Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
PLoS ONE (Impact Factor: 3.23). 02/2007; 2(9):e928. DOI: 10.1371/journal.pone.0000928
Source: PubMed


Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, gamma-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species.
The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species.
This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.

Download full-text


Available from: George E Fox,
33 Reads
  • Source
    • "comprehensive studies on the com - plex genetic and metabolic system shared by UV - resistant HAAL microbial communities , herein named as UV - resistome . Current model radiation resistant extremophiles are Deinococcus spp . ( Makarova et al . , 2001 ) , Halobacterium spp . ( Baliga et al . , 2004 ; Crowley et al . , 2006 ) , and Bacillus spp . ( Gioia et al . , 2007 ) . More recently , Acinetobacter radioresistans and other species have been isolated from spacecraft assembly rooms ( McCoy et al . , 2012 ; Derecho et al . , 2014 ) . All these strains were stud - ied for their resistance to high - energy radiation , mainly gamma rays or UV - C ; however , the mechanisms described may not be applicabl"
    [Show abstract] [Hide abstract]
    ABSTRACT: Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.
    Frontiers in Microbiology 04/2015; 6:328. DOI:10.3389/fmicb.2015.00328 · 3.99 Impact Factor
  • Source
    • "Genome sequencing revealed the presence of some unique SAFR-032 genes, genes homologous to previously characterized resistance genes of other Bacilli species. Moreover, it showed the absence of some genes that play roles in protection from UV and H 2 O 2 in other Bacilli species (Gioia et al. 2007). Two manganese catalases, YjqC and BPUM_1305, coded by the suggested resistance genes, were recently identified in this species' spores by liquid chromatography/mass spectrometry proteomic analysis in purified SAFR-032 spore samples (Checinska et al. 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The ubiquity of Bacilli endospores in soils facilitates their easy transfer routes to other environments, including cleanrooms and low-biomass sites required by many industries such as food production and processing. A bacterial endospore is a metabolically dormant form of life that is much more resistant to heat, desiccation, lack of nutrients, exposure to UV and gamma radiation, organic chemicals, and oxidizing agents than is a vegetative cell. For example, the heat tolerance of endospores depends on multiple factors such as sporulation temperature, core dehydration, and the presence of minerals and small, acid-soluble proteins (SASPs) in the core. This review describes our current understanding of the persistence mechanisms related to sporeformers' biochemical properties and discusses in detail spores' heat, radiation, and reactive chemical resistance. In addition, it discusses the impact of contamination with spores on many areas of human activity, spore adhesive properties, and biofilm contribution to resistance. Expected final online publication date for the Annual Review of Food Science and Technology Volume 6 is February 28, 2015. Please see for revised estimates.
    Review of Food Science and Technology 02/2015; 6(1). DOI:10.1146/annurev-food-030713-092332 · 6.29 Impact Factor
  • Source
    • "B. pumilus spores are highly resistant against oxidative as well as thermal stress and thereby cause significant difficulties in sterilization procedures [14,15]. Thus, as a first step the endospore formation was knocked out in B. pumilus strain derivative Jo2.1 [13]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Since volatile and rising cost factors such as energy, raw materials and market competitiveness have a significant impact on the economic efficiency of biotechnological bulk productions, industrial processes need to be steadily improved and optimized. Thereby the current production hosts can undergo various limitations. To overcome those limitations and in addition increase the diversity of available production hosts for future applications, we suggest a Production Strain Blueprinting (PSB) strategy to develop new production systems in a reduced time lapse in contrast to a development from scratch.To demonstrate this approach, Bacillus pumilus has been developed as an alternative expression platform for the production of alkaline enzymes in reference to the established industrial production host Bacillus licheniformis. To develop the selected B. pumilus as an alternative production host the suggested PSB strategy was applied proceeding in the following steps (dedicated product titers are scaled to the protease titer of Henkel's industrial production strain B. licheniformis at lab scale): Introduction of a protease production plasmid, adaptation of a protease production process (44%), process optimization (92%) and expression optimization (114%). To further evaluate the production capability of the developed B. pumilus platform, the target protease was substituted by an alpha-amylase. The expression performance was tested under the previously optimized protease process conditions and under subsequently adapted process conditions resulting in a maximum product titer of 65% in reference to B. licheniformis protease titer. In this contribution the applied PSB strategy performed very well for the development of B. pumilus as an alternative production strain. Thereby the engineered B. pumilus expression platform even exceeded the protease titer of the industrial production host B. licheniformis by 14%. This result exhibits a remarkable potential of B. pumilus to be the basis for a next generation production host, since the strain has still a large potential for further genetic engineering. The final amylase titer of 65% in reference to B. licheniformis protease titer suggests that the developed B. pumilus expression platform is also suitable for an efficient production of non-proteolytic enzymes reaching a final titer of several grams per liter without complex process modifications.
    Microbial Cell Factories 03/2014; 13(1):46. DOI:10.1186/1475-2859-13-46 · 4.22 Impact Factor
Show more