Ubiquitin protein modification and signal transduction: implications for inflammatory bowel diseases

The Ubiquitination System within Bacterial Host-Pathogen Interactions

Ubiquitination of proteins, like phosphorylation and acetylation, is an important regulatory aspect influencing numerous and various cell processes, such as immune response signaling and autophagy. The study of ubiquitination has become essential to learning about host-pathogen interactions, and a better understanding of the detailed mechanisms through which pathogens affect ubiquitination processes in host cell will contribute to vaccine development and effective treatment of diseases. Pathogenic bacteria (e.g., Salmonella enterica, Legionella pneumophila and Shigella flexneri) encode many effector proteins, such as deubiquitinating enzymes (DUBs), targeting the host ubiquitin machinery and thus disrupting pertinent ubiquitin-dependent anti-bacterial response. We focus here upon the host ubiquitination system as an integral unit, its interconnection with the regulation of inflammation and autophagy, and primarily while examining pathogens manipulating the host ubiquitination system. Many bacterial effector proteins have already been described as being translocated into the host cell, where they directly regulate host defense processes. Due to their importance in pathogenic bacteria progression within the host, they are regarded as virulence factors essential for bacterial evasion. However, in some cases (e.g., Francisella tularensis) the host ubiquitination system is influenced by bacterial infection, although the responsible bacterial effectors are still unknown.

Roles of protein ubiquitination in inflammatory bowel disease

Inflammatory bowel disease (IBD) including Crohn's disease (CD) and ulcerative colitis (UC) seriously affects the quality of life for patients. The pathogenesis of IBD contains the environmental, host genetic and epigenetic factors. In recent years, the studies of protein ubiquitination, an important protein post-translational modification as an epigenetic factor, have emerged in the pathogenesis and development of IBD. In the past few years, accumulative evidence illustrated that six E3 ubiquitin ligases, namely, ring finger protein (RNF) 183, RNF 20, A20, Pellino 3, TRIM62 and Itch, exhibited clear mechanisms in the development of IBD. They regulate the intestinal inflammation by facilitating the ubiquitination of targeted proteins which participate in different inflammatory signaling pathways. Besides, it was reported that some deubiquitinating enzymes such as Cylindromatosis and USP7 were involved in the development of IBD, but the molecular mechanism was still unclear. This review summarized the role and regulatory mechanism of protein ubiquitination in the pathogenesis and development of IBD, providing insights to develop a new therapeutic strategy in IBD treatments.

Proteolytic and non-proteolytic roles of ubiquitin and the ubiquitin proteasome system in transcriptional regulation

The ubiquitin proteasome system (UPS) regulates perhaps the most intriguing balance in all of biology: how cells control protein function and malfunction in order to regulate, and eventually eliminate, the old and error prone while simultaneously synthesizing and orchestrating the new. In light of the growing notion that ubiquitination and the 26S proteasome are central to a multiplicity of diverse cellular functions, we discuss here the proteolytic and non-proteolytic roles of the UPS in regulating pathways ultimately involved in protein synthesis and activity including roles in epigenetics, transcription, and post-translational modifications. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!

Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies

Inflammatory bowel diseases (IBD) are chronic, heterogeneous, and multifactorial intestinal inflammatory disorders. Major challenges in IBD research include identification of major pathogenic alterations of genes/proteins as well as effective biomarkers for early diagnosis, prognosis, and prediction of therapeutic response. Since proteins govern cellular structure and biological function, a wide selection of proteomic approaches enables effective characterization of IBD pathogenesis by investigating the dynamic nature of protein expression, cellular and subcellular distribution, posttranslational modifications, and interactions at both the cellular and subcellular levels. The aims of this review are to 1) highlight the current status of proteomic studies of IBD, and 2) introduce the available and emerging proteomic technologies that have potential applications in the study of IBD. These technologies include various mass spectrometry technologies, quantitative proteomics (2D-PAGE, ICAT, SILAC, iTRAQ), protein/antibody arrays, and multi-epitope-ligand cartography. This review also presents information and methodologies, from sample selection and enrichment to protein identification, that are not only essential but also particularly relevant to IBD research. The potential future application of these technologies is expected to have a significant impact on the discovery of novel biomarkers and key pathogenic factors for IBD.

Early molecular and functional changes in colonic epithelium that precede increased gut permeability during colitis development in mdr1a(-/-) mice

BACKGROUND

The early molecular changes preceding the onset of mucosal inflammation in colitis and their temporal relationship with gut permeability remain poorly defined. This study investigated functional and transcriptomic changes in mdr1a(-/-) mice lacking the intestinal transporter P-glycoprotein, which develop colitis spontaneously when exposed to normal enteric flora.

