<i>Deinococcus</i>
            as new chassis for industrial biotechnology: biology, physiology and tools

Gerber, Eva; Bernard, Rémi; Castang, Sandra; Chabot, Nicolas; Coze, Fabien; Dreux-Zigha, A.; Hauser, Ernst A.; Hivin, P.; Joseph, Patrice; Lazarelli, C.; Letellier, Guy; Olive, Jacqueline; Leonetti, Jean-Paul

doi:10.1111/jam.12808

Cited by 82 publications

(57 citation statements)

References 61 publications

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“…percentage of unmapped reads across the samples (∼10%) falls within the expected for 422 RNA-seq experiments in which reads are mapped to a reference genome different from 423 the evaluated isolate [63] [57], and is also consistent with the reported variability among 424 Deinococcus genomes [21]. However, 30% of these unmapped reads showed identity 425 values over 85% against the reference genome through a blast alignment, which reasserts 426 the idea of intraspecific diversity for Deinococcus sp.…”

supporting

confidence: 69%

“…swuensis CG1225, with >60% survival at the highest dose tested (800J/m 2 ), was 345 the most resistant isolate recovered based on our radiation resistance experiments. The 346 UV resistance of Deinococcus spp., a group described as being "among the most 347 radiation-resistant microorganisms that have been discovered", has been widely 348 recognized since 1956 [21]. Some Deinococcus members have shown tolerance to UV 349 radiation (100 to 295 nm), and tolerance to ionizing radiation (5000 -30000 Gy) [60].…”

mentioning

confidence: 99%

“…The high variability in genomic organization 414 (genome size, number of chromosomes, plasmids, etc.) in Deinococcus sequenced isolates 415 has been proposed as a potential source of interesting adaptations [21]. A comparison 416 among D. geothermalis, D gobiensis and D. proteolyticus showed, for example, a core 417 genome of 1369 genes and ∼600-1700 accessory species-specific genes [21], which could 418 harbor potential functional differences even among related species.…”

mentioning

confidence: 99%

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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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supporting

confidence: 69%

mentioning

confidence: 99%

mentioning

confidence: 99%

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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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“…Other features such as the ability to degrade and metabolize sugars and polymeric sugars make Deinococcus spp. an attractive alternative for use in industrial biotechnology (Gerber et al . 2015).…”

Section: Discussionmentioning

confidence: 99%

Gut Microbiome Analysis In Adult Tropical Gars (Atractosteus tropicus)

Méndez-Pérez

García-López

Bautista-López

et al. 2019

Preprint

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Tropical gar (Atractosteus tropicus), is freshwater and estuarine fish that has inhabited 17 the Earth since the Mesozoic era, undergoing limited physiological variation ever since. This 18 omnivorous fish is endemic to southern Mexico and part of Central America. Besides its 19 recognized cultural and scientific relevance, the species has seen remarkable growth in its 20 economic impact due to pisciculture. Previous studies have highlighted the role of microbial 21 communities in fish, particularly those in the gut microbiome, in maintaining their host 22 homeostasis or disease. In this study, we present the first report of the whole taxonomic 23 composition of microbial communities in gut contents of adults' A. tropicus, by sex (female/male) 24 and origin (wild/cultivated). Using culture-independent techniques, we extracted metagenomic 25 DNA that was used for high throughput 16S rDNA profiling by amplifying the V4 -V5 26 hypervariable regions of the bacterial gene. A total of 364,735 total paired-end reads were 27 obtained on an Illumina MiSeq sequencing platform, belonging to 508 identified genera, with the 28 most and least abundant are Cetobacterium, Edwardsiella, Serratia, Clostridium sensu stricto, 29Paludibacter and Campylobacter, Snodgrassella, Albirhodobacter, Lentilitoribacter, respectively. We 30 detected that, by sex and origin, Proteobacteria, Fusobacteria, Firmicutes and Bacteroidetes phyla 31 are the core gut microbiome of the adults' A. tropicus. We discover the Deinococcus-Thermus 32 phylum sequence, wildtype males only, with extremophile capacity in another freshwater fish. 33We also identified the species Lactococcus lactis strains CAU929 and CAU6600, Cp6 and CAU9951, 34Cetobacterium strain H69, Aeromonas hydrophila strains P5 and WR-5-3-2, Aeromonas sobria strain 35 CP DC28 and Aeromonas hydrophila with probiotic potential in aquaculture within the three 36 dominant phyla, especially in wild-type organisms. 37

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“…The selected examples include Vibrio natriegens (endowed with a remarkably fast growth), cyanobacteria (due to their photosynthetic capabilities) and Roseobacter and Halomonas as marine bacterial species with an unique tolerance to saline stress. Other relevant, emerging bacterial species that could be potentially developed as chassis for specific applications include both Shewanella and Geobacter sp., which can be used to engineer microbial fuel cells due to their electron-accepting capabilities; Klebsiella sp., which can produce a variety of low-molecular-weight bulk products using glycerol as carbon source; and Deinococcus, due to its high resistance to DNA damage and broad range of feedstock utilization (Fredrickson et al, 2008;Dantas et al, 2015;Gerber et al, 2015;Kumar and Park, 2018). Although significant research efforts have been invested on alternative bacterial chassis in recent years, much work is still lying ahead to place them at a similar state of acceptance and widespread use as E. coli or B. subtilis.…”

Section: Emergent Bacterial Chassismentioning

confidence: 99%

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Calero

Nikel

2018

Microbial Biotechnology

243

184

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The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.

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Deinococcus as new chassis for industrial biotechnology: biology, physiology and tools

Cited by 82 publications

References 61 publications

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

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

Gut Microbiome Analysis In Adult Tropical Gars (Atractosteus tropicus)

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

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