Impact of a short-term exposure to spaceflight on the phenotype, genome, transcriptome and proteome ofEscherichia coli

Abstract

Escherichia coli (E. coli) is the most widely applied model organism in current biological science. As a widespread opportunistic pathogen, E. coli can survive not only by symbiosis with human, but also outside the host as well, which necessitates the evaluation of its response to the space environment. Therefore, to keep humans safe in space, it is necessary to understand how the bacteria respond to this environment. Despite extensive investigations for a few decades, the response of E. coli to the real space environment is still controversial. To better understand the mechanisms how E. coli overcomes harsh environments such as microgravity in space and to investigate whether these factors may induce pathogenic changes in E. coli that are potentially detrimental to astronauts, we conducted detailed genomics, transcriptomic and proteomic studies on E. coli that experienced 17 days of spaceflight. By comparing two flight strains LCT-EC52 and LCT-EC59 to a control strain LCT-EC106 that was cultured under the same temperature conditions on the ground, we identified metabolism changes, polymorphism changes, differentially expressed genes and proteins in the two flight strains. The flight strains differed from the control in the utilization of more than 30 carbon sources. Two single nucleotide polymorphisms (SNPs) and one deletion were identified in the flight strains. The expression level of more than 1000 genes altered in flight strains. Genes involved in chemotaxis, lipid metabolism and cell motility express differently. Moreover, the two flight strains also differed extensively from each other in terms of metabolism, transcriptome and proteome, indicating the impact of space environment on individual cells is heterogeneous and probably genotype-dependent. This study presents the first systematic profile of E. coli genome, transcriptome and proteome after spaceflight, which helps to elucidate the mechanism that controls the adaptation of microbes to the space environment.

Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission

“…radiodurans ( Fig 6 ). The surface-active compound stearic acid was identified in biosurfactants of several bacterial species [ 76 , 77 ]. Decreased levels of stearic acid associated with the dramatic reduction in biofilm formation of Streptococcus sanguinis nox mutant [ 78 ], suggesting its involvement in stress-related reactions.…”

Molecular Mechanisms of Microbial Survivability in Outer Space: A Systems Biology Approach

“…In response to space environmental stress, microorganisms with great adaptability to survive successfully exhibit certain flexibility in carbon source utilization. Strains of Serratia marcescens, Escherichia coli, and Klebsiella pneumoniae after a long-term flight on-board of the SHENZHOU-8 spacecraft exhibited a difference in carbon source utilization (as suggested by multi-omics analysis), while their morphology or growth patterns were not affected (Li et al, 2014(Li et al, , 2015Wang et al, 2014;Guo et al, 2015;Zhang et al, 2015). Strains of S. marcescens after spaceflight displayed a positive reaction in the sole-carbon-source utilization of D-Mannitol, D-Raffinose, and N-Acetyl neuraminic acid (Wang et al, 2014).…”

“…Frequently observed down-regulation of enzymes involved in amino acid transport and metabolism of space-exposed microorganisms is usually associated with their arrest in growth. Among all the genes of K. pneumonia, E. coli and B. cereus affected during spaceflight on-board of space vehicle, functional category of amino acid transport and metabolism was the most represented (Li et al, 2014(Li et al, , 2015Su et al, 2014;Guo et al, 2015;Zhang et al, 2015). The strain of K. pneumoniae after spaceflight characterized by increased biofilm formation was suggested to use amino acids as an indirect carbon source through TCA cycle in stress-related space conditions (Li et al, 2014).…”

“…Transcriptomic analysis of space exposed B. subtilis spores and Rhodospirillum rubrum exposed to modeled microgravity in frames of the Micro-Ecological Life Support System Alternative (MELiSSA) project showed the down-regulation of genes encoding lipid biosynthetic enzymes (Nicholson et al, 2012;Mastroleo et al, 2013). Multiomic analyses showed that metabolic pathways associated with fatty acid metabolism, phospholipid biosynthetic process, and cellular lipid biosynthetic processes were affected in E. coli and Enterococcus faecium strains after spaceflight (Chang et al, 2013a;Li et al, 2015).…”

“…Comparative genomic analysis of returned after spaceflight E. faecium strain revealed mutation of the arpU gene associated with cell wall growth, which in turn may affect the expression of molecular players responsible for cell wall and membrane biogenesis of E. faecium (Chang et al, 2013a). The post-flight transcriptomic and proteomic studies of E. coli revealed the up-regulation of the envelope stress induced periplasmic protein Spy and the yfbE gene encoding predicted pyridoxal phosphate-dependent enzyme with regulatory functions in cell wall biogenesis (Li et al, 2015;Zhang et al, 2015). A number of differentially expressed genes involved in cell wall and spore structure were described microarray-based analysis of Streptomyces coelicolor during spaceflight and simulated microgravity (Huang et al, 2015).…”