1
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Soundararajan M, Paddock MB, Dougherty M, Jones HW, Hogan JA, Donovan FM, Galazka JM, Settles AM. Theoretical design of a space bioprocessing system to produce recombinant proteins. NPJ Microgravity 2023; 9:78. [PMID: 37717090 PMCID: PMC10505218 DOI: 10.1038/s41526-023-00324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/06/2023] [Indexed: 09/18/2023] Open
Abstract
Space-based biomanufacturing has the potential to improve the sustainability of deep space exploration. To advance biomanufacturing, bioprocessing systems need to be developed for space applications. Here, commercial technologies were assessed to design space bioprocessing systems to supply a liquid amine carbon dioxide scrubber with active carbonic anhydrase produced recombinantly. Design workflows encompassed biomass dewatering of 1 L Escherichia coli cultures through to recombinant protein purification. Non-crew time equivalent system mass (ESM) analyses had limited utility for selecting specific technologies. Instead, bioprocessing system designs focused on minimizing complexity and enabling system versatility. Three designs that differed in biomass dewatering and protein purification approaches had nearly equivalent ESM of 357-522 kg eq. Values from the system complexity metric (SCM), technology readiness level (TRL), integration readiness level (IRL), and degree of crew assistance metric identified a simpler, less costly, and easier to operate design for automated biomass dewatering, cell lysis, and protein affinity purification.
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Affiliation(s)
| | - Matthew B Paddock
- KBR, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA
| | - Michael Dougherty
- KBR, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA
| | - Harry W Jones
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA
| | - John A Hogan
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA
| | - Frances M Donovan
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA
| | - A Mark Settles
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, Mountain View, CA, 94035, USA.
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2
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Flores P, McBride SA, Galazka JM, Varanasi KK, Zea L. Biofilm formation of Pseudomonas aeruginosa in spaceflight is minimized on lubricant impregnated surfaces. NPJ Microgravity 2023; 9:66. [PMID: 37587131 PMCID: PMC10432549 DOI: 10.1038/s41526-023-00316-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/02/2023] [Indexed: 08/18/2023] Open
Abstract
The undesirable, yet inevitable, presence of bacterial biofilms in spacecraft poses a risk to the proper functioning of systems and to astronauts' health. To mitigate the risks that arise from them, it is important to understand biofilms' behavior in microgravity. As part of the Space Biofilms project, biofilms of Pseudomonas aeruginosa were grown in spaceflight over material surfaces. Stainless Steel 316 (SS316) and passivated SS316 were tested for their relevance as spaceflight hardware components, while a lubricant impregnated surface (LIS) was tested as potential biofilm control strategy. The morphology and gene expression of biofilms were characterized. Biofilms in microgravity are less robust than on Earth. LIS strongly inhibits biofilm formation compared to SS. Furthermore, this effect is even greater in spaceflight than on Earth, making LIS a promising option for spacecraft use. Transcriptomic profiles for the different conditions are presented, and potential mechanisms of biofilm reduction on LIS are discussed.
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Affiliation(s)
- Pamela Flores
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder, CO, 80309, USA.
- Molecular, Cellular, and Developmental Biology Department, University of Colorado Boulder, Boulder, CO, 80309, USA.
| | | | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Kripa K Varanasi
- Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
| | - Luis Zea
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder, CO, 80309, USA.
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3
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Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. Cell Rep Methods 2022; 2:100325. [PMID: 36452864 PMCID: PMC9701605 DOI: 10.1016/j.crmeth.2022.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.
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Affiliation(s)
- Eliah G. Overbey
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca Klotz
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German
- yuri GmbH, Meckenbeuren, Germany
| | | | - Ryan T. Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher E. Mason
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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4
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Nwanaji‐Enwerem JC, Boileau P, Galazka JM, Cardenas A. In vitro relationships of galactic cosmic radiation and epigenetic clocks in human bronchial epithelial cells. Environ Mol Mutagen 2022; 63:184-189. [PMID: 35470505 PMCID: PMC9233067 DOI: 10.1002/em.22483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Ionizing radiation is a well-appreciated health risk, precipitant of DNA damage, and contributor to DNA methylation variability. Nevertheless, relationships of ionizing radiation with DNA methylation-based markers of biological age (i.e. epigenetic clocks) remain poorly understood. Using existing data from human bronchial epithelial cells, we examined in vitro relationships of three epigenetic clock measures (Horvath DNAmAge, MiAge, and epiTOC2) with galactic cosmic radiation (GCR), which is particularly hazardous due to its high linear energy transfer (LET) heavy-ion components. High-LET 56Fe was significantly associated with accelerations in epiTOC2 (β = 192 cell divisions, 95% CI: 71, 313, p-value = .003). We also observed a significant, positive interaction of 56Fe ions and time-in-culture with epiTOC2 (95% CI: 42, 441, p-value = .019). However, only the direct 56Fe ion association remained statistically significant after adjusting for multiple hypothesis testing. Epigenetic clocks were not significantly associated with high-LET 28Si and low-LET X-rays. Our results demonstrate sensitivities of specific epigenetic clock measures to certain forms of GCR. These findings suggest that epigenetic clocks may have some utility for monitoring and better understanding the health impacts of GCR.
