UV hyper‐resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase

Abstract

Exposure to solar radiation can cause mortality in natural communities of pico-phytoplankton, both at the surface and to a depth of at least 30 m. DNA damage is a significant cause of death, mainly due to cyclobutane pyrimidine dimer formation, which can be lethal if not repaired. While developing a UV mutagenesis protocol for the marine cyanobacterium Prochlorococcus, we isolated a UV-hyper-resistant variant of high light-adapted strain MED4. The hyper-resistant strain was constitutively upregulated for expression of the mutT-phrB operon, encoding nudix hydrolase and photolyase, both of which are involved in repair of DNA damage that can be caused by UV light. Photolyase (PhrB) breaks pyrimidine dimers typically caused by UV exposure, using energy from visible light in the process known as photoreactivation. Nudix hydrolase (MutT) hydrolyses 8-oxo-dGTP, an aberrant form of GTP that results from oxidizing conditions, including UV radiation, thus impeding mispairing and mutagenesis by preventing incorporation of the aberrant form into DNA. These processes are error-free, in contrast to error-prone SOS dark repair systems that are widespread in bacteria. The UV-hyper-resistant strain contained only a single mutation: a 1 bp deletion in the intergenic region directly upstream of the mutT-phrB operon. Two subsequent enrichments for MED4 UV-hyper-resistant strains from MED4 wild-type cultures gave rise to strains containing this same 1 bp deletion, affirming its connection to the hyper-resistant phenotype. These results have implications for Prochlorococcus DNA repair mechanisms, genome stability and possibly lysogeny.

The spontaneous mutation frequencies of Prochlorococcus strains are commensurate with those of other bacteria

“…For antibiotic resistance, the mutation frequency data for MED4 leads to a maximum spontaneous mutation rate of 10 −7 −10 −8 per gene per generation, about the same or slightly lower than that found for other bacteria (Drake et al ., 1998; Whitman et al ., 1998). These results are also consistent with our previous findings regarding the number of SNPs in one MED4 isolate after growth in culture for more than 1500 generations (Osburne et al ., 2010). Although the sporatic appearance of mutator strains may have played a past role in shaping Prochlorococcus genomes, potentially affecting their rate of protein evolution, it is clear that despite the lack of some ‘mutator’ DNA repair genes, these Prochlorococcus strains do not appear to have a mutator phenotype.…”

“…We recently determined that after over 1500 generations, the number of single nucleotide substitutions (SNPs) in the genome of the high‐light‐adapted Prochlorococcus strain MED4 was in the range expected for non‐mutator bacteria (Osburne et al ., 2010). As this finding appeared inconsistent with a mutator phenotype in MED4, we decided to investigate further by measuring the spontaneous mutation frequency (the fraction of mutantcells in a population) in MED4 and in two other Prochlorococcus strains, allowing us to then bound the upper limit of their spontaneous mutation rates.…”

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

“…Indeed, the high-light adapted strain MED4, which encodes photolyase, has a greater tolerance to UV exposure than low-light adapted strain MIT9313 (Osburne et al, 2010), which lacks photolyase but encodes pyrimidine dimmer glycosylase. Thus, the protection from UV exposure provided by photolyase may explain, at least in part, why the eNATL clade can better survive transport to UV-rich surface waters.…”

UV-B stress induced metabolic rearrangements explored with comparative proteomics in three Anabaena species

“…Additionally these 3 proteins appeared as 20 isoforms across three species showed similar as well as opposite expression pattern in Anabaena L31 and Anabaena doliolum respectively suggesting their specific roles in modulating UV-B stress (Supplementary Figures S5, S6, and S7). Alr 2954 encompassing nudix hydrolase domain registered marked accumulation of 18.7 fold on day one in Anabaena L31 connoted acquiring strategy for error free repair of damaged GTPs produced under UV-B stress (Supplementary Table S4) [37]. All5091 with slightly higher accumulation in Anabaena L31 contains sugar kinase/HSP70/actin superfamily, members of which share a core structural fold coupled with ATP hydrolysis leading to conformational changes which affect the affinity of HSP70 towards unfolded protein hence preventing protein misfolding [38].…”