Research

(1) Metabolic Control Mechanisms via Proteolysis

To metabolically engineer microorganisms for the large-scale production of valuable substances, it is essential to elucidate the fundamental regulatory mechanisms of metabolism. Traditionally, studies have focused on allosteric regulation, feedback control, and feed-forward regulation of metabolic enzymes. With the advent of molecular biology, transcriptional regulation of metabolic enzymes has also been extensively studied.

In recent years, growing evidence has shown that metabolic pathways are regulated by protein degradation systems. For instance, the transition between glycolysis and gluconeogenesis (illustrated in the lower-left figure), the switch in the glyoxylate cycle (also shown in the lower-left figure), and the regulation of the sterol biosynthetic pathway (depicted in the lower-right figure) are all significantly influenced by the degradation of metabolic enzymes via ubiquitin ligase complexes (as detailed in Crit. Rev. Biochem. Mol. Biol., 2015).

While metabolic regulation through protein post-translational modifications and the ubiquitin-proteasome system has been sporadically reported, systematic investigations remain scarce. Our laboratory is committed to uncovering novel regulatory mechanisms of material metabolism by rigorously examining metabolic pathways through the lens of protein post-translational modifications and degradation processes.

This research holds great promise for advancing metabolic engineering strategies, particularly for enhancing the production capacity of microbial-derived substances, such as biofuels.

(2) Protein Quality Control Mechanisms

Proteins synthesized by ribosomes can fulfill their functions only when they adopt the correct three-dimensional structure. However, the "yield" of properly folded, functional proteins is not always optimal, and defective products—misfolded or aberrant proteins—are inevitably produced. While misfolding can occur randomly, it may also result from various factors such as stress, aging, or genetic mutations.

Cells are equipped with a "quality control" mechanism that specifically recognizes and either repairs or degrades (removes) abnormal proteins, thus maintaining cellular homeostasis. Under normal conditions, this system effectively prevents the accumulation of defective proteins. However, when the quantity of misfolded proteins exceeds the capacity of the quality control machinery, or if the system itself is impaired, it can lead to severe diseases in humans.

The fundamental principles of protein quality control are highly conserved across species, from single-celled yeast to higher organisms. Research using yeast as a model organism has been instrumental in establishing the concept of biopolymer quality control. Eukaryotic cells contain various subcellular compartments, including the cytoplasm, nucleus, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, mitochondria, chloroplasts, and the plasma membrane. Recent studies have revealed that each compartment possesses its own distinct quality control mechanisms.

Among these, the quality control system in the endoplasmic reticulum (ER) has been the focus of intensive research. When misfolded proteins accumulate in the ER, a response known as the "endoplasmic reticulum stress response" is activated to restore ER homeostasis. This response involves: (1) Translational repression, which reduces the burden on the ER; (2) Induction of molecular chaperones, which enhance the protein folding capacity; (3) Degradation of misfolded proteins, mediated by specialized pathways.

In our laboratory, we focus on the degradation of misfolded proteins in the ER, a process known as endoplasmic reticulum-associated degradation (ERAD). By combining in vitro assay systems with genetic approaches, we aim to elucidate the molecular mechanisms underlying ERAD (for further details, see Curr. Opin. Cell Biol., 2014).