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Affiliation(s)
- Jamaji C. Nwanaji‐Enwerem
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, and Department of Emergency MedicineEmory University School of MedicineAtlantaGeorgiaUSA
- Division of Environmental Health Sciences, School of Public Health and Center for Computational BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Philippe Boileau
- Graduate Group in Biostatistics and Center for Computational BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | | | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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5
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Bowen CH, Sargent CJ, Wang A, Zhu Y, Chang X, Li J, Mu X, Galazka JM, Jun YS, Keten S, Zhang F. Microbial production of megadalton titin yields fibers with advantageous mechanical properties. Nat Commun 2021; 12:5182. [PMID: 34462443 PMCID: PMC8405620 DOI: 10.1038/s41467-021-25360-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Manmade high-performance polymers are typically non-biodegradable and derived from petroleum feedstock through energy intensive processes involving toxic solvents and byproducts. While engineered microbes have been used for renewable production of many small molecules, direct microbial synthesis of high-performance polymeric materials remains a major challenge. Here we engineer microbial production of megadalton muscle titin polymers yielding high-performance fibers that not only recapture highly desirable properties of natural titin (i.e., high damping capacity and mechanical recovery) but also exhibit high strength, toughness, and damping energy - outperforming many synthetic and natural polymers. Structural analyses and molecular modeling suggest these properties derive from unique inter-chain crystallization of folded immunoglobulin-like domains that resists inter-chain slippage while permitting intra-chain unfolding. These fibers have potential applications in areas from biomedicine to textiles, and the developed approach, coupled with the structure-function insights, promises to accelerate further innovation in microbial production of high-performance materials.
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Affiliation(s)
- Christopher H Bowen
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Cameron J Sargent
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Ao Wang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Yaguang Zhu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyuan Chang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyue Mu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Young-Shin Jun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
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6
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Nguyen H, Tran D, Galazka JM, Costes SV, Beheshti A, Petereit J, Draghici S, Nguyen T. CPA: a web-based platform for consensus pathway analysis and interactive visualization. Nucleic Acids Res 2021; 49:W114-W124. [PMID: 34037798 PMCID: PMC8262702 DOI: 10.1093/nar/gkab421] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/16/2021] [Accepted: 05/05/2021] [Indexed: 01/06/2023] Open
Abstract
In molecular biology and genetics, there is a large gap between the ease of data collection and our ability to extract knowledge from these data. Contributing to this gap is the fact that living organisms are complex systems whose emerging phenotypes are the results of multiple complex interactions taking place on various pathways. This demands powerful yet user-friendly pathway analysis tools to translate the now abundant high-throughput data into a better understanding of the underlying biological phenomena. Here we introduce Consensus Pathway Analysis (CPA), a web-based platform that allows researchers to (i) perform pathway analysis using eight established methods (GSEA, GSA, FGSEA, PADOG, Impact Analysis, ORA/Webgestalt, KS-test, Wilcox-test), (ii) perform meta-analysis of multiple datasets, (iii) combine methods and datasets to accurately identify the impacted pathways underlying the studied condition and (iv) interactively explore impacted pathways, and browse relationships between pathways and genes. The platform supports three types of input: (i) a list of differentially expressed genes, (ii) genes and fold changes and (iii) an expression matrix. It also allows users to import data from NCBI GEO. The CPA platform currently supports the analysis of multiple organisms using KEGG and Gene Ontology, and it is freely available at http://cpa.tinnguyen-lab.com.
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Affiliation(s)
- Hung Nguyen
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| | - Duc Tran
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| | - Jonathan M Galazka
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Sylvain V Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Juli Petereit
- University of Nevada Reno, Nevada Bioinformatics Center, Reno, NV 89557, USA
| | - Sorin Draghici
- Wayne State University, Department of Computer Science, Detroit, MI 48202, USA
| | - Tin Nguyen
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
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7
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Paul AM, Overbey EG, da Silveira WA, Szewczyk N, Nishiyama NC, Pecaut MJ, Anand S, Galazka JM, Mao XW. Immunological and hematological outcomes following protracted low dose/low dose rate ionizing radiation and simulated microgravity. Sci Rep 2021; 11:11452. [PMID: 34075076 PMCID: PMC8169688 DOI: 10.1038/s41598-021-90439-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/10/2021] [Indexed: 11/09/2022] Open
Abstract
Using a ground-based model to simulate spaceflight [21-days of single-housed, hindlimb unloading (HLU) combined with continuous low-dose gamma irradiation (LDR, total dose of 0.04 Gy)], an in-depth survey of the immune and hematological systems of mice at 7-days post-exposure was performed. Collected blood was profiled with a hematology analyzer and spleens were analyzed by whole transcriptome shotgun sequencing (RNA-sequencing). The results revealed negligible differences in immune differentials. However, hematological system analyses of whole blood indicated large disparities in red blood cell differentials and morphology, suggestive of anemia. Murine Reactome networks indicated majority of spleen cells displayed differentially expressed genes (DEG) involved in signal transduction, metabolism, cell cycle, chromatin organization, and DNA repair. Although immune differentials were not changed, DEG analysis of the spleen revealed expression profiles associated with inflammation and dysregulated immune function persist to 1-week post-simulated spaceflight. Additionally, specific regulation pathways associated with human blood disease gene orthologs, such as blood pressure regulation, transforming growth factor-β receptor signaling, and B cell differentiation were noted. Collectively, this study revealed differential immune and hematological outcomes 1-week post-simulated spaceflight conditions, suggesting recovery from spaceflight is an unremitting process.
