Genomics of Antarctic polyextremophile Nesterenkonia

Abstract

Nesterenkonia sp. AN1 was isolated from soil samples obtained from the Miers Valley, McMurdo region in eastern Antarctica, where the organism survives under 'extreme' environmental conditions, including extreme cold, osmotic and oxidative stresses, desiccation and starvation as well as elevated fluxes of ultraviolet radiation. The isolate is the first member of the genus Nesterenkonia to be reported from Antarctic soils. This thesis provides insights into the molecular determinants underlying the ability of the Antarctic Nesterenkonia sp. AN1 to survive under multiple stress conditions. A range of genomic and comparative genomic analyses was applied to elucidate the genetic determinants underlying survival strategies of Nesterenkonia sp. AN1. To highlight psychrotolerance mechanisms, the transcriptome of the Nesterenkonia sp. AN1grown at 5 ºC and 21 ºC were also compared. The draft genome of Nesterenkonia sp. AN1 represents the first genome sequence of a cold adapted member of the genus Nesterenkonia. The genome was 3.04 Mb in size, was assembled into forty-one contigs and encoded 2,852 proteins. These proteins include those putatively involved in cold shock, cold acclimation, osmotic and oxidative stress responses as well as the modulation of membrane fluidity. Genome-wide comparisons of the cold-active Nesterenkonia sp. AN1 and three mesophilic strains revealed that members of the genus Nesterenkonia encodes an open pan-genome, which is consistent with their ecological diversity and niche specializations. Further evaluation of the pan-genome compartments showed that the majority of the adaptation genes are shared by all the strains, suggesting that members of the genus are naturally resilient to environmental stresses. The genome of Nesterenkonia sp. AN1, however, encodes unique putative adaptation proteins within the strain-specific genome fraction and also showed evidence of molecular evolution in a large number of the core genes. These events indicate that the evolution of the Nesterenkonia sp. AN1 genome may have involved a significant number of gene acquisition events and the incorporation of advantageous mutations in the ancestral genetic stock. Transcriptome data of Nesterenkonia sp. AN1 revealed that ~ 97 % of the genes predicted in Nesterenkonia sp. AN1 were expressed under the experimental conditions. Analyses of the transcriptome showed that there was significant induction at 5 ºC of transcripts that coded for proteins associated with antioxidant activity. There was also overexpression of universal stress protein genes related to uspA, along with genes encoding other characterised cold stress features. Genes encoding key enzymes of the glyoxylate cycle were also induced at 5 ºC, suggesting possible adaptation strategies for energy metabolism in cold habitats. Taken together, the combined data revealed the presence of pervasive adaptive strategies which likely determine niche specialization of Nesterenkonia sp. AN1 and support its survival in the arid soils of Antarctica.