DEEP RNA-SEQUENCING ANALYSIS OF THE ANTARCTIC BACTERIUM Pseudomonas extremaustralis IN RESPONSE TO LOW TEMPERATURE

PAULA M TRIBELL; MARTINIANO M RICARDI; SØREN MOLIN; NANCY I LOPEZ

Mar del Plata

Congreso; Congreso de Microbiologia General (SAMIGE); 2014

Sociedad argentina de microbiologia general

In cold environments low temperatures and ice presence exerts severe constraints on living organisms and those ones able to survive in this conditions presents several adaptation to cope with unfavorable conditions. Environmental adaptability involves different physiological and genetic strategies including the response ofindividual genes or operons and complex regulatory networks that coordinate the control of several genes. RNAdeep sequence is a powerful tool in bacterial species to analyze gene expression, discover previously unannotated genes and detect small regulatory RNA. We used RNA-seq technology in Pseudomonas extremaustralis, anAntarctic bacterium able to grow under low temperatures and survive to freezing. Total RNA was extracted fromcultures grown at 30oC and 5oC and the rRNA was depleted from the samples to allow a better coverageDirectional libraries were prepared with ScriptSeq v2RNA-Seq Library Preparation Kit (Epicentre) and were sequenced using the Illumina HiSeq2000 platform with a paired-end protocol and read lengths of 100 nt. For each condition duplicated independent RNA extraction andlibraries were used. Bioinformatics analysis of around 6000 transcripts expression levels in both conditions using Rockhoper software showed thatthe majority of transcripts did not present a statistical significant change in the expression level. Down-regulated genes were around 750 and included cytochromes and enzymes belonging todifferent catabolic pathways. Interestingly, 76 geneswere up-regulated under cold conditions including several lipoproteins, transcriptional regulators with unknown function, alginate biosynthesis activator, osmotic response elements and other cellular functions. We also detected several unnanotated transcripts in both conditions. Additionally, we have found around 170 putative non-coding small RNAs. Some of them presented altered expression levels under low temperatures with unknown function. The results showed a novel varietyof transcripts and regulatory elements that could explain growth and survival under low temperatures in this psycrotolerant bacterium