Systems-level analysis and evolution of the phototransduction network in Drosophila

Abstract

Networks of interacting genes are responsible for generating life's complexity and for mediating how organisms respond to their environment. Thus, a basic understanding of genetic variation in gene networks in natural populations is important for elucidating how changes at the genetic level map to higher levels of biological organization. Here, using the well-characterized phototransduction network in Drosophila, we analyze variation in gene expression within and between two closely related species, Drosophila melanogaster and Drosophila simulans, under different environmental conditions. Gene expression levels in the pathway are largely conserved between these two sibling species. For most genes in the network, differences in level of gene expression between species are correlated with degree of polymorphism within species. However, one gene encoding the light-induced ion channel TRPL (transient receptor potential-like) shows an excess of expression divergence relative to polymorphism, suggesting a possible role for natural selection in shaping this expression difference between species. Finally, this difference in TRPL expression likely has significant functional consequences, because it is known that a high level of rhabdomeral TRPL leads to increased sensitivity to dim background light and an increased response to a wider range of light intensities. These results provide a preliminary quantification of variation and divergence of gene expression between species in a known gene network and provide a foundation for a system-level understanding of functional and evolutionary change.

Fig. 1.

Major proteins of the phototransduction network. Colors indicate the observed relative levels of gene expression between D. melanogaster and D. simulans. Color coding indicates expression difference between species as a ratio (D. melanogaster/D. simulans). Red is ≤1/4; orange is >1/2; yellow is 1/1; light blue is <2/1; dark blue is ≥2/1; black, no data. The Drosophila phototransduction network is a paradigm for the study of signal transduction (3, 14, 23, 31, 32). The end point of the cascade is the depolarization of the photoreceptor cell, resulting from the opening of Na⁺- and Ca²⁺-permeable channels, TRP and TRPL. Light initially activates rhodopsin into active metarhodopsin, which catalyzes the activation of a heterotrimeric G protein. The Gα subunit of the activated heterotrimer then activates an effector enzyme, phosphoinositide-specific phospholipase C (PLCβ, encoded by the gene norpA), which leads to the production of two signaling molecules, DAG (diacylglycerol) and InsP₃ (inositol triphosphate) from PIP₂ (phosphatidylinositol-4,5-biphosphate). This ultimately leads to the activation of the light-sensitive channels TRP, TRPL, and TRPγ (the latter is not studied here). The gray arrow indicates a mechanism of action that is not totally elucidated. TRPL and TRPγ form heteromultimers with TRP and with each other. Modulation of the ratio of TRP/TRPL subunits in the rabdhomeres through the light-sensitive translocation of TRPL has been suggested as a physiological mechanism increasing sensitivity to dim background light and allowing response to a wider dynamic range of light intensities (13). A sharp response is provided by the inactivation reactions that take place soon after activation. Two important players in the inactivation are the arrestins, which bind to and inactivate rhodopsin. Activity of both the GTP-bound Gqα subunit and PLC is terminated by the GTPase activity of the G protein and other components. Light-sensitive channels are inactivated by Ca²⁺ through the action of calmodulin. RDGC is a rhodopsin phosphatase that is regulated by calmodulin. Its function in deactivation of the response, by means of the deactivation of rhodopsin-mediated signaling, is mostly inferred from mutant phenotypes. Many of the molecules are assembled in a signalplex whose core component is INAD, a scaffold protein with five PDZ protein-interaction modules. Other proteins interact with INAD, but their localization in the rabdhomeres does not depend on INAD. InaF serves as a regulator of the calcium-channel activity, but its mode of action is not completely elucidated. NinaA is responsible for transporting rhodopsin from the endoplasmic reticulum to the cell membrane. PKC is a protein kinase encoded by inaC, whose role is not fully understood, but mutant phenotypes suggest a role in adaptation to light and termination response.

Fig. 2.

Relative transcript abundance. Expression level of the genes of the phototransduction pathway in D. melanogaster and D. simulans are largely conserved between the two sibling species (Pearson correlation, r = 0.94, P = 4.6 × 10⁻¹⁰, n = 20).

Fig. 3.

Expression level of trpl in D. melanogaster and D. simulans in light and after a 1-h exposure to complete darkness. Expression level is shown relative to the lowest expression level, which is arbitrarily set to one. ANOVA: P_sp < 0.0001; P_env = 0.03; P_int = 0.88.

Fig. 4.

Distribution of divergence (MS_species) to polymorphism (MS_strain) ratio across the phototransduction pathway. The solid lines represent the theoretical expectation; i.e., 2.7 times the F_1,10 distribution. The gene at the far right of the distribution is trpl.