Progress 12/17/14 to 09/30/19
Outputs
Target Audience:Programmed cell death and cell fusion: Scientific researchers in academia and researchers in the health (focused on treatment of fungal infections), pharmaceutical, biotechnological, and agricultural chemical sectors. Plant biomass deconstruction: Scientific researchers in academia and biotechnology fields, particularly those involved in specialty chemical and biofuel production. Amateur Mycological Societies: Regular presentations to the general public on fungal communication and networks. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Oct. 1 2018-Sept. 30, 2019 Trained two graduate students: Darae Jun and Gabriel Rosenfield Trained undergraduate: Karen Chow Trained post-doctoral scholars: Dr. Lori Huberman, Dr. Asen Daskalov, Dr. Pedro Goncalves, Dr. Adria Rico-Ramirez, Dr. Yang Li and Dr. Kaila Pianalto Trained project scientist: Jens Heller How have the results been disseminated to communities of interest?Huberman: Posters: 2018 Gordon Research Conference on Cellular and Molecular Biology of the Fungi (Poster Award); 2019, 30th Fungal Genetics Conference (poster award) P Rico-Ramirez: Poster: 2019, 30th Fungal Genetics Conference Li: Poster: 2019, 30th Fungal Genetics Conference Rosenfield: Poster: 2019, 30th Fungal Genetics Conference Jun: Poster: 2019, 30th Fungal Genetics Conference Heller: Poster: 2019 DOE Genomic Sciences Meeting Daskalov: Poster: 2019, 30th Fungal Genetics Conference Glass: 2018 University of Nebraska, Lincoln, Biotechnology/Life Sciences; 2018 Cellular and Molecular Fungal Biology Gordon Conference; 2018 CMDB/GGB/MCBL Seminar Series, University of California, Riverside; 2018 Gordon Research Conference on Cellular and Molecular Biology of the Fungi What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
A. Plant Biomass Deconstruction Biofuels derived from lignocellulosic biomass are a viable alternative to fossil fuels required for transportation. Following plant biomass pretreatment, the furan derivative furfural is present at concentrations which are inhibitory to yeasts. Detoxification of furfural is thus important for efficient fermentation. Here, we searched for new genetic attributes in the fungus Neurospora crassa that may be linked to furfural tolerance. The fact that furfural is involved in the natural process of sexual spore germination of N. crassa and that this fungus is highly amenable to genetic manipulations makes it a rational candidate for this study. Both hypothesis-based and unbiased (random promotor mutagenesis) approaches were performed to identify N. crassa genes associated with the response to furfural. Changes in the transcriptional profile following exposure to furfural revealed that the affected processes were, overall, similar to those observed in Saccharomyces cerevisiae. N. crassa was more tolerant (by ~ 30%) to furfural when carboxymethyl cellulose was the main carbon source as opposed to sucrose, indicative of a link between carbohydrate metabolism and furfural tolerance. We also observed increased tolerance in a Δcre-1 mutant (CRE-1 is a key transcription factor that regulates the ability of fungi to utilize non-preferred carbon sources). In addition, analysis of aldehyde dehydrogenase mutants showed that ahd-2 (NCU00378) was involved in tolerance to furfural as well as the predicted membrane transporter NCU05580 (flr-1), a homolog of FLR1 in S. cerevisiae. Further to the rational screening, an unbiased approach revealed additional genes whose inactivation conferred increased tolerance to furfural: (i) NCU02488, which affected the abundance of the non-anchored cell wall protein NCW-1 (NCU05137), and (ii) the zinc finger protein NCU01407. We identified attributes in N. crassa associated with tolerance or degradation of furfural, using complementary research approaches. The manipulation of the genes involved in furan sensitivity can provide a means for improving the production of biofuel producing strains. Similar research approaches can be utilized in N. crassa and other filamentous fungi to identify additional attributes relevant to other furans or toxic chemicals. Regulation of the secretory pathway improves the efficiency of secretion and plant cell wall degradation. We conducted a forward genetic screen to identify and characterize defective trafficking mutants that cannot translocate cellulases in the ER or that improperly retain cellulases in the ER instread of secreting them into the extracellular environment. We