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Affiliation(s)
- Amber M Paul
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA. .,Universities Space Research Association, Columbia, MD, 21046, USA. .,Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA.
| | - Eliah G Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Willian A da Silveira
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), Queen's University, Belfast, BT9 5DL, Northern Ireland, UK
| | - Nathaniel Szewczyk
- Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, 45701, USA
| | - Nina C Nishiyama
- Division of Biomedical Engineering Sciences (BMES), Department of Basic Sciences, Loma Linda University, Loma Linda, CA, 92354, USA
| | - Michael J Pecaut
- Division of Biomedical Engineering Sciences (BMES), Department of Basic Sciences, Loma Linda University, Loma Linda, CA, 92354, USA
| | - Sulekha Anand
- Department of Biological Sciences, San Jose University, San Jose, CA, 95192, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Xiao Wen Mao
- Division of Biomedical Engineering Sciences (BMES), Department of Basic Sciences, Loma Linda University, Loma Linda, CA, 92354, USA
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8
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Overbey EG, Saravia-Butler AM, Zhang Z, Rathi KS, Fogle H, da Silveira WA, Barker RJ, Bass JJ, Beheshti A, Berrios DC, Blaber EA, Cekanaviciute E, Costa HA, Davin LB, Fisch KM, Gebre SG, Geniza M, Gilbert R, Gilroy S, Hardiman G, Herranz R, Kidane YH, Kruse CPS, Lee MD, Liefeld T, Lewis NG, McDonald JT, Meller R, Mishra T, Perera IY, Ray S, Reinsch SS, Rosenthal SB, Strong M, Szewczyk NJ, Tahimic CGT, Taylor DM, Vandenbrink JP, Villacampa A, Weging S, Wolverton C, Wyatt SE, Zea L, Costes SV, Galazka JM. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data. iScience 2021; 24:102361. [PMID: 33870146 PMCID: PMC8044432 DOI: 10.1016/j.isci.2021.102361] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab. Analysis of omics data from different spaceflight studies presents unique challenges A standardized pipeline for RNA-seq analysis eliminates data processing variation The GeneLab RNA-seq pipeline includes QC, trimming, mapping, quantification, and DGE Space-relevant data processed with this pipeline are available at genelab.nasa.gov
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Affiliation(s)
- Eliah G Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Amanda M Saravia-Butler
- Logyx, LLC, Mountain View, CA 94043, USA.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Komal S Rathi
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Homer Fogle
- The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Willian A da Silveira
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Richard J Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Joseph J Bass
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Royal Derby Hospital, University of Nottingham & National Institute for Health Research Nottingham Biomedical Research Centre, Derby DE22 3DT, UK
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel C Berrios
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Elizabeth A Blaber
- Center for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Helio A Costa
- Departments of Pathology, and of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samrawit G Gebre
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.,KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Gary Hardiman
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Medical University of South Carolina, Charleston, SC, USA
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219, USA
| | - Colin P S Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA 94035, USA.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA
| | - Ted Liefeld
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - J Tyson McDonald
- Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Robert Meller
- Department of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Strong
- National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson Street, Denver, CO 80206, USA
| | - Nathaniel J Szewczyk
- Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USA
| | - Candice G T Tahimic
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and the Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Silvio Weging
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle 06120, Germany
| | - Chris Wolverton
- Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, USA
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA.,Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Luis Zea
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder 80303 USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
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9
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Rutter L, Barker R, Bezdan D, Cope H, Costes SV, Degoricija L, Fisch KM, Gabitto MI, Gebre S, Giacomello S, Gilroy S, Green SJ, Mason CE, Reinsch SS, Szewczyk NJ, Taylor DM, Galazka JM, Herranz R, Muratani M. A New Era for Space Life Science: International Standards for Space Omics Processing. Patterns (N Y) 2020; 1:100148. [PMID: 33336201 PMCID: PMC7733874 DOI: 10.1016/j.patter.2020.100148] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Space agencies have announced plans for human missions to the Moon to prepare for Mars. However, the space environment presents stressors that include radiation, microgravity, and isolation. Understanding how these factors affect biology is crucial for safe and effective crewed space exploration. There is a need to develop countermeasures, to adapt plants and microbes for nutrient sources and bioregenerative life support, and to limit pathogen infection. Scientists across the world are conducting space omics experiments on model organisms and, more recently, on humans. Optimal extraction of actionable scientific discoveries from these precious datasets will only occur at the collective level with improved standardization. To address this shortcoming, we established ISSOP (International Standards for Space Omics Processing), an international consortium of scientists who aim to enhance standard guidelines between space biologists at a global level. Here we introduce our consortium and share past lessons learned and future challenges related to spaceflight omics.
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Affiliation(s)
- Lindsay Rutter
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Henry Cope
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Kathleen M. Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mariano I. Gabitto
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Samrawit Gebre
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Stefan J. Green
- Genome Research Core, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sigrid S. Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Nathaniel J. Szewczyk
- Ohio Musculoskeletal and Neurological Institute (OMNI), Ohio University, Athens, OH 45701, USA
| | - Deanne M. Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Masafumi Muratani
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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10
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Nwanaji-Enwerem JC, Nwanaji-Enwerem U, Van Der Laan L, Galazka JM, Redeker NS, Cardenas A. A Longitudinal Epigenetic Aging and Leukocyte Analysis of Simulated Space Travel: The Mars-500 Mission. Cell Rep 2020; 33:108406. [PMID: 33242403 PMCID: PMC7786521 DOI: 10.1016/j.celrep.2020.108406] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/24/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
Astronauts undertaking long-duration space missions may be vulnerable to unique stressors that can impact human aging. Nevertheless, few studies have examined the relationship of mission duration with DNA-methylation-based biomarkers of aging in astronauts. Using data from the six participants of the Mars-500 mission, a high-fidelity 520-day ground simulation experiment, we tested relationships of mission duration with five longitudinally measured blood DNA-methylation-based metrics: DNAmGrimAge, DNAmPhenoAge, DNA-methylation-based estimator of telomere length (DNAmTL), mitotic divisions (epigenetic mitotic clock [epiTOC2]), and pace of aging (PoA). We provide evidence that, relative to baseline, mission duration was associated with significant decreases in epigenetic aging. However, only decreases in DNAmPhenoAge remained significant 7 days post-mission. We also observed significant changes in estimated proportions of plasmablasts, CD4T, CD8 naive, and natural killer (NK) cells. Only decreases in NK cells remained significant post-mission. If confirmed more broadly, these findings contribute insights to improve the understanding of the biological aging implications for individuals experiencing long-duration space travel. Long-duration space travel is marked by a unique combination of stressors known to impact human aging. Using data from six participants of the Mars-500 mission, a high-fidelity 520-day ground simulation experiment, Nwanaji-Enwerem et al. report significant associations of mission duration with decreased biological aging measured via blood DNA methylation.
