Vps34

This post was initiated by a request to take a quick look at a review on the catalytic subunit of the class III phosphoatidylinositol 3-kinase catalytic subunit called vps34 in yeast. [1] The mammalian homolog is coded for by the PIK3c3 gene. The featured image came from UniProt.org. For a nice diagram of the phylogenetic tree and some Pt click Ohashi 2021 Fig 1

When we think about Vps34/PIK3c3 we have to remember that PtdIns(3)P is a precursor to PIP₃.

Data from UniProt

Human Vps34 Catalytic subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Expression is ubiquitous with the highest expression in muscle.

UniProt AI annotation mirrors the Redlick review [1] with exerts like ” May be a component of a complex composed of RAB5A (in GDP-bound form), DYN2 and PIK3C3 (By similarity). Interacts with NCKAP1L” RAB5A and DYN2 are G proteins.

Acetylation of Vps34 aka PIK3C3 [2]

A summary, “Utilizing approaches combining protein acetylation analysis, mass spectrometry, and site-directed mutagenesis, we proved that PIK3C3/VPS34 is indeed an acetylation substrate specifically for EP300, and that K29 and K771 are the major acetylation sites. In addition, we revealed that acetylation by EP300 suppresses PIK3C3/VPS34 activity for PtdIns3P production, whereas deacetylation activates it. Furthermore, we determined that the suppression is dominantly derived from K771 acetylation.” [2]

EP300 is a histone acetylase. EP300 not only acetylates all four histones but also many other enzymes according to UniPort. EP300 can use different acyl-CoA substrates, such as (2E)-butenoyl-CoA (crotonyl-CoA), butanoyl-CoA, 2-hydroxyisobutanoyl-CoA, lactoyl-CoA or propanoyl-CoA.

“Both EP300 inactivation and PIK3C3/VPS34 deacetylation were confirmed in starved cells and in liver tissues of starved mice. PIK3C3/VPS34 knockdown and rescue experiments then suggested that this EP300 inactivation-derived PIK3C3/VPS34 deacetylation is required for starvation-induced autophagy and intracellular lipid droplet clearance. More intriguingly, inactivation of EP300 by EP300 inhibitors or EP300 knockdown effectively trigger PtdIns3P production and autophagy in AMPK^−/−, TSC2^−/−, RB1CC1/FIP200^−/−, or ULK1^−/− cells, which was prevented by over expression of the acetylation-mimicking PIK3C3/VPS34. Similar phenomena are observed in cells treated with low concentration of NH₄Cl, which stimulates autophagy in a ULK1-independent manner without inhibiting lysosomal function.” [2]

Acetylation and autophagy, the Xu and Wan review [3]

A Xu and Wan review paints a much more complicated picture of every aspect of autophagy that is controlled by acetylation. [3] This review has five colorful images explaining the role of acetylation in controlling autophagy.

Figure 1.Autophagy initiation

Acetylation of autophagy initiation machinery. The amazing thing about this figure that can be viewed from the link above is the role that Sirt1 plays in controlling the process and the number of proteins invovled in the process.

Since we have been interested in regulation of genes that code for lysosome proteins.

Figure 2. Autophagy progression to LC 3 and lysosomes.

Acetylation of LC3 conjugation machinery. Transcription is involved as are ADP/ATP sensing AMPK and Sirt1.

Going back to the Eeidick review [1], Ohashi has publised a similar review on complexes that regulate PIK3c3/Vps34. [4]

The Ohashi review, phosphorylation, G proteins…[4]

The Ohashi review covers three different complexes that contain Vsp34. These three complexes have slightly different roles and may be regulated by slightly different G proteins. Myotubularins, , was introduced in this review. [4] Complex II seems to be more involved in plasma membrane trafficking. VPS15 is the regulatory subunit. ATG14L is the gene that codes or the Beclin 1-associated autophagy-related key regulator. According to UniProt this protein stimulates the phosphorylation of BECN1, but suppresses the phosphorylation PIK3C3 by AMPK (PubMed:23878393).

Figure 4 Vps34 complexes regulation by ULK1 and mTorc1

• ULK1 complex senses starvation and functions as an on switch. mTORC1 acts as an off switch in nutrient-replete conditions. This panel depicts their phosphorylatoin sites.
• : Vps34 complexes I and II regulation lysosomes under slightly different conditions.
• (C) VPS34–mTORC1 activation by lysosome translocation to the plasma membrane, mechanisms.

Tying things up

Things are getting very complicated for regulation of Vps34 and autophagosomes. A common theme of nutrient availability is emerging. The literature on Vps34 and autophagy of protein aggregates associated wit neuro degenerative diseases is there but beyond the scope of this post to summarize. What the roles of dietary interventions and PEMF remain to be established.

References

1. Reidick C, Boutouja F, Platta HW. The class III phosphatidylinositol 3-kinase Vps34 in Saccharomyces cerevisiae. Biol Chem. 2017 May 1;398(5-6):677-685. free article
2. Su H, Liu W. PIK3C3/VPS34 control by acetylation. Autophagy. 2018; 14(6):1086-1087. free paper
3. Xu Y, Wan W. Acetylation in the regulation of autophagy. Autophagy. 2023 Feb;19(2):379-387. PMC free paper
4. Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells. 2021 Nov 11;10(11):3124. PMC free paper