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Jenkinson CB, Lin SY, Villarreal M, Oakley CE, Sherman DH, Lee CK, Wang CCC, Oakley BR. Discovery of Uncommon Tryptophan-Containing Diketopiperazines from Aspergillus homomorphus CBS 101889 Using an Aspergillus nidulans Heterologous Expression System. JOURNAL OF NATURAL PRODUCTS 2024; 87:1704-1713. [PMID: 38990199 DOI: 10.1021/acs.jnatprod.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Fungal secondary metabolite (SM) biosynthetic gene clusters (BGCs) containing dimethylallyltryptophan synthases (DMATSs) produce structurally diverse prenylated indole alkaloids with wide-ranging activities that have vast potential as human therapeutics. To discover new natural products produced by DMATSs, we mined the Department of Energy Joint Genome Institute's MycoCosm database for DMATS-containing BGCs. We found a DMATS BGC in Aspergillus homomorphus CBS 101889, which also contains a nonribosomal peptide synthetase (NRPS). This BGC appeared to have a previously unreported combination of genes, which suggested the cluster might make novel SMs. We refactored this BGC with highly inducible promoters into the model fungus Aspergillus nidulans. The expression of this refactored BGC in A. nidulans resulted in the production of eight tryptophan-containing diketopiperazines, six of which are new to science. We have named them homomorphins A-F (2, 4-8). Perhaps even more intriguingly, to our knowledge, this is the first discovery of C4-prenylated tryptophan-containing diketopiperazines and their derivatives. In addition, the NRPS from this BGC is the first described that has the ability to promiscuously combine tryptophan with either of two different amino acids, in this case, l-valine or l-allo-isoleucine.
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Affiliation(s)
- Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Shu-Yi Lin
- School of Pharmacy, National Defense Medical Center, Taipei, 11490, Taiwan
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Mary Villarreal
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ching-Kuo Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
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2
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Kourkoulou A, Martzoukou O, Fischer R, Amillis S. A type II phosphatidylinositol-4-kinase coordinates sorting of cargo polarizing by endocytic recycling. Commun Biol 2024; 7:855. [PMID: 38997419 PMCID: PMC11245547 DOI: 10.1038/s42003-024-06553-3] [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] [Received: 10/30/2023] [Accepted: 07/04/2024] [Indexed: 07/14/2024] Open
Abstract
Depending on their phosphorylation status, derivatives of phosphatidylinositol play important roles in vesicle identity, recognition and intracellular trafficking processes. In eukaryotic cells, phosphatidylinositol-4 phosphate pools generated by specific kinases are key determinants of the conventional secretion pathways. Earlier work in yeast has classified phosphatidylinositol-4 kinases in two types, Stt4p and Pik1p belonging to type III and Lsb6p to type II, with distinct cellular localizations and functions. Eurotiomycetes appear to lack Pik1p homologues. In Aspergillus nidulans, unlike homologues in other fungi, AnLsb6 is associated to late Golgi membranes and when heterologously overexpressed, it compensates for the thermosensitive phenotype in a Saccharomyces cerevisiae pik1 mutant, whereas its depletion leads to disorganization of Golgi-associated PHOSBP-labelled membranes, that tend to aggregate dependent on functional Rab5 GTPases. Evidence provided herein, indicates that the single type II phosphatidylinositol-4 kinase AnLsb6 is the main contributor for decorating secretory vesicles with relevant phosphatidylinositol-phosphate species, which navigate essential cargoes following the route of apical polarization via endocytic recycling.
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Affiliation(s)
- Anezia Kourkoulou
- National and Kapodistrian University of Athens, Department of Biology, Athens, Hellas, Greece
| | - Olga Martzoukou
- National and Kapodistrian University of Athens, Department of Biology, Athens, Hellas, Greece
| | - Reinhard Fischer
- Karlsruhe Institute of Technology - South Campus, Institute for Applied Biosciences, Department of Microbiology, Karlsruhe, Germany
| | - Sotiris Amillis
- National and Kapodistrian University of Athens, Department of Biology, Athens, Hellas, Greece.
- Karlsruhe Institute of Technology - South Campus, Institute for Applied Biosciences, Department of Microbiology, Karlsruhe, Germany.
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3
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Yamamoto R, Miki H, Itani A, Takeshita N. Hyphae of the fungus Aspergillus nidulans demonstrate chemotropism to nutrients and pH. PLoS Biol 2024; 22:e3002726. [PMID: 39078817 PMCID: PMC11288418 DOI: 10.1371/journal.pbio.3002726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
The importance of fungi in ecological systems and pathogenicity hinges on their ability to search for nutrients, substrates, and hosts. Despite this, the question of whether fungal hyphae exhibit chemotropism toward them remains largely unresolved and requires close examination at the cellular level. Here, we designed a microfluidic device to assess hyphal chemotropism of Aspergillus nidulans in response to carbon and nitrogen sources, as well as pH. Within this device, hyphae could determine their growth direction in a two-layer flow with distinct compositions that were adjacent but non-mixing. Under conditions with and without a carbon source, hyphae changed growth direction to remain in the presence of a carbon source, but it was still difficult to distinguish between differences in growth and chemotropism. Although nitrogen sources such as ammonia and nitrate are important for growth, the hyphae indicated negative chemotropism to avoid them depending on the specific transporters. This fungus grows equally well at the colony level in the pH range of 4 to 9, but the hyphae exhibited chemotropism to acidic pH. The proton pump PmaA is vital for the chemotropism to acid pH, while the master regulatory for pH adaptation PacC is not involved, suggesting that chemotropism and adaptive growth via gene expression regulation are distinct regulatory mechanisms. Despite various plasma membrane transporters are distributed across membranes except at the hyphal tip, the control of growth direction occurs at the tip. Finally, we explored the mechanisms linking these two phenomena, tip growth and chemotropism.
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Affiliation(s)
- Riho Yamamoto
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hinata Miki
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ayaka Itani
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Yu X, Ma C, Wang W, Ge J, Wang Z, Lin J, Che Q, Zhang G, Zhu T, Li D. Genome Mining Reveals a UbiA-Type Prenyltransferase Access to Farnesylation of Diketopiperazines. Org Lett 2024; 26:3349-3354. [PMID: 38607994 DOI: 10.1021/acs.orglett.4c00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
UbiA-type prenyltransferases (PTases) are significant enzymes that lead to structurally diverse meroterpenoids. Herein, we report the identification and characterization of an undescribed UbiA-type PTase, FtaB, that is responsible for the farnesylation of indole-containing diketopiperazines (DKPs) through genome mining. Heterologous expression of the fta gene cluster and non-native pathways result in the production of a series of new C2-farnesylated DKPs. This study broadens the reaction scope of UbiA-type PTases and expands the chemical diversity of meroterpenoids.
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Affiliation(s)
- Xiaotian Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Chuanteng Ma
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Wenxue Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Jing Ge
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zian Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Jiaqi Lin
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Qian Che
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Guojian Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao 266237, People's Republic of China
| | - Tianjiao Zhu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
- Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, People's Republic of China
| | - Dehai Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao 266237, People's Republic of China
- Sanya Oceanographic Institute, Ocean University of China, Sanya 572025, People's Republic of China
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Zhang J, Qiu R, Xie S, Rasmussen M, Xiang X. VezA/vezatin facilitates proper assembly of the dynactin complex in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590248. [PMID: 38659795 PMCID: PMC11042379 DOI: 10.1101/2024.04.19.590248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cytoplasmic dynein-mediated intracellular transport needs the multi-component dynactin complex for cargo binding and motor activation. However, cellular factors involved in dynactin assembly remain unexplored. Here we found in Aspergillus nidulans that the vezatin homolog VezA is important for dynactin assembly. VezA affects the microtubule plus-end accumulation of dynein before cargo binding and cargo adapter-mediated dynein activation, two processes that both need dynactin. The dynactin complex contains multiple components including an Arp1 (actin-related protein 1) mini-filament associated with a pointed-end sub-complex. VezA physically interacts with dynactin either directly or indirectly via the Arp1 mini-filament and its pointed-end sub-complex. Loss of VezA causes a defect in dynactin integrity, most likely by affecting the connection between the Arp1 mini-filament and its pointed-end sub-complex. Using various dynactin mutants, we further revealed that assembly of the dynactin complex must be highly coordinated. Together, these results shed important new light on dynactin assembly in vivo.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
| | - Rongde Qiu
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
| | - Sean Xie
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
- Montgomery Blair High School, Silver Spring, Maryland, USA
| | - Megan Rasmussen
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
| | - Xin Xiang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
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6
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Picazo I, Espeso EA. Interconnections between the Cation/Alkaline pH-Responsive Slt and the Ambient pH Response of PacC/Pal Pathways in Aspergillus nidulans. Cells 2024; 13:651. [PMID: 38607089 PMCID: PMC11011638 DOI: 10.3390/cells13070651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
In the filamentous ascomycete Aspergillus nidulans, at least three high hierarchy transcription factors are required for growth at extracellular alkaline pH: SltA, PacC and CrzA. Transcriptomic profiles depending on alkaline pH and SltA function showed that pacC expression might be under SltA regulation. Additional transcriptional studies of PacC and the only pH-regulated pal gene, palF, confirmed both the strong dependence on ambient pH and the function of SltA. The regulation of pacC expression is dependent on the activity of the zinc binuclear (C6) cluster transcription factor PacX. However, we found that the ablation of sltA in the pacX- mutant background specifically prevents the increase in pacC expression levels without affecting PacC protein levels, showing a novel specific function of the PacX factor. The loss of sltA function causes the anomalous proteolytic processing of PacC and a reduction in the post-translational modifications of PalF. At alkaline pH, in a null sltA background, PacC72kDa accumulates, detection of the intermediate PacC53kDa form is extremely low and the final processed form of 27 kDa shows altered electrophoretic mobility. Constitutive ubiquitination of PalF or the presence of alkalinity-mimicking mutations in pacC, such as pacCc14 and pacCc700, resembling PacC53kDa and PacC27kDa, respectively, allowed the normal processing of PacC but did not rescue the alkaline pH-sensitive phenotype caused by the null sltA allele. Overall, data show that Slt and PacC/Pal pathways are interconnected, but the transcription factor SltA is on a higher hierarchical level than PacC on regulating the tolerance to the ambient alkalinity in A. nidulans.