generated a mutant library using random mutagenesis of a strain with a GFP-tagged endoglucanase (EG-2), to screen via microscopy for mutants with mislocalized EG-2. From the screen, we identified a mutant that mislocalized EG-2-GFP to the ER. We used bulked segregant analysis to identify the putative causal mutation. The putative causal gene encoded a scaffolding protein. B. Cell Fusion Cells rarely exist alone, which drives the evolution of diverse mechanisms for identifying and responding appropriately to the presence of other nearby cells. Filamentous fungi depend on somatic cell-to-cell communication and fusion for the development and maintenance of a multicellular, interconnected colony that is characteristic of this group of organisms. The filamentous fungus Neurospora crassa is a model for investigating the mechanisms of somatic cell-to-cell communication and fusion. N. crassa cells chemotropically grow toward genetically similar cells, which ultimately make physical contact and undergo cell fusion. Here, we describe the development of a Pprm1-luciferase reporter system that differentiates whether genes function upstream or downstream of a conserved MAP kinase (MAPK) signaling complex, by using a set of mutants required for communication and cell fusion. The vast majority of these mutants are deficient for self-fusion and for fusion when paired with wild-type cells. However, the Δham-11 mutant is unique in that it fails to undergo self-fusion, but chemotropic interactions and cell fusion are restored in Δham-11 + wild-type interactions. In genetically dissimilar cells, chemotropic interactions are regulated by genetic differences at doc-1 and doc-2, which regulate prefusion non-self recognition; cells with dissimilar doc-1 and doc-2 alleles show greatly reduced cell-fusion frequencies. HAM-11 functions in parallel with the DOC-1 and DOC-2 proteins to regulate the activity of the MAPK signaling complex. Together, our data support a model of integrated self and non-self recognition processes that modulate somatic cell-to-cell communication in N. crassa. C. PCD Somatic cell fusion and conspecific cooperation are crucial social traits for microbial unicellular-to-multicellular transitions, colony expansion, and substrate foraging but are also associated with risks of parasitism. We identified a cell wall remodeling (cwr) checkpoint that acts upon cell contact to assess genetic compatibility and regulate cell wall dissolution during somatic cell fusion in a wild population of the filamentous fungus Neurospora crassa. Non-allelic interactions between two linked loci, cwr-1 and cwr-2, were necessary and sufficient to block cell fusion: cwr-1 encodes a polysaccharide monooxygenase (PMO), a class of enzymes associated with extracellular degradative capacities, and cwr-2 encodes a predicted transmembrane protein. Mutations of sites in CWR-1 essential for PMO catalytic activity abolished the block in cell fusion between formerly incompatible strains. In Neurospora, alleles cwr-1 and cwr-2 were highly polymorphic, fell into distinct haplogroups, and showed trans-species polymorphisms. Distinct haplogroups and trans-species polymorphisms at cwr-1 and cwr-2 were also identified in the distantly related genus Fusarium, suggesting convergent evolution. Proteins involved in chemotropic processes showed extended localization at contact sites, suggesting that cwr regulates the transition between chemotropic growth and cell wall dissolution. Our work revealed an allorecognition surveillance system based on kind discrimination that inhibits cooperative behavior in fungi by blocking cell fusion upon contact, contributing to fungal immunity by preventing formation of chimeras between genetically non-identical colonies. The develoment and validation of a flow cytometry-based communication communication assay and analysis pipeline to evaluate the communication behavior of enabled the the evaluation of communication group (CG)-specific signals. If the determinanat of communication (DOC) system does not recieve a compatible CG signal, DOC-1 and DOC-2 both prevent reinforcement of MAK-2 complex oscillations and suppresses communication. This suppression involves the actions of the middle and C-terminal regions of DOC-1 and does not require the N-terminal region of DOC-2. The N-terminal region of DOC-1 is required to properly derepress communication.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural.
Feldman D, Kowbel DJ, Cohen A, Glass NL, Hadar Y, Yarden O.
