A Residue Specific Insight into the Arkadia E3 Ubiquitin Ligase Activity and Conformational Plasticity

Preserving genome integrity: The vital role of SUMO-targeted ubiquitin ligases

Various post-translational modifications (PTMs) collaboratively fine-tune protein activities. SUMO-targeted ubiquitin E3 ligases (STUbLs) emerge as specialized enzymes that recognize SUMO-modified substrates through SUMO-interaction motifs and subsequently ubiquitinate them via the RING domain, thereby bridging the SUMO and ubiquitin signaling pathways. STUbLs participate in a wide array of molecular processes, including cell cycle regulation, DNA repair, replication, and mitosis, operating under both normal conditions and in response to challenges such as genotoxic stress. Their ability to catalyze various types of ubiquitin chains results in diverse proteolytic and non-proteolytic outcomes for target substrates. Importantly, STUbLs are strategically positioned in close proximity to SUMO proteases and deubiquitinases (DUBs), ensuring precise and dynamic control over their target proteins. In this review, we provide insights into the unique properties and indispensable roles of STUbLs, with a particular emphasis on their significance in preserving genome integrity in humans.

E2 Partner Tunes the Ubiquitylation Specificity of Arkadia E3 Ubiquitin Ligase

Arkadia (RNF111) is a positive regulator of the TGF-β signaling that mediates the proteasome-dependent degradation of negative factors of the pathway. It is classified as an E3 ubiquitin ligase and a SUMO-targeted ubiquitin ligase (STUBL), implicated in various pathological conditions including cancer and fibrosis. The enzymatic (ligase) activity of Arkadia is located at its C-terminus and involves the RING domain. Notably, E3 ligases require E2 enzymes to perform ubiquitylation. However, little is known about the cooperation of Arkadia with various E2 enzymes and the type of ubiquitylation that they mediate. In the present work, we study the interaction of Arkadia with the E2 partners UbcH5B and UbcH13, as well as UbcH7. Through NMR spectroscopy, we found that the E2-Arkadia interaction surface is similar in all pairs examined. Nonetheless, the requirements and factors that determine an enzymatically active E2-Arkadia complex differ in each case. Furthermore, we revealed that the cooperation of Arkadia with different E2s results in either monoubiquitylation or polyubiquitin chain formation via K63, K48, or K11 linkages, which can determine the fate of the substrate and lead to distinct biological outcomes.

Structural modeling of protein ensembles between E3 RING ligases and SARS-CoV-2: The role of zinc binding domains

BACKGROUND

The ubiquitin system is a modification process with many different cellular functions including immune signaling and antiviral functions. E3 ubiquitin ligases are enzymes that recruit an E2 ubiquitin-conjugating enzyme bound to ubiquitin in order to catalyze the transfer of ubiquitin from the E2 to a protein substrate. The RING E3s, the most abundant type of ubiquitin ligases, are characterized by a zinc (II)-binding domain called RING (Really Interesting New Gene). Viral replication requires modifying and hijacking key cellular pathways within host cells such as cellular ubiquitination. There are well-established examples where a viral proteins bind to RING E3s, redirecting them to degrade otherwise long-lived host proteins or inhibiting E3's ubiquitination activity. Recently, three binary interactions between SARS-CoV-2 proteins and innate human immune signaling Ε3 RING ligases: NSP15-RNF41, ORF3a-TRIM59 and NSP9-MIB1 have been experimentally established.

METHODS

In this work, we have investigated the mode of the previous experimentally supported NSP15-RNF41, ORF3a,-TRIM59 and NSP9-MIB1 binary interactions by in silico methodologies intending to provide structural insights of E3-virus interplay that can help identify potential inhibitors that could block SARS-CoV-2 infection of immune cells.

CONCLUSION

In silico methodologies have shown that the above human E3 ligases interact with viral partners through their Zn(II) binding domains. This RING mediated formation of stable SARS-CoV-2-E3 complexes indicates a critical structural role of RING domains in immune system disruption by SARS-CoV-2-infection.

DATA AVAILABILITY

The data used to support the findings of this research are included within the article and are labeled with references.

