Rubicon (run domain

Beclin-1 Beclin-1 is a protein that in humans is encoded by the ''BECN1'' gene. Beclin-1 is a mammalian ortholog of the yeast autophagy-related gene 6 (Atg6) and BEC-1 in the C. elegans nematode. This protein interacts with either BCL-2 or PI3k cla ...

-interacting and cysteine-rich domain-containing protein) is a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

that in humans is encoded by the RUBCN gene. Rubicon is one of the few known negative regulators of

autophagy Autophagy (or autophagocytosis; from the Ancient Greek , , meaning "self-devouring" and , , meaning "hollow") is the natural, conserved degradation of the cell that removes unnecessary or dysfunctional components through a lysosome-dependent re ...

, a cellular process that degrades unnecessary or damaged cellular components. Rubicon is recruited to its sites of action through interaction with the

small GTPase Small GTPases (), also known as small G-proteins, are a family of hydrolase enzymes that can bind and hydrolyze guanosine triphosphate (GTP). They are a type of G-protein found in the cytosol that are homologous to the alpha subunit of heterotrim ...

Rab7, and impairs the autophagosome-

lysosome A lysosome () is a membrane-bound organelle found in many animal cells. They are spherical vesicles that contain hydrolytic enzymes that can break down many kinds of biomolecules. A lysosome has a specific composition, of both its membrane ...

fusion step of autophagy through inhibition of PI3KC3-C2 (class III phosphatidylinositol 3-kinase complex 2). Negative modulation of Rubicon is associated with reduction of

aging Ageing ( BE) or aging ( AE) is the process of becoming older. The term refers mainly to humans, many other animals, and fungi, whereas for example, bacteria, perennial plants and some simple animals are potentially biologically immortal. In ...

and

aging-associated diseases An aging-associated disease (commonly termed age-related disease, ARD) is a disease that is most often seen with increasing frequency with increasing senescence. They are essentially complications of senescence, distinguished from the aging proc ...

: knockout of Rubicon increases lifespan in roundworms and female fruit flies, and in mice decreases kidney fibrosis and

α-synuclein Alpha-synuclein is a protein that, in humans, is encoded by the ''SNCA'' gene. Alpha-synuclein is a neuronal protein that regulates synaptic vesicle trafficking and subsequent neurotransmitter release. It is abundant in the brain, while smaller ...

accumulation. In addition to regulation of autophagy, Rubicon has been shown to be required for LC3-associated phagocytosis (LAP) and LC3-associated endocytosis (LANDO). Rubicon has also been shown to negatively regulate the

innate immune response The innate, or nonspecific, immune system is one of the two main immunity strategies (the other being the adaptive immune system) in vertebrates. The innate immune system is an older evolutionary defense strategy, relatively speaking, and is th ...

through direct interaction with multiple downstream regulatory molecules.

Structure

Rubicon consists of 972 amino acids and has an N-terminal

RUN domain The RUN domain is an evolutionary conserved protein–protein binding protein domain. They often interact with GTPases and could play a role in multiple Ras superfamily, Ras-like GTPase Cell signaling, signalling pathways. This domain is pres ...

, a middle region (MR), and a C-terminal Rubicon homology (RH) domain. The Rubicon homology domain is rich in cysteine residues and binds at least 4 divalent Zinc ions, forming zinc finger motifs. The structural basis for interaction between Rubicon and GTP-bound Rab7 has been experimentally determined
PDB ID: 6WCW
.

Function

The function of the N-terminal RUN domain are unknown, but it is required for autophagy suppression. The middle region contains the

PI3K Phosphoinositide 3-kinases (PI3Ks), also called phosphatidylinositol 3-kinases, are a family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, survival and intracellular trafficking, which i ...

-binding domain (PIKBD), which mediates inhibition of PI3KC3-C2. The C-terminal Rubicon homology domain mediates interaction with Rab7, and is shared by other RH domain-containing autophagy regulatory proteins, including PLEKHM1 and Pacer (also known as RUBCNL, Rubicon-like Autophagy Enhancer).

