Isolation of rpoB mutations causing rifampicin resistance in Bacillus subtilis spores exposed to simulated Martian surface conditions

Environmental dependence of competitive fitness in rifampin-resistant rpoB mutants of Bacillus subtilis

RNA polymerase (RNAP) is a highly conserved macromolecular machine that contributes to the flow of genetic information from genotype to phenotype. In Bacillus subtilis , mutations in the rpoB gene encoding the β-subunit of RNAP have been shown to alter a number of global phenotypes including growth, utilization of unusual nutrient sources, sporulation, germination, and production of secondary metabolites. In addition, the spectrum of mutations in rpoB leading to rifampin resistance (Rif R ) can change dramatically depending upon the environment to which B. subtilis cells or spores are exposed. Rif R rpoB mutations have historically been associated with slower growth and reduced fitness; however, these assessments of fitness were conducted on limited collections of mutants in rich laboratory media that poorly reflect natural environments typically inhabited by B. subtilis . Using a novel, deep-sequencing approach in addition to traditional measurements of growth rate, lag time, and pairwise competitions, we demonstrated the competitive advantage of specific rpoB alleles differs depending on the growth environment in which they are determined.

IMPORTANCE

Microbial resistance to antibiotics is a growing threat to public health across the world. Historically, resistance to antibiotics has been associated with reduced fitness. A growing body of evidence indicates that resistance to rifampin, a frontline antibiotic used to treat mycobacterial and biofilm-associated infections, may increase fitness given an appropriate environment even in the absence of the selective antibiotic. Here we experimentally confirm this phenomenon by directly comparing the fitness of multiple rifampin-resistant mutants of Bacillus subtilis in rich LB medium and an asparagine minimal medium. Our research demonstrates that the fitness cost of rifampin resistance can vary greatly depending upon the environment. This has important implications for understanding how microbes develop antimicrobial resistance in the absence of antibiotic selection.

Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii

Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth's biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10^-10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20-45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

Alterations in the Spectrum of Spontaneous Rifampicin-Resistance Mutations in the Bacillus subtilis rpoB Gene after Cultivation in the Human Spaceflight Environment

The effect of Bacillus subtilis exposure to the human spaceflight environment on growth, mutagenic frequency, and spectrum of mutations to rifampicin resistance (RifR) was investigated. B. subtilis cells were cultivated in Biological Research in Canister-Petri Dish Fixation Units (BRIC-PDFUs) on two separate missions to the International Space Station (ISS), dubbed BRIC-18 and BRIC-21, with matching asynchronous ground controls. No statistically significant difference in either growth or in the frequency of mutation to RifR was found in either experiment. However, nucleotide sequencing of the RifR regions of the rpoB gene from RifR mutants revealed dramatic differences in the spectrum of mutations between flight (FL) and ground control (GC) samples, including two newly discovered rpoB alleles in the FL samples (Q137R and L489S). The results strengthen the idea that exposure to the human spaceflight environment causes unique stresses on bacteria, leading to alterations in their mutagenic potential.

Cultivation of Staphylococcus epidermidis in the Human Spaceflight Environment Leads to Alterations in the Frequency and Spectrum of Spontaneous Rifampicin-Resistance Mutations in the rpoB Gene

Bacteria of the genus Staphylococcus are persistent inhabitants of human spaceflight habitats and represent potential opportunistic pathogens. The effect of the human spaceflight environment on the growth and the frequency of mutations to antibiotic resistance in the model organism Staphylococcus epidermidis strain ATCC12228 was investigated. Six cultures of the test organism were cultivated in biological research in canisters-Petri dish fixation units for 122 h on orbit in the International Space Station (ISS) as part of the SpaceX-3 resupply mission. Asynchronous ground controls (GCs) consisted of identical sets of cultures cultivated for 122 h in the ISS Environmental Simulator at Kennedy Space Center. S. epidermidis exhibited significantly lower viable counts but significantly higher frequencies of mutation to rifampicin (Rif) resistance in space vs. GC cultures. The spectrum of mutations in the rpoB gene leading to Rif(R) was altered in S. epidermidis isolates cultivated in the ISS compared to GCs. The results suggest that the human spaceflight environment induces unique physiologic stresses on growing bacterial cells leading to changes in mutagenic potential.

