Nutrient-sensing mechanisms across evolution

Abstract

For organisms to coordinate their growth and development with nutrient availability, they must be able to sense nutrient levels in their environment. Here, we review select nutrient-sensing mechanisms in a few diverse organisms. We discuss how these mechanisms reflect the nutrient requirements of specific species and how they have adapted to the emergence of multicellularity in eukaryotes.

Figure 1. Nutrient sensing pathways throughout evolution

An overview of the nutrient sensing pathways described in this review. Pathways specific to unicellular organisms are denoted, followed by the sensing pathways that are conserved from yeast to man. Black bars indicate the presence of the pathway within the denoted species or organism.

Figure 2. Select sensing pathways in unicellular organisms

A. Chemotaxis in E. coli: In the absence of nutrients, the chemoreceptor activates the CheA kinase associated with CheW. CheA in turn phosphorylates and activates two critical effectors: CheY, which promotes clockwise rotation in the flagellar motor and random tumbling motions, and CheB, a demethylase involved in the adaptation process which counteracts CheR, the constitutive methylase. Conversely, the presence of nutrients suppresses this pathway and the default counterclockwise rotation of the rotor ensues to yield smooth runs. B. PII proteins in alpha-proteobacteria: This tightly regulated protein family serves to control the adenylylation state and activity of glutamine synthase (GS). When nitrogen is absent, the precursor of nitrogen assimilation reactions, 2-OG, accumulates, binds to, and inhibits the unmodified PII protein GlnB, which is unable to stimulate the adenylylation reaction of ATase. The unmodified and active form of GS accumulates. When nitrogen is abundant, glutamine levels are high, and this molecule binds and inhibits UTase, which permits the unmodified form of GlnB to accumulate and promote GS inhibition, by activating the adenylylation of GS by ATase. C. SPS pathway in S. cerevisiae: Extracellular amino acids bind directly to Ssy1, a transceptor with homology to amino acid permeases but lacking transport activity, to activate the SPS (Ssy1-Ptr3-Ssy5) pathway. Amino acids bind to Ssy1 to stimulate a conformational change in Ssy5, resulting in the phosphorylation and subsequent ubiquitin-mediated degradation of its inhibitory pro-domain. Ptr3 acts as an adapter to mediate this process. Release of the catalytic domain of Ssy5 permits it to cleave the latent transcription factors Stp1 and Stp2, which translocate to the nucleus to activate transcription of genes involved in amino acid transport and metabolism. (Figure adapted from Conrad et al, 2014).

Figure 3. Nutrient sensing by the TOR pathway

A. In the absence of amino acids and growth factors, mTORC1 is inactive. This is controlled by two separate signaling pathways. First, in the absence of amino acids GATOR1 is an active GAP towards RagA, causing it to become GDP bound. In this state, mTORC1 does not localize to the lysosomal surface. Secondly, in the absence of insulin or growth factors, TSC is an active GAP towards Rheb and stimulates it to be GDP bound. B. In the presence of amino acids and growth factors, mTORC1 is active. Amino acids within the lysosome signal through SLC38A9 to activate the amino acid sensing branch. Ragulator is active, causing RagA to be GTP bound. This binding state is reinforced by the fact that GATOR1 in inactive in the presence of amino acids, as GATOR2 inhibits it. The Rag heterodimer in this nucleotide conformation state recruits mTORC1 to the lysosomal surface. In addition, the presence of insulin or growth factors activates a pathway that inhibits TSC, leaving Rheb GTP bound. In this state, Rheb activates mTORC1 when it translocates to the lysosomal surface.

Figure 4. Evolution of nutrient sensing with the emergence of multicellularity and compartmentalization

A. Prokaryotes have two compartments that may contain amino acids: the extracellular space and the cytosol. Amino acid transporters such as the chemoreceptors Tsr and Tar can sense extracellular amino acids. A variety of sensors, including the PII proteins, can detect intracellular amino acids. B. Similar to prokaryotes, yeast sense extracellular amino acids via plasma membrane transporters, such as Ssy1. In addition, they sense cytosolic amino acid availability with sensors like GCN2. Unlike prokaryotes, however, eukaryotes have organelles such as the vacuole, an additional compartment which may contain amino acids. While it has not yet been established if yeast directly sense amino acid levels within the vacuole, they do contain organelles which can act as alternate storage depots for nutrients and are therefore another potential compartment in which sensing may occur. C. In mammalian cells, there are three distinct compartments in which sensing may occur, similar to yeast. First, extracellular nutrients are sensed via transporters, not discussed in detail in this review. In addition, cytosolic amino acids are sensed by the GCN2 pathway. Finally, amino acids stored within the lysosome are sensed by the mTORC1 pathway.