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55. T-toxin virulence genes: unconnected dots in a sea of repeats

Author

Haridas, Sajeet, primary, González, Jennifer B., additional, Riley, Robert, additional, Koriabine, Maxim, additional, Yan, Mi, additional, Ng, Vivian, additional, Rightmyer, Adriana, additional, Grigoriev, Igor V., additional, Baker, Scott E., additional, and Turgeon, B. Gillian, additional

Published
2023
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57. Aspergillus: Genomics of a Cosmopolitan Fungus

Author

Benoit, Isabelle, Malavazi, Iran, Goldman, Gustavo Henrique, Baker, Scott E., de Vries, Ronald P., Varma, Ajit, Series editor, Horwitz, Benjamin A., editor, Mukherjee, Prasun K., editor, Mukherjee, Mala, editor, and Kubicek, Christian P., editor

Published
2013
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59. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, Robert, Salamov, Asaf A., Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitrios, Held, Benjamin W., Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika A., Sun, Hui, LaButti, Kurt M., Schmutz, Jeremy, Jabbour, Dina, Luoi, Hong, Baker, Scott E., Pisabarro, Antonio G., Walton, Jonathan D., Blanchette, Robert A., Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David S., and Grigoriev, Igor V.

Published
2014

68. Online Hydrophilic Interaction Chromatography (HILIC) Enhanced Top-Down Mass Spectrometry Characterization of the SARS-CoV-2 Spike Receptor-Binding Domain

Author

Wilson, Jesse W., primary, Bilbao, Aivett, additional, Wang, Juan, additional, Liao, Yen-Chen, additional, Velickovic, Dusan, additional, Wojcik, Roza, additional, Passamonti, Marta, additional, Zhao, Rui, additional, Gargano, Andrea F. G., additional, Gerbasi, Vincent R., additional, Pas̆a-Tolić, Ljiljana, additional, Baker, Scott E., additional, and Zhou, Mowei, additional

Published
2022
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71. Tracking the Roots of Cellulase Hyperproduction by the Fungus Trichoderma Reesei Using Massively Parallel DNA Sequencing

Author

Le Crom, Stéphane, Schackwitz, Wendy, Pennacchio, Len, Magnuson, Jon K., Culley, David E., Collett, James R., Martin, Joel, Druzhinina, Irina S., Mathis, Hugues, Monot, Frédéric, Seiboth, Bernhard, Cherry, Barbara, Rey, Michael, Berka, Randy, Kubicek, Christian P., Baker, Scott E., Margeot, Antoine, and Bennett, Joan Wennstrom

Published
2009
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72. Genome, Transcriptome, and Secretome Analysis of Wood Decay Fungus Postia placenta Supports Unique Mechanisms of Lignocellulose Conversion

Author

Martinez, Diego, Challacombe, Jean, Morgenstern, Ingo, Hibbett, David, Schmoll, Monika, Kubicek, Christian P., Ferreira, Patricia, Ruiz-Duenas, Francisco J., Martinez, Angel T., Kersten, Phil, Hammel, Kenneth E., Vanden Wymelenberg, Amber, Gaskell, Jill, Lindquist, Erika, Sabat, Grzegorz, BonDurant, Sandra Splinter, Larrondo, Luis F., Canessa, Paulo, Vicuna, Rafael, Yadav, Jagjit, Doddapaneni, Harshavardhan, Subramanian, Venkataramanan, Pisabarro, Antonio G., Lavin, José L., Oguiza, José A., Master, Emma, Henrissat, Bernard, Coutinho, Pedro M., Harris, Paul, Magnuson, Jon Karl, Baker, Scott E., Bruno, Kenneth, Kenealy, William, Hoegger, Patrik J., Kües, Ursula, Ramaiya, Preethi, Lucas, Susan, Salamov, Asaf, Shapiro, Harris, Tu, Hank, Chee, Christine L., Misra, Monica, Xie, Gary, Teter, Sarah, Yaver, Debbie, James, Tim, Mokrejs, Martin, Pospisek, Martin, Grigoriev, Igor V., Brettin, Thomas, Rokhsar, Dan, Berka, Randy, Cullen, Dan, and Dixon, Richard A.