Biotechnol Biofuels. 2019 Sep 4;12:210. doi: 10.1186/s13068-019-1550-4.
PMID:31508149
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Allorecognition upon Fungal Cell-Cell Contact Determines Social Cooperation and Impacts the Acquisition of Multicellularity. Gon�alves AP, Heller J, Span EA, Rosenfield G, Do HP, Palma-Guerrero J, Requena N, Marletta MA, Glass NL. Curr Biol. 2019 Sep 23;29(18):3006-3017.e3. doi: 10.1016/j.cub.2019.07.060. PMID: 31474536
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Communicate and Fuse: How Filamentous Fungi Establish and Maintain an Interconnected Mycelial Network. Fischer MS, Glass NL. Front Microbiol. 2019 Mar 29;10:619. doi: 10.3389/fmicb.2019.00619. Review. PMID:31001214
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
The power of discussion: Support for women at the fungal Gordon Research Conference. Riquelme M, Aime MC, Branco S, Brand A, Brown A, Glass NL, Kahmann R, Momany M, Rokas A, Trail F. Fungal Genet Biol. 2018 Dec;121:65-67. doi: 10.1016/j.fgb.2018.09.007. PMID:30261275
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2019
Citation:
Long-Distance Non-Self Recognition and Control of Intercellular Communication in Neurospora crassa Gabriel R. Rosenfield 08/2019
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2019
Citation:
Dissecting the mechanism of cell fusion and secretion in Neurospora crassa. Darae Jun 05/2019
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Integration of Self and Non-self Recognition Modulates Asexual Cell-to-Cell Communication in Neurospora crassa. Fischer MS, Jonkers W, Glass NL. Genetics. 2019 Apr;211(4):1255-1267. doi: 10.1534/genetics.118.301780. PMID:30718271
|
Progress 10/01/17 to 09/30/18
Outputs
Target Audience:Programmed cell death and cell fusion: Scientific researchers in academia and researchers in the health (focused on treatment of fungal infections), pharmaceutical, biotechnological, and agricultural chemical sectors. Plant biomass deconstruction: Scientific researchers in academia and biotechnology fields, particularly those involved in specialty chemical and biofuel production. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work provided training and professional development for four post-doctoral associates, four graduate students and three undergraduate students. The post-doctoral associates and graduate students all attend at least one scientific meeting a year and present their work as oral presentations, posters or both. The graduate students, undergraduate students and post-doctoral associates attend weekly laboratory meetings, where they present their research and receive feedback and discussions. We participate in supergroup on campus, where students/post-docs present their work to a wider audience. The graduate students/post-docs are encouraged to participate in additional activities (volunteering in K-12 educational activities) that enrich their educational experience. Post-doctoral associates also participate in grant writing and both graduate students and post-doctoral associates participate heavily in manuscript writing/editing. How have the results been disseminated to communities of interest?The results of this work have been disseminated via publication in peer reviewed scientific journals and presentation at national and international meetings. What do you plan to do during the next reporting period to accomplish the goals?Plant Biomass Deconstruction: Complete Fungal EnCode project in collaboration with the Joint Genome Institute to define the Neurospora metabolic model. Cell fusion: Define the interconnection between tpolysaccharide monooxygenases role in cell fusion versus fungal cell wall functions and determine if these enzymes serve a signaing function. Programmed cell death: Explore the function of Gasdermin homologs in Neurospora that mediate nonself recognition and death versus their function in mammalian cells during innate immunity functions.
Impacts
What was accomplished under these goals?