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Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, and MD/PhD Program, Harvard Medical School, Boston, MA 02115, USA; Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | | | - Lars Van Der Laan
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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11
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Lai Polo SH, Saravia-Butler AM, Boyko V, Dinh MT, Chen YC, Fogle H, Reinsch SS, Ray S, Chakravarty K, Marcu O, Chen RB, Costes SV, Galazka JM. RNAseq Analysis of Rodent Spaceflight Experiments Is Confounded by Sample Collection Techniques. iScience 2020; 23:101733. [PMID: 33376967 PMCID: PMC7756143 DOI: 10.1016/j.isci.2020.101733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/04/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
To understand the physiological changes that occur in response to spaceflight, mice are transported to the International Space Station (ISS) and housed for variable periods of time before euthanasia on-orbit or return to Earth. Sample collection under such difficult conditions introduces confounding factors that need to be identified and addressed. We found large changes in the transcriptome of mouse tissues dissected and preserved on-orbit compared with tissues from mice euthanized on-orbit, preserved, and dissected after return to Earth. Changes due to preservation method eclipsed those between flight and ground samples, making it difficult to identify spaceflight-specific changes. Follow-on experiments to interrogate the roles of euthanasia methods, tissue and carcass preservation protocols, and library preparation methods suggested that differences due to preservation protocols are exacerbated when coupled with polyA selection. This has important implications for the interpretation of existing datasets and the design of future experiments. Experimentation is necessary to understand how organisms respond to space Specialized protocols are used for preserving biological samples on the ISS RNAseq datasets are impacted by preservation protocols used on the ISS Impacts can be alleviated with improved carcass preservation protocols
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Affiliation(s)
- San-Huei Lai Polo
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Amanda M Saravia-Butler
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,Logyx, LLC, Mountain View, CA 94043, USA
| | - Valery Boyko
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Marie T Dinh
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,Logyx, LLC, Mountain View, CA 94043, USA
| | - Yi-Chun Chen
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Homer Fogle
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | | | - Oana Marcu
- Carl Sagan Center, SETI Institute, Mountain View, CA 94043, USA
| | - Rick B Chen
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
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12
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Beheshti A, Chakravarty K, Fogle H, Fazelinia H, Silveira WAD, Boyko V, Polo SHL, Saravia-Butler AM, Hardiman G, Taylor D, Galazka JM, Costes SV. Author Correction: Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. Sci Rep 2020; 10:1517. [PMID: 31988426 PMCID: PMC6985101 DOI: 10.1038/s41598-020-58490-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Afshin Beheshti
- Wyle Labs, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
| | | | - Homer Fogle
- Wyle Labs, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core Facility, and the Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | - Valery Boyko
- Wyle Labs, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - San-Huei Lai Polo
- Wyle Labs, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | | | - Gary Hardiman
- Institute for Global Food Security, Queens University Belfast, Belfast, UK
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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13
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Abstract
Microbially produced protein-based materials (PBMs) are appealing due to use of renewable feedstock, low energy requirements, tunable side-chain chemistry, and biodegradability. However, high-strength PBMs typically have high molecular weights (HMW) and repetitive sequences that are difficult to microbially produce due to genetic instability and metabolic burden. We report the development of a biosynthetic strategy termed seeded chain-growth polymerization (SCP) for synthesis of HMW PBMs in living bacterial cells. SCP uses split intein (SI) chemistry to cotranslationally polymerize relatively small, genetically stable material protein subunits, effectively preventing intramolecular cyclization. We apply SCP to bioproduction of spider silk in Escherichia coli, generating HMW spider silk proteins (spidroins) up to 300 kDa, resulting in spidroin fibers of high strength, modulus, and toughness. SCP provides a modular strategy to synthesize HMW, repetitive material proteins, and may facilitate bioproduction of a variety of high-performance PBMs for broad applications.
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Affiliation(s)
| | | | | | | | - Jonathan M. Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, California 94035, United States
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14
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Overbey EG, Paul AM, da Silveira WA, Tahimic CGT, Reinsch SS, Szewczyk N, Stanbouly S, Wang C, Galazka JM, Mao XW. Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae. Int J Mol Sci 2019; 20:ijms20174094. [PMID: 31443374 PMCID: PMC6747492 DOI: 10.3390/ijms20174094] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 02/07/2023] Open
Abstract
Spaceflight poses many challenges for humans. Ground-based analogs typically focus on single parameters of spaceflight and their associated acute effects. This study assesses the long-term transcriptional effects following single and combination spaceflight analog conditions using the mouse model: simulated microgravity via hindlimb unloading (HLU) and/or low-dose γ-ray irradiation (LDR) for 21 days, followed by 4 months of readaptation. Changes in gene expression and epigenetic modifications in brain samples during readaptation were analyzed by whole transcriptome shotgun sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS). The results showed minimal gene expression and cytosine methylation alterations at 4 months readaptation within single treatment conditions of HLU or LDR. In contrast, following combined HLU+LDR, gene expression and promoter methylation analyses showed multiple altered pathways involved in neurogenesis and neuroplasticity, the regulation of neuropeptides, and cellular signaling. In brief, neurological readaptation following combined chronic LDR and HLU is a dynamic process that involves pathways that regulate neuronal function and structure and may lead to late onset neurological sequelae.