Mutagenesis in bacterial spores exposed to space and simulated martian conditions: data from the EXPOSE-E spaceflight experiment PROTECT

As part of the PROTECT experiment of the EXPOSE-E mission on board the International Space Station (ISS), the mutagenic efficiency of space was studied in spores of Bacillus subtilis 168. After 1.5 years' exposure to selected parameters of outer space or simulated martian conditions, the rates of induced mutations to rifampicin resistance (Rif(R)) and sporulation deficiency (Spo(-)) were quantified. In all flight samples, both mutations, Rif(R) and Spo(-), were induced and their rates increased by several orders of magnitude. Extraterrestrial solar UV radiation (>110 nm) as well as simulated martian UV radiation (>200 nm) led to the most pronounced increase (up to nearly 4 orders of magnitude); however, mutations were also induced in flight samples shielded from insolation, which were exposed to the same conditions except solar irradiation. Nucleotide sequencing located the Rif(R) mutations in the rpoB gene encoding the β-subunit of RNA polymerase. Mutations isolated from flight and parallel mission ground reference (MGR) samples were exclusively localized to Cluster I. The 21 Rif(R) mutations isolated from the flight experiment showed all a C to T transition and were all localized to one hotspot: H482Y. In mutants isolated from the MGR, the spectrum was wider with predicted amino acid changes at residues Q469K/L/R, H482D/P/R/Y, and S487L. The data show the unique mutagenic power of space and martian surface conditions as a consequence of DNA injuries induced by solar UV radiation and space vacuum or the low pressure of Mars.

Transcriptomic responses of germinating Bacillus subtilis spores exposed to 1.5 years of space and simulated martian conditions on the EXPOSE-E experiment PROTECT

Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus, it is important to understand their global responses to long-term exposure to space or martian environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low-Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted, fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon), and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated martian conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.

Role of altered rpoB alleles in Bacillus subtilis sporulation and spore resistance to heat, hydrogen peroxide, formaldehyde, and glutaraldehyde

Mutations in the RNA polymerase β-subunit gene rpoB causing resistance to rifampicin (Rif(R)) in Bacillus subtilis were previously shown to lead to alterations in the expression of a number of global phenotypes known to be under transcriptional control. To better understand the influence of rpoB mutations on sporulation and spore resistance to heat and chemicals, cells and spores of the wild-type and twelve distinct congenic Rif(R) mutant strains of B. subtilis were tested. Different levels of glucose catabolite repression during sporulation and spore resistance to heat and chemicals were observed in the Rif(R) mutants, indicating the important role played by the RNA polymerase β-subunit, not only in the catalytic aspect of transcription, but also in the initiation of sporulation and in the spore resistance properties of B. subtilis.

Enhanced S-adenosyl-l-methionine production in Saccharomyces cerevisiae by spaceflight culture, overexpressing methionine adenosyltransferase and optimizing cultivation

AIMS

S-adenosyl-l-methionine (SAM) is an important biochemical molecule with great potential in the pharmacological and chemotherapeutic fields. In this study, our aims were to enhance SAM production in Saccharomyces cerevisiae.

METHODS AND RESULTS

Through spaceflight culture, a SAM-accumulating strain, S. cerevisiae H5M147, was isolated and found to produce 86·89% more SAM than its ground control strain H5. Amplified fragment length polymorphism (AFLP) analysis demonstrated that there were genetic variations between strain H5M147 and its ground control. Through recombinant DNA technology, the heterologous gene encoding methionine adenosyltransferase was integrated into the genome of strain H5M147. The recombinant strain H5MR83 was selected because its SAM production was increased by 42·98% when compared to strain H5M147. Furthermore, cultivation conditions were optimized using the one-factor-at-a-time and Taguchi methods. Under optimal conditions, strain H5MR83 yielded 7·76 g l(-1) of SAM in shake flask, an increase of 536·07% when compared to the strain H5. Furthermore, 9·64 g l(-1) of SAM was produced in fermenter cultivation.