Plant Biomass Deconstruction: During this reporting period, we elucidated signaling pathways the regulate the production of plant cell wall degrading enzymes in the filamentous fungus Neurospora crassa (Huberman et al., PNAS). In collaboration with the Hong laboratory, we constructed synthetic fungal strains that showed a signficant increase in regulation production of plant cell wall degrading enzymes (Matsu-Ura et al., ACS Synth Biol). The production of secreted enzymes depends of high trafficking of proteins through the secretory pathway. We determined that specific cargo adaptors are important for trafficking cellulase enzymes (CBH-1 and CBH-2) (Starr et al., Mol Microbiol). In collaboration with the Hadar laboratory, we investigated the expression patterns of cell wall degrading enzymes in the basidiomycete species Pleurotus ostreatus (Feldman et al., Sci Rep). Cell Fusion: We defined the signaling pathways that regulate specific transcription factors that are essential for regulation of genes involved in cell fusion (Fischer et al., Genetics). Programmed cell death: We identified proteins the regulate nonself recognition and death in filamentous fungi that have structural and signaling similarities to proteins involved in innate immunity in plants and animals.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Fischer MS, Wu VW, Lee JE, O'Malley RC, Glass NL, 2018. Regulation of cell-to-cell communication and cell wall integrity by a network of MAP-kinase pathways and transcription factors, in Neurospora crassa. Genetics 209(2):489-506. doi: 10.1534/genetics.118.300904. PMID: 29678830.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Matsu-Ura T, Dovzhenok AA, Coradetti ST, Subramanian KR, Meyer DR, Kwon JJ, Kim C, Salomonis N, Glass NL, Lim S, Hong CI. Synthetic gene network with positive feedback loop amplifies cellulase gene expression in Neurospora crassa, 2018. ACS Synth Biol 7(5):1395-1405. doi: 10.1021/acssynbio.8b00011. PMID:29625007
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Heller J, Clave C, Gladieux P, Saupe SJ, Glass NL, 2018. NLR surveillance of essential SEC-9 SNARE proteins induces programmed cell death upon allorecognition in filamentous fungi. Proc Natl Acad Sci USA 115(10):E2292-E2301. doi: 10.1073/pnas.1719705115. PMID: 29463729.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y, 2017. A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus. Sci Rep 7:14553. doi: 10.1038/s41598-017-15112-2.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Glass NL, 2017. Near-cognate codons contribute complexity to translation regulation. MBio 8(6). pii: e01820-17. doi: 10.1128/mBio.01820-17.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Starr TL, Goncalves AP, Meshgin N, Glass NL, 2017. The major cellulases CBH-1 and CBH-2 of Neurospora crassa rely on distinct ER cargo adaptors for efficient ER-exit. Mol Microbiol 107:229-248. doi: 10.1111/mmi.13879.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Huberman LB, Coradetti ST, Glass NL, 2017. Network of nutrient-sensing pathways and a conservative kinase cascade integrate osmolarity and carbon sensing in Neurospora crassa. Proc Natl Acad Sci USA 14:E8665-E8674. doi: 10.1073/pnas.1707713114.
|
Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Plant Biomass Deconstruction: Scientific researchers in academics and industry who work on filamentous fungi for industrial applications. Government personnel in the Department of Energy. Cell Fusion: Scientific researchers in the academic and biotechnology sector. Programmed Cell Death: Scientific researchers in academia and researchers in the pharmaceutical, biotechnological and agricultural chemical sectors. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Post-doctoral Associates Jens Heller: Dr. Heller discussed his work at the Fungal Genetics Conference (invited speaker, March 2017); participated in grant writing for NSF; mentored graduate students/undergraduate students Lori Huberman: Dr. Huberman discussed her work at the Fungal Genetics Conference (invited speaker, March 2017); participated in grant writing (as a PI and as a co-PI); mentored graduate/undergraduate students Pedro Goncalves: Dr. Goncalves was an invited speaker to the Fungal Cell Wall meeting ( Sept 2017); participated in grant writing; mentored graduate/undergraduate students Asen Daskalov: Dr. Daskalov was invited to participate in a small Cold Spring Harbor meeting on innate immunity led by Jonathan Jones (fall 2017); participated in grant writing. Lina Qin: Poster presentation at the Fungal Genetics Meeting (March 2017); left in May 2017 for a faculty position in China. Graduate Students:Jason Liu, Monika Fischer, Gabe Rosenfield, Darae Jun and Vince Wu participated in the Fungal Genetics meeting (poster presentation). Wu presented at the JGI user meeting. Wu and Fischer participated in grant writing/proposal development. Fischer and Rosenfield mentored undergraduate students. Wu spent 4 months at the JGI to learn computatational biology methods. How have the results been disseminated to communities of interest?Seminars given by PI during reporting period 