG)
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7
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Xu X, Fan C, Song L, Li J, Chen Y, Zhang Y, Liu B, Zhang W. A Novel CreA-Mediated Regulation Mechanism of Cellulase Expression in the Thermophilic Fungus Humicola insolens. Int J Mol Sci 2019; 20:ijms20153693. [PMID: 31357701 PMCID: PMC6696435 DOI: 10.3390/ijms20153693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
The thermophilic fungus Humicola insolens produces cellulolytic enzymes that are of great scientific and commercial interest; however, few reports have focused on its cellulase expression regulation mechanism. In this study, we constructed a creA gene (carbon catabolite repressor gene) disruption mutant strain of H. insolens that exhibited a reduced radial growth rate and stouter hyphae compared to the wild-type (WT) strain. The creA disruption mutant also expressed elevated pNPCase (cellobiohydrolase activities), pNPGase (β-glucosidase activities), and xylanase levels in non-inducing fermentation with glucose. Unlike other fungi, the H. insolenscreA disruption mutant displayed lower FPase (filter paper activity), CMCase (carboxymethyl cellulose activity), pNPCase, and pNPGase activity than observed in the WT strain when fermentation was induced using Avicel, whereas its xylanase activity was higher than that of the parental strain. These results indicate that CreA acts as a crucial regulator of hyphal growth and is part of a unique cellulase expression regulation mechanism in H. insolens. These findings provide a new perspective to improve the understanding of carbon catabolite repression regulation mechanisms in cellulase expression, and enrich the knowledge of metabolism diversity and molecular regulation of carbon metabolism in thermophilic fungi.
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Affiliation(s)
- Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Chao Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Liya Song
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, No.11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Jinyang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Yuan Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China.
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China.
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Pei XY, Dendooven T, Sonnleitner E, Chen S, Bläsi U, Luisi BF. Architectural principles for Hfq/Crc-mediated regulation of gene expression. eLife 2019; 8:e43158. [PMID: 30758287 PMCID: PMC6422490 DOI: 10.7554/elife.43158] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/11/2019] [Indexed: 12/24/2022] Open
Abstract
In diverse bacterial species, the global regulator Hfq contributes to post-transcriptional networks that control expression of numerous genes. Hfq of the opportunistic pathogen Pseudomonas aeruginosa inhibits translation of target transcripts by forming a regulatory complex with the catabolite repression protein Crc. This repressive complex acts as part of an intricate mechanism of preferred nutrient utilisation. We describe high-resolution cryo-EM structures of the assembly of Hfq and Crc bound to the translation initiation site of a target mRNA. The core of the assembly is formed through interactions of two cognate RNAs, two Hfq hexamers and a Crc pair. Additional Crc protomers are recruited to the core to generate higher-order assemblies with demonstrated regulatory activity in vivo. This study reveals how Hfq cooperates with a partner protein to regulate translation, and provides a structural basis for an RNA code that guides global regulators to interact cooperatively and regulate different RNA targets.