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Affiliation(s)
- Eliah G Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Amber M Paul
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Universities Space Research Association, Columbia, MD 21046, USA
| | - Willian A da Silveira
- Institute for Global Food Security (IGF), School of Biological Sciences, Queen's University, Belfast, Northern Ireland BT7 1NN, UK
| | - Candice G T Tahimic
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- KBR, Moffett Field, CA 94035, USA
| | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Nathaniel Szewczyk
- MRC/ARUK Centre for Musculoskeletal Ageing Research & National Institute for Health Research Nottingham Biomedical Research Centre, Royal Derby Hospital, University of Nottingham, Derby DE22 3DT, UK
| | - Seta Stanbouly
- Division of Biomedical Engineering Sciences (BMES), Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| | - Xiao Wen Mao
- Division of Biomedical Engineering Sciences (BMES), Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA.
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15
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Beheshti A, Shirazi-Fard Y, Choi S, Berrios D, Gebre SG, Galazka JM, Costes SV. Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform. J Vis Exp 2019. [PMID: 30688299 DOI: 10.3791/58447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Performing biological experiments in space requires special accommodations and procedures to ensure that these investigations are performed effectively and efficiently. Moreover, given the infrequency of these experiments it is imperative that their impacts be maximized. The rapid advancement of omics technologies offers an opportunity to dramatically increase the volume of data produced from precious spaceflight specimens. To capitalize on this, NASA has developed the GeneLab platform to provide unrestricted access to spaceflight omics data and encourage its widespread analysis. Rodents (both rats and mice) are common model organisms used by scientists to investigate space-related biological impacts. The enclosure that house rodents during spaceflight are called Rodent Habitats (formerly Animal Enclosure Modules), and are substantially different from standard vivarium cages in their dimensions, air flow, and access to water and food. In addition, due to environmental and atmospheric conditions on the International Space Station (ISS), animals are exposed to a higher CO2 concentration. We recently reported that mice in the Rodent Habitats experience large changes in their transcriptome irrespective of whether animals were on the ground or in space. Furthermore, these changes were consistent with a hypoxic response, potentially driven by higher CO2 concentrations. Here we describe how a typical rodent experiment is performed in space, how omics data from these experiments can be accessed through the GeneLab platform, and how to identify key factors in this data. Using this process, any individual can make critical discoveries that could change the design of future space missions and activities.
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Affiliation(s)
- Afshin Beheshti
- WYLE Labs, Space Biosciences Division, NASA Ames Research Center;
| | | | - Sungshin Choi
- WYLE Labs, Space Biosciences Division, NASA Ames Research Center
| | | | - Samrawit G Gebre
- WYLE Labs, Space Biosciences Division, NASA Ames Research Center
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16
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Ray S, Gebre S, Fogle H, Berrios DC, Tran PB, Galazka JM, Costes SV. GeneLab: Omics database for spaceflight experiments. Bioinformatics 2018; 35:1753-1759. [DOI: 10.1093/bioinformatics/bty884] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Shayoni Ray
- Space Biosciences Division, USRA/NASA Ames Research Center, Moffett Field, CA, USA
| | - Samrawit Gebre
- Space Biosciences Division, KBRwyle/NASA Ames Research Center, Moffett Field, CA, USA
| | - Homer Fogle
- Space Biosciences Division, KBRwyle/NASA Ames Research Center, Moffett Field, CA, USA
| | - Daniel C Berrios
- Space Biosciences Division, USRA/NASA Ames Research Center, Moffett Field, CA, USA
| | - Peter B Tran
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
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17
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Bowen CH, Dai B, Sargent CJ, Bai W, Ladiwala P, Feng H, Huang W, Kaplan DL, Galazka JM, Zhang F. Recombinant Spidroins Fully Replicate Primary Mechanical Properties of Natural Spider Silk. Biomacromolecules 2018; 19:3853-3860. [DOI: 10.1021/acs.biomac.8b00980] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | | | | | | | | | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Jonathan M. Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, California 94035, United States
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18
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Xiao Y, Wang S, Rommelfanger S, Balassy A, Barba-Ostria C, Gu P, Galazka JM, Zhang F. Developing a Cas9-based tool to engineer native plasmids in Synechocystis sp. PCC 6803. Biotechnol Bioeng 2018; 115:2305-2314. [PMID: 29896914 DOI: 10.1002/bit.26747] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/06/2018] [Accepted: 06/05/2018] [Indexed: 01/05/2023]
Abstract
The oxygenic photosynthetic bacterium Synechocystis sp. PCC 6803 (S6803) is a model cyanobacterium widely used for fundamental research and biotechnology applications. Due to its polyploidy, existing methods for genome engineering of S6803 require multiple rounds of selection to modify all genome copies, which is time-consuming and inefficient. In this study, we engineered the Cas9 tool for one-step, segregation-free genome engineering. We further used our Cas9 tool to delete three of seven S6803 native plasmids. Our results show that all three small-size native plasmids, but not the large-size native plasmids, can be deleted with this tool. To further facilitate heterologous gene expression in S6803, a shuttle vector based on the native plasmid pCC5.2 was created. The shuttle vector can be introduced into Cas9-containing S6803 in one step without requiring segregation and can be stably maintained without antibiotic pressure for at least 30 days. Moreover, genes encoded on the shuttle vector remain functional after 30 days of continuous cultivation without selective pressure. Thus, this study provides a set of new tools for rapid modification of the S6803 genome and for stable expression of heterologous genes, potentially facilitating both fundamental research and biotechnology applications using S6803.