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Affiliation(s)
| | - Eduardo A. Espeso
- Department of Molecular and Cellular Biology, Centro de Investigaciones Biológicas (CIB) Margarita Salas, Spanish Research Council (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain;
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7
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Lu M, Billerbeck S. Improving homology-directed repair by small molecule agents for genetic engineering in unconventional yeast?-Learning from the engineering of mammalian systems. Microb Biotechnol 2024; 17:e14398. [PMID: 38376092 PMCID: PMC10878012 DOI: 10.1111/1751-7915.14398] [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: 08/30/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
The ability to precisely edit genomes by deleting or adding genetic information enables the study of biological functions and the building of efficient cell factories. In many unconventional yeasts, such as those promising new hosts for cell factory design but also human pathogenic yeasts and food spoilers, this progress has been limited by the fact that most yeasts favour non-homologous end joining (NHEJ) over homologous recombination (HR) as a DNA repair mechanism, impairing genetic access to these hosts. In mammalian cells, small molecules that either inhibit proteins involved in NHEJ, enhance protein function in HR, or arrest the cell cycle in HR-dominant phases are regarded as promising agents for the simple and transient increase of HR-mediated genome editing without the need for a priori host engineering. Only a few of these chemicals have been applied to the engineering of yeast, although the targeted proteins are mostly conserved, making chemical agents a yet-underexplored area for enhancing yeast engineering. Here, we consolidate knowledge of the available small molecules that have been used to improve HR efficiency in mammalian cells and the few ones that have been used in yeast. We include available high-throughput-compatible NHEJ/HR quantification assays that could be used to screen for and isolate yeast-specific inhibitors.
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Affiliation(s)
- Min Lu
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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8
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Oakley CE, Barton TS, Oakley BR. Identification of the chaA and fwA Spore Color Genes of Aspergillus nidulans. J Fungi (Basel) 2024; 10:104. [PMID: 38392776 PMCID: PMC10890192 DOI: 10.3390/jof10020104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Wild-type Aspergillus nidulans asexual spores (conidia) are green due to a pigment that protects the spores against ultraviolet light. The pigment is produced by a biosynthetic pathway, the genes of which are dispersed in the genome. The backbone molecule of the pigment is a polyketide synthesized by a polyketide synthase encoded by the wA gene. If wA is not functional, the conidia are white. The polyketide is modified by a laccase encoded by the yA gene and inactivation of yA in an otherwise wild-type background results in yellow spores. Additional spore color mutations have been isolated and mapped to a locus genetically, but the genes that correspond to these loci have not been determined. Spore color markers have been useful historically, and they remain valuable in the molecular genetics era. One can determine if a transforming fragment has been successfully integrated at the wA or yA locus by simply looking at the color of transformant conidia. The genes of the potentially useful color loci chaA (chartreuse conidia) and fwA (fawn conidia) have not been identified previously. We chose a set of candidate genes for each locus by comparing the assembled genome with the genetic map. By systematically deleting these candidate genes, we identified a cytochrome P450 gene (AN10028) corresponding to chaA. Deletions of this gene result in chartreuse conidia and chartreuse mutations can be complemented in trans by a functional copy of this gene. With fwA, we found that the existing fawn mutation, fwA1, is a deletion of 2241 base pairs that inactivates three genes. By deleting each of these genes, we determined that fwA is AN1088, an EthD domain protein. Deletion of AN1088 results in fawn conidia as expected. Neither deletion of chaA nor fwA restricts growth and both should be valuable target loci for transformations. Combinations of deletions have allowed us to investigate the epistasis relationships of wA, yA, chaA and fwA.
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Affiliation(s)
- C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave., Lawrence, KS 66045, USA
| | - Thomas S Barton
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave., Lawrence, KS 66045, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave., Lawrence, KS 66045, USA
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Amahisa M, Tsukagoshi M, Kadooka C, Masuo S, Takeshita N, Doi Y, Takagi H, Takaya N. The Metabolic Regulation of Amino Acid Synthesis Counteracts Reactive Nitrogen Stress via Aspergillus nidulans Cross-Pathway Control. J Fungi (Basel) 2024; 10:58. [PMID: 38248967 PMCID: PMC10817288 DOI: 10.3390/jof10010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
Nitric oxide (NO) is a natural reactive nitrogen species (RNS) that alters proteins, DNA, and lipids and damages biological activities. Although microorganisms respond to and detoxify NO, the regulation of the cellular metabolic mechanisms that cause cells to tolerate RNS toxicity is not completely understood. We found that the proline and arginine auxotrophic proA5 and argB2 mutants of the fungus Aspergillus nidulans require more arginine and proline for normal growth under RNS stress that starves cells by accumulating fewer amino acids. Fungal transcriptomes indicated that RNS stress upregulates the expression of the biosynthetic genes required for global amino acids, including proline and arginine. A mutant of the gene disruptant, cpcA, which encodes the transcriptional regulation of the cross-pathway control of general amino acid synthesis, did not induce these genes, and cells accumulated fewer amino acids under RNS stress. These results indicated a novel function of CpcA in the cellular response to RNS stress, which is mediated through amino acid starvation and induces the transcription of genes for general amino acid synthesis. Since CpcA also controls organic acid biosynthesis, impaired intermediates of such biosynthesis might starve cells of amino acids. These findings revealed the importance of the mechanism regulating amino acid homeostasis for fungal responses to and survival under RNS stress.
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Affiliation(s)
- Madoka Amahisa
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Madoka Tsukagoshi
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Chihiro Kadooka
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Norio Takeshita
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Yuki Doi
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
| | - Hiroshi Takagi
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan;
| | - Naoki Takaya
- Microbiology Research Center for Sustainability, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan; (M.A.); (C.K.); (S.M.); (N.T.); (Y.D.)
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10
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Garrido-Bazán V, Guzmán-Ocampo DC, Domínguez L, Aguirre J. Filamentous actin destabilization by H 2O 2 favors DnmA aggregation, with crucial roles of cysteines 450 and 776 in mitochondrial and peroxisomal division in Aspergillus nidulans. mBio 2023; 14:e0282223. [PMID: 38014993 PMCID: PMC10746283 DOI: 10.1128/mbio.02822-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Mitochondria constitute major sources of H2O2 and other reactive oxygen species in eukaryotic cells. The division of these organelles is crucial for multiple processes in cell biology and relies on highly regulated mechano-GTPases that are oligomerization dependent and belong to the dynamin-related protein family, like A. nidulans DnmA. Our previous work demonstrated that H2O2 induces mitochondrial constriction, division, and remodeling of the outer membrane. Here, we show that H2O2 also induces a DnmA aggregation consistent with higher-order oligomerization and its recruitment to mitochondria. The study of this response uncovered that H2O2 induces the depolymerization and reorganization of actin as well as the critical role that cysteines 450 and 776 play in DnmA function. Our results provide new insights into the mechanisms of reactive oxygen species cell signaling and how they can regulate the dynamics of the actin cytoskeleton and the division of mitochondria and peroxisomes.
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Affiliation(s)
- Verónica Garrido-Bazán
- Instituto de Fisiología Celular, Departamento de Biología Celular y Desarrollo, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Dulce C. Guzmán-Ocampo
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Laura Domínguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jesús Aguirre
- Instituto de Fisiología Celular, Departamento de Biología Celular y Desarrollo, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Qin L, Guo S, Li A, Fan L, Tan K, Wong KH. An effective strategy for identifying autogenous regulation of transcription factors in filamentous fungi. Microbiol Spectr 2023; 11:e0234723. [PMID: 37929986 PMCID: PMC10714999 DOI: 10.1128/spectrum.02347-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/08/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Transcription factors (TFs) play a crucial role in deciphering biological information from the DNA of living organisms. Improper regulation of their functions can disrupt cellular physiology and lead to diseases in humans. As one of the key regulatory mechanisms, some TFs control their own expression levels through autogenous regulation. However, identifying autogenous regulation events of TFs has been a tedious task. In this study, we present a straightforward approach that provides a reliable means to identify TF autogenous regulation events. Our method provides a valuable means for understanding the function of this important class of proteins in cells.
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Affiliation(s)
- Longguang Qin
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
| | - Shuhui Guo
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
| | - Ang Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
| | - Lu Fan
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
- Gene Expression, Genomics and Bioinformatics core, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
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12
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Zhang J, Qiu R, Bieger BD, Oakley CE, Oakley BR, Egan MJ, Xiang X. Aspergillus SUMOylation mutants exhibit chromosome segregation defects including chromatin bridges. Genetics 2023; 225:iyad169. [PMID: 37724751 PMCID: PMC10697819 DOI: 10.1093/genetics/iyad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
Functions of protein SUMOylation remain incompletely understood in different cell types. Via forward genetics, here we identified ubaBQ247*, a loss-of-function mutation in a SUMO activation enzyme UbaB in the filamentous fungus Aspergillus nidulans. The ubaBQ247*, ΔubaB, and ΔsumO mutants all produce abnormal chromatin bridges, indicating the importance of SUMOylation in the completion of chromosome segregation. The bridges are enclosed by nuclear membrane containing peripheral nuclear pore complex proteins that normally get dispersed during mitosis, and the bridges are also surrounded by cytoplasmic microtubules typical of interphase cells. Time-lapse sequences further indicate that most bridges persist through interphase prior to the next mitosis, and anaphase chromosome segregation can produce new bridges that persist into the next interphase. When the first mitosis happens at a higher temperature of 42°C, SUMOylation deficiency produces not only chromatin bridges but also many abnormally shaped single nuclei that fail to divide. UbaB-GFP localizes to interphase nuclei just like the previously studied SumO-GFP, but the nuclear signals disappear during mitosis when the nuclear pores are partially open, and the signals reappear after mitosis. The nuclear localization is consistent with many SUMO targets being nuclear proteins. Finally, although the budding yeast SUMOylation machinery interacts with LIS1, a protein critical for dynein activation, loss of SUMOylation does not cause any obvious defect in dynein-mediated transport of nuclei and early endosomes, indicating that SUMOylation is unnecessary for dynein activation in A. nidulans.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences-F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Rongde Qiu
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences-F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Baronger D Bieger
- Department of Entomology and Plant Pathology, University of Arkansas Systems Division of Agriculture, Fayetteville, AR 72701, USA
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Martin J Egan
- Department of Entomology and Plant Pathology, University of Arkansas Systems Division of Agriculture, Fayetteville, AR 72701, USA
| | - Xin Xiang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences-F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
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13
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Nishitani A, Hiramatsu K, Kadooka C, Mori K, Okutsu K, Yoshizaki Y, Takamine K, Tashiro K, Goto M, Tamaki H, Futagami T. Expression of heterochromatin protein 1 affects citric acid production in Aspergillus luchuensis mut. kawachii. J Biosci Bioeng 2023; 136:443-451. [PMID: 37775438 DOI: 10.1016/j.jbiosc.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
A putative methyltransferase, LaeA, controls citric acid production through epigenetic regulation of the citrate exporter gene, cexA, in the white koji fungus Aspergillus luchuensis mut. kawachii. In this study, we investigated the role of another epigenetic regulator, heterochromatin protein 1, HepA, in citric acid production. The ΔhepA strain exhibited reduced citric acid production in liquid culture, although to a lesser extent compared to the ΔlaeA strain. In addition, the ΔlaeA ΔhepA strain showed citric acid production similar to the ΔlaeA strain, indicating that HepA plays a role in citric acid production, albeit with a less-significant regulatory effect than LaeA. RNA-seq analysis revealed that the transcriptomic profiles of the ΔhepA and ΔlaeA strains were similar, and the expression level of cexA was reduced in both strains. These findings suggest that the genes regulated by HepA are similar to those regulated by LaeA in A. luchuensis mut. kawachii. However, the reductions in citric acid production and cexA expression observed in the disruptants were mitigated in rice koji, a solid-state culture. Thus, the mechanism by which citric acid production is regulated differs between liquid and solid cultivation. Further investigation is thus needed to understand the regulatory mechanism in koji.