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Affiliation(s)
- Xue Yuan Pei
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Tom Dendooven
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F Perutz Laboratories, Center of Molecular BiologyUniversity of Vienna, Vienna BiocenterViennaAustria
| | - Shaoxia Chen
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F Perutz Laboratories, Center of Molecular BiologyUniversity of Vienna, Vienna BiocenterViennaAustria
| | - Ben F Luisi
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
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9
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Martínez-Valenzuela M, Guzmán J, Moreno S, Ahumada-Manuel CL, Espín G, Núñez C. Expression of the sRNAs CrcZ and CrcY modulate the strength of carbon catabolite repression under diazotrophic or non-diazotrophic growing conditions in Azotobacter vinelandii. PLoS One 2018; 13:e0208975. [PMID: 30543677 PMCID: PMC6292655 DOI: 10.1371/journal.pone.0208975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/28/2018] [Indexed: 12/25/2022] Open
Abstract
Azotobacter vinelandii is a nitrogen-fixing bacterium of the Pseudomonadaceae family that prefers the use of organic acids rather than carbohydrates. Thus, in a mixture of acetate-glucose, glucose is consumed only after acetate is exhausted. In a previous work, we investigated the molecular basis of this carbon catabolite repression (CCR) process under diazotrophic conditions. In the presence of acetate, Crc-Hfq inhibited translation of the gluP mRNA, encoding the glucose transporter in A. vinelandii. Herein, we investigated the regulation in the expression of the small non-coding RNAs (sRNAs) crcZ and crcY, which are known to antagonize the repressing activity of Hfq-Crc. Our results indicated higher expression levels of the sRNAs crcZ and crcY under low CCR conditions (i.e. glucose), in relation to the strong one (acetate one). In addition, we also explored the process of CCR in the presence of ammonium. Our results revealed that CCR also occurs under non-diazotrophic conditions as we detected a hierarchy in the utilization of the supplied carbon sources, which was consistent with the higher expression level of the crcZ/Y sRNAs during glucose catabolism. Analysis of the promoters driving transcription of crcZ and crcY confirmed that they were RpoN-dependent but we also detected a processed form of CrcZ (CrcZ*) in the RpoN-deficient strain derived from a cbrB-crcZ co-transcript. CrcZ* was functional and sufficient to allow the assimilation of acetate.
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Affiliation(s)
- Marcela Martínez-Valenzuela
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, México
| | - Josefina Guzmán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Carlos Leonel Ahumada-Manuel
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- * E-mail:
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Alcaíno J, Bravo N, Córdova P, Marcoleta AE, Contreras G, Barahona S, Sepúlveda D, Fernández-Lobato M, Baeza M, Cifuentes V. The Involvement of Mig1 from Xanthophyllomyces dendrorhous in Catabolic Repression: An Active Mechanism Contributing to the Regulation of Carotenoid Production. PLoS One 2016; 11:e0162838. [PMID: 27622474 PMCID: PMC5021340 DOI: 10.1371/journal.pone.0162838] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/29/2016] [Indexed: 11/18/2022] Open
Abstract
The red yeast X. dendrorhous is one of the few natural sources of astaxanthin, a carotenoid used in aquaculture for salmonid fish pigmentation and in the cosmetic and pharmaceutical industries for its antioxidant properties. Genetic control of carotenogenesis is well characterized in this yeast; however, little is known about the regulation of the carotenogenesis process. Several lines of evidence have suggested that carotenogenesis is regulated by catabolic repression, and the aim of this work was to identify and functionally characterize the X. dendrorhous MIG1 gene encoding the catabolic repressor Mig1, which mediates transcriptional glucose-dependent repression in other yeasts and fungi. The identified gene encodes a protein of 863 amino acids that demonstrates the characteristic conserved features of Mig1 proteins, and binds in vitro to DNA fragments containing Mig1 boxes. Gene functionality was demonstrated by heterologous complementation in a S. cerevisiae mig1- strain; several aspects of catabolic repression were restored by the X. dendrorhous MIG1 gene. Additionally, a X. dendrorhous mig1- mutant was constructed and demonstrated a higher carotenoid content than the wild-type strain. Most important, the mig1- mutation alleviated the glucose-mediated repression of carotenogenesis in X. dendrorhous: the addition of glucose to mig1- and wild-type cultures promoted the growth of both strains, but carotenoid synthesis was observed only in the mutant strain. Transcriptomic and RT-qPCR analyses revealed that several genes were differentially expressed between X. dendrorhous mig1- and the wild-type strain when cultured with glucose as the sole carbon source. The results obtained in this study demonstrate that catabolic repression in X. dendrorhous is an active process in which the identified MIG1 gene product plays a central role in the regulation of several biological processes, including carotenogenesis.