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Affiliation(s)
- Yi Xiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Present address: State Key Laboratory for Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaojie Wang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Sarah Rommelfanger
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missori
| | - Andrea Balassy
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Carlos Barba-Ostria
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Present address: Department of Health Sciences, Ambato Technical University, Ambato, Ecuador
| | - Pengfei Gu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Jonathan M Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Mountain View, California
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missori
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Misssori
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19
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Galazka JM, Klocko AD, Uesaka M, Honda S, Selker EU, Freitag M. Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3. Genome Res 2016; 26:1069-80. [PMID: 27260477 PMCID: PMC4971769 DOI: 10.1101/gr.203182.115] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 06/02/2016] [Indexed: 01/14/2023]
Abstract
Eukaryotic genomes are organized into chromatin domains with three-dimensional arrangements that presumably result from interactions between the chromatin constituents—proteins, DNA, and RNA—within the physical constraints of the nucleus. We used chromosome conformation capture (3C) followed by high-throughput sequencing (Hi-C) with wild-type and mutant strains of Neurospora crassa to gain insight into the role of heterochromatin in the organization and function of the genome. We tested the role of three proteins thought to be important for establishment of heterochromatin, namely, the histone H3 lysine 9 methyltransferase DIM-5, Heterochromatin Protein 1 (HP1), which specifically binds to the product of DIM-5 (trimethylated H3 lysine 9 [H3K9me3]), and DIM-3 (importin alpha), which is involved in DIM-5 localization. The average genome configuration of the wild-type strain revealed strong intra- and inter-chromosomal associations between both constitutive and facultative heterochromatic domains, with the strongest interactions among the centromeres, subtelomeres, and interspersed heterochromatin. Surprisingly, loss of either H3K9me3 or HP1 had only mild effects on heterochromatin compaction, whereas dim-3 caused more drastic changes, specifically decreasing interactions between constitutive heterochromatic domains. Thus, associations between heterochromatic regions are a major component of the chromosome conformation in Neurospora, but two widely studied key heterochromatin proteins are not necessary, implying that undefined protein factors play key roles in maintaining overall chromosome organization.
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Affiliation(s)
- Jonathan M Galazka
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Andrew D Klocko
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Miki Uesaka
- Department of Biochemistry and Bioinformative Sciences, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Shinji Honda
- Department of Biochemistry and Bioinformative Sciences, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
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20
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Abstract
Chromatin structure can affect the organization and maintenance of chromosomes. Recent discoveries in several filamentous fungi suggest mechanisms for the clustering and co-regulation of secondary metabolite genes or pathogenicity islands. An extreme case of this may be fungal 'accessory', 'conditionally dispensable', or 'supernumerary' chromosomes that often confer beneficial traits. Fungal supernumerary chromosomes may be derived by similar mechanisms as animal or plant B chromosomes, and we thus propose that this term should be reconsidered to capture the wide variety of fungal accessory chromosomes. In some fungi, both the 'ends' of chromosomes and these 'odd B chromosomes are enriched with a silencing histone modification, H3 lysine 27 trimethylation (H3K27me3), suggesting parallel mechanisms in evolving subtelomeric or B-chromosomal pathogenicity islands and secondary metabolite clusters (SMCs).
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Affiliation(s)
- Jonathan M Galazka
- Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States.
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21
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Chomvong K, Kordić V, Li X, Bauer S, Gillespie AE, Ha SJ, Oh EJ, Galazka JM, Jin YS, Cate JHD. Overcoming inefficient cellobiose fermentation by cellobiose phosphorylase in the presence of xylose. Biotechnol Biofuels 2014; 7:85. [PMID: 24944578 PMCID: PMC4061319 DOI: 10.1186/1754-6834-7-85] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/21/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cellobiose and xylose co-fermentation holds promise for efficiently producing biofuels from plant biomass. Cellobiose phosphorylase (CBP), an intracellular enzyme generally found in anaerobic bacteria, cleaves cellobiose to glucose and glucose-1-phosphate, providing energetic advantages under the anaerobic conditions required for large-scale biofuel production. However, the efficiency of CBP to cleave cellobiose in the presence of xylose is unknown. This study investigated the effect of xylose on anaerobic CBP-mediated cellobiose fermentation by Saccharomyces cerevisiae. RESULTS Yeast capable of fermenting cellobiose by the CBP pathway consumed cellobiose and produced ethanol at rates 61% and 42% slower, respectively, in the presence of xylose than in its absence. The system generated significant amounts of the byproduct 4-O-β-d-glucopyranosyl-d-xylose (GX), produced by CBP from glucose-1-phosphate and xylose. In vitro competition assays identified xylose as a mixed-inhibitor for cellobiose phosphorylase activity. The negative effects of xylose were effectively relieved by efficient cellobiose and xylose co-utilization. GX was also shown to be a substrate for cleavage by an intracellular β-glucosidase. CONCLUSIONS Xylose exerted negative impacts on CBP-mediated cellobiose fermentation by acting as a substrate for GX byproduct formation and a mixed-inhibitor for cellobiose phosphorylase activity. Future efforts will require efficient xylose utilization, GX cleavage by a β-glucosidase, and/or a CBP with improved substrate specificity to overcome the negative impacts of xylose on CBP in cellobiose and xylose co-fermentation.
