Genome mining revealed coding genes belonging to the photolyase-cryptochrome family in UV-resistant bacteria isolated from High-Altitude Andean Lakes

ALBARRACÍN V.H.; KURTH D.; FERRER M.G.; ORDOÑEZ O.F.; REVALE S.; MANCINI S.; ROMERO S.; VAZQUEZ M.P.; FARIAS M.E.

COPENHAGEN

Simposio; 14TH INTERNATIONAL SYMPOSIUM ON MICROBIAL ECOLOGY; 2012

High-Altitude Andean Lakes (HAAL) are a disperse group of shallow lakes allocated in the Puna- High Andes ecoregion above 4,000 m, at Northwestern Argentina. Environmental conditions in the HAAL are stressful for life, but UV irradiation is giving the greatest pressure on the ecology of its outstanding microbial diversity. This work presents the analysis of recently made available genomes of three UV resistant bacterial strains, isolated from these extreme environments and highlights the presence of coding-genes for members of the photolyase-cryptochrome protein family (PL-Cry). We used Acinetobacter sp. Ver3, Exiguobacterium sp. S17, and Nesterenkonia sp. Act20, isolated from shallow water of Laguna Verde (4,400 m asl), from modern stromatolites and from the surrounding soil of Laguna Socompa (4,000 m asl), respectively. Maximal UV-B intensity registered in situ was 10.78 W m-2. Genome sequences were obtained using a whole-genome shotgun strategy with a 454 GS Titanium pyrosequencer at INDEAR, Argentina. Genomes were annotated and analyzed in the RAST annotation server. PSI-BLAST and ClustalW were used to compare and align sequences, and phylogenetic trees were built using Mega4. Genome sizes were 3,349 Mb for Ver3, 3,139 Mb for S17 and 2,941 Mb for Act20. A total of 3,213 Coding Sequences (CDS) and 66 structural RNAs were predicted in Ver3. Annotation covered 320 RAST subsystems (45%) with 1417 CDS and 55 hypothetical proteins; S17 displayed 3220 CDS and 49 structural RNAs. Only 43% CDS were annotated in RAST subsystems with 1381 CDS and 73 hypothetical proteins. In Act20, we found 2,666 CDS and 50 structural RNAs. Annotation covered 302 RAST subsystems (41%) with 1070 CDS and 34 hypothetical proteins. PL-Cry proteins were found in all the studied genomes, and were classified phylogenetically. These photolyases fell within three groups: CPD-PLs, photolyase-related proteins (PRPs), and Cryptochromes. The first two groups were represented in the three organisms studied, while a Cry- DASH related protein with 72% identity with Exiguobacterium sibiricum was found only in S17. CPD-PLs from Ver3 and S17 cluster within the Class I-CPD PLs. Interestingly, Act20-PL1 does not cluster within the group of the so-called actinomycetes CPD-photolyases but as a sister branch of the plant cryptochromes and Class III CPD-photolyases. Finally, Ver3 PRPs is related to the newly described FeS bacterial cryptochromes and photolyases (FeS-BCPs). S17 and Act20 also bear PRPs in the same group, but more distantly related to the known characterized FeS-BCPs. We have found a rich diversity and complex phylogenetic arrangement of the Cry-PL genes in different strains from HAAL. These gene products most probably enable them to sense and respond to the high UV light intensity they suffered in their original environment. Overexpression experiments are currently processed aiming to demonstrate that these ?extreme? photoreceptors are functional and effective for these purposes.