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Affiliation(s)
- Atsushi Nishitani
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Center for Advanced Science Research and Promotion, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kentaro Hiramatsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto 860-0082, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Kayu Okutsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masatoshi Goto
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
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14
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Zhang L, Zhang B, Zhu A, Liu SH, Wu R, Zhang X, Xu Z, Tan RX, Ge HM. Biosynthesis of Phomactin Platelet Activating Factor Antagonist Requires a Two-Enzyme Cascade. Angew Chem Int Ed Engl 2023; 62:e202312996. [PMID: 37804495 DOI: 10.1002/anie.202312996] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
Phomactin diterpenoids possess a unique bicyclo[9.3.1]pentadecane skeleton with multiple oxidative modifications, and are good platelet-activating factor (PAF) antagonists that can inhibit PAF-induced platelet aggregation. In this study, we identified the gene cluster (phm) responsible for the biosynthesis of phomactins from a marine fungus, Phoma sp. ATCC 74077. Despite the complexity of their structures, phomactin biosynthesis only requires two enzymes: a type I diterpene cyclase PhmA and a P450 monooxygenase PhmC. PhmA was found to catalyze the formation of the phomactatriene, while PhmC sequentially catalyzes the oxidation of multiple sites, leading to the generation of structurally diverse phomactins. The rearrangement mechanism of the diterpene scaffold was investigated through isotope labeling experiments. Additionally, we obtained the crystal complex of PhmA with its substrate analogue FGGPP and elucidated the novel metal-ion-binding mode and enzymatic mechanism of PhmA through site-directed mutagenesis. This study provides the first insight into the biosynthesis of phomactins, laying the foundation for the efficient production of phomactin natural products using synthetic biology approaches.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Shuang He Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Rui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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15
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Han X, D'Angelo C, Otamendi A, Cifuente JO, de Astigarraga E, Ochoa-Lizarralde B, Grininger M, Routier FH, Guerin ME, Fuehring J, Etxebeste O, Connell SR. CryoEM analysis of the essential native UDP-glucose pyrophosphorylase from Aspergillus nidulans reveals key conformations for activity regulation and function. mBio 2023; 14:e0041423. [PMID: 37409813 PMCID: PMC10470519 DOI: 10.1128/mbio.00414-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Invasive aspergillosis is one of the most serious clinical invasive fungal infections, resulting in a high case fatality rate among immunocompromised patients. The disease is caused by saprophytic molds in the genus Aspergillus, including Aspergillus fumigatus, the most significant pathogenic species. The fungal cell wall, an essential structure mainly composed of glucan, chitin, galactomannan, and galactosaminogalactan, represents an important target for the development of antifungal drugs. UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) is a central enzyme in the metabolism of carbohydrates that catalyzes the biosynthesis of UDP-glucose, a key precursor of fungal cell wall polysaccharides. Here, we demonstrate that the function of UGP is vital for Aspergillus nidulans (AnUGP). To understand the molecular basis of AnUGP function, we describe a cryoEM structure (global resolution of 3.5 Å for the locally refined subunit and 4 Å for the octameric complex) of a native AnUGP. The structure reveals an octameric architecture with each subunit comprising an N-terminal α-helical domain, a central catalytic glycosyltransferase A-like (GT-A-like) domain, and a C-terminal (CT) left-handed β-helix oligomerization domain. AnUGP displays unprecedented conformational variability between the CT oligomerization domain and the central GT-A-like catalytic domain. In combination with activity measurements and bioinformatics analysis, we unveil the molecular mechanism of substrate recognition and specificity for AnUGP. Altogether, our study not only contributes to understanding the molecular mechanism of catalysis/regulation of an important class of enzymes but also provides the genetic, biochemical, and structural groundwork for the future exploitation of UGP as a potential antifungal target. IMPORTANCE Fungi cause diverse diseases in humans, ranging from allergic syndromes to life-threatening invasive diseases, together affecting more than a billion people worldwide. Increasing drug resistance in Aspergillus species represents an emerging global health threat, making the design of antifungals with novel mechanisms of action a worldwide priority. The cryoEM structure of UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) from the filamentous fungus Aspergillus nidulans reveals an octameric architecture displaying unprecedented conformational variability between the C-terminal oligomerization domain and the central glycosyltransferase A-like catalytic domain in the individual protomers. While the active site and oligomerization interfaces are more highly conserved, these dynamic interfaces include motifs restricted to specific clades of filamentous fungi. Functional study of these motifs could lead to the definition of new targets for antifungals inhibiting UGP activity and, thus, the architecture of the cell wall of filamentous fungal pathogens.
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Affiliation(s)
- Xu Han
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Cecilia D'Angelo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Ainara Otamendi
- Laboratory of Biology, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, UPV/EHU, San Sebastian, Spain
| | - Javier O. Cifuente
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Elisa de Astigarraga
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Borja Ochoa-Lizarralde
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Marcelo E. Guerin
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jana Fuehring
- Institute for Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Oier Etxebeste
- Laboratory of Biology, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, UPV/EHU, San Sebastian, Spain
| | - Sean R. Connell
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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16
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Mendoza-Martínez AE, Sánchez O, Aguirre J. The role of peroxiredoxins PrxA and PrxB in the antioxidant response, carbon utilization and development in Aspergillus nidulans. Fungal Biol 2023; 127:1198-1208. [PMID: 37495309 DOI: 10.1016/j.funbio.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
In addition to their role in the breakdown of H2O2, some peroxiredoxins (Prxs) have chaperone and H2O2 sensing functions. Acting as an H2O2 sensor, Prx Gpx3 transfers the oxidant signal to the transcription factor Yap1, involved in the antioxidant response in Saccharomyces cerevisiae. We have shown that Aspergillus nidulans Yap1 ortholog NapA is necessary for the antioxidant response, the utilization of arabinose, fructose and ethanol, and for proper development. To address the Prx roles in these processes, we generated and characterized mutants lacking peroxiredoxins PrxA, PrxB, PrxC, or TpxC. Our results show that the elimination of peroxiredoxins PrxC or TpxC does not produce any distinguishable phenotype. In contrast, the elimination of atypical 2-cysteine peroxiredoxins PrxA and PrxB produce different mutant phenotypes. ΔprxA, ΔnapA and ΔprxA ΔnapA mutants are equally sensitive to H2O2 and menadione, while PrxB is dispensable for this. However, the sensitivity of ΔprxA and ΔprxA ΔnapA mutants is increased by the lack of PrxB. Moreover, PrxB is required for arabinose and ethanol utilization and fruiting body cell wall pigmentation. PrxA expression is partially independent of NapA, and the replacement of peroxidatic cysteine 61 by serine (C61S) is enough to cause oxidative stress sensitivity and prevent NapA nuclear accumulation in response to H2O2, indicating its critical role in H2O2 sensing. Our results show that despite their high similarity, PrxA and PrxB play differential roles in Aspergillus nidulans antioxidant response, carbon utilization and development.
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Affiliation(s)
- Ariann E Mendoza-Martínez
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510, México, D.F., Mexico
| | - Olivia Sánchez
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510, México, D.F., Mexico
| | - Jesús Aguirre
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510, México, D.F., Mexico.
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17
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Bravo-Plaza I, Tagua VG, Arst HN, Alonso A, Pinar M, Monterroso B, Galindo A, Peñalva MA. The Uso1 globular head interacts with SNAREs to maintain viability even in the absence of the coiled-coil domain. eLife 2023; 12:e85079. [PMID: 37249218 PMCID: PMC10275640 DOI: 10.7554/elife.85079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Uso1/p115 and RAB1 tether ER-derived vesicles to the Golgi. Uso1/p115 contains a globular-head-domain (GHD), a coiled-coil (CC) mediating dimerization/tethering, and a C-terminal region (CTR) interacting with golgins. Uso1/p115 is recruited to vesicles by RAB1. Genetic studies placed Uso1 paradoxically acting upstream of, or in conjunction with RAB1 (Sapperstein et al., 1996). We selected two missense mutations in uso1 resulting in E6K and G540S in the GHD that rescued lethality of rab1-deficient Aspergillus nidulans. The mutations are phenotypically additive, their combination suppressing the complete absence of RAB1, which emphasizes the key physiological role of the GHD. In living hyphae Uso1 recurs on puncta (60 s half-life) colocalizing partially with the Golgi markers RAB1, Sed5, and GeaA/Gea1/Gea2, and totally with the retrograde cargo receptor Rer1, consistent with Uso1 dwelling in a very early Golgi compartment from which ER residents reaching the Golgi recycle back to the ER. Localization of Uso1, but not of Uso1E6K/G540S, to puncta is abolished by compromising RAB1 function, indicating that E6K/G540S creates interactions bypassing RAB1. That Uso1 delocalization correlates with a decrease in the number of Gea1 cisternae supports that Uso1-and-Rer1-containing puncta are where the protein exerts its physiological role. In S-tag-coprecipitation experiments, Uso1 is an associate of the Sed5/Bos1/Bet1/Sec22 SNARE complex zippering vesicles with the Golgi, with Uso1E6K/G540S showing a stronger association. Using purified proteins, we show that Bos1 and Bet1 bind the Uso1 GHD directly. However, Bet1 is a strong E6K/G540S-independent binder, whereas Bos1 is weaker but becomes as strong as Bet1 when the GHD carries E6K/G540S. G540S alone markedly increases GHD binding to Bos1, whereas E6K causes a weaker effect, correlating with their phenotypic contributions. AlphaFold2 predicts that G540S increases the binding of the GHD to the Bos1 Habc domain. In contrast, E6K lies in an N-terminal, potentially alpha-helical, region that sensitive genetic tests indicate as required for full Uso1 function. Remarkably, this region is at the end of the GHD basket opposite to the end predicted to interact with Bos1. We show that, unlike dimeric full-length and CTR∆ Uso1 proteins, the GHD lacking the CC/CTR dimerization domain, whether originating from bacteria or Aspergillus extracts and irrespective of whether it carries or not E6K/G540S, would appear to be monomeric. With the finding that overexpression of E6K/G540S and wild-type GHD complement uso1∆, our data indicate that the GHD monomer is capable of providing, at least partially, the essential Uso1 functions, and that long-range tethering activity is dispensable. Rather, these findings strongly suggest that the essential role of Uso1 involves the regulation of SNAREs.
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Affiliation(s)
- Ignacio Bravo-Plaza
- Department of Cellular and Molecular Biology, CSIC Centro de Investigaciones BiológicasMadridSpain
| | - Victor G Tagua
- Instituto de Tecnologías Biomédicas, Hospital Universitario Nuestra Señora de CandelariaSanta Cruz de TenerifeSpain
| | - Herbert N Arst
- Department of Infectious Diseases, Faculty of Medicine, Flowers Building, Imperial CollegeLondonUnited Kingdom
| | - Ana Alonso
- Department of Cellular and Molecular Biology, CSIC Centro de Investigaciones BiológicasMadridSpain
| | - Mario Pinar
- Department of Cellular and Molecular Biology, CSIC Centro de Investigaciones BiológicasMadridSpain
| | - Begoña Monterroso
- Department of Structural and Chemical Biology, CSIC Centro de Investigaciones BiológicasMadridSpain
| | - Antonio Galindo
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
| | - Miguel A Peñalva
- Department of Cellular and Molecular Biology, CSIC Centro de Investigaciones BiológicasMadridSpain
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18
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Zhang J, Qiu R, Bieger BD, Oakley CE, Oakley BR, Egan MJ, Xiang X. Aspergillus SUMOylation mutants have normal dynein function but exhibit chromatin bridges. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.16.537086. [PMID: 37131833 PMCID: PMC10153134 DOI: 10.1101/2023.04.16.537086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Functions of protein SUMOylation remain incompletely understood in different cell types. The budding yeast SUMOylation machinery interacts with LIS1, a protein critical for dynein activation, but dynein-pathway components were not identified as SUMO-targets in the filamentous fungus Aspergillus nidulans. Via A. nidulans forward genetics, here we identified ubaBQ247*, a loss-of-function mutation in a SUMO-activation enzyme UbaB. Colonies of the ubaBQ247*, ΔubaB and ΔsumO mutants looked similar and less healthy than the wild-type colony. In these mutants, about 10% of nuclei are connected by abnormal chromatin bridges, indicating the importance of SUMOylation in the completion of chromosome segregation. Nuclei connected by chromatin bridges are mostly in interphase, suggesting that these bridges do not prevent cell-cycle progression. UbaB-GFP localizes to interphase nuclei just like the previously studied SumO-GFP, but the nuclear signals disappear during mitosis when the nuclear pores are partially open, and the signals reappear after mitosis. The nuclear localization is consistent with many SUMO-targets being nuclear proteins, for example, topoisomerase II whose SUMOylation defect gives rise to chromatin bridges in mammalian cells. Unlike in mammalian cells, however, loss of SUMOylation in A. nidulans does not apparently affect the metaphase-to-anaphase transition, further highlighting differences in the requirements of SUMOylation in different cell types. Finally, loss of UbaB or SumO does not affect dynein- and LIS1-mediated early-endosome transport, indicating that SUMOylation is unnecessary for dynein or LIS1 function in A. nidulans.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
| | - Rongde Qiu
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
| | - Baronger D. Bieger
- Department of Entomology and Plant Pathology, University of Arkansas Systems Division of Agriculture, Fayetteville, AR, USA
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Martin J. Egan
- Department of Entomology and Plant Pathology, University of Arkansas Systems Division of Agriculture, Fayetteville, AR, USA
| | - Xin Xiang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, Maryland 20814, USA
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19
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Unraveling the Gene Regulatory Networks of the Global Regulators VeA and LaeA in Aspergillus nidulans. Microbiol Spectr 2023:e0016623. [PMID: 36920196 PMCID: PMC10101098 DOI: 10.1128/spectrum.00166-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
In the filamentous fungus Aspergillus nidulans, the velvet family protein VeA and the global regulator of secondary metabolism LaeA govern development and secondary metabolism mostly by acting as the VelB/VeA/LaeA heterotrimeric complex. While functions of these highly conserved controllers have been well studied, the genome-wide regulatory networks governing cellular and chemical development remain to be uncovered. Here, by integrating transcriptomic analyses, protein-DNA interactions, and the known A. nidulans gene/protein interaction data, we have unraveled the gene regulatory networks governed by VeA and LaeA. Within the networks, VeA and LaeA directly control the expression of numerous genes involved in asexual/sexual development and primary/secondary metabolism in A. nidulans. Totals of 3,190 and 1,834 potential direct target genes of VeA and LaeA were identified, respectively, including several important developmental and metabolic regulators such as flbA·B·C, velB·C, areA, mpkB, and hogA. Moreover, by analyzing over 8,800 ChIP-seq peaks, we have revealed the predicted common consensus sequences 5'-TGATTGGCTG-3' and 5'-TCACGTGAC-3' that VeA and LaeA might bind to interchangeably. These findings further expand the biochemical and genomic studies of the VelB/VeA/LaeA complex functionality in the gene regulation. In summary, this study unveils genes that are under the regulation of VeA and LaeA, proposes the VeA- and LaeA-mediated gene regulatory networks, and demonstrates their genome-wide developmental and metabolic regulations in A. nidulans. IMPORTANCE Fungal development and metabolism are genetically programmed events involving specialized cellular differentiation, cellular communication, and temporal and spatial regulation of gene expression. In genus Aspergillus, the global regulators VeA and LaeA govern developmental and metabolic processes by affecting the expression of downstream genes, including multiple transcription factors and signaling elements. Due to their vital roles in overall biology, functions of VeA and LaeA have been extensively studied, but there still has been a lack of knowledge about their genome-wide regulatory networks. In this study, employing the model fungus A. nidulans, we have identified direct targets of VeA and LaeA and their gene regulatory networks by integrating transcriptome, protein-DNA interaction, and protein-protein interaction analyses. Our results demonstrate the genome-wide regulatory mechanisms of these global regulators, thereby advancing the knowledge of fungal biology and genetics.
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srdA mutations suppress the rseA/cpsA deletion mutant conidiation defect in Aspergillus nidulans. Sci Rep 2023; 13:4285. [PMID: 36922566 PMCID: PMC10017718 DOI: 10.1038/s41598-023-31363-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Conidiation is an important reproductive process in Aspergillus. We previously reported, in A. nidulans, that the deletion of a putative glycosyltransferase gene, rseA/cpsA, causes an increase in the production of extracellular hydrolases and a severe reduction in conidiation. The aim of this study was to obtain novel genetic factors involved in the repression of conidiation in the rseA deletion mutant. We isolated mutants in which the rseA deletion mutant conidiation defect is suppressed and performed a comparative genomic analysis of these mutants. A gene encoding a putative transcription factor was identified as the associated candidate causative gene. The candidate gene was designated as srdA (suppressor gene for the conidiation defect of the rseA deletion mutant). The conidiation efficiency of the rseAsrdA double-deletion mutant was increased. Introduction of wild-type srdA into the suppressor mutants caused a conidiation defect similar to that of the rseA deletion mutant. Notably, the conidiation efficiencies of the rseAsrdA double-deletion and srdA single-deletion mutants were higher than that of the wild-type strain. These results indicate that srdA is a novel genetic factor that strongly represses conidiation of the rseA deletion mutant, and a putative transcriptional regulator, SrdA is a negative regulator of conidiation in A. nidulans.
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Mining an O-methyltransferase for de novo biosynthesis of physcion in Aspergillus nidulans. Appl Microbiol Biotechnol 2023; 107:1177-1188. [PMID: 36648527 DOI: 10.1007/s00253-023-12373-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/18/2023]
Abstract
Physcion is one of natural anthraquinones, registered as a novel plant-derived fungicide due to its excellent prevention of plant disease. However, the current production of physcion via plant extraction limits its yield promotion and application. Here, a pair of polyketide synthases (PKS) in emodin biosynthesis were used as probes to mining the potential O-methyltransferase (OMT) responsible for physcion biosynthesis. Further refinement using the phylogenetic analysis of the mined OMTs revealed a distinct OMT (AcOMT) with the ability of transferring a methyl group to C-6 hydroxyl of emodin to form physcion. Through introducing AcOMT, we successfully obtained the de novo production of physcion in Aspergillus nidulans. The physcion biosynthetic pathway was further rationally engineered by expressing the decarboxylase genes from different fungi. Finally, the titer of physcion reached to 64.6 mg/L in shake-flask fermentation through enhancing S-adenosylmethionine supply. Our work provides a native O-methyltransferase for physcion biosynthesis and lays the foundation for further improving the production of physcion via a sustainable route. KEY POINTS: • Genome mining of the native O-methyltransferase responsible for physcion biosynthesis • De novo biosynthesis of physcion in the engineered Aspergillus nidulans • Providing an alternative way to produce plant-derived fungicide physcion.
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Kirchgaessner L, Wurlitzer JM, Seibold PS, Rakhmanov M, Gressler M. A genetic tool to express long fungal biosynthetic genes. Fungal Biol Biotechnol 2023; 10:4. [PMID: 36726159 PMCID: PMC9893682 DOI: 10.1186/s40694-023-00152-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/22/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Secondary metabolites (SMs) from mushroom-forming fungi (Basidiomycota) and early diverging fungi (EDF) such as Mucoromycota are scarcely investigated. In many cases, production of SMs is induced by unknown stress factors or is accompanied by seasonable developmental changes on fungal morphology. Moreover, many of these fungi are considered as non-culturable under laboratory conditions which impedes investigation into SM. In the post-genomic era, numerous novel SM genes have been identified especially from EDF. As most of them encode multi-module enzymes, these genes are usually long which limits cloning and heterologous expression in traditional hosts. RESULTS An expression system in Aspergillus niger is presented that is suitable for the production of SMs from both Basidiomycota and EDF. The akuB gene was deleted in the expression host A. niger ATNT∆pyrG, resulting in a deficient nonhomologous end-joining repair mechanism which in turn facilitates the targeted gene deletion via homologous recombination. The ∆akuB mutant tLK01 served as a platform to integrate overlapping DNA fragments of long SM genes into the fwnA locus required for the black pigmentation of conidia. This enables an easy discrimination of correct transformants by screening the transformation plates for fawn-colored colonies. Expression of the gene of interest (GOI) is induced dose-dependently by addition of doxycycline and is enhanced by the dual TetON/terrein synthase promoter system (ATNT) from Aspergillus terreus. We show that the 8 kb polyketide synthase gene lpaA from the basidiomycete Laetiporus sulphureus is correctly assembled from five overlapping DNA fragments and laetiporic acids are produced. In a second approach, we expressed the yet uncharacterized > 20 kb nonribosomal peptide synthetase gene calA from the EDF Mortierella alpina. Gene expression and subsequent LC-MS/MS analysis of mycelial extracts revealed the production of the antimycobacterial compound calpinactam. This is the first report on the heterologous production of a full-length SM multidomain enzyme from EDF. CONCLUSIONS The system allows the assembly, targeted integration and expression of genes of > 20 kb size in A. niger in one single step. The system is suitable for evolutionary distantly related SM genes from both Basidiomycota and EDF. This uncovers new SM resources including genetically intractable or non-culturable fungi.