Autophagy-dependent

Rubicon suppresses autophagy through association with and inhibition of PI3KC3-C2. Specifically, Rubicon directly binds PI3KC3-C2 and inhibits recruitment of PI3KC3-C2 to the membrane through conformational modulation of the

subunit. This activity prevents PI3KC3-directed generation of

phosphatidylinositol 3-phosphate Phosphatidylinositol 3-phosphate (PtdIns3''P'') is a phospholipid found in cell membranes that helps to recruit a range of proteins, many of which are involved in protein trafficking, to the membranes. It is the product of both the class II and II ...

(PI3P) at the autophagosome membrane, and a resulting failure to recruit machinery that directs autophagosome-lysosome fusion. Rubicon is targeted to its site of action through direct interaction with Rab7, which decorates late endosomes and late autophagosomes.

Autophagy-independent

Rubicon is required for LC3-associated phagocytosis (LAP) and LC3-associated endocytosis (LANDO). Rubicon plays a role in PI3KC3 localization to phagosomes, which is important for PI3P production at the membrane and recruitment of downstream effectors including

NOX2 NADPH oxidase 2 (Nox2), also known as cytochrome b(558) subunit beta or Cytochrome b-245 heavy chain, is a protein that in humans is encoded by the ''NOX2'' gene (also called ''CYBB'' gene). The protein is a superoxide generating enzyme which for ...

. Rubicon has been shown to suppress the innate immune response and in some cases exacerbate viral replication. Rubicon suppresses

cytokine Cytokines are a broad and loose category of small proteins (~5–25 kDa) important in cell signaling. Cytokines are peptides and cannot cross the lipid bilayer of cells to enter the cytoplasm. Cytokines have been shown to be involved in a ...

responses through interaction with NF-κB essential modulator (NEMO), interferon regulatory factor 3 (IRF3) and caspase recruitment domain-containing protein 9 (CARD9).

Role in aging and disease

Aging-related diseases

Rubicon expression levels increase with age in mice and other model organisms, suggesting that Rubicon may cause age-associated decrease of autophagy. Since reduced autophagy is associated with aging and age-related diseases, modulation of Rubicon has been identified as a potential therapeutic target. In mice, Rubicon knockout reduces

accumulation in the brain and reduces interstitial fibrosis in the kidney.

Aging

Rubicon knockout increases lifespan in roundworms ( ''C. elegans'') through modulation of autophagy, and also increases lifespan in female fruit flies ( ''D. melanogaster'').

Nonalcoholic fatty liver disease (NAFLD)

Rubicon levels are increased in mouse models of

nonalcoholic fatty liver disease Non-alcoholic fatty liver disease (NAFLD), also known as metabolic (dysfunction) associated fatty liver disease (MAFLD), is excessive fat build-up in the liver without another clear cause such as alcohol use. There are two types; non-alcoholic ...

(NAFLD). Knockout of Rubicon in

hepatocytes A hepatocyte is a cell of the main parenchymal tissue of the liver. Hepatocytes make up 80% of the liver's mass. These cells are involved in: * Protein synthesis * Protein storage * Transformation of carbohydrates * Synthesis of cholesterol, bi ...

improves liver steatosis and autophagy, suggesting that Rubicon contributes to NAFLD pathogenesis.

Metabolic disease

Age-dependent decline of Rubicon expression in adipose tissues may exacerbate metabolic disorders due to excessive autophagic activity.

Salih ataxia (SCAR15)

A single nucleotide deletion mutation within Rubicon is the cause of Salih ataxia
OMIM ID: 615705
. Salih ataxia (also known as spinocerebellar ataxia, autosomal recessive 15 or SCAR15) is a form of

spinocerebellar ataxia Spinocerebellar ataxia (SCA) is a progressive, degenerative, genetic disease with multiple types, each of which could be considered a neurological condition in its own right. An estimated 150,000 people in the United States have a diagnosis of s ...

characterized by progressive loss of coordination of hands, gait, speech, and eye movement. The disease was discovered in children carrying a mutation (c.2624delC p.Ala875ValfsX146) causing a

frameshift mutation A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation caused by indels (gene insertion, insertions or genetic deletion, deletions) of a number of nucleotides in a DNA sequence that is not divisible by ...

and an erroneous

open reading frame In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a Prokaryote, prokaryotic DNA sequence, where only one of the #Six-fra ...

in the Rubicon-coding gene starting from Alanine 875. The resulting disruption of the

C-terminal domain The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain ( protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein ...

impairs Rubicon subcellular localization with Rab7 and late endosomes.

References

{{reflist Human genes