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Affiliation(s)
- Jennifer Alcaíno
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Natalia Bravo
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pamela Córdova
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Andrés E. Marcoleta
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Gabriela Contreras
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Salvador Barahona
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María Fernández-Lobato
- Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular (UAM-CSIC), Universidad Autónoma, Madrid, Cantoblanco, España
| | - Marcelo Baeza
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail:
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11
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Zhu M, Lu Y, Wang J, Li S, Wang X. Carbon Catabolite Repression and the Related Genes of ccpA, ptsH and hprK in Thermoanaerobacterium aotearoense. PLoS One 2015; 10:e0142121. [PMID: 26540271 PMCID: PMC4634974 DOI: 10.1371/journal.pone.0142121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/16/2015] [Indexed: 01/09/2023] Open
Abstract
The strictly anaerobic, Gram-positive bacterium, Thermoanaerobacterium aotearoense SCUT27, is capable of producing ethanol, hydrogen and lactic acid by directly fermenting glucan, xylan and various lignocellulosically derived sugars. By using non-metabolizable and metabolizable sugars as substrates, we found that cellobiose, galactose, arabinose and starch utilization was strongly inhibited by the existence of 2-deoxyglucose (2-DG). However, the xylose and mannose consumptions were not markedly affected by 2-DG at the concentration of one-tenth of the metabolizable sugar. Accordingly, T. aotearoense SCUT27 could consume xylose and mannose in the presence of glucose. The carbon catabolite repression (CCR) related genes, ccpA, ptsH and hprK were confirmed to exist in T. aotearoense SCUT27 through gene cloning and protein characterization. The highly purified Histidine-containing Protein (HPr) could be specifically phosphorylated at Serine 46 by HPr kinase/phosphatase (HPrK/P) with no need to add fructose-1,6-bisphosphate (FBP) or glucose-6-phosphate (Glc-6-P) in the reaction mixture. The specific protein-interaction of catabolite control protein A (CcpA) and phosphorylated HPr was proved via affinity chromatography in the absence of formaldehyde. The equilibrium binding constant (KD) of CcpA and HPrSerP was determined as 2.22 ± 0.36 nM by surface plasmon resonance (SPR) analysis, indicating the high affinity between these two proteins.
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Affiliation(s)
- Muzi Zhu
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Yanping Lu
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
- * E-mail:
| | - Xiaoning Wang
- State Key Laboratory of Kidney, the Institute of Life Sciences, Chinese PLA General Hospital, Beijing, China
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Xiong Y, Sun J, Glass NL. VIB1, a link between glucose signaling and carbon catabolite repression, is essential for plant cell wall degradation by Neurospora crassa. PLoS Genet 2014; 10:e1004500. [PMID: 25144221 PMCID: PMC4140635 DOI: 10.1371/journal.pgen.1004500] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/27/2014] [Indexed: 11/18/2022] Open
Abstract
Filamentous fungi that thrive on plant biomass are the major producers of hydrolytic enzymes used to decompose lignocellulose for biofuel production. Although induction of cellulases is regulated at the transcriptional level, how filamentous fungi sense and signal carbon-limited conditions to coordinate cell metabolism and regulate cellulolytic enzyme production is not well characterized. By screening a transcription factor deletion set in the filamentous fungus Neurospora crassa for mutants unable to grow on cellulosic materials, we identified a role for the transcription factor, VIB1, as essential for cellulose utilization. VIB1 does not directly regulate hydrolytic enzyme gene expression or function in cellulosic inducer signaling/processing, but affects the expression level of an essential regulator of hydrolytic enzyme genes, CLR2. Transcriptional profiling of a Δvib-1 mutant suggests that it has an improper expression of genes functioning in metabolism and energy and a deregulation of carbon catabolite repression (CCR). By characterizing new genes, we demonstrate that the transcription factor, COL26, is critical for intracellular glucose sensing/metabolism and plays a role in CCR by negatively regulating cre-1 expression. Deletion of the major player in CCR, cre-1, or a deletion of col-26, did not rescue the growth of Δvib-1 on cellulose. However, the synergistic effect of the Δcre-1; Δcol-26 mutations circumvented the requirement of VIB1 for cellulase gene expression, enzyme secretion and cellulose deconstruction. Our findings support a function of VIB1 in repressing both glucose signaling and CCR under carbon-limited conditions, thus enabling a proper cellular response for plant biomass deconstruction and utilization.