Biological Effects of Human Exposure to Environmental Cadmium

Cadmium (Cd) is a toxic metal for the human organism and for all ecosystems. Cd is naturally found at low levels; however, higher amounts of Cd in the environment result from human activities as it spreads into the air and water in the form of micropollutants as a consequence of industrial processes, pollution, waste incineration, and electronic waste recycling. The human body has a limited ability to respond to Cd exposure since the metal does not undergo metabolic degradation into less toxic species and is only poorly excreted. The extremely long biological half-life of Cd essentially makes it a cumulative toxin; chronic exposure causes harmful effects from the metal stored in the organs. The present paper considers exposure and potential health concerns due to environmental cadmium. Exposure to Cd compounds is primarily associated with an elevated risk of lung, kidney, prostate, and pancreatic cancer. Cd has also been linked to cancers of the breast, urinary system, and bladder. The multiple mechanisms of Cd-induced carcinogenesis include oxidative stress with the inhibition of antioxidant enzymes, the promotion of lipid peroxidation, and interference with DNA repair systems. Cd²⁺ can also replace essential metal ions, including redox-active ones. A total of 12 cancer types associated with specific genes coding for the Cd-metalloproteome were identified in this work. In addition, we summarize the proper treatments of Cd poisoning, based on the use of selected Cd detoxifying agents and chelators, and the potential for preventive approaches to counteract its chronic exposure.

Natural Dietary Compounds in the Treatment of Arsenic Toxicity

Chronic exposure to arsenic (As) compounds leads to its accumulation in the body, with skin lesions and cancer being the most typical outcomes. Treating As-induced diseases continues to be challenging as there is no specific, safe, and efficacious therapeutic management. Therapeutic and preventive measures available to combat As toxicity refer to chelation therapy, antioxidant therapy, and the intake of natural dietary compounds. Although chelation therapy is the most commonly used method for detoxifying As, it has several side effects resulting in various toxicities such as hepatotoxicity, neurotoxicity, and other adverse consequences. Drugs of plant origin and natural dietary compounds show efficient and progressive relief from As-mediated toxicity without any particular side effects. These natural compounds have also been found to aid the elimination of As from the body and, therefore, can be more effective than conventional therapeutic agents in ameliorating As toxicity. This review provides an overview of the recently updated knowledge on treating As poisoning through natural dietary compounds. This updated information may serve as a basis for defining novel prophylactic and therapeutic formulations.

Impact of a Single Nucleotide Polymorphism on the 3D Protein Structure and Ubiquitination Activity of E3 Ubiquitin Ligase Arkadia

Single nucleotide polymorphisms (SNPs) are genetic variations which can play a vital role in the study of human health. SNP studies are often used to identify point mutations that are associated with diseases. Arkadia (RNF111) is an E3 ubiquitin ligase that enhances transforming growth factor-beta (TGF-β) signaling by targeting negative regulators for degradation. Dysregulation of the TGF-β pathway is implicated in cancer because it exhibits tumor suppressive activity in normal cells while in tumor cells it promotes invasiveness and metastasis. Τhe SNP CGT > TGT generated an amino-acid (aa) substitution of Arginine 957 to Cysteine on the enzymatic RING domain of Arkadia. This was more prevalent in a tumor than in a normal tissue sample of a patient with colorectal cancer. This prompted us to investigate the effect of this mutation in the structure and activity of Arkadia RING. We used nuclear magnetic resonance (NMR) to analyze at an atomic-level the structural and dynamic properties of the R957C Arkadia RING domain, while ubiquitination and luciferase assays provided information about its enzymatic functionality. Our study showed that the R957C mutation changed the electrostatic properties of the RING domain however, without significant effects on the structure of its core region. However, the functional studies revealed that the R957C Arkadia exhibits significantly increased enzymatic activity supporting literature data that Arkadia within tumor cells promotes aggressive and metastatic behavior.