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Affiliation(s)
- Leo Kirchgaessner
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.413047.50000 0001 0658 7859Faculty Medical Technology and Biotechnology, Ernst Abbe University of Applied Sciences Jena, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Jacob M. Wurlitzer
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Paula S. Seibold
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Malik Rakhmanov
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Markus Gressler
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
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23
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Pinheiro Â, Piontkivska D, Sequeira P, Martins TM, Silva Pereira C. Aspergillus nidulans. Trends Microbiol 2023; 31:212-213. [PMID: 36272887 DOI: 10.1016/j.tim.2022.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Ângela Pinheiro
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Daryna Piontkivska
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Patrícia Sequeira
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago M Martins
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristina Silva Pereira
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Chiang CY, Ohashi M, Tang Y. Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining. Nat Prod Rep 2023; 40:89-127. [PMID: 36125308 PMCID: PMC9906657 DOI: 10.1039/d2np00050d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.
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Affiliation(s)
- Chen-Yu Chiang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Masao Ohashi
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Yi Tang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
- Dept. of Chemistry and Biochemistry, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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25
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Cell wall dynamics stabilize tip growth in a filamentous fungus. PLoS Biol 2023; 21:e3001981. [PMID: 36649360 PMCID: PMC9882835 DOI: 10.1371/journal.pbio.3001981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 01/27/2023] [Accepted: 12/22/2022] [Indexed: 01/18/2023] Open
Abstract
Hyphal tip growth allows filamentous fungi to colonize space, reproduce, or infect. It features remarkable morphogenetic plasticity including unusually fast elongation rates, tip turning, branching, or bulging. These shape changes are all driven from the expansion of a protective cell wall (CW) secreted from apical pools of exocytic vesicles. How CW secretion, remodeling, and deformation are modulated in concert to support rapid tip growth and morphogenesis while ensuring surface integrity remains poorly understood. We implemented subresolution imaging to map the dynamics of CW thickness and secretory vesicles in Aspergillus nidulans. We found that tip growth is associated with balanced rates of CW secretion and expansion, which limit temporal fluctuations in CW thickness, elongation speed, and vesicle amount, to less than 10% to 20%. Affecting this balance through modulations of growth or trafficking yield to near-immediate changes in CW thickness, mechanics, and shape. We developed a model with mechanical feedback that accounts for steady states of hyphal growth as well as rapid adaptation of CW mechanics and vesicle recruitment to different perturbations. These data provide unprecedented details on how CW dynamics emerges from material secretion and expansion, to stabilize fungal tip growth as well as promote its morphogenetic plasticity.
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26
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Qiu R, Zhang J, McDaniel D, Peñalva MA, Xiang X. Live-Cell Imaging of Dynein-Mediated Cargo Transport in Aspergillus nidulans. Methods Mol Biol 2023; 2623:3-23. [PMID: 36602676 DOI: 10.1007/978-1-0716-2958-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Filamentous fungi have been used for studying long-distance transport of cargoes driven by cytoplasmic dynein. Aspergillus nidulans is a well-established genetic model organism used for studying dynein function and regulation in vivo. Here, we describe how we grow A. nidulans strains for live-cell imaging and how we observe the dynein-mediated distribution of early endosomes and secretory vesicles. Using an on-stage incubator and culture chambers for inverted microscopes, we can image fungal hyphae that naturally attach to the bottom of the chambers, using wide-field epifluorescence microscopes or the new Zeiss LSM 980 (with Airyscan 2) microscope. In addition to methods for preparing cells for imaging, a procedure for A. nidulans transformation is also described.
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Affiliation(s)
- Rongde Qiu
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD, USA
| | - Jun Zhang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD, USA
| | - Dennis McDaniel
- Department of Microbiology and Immunology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD, USA
| | - Miguel A Peñalva
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain.
| | - Xin Xiang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD, USA.
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Qiu R, Zhang J, Xiang X. Kinesin-1 autoinhibition facilitates the initiation of dynein cargo transport. J Biophys Biochem Cytol 2022; 222:213766. [PMID: 36524956 PMCID: PMC9802684 DOI: 10.1083/jcb.202205136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The functional significance of Kinesin-1 autoinhibition has been unclear. Kinesin-1 transports multiple cargoes including cytoplasmic dynein to microtubule plus ends. From a genetic screen for Aspergillus mutants defective in dynein-mediated early endosome transport, we identified a kinesin-1 mutation kinAK895* at the C-terminal IAK motif involved in autoinhibition. The kinA∆IAK and kinAK895E mutants exhibited a similar defect in dynein-mediated early endosome transport, verifying the importance of kinesin-1 autoinhibition in dynein-mediated transport. Kinesin-1 autoinhibition is not critical for dynein accumulation at microtubule plus ends or for the secretory vesicle cargoes of kinesin-1 to reach the hyphal tip. However, it facilitates dynein to initiate early endosome transport. This is unrelated to a direct competition between dynein and kinesin-1 on early endosomes because kinesin-3 rather than kinesin-1 drives the plus-end-directed early endosome movement. This effect of kinesin-1 autoinhibition on dynein-mediated early endosome transport is related to cargo adapter-mediated dynein activation but at a step beyond the switching of dynein from its autoinhibited conformation.
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Affiliation(s)
- Rongde Qiu
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MA, USA
| | - Jun Zhang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MA, USA
| | - Xin Xiang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MA, USA,Correspondence to Xin Xiang:
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28
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Dionysopoulou M, Yan N, Wang B, Pliotas C, Diallinas G. Genetic and cellular characterization of MscS-like putative channels in the filamentous fungus Aspergillus nidulans. Channels (Austin) 2022; 16:148-158. [PMID: 35941834 PMCID: PMC9367656 DOI: 10.1080/19336950.2022.2098661] [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
Mechanosensitive ion channels are integral membrane proteins ubiquitously present in bacteria, archaea, and eukarya. They act as molecular sensors of mechanical stress to serve vital functions such as touch, hearing, osmotic pressure, proprioception and balance, while their malfunction is often associated with pathologies. Amongst them, the structurally distinct MscL and MscS channels from bacteria are the most extensively studied. MscS-like channels have been found in plants and Schizosaccharomyces pombe, where they regulate intracellular Ca2+ and cell volume under hypo-osmotic conditions. Here we characterize two MscS-like putative channels, named MscA and MscB, from the model filamentous fungus Aspergillus nidulans. Orthologues of MscA and MscB are present in most fungi, including relative plant and animal pathogens. MscA/MscB and other fungal MscS-like proteins share the three transmembrane helices and the extended C-terminal cytosolic domain that form the structural fingerprint of MscS-like channels with at least three additional transmembrane segments than Escherichia coli MscS. We show that MscA and MscB localize in Endoplasmic Reticulum and the Plasma Membrane, respectively, whereas their overexpression leads to increased CaCl2 toxicity or/and reduction of asexual spore formation. Our findings contribute to understanding the role of MscS-like channels in filamentous fungi and relative pathogens.
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Affiliation(s)
- Mariangela Dionysopoulou
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom.,Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece
| | - Nana Yan
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom
| | - Bolin Wang
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 70013 Heraklion, Greece
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29
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Rajasenan S, Osmani AH, Osmani SA. Modulation of sensitivity to gaseous signaling by sterol-regulatory hypoxic transcription factors in Aspergillus nidulans biofilm cells. Fungal Genet Biol 2022; 163:103739. [PMID: 36089227 DOI: 10.1016/j.fgb.2022.103739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 01/06/2023]
Abstract
Fungal biofilm founder cells experience self-generated hypoxia leading to dramatic changes in their cell biology. For example, during Aspergillus nidulans biofilm formation microtubule (MT) disassembly is triggered causing dispersal of EB1 from MT tips. This process is dependent on SrbA, a sterol regulatory element-binding transcription factor required for adaptation to hypoxia. We show that SrbA, an ER resident protein prior to activation, is proteolytically activated during early stages of biofilm formation and that, like SrbA itself, its activating proteases are also required for normal biofilm MT disassembly. In addition to SrbA, the AtrR transcription factor is also found to be required to modulate cellular responses to gaseous signaling during biofilm development. Using co-cultures, we further show that cells lacking srbA or atrR are capable of responding to biofilm generated gaseous microenvironments but are actually more sensitive to this signal than wild type cells. SrbA is a regulator of ergosterol biosynthetic genes and we find that the levels of seven GFP-tagged Erg proteins differentially accumulate during biofilm formation with various dependencies on SrbA for their accumulation. This uncovers a complex pattern of regulation with biofilm accumulation of only some Erg proteins being dependent on SrbA with others accumulating to higher levels in its absence. Because different membrane sterols are known to influence cell permeability to gaseous molecules, including oxygen, we propose that differential regulation of ergosterol biosynthetic proteins by SrbA potentially calibrates the cell's responsiveness to gaseous signaling which in turn modifies the cell biology of developing biofilm cells.
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Affiliation(s)
- Shobhana Rajasenan
- Ohio State University, Department of Molecular Genetics, 105 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Aysha H Osmani
- Ohio State University, Department of Molecular Genetics, 105 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Stephen A Osmani
- Ohio State University, Department of Molecular Genetics, 105 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH 43210, United States.
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30
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Chiang YM, Lin TS, Wang CCC. Total Heterologous Biosynthesis of Fungal Natural Products in Aspergillus nidulans. JOURNAL OF NATURAL PRODUCTS 2022; 85:2484-2518. [PMID: 36173392 PMCID: PMC9621686 DOI: 10.1021/acs.jnatprod.2c00487] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fungal natural products comprise a wide range of bioactive compounds including important drugs and agrochemicals. Intriguingly, bioinformatic analyses of fungal genomes have revealed that fungi have the potential to produce significantly more natural products than what have been discovered so far. It has thus become widely accepted that most biosynthesis pathways of fungal natural products are silent or expressed at very low levels under laboratory cultivation conditions. To tap into this vast chemical reservoir, the reconstitution of entire biosynthetic pathways in genetically tractable fungal hosts (total heterologous biosynthesis) has become increasingly employed in recent years. This review summarizes total heterologous biosynthesis of fungal natural products accomplished before 2020 using Aspergillus nidulans as heterologous hosts. We review here Aspergillus transformation, A. nidulans hosts, shuttle vectors for episomal expression, and chromosomal integration expression. These tools, collectively, not only facilitate the discovery of cryptic natural products but can also be used to generate high-yield strains with clean metabolite backgrounds. In comparison with total synthesis, total heterologous biosynthesis offers a simplified strategy to construct complex molecules and holds potential for commercial application.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
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Jarczynska Z, Garcia Vanegas K, Deichmann M, Nørskov Jensen C, Scheeper MJ, Futyma ME, Strucko T, Jares Contesini F, Sparholt Jørgensen T, Blæsbjerg Hoof J, Hasbro Mortensen U. A Versatile in Vivo DNA Assembly Toolbox for Fungal Strain Engineering. ACS Synth Biol 2022; 11:3251-3263. [PMID: 36126183 PMCID: PMC9594312 DOI: 10.1021/acssynbio.2c00159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Efficient homologous recombination in baker's yeast allows accurate fusion of DNA fragments via short identical sequence tags in vivo. Eliminating the need for an Escherichia coli cloning step speeds up genetic engineering of this yeast and sets the stage for large high-throughput projects depending on DNA construction. With the aim of developing similar tools for filamentous fungi, we first set out to determine the genetic- and sequence-length requirements needed for efficient fusion reactions, and demonstrated that in nonhomologous end-joining deficient strains of Aspergillus nidulans, efficient fusions can be achieved by 25 bp sequence overlaps. Based on these results, we developed a novel fungal in vivo DNA assembly toolbox for simple and flexible genetic engineering of filamentous fungi. Specifically, we have used this method for construction of AMA1-based vectors, complex gene-targeting substrates for gene deletion and gene insertion, and for marker-free CRISPR based gene editing. All reactions were done via single-step transformations involving fusions of up to six different DNA fragments. Moreover, we show that it can be applied in four different species of Aspergilli. We therefore envision that in vivo DNA assembly can be advantageously used for many more purposes and will develop into a popular tool for fungal genetic engineering.