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Affiliation(s)
- Yi Xiong
- Plant and Microbial Biology Department and The Energy Biosciences Institute, The University of California, Berkeley, Berkeley, California, United States of America
| | - Jianping Sun
- Plant and Microbial Biology Department and The Energy Biosciences Institute, The University of California, Berkeley, Berkeley, California, United States of America
| | - N. Louise Glass
- Plant and Microbial Biology Department and The Energy Biosciences Institute, The University of California, Berkeley, Berkeley, California, United States of America
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13
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Abstract
Carbon Catabolite repression (CCR) allows a fast adaptation of Bacteria to changing nutrient supplies. The Pseudomonas aeruginosa (PAO1) catabolite repression control protein (Crc) was deemed to act as a translational regulator, repressing functions involved in uptake and utilization of carbon sources. However, Crc of PAO1 was recently shown to be devoid of RNA binding activity. In this study the RNA chaperone Hfq was identified as the principle post-transcriptional regulator of CCR in PAO1. Hfq is shown to bind to A-rich sequences within the ribosome binding site of the model mRNA amiE, and to repress translation in vitro and in vivo. We further report that Crc plays an unknown ancillary role, as full-fledged repression of amiE and other CCR-regulated mRNAs in vivo required its presence. Moreover, we show that the regulatory RNA CrcZ, transcription of which is augmented when CCR is alleviated, binds to Hfq with high affinity. This study on CCR in PAO1 revealed a novel concept for Hfq function, wherein the regulatory RNA CrcZ acts as a decoy to abrogate Hfq-mediated translational repression of catabolic genes and thus highlights the central role of RNA based regulation in CCR of PAO1. Carbon assimilation in Bacteria is governed by a mechanism known as carbon catabolite repression (CCR). In contrast to several other bacterial clades CCR in Pseudomonas species appears to be primarily regulated at the post-transcriptional level. In this study, we have identified the RNA chaperone Hfq as the principle post-transcriptional regulator of CCR in P. aeruginosa (PAO1). Hfq is shown to act as a translational regulator and to prevent ribosome loading through binding to A-rich sequences within the ribosome binding site of mRNAs, which encode enzymes involved in carbon utilization. It has been previously shown that the synthesis of the RNA CrcZ is augmented in the presence of non-preferred carbon sources. Here, we show that the CrcZ RNA binds to and sequesters Hfq, which in turn abrogates Hfq-mediated translational repression of mRNAs, the encoded functions of which are required for the breakdown of non-preferred carbon sources. This novel mechanistic twist on Hfq function not only highlights the central role of RNA based regulation in CCR of PAO1 but also broadens the view of Hfq-mediated post-transcriptional mechanisms.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna, Austria
- * E-mail: (ES); (UB)
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna, Austria
- * E-mail: (ES); (UB)
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Forment JV, Flipphi M, Ventura L, González R, Ramón D, MacCabe AP. High-affinity glucose transport in Aspergillus nidulans is mediated by the products of two related but differentially expressed genes. PLoS One 2014; 9:e94662. [PMID: 24751997 PMCID: PMC3994029 DOI: 10.1371/journal.pone.0094662] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/18/2014] [Indexed: 11/18/2022] Open
Abstract
Independent systems of high and low affinity effect glucose uptake in the filamentous fungus Aspergillus nidulans. Low-affinity uptake is known to be mediated by the product of the mstE gene. In the current work two genes, mstA and mstC, have been identified that encode high-affinity glucose transporter proteins. These proteins' primary structures share over 90% similarity, indicating that the corresponding genes share a common origin. Whilst the function of the paralogous proteins is little changed, they differ notably in their patterns of expression. The mstC gene is expressed during the early phases of germination and is subject to CreA-mediated carbon catabolite repression whereas mstA is expressed as a culture tends toward carbon starvation. In addition, various pieces of genetic evidence strongly support allelism of mstC and the previously described locus sorA. Overall, our data define MstC/SorA as a high-affinity glucose transporter expressed in germinating conidia, and MstA as a high-affinity glucose transporter that operates in vegetative hyphae under conditions of carbon limitation.