Structural Identification of Metalloproteomes in Marine Diatoms, an Efficient Algae Model in Toxic Metals Bioremediation

The biosorption of pollutants using microbial organisms has received growing interest in the last decades. Diatoms, the most dominant group of phytoplankton in oceans, are (i) pollution tolerant species, (ii) excellent biological indicators of water quality, and (iii) efficient models in assimilation and detoxification of toxic metal ions. Published research articles connecting proteomics with the capacity of diatoms for toxic metal removal are very limited. In this work, we employed a structural based systematic approach to predict and analyze the metalloproteome of six species of marine diatoms: Thalassiosira pseudonana, Phaeodactylum tricornutum, Fragilariopsis cylindrus, Thalassiosira oceanica, Fistulifera solaris, and Pseudo-nitzschia multistriata. The results indicate that the metalloproteome constitutes a significant proportion (~13%) of the total diatom proteome for all species investigated, and the proteins binding non-essential metals (Cd, Hg, Pb, Cr, As, and Ba) are significantly more than those identified for essential metals (Zn, Cu, Fe, Ca, Mg, Mn, Co, and Ni). These findings are most likely related to the well-known toxic metal tolerance of diatoms. In this study, metalloproteomes that may be involved in metabolic processes and in the mechanisms of bioaccumulation and detoxification of toxic metals of diatoms after exposure to toxic metals were identified and described.

SUMO-Targeted Ubiquitin Ligases and Their Functions in Maintaining Genome Stability

Small ubiquitin-like modifier (SUMO)-targeted E3 ubiquitin ligases (STUbLs) are specialized enzymes that recognize SUMOylated proteins and attach ubiquitin to them. They therefore connect the cellular SUMOylation and ubiquitination circuits. STUbLs participate in diverse molecular processes that span cell cycle regulated events, including DNA repair, replication, mitosis, and transcription. They operate during unperturbed conditions and in response to challenges, such as genotoxic stress. These E3 ubiquitin ligases modify their target substrates by catalyzing ubiquitin chains that form different linkages, resulting in proteolytic or non-proteolytic outcomes. Often, STUbLs function in compartmentalized environments, such as the nuclear envelope or kinetochore, and actively aid in nuclear relocalization of damaged DNA and stalled replication forks to promote DNA repair or fork restart. Furthermore, STUbLs reside in the same vicinity as SUMO proteases and deubiquitinases (DUBs), providing spatiotemporal control of their targets. In this review, we focus on the molecular mechanisms by which STUbLs help to maintain genome stability across different species.

RNF111-facilitated neddylation potentiates cGAS-mediated antiviral innate immune response

The cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthetase (cGAS) has emerged as a fundamental component fueling the anti-pathogen immunity. Because of its pivotal role in initiating innate immune response, the activity of cGAS must be tightly fine-tuned to maintain immune homeostasis in antiviral response. Here, we reported that neddylation modification was indispensable for appropriate cGAS-STING signaling activation. Blocking neddylation pathway using neddylation inhibitor MLN4924 substantially impaired the induction of type I interferon and proinflammatory cytokines, which was selectively dependent on Nedd8 E2 enzyme Ube2m. We further found that deficiency of the Nedd8 E3 ligase Rnf111 greatly attenuated DNA-triggered cGAS activation while not affecting cGAMP induced activation of STING, demonstrating that Rnf111 was the Nedd8 E3 ligase of cGAS. By performing mass spectrometry, we identified Lys231 and Lys421 as essential neddylation sites in human cGAS. Mechanistically, Rnf111 interacted with and polyneddylated cGAS, which in turn promoted its dimerization and enhanced the DNA-binding ability, leading to proper cGAS-STING pathway activation. In the same line, the Ube2m or Rnf111 deficiency mice exhibited severe defects in innate immune response and were susceptible to HSV-1 infection. Collectively, our study uncovered a vital role of the Ube2m-Rnf111 neddylation axis in promoting the activity of the cGAS-STING pathway and highlighted the importance of neddylation modification in antiviral defense.