Published
2009
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74. The Fusarium graminearum Genome Reveals a Link between Localized Polymorphism and Pathogen Specialization

Author

Cuomo, Christina A., Güldener, Ulrich, Xu, Jin-Rong, Trail, Frances, Turgeon, B. Gillian, Di Pietro, Antonio, Walton, Jonathan D., Ma, Li-Jun, Baker, Scott E., Rep, Martijn, Adam, Gerhard, Antoniw, John, Baldwin, Thomas, Calvo, Sarah, Chang, Yueh-Long, DeCaprio, David, Gale, Liane R., Gnerre, Sante, Goswami, Rubella S., Hammond-Kosack, Kim, Harris, Linda J., Hilburn, Karen, Kennell, John C., Kroken, Scott, Magnuson, Jon K., Mannhaupt, Gertrud, Mauceli, Evan, Mewes, Hans-Werner, Mitterbauer, Rudolf, Muehlbauer, Gary, Münsterkötter, Martin, Nelson, David, O'Donnell, Kerry, Ouellet, Thérèse, Qi, Weihong, Quesneville, Hadi, Roncero, M. Isabel G., Seong, Kye-Yong, Tetko, Igor V., Urban, Martin, Waalwijk, Cees, Ward, Todd J., Yao, Jiqiang, Birren, Bruce W., and Kistler, H. Corby

Published
2007
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76. Optimizing a High Performing Multiplex-CRISPRi P. putida strain with Integrated Metabolomics and 13C-Metabolic Flux Analyses

Author

Czajka, Jeffrey J, primary, Banerjee, Deepanwita, additional, Eng, Thomas T, additional, Menasalvas, Javier, additional, Yan, Chunsheng, additional, Munoz Munoz, Nathalie, additional, Poirier, Brenton C, additional, Kim, Young-Mo, additional, Baker, Scott E, additional, Tang, Yinjie J, additional, and Mukhopadhyay, Aindrila, additional

Published
2021
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79. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling

Author

McNaughton, Andrew D., primary, Bredeweg, Erin L., additional, Manzer, James, additional, Zucker, Jeremy, additional, Munoz Munoz, Nathalie, additional, Burnet, Meagan C., additional, Nakayasu, Ernesto S., additional, Pomraning, Kyle R., additional, Merkley, Eric D., additional, Dai, Ziyu, additional, Chrisler, William B., additional, Baker, Scott E., additional, St. John, Peter C., additional, and Kumar, Neeraj, additional

Published
2021
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83. Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

Author

Chroumpi, Tania, Peng, Mao, Markillie, Lye Meng, Mitchell, Hugh D, Nicora, Carrie D, Hutchinson, Chelsea M, Paurus, Vanessa, Tolic, Nikola, Clendinen, Chaevien S, Orr, Galya, Baker, Scott E, Mäkelä, Miia R, de Vries, Ronald P, Molecular Plant Physiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Sub Molecular Plant Physiology, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Department of Microbiology, Fungal Genetics and Biotechnology, and Helsinki Institute of Sustainability Science (HELSUS)

Subjects
0301 basic medicine, Histology, lcsh:Biotechnology, 030106 microbiology, Biomedical Engineering, Pentose, Biomass, Bioengineering, Polysaccharide, 03 medical and health sciences, chemistry.chemical_compound, lcsh:TP248.13-248.65, sugar beet pulp, Monosaccharide, L-rhamnose catabolic pathway, Sugar, pentose catabolic pathway, Original Research, 2. Zero hunger, chemistry.chemical_classification, biology, lignocellulosic substrates, Aspergillus niger, Bioengineering and Biotechnology, food and beverages, 15. Life on land, biology.organism_classification, 220 Industrial biotechnology, Xyloglucan, 030104 developmental biology, chemistry, Biochemistry, D-galacturonic acid catabolic pathway, Sugar beet, wheat bran, CAZymes, Biotechnology
Abstract

The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after the hexose D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.

Published
2021

84. Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Chroumpi, Tania, Peng, Mao, Markillie, Lye Meng, Mitchell, Hugh D, Nicora, Carrie D, Hutchinson, Chelsea M, Paurus, Vanessa, Tolic, Nikola, Clendinen, Chaevien S, Orr, Galya, Baker, Scott E, Mäkelä, Miia R, de Vries, Ronald P, Molecular Plant Physiology, Sub Molecular Plant Physiology, Chroumpi, Tania, Peng, Mao, Markillie, Lye Meng, Mitchell, Hugh D, Nicora, Carrie D, Hutchinson, Chelsea M, Paurus, Vanessa, Tolic, Nikola, Clendinen, Chaevien S, Orr, Galya, Baker, Scott E, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

87. Fungal genome sequencing and bioenergy

Author

Baker, Scott E., Thykaer, Jette, Adney, William S., Brettin, Thomas S., Brockman, Fred J., D'haeseleer, Patrik, Martinez, A. Diego, Miller, R. Michael, Rokhsar, Daniel S., Schadt, Christopher W., Torok, Tamas, Tuskan, Gerald, Bennett, Joan, Berka, Randy M., Briggs, Steven P., Heitman, Joseph, Taylor, John, Gillian Turgeon, B., Werner-Washburne, Margaret, and Himmel, Michael E.