CONCLUSIONS

A new SAM-accumulating strain, S. cerevisiae H5MR83, was obtained through spaceflight culture and genetic modification. Under optimal conditions, SAM production was increased to a relative high level in our study.

SIGNIFICANCE AND IMPACT OF THE STUDY

Through comprehensive application of multiple methods including spaceflight culture, genetic modification and optimizing cultivation, the yield of SAM could be increased by 6·4 times compared to that in the control strain H5. The obtained S. cerevisiae H5MR83 produced 7·76 g l(-1) of SAM in the flask cultures, a significant improvement on previously reported results. The SAM production period with S. cerevisiae H5MR83 was 84 h, which is shorter than previously reported results. Saccharomyces cerevisiae H5MR83 has considerable potential for use in industrial applications.

Astrobiological aspects of the mutagenesis of cosmic radiation on bacterial spores

Based on their unique resistance to various space parameters, Bacillus endospores are one of the model systems used for astrobiological studies. In this study, spores of B. subtilis were used to study the effects of galactic cosmic radiation (GCR) on spore survival and induced mutagenesis. In interplanetary space, outside Earth's protective magnetic field, spore-containing rocks would be exposed to bombardment by high-energy charged particle radiation from galactic sources and from the Sun, which consists of photons (X-rays, gamma rays), protons, electrons, and heavy, high-energy charged (HZE) particles. B. subtilis spores were irradiated with X-rays and accelerated heavy ions (helium, carbon, silicon and iron) in the linear energy transfer (LET) range of 2-200 keV/mum. Spore survival and the rate of the induced mutations to rifampicin resistance (Rif(R)) depended on the LET of the applied species of ions and radiation, whereas the exposure to high-energy charged particles, for example, iron ions, led to a low level of spore survival and increased frequency of mutation to Rif(R) compared to low-energy charged particles and X-rays. Twenty-one Rif(R) mutant spores were isolated from X-ray and heavy ion-irradiated samples. Nucleotide sequencing located the Rif(R) mutations in the rpoB gene encoding the beta-subunit of RNA polymerase. Most mutations were primarily found in Cluster I and were predicted to result in amino acid changes at residues Q469L, A478V, and H482P/Y. Four previously undescribed alleles in B. subtilis rpoB were isolated: L467P, R484P, and A488P in Cluster I and H507R in the spacer between Clusters I and II. The spectrum of Rif(R) mutations arising from spores exposed to components of GCR is distinctly different from those of spores exposed to simulated space vacuum and martian conditions.

Exposure of DNA and Bacillus subtilis spores to simulated martian environments: use of quantitative PCR (qPCR) to measure inactivation rates of DNA to function as a template molecule

Several NASA and ESA missions are planned for the next decade to investigate the possibility of present or past life on Mars. Evidence of extraterrestrial life will likely rely on the detection of biomolecules, which highlights the importance of preventing forward contamination not only with viable microorganisms but also with biomolecules that could compromise the validity of life-detection experiments. The designation of DNA as a high-priority biosignature makes it necessary to evaluate its persistence in extraterrestrial environments and the effects of those conditions on its biological activity. We exposed DNA deposited on spacecraft-qualified aluminum coupons to a simulated martian environment for periods ranging from 1 minute to 1 hour and measured its ability to function as a template for replication in a quantitative polymerase chain reaction (qPCR) assay. We found that inactivation of naked DNA or DNA extracted from exposed spores of Bacillus subtilis followed a multiphasic UV-dose response and that a fraction of DNA molecules retained functionality after 60 minutes of exposure to simulated full-spectrum solar radiation in martian atmospheric conditions. The results indicate that forward-contaminant DNA could persist for considerable periods of time at the martian surface.