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Affiliation(s)
- Zofia
Dorota Jarczynska
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Katherina Garcia Vanegas
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Marcus Deichmann
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christina Nørskov Jensen
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Marouschka Jasmijn Scheeper
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Malgorzata Ewa Futyma
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Tomas Strucko
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Fabiano Jares Contesini
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jakob Blæsbjerg Hoof
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Eukaryotic
Molecular Cell Biology, Section for Synthetic Biology, Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark,
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32
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James SW, Palmer J, Keller NP, Brown ML, Dunworth MR, Francisco SG, Watson KG, Titchen B, Achimovich A, Mahoney A, Artemiou JP, Buettner KG, Class M, Sydenstricker AL, Anglin SL. A reciprocal translocation involving Aspergillus nidulans snxAHrb1/Gbp2 and gyfA uncovers a new regulator of the G2-M transition and reveals a role in transcriptional repression for the setBSet2 histone H3-lysine-36 methyltransferase. Genetics 2022; 222:iyac130. [PMID: 36005881 PMCID: PMC9526064 DOI: 10.1093/genetics/iyac130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Aspergillus nidulans snxA, an ortholog of Saccharomyces cerevisiae Hrb1/Gbp2 messenger RNA shuttle proteins, is-in contrast to budding yeast-involved in cell cycle regulation, in which snxA1 and snxA2 mutations as well as a snxA deletion specifically suppress the heat sensitivity of mutations in regulators of the CDK1 mitotic induction pathway. snxA mutations are strongly cold sensitive, and at permissive temperature snxA mRNA and protein expression are strongly repressed. Initial attempts to identify the causative snxA mutations revealed no defects in the SNXA protein. Here, we show that snxA1/A2 mutations resulted from an identical chromosome I-II reciprocal translocation with breakpoints in the snxA first intron and the fourth exon of a GYF-domain gene, gyfA. Surprisingly, a gyfA deletion and a reconstructed gyfA translocation allele suppressed the heat sensitivity of CDK1 pathway mutants in a snxA+ background, demonstrating that 2 unrelated genes, snxA and gyfA, act through the CDK1-CyclinB axis to restrain the G2-M transition, and for the first time identifying a role in G2-M regulation for a GYF-domain protein. To better understand snxA1/A2-reduced expression, we generated suppressors of snxA cold sensitivity in 2 genes: (1) loss of the abundant nucleolar protein Nsr1/nucleolin bypassed the requirement for snxA and (2) loss of the Set2 histone H3 lysine36 (H3K36) methyltransferase or a nonmethylatable histone H3K36L mutant rescued hypomorphic snxA mutants by restoring full transcriptional proficiency, indicating that methylation of H3K36 acts normally to repress snxA transcription. These observations are in line with known Set2 functions in preventing excessive and cryptic transcription of active genes.
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Affiliation(s)
- Steven W James
- Department of Biology, Gettysburg College, Gettysburg, PA 17325, USA
| | - Jonathan Palmer
- Data Analytics, Genencor Technology Center, IFF, Palo Alto, CA, 94306, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Morgan L Brown
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Dunworth
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Sarah G Francisco
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Katherine G Watson
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, USA
| | - Breanna Titchen
- Department of Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alecia Achimovich
- Department of Chemistry, Gettysburg College, Gettysburg, PA 17325, USA
| | - Andrew Mahoney
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Kyra G Buettner
- School of Medicine, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Madelyn Class
- School of Medicine, Temple University, Philadelphia, PA 19140, USA
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Gawlik J, Koper M, Bogdanowicz A, Weglenski P, Dzikowska A. Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in Aspergillus nidulans. Int J Mol Sci 2022; 23:ijms231911138. [PMID: 36232439 PMCID: PMC9570407 DOI: 10.3390/ijms231911138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
Kae1 is a subunit of the highly evolutionarily conserved KEOPS/EKC complex, which is involved in universal (t6A37) tRNA modification. Several reports have discussed the participation of this complex in transcription regulation in yeast and human cells, including our previous observations of KaeA, an Aspergillus nidulans homologue of Kae1p. The aim of this project was to confirm the role of KaeA in transcription, employing high-throughput transcriptomic (RNA-Seq and ChIP-Seq) and proteomic (LC-MS) analysis. We confirmed that KaeA is a subunit of the KEOPS complex in A. nidulans. An analysis of kaeA19 and kaeA25 mutants showed that, although the (t6A37) tRNA modification is unaffected in both mutants, they reveal significantly altered transcriptomes compared to the wild type. The finding that KaeA is localized in chromatin and identifying its protein partners allows us to postulate an additional nuclear function for the protein. Our data shed light on the universal bi-functional role of this factor and proves that the activity of this protein is not limited to tRNA modification in cytoplasm, but also affects the transcriptional activity of a number of nuclear genes. Data are available via the NCBI’s GEO database under identifiers GSE206830 (RNA-Seq) and GSE206874 (ChIP-Seq), and via ProteomeXchange with identifier PXD034554 (proteomic).
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Affiliation(s)
- Joanna Gawlik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5A, 02-106 Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Michal Koper
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Albert Bogdanowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Piotr Weglenski
- Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Agnieszka Dzikowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5A, 02-106 Warsaw, Poland
- Correspondence: or
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34
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CRISPR/Cas9-Mediated Gene Editing of BnFAD2 and BnFAE1 Modifies Fatty Acid Profiles in Brassica napus. Genes (Basel) 2022; 13:genes13101681. [PMID: 36292566 PMCID: PMC9602045 DOI: 10.3390/genes13101681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Fatty acid (FA) composition determines the quality of oil from oilseed crops, and thus is a major target for genetic improvement. FAD2 (Fatty acid dehydrogenase 2) and FAE1 (fatty acid elongase 1) are critical FA synthetic genes, and have been the focus of genetic manipulation to alter fatty acid composition in oilseed plants. In this study, to improve the nutritional quality of rapeseed cultivar CY2 (about 50% oil content; of which 40% erucic acid), we generated novel knockout plants by CRISPR/Cas9 mediated genome editing of BnFAD2 and BnFAE1 genes. Two guide RNAs were designed to target one copy of the BnFAD2 gene and two copies of the BnFAE1 gene, respectively. A number of lines with mutations at three target sites of BnFAD2 and BnFAE1 genes were identified by sequence analysis. Three of these lines showed mutations in all three target sites of the BnFAD2 and BnFAE1 genes. Fatty acid composition analysis of seeds revealed that mutations at all three sites resulted in significantly increased oleic acid (70–80%) content compared with that of CY2 (20%), greatly reduced erucic acid levels and slightly decreased polyunsaturated fatty acids content. Our results confirmed that the CRISPR/Cas9 system is an effective tool for improving this important trait.
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35
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Zehetbauer F, Seidl A, Berger H, Sulyok M, Kastner F, Strauss J. RimO (SrrB) is required for carbon starvation signaling and production of secondary metabolites in Aspergillus nidulans. Fungal Genet Biol 2022; 162:103726. [PMID: 35843417 DOI: 10.1016/j.fgb.2022.103726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/17/2022] [Accepted: 07/09/2022] [Indexed: 11/20/2022]
Abstract
Depending on the prevailing environmental, developmental and nutritional conditions, fungi activate biosynthetic gene clusters (BGCs) to produce condition-specific secondary metabolites (SMs). For activation, global chromatin-based de-repression must be integrated with pathway-specific induction signals. Here we describe a new global regulator needed to activate starvation-induced SMs. In our transcriptome dataset, we found locus AN7572 strongly transcribed solely under conditions of starvation-induced SM production. The predicted AN7572 protein is most similar to the stress and nutritional regulator Rim15 of Saccharomyces cerevisiae, and to STK-12 of Neurospora crassa. Based on this similarity and on stress and nutritional response phenotypes of A. nidulans knock-out and overexpression strains, AN7572 is designated rimO. In relation to SM production, we found that RimO is required for the activation of starvation-induced BGCs, including the sterigmatocystin (ST) gene cluster. Here, RimO regulates the pathway-specific transcription factor AflR both at the transcriptional and post-translational level. At the transcriptional level, RimO mediates aflR induction following carbon starvation and at the post-translational level, RimO is required for nuclear accumulation of the AflR protein. Genome-wide transcriptional profiling showed that cells lacking rimO fail to adapt to carbon starvation that, in the wild type, leads to down-regulation of genes involved in basic metabolism, membrane biogenesis and growth. Consistently, strains overexpressing rimO are more resistant to oxidative and osmotic stress, largely insensitive to glucose repression and strongly overproduce several SMs. Our data indicate that RimO is a positive regulator within the SM and stress response network, but this requires nutrient depletion that triggers both, rimO gene transcription and activation of the RimO protein.
