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

Ott, Emanuel; Kawaguchi, Yuko; Kölbl, Denise; Chaturvedi, Palak; Nakagawa, Kazumichi; Yamagishi, Akihiko; Weckwerth, Wolfram; Milojevic, Tetyana

doi:10.1371/journal.pone.0189381

Cited by 26 publications

(46 citation statements)

References 80 publications

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“…The protein band observed at~40 kDa was excised (Uni-Prot Acession: A0A0E3K5T7-slaB = 41 kDa), processed for mass spectrometric analysis and subsequent protein identification as described in ref. 72 .…”

Section: Methodsmentioning

confidence: 99%

CRISPR-mediated gene silencing reveals involvement of the archaeal S-layer in cell division and virus infection

et al. 2019

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The S-layer is a proteinaceous surface lattice found in the cell envelope of bacteria and archaea. In most archaea, a glycosylated S-layer constitutes the sole cell wall and there is evidence that it contributes to cell shape maintenance and stress resilience. Here we use a gene-knockdown technology based on an endogenous CRISPR type III complex to gradually silence slaB, which encodes the S-layer membrane anchor in the hyperthermophilic archaeon Sulfolobus solfataricus. Silenced cells exhibit a reduced or peeled-off S-layer lattice, cell shape alterations and decreased surface glycosylation. These cells barely propagate but increase in diameter and DNA content, indicating impaired cell division; their phenotypes can be rescued through genetic complementation. Furthermore, S-layer depleted cells are less susceptible to infection with the virus SSV1. Our study highlights the usefulness of the CRISPR type III system for gene silencing in archaea, and supports that an intact S-layer is important for cell division and virus susceptibility.

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Section: Methodsmentioning

confidence: 99%

CRISPR-mediated gene silencing reveals involvement of the archaeal S-layer in cell division and virus infection

et al. 2019

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“…Although limited under space-simulated conditions, previous studies have shown a similar tendency after exposure of D . radiodurans to UVC radiation combined with vacuum and solely vacuum [ 23 , 24 ]. Our untargeted metabolomics approach indicated a reduced level of sugars during repair after LEO exposure (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Preliminary experiments with monochromatic lamps at UV 172 nm UV 254 nm, indicated that cells of D. radiodurans should be able to withstand solar UV radiation on the ISS for 1 year as multi-layers of more than 200 μm thickness [ 21 ]. Additionally, several initial investigations prior to the Tanpopo space mission already resolved molecular responses of D. radiodurans to selected simulated parameters of the outer space environment [ 23 , 24 ]. Exposure to extreme conditions such as ionizing radiation, UV radiation and desiccation cause an increase of reactive oxygen species, which severely damage nucleic acids, by forming bipyrimidine dimers or introducing DNA double strand breaks.…”

Section: Introductionmentioning

confidence: 99%

“…It consists of four crucial proteins, UvrA, UvrB, UvrC and UvrD, which in conjunction with each other orchestrate effective DNA repair performance. The Uvr cluster proteins are triggered by the exposure of D. radiodurans to several space-related conditions (UVC and vacuum), albeit the response to these factors is a multi-layered process, in which many other molecular components, in addition to DNA damage repair, are involved [ 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

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Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission

et al. 2020

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Background The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from low Earth orbit, was performed. Methods We monitored Deinococcus radiodurans cells during early stage of recovery after low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in low Earth orbit. Results D. radiodurans cells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane-associated vesicles was observed. On levels of proteins and transcripts, a multi-faceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine, which works as reactive oxygen species scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicates alternations in the energy status, which is needed to repair damaged molecules. Conclusion Low Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacterium Deinococcus radiodurans survived long-term low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2 effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions.

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“…The activity of hydrolases 390 modulating cellular redox processes has been described for many organisms [56] and in 391 D. radiodurans it prevents incorporation of damaged nucleotides into DNA [1] [38]. RNA enzymes are essential for stress resistance [43] [1] [39] [38].…”

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confidence: 99%

Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems

Diaz-Riano

Posada

Garcia

et al. 2019

Preprint

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Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m 2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m 2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the early resistance strategy used by D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions. 2 and/or radiation conditions are attractive sources of microorganisms with exceptional 3 phenotypic and genotypic properties. The high-mountain Paramo biome, similar to the 4 tundra biome of high latitudes, consists of high-elevation areas subject to harsh 5 environmental conditions. The Paramo biome has a high solar incidence that can induce 6 damage by ultraviolet radiation (UVR) that represents a survival challenge for 7 organisms [50]. Ionizing radiation and UVR affect organisms by damaging cellular 8 components such as nucleic acids, proteins, and lipids [30]. The deleterious effect on 9 cells is caused by direct damage to DNA, such as chromosomal lesions that introduce 10 both double-strand breaks (DSBs) and single-strand breaks (SSBs), and damage due to 11 pyrimidine dimerization and photoproducts that inhibit DNA replication and 12 July 31, 2019 1/19 transcription [2]. Most of the damage, however, is caused indirectly by the production of 13 reactive oxygen species (ROS), such as the chemically reactive superoxide and hydroxyl 14 radicals that in turn affect various cellular constituents, including proteins [30]. 15 The electromagnetic spectrum of UVR is divided into ultraviolet A (UVA) with 16 wavelengths from 315-400 nm (6.31e-19 -4.97e-19 J/m 2 s), ultraviolet B (UVB, from 17 280-315 nm, 7.10e-19 -6.31e-19 J/m 2 s) and ultraviolet C (UVC, from 100-280 nm, 18 1.99e-18 -7.10e-19 J/m 2 s) [64]. The UV electromagnetic spectrum covering UVB and 19 UVC is considered ionizing radiation [51]. While UVC is absorbed by the ozone layer 20 and the atmosphere, about 8% of UVA and 1% of UVB reach the Earth's surface [51]. 21 The harmful effects of UVR on cellular components depend on the wavelength: UVA 22 can travel farther into tissues and contributes to ROS (damage to lipids, proteins, and 23 DNA) whereas UVB produces direct breaks...

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

Cited by 26 publications

References 80 publications

CRISPR-mediated gene silencing reveals involvement of the archaeal S-layer in cell division and virus infection

CRISPR-mediated gene silencing reveals involvement of the archaeal S-layer in cell division and virus infection

Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission

Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems

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