Adapting to UV: Integrative Genomic and Structural Analysis in Bacteria from Chilean Extreme Environments

Abstract

Extremophilic bacteria from extreme environments, such as the Atacama Desert, Salar de Huasco, and Antarctica, exhibit adaptations to intense UV radiation. In this study, we investigated the genomic and structural mechanisms underlying UV resistance in three bacterial isolates identified as Bacillus velezensis PQ169, Pseudoalteromonas sp. AMH3-8, and Rugamonas violacea T1-13. Through integrative genomic analyses, we identified key genes involved in DNA-repair systems, pigment production, and spore formation. Phylogenetic analyses of aminoacidic sequences of the nucleotide excision repair (NER) system revealed conserved evolutionary patterns, indicating their essential role across diverse bacterial taxa. Structural modeling of photolyases from Pseudoalteromonas sp. AMH3-8 and R. violacea T1-13 provided further insights into protein function and interactions critical for DNA repair and UV resistance. Additionally, the presence of a complete violacein operon in R. violacea T1-13 underscores pigment biosynthesis as a crucial protective mechanism. In B. velezensis PQ169, we identified the complete set of genes responsible for sporulation, suggesting that sporulation may represent a key protective strategy employed by this bacterium in response to environmental stress. Our comprehensive approach underscores the complexity and diversity of microbial adaptations to UV stress, offering potential biotechnological applications and advancing our understanding of microbial resilience in extreme conditions.

Keywords: DNA repair; UV resistance; extremophilic bacteria; photolyase; pigment biosynthesis; sporulation.

Figure 1

Isolation sites, genomic assembly characteristics, and ANI-based taxonomic assignment of three extremophilic bacterial isolates. (a–c) Representative sampling sites of bacterial isolates: (a) Atacama Desert, (b) Salar de Huasco, and (c) Antarctic soil. (d–f) Circular genome representations illustrating variability in genome size, contiguity, and genetic content: (d) Bacillus velezensis PQ169 (76 contigs, 4.18 Mb), (e) Pseudoalteromonas sp. AMH3-8 (single contig, 4.74 Mb), and (f) Rugamonas violacea T1-13 (171 contigs, 6.85 Mb). Rings (outer to inner) represent predicted CDSs, RNA genes (rRNA, tRNA, and tmRNA), GC content, and GC skew. (g–i) Heatmaps depicting average nucleotide identity based on MUMmer (ANIm) analysis between each isolate and closely related reference strains, supporting definitive taxonomic assignment: (g) Bacillus velezensis PQ169, (h) Pseudoalteromonas sp. AMH3-8, and (i) Rugamonas violacea T1-13. Color gradients indicate similarity percentages, with red color representing higher ANI values, and blue lower values.

Figure 2

Phylogenetic tree based on the amino acid sequences of UvrA, UvrB, and UvrC proteins (NER system). Multiple sequence alignment was performed using MUSCLE on the Phylogeny.fr platform, followed by tree construction with PhyML and visualization using TreeDyn. The resulting tree was further arranged and refined using the Interactive Tree of Life (iTOL v7) tool. The maximum likelihood method was employed with 1000 bootstrap replicates, where the node sizes reflect the level of bootstrap support. Each label includes the gene name, the bacterial species, and the corresponding NCBI accession number. Three environmental strains are highlighted: Bacillus velezensis PQ-169 (green), Pseudoalteromonas sp. AMH3-8 (yellow), and Rugamonas violacea T1-13 (purple). These strains, along with other extremophilic, UV-resistant, and pathogenic bacteria, were included to compare UvrA (red clade), UvrB (blue clade), and UvrC (green clade) variations under extreme environmental conditions.

Figure 3

Multiple sequence alignment between the photolyase of Vibrio cholerae and photolyase-related proteins from Pseudoalteromonas sp. AMH3-8 and Rugamonas violacea T1-13. The alignment was generated in MEGA12, using the MUSCLE algorithm, and visualized in Jalview, where blue shading indicates residues with over 50% conservation. The consensus sequence (bottom line) and the associated histogram (in yellow/brown) further highlight highly conserved regions, supporting the structural and functional similarities observed among these photolyase-like proteins.

Figure 4

Comparative structural analysis of photolyase-related proteins from Pseudoalteromonas sp. AMH3-8, Vibrio cholerae, and Rugamonas violacea T1-13. (a) Three-dimensional (3D) model of the putative deoxyribodipyrimidine photolyase-related protein from Pseudoalteromonas sp. AMH3-8. (b) X-ray structure of the Vibrio cholerae photolyase (PDB ID: 7YKN), used as a reference in the structural comparisons. (c) Three-dimensional model of the photolyase-related protein from R. violacea T1-13. The recoloring (d–f) facilitates the identification of each model’s overall topology. (g) Superposition of the Pseudoalteromonas sp. AMH3-8 model and the V. cholerae photolyase, illustrating the high overall structural similarity. (h) Superposition of the Pseudoalteromonas sp. AMH3-8 and R. violacea T1-13 models, showing conserved folds. (i) Superposition of the V. cholerae photolyase and the R. violacea T1-13 model. (j) Combined overlay of all three structures (Pseudoalteromonas sp. AMH3-8, V. cholerae, and R. violacea T1-13), highlighting the putative FAD-binding pocket. These comparisons reveal a shared photolyase-like architecture among the three proteins, suggesting a conserved role in UV-induced DNA repair.

Figure 5

Genetic organization and biosynthetic pathway of violacein in Rugamonas violacea T1-13. (a) Genomic arrangement of the violacein operon in R. violacea T1-13, showing the sequential organization of key biosynthetic genes (e.g., vioA, vioB, vioC, vioD, and vioE) within a ~6 kb region. Different colored arrows indicate individual genes and their transcriptional orientation. (b) Proposed biosynthetic pathway for violacein production, starting from L-tryptophan and progressing through various intermediates (such as IPA imine and protodeoxyviolaceinic intermediates) to yield the final product, violacein. The pathway diagram also identifies the cytoplasmic localization of pigment biosynthesis in this Gram-negative bacterium.

Figure 6

Spore-formation cycle in Bacillus due to UV damage. (a) Activation of the UV damage-response pathway at the membrane, where kinases KinA, KinB, and KinC are activated, leading to the phosphorylation of Spo0A. This process triggers the differentiation of the mother cell and the forespore. (b) Stages of spore formation, including asymmetric division; engulfment of the forespore by the mother cell; and the roles of σ^F, σ^E, σ^G, and σ^K in spore maturation and the eventual lysis of the mother cell, leading to spore release and germination.