Published
2008
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89. Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

Author

Pomraning, Kyle R., primary, Dai, Ziyu, additional, Munoz, Nathalie, additional, Kim, Young-Mo, additional, Gao, Yuqian, additional, Deng, Shuang, additional, Kim, Joonhoon, additional, Hofstad, Beth A., additional, Swita, Marie S., additional, Lemmon, Teresa, additional, Collett, James R., additional, Panisko, Ellen A., additional, Webb-Robertson, Bobbie-Jo M., additional, Zucker, Jeremy D., additional, Nicora, Carrie D., additional, De Paoli, Henrique, additional, Baker, Scott E., additional, Burnum-Johnson, Kristin E., additional, Hillson, Nathan J., additional, and Magnuson, Jon K., additional

Published
2021
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90. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Author

Daly, Paul, Peng, Mao, Mitchell, Hugh D., Kim, Young‐mo, Ansong, Charles, Brewer, Heather, Gijsel, Peter, Lipton, Mary S., Markillie, Lye Meng, Nicora, Carrie D., Orr, Galya, Wiebenga, Ad, Hildén, Kristiina S., Kabel, Mirjam A., Baker, Scott E., Mäkelä, Miia R., Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Fungal Genetics and Biotechnology, Department of Microbiology, Helsinki Institute of Sustainability Science (HELSUS), Department of Food and Nutrition, Molecular Plant Physiology, and Sub Molecular Plant Physiology

Subjects
EXPRESSION, GENES, Hypha, DATABASE, Hyphae, Fungus, Microbiology, SUGAR CATABOLISM, 03 medical and health sciences, STANDARD, Nutrient, Levensmiddelenchemie, Carbon source, Botany, Life Science, PLANTS, Biomass, Research Articles, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 11832 Microbiology and virology, 0303 health sciences, Food Chemistry, biology, Bran, 030306 microbiology, High ability, Aspergillus niger, fungi, food and beverages, 15. Life on land, biology.organism_classification, Adaptation, Physiological, Carbon, ACCURATE MASS, GENOME, VEGETATIVE MYCELIUM, GROWTH, Pectins, Sugar beet, Research Article
Abstract

Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels, respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony. This article is protected by copyright. All rights reserved.

Published
2020

92. A comparative genomics study of 23 Aspergillus species from section Flavi

Author

Sub Molecular Plant Physiology, Molecular Plant Physiology, Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J.M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., Andersen, Mikael R., Sub Molecular Plant Physiology, Molecular Plant Physiology, Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J.M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R.

Published
2020

93. A comparative genomics study of 23 Aspergillus species from section Flavi

Author

Kjaerbolling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Makela, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., Andersen, Mikael R., Kjaerbolling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Makela, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R.

Published
2020

94. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Daly, Paul, Peng, Mao, Mitchell, Hugh D., Kim, Young‐mo, Ansong, Charles, Brewer, Heather, Gijsel, Peter, Lipton, Mary S., Markillie, Lye Meng, Nicora, Carrie D., Orr, Galya, Wiebenga, Ad, Hildén, Kristiina S., Kabel, Mirjam A., Baker, Scott E., Mäkelä, Miia R., Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Daly, Paul, Peng, Mao, Mitchell, Hugh D., Kim, Young‐mo, Ansong, Charles, Brewer, Heather, Gijsel, Peter, Lipton, Mary S., Markillie, Lye Meng, Nicora, Carrie D., Orr, Galya, Wiebenga, Ad, Hildén, Kristiina S., Kabel, Mirjam A., Baker, Scott E., Mäkelä, Miia R., and Vries, Ronald P.

Published
2020

97. Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

Author

Kim, Joonhoon, primary, Coradetti, Samuel T., additional, Kim, Young-Mo, additional, Gao, Yuqian, additional, Yaegashi, Junko, additional, Zucker, Jeremy D., additional, Munoz, Nathalie, additional, Zink, Erika M., additional, Burnum-Johnson, Kristin E., additional, Baker, Scott E., additional, Simmons, Blake A., additional, Skerker, Jeffrey M., additional, Gladden, John M., additional, and Magnuson, Jon K., additional

Published
2021
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100. Genomes to Proteomes

Author

Panisko, Ellen A., Grigoriev, Igor, Daly, Don S., Webb-Robertson, Bobbie-Jo, and Baker, Scott E.

Subjects
genomes to proteomes, gene modeling, eukaryotic gene predictors, ENSEMBL pipeline for vertebrate genomes, proteomics - experimental design, mixed-effects linear statistical modeling, data quality issues, Bioinformatics Resource Manager (BRM) working environment, gene models crucial to proteomics
Abstract

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form.While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic annotation and the generation of high quality gene models, the setup and execution of global proteomics experiments that are quantitative and statistically rigorous and finally add biological context to proteomics.

Published
2009

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