Elucidating the Role of Nrf2 Factor Interactions in Various Disorders of Human System and It’s Proteomic Approaches: A Novel Study

Nuclear factor erythroid 2-related factor 2 (Nrf2), which is also known as nuclear factor erythroid-derived-like-2, is a transcription factor which is encoded by the NFE2L2 gene. It is a basic leucine zipper (bZIP) protein which coordinates the basal and stress-inducible activation of a vast array of cytoprotective genes. It modulates a cellular antioxidant response program and plays a major role in the protection against oxidants and electrophiles; extracellular and intracellular oxidant/electrophiles have great contributions to the damages in cellular macromolecules such as proteins, lipids or DNA. Keap1 protein which is a regulator of Nrf2, is a highly redox-sensitive member of BTB-Kelch family assembling with Cul3 protein to form a Cullin-RING E3 ligase complex for Nrf2 degradation. Thus, this factor is a regulator of many processes of life and it’s signalling system (Nrf2-KEAP-1-ARE pathway) has been found to participate in various ocular or eye diseases and even other systemic diseases such as respiratory disease, chronic diseases or cancer. In microbial infections, the host oxidative stress response may lead to the production of cytoprotective molecules, which in turn induces the activation of cellular Nrf2 factor. The crystallins or eye lens proteins, (?B-crystallin being one of them) may possibly interact with Nrf2 factor and regulate oxidative stress, but it is yet to be deciphered. Proteomic studies may provide valuable information, regarding such detailed protein interactions and their pathways especially in case of diseases or infections in the upcoming days.

NEDD8 Deamidation Inhibits Cullin RING Ligase Dynamics

Cullin-RING ligases (CRLs) are a significant subset of Ubiquitin E3 ligases that regulate multiple cellular substrates involved in innate immunity, cytoskeleton modeling, and cell cycle. The glutamine deamidase Cycle inhibitory factor (Cif) from enteric bacteria inactivates CRLs to modulate these processes in the host cell. The covalent attachment of a Ubiquitin-like protein NEDD8 catalytically activates CRLs by driving conformational changes in the Cullin C-terminal domain (CTD). NEDDylation results in a shift from a compact to an open CTD conformation through non-covalent interactions between NEDD8 and the WHB subdomain of CTD, eliminating the latter’s inhibitory interactions with the RING E3 ligase-Rbx1/2. It is unknown whether the non-covalent interactions are sufficient to stabilize Cullin CTD’s catalytic conformation. We studied the dynamics of Cullin-CTD in the presence and absence of NEDD8 using atomistic molecular dynamics (MD) simulations. We uncovered that NEDD8 engages in non-covalent interactions with 4HB/αβ subdomains in Cullin-CTD to promote open conformations. Cif deamidates glutamine 40 in NEDD8 to inhibit the conformational change in CRLs by an unknown mechanism. We investigated the effect of glutamine deamidation on NEDD8 and its interaction with the WHB subdomain post-NEDDylation using MD simulations and NMR spectroscopy. Our results suggest that deamidation creates a new intramolecular salt bridge in NEDD8 to destabilize the NEDD8/WHB complex and reduce CRL activity.

SIRT1 coordinates with the CRL4B complex to regulate pancreatic cancer stem cells to promote tumorigenesis

Pancreatic cancer is a common malignant tumor with poor prognosis. Recently, cancer stem cells (CSCs) were identified in several solid tumors, including pancreatic cancer. Although accumulating evidence indicates that sirtuin 1 (SIRT1) exerts biological functions in various cancers, how it contributes to tumorigenesis and metastasis of pancreatic cancer, as well as its role in CSCs, is still poorly defined. Here we show that SIRT1 interacts with the Cullin 4B (CUL4B)-Ring E3 ligase (CRL4B) complex, which is responsible for H2AK119 monoubiquitination (H2AK119ub1), collaborating as a functional unit. Genome-wide analysis of SIRT1/CUL4B targets identified a cohort of genes, including GRHL3 and FOXO3, critically involved in cell differentiation, growth, and migration. Furthermore, we found that SIRT1 and CUL4B collectively promote the proliferation, autophagy, and invasion of pancreatic cancer cells. Remarkably, we demonstrate that SIRT1/CUL4B promotes CSC-like properties, including increased stemness marker expression and sphere formation. In vivo experiments implied that SIRT1 promoted established tumor xenograft growth, increased tumor-initiating capacity in NOD/SCID mice, and increased CSC frequency. Strikingly, SIRT1 and CUL4B expression is markedly upregulated in a variety of human cancers, including pancreatic cancer. Our data provide a molecular basis for the functional interplay between histone deacetylation and ubiquitination. The results also implicate the SIRT1/CRL4B complex in pancreatic cancer metastasis and stem cell properties, thus supporting SIRT1 as a promising potential target for cancer therapy development.