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Affiliation(s)
- Franz Zehetbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
| | - Angelika Seidl
- University of Natural Resources and Life Sciences, Vienna, Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
| | - Harald Berger
- University of Natural Resources and Life Sciences, Vienna, Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
| | - Michael Sulyok
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Straße 20, 3430 Tulln an der Donau, Austria.
| | - Florian Kastner
- University of Natural Resources and Life Sciences, Vienna, Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
| | - Joseph Strauss
- University of Natural Resources and Life Sciences, Vienna, Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
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36
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Garrido-Bazán V, Aguirre J. H 2O 2 Induces Calcium and ERMES Complex-Dependent Mitochondrial Constriction and Division as Well as Mitochondrial Outer Membrane Remodeling in Aspergillus nidulans. J Fungi (Basel) 2022; 8:829. [PMID: 36012817 PMCID: PMC9410301 DOI: 10.3390/jof8080829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
The dynamin-like protein DnmA and its receptor FisA are essential for H2O2-induced mitochondrial division in Aspergillus nidulans. Here, we show that in the absence of DnmA or FisA, mitochondria show few spontaneous transient constrictions, the frequency of which is extensively increased by H2O2 or the carbonyl cyanide m-chlorophenyl hydrazone (CCCP). While H2O2-induced constrictions are transient, CCCP induces a drastic and irreversible alteration of mitochondrial filaments. H2O2 induces a gradual mitochondrial depolarization, while CCCP-induced depolarization is abrupt. The calcium chelator BAPTA-AM prevents the formation of mitochondrial constrictions induced by either H2O2 or CCCP. H2O2 also induces major rearrangements of the mitochondrial outer membrane, which remain after constrictions dissipate, as well as changes in endoplasmic reticulum (ER) and nuclear morphology. Similar mitochondrial constriction, ER and nuclear morphology changes are detected during the early stages of asexual development. ER and ER-Mitochondria encounter structure (ERMES) complex-composed of proteins Mdm10, Mmm1, Mdm43 and Mdm12-are important for mitochondrial division in Saccharomyces cerevisiae. As the Mdm10 ortholog MdmB was found to be essential in A. nidulans, we evaluated its functions in ΔmdmB terminal mutants and ΔmdmB heterokaryons. ΔmdmB conidia produce a short germ tube that fails to grow further, in which inherited mitochondria become gigantic and round shaped, lacking clear contacts with the ER. In slow-growing ΔmdmB heterokaryotic mycelia, multiple hyphae contain very long mitochondria with high ROS levels, as occur in ΔdnmA and ΔfisA mutants. In this hyphae, H2O2 fails to induce mitochondrial constrictions but not outer mitochondrial membrane reshaping, indicating that these are two separate effects of H2O2. Our results indicate that H2O2 induces a generalized mitochondrial constriction response, prior to actual division, involving gradual depolarization; they also indicate that Ca2+ and the ERMES complex are critical for both mitochondrial constriction and division. This supports a view of mitochondrial dynamics as the result of a cascade of signaling events that can be initiated in vivo by H2O2.
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Affiliation(s)
| | - Jesús Aguirre
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, Ciudad de México 04510, Mexico
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37
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Pinar M, Alonso A, de los Ríos V, Bravo-Plaza I, de la Gandara Á, Galindo A, Arias-Palomo E, Peñalva MÁ. The type V myosin-containing complex HUM is a RAB11 effector powering movement of secretory vesicles. iScience 2022; 25:104514. [PMID: 35754728 PMCID: PMC9213775 DOI: 10.1016/j.isci.2022.104514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 01/01/2023] Open
Abstract
In the apex-directed RAB11 exocytic pathway of Aspergillus nidulans, kinesin-1/KinA conveys secretory vesicles (SVs) to the hyphal tip, where they are transferred to the type V myosin MyoE. MyoE concentrates SVs at an apical store located underneath the PM resembling the presynaptic active zone. A rod-shaped RAB11 effector, UDS1, and the intrinsically disordered and coiled-coil HMSV associate with MyoE in a stable HUM (HMSV-UDS1-MyoE) complex recruited by RAB11 to SVs through an interaction network involving RAB11 and HUM components, with the MyoE globular tail domain (GTD) binding both HMSV and RAB11-GTP and RAB11-GTP binding both the MyoE-GTD and UDS1. UDS1 bridges RAB11-GTP to HMSV, an avid interactor of the MyoE-GTD. The interaction between the UDS1-HMSV sub-complex and RAB11-GTP can be reconstituted in vitro. Ablating UDS1 or HMSV impairs actomyosin-mediated transport of SVs to the apex, resulting in spreading of RAB11 SVs across the apical dome as KinA/microtubule-dependent transport gains prominence.
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Affiliation(s)
- Mario Pinar
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana Alonso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Vivian de los Ríos
- Proteomics Facility, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ignacio Bravo-Plaza
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Álvaro de la Gandara
- Department of Chemical and Structural Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Galindo
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK
| | - Ernesto Arias-Palomo
- Department of Chemical and Structural Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Á. Peñalva
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Corresponding author
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38
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Mózsik L, Iacovelli R, Bovenberg RAL, Driessen AJM. Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi. Front Bioeng Biotechnol 2022; 10:901037. [PMID: 35910033 PMCID: PMC9335490 DOI: 10.3389/fbioe.2022.901037] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are highly productive cell factories, many of which are industrial producers of enzymes, organic acids, and secondary metabolites. The increasing number of sequenced fungal genomes revealed a vast and unexplored biosynthetic potential in the form of transcriptionally silent secondary metabolite biosynthetic gene clusters (BGCs). Various strategies have been carried out to explore and mine this untapped source of bioactive molecules, and with the advent of synthetic biology, novel applications, and tools have been developed for filamentous fungi. Here we summarize approaches aiming for the expression of endogenous or exogenous natural product BGCs, including synthetic transcription factors, assembly of artificial transcription units, gene cluster refactoring, fungal shuttle vectors, and platform strains.
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Affiliation(s)
- László Mózsik
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, Netherlands
- Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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39
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Dimou S, Dionysopoulou M, Sagia GM, Diallinas G. Golgi-Bypass Is a Major Unconventional Route for Translocation to the Plasma Membrane of Non-Apical Membrane Cargoes in Aspergillus nidulans. Front Cell Dev Biol 2022; 10:852028. [PMID: 35465316 PMCID: PMC9021693 DOI: 10.3389/fcell.2022.852028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Nutrient transporters have been shown to translocate to the plasma membrane (PM) of the filamentous fungus Aspergillus nidulans via an unconventional trafficking route that bypasses the Golgi. This finding strongly suggests the existence of distinct COPII vesicle subpopulations, one following Golgi-dependent conventional secretion and the other directed towards the PM. Here, we address whether Golgi-bypass concerns cargoes other than nutrient transporters and whether Golgi-bypass is related to cargo structure, size, abundance, physiological function, or polar vs. non-polar distribution in the PM. To address these questions, we followed the dynamic subcellular localization of two selected membrane cargoes differing in several of the aforementioned aspects. These are the proton-pump ATPase PmaA and the PalI pH signaling component. Our results show that neosynthesized PmaA and PalI are translocated to the PM via Golgi-bypass, similar to nutrient transporters. In addition, we showed that the COPII-dependent exit of PmaA from the ER requires the alternative COPII coat subunit LstA, rather than Sec24, whereas PalI requires the ER cargo adaptor Erv14. These findings strengthen the evidence of distinct cargo-specific COPII subpopulations and extend the concept of Golgi-independent biogenesis to essential transmembrane proteins, other than nutrient transporters. Overall, our findings point to the idea that Golgi-bypass might not constitute a fungal-specific peculiarity, but rather a novel major and cargo-specific sorting route in eukaryotic cells that has been largely ignored.
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Affiliation(s)
- Sofia Dimou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, Greece
| | - Mariangela Dionysopoulou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, Greece
| | - Georgia Maria Sagia
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece
- *Correspondence: George Diallinas,
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40
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Roux I, Chooi YH. Cre/ lox-Mediated Chromosomal Integration of Biosynthetic Gene Clusters for Heterologous Expression in Aspergillus nidulans. ACS Synth Biol 2022; 11:1186-1195. [PMID: 35168324 DOI: 10.1021/acssynbio.1c00458] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Building strains of filamentous fungi for stable long-term heterologous expression of large biosynthetic pathways is limited by the low transformation efficiency or genetic stability of current methods. Here, we developed a system for targeted chromosomal integration of large biosynthetic gene clusters in Aspergillus nidulans based on site-specific recombinase-mediated cassette exchange. We built A. nidulans strains harboring a chromosomal landing pad for Cre/lox-mediated recombination and demonstrated efficient targeted integration of a 21 kb DNA fragment in a single step. We further evaluated the integration at two loci by analyzing the expression of a fluorescent reporter and the production of a heterologous polyketide metabolite. We compared chromosomal expression at those landing loci to episomal AMA1-based expression, which also shed light on uncharacterized aspects of episomal expression in filamentous fungi. This is the first demonstration of site-specific recombinase-mediated integration in filamentous fungi, setting the foundations for the further development of this tool.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
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41
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Kellner N, Griesel S, Hurt E. A Homologous Recombination System to Generate Epitope-Tagged Target Genes in Chaetomium thermophilum: A Genetic Approach to Investigate Native Thermostable Proteins. Int J Mol Sci 2022; 23:ijms23063198. [PMID: 35328616 PMCID: PMC8951082 DOI: 10.3390/ijms23063198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Chaetomium thermophilum is an attractive eukaryotic model organism which, due to its unusually high temperature tolerance (optimal growth at 50-52 °C), has a thermostable proteome that can be exploited for biochemical, structural and biotechnological applications. Site directed gene manipulation for the expression of labeled target genes is a desirable approach to study the structure and function of thermostable proteins and their organization in complexes, which has not been established for this thermophile yet. Here, we describe the development of a homologous recombination system to epitope-tag chromosomal genes of interest in Chaetomium thermophilum with the goal to exploit the derived thermostable fusion proteins for tandem-affinity purification. This genetic approach was facilitated by the engineering of suitable strains, in which factors of the non-homologous end-joining pathway were deleted, thereby improving the efficiency of homologous integration at specific gene loci. Following this strategy, we could demonstrate that gene tagging via homologous recombination improved the yield of purified bait proteins and co-precipitated factors, paving the way for related studies in fundamental research and industrial applications.
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Affiliation(s)
| | | | - Ed Hurt
- Correspondence: (N.K.); (E.H.)
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42
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Madhavan A, Arun KB, Sindhu R, Alphonsa Jose A, Pugazhendhi A, Binod P, Sirohi R, Reshmy R, Kumar Awasthi M. Engineering interventions in industrial filamentous fungal cell factories for biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126209. [PMID: 34715339 DOI: 10.1016/j.biortech.2021.126209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Filamentous fungi possess versatile capabilities for synthesizing a variety of valuable bio compounds, including enzymes, organic acids and small molecule secondary metabolites. The advancements of genetic and metabolic engineering techniques and the availability of sequenced genomes discovered their potential as expression hosts for recombinant protein production. Remarkably, plant-biomass degrading filamentous fungi show the unique capability to decompose lignocellulose, an extremely recalcitrant biopolymer. The basic biochemical approaches have motivated several industrial processes for lignocellulose biomass valorisation into fermentable sugars and other biochemical for biofuels, biomolecules, and biomaterials. The review gives insight into current trends in engineering filamentous fungi for enzymes, fuels, and chemicals from lignocellulose biomass. This review describes the variety of enzymes and compounds that filamentous fungi produce, engineering of filamentous fungi for biomass valorisation with a special focus on lignocellulolytic enzymes and other bulk chemicals.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India.
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Anju Alphonsa Jose
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | | | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy & Environmental Sustainability, Lucknow 226001. Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, PR China
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Suresh S, Osmani SA. Protein Retargeting in Aspergillus nidulans to Study the Function of Nuclear Pore Complex Proteins. Methods Mol Biol 2022; 2502:183-201. [PMID: 35412239 DOI: 10.1007/978-1-0716-2337-4_12] [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: 06/14/2023]
Abstract
Targeting a protein of interest to a subcellular location by linking it to another protein is a commonly used approach to help determine function in many model systems. Such targeting strategies rely on the creation of functional protein-protein fusions followed by microscopic examination if one or both proteins have fluorescent tags. In this paper, using the model filamentous fungus Aspergillus nidulans, we describe methods to link GFP-tagged proteins to other proteins in the cell by fusing the latter with a GFP-Binding Protein (GBP) that has a high affinity for GFP. This method enables rapid generation of strains with linked proteins in filamentous fungi by sexual crossing or transformations. Additionally, if these two linked proteins stably associate with subcellular structures, it is possible to link the structures using this approach. For example, we used this method to link Nuclear Pore Complexes (NPCs) with mitotic chromatin in A. nidulans. This was done to show that the NPC protein Nup2, that uniquely transitions from NPC onto mitotic chromatin, couples NPC segregation with chromatin segregation by bridging these two structures. In the absence of Nup2, we used the described approach to show that an artificial NPC-chromatin bridge was sufficient for faithful NPC segregation.