METHODS

Mdr1a(-/-) mice were housed in specific pathogen-free conditions to slow colitis development and compared to congenic controls. Mucosal permeability and cytokine secretion were analyzed in ex vivo colon. Gene expression in colonic mucosal and epithelial preparations was analyzed by microarray and qPCR. Colonocyte responsiveness to bacterial antigens was measured in short-term culture.

RESULTS

Colon from 4-5-week-old, disease-free mdr1a(-/-) mice was histologically normal with no evidence of increased permeability compared to controls. However, these tissues display a distinctive pattern of gene expression involving significant changes in a small number of genes. The majority of upregulated genes were associated with bacterial recognition and the ubiquitin-proteasome system and were gamma-interferon (IFN-gamma) responsive. Expression of the antiinflammatory factor pancreatitis-associated protein (PAP) and the related gene RegIIIgamma were markedly reduced. Colonocytes from 4-5-week mdr1a(-/-) exhibit similar transcriptomic changes, accompanied by higher basal chemokine secretion and increased responsiveness to LPS. Significant increases in colonic permeability were associated with older (12-16-week) mdr1a(-/-) mice displaying molecular and functional evidence of active inflammation.

CONCLUSIONS

These studies show that early epithelial changes associated with altered responsiveness to bacteria precede increased permeability and mucosal inflammation in this model of colitis, highlighting the importance of P-glycoprotein in regulating interactions with the commensal microflora.

NF-kappaB and the intestine: friend or foe?

The biological impact of the NF-kappaB transcriptional system in various intestinal biological processes such as cellular proliferation, differentiation and survival, inflammation, and carcinogenesis is a relatively young field of research. Less than a decade ago, reviews addressing NF-kappaB regulation and function in the intestine had to borrow concepts and hypotheses from other bodily systems such as the joints (rheumatoid arthritis), the lungs (asthma), or the cardiovascular system (systemic inflammatory states, sepsis). Since then, important progress has been made in defining the various functional aspects of NF-kappaB signaling in intestinal homeostasis and diseases, and exciting new paradigms have emerged from this research. This review will discuss the function of NF-kappaB in intestinal homeostasis and diseases in relation to injury responses and microbial colonization/infection.

Role of proteasomes in disease

A functional ubiquitin proteasome system is essential for all eukaryotic cells and therefore any alteration to its components has potential pathological consequences. Though the exact underlying mechanism is unclear, an age-related decrease in proteasome activity weakens cellular capacity to remove oxidatively modified proteins and favours the development of neurodegenerative and cardiac diseases. Up-regulation of proteasome activity is characteristic of muscle wasting conditions including sepsis, cachexia and uraemia, but may not be rate limiting. Meanwhile, enhanced presence of immunoproteasomes in aging brain and muscle tissue could reflect a persistent inflammatory defence and anti-stress mechanism, whereas in cancer cells, their down-regulation reflects a means by which to escape immune surveillance. Hence, induction of apoptosis by synthetic proteasome inhibitors is a potential treatment strategy for cancer, whereas for other diseases such as neurodegeneration, the use of proteasome-activating or -modulating compounds could be more effective. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).

Aluminum is a potential environmental factor for Crohn's disease induction: extended hypothesis

Aluminum (Al) is a common environmental compound with immune-adjuvant activity and granulomatous inflammation inducer. Al exposure in food, additives, air, pharmaceuticals, and water pollution is ubiquitous in Western culture. Crohn's disease (CD) is a chronic relapsing intestinal inflammation in genetically susceptible individuals and is influenced by yet unidentified environmental factors. It is hypothesized, in the present review, that Al is a potential factor for induction or maintaining the inflammation in CD. Epidemiologically, CD incidence is higher in urban areas, where microparticle pollution is prevalent. Al immune activities share many characteristics with the immune pathology of CD: increased antigen presentation and APCs activation, many luminal bacterial or dietary compounds can be adsorbed to the metal and induce Th1 profile activity, promotion of humoral and cellular immune responses, proinflammatory, apoptotic, oxidative activity, and stress-related molecule expression enhancement, affecting intestinal bacterial composition and virulence, granuloma formation, colitis induction in an animal model of CD, and terminal ileum uptake. The Al-bacterial interaction, the microparticles homing the intestine together with the extensive immune activity, put Al as a potential environmental candidate for CD induction and maintenance.

Role of neuropeptides in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic, relapsing condition involving complex interactions between genes and the environment. The mechanisms triggering the initial attack and relapses, however, are not well understood. In the past several years the enteric nervous system (ENS) has been implicated in the pathophysiology of IBD. Both the ENS and the central nervous system (CNS) can amplify or modulate aspects of intestinal inflammation through secretion of neuropeptides that serve as a link between the ENS and CNS. Neuropeptides are defined as any peptide released from the nervous system that serves as an intercellular signaling molecule. Neuropeptides thought to play a potentially key role in IBD include substance P, corticotropin-releasing hormone, neurotensin, vasoactive intestinal peptide, mu-opