Genes Required for Survival in Microgravity Revealed by Genome-Wide Yeast Deletion Collections Cultured during Spaceflight

Spaceflight is a unique environment with profound effects on biological systems including tissue redistribution and musculoskeletal stresses. However, the more subtle biological effects of spaceflight on cells and organisms are difficult to measure in a systematic, unbiased manner. Here we test the utility of the molecularly barcoded yeast deletion collection to provide a quantitative assessment of the effects of microgravity on a model organism. We developed robust hardware to screen, in parallel, the complete collection of ~4800 homozygous and ~5900 heterozygous (including ~1100 single-copy deletions of essential genes) yeast deletion strains, each carrying unique DNA that acts as strain identifiers. We compared strain fitness for the homozygous and heterozygous yeast deletion collections grown in spaceflight and ground, as well as plus and minus hyperosmolar sodium chloride, providing a second additive stressor. The genome-wide sensitivity profiles obtained from these treatments were then queried for their similarity to a compendium of drugs whose effects on the yeast collection have been previously reported. We found that the effects of spaceflight have high concordance with the effects of DNA-damaging agents and changes in redox state, suggesting mechanisms by which spaceflight may negatively affect cell fitness.

[1]  Michael I. Jordan,et al.  Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[3]  M. Hughes-Fulford,et al.  To infinity … and beyond! Human spaceflight and life science , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[4]  M. Serrano,et al.  Depletion of ribosomal protein L37 occurs in response to DNA damage and activates p53 through the L11/MDM2 pathway , 2010, Cell cycle.

[5]  Corey Nislow,et al.  Bugs, drugs and chemical genomics. , 2011, Nature chemical biology.

[6]  Gabriela F. Ribeiro,et al.  Characterization of DNA damage in yeast apoptosis induced by hydrogen peroxide, acetic acid, and hyperosmotic shock. , 2006, Molecular biology of the cell.

[7]  Brenda J. Andrews,et al.  Functional Analysis With a Barcoder Yeast Gene Overexpression System , 2012, G3: Genes | Genomes | Genetics.

[8]  David Botstein,et al.  Yeast as a Model Organism , 1997, Science.

[9]  D. Botstein,et al.  Yeast: An Experimental Organism for 21st Century Biology , 2011, Genetics.

[10]  D. Colomer,et al.  Mitoxantrone, a topoisomerase II inhibitor, induces apoptosis of B‐chronic lymphocytic leukaemia cells , 1998, British journal of haematology.

[11]  Robert P. St.Onge,et al.  The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes , 2008, Science.

[12]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[13]  Ronald W. Davis,et al.  Mechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling in Yeast , 2005, Genetics.

[14]  N. Doudican,et al.  Oxidative DNA Damage Causes Mitochondrial Genomic Instability in Saccharomyces cerevisiae , 2005, Molecular and Cellular Biology.

[15]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[16]  Gary D. Bader,et al.  Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures , 2014, Science.

[17]  J. Veldhuijzen,et al.  Inertial shear forces and the use of centrifuges in gravity research. What is the proper control? , 2003, Journal of biomechanical engineering.

[18]  J Kiefer,et al.  Space radiation effects and microgravity. , 1999, Mutation research.

[19]  D M Klaus,et al.  Buoyant plumes from solute gradients generated by non-motile Escherichia coli , 2008, Physical biology.

[20]  G. Giaever,et al.  Quantitative Phenotyping via Deep Barcode Sequencing , 2022 .

[21]  J. Loon.  Microgravity and mechanomics , 2007 .

[22]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[23]  Jens Hauslage,et al.  Ground-based facilities for simulation of microgravity: organism-specific recommendations for their use, and recommended terminology. , 2013, Astrobiology.

[24]  Corey Nislow,et al.  The Yeast Deletion Collection: A Decade of Functional Genomics , 2014, Genetics.

[25]  P. Vejpongsa,et al.  Topoisomerase 2β: A Promising Molecular Target for Primary Prevention of Anthracycline‐Induced Cardiotoxicity , 2013, Clinical pharmacology and therapeutics.

[26]  T G Hammond,et al.  Optimized suspension culture: the rotating-wall vessel. , 2001, American journal of physiology. Renal physiology.

[27]  J. Butler,et al.  5-Fluorouracil Enhances Exosome-Dependent Accumulation of Polyadenylated rRNAs , 2004, Molecular and Cellular Biology.

[28]  Soile Tapio,et al.  Supplementary table 1 , 2014 .

[29]  D. Benos,et al.  Focus on "contrasting effects of cPLA2 on epithelial Na+ transport". , 2001, American journal of physiology. Cell physiology.

[30]  A. Takahashi,et al.  Analysis of deletion mutations of the rpsL gene in the yeast Saccharomyces cerevisiae detected after long-term flight on the Russian space station Mir. , 2000, Mutation research.

[31]  Corey Nislow,et al.  Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures , 2007, Nature Protocols.

[32]  T. Hsia,et al.  Diallyl disulfide (DADS) induces apoptosis in human cervical cancer Ca Ski cells via reactive oxygen species and Ca2+-dependent mitochondria-dependent pathway. , 2008, Anticancer research.

[33]  M. D’Incalci,et al.  DNA damage and cytotoxicity of mitoxantrone and doxorubicin in doxorubicin-sensitive and-resistant human colon carcinoma cells , 2004, Cancer Chemotherapy and Pharmacology.

[34]  A. Takahashi,et al.  The effects of microgravity on induced mutation in Escherichia coli and Saccharomyces cerevisiae. , 2001, Advances in space research : the official journal of the Committee on Space Research.