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Affiliation(s)
- Josep V. Forment
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michel Flipphi
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Luisa Ventura
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Ramón González
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Daniel Ramón
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- Biopolis SL, Parc Cientific Universitat de València, Paterna, Valencia, Spain
| | - Andrew P. MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
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15
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Krin E, Cambray G, Mazel D. The superintegron integrase and the cassette promoters are co-regulated in Vibrio cholerae. PLoS One 2014; 9:e91194. [PMID: 24614503 PMCID: PMC3948777 DOI: 10.1371/journal.pone.0091194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/10/2014] [Indexed: 12/23/2022] Open
Abstract
Chromosome 2 of Vibrio cholerae carries a chromosomal superintegron, composed of an integrase, a cassette integration site (attI) and an array of mostly promoterless gene cassettes. We determined the precise location of the promoter, Pc, which drives the transcription of the first cassettes of the V. cholerae superintegron. We found that cassette mRNA starts 65 bp upstream of the attI site, so that the inversely oriented promoters Pc and Pint (integrase promoter) partly overlap, allowing for their potential co-regulation. Pint was previously shown to be induced during the SOS response and is further controlled by the catabolite repression cAMP-CRP complex. We found that cassette expression from Pc was also controlled by the cAMP-CRP complex, but is not part of the SOS regulon. Pint and Pc promoters were both found to be induced in rich medium, at high temperature, high salinity and at the end of exponential growth phase, although at very different levels and independently of sigma factor RpoS. All these results show that expression from the integrase and cassette promoters can take place at the same time, thus leading to coordinated excisions and integrations within the superintegron and potentially coupling cassette shuffling to immediate selective advantage.
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Affiliation(s)
- Evelyne Krin
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, UMR 3525, Paris, France
| | - Guillaume Cambray
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, UMR 3525, Paris, France
- * E-mail:
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16
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Oh BR, Hong WK, Heo SY, Luo LH, Kondo A, Seo JW, Kim CH. The production of 1,3-propanediol from mixtures of glycerol and glucose by a Klebsiella pneumoniae mutant deficient in carbon catabolite repression. Bioresour Technol 2013; 130:719-724. [PMID: 23334032 DOI: 10.1016/j.biortech.2012.12.076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 06/01/2023]
Abstract
In the present study, mutant strain of Klebsiella pneumoniae with deletion of the crr gene encoding EIIA(Glc) (a component of the glucose-specific phosphoenolpyruvate-dependent transferase system [PTS]) was prepared. This eliminated the ability of the strain to mediate carbon catabolite repression (CCR). Production of 1,3-propanediol (1,3-PD) from glycerol by the crr mutant strain was enhanced (compared to that of the parent) in the presence of glucose. Using molasses as a co-substrate of glycerol, the maximum yield of 1,3-PD was 60.4% greater (81.2g/l) than that obtained when glycerol was used alone, under optimum fermentation conditions.
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Affiliation(s)
- Baek-Rock Oh
- Applied Microbiology Research Center, Bio-Materials Research Institute, KRIBB, Jeongeup, Jeonbuk 580-185, South Korea
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Tomás-Gallardo L, Santero E, Floriano B. Involvement of a putative cyclic amp receptor protein (CRP)-like binding sequence and a CRP-like protein in glucose-mediated catabolite repression of thn genes in Rhodococcus sp. strain TFB. Appl Environ Microbiol 2012; 78:5460-2. [PMID: 22636000 PMCID: PMC3416400 DOI: 10.1128/aem.00700-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/16/2012] [Indexed: 11/20/2022] Open
Abstract
Glucose catabolite repression of tetralin catabolic genes in Rhodococcus sp. strain TFB was shown to be exerted by a protein homologous to transcriptional regulators of the cyclic AMP receptor (CRP)-FNR family. The protein was detected bound to putative CRP-like boxes localized at the promoters of the thnA1 and thnS genes.
