Differential expression analysis of TOR3 knockouts in arginine-starved Leishmania major

Abstract

The Arginine Deprivation Response (ADR) pathway is essential for Leishmania parasites to overcome host macrophage defense mechanisms and establish infection. The activation of this pathway appears to rely in part on regulation by target of rapamycin kinase 3 (TOR3), since TOR3 knockouts do not respond to arginine starvation consistent with ADR activation. Here, we investigate the role of TOR3 in response to arginine starvation via TOR3 knockout in Leishmania major. We analyzed mRNA abundance changes in L. major by differential gene expression analysis across four conditions: wild type (WT) in the presence of arginine, WT starved of arginine, knockout (KO) in arginine, and KO starved. As expected, we found a small number of changes between starved and unstarved WT samples, with relatively low magnitude (22 up-regulated, 1 down-regulated; fold change ≤ 2.5). Conversely, comparison of starved and unstarved knockout samples yielded man more differentially expressed genes (1263 up-regulated, 1158 down-regulated) with overall higher fold changes. Comparison of WT and KO samples under starved conditions showed similar results (1533 up-regulated, 1383 down-regulated) while comparison of WT and KO under unstarved showed fewer changes, even in the presence of arginine (463 up-regulated, 261 down-regulated). Together, our results support the hypothesis that TOR3 is involved in the ADR pathway and suggest that it also plays a wider regulatory role in cell homeostasis.