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Affiliation(s)
- Kulika Chomvong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Vesna Kordić
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Xin Li
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Stefan Bauer
- Energy Biosciences Institute, University of California, Berkeley, CA, USA
| | - Abigail E Gillespie
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Suk-Jin Ha
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Bioengineering and Technology, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun Joong Oh
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Jonathan M Galazka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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22
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Lin Y, Chomvong K, Acosta-Sampson L, Estrela R, Galazka JM, Kim SR, Jin YS, Cate JHD. Leveraging transcription factors to speed cellobiose fermentation by Saccharomyces cerevisiae. Biotechnol Biofuels 2014; 7:126. [PMID: 25435910 PMCID: PMC4243952 DOI: 10.1186/s13068-014-0126-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/06/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae, a key organism used for the manufacture of renewable fuels and chemicals, has been engineered to utilize non-native sugars derived from plant cell walls, such as cellobiose and xylose. However, the rates and efficiencies of these non-native sugar fermentations pale in comparison with those of glucose. Systems biology methods, used to understand biological networks, hold promise for rational microbial strain development in metabolic engineering. Here, we present a systematic strategy for optimizing non-native sugar fermentation by recombinant S. cerevisiae, using cellobiose as a model. RESULTS Differences in gene expression between cellobiose and glucose metabolism revealed by RNA deep sequencing indicated that cellobiose metabolism induces mitochondrial activation and reduces amino acid biosynthesis under fermentation conditions. Furthermore, glucose-sensing and signaling pathways and their target genes, including the cAMP-dependent protein kinase A pathway controlling the majority of glucose-induced changes, the Snf3-Rgt2-Rgt1 pathway regulating hexose transport, and the Snf1-Mig1 glucose repression pathway, were at most only partially activated under cellobiose conditions. To separate correlations from causative effects, the expression levels of 19 transcription factors perturbed under cellobiose conditions were modulated, and the three strongest promoters under cellobiose conditions were applied to fine-tune expression of the heterologous cellobiose-utilizing pathway. Of the changes in these 19 transcription factors, only overexpression of SUT1 or deletion of HAP4 consistently improved cellobiose fermentation. SUT1 overexpression and HAP4 deletion were not synergistic, suggesting that SUT1 and HAP4 may regulate overlapping genes important for improved cellobiose fermentation. Transcription factor modulation coupled with rational tuning of the cellobiose consumption pathway significantly improved cellobiose fermentation. CONCLUSIONS We used systems-level input to reveal the regulatory mechanisms underlying suboptimal metabolism of the non-glucose sugar cellobiose. By identifying key transcription factors that cause suboptimal cellobiose fermentation in engineered S. cerevisiae, and by fine-tuning the expression of a heterologous cellobiose consumption pathway, we were able to greatly improve cellobiose fermentation by engineered S. cerevisiae. Our results demonstrate a powerful strategy for applying systems biology methods to rapidly identify metabolic engineering targets and overcome bottlenecks in performance of engineered strains.
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Affiliation(s)
- Yuping Lin
- />Departments of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Kulika Chomvong
- />Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Ligia Acosta-Sampson
- />Departments of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Raíssa Estrela
- />Departments of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Jonathan M Galazka
- />Departments of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Soo Rin Kim
- />Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
- />Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Yong-Su Jin
- />Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
- />Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Jamie HD Cate
- />Departments of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- />Chemistry, University of California, Berkeley, CA 94720 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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23
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Znameroski EA, Li X, Tsai JC, Galazka JM, Glass NL, Cate JHD. Evidence for transceptor function of cellodextrin transporters in Neurospora crassa. J Biol Chem 2013; 289:2610-9. [PMID: 24344125 DOI: 10.1074/jbc.m113.533273] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Neurospora crassa colonizes burnt grasslands and metabolizes both cellulose and hemicellulose from plant cell walls. When switched from a favored carbon source to cellulose, N. crassa dramatically up-regulates expression and secretion of genes encoding lignocellulolytic enzymes. However, the means by which N. crassa and other filamentous fungi sense the presence of cellulose in the environment remains unclear. Previously, we have shown that a N. crassa mutant carrying deletions of three β-glucosidase enzymes (Δ3βG) lacks β-glucosidase activity, but efficiently induces cellulase gene expression and cellulolytic activity in the presence of cellobiose as the sole carbon source. These observations indicate that cellobiose, or a modified version of cellobiose, functions as an inducer of lignocellulolytic gene expression and activity in N. crassa. Here, we show that in N. crassa, two cellodextrin transporters, CDT-1 and CDT-2, contribute to cellulose sensing. A N. crassa mutant carrying deletions for both transporters is unable to induce cellulase gene expression in response to crystalline cellulose. Furthermore, a mutant lacking genes encoding both the β-glucosidase enzymes and cellodextrin transporters (Δ3βGΔ2T) does not induce cellulase gene expression in response to cellobiose. Point mutations that severely reduce cellobiose transport by either CDT-1 or CDT-2 when expressed individually do not greatly impact cellobiose induction of cellulase gene expression. These data suggest that the N. crassa cellodextrin transporters act as "transceptors" with dual functions - cellodextrin transport and receptor signaling that results in downstream activation of cellulolytic gene expression. Similar mechanisms of transceptor activity likely occur in related ascomycetes used for industrial cellulase production.