2017 Temasek Life Sciences Laboratory, The National University of Singapore, Singapore 2017 XXII Mexican Congress of Molecular and Cell Biology of Fungi, Queretaro, Mexico 2017 International Fungal Biology Conference, Seoul, S. Korea 2017 FungiBrain, Cordoba, Spain 2017 Plant Gene Expression Center, Albany, CA 2017 German Genetics Society Meeting, Bochum, Germany 2017 Alexander von Humboldt Foundation Colloquium, Washington DC 2017 Institute of Molecular Biology (IMB), Academia Sinica, Nankang, Taipei 2016 PPPMB Section, Cornell University 2016 Max Planck Institute for Terrestrial Microbiology, Marburg Germany 2016 ETH Zurich, Department of Agricultural Sciences 2016 University of Braunschweig, Germany, Symposium on Cell Fusion What do you plan to do during the next reporting period to accomplish the goals?Plant Biomass Deconstruction: 1.In collaboration with the JGI, we have developed DAP-seq, a technique that identifies direct target sites of transcription factors using high throughput sequencing methods. We focused on transcription factors important for plant biomass deconstruction. This work is finished, but we are not refining computational methods to define transcriptional regulatory networks and test hypotheses regarding function.2. We will continue to probe the interaction between the kinase pathway and induction of cellulases mediated by the transcription factor CLR-1 to understand the biochemical mechanisms oif induction and regulations. Cell Fusion: 1. To identify the mechanistic basis of chemical languages in fungi, we have been targeting interacting proteins of DOC-1 and DOC-2, which are essential for communication group. We anticipate follow up experiments in the coming year. 2.We will finalize our understanding of the relationship between the two cell fusion regulators ADV-1 and PP-1.3.We will define the function of chitin PMOs in the regulation of cell wall breakdown during cell fusion. PCD: 1. We will identify suppressor of death induced by innate immunity to determine downstream signaling functions.2. We will define the function of the fungal homolog of human Gasdermin, which is implicated in innate immunity and PCD, as a comparative death inducing pore complex formation.
Impacts
What was accomplished under these goals?
Plant Biomass Deconstruction: 1.During this review period, we completed a metabolic model forNeurospora crassagrowing on plant biomass that incorporated large amounts of data from diverse sources. The development of this metabolic model led to the hypothesis that cellulose and mannan utilization in N. crassa are linked, which was subsequently shown to be true. Published in Biotechnology for Biofuels 2. We identified a kinase pathway, previously reported to be involved is osmosensing, that is required fo negative regulation of the transcription of plant cell wall degrading enzymes. We hypothesize that Neurospora is using this pathway to sense soluble sugars to fine tune its plant cell wall enzyme production. Published in the Proc Natl Acad Sci USA. 3. In a collaborative effort, we identified a new transcription factor that is involved in the regulation of genes encoding enzymes needed for pectin degradation. Published in Biotechnology for Biofuels. 4. We determined that a transcription factor COL-26 integrates nutrient sensing (nitrogen and carbon) important for transcriptional activation of genes encoding cellulases. This was one of the first cases of the characterization of a transcription factor involved in both nitrogen and carbon metabolism. Published in PLoS Genetics. 5. We determined that the SREPB pathway, which is involved in regulating the response to hypoxia in a large number of species, also negatively regulates cellulase production. Importantly, our work showed a relationship between the unfolded response pathway (UPR) and the SREBP pathway that is important to the regulation of cellulase gene transcription. This work was published in MBio. 6. Plant cell wall degrading enzymes have a N-terminal modification, termed pyroglutamate. However, the enzymes involved in this modification in fungi were unknown. We identified two ER-localized glutaminyl cyclases, which are essential for the formation of the N-terminal pyroglutamate on secreted cellulases. We show that the pyroglutamate modification is important for thermostability and resistance to proteases. Published in MBio. Cell Fusion:We wrote a review on the Cell fusion and Heterokaryon Formation (Microbiol Spectrum). We anticipate two to three publications on this topic in the coming year. We showed that two kinase pathway (MAK-1 and MAK-2) function to regulate two transcription factors essential for expression of cell fusion genes. PCD:We rote a review on Regulated Forms of Cell Death for Front Microbiol. We published a paper in PNAS in Feb 2018 showing that PCD in filamentous fungi is regulated by innate immunity genes, a first biochemical and genetic report of the function of the NLR-like receptors in fungi.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Wu VW, Dana CM, Iavarone AT, Clark DS, Glass NL. Identification of Glutaminyl Cyclase Genes Involved in Pyroglutamate Modification of Fungal Lignocellulolytic Enzymes. MBio. 2017 Jan 17;8(1). pii: e02231-16. doi: 10.1128/mBio.02231-16. PMID: 28096492