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Affiliation(s)
- Subbulakshmi Suresh
- The Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
| | - Stephen A Osmani
- The Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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44
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Roux I, Chooi YH. Heterologous Expression of Fungal Biosynthetic Pathways in Aspergillus nidulans Using Episomal Vectors. Methods Mol Biol 2022; 2489:75-92. [PMID: 35524046 DOI: 10.1007/978-1-0716-2273-5_5] [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: 06/14/2023]
Abstract
Filamentous fungi produce a wide diversity of secondary metabolites, whose biosynthesis is encoded in biosynthetic gene clusters (BGCs). As novel BGCs are often found in fungal species that are genetically intractable or difficult to cultivate, heterologous expression is increasingly being used for compound discovery. In addition, heterologous expression is a useful strategy to elucidate the function of the genes within a BGC and shed light on their enzymatic mechanisms. Here, we describe a method for BGC elucidation using multi-marker AMA1-based pYFAC vectors for episomal expression in the fungal host Aspergillus nidulans. The pYFAC vectors have the advantage of high transformation efficiency and support high compound production. In addition, different pathway intermediates can be easily evaluated by testing different vector combinations. This protocol encompasses different AMA1-based strategies for BGC expression such as cloning of a BGC native sequence, promoter exchange or transcription factor overexpression. We also describe procedures for A. nidulans protoplasting, transformation, and small-scale culture analysis of strains containing AMA1 vectors.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Yit Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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45
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Li A, Parsania C, Tan K, Todd RB, Wong KH. Co-option of an extracellular protease for transcriptional control of nutrient degradation in the fungus Aspergillus nidulans. Commun Biol 2021; 4:1409. [PMID: 34921231 PMCID: PMC8683493 DOI: 10.1038/s42003-021-02925-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
Nutrient acquisition is essential for all organisms. Fungi regulate their metabolism according to environmental nutrient availability through elaborate transcription regulatory programs. In filamentous fungi, a highly conserved GATA transcription factor AreA and its co-repressor NmrA govern expression of genes involved in extracellular breakdown, uptake, and metabolism of nitrogen nutrients. Here, we show that the Aspergillus nidulans PnmB protease is a moonlighting protein with extracellular and intracellular functions for nitrogen acquisition and metabolism. PnmB serves not only as a secreted protease to degrade extracellular nutrients, but also as an intracellular protease to control the turnover of the co-repressor NmrA, accelerating AreA transcriptional activation upon nitrogen starvation. PnmB expression is controlled by AreA, which activates a positive feedback regulatory loop. Hence, we uncover a regulatory mechanism in the well-established controls determining the response to nitrogen starvation, revealing functional evolution of a protease gene for transcriptional regulation and extracellular nutrient breakdown.
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Affiliation(s)
- Ang Li
- grid.437123.00000 0004 1794 8068Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR China ,grid.470124.4Present Address: Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 China
| | - Chirag Parsania
- grid.437123.00000 0004 1794 8068Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR China ,Present Address: Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW 2050 China
| | - Kaeling Tan
- grid.437123.00000 0004 1794 8068Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR China ,grid.437123.00000 0004 1794 8068Gene Expression, Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR China
| | - Richard B. Todd
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China. .,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China. .,MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China.
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46
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Yao Y, Wang W, Shi W, Yan R, Zhang J, Wei G, Liu L, Che Y, An C, Gao SS. Overproduction of medicinal ergot alkaloids based on a fungal platform. Metab Eng 2021; 69:198-208. [PMID: 34902590 DOI: 10.1016/j.ymben.2021.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022]
Abstract
Privileged ergot alkaloids (EAs) produced by the fungal genus Claviceps are used to treat a wide range of diseases. However, their use and research have been hampered by the challenging genetic engineering of Claviceps. Here we systematically refactored and rationally engineered the EA biosynthetic pathway in heterologous host Aspergillus nidulans by using a Fungal-Yeast-Shuttle-Vector protocol. The obtained strains allowed the production of diverse EAs and related intermediates, including prechanoclavine (PCC, 333.8 mg/L), chanoclavine (CC, 241.0 mg/L), agroclavine (AC, 78.7 mg/L), and festuclavine (FC, 99.2 mg/L), etc. This fungal platform also enabled the access to the methyl-oxidized EAs (MOEAs), including elymoclavine (EC), lysergic acid (LA), dihydroelysergol (DHLG), and dihydrolysergic acid (DHLA), by overexpressing a P450 enzyme CloA. Furthermore, by optimizing the P450 electron transfer (ET) pathway and using multi-copy of cloA, the titers of EC and DHLG have been improved by 17.3- and 9.4-fold, respectively. Beyond our demonstration of A. nidulans as a robust platform for EA overproduction, our study offers a proof of concept for engineering the eukaryotic P450s-contained biosynthetic pathways in a filamentous fungal host.
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Affiliation(s)
- Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Wei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Rui Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Yongsheng Che
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, PR China
| | - Chunyan An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.
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47
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Caesar LK, Montaser R, Keller NP, Kelleher NL. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. Nat Prod Rep 2021; 38:2041-2065. [PMID: 34787623 PMCID: PMC8691422 DOI: 10.1039/d1np00036e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2010 to 2021Organisms in nature have evolved into proficient synthetic chemists, utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of secondary metabolites. Often serving to boost competitive advantage for their producers, these secondary metabolites have widespread human impacts as antibiotics, anti-inflammatories, and antifungal drugs. The natural products discovery field has begun a shift away from traditional activity-guided approaches and is beginning to take advantage of increasingly available metabolomics and genomics datasets to explore undiscovered chemical space. Major strides have been made and now enable -omics-informed prioritization of chemical structures for discovery, including the prospect of confidently linking metabolites to their biosynthetic pathways. Over the last decade, more integrated strategies now provide researchers with pipelines for simultaneous identification of expressed secondary metabolites and their biosynthetic machinery. However, continuous collaboration by the natural products community will be required to optimize strategies for effective evaluation of natural product biosynthetic gene clusters to accelerate discovery efforts. Here, we provide an evaluative guide to scientific literature as it relates to studying natural product biosynthesis using genomics, metabolomics, and their integrated datasets. Particular emphasis is placed on the unique insights that can be gained from large-scale integrated strategies, and we provide source organism-specific considerations to evaluate the gaps in our current knowledge.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Rana Montaser
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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48
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Casado-del Castillo V, MacCabe AP, Orejas M. Agrobacterium tumefaciens-Mediated Transformation of NHEJ Mutant Aspergillus nidulans Conidia: An Efficient Tool for Targeted Gene Recombination Using Selectable Nutritional Markers. J Fungi (Basel) 2021; 7:961. [PMID: 34829246 PMCID: PMC8623315 DOI: 10.3390/jof7110961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Protoplast transformation for the introduction of recombinant DNA into Aspergillus nidulans is technically demanding and dependant on the availability and batch variability of commercial enzyme preparations. Given the success of Agrobacterium tumefaciens-mediated transformation (ATMT) in diverse pathogenic fungi, we have adapted this method to facilitate transformation of A. nidulans. Using suitably engineered binary vectors, gene-targeted ATMT of A. nidulans non-homologous end-joining (NHEJ) mutant conidia has been carried out for the first time by complementation of a nutritional requirement (uridine/uracil auxotrophy). Site-specific integration in the ΔnkuA host genome occurred at high efficiency. Unlike other transformation techniques, however, cross-feeding of certain nutritional requirements from the bacterium to the fungus was found to occur, thus limiting the choice of auxotrophies available for ATMT. In complementation tests and also for comparative purposes, integration of recombinant cassettes at a specific locus could provide a means to reduce the influence of position effects (chromatin structure) on transgene expression. In this regard, targeted disruption of the wA locus permitted visual identification of transformants carrying site-specific integration events by conidial colour (white), even when auxotrophy selection was compromised due to cross-feeding. The protocol described offers an attractive alternative to the protoplast procedure for obtaining locus-targeted A. nidulans transformants.
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Affiliation(s)
| | - Andrew P. MacCabe
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), c/Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain; (V.C.-d.C.); (M.O.)
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49
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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50
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Qiu R, Zhang J, Rotty JD, Xiang X. Dynein activation in vivo is regulated by the nucleotide states of its AAA3 domain. Curr Biol 2021; 31:4486-4498.e6. [PMID: 34428469 DOI: 10.1016/j.cub.2021.07.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 07/29/2021] [Indexed: 01/02/2023]
Abstract
Cytoplasmic dynein is activated by the dynactin complex, cargo adapters and LIS1 (Lissencephaly 1). How this process is regulated in vivo remains unclear. The dynein motor ring contains six AAA+ (ATPases associated with diverse cellular activities) domains. Here, we used the filamentous fungus Aspergillus nidulans to examine whether ATP hydrolysis at AAA3 regulates dynein activation in the context of other regulators. In fungal hyphae, early endosomes undergo dynein-mediated movement away from the microtubule plus ends near the hyphal tip. Dynein normally accumulates at the microtubule plus ends. The early endosomal adaptor Hook protein, together with dynactin, drives dynein activation to cause its relocation to the microtubule minus ends. This activation process depends on LIS1, but LIS1 tends to dissociate from dynein after its activation. In this study, we found that dynein containing a mutation-blocking ATP hydrolysis at AAA3 can undergo LIS1-independent activation, consistent with our genetic data that the same mutation suppresses the growth defect of the A. nidulans LIS1-deletion mutant. Our data also suggest that blocking AAA3 ATP hydrolysis allows dynein activation by dynactin without the early endosomal adaptor. As a consequence, dynein accumulates at microtubule minus ends whereas early endosomes stay near the plus ends. Dynein containing a mutation-blocking ATP binding at AAA3 largely depends on LIS1 for activation, but this mutation abnormally prevents LIS1 dissociation upon dynein activation. Together, our data suggest that the AAA3 ATPase cycle regulates the coordination between dynein activation and cargo binding as well as the dynamic dynein-LIS1 interaction.
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Affiliation(s)
- Rongde Qiu
- Department of Biochemistry and Molecular Biology, the Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Jun Zhang
- Department of Biochemistry and Molecular Biology, the Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Jeremy D Rotty
- Department of Biochemistry and Molecular Biology, the Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Xin Xiang
- Department of Biochemistry and Molecular Biology, the Uniformed Services University of the Health Sciences- F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA.
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