Neddylation inhibition protects against ischemic brain injury

Neddylation is a ubiquitylation-like pathway that is critical in various cellular functions by conjugating NEDD8 to target proteins. However, the roles of neddylation in stroke, remain elusive. Here, we report that NEDD8 conjugation increased after ischemic stroke and was abundantly present in neutrophils, whereas cullin-1, a key substrate of neddylation, was upregulated in endothelium. Inhibition of neddylation by MLN4924, inactivated cullin-RING E3 ligase (CRL), reduced brain infarction and improved functional outcomes. MLN4924 treatment induced accumulation of the CRL substrate NF1. Knockdown of NF1 abolished MLN4924-dependent inhibition of neutrophil trafficking. These effects were mediated through activation of endothelial P-selectin and ICAM-1. Moreover, NF1 silencing blocked MLN4924-afforded BBB protection and neuroprotection through activation of PKCδ, MARCKS and MLC in cerebral microvessels. Our results demonstrate that increased neddylation promoted neutrophil trafficking and thus exacerbated injury of the BBB and stroke outcomes. We suggest that the neddylation inhibition may be beneficial in ischemic stroke.

The RING E3 ligase SDIR1 destabilizes EBF1/EBF2 and modulates the ethylene response to ambient temperature fluctuations in Arabidopsis

The gaseous phytohormone ethylene mediates numerous aspects of plant growth and development as well as stress responses. The F-box proteins EIN3-binding F-box protein 1 (EBF1) and EBF2 are key components that ubiquitinate and degrade the master transcription factors ethylene insensitive 3 (EIN3) and EIN3-like 1 (EIL1) in the ethylene response pathway. Notably, EBF1 and EBF2 themselves undergo the 26S proteasome-mediated proteolysis induced by ethylene and other stress signals. However, despite their importance, little is known about the mechanisms regulating the degradation of these proteins. Here, we show that a really interesting new gene (RING)-type E3 ligase, salt- and drought-induced ring finger 1 (SDIR1), positively regulates the ethylene response and promotes the accumulation of EIN3. Further analyses indicate that SDIR1 directly interacts with EBF1/EBF2 and targets them for ubiquitination and proteasome-dependent degradation. We show that SDIR1 is required for the fine tuning of the ethylene response to ambient temperature changes by mediating temperature-induced EBF1/EBF2 degradation and EIN3 accumulation. Thus, our work demonstrates that SDIR1 functions as an important modulator of ethylene signaling in response to ambient temperature changes, thereby enabling plant adaptation under fluctuating environmental conditions.

Ubiquitination of phytoene synthase 1 precursor modulates carotenoid biosynthesis in tomato

Carotenoids are natural pigments that are indispensable to plants and humans, whereas the regulation of carotenoid biosynthesis by post-translational modification remains elusive. Here, we show that a tomato E3 ubiquitin ligase, Plastid Protein Sensing RING E3 ligase 1 (PPSR1), is responsible for the regulation of carotenoid biosynthesis. PPSR1 exhibits self-ubiquitination activity and loss of PPSR1 function leads to an increase in carotenoids in tomato fruit. PPSR1 affects the abundance of 288 proteins, including phytoene synthase 1 (PSY1), the key rate-limiting enzyme in the carotenoid biosynthetic pathway. PSY1 contains two ubiquitinated lysine residues (Lys380 and Lys406) as revealed by the global analysis and characterization of protein ubiquitination. We provide evidence that PPSR1 interacts with PSY1 precursor protein and mediates its degradation via ubiquitination, thereby affecting the steady-state level of PSY1 protein. Our findings not only uncover a regulatory mechanism for controlling carotenoid biosynthesis, but also provide a strategy for developing carotenoid-enriched horticultural crops.