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Daskalov A, Heller J, Herzog S, Flei�ner A, Glass NL. Molecular Mechanisms Regulating Cell Fusion and Heterokaryon Formation in Filamentous Fungi. Microbiol Spectr. 2017 Mar;5(2). doi: 10.1128/microbiolspec.FUNK-0015-2016. PMID: 28256191
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Glass NL. The Enigmatic Universe of the Herbivore Gut. Trends Biochem Sci. 2016 Jul;41(7):561-562. doi: 10.1016/j.tibs.2016.05.007. PMID: 27257096
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Qin L, Wu VW, Glass NL. Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in Neurospora crassa. MBio. 2017 Apr 18;8(2). pii: e00233-17. doi: 10.1128/mBio.00233-17. PMID: 28420736
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Xiong Y, Wu VW, Lubbe A, Qin L, Deng S, Kennedy M, Bauer D, Singan VR, Barry K, Northen TR, Grigoriev IV, Glass NL. A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism. PLoS Genet. 2017 May 3;13(5):e1006737. doi: 10.1371/journal.pgen.1006737. PMID: 28467421
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Thieme N, Wu VW, Dietschmann A, Salamov AA, Wang M, Johnson J, Singan VR, Grigoriev IV, Glass NL, Somerville CR, Benz JP. The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa. Biotechnol Biofuels. 2017 Jun 12;10:149. doi: 10.1186/s13068-017-0807-z. PMID: 28616073
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL. Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa. Biotechnol Biofuels. 2017 Sep 21;10:225. doi: 10.1186/s13068-017-0901-2. PMID: 28947916
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Gon�alves AP, Heller J, Daskalov A, Videira A, Glass NL. Regulated Forms of Cell Death in Fungi. Front Microbiol. 2017 Sep 21;8:1837. doi: 10.3389/fmicb.2017.01837. PMID: 28983298
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Plant Biomass Deconstruction:Scientific researchers in academia and biotechnology fields; biofuelproduction agencies. Cell Fusion: Scientific researchers working on human, animal and plant systems interested in cell fusion mechanisms. Application of cell fusion to biotechnology sector and industrial fermentation using filamentous fungi. Programmed Cell Death:Scientific researchers in academia and researchers in pharmaceutical, biotechnological and agricultural chemical sectors. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work provided training and professional development for five post-doctoral associates, fivegraduate students and 3 undergraduate students. The post-doctoral students and graduate students attended national meetings where they presented their work either via poster presentations or by selected talks. Weekly meeting and presentations as well as biweekly journal clubs were attended and participated in by post-doctoral associates, graduate students and undergraduate students. Additional, graduate students and post-doctoral associates participate in a departmental seminar series geared for presentations by students/post-docs, in addition to a campus wide group focused on fungal research. Undergraduate students were expected to make presentations and write up their projects prior to graduation. How have the results been disseminated to communities of interest?The results of this work have been disseminated via publication in peer-reviewed journal articles and presentations at national and international meetings. What do you plan to do during the next reporting period to accomplish the goals?Plant Biomass Deconstruction: We have identified new mutants that result in the hyper- production of lignocellulolytic enzymes and have clarifiedthe biochemical and physiological pathways involved. In addition, in collaboration with the Joint Genome Institute, we are developing a regulatory map of N. crassa in response to plant biomass that includes ~50 transcription factors and a wide variety of carbon, nitrogen, phosphorus and sulfur souces. The data for this project has been generated and is currently being analyzed. Cell Fusion: We determined that N. crassa populations have fungal languages that affect interactions of genetically different colonies and opens that door to assessing how eukaryotic microbes comunicate with each other. We have also determined that cell fusion between isolates results in rapid cell death that is mediated by Gasdermin homologs, that function in pyroptosis in mammalian cells in response to infection. We will continue to assess the role and function of these chemical languages on the behavior and interactions of fungi. Programmed Cell Death: Polymorphisms at certain genes result in death of germinated asexual spores (germlings) in N. crassa; we have developed high throughput methods to evaluate this proces and have identified conserved genes involved in this process. As asexual spores are the most common infection structure for both plant and animal diseases, this work opens the door to development of drugs that trigger this pathway when asexual spores germinate on their host.