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24
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Li S, Ha SJ, Kim HJ, Galazka JM, Cate JHD, Jin YS, Zhao H. Investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization. J Biotechnol 2013; 168:1-6. [PMID: 23954547 DOI: 10.1016/j.jbiotec.2013.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
Functional expression of a cellodextrin transporter and an intracellular β-glucosidase from Neurospora crassa in Saccharomyces cerevisiae enables simultaneous co-fermentation of cellobiose and non-glucose sugars such as xylose. Here we investigate the functional role of aldose 1-epimerase (AEP) in engineered cellobiose utilization. One AEP (Gal10) and two putative AEPs (Yhr210c and Ynr071c sharing 50.6% and 51.0% amino acid identity with Gal10, respectively) were selected. Deletion of GAL10 led to complete loss of both AEP activity and cell growth on cellobiose, while GAL10 complementation restored the AEP activity and cell growth. In addition, deletion of YHR210C or YNR071C resulted in improved cellobiose utilization. These results suggest that the intracellular mutarotation of β-glucose to α-glucose might be a rate controlling step and Gal10 play a crucial role in cellobiose fermentation by engineered S. cerevisiae.
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Affiliation(s)
- Sijin Li
- Energy Biosciences Institute, Institute for Genomic Biology, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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25
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Oh EJ, Ha SJ, Rin Kim S, Lee WH, Galazka JM, Cate JH, Jin YS. Enhanced xylitol production through simultaneous co-utilization of cellobiose and xylose by engineered Saccharomyces cerevisiae. Metab Eng 2013; 15:226-34. [DOI: 10.1016/j.ymben.2012.09.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 08/17/2012] [Accepted: 09/14/2012] [Indexed: 11/26/2022]
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26
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Abstract
How centromeres are assembled and maintained remains one of the fundamental questions in cell biology. Over the past 20 years, the idea of centromeres as precise genetic loci has been replaced by the realization that it is predominantly the protein complement that defines centromere localization and function. Thus, placement and maintenance of centromeres are excellent examples of epigenetic phenomena in the strict sense. In contrast, the highly derived "point centromeres" of the budding yeast Saccharomyces cerevisiae and its close relatives are counter-examples for this general principle of centromere maintenance. While we have learned much in the past decade, it remains unclear if mechanisms for epigenetic centromere placement and maintenance are shared among various groups of organisms. For that reason, it seems prudent to examine species from many different phylogenetic groups with the aim to extract comparative information that will yield a more complete picture of cell division in all eukaryotes. This review addresses what has been learned by studying the centromeres of filamentous fungi, a large, heterogeneous group of organisms that includes important plant, animal and human pathogens, saprobes, and symbionts that fulfill essential roles in the biosphere, as well as a growing number of taxa that have become indispensable for industrial use.
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Affiliation(s)
- Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
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27
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Ha SJ, Galazka JM, Joong Oh E, Kordić V, Kim H, Jin YS, Cate JHD. Energetic benefits and rapid cellobiose fermentation by Saccharomyces cerevisiae expressing cellobiose phosphorylase and mutant cellodextrin transporters. Metab Eng 2012. [PMID: 23178501 DOI: 10.1016/j.ymben.2012.11.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Anaerobic bacteria assimilate cellodextrins from plant biomass by using a phosphorolytic pathway to generate glucose intermediates for growth. The yeast Saccharomyces cerevisiae can also be engineered to ferment cellobiose to ethanol using a cellodextrin transporter and a phosphorolytic pathway. However, strains with an intracellular cellobiose phosphorylase initially fermented cellobiose slowly relative to a strain employing an intracellular β-glucosidase. Fermentations by the phosphorolytic strains were greatly improved by using cellodextrin transporters with elevated rates of cellobiose transport. Furthermore under stress conditions, these phosphorolytic strains had higher biomass and ethanol yields compared to hydrolytic strains. These observations suggest that, although cellobiose phosphorolysis has energetic advantages, phosphorolytic strains are limited by the thermodynamics of cellobiose phosphorolysis (ΔG°=+3.6kJmol(-1)). A thermodynamic "push" from the reaction immediately upstream (transport) is therefore likely to be necessary to achieve high fermentation rates and energetic benefits of phosphorolysis pathways in engineered S. cerevisiae.
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Affiliation(s)
- Suk-Jin Ha
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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28
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Abstract
In 2010, our group announced the discovery of two cellodextrin transporter families from the cellulolytic fungus, Neurospora crassa. Furthermore, we demonstrated the utility of these transporters in the production of lignocellulosic biofuels. This discovery was made possible by a decision to systematically study cell wall degradation by N. crassa. The identified transport pathway has opened up a new way of thinking about microbial fermentation of hexoses as well as pentoses derived from plant cell walls. Integrating this pathway with the endogenous metabolism and signaling networks of S. cerevisiae is now a major goal of our group.
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Affiliation(s)
- Jonathan M Galazka
- Department of Molecular and Cell Biology, University of California at Berkeley, USA
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29
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Abstract
Fungal degradation of plant biomass may provide insights for improving cellulosic biofuel production. We show that the model cellulolytic fungus Neurospora crassa relies on a high-affinity cellodextrin transport system for rapid growth on cellulose. Reconstitution of the N. crassa cellodextrin transport system in Saccharomyces cerevisiae promotes efficient growth of this yeast on cellodextrins. In simultaneous saccharification and fermentation experiments, the engineered yeast strains more rapidly convert cellulose to ethanol when compared with yeast lacking this system.
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Affiliation(s)
- Jonathan M Galazka
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
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30
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Li S, Du J, Sun J, Galazka JM, Glass NL, Cate JHD, Yang X, Zhao H. Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a β-glucosidase in Saccharomyces cerevisiae. Mol BioSyst 2010; 6:2129-32. [DOI: 10.1039/c0mb00063a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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