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Affiliation(s)
- Laura Tomás-Gallardo
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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18
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Fernandez J, Wright JD, Hartline D, Quispe CF, Madayiputhiya N, Wilson RA. Principles of carbon catabolite repression in the rice blast fungus: Tps1, Nmr1-3, and a MATE-family pump regulate glucose metabolism during infection. PLoS Genet 2012; 8:e1002673. [PMID: 22570632 PMCID: PMC3342947 DOI: 10.1371/journal.pgen.1002673] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 03/12/2012] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic pathways that regulate how pathogenic fungi respond to their environment is paramount to developing effective mitigation strategies against disease. Carbon catabolite repression (CCR) is a global regulatory mechanism found in a wide range of microbial organisms that ensures the preferential utilization of glucose over less favourable carbon sources, but little is known about the components of CCR in filamentous fungi. Here we report three new mediators of CCR in the devastating rice blast fungus Magnaporthe oryzae: the sugar sensor Tps1, the Nmr1-3 inhibitor proteins, and the multidrug and toxin extrusion (MATE)–family pump, Mdt1. Using simple plate tests coupled with transcriptional analysis, we show that Tps1, in response to glucose-6-phosphate sensing, triggers CCR via the inactivation of Nmr1-3. In addition, by dissecting the CCR pathway using Agrobacterium tumefaciens-mediated mutagenesis, we also show that Mdt1 is an additional and previously unknown regulator of glucose metabolism. Mdt1 regulates glucose assimilation downstream of Tps1 and is necessary for nutrient utilization, sporulation, and pathogenicity. This is the first functional characterization of a MATE–family protein in filamentous fungi and the first description of a MATE protein in genetic regulation or plant pathogenicity. Perturbing CCR in Δtps1 and MDT1 disruption strains thus results in physiological defects that impact pathogenesis, possibly through the early expression of cell wall–degrading enzymes. Taken together, the importance of discovering three new regulators of carbon metabolism lies in understanding how M. oryzae and other pathogenic fungi respond to nutrient availability and control development during infection. To succeed as pathogens, fungi such as the rice blast fungus M. oryzae must adapt their metabolism to nutrient availability within the host, but little is known about the genetic regulatory mechanisms involved. M. oryzae destroys enough rice to feed 60 million people annually, and understanding how the infection process is controlled would afford new targets for anti-rice blast strategies and shed light on regulatory pathways common to other pathogenic fungi. Here we use M. oryzae to identify and describe three new regulators of global carbon metabolism in filamentous fungi: the sugar-sensor Tps1; the transcription factor inhibitor proteins Nmr1-3; and a transmembrane efflux pump Mdt1 (the first pump of its type to be described in pathogenic filamentous fungi), which is essential for sporulation and pathogenicity. Tps1, Nmr1-3, and Mdt1 are shown to control the fungal response to glucose availability, and perturbation of this regulatory pathway abolishes disease. This work gives fresh insights into nutrient adaptation and the control of fungal development during infection and is thus applicable to a wide range of fungal pathogens.
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Affiliation(s)
- Jessie Fernandez
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
| | - Janet D. Wright
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
| | - David Hartline
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
| | - Cristian F. Quispe
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
| | - Nandakumar Madayiputhiya
- Proteomic and Metabolomic Core Facility, Redox Biology Center, Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
| | - Richard A. Wilson
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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19
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Chulkin AM, Vavilova EA, Benevolenskiĭ SV. [The mutational analysis of carbon catabolite repression in filamentous fungus Penicillium canescens]. Mol Biol (Mosk) 2011; 45:871-878. [PMID: 22393784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Penicillium canescens strain F178 is a natural producer of beta-galactosidase and endo-1,4-beta-xylanase. The transcription of genes bgaS and xylA, coding for these proteins, is subject to carbon catabolite repression. The system for selective isolation of regulatory mutants in P. canescens is developed. Two strains from the mutant collection are studied in details. It is shown that both mutations can be complement by creA gene of P. canescens, encoding global regulator of carbon catabolite repression in filamentous fungi. creA(-) alleles contain frameshift mutations in C-domain of CreA. Gene xylA is derepressed in mutants at transcription level in the presence of D-glucose. A transcription of creA gene in mutants is also derepressed proving effect of autoregulation for this gene.
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