Impacts
What was accomplished under these goals?
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 9.5px Helvetica} p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; font: 7.5px Helvetica} Plant Biomass Deconstruction: During this reporting period, we further defined the regulatory network required for production of plant cell wall degrading enzymes in filamentous fungi, using Neurospora crassa as a model organism. Additionaly, using forward and reverse genetics methods, we identified new enzymes associated with modification of lignocellulosic enzymes. Cell Fusion: During this reporting period, we determined that Neurospora uses chemical languages that mediate fungal behavior. This work was published in the high impact journal PLoS Biol. This article was highlighted both in UCB campus communiques and in Science highlights. Programmed Cell Death: In collaboration with a laboratory in Spain (Lopez-LLorca) and a laboratory in Brazil (Bertolini), we showed that various stresses (membrane disrupting anti-fungals) and nutrient/heat shock stress have specific transcriptional response that revealed novel players in the adaptation of fungi to the stress conditions.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Heller J, Zhao J, Rosenfield G, Kowbel DJ, Gladieux P, Glass NL, 2016. Characterization of greenbeard genes involved in long distance discrimination in a microbial eukaryote. PLoS Biol 14:e1002431.
Jonkers W, Fischer MS, Do HP, Starr TL, Glass NL, 2016. Chemotropisim and cell fusion in Neurospora crassa relies on the formation of distinct protein complexes by HAM-5 and a novel protein HAM-15. Genetics 203:319-334.
Freitas FZ, Virgilio S, Cupertino FB, Kowbel DJ, Fioramonte M, Gozzo FC, Glass NL, Bertolini MC, 2016. The SEB-1 transcription factor binds to the STRE motif in Neurospora crassa and regulates a variety of cellular processes including the stress response and reserve carbohydrate metabolism. G3 6:1327-1343.
Lopez-Moya F, Kowbel DJ, Nueda MJ, Palma-Guerrero J, Glass NL, Lopez-Llorca LV, 2016. Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan. Mol Biosyst 12:391-403.
|
Progress 12/17/14 to 09/30/15
Outputs
Target Audience:Plant Biomass Deconstruction:Scientific researchers in academics and industry who work on filamentous fungi for industrial applications. Government personnel in the Department of Energy. Cell Fusion:Scientific researchers in the academic and biotechnology sector. Programmed Cell Death:Scientific researchers in academia and researchers in the pharmaceutical, biotechnologicaland agricultural chemical sectors. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work provided training and professional development for eightpost-doctoral associates, six graduate students and 5 undergraduate students. The post-doctoral students and graduate students attended international meetings where they presented their work either via poster presentations or by selected talks. Weekly meeting and presentations as well as bi-weekly journal clubs were attended and participated in by post-doctoral associates, graduate students and undergraduate students. Undergraduate students were expected to make presentations and write up their projects prior to graduation. How have the results been disseminated to communities of interest?The results of this work have been disseminated via publication in peer-reviewed journal articles and presentations at national and international meetings. What do you plan to do during the next reporting period to accomplish the goals?Plant Biomass Deconstruction:We have identified additional mutations that result in the production of lignocellulolytic enzymes in N. crassa at industrial levels and are clarifying the biochemical and physiological pathways affected by these mutations. In addition, in collaboration with the Joint Genome Institute, we are developing a regulatory map of N. crassa in response to plant biomass that includes ~50 transcription factors and a wide variety of carbon, nitrogen, phosphorus and sulfur souces. Cell Fusion:We determined that N. crassa populations havefungal languages that affect interactions of genetically different colonies and opens that door to assessing how eukaryotic microbes comunicate with each other. We will continue to assess the role and function of these chemical languages on the behavior and interactions of fungi. Programmed Cell Death:We have determined that polymorphisms at certain genes result in death of germinated asexual spores (germlings) in N. crassa. As asexual spores are the most common infection structure for both plant and animal diseases, this work opens the door to development of drugs that trigger this pathway when asexual spores germinate on their host.