A SARS-CoV-2 -human metalloproteome interaction map

The recent pandemic caused by the novel coronavirus resulted in the greatest global health crisis since the Spanish flu pandemic of 1918. There is limited knowledge of whether SARS-CoV-2 is physically associated with human metalloproteins. Recently, high-confidence, experimentally supported protein-protein interactions between SARS-CoV-2 and human proteins were reported. In this work, 58 metalloproteins among these human targets have been identified by a structure-based approach. This study reveals that most human metalloproteins interact with the recently discovered SARS-CoV-2 orf8 protein, whose antibodies are one of the principal markers of SARS-CoV-2 infections. Furthermore, this work provides sufficient evidence to conclude that Zn²⁺ plays an important role in the interplay between the novel coronavirus and humans. First, the content of Zn-binding proteins in the involved human metalloproteome is significantly higher than that of the other metal ions. Second, a molecular linkage between the identified human Zn-binding proteome with underlying medical conditions, that might increase the risk of severe illness from the SARS-CoV-2 virus, has been found. Likely perturbations of host cellular metal homeostasis by SARS-CoV-2 infection are highlighted.

The Role of Conformational Dynamics in the Recognition and Regulation of Ubiquitination

The ubiquitination pathway is central to many cell signaling and regulatory events. One of the intriguing aspects of the pathway is the combinatorial sophistication of substrate recognition and ubiquitin chain building determinations. The abundant structural and biological data portray several characteristic protein folds among E2 and E3 proteins, and the understanding of the combinatorial complexity that enables interaction with much of the human proteome is a major goal to developing targeted and selective manipulation of the pathway. With the commonality of some folds, there are likely other aspects that can provide differentiation and recognition. These aspects involve allosteric effects and conformational dynamics that can direct recognition and chain building processes. In this review, we will describe the current state of the knowledge for conformational dynamics across a wide timescale, address the limitations of present approaches, and illustrate the potential to make new advances in connecting dynamics with ubiquitination regulation.

Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network

The ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the pathway. Its RING domain binds both E2-Ub and free Ub with high affinity, resulting in a catalytic active Ub_R-RING-E2-Ub_D complex formation. We examined potential changes in the conformational plasticity of the Ark2C RING domain and its ligands in their complexed form within the ubiquitin pathway through molecular dynamics (MD). Three molecular mechanics force fields compared to previous NMR relaxation studies of RING domain of Arkadia were used for effective and accurate assessment of MDs. Our results suggest the Ark2C Ub-RING docking site has a substantial impact on maintaining the conformational rigidity of E2-E3 assembly, necessary for the E3’s catalytic activity. In the Ub_R-RING-E2-Ub_D catalytic complex, the Ub_R molecule was found to have greater mobility than the other Ub, bound to E2. Furthermore, network-based bioinformatics helped us identify E3 RING ligase candidates which potentially exhibit similar structural modules as Ark2C, along with predicted substrates targeted by the Ub-binding RING Ark2C. Our findings could trigger a further exploration of related unrevealed functions of various other E3 RING ligases.

Recent aspects of the effects of zinc on human health

Zinc (Zn) is one of the most important essential nutrients of great public health significance. It is involved in numerous biological functions and it is considered as a multipurpose trace element, due to its capacity to bind to more than 300 enzymes and more than 2000 transcriptional factors. Its role in biochemical pathways and cellular functions, such as the response to oxidative stress, homeostasis, immune responses, DNA replication, DNA damage repair, cell cycle progression, apoptosis and aging is significant. Zn is required for the synthesis of protein and collagen, thus contributing to wound healing and a healthy skin. Metallothioneins are metal-binding proteins and they are potent scavengers of heavy metals, including Zn, and protect the organism against stress. Zn deficiency is observed almost in 17% of the global population and affects many organ systems, leading to dysfunction of both humoral and cell-mediated immunity, thus increasing the susceptibility to infection. This review gives a thorough insight into the most recent evidence on the association between Zn biochemistry and human pathologies, epigenetic processes, gut microbial composition, drug targets and nanomedicine.

Smad2 and Smad3 play antagonistic roles in high glucose-induced renal tubular fibrosis via the regulation of SnoN

Diabetic nephropathy (DN) is a serious microvascular complication of diabetes mellitus.The main pathological features of DN include glomerular sclerosis and renal tubular interstitial fibrosis, which results in epithelial mesenchymal transition (EMT) and excessive extracellular matrix (ECM) deposition.Transforming growth factor-β1(TGF-β1) is a critical factor that regulates the manifestation of renal fibrosis.Smad2 and Smad3 are the main downstream of the TGF-β1 pathway. Ski-related novel protein N(SnoN) is a negative regulator of TGF-β1, and inhibits the activation of the TGF-β1/Smad2/3 signalling pathway. In this study, the expression of Smad2 and Smad3 proteins, SnoN mRNA, SnoN proteins, and the ubiquitination levels of SnoN were determined in DN rats and renal tubular epithelial cells(NRK52E cells). Knockdown and overexpression of Smad2 or Smad3 in NRK52E cells were used to investigate the specific roles of Smad2 and Smad3 in the development of high glucose-induced renal tubular fibrosis, with a specific focus on their effect on the regulation of SnoN expression. Our study demonstrated that Smad3 could inhibit SnoN expression and increase ECM deposition in NRK52E cells, to promote high glucose-induced renal tubular fibrosis. In contrast, Smad2 could induce SnoN expression and reduce ECM deposition, to inhibit high glucose-induced fibrosis. The underlying mechanism involves regulation of SnoN expression. These findings provide a novel mechanism to understanding the significant role of the TGF-β1/ Smad2/3 pathway in DN.

Protein isoelectric point distribution in the interactomes across the domains of life

The distribution of the protein isoelectric point (pI) in the protein-protein interaction (PPI) networks across the domains of life has not been investigated yet. This work attempts to correlate the pI with the number of direct interacting partners in the experimentally supported networks involving 226.085 PPIs from 14 various organisms including human, mouse, yeast, bacteria, viruses and 53.606 virus-host interactions. The results showed that the acidic proteins (pI<3) have the highest average number of interactions in eukaryotes, while in bacteria more neutral proteins. On the contrary, the basic proteins (pI>11) have the lowest average number of interactions in human, mouse, yeast, bacteria and human-viral interactomes and the highest average in intraviral interactomes. We examined the correlation of the pI of the interacting partners by calculating the assortativity index of various PPI networks. We found that the interactions between the acidic, neutral and basic proteins have a fairly random mix, implying weak if any association between the acidic and basic proteins. Furthermore, protein features such as biological function, structurally order and disorder, subcellular localization, and homodimerization were classified according to pI in prokaryote and eukaryote proteomes.

Lead Identification Through the Synergistic Action of Biomolecular NMR and In Silico Methodologies

The combination of virtual screening with biomolecular NMR can be a powerful approach in the first steps toward drug discovery. Here, we describe how computational methodologies to screen large databases readily available for testing small molecules, in synergy with NMR techniques focused on protein-ligand interactions, can be used in the early lead compound identification process against a protein drug target.

Preliminary results from structural systems biology approach in Tetrahymena thermophila reveal novel perspectives for this toxicological model

Tetrahymena is a unicellular microbial eukaryotic organism that has been used extensively in toxicology and environmental research. This work attempts to model for the first time the wiring of proteins involved in cellular mechanisms of Cd toxicity in Tetrahymena thermophila. 1975 high-confidence PPIs between 68 Cd-binding proteins and 422 partners were inferred through a novel structural systems biology approach that utilizes comparative analysis between Tetrahymena and other eukaryotes for which experimentally supported protein interactomes exist. The PPIs of the potential network were confirmed by known domain interactions in the Protein Data Bank and its topological characteristics were compared with publicly available experimental information for T. thermophila. To experimentally validate the robustness of the proposed PPI network, the interaction between the two most interconnected hub proteins was detected through GST pull-down assay. Potential effects on Tetrahymena's cellular and metabolic processes by PPIs involving Cd-binding proteins were uncovered. Furthermore, 244 PPIs in which Cd-binding proteins or/and their partners are encoded by orthologs of human disease genes in T. thermophila, but not in yeast, were identified and analyzed. The findings suggest that Tetrahymena could be possibly a useful model for an improved understanding of molecular mechanisms of Cd toxicity in human diseases.

Shared gene-network signatures between the human heavy metal proteome and neurological disorders and cancer types

In this work, for the first time, the human heavy metal proteome was predicted.