Impacts
What was accomplished under these goals?
Plant Biomass Deconstruction:During this reporting period, we further defined the regulatory network required for production of plant cell wall degrading enzymes in filamentous fungi, using Neurospora crassa as a model organism. This work led to the incorporation of genes from N. crassa into the fermention/biofuel producing organism Saccharomyces cerevisiae, which enabled this organism to utilize components of the plant cell wall that it previously was not capable of utilizing to make fuels. This work led to the patent that was issued in April 2015 entitled "Methods and compositions for improving sugar transport, mixed sugar fermentation and production of biofuels" patent number US8431360. We also identified mutations in N. crassa that resulted in hyper-production of lignocellulolytic enzymes, which are being incorporated into production hosts. Cell Fusion:We identified a new component required for productive cell fusion and membrane merger in N. crassa, and which is conserved among filamentous fungi. These findings are also applicable to membrane merger/cell fusion events that occur during development of bone, placenta and muscle in animals. Programmed Cell Death:We used genomic and chemical approaches to define genes and pathways required for programmed cell death in filamentous fungi. We identified a number of conserved loci involved in the recognition aspect of death and also determined the physiological response, based on transcriptional profiling, of N. crassa to synthetic xanthones that have potential as fungicidal drugs.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
1. Palma-Guerrero J, Zhao J, Gon�alves AP, Starr TL, Glass NL. 2015. Identification and characterization of LDF-2, a predicted FRINGE protein required for membrane integrity during cell fusion in Neurospora crassa. Eukaryot Cell 14:265-77.
2. Goncalves AP, Silva N, Oliveira C, Kowbel DJ, Glass NL, Kijjoe A, Pameira A, Sousa e, Pinto M, Videira A. 2015. Transcription profiling of the Neurospora crassa response to a group of synthetic (thio)xanthones and a natural acetophenone. Genomics Data 4:26-32.
Li X, Yu VY, Lin Y, Chomvong K, Estrela R, Park A, Liang JM, Znameroski EA, Feehan J, Kim SR, Jin YS, Glass NL, Cate JH. 2015. Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels. Elife 4. doi: 10.7554/eLife.05896.
3. Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y. 2015. Detoxification of 5-hydroxymethylfurfural by the Pleurotus ostreatus lignolytic enzymes aryl alcohol oxidase and dehydrogenase. Biotechnol Biofuels 8:63.
4. Zhao J, Gladieux P, Hutchison E, Bueche J, Hall C, Perraudeau F, Glass NL. 2015. Identification of allorecognition loci in Neurospora crassa by genomics and evolutionary approaches. Mol Biol Evol 32:2417-32. doi: 10.1093/molbev/msv125.
6. Reilly MC, Qin L, Craig JP, Starr TL, Glass NL. 2015. Deletion of homologs of the SREBP pathway results in hyper-production of cellulases in Neurospora crassa and Trichoderma reesei. Biotechnol Biofuels. 19;8:121. doi: 10.1186/s13068-015-0297-9.
7. Craig JP, Coradetti ST, Starr TL, Glass NL, 2015. Direct target network of the Neurospora crassa plant cell wall deconstruction regulators, CLR-1, CLR-2 and XLR-1. MBio. 13;6. pii: e01452-15. doi: 10.1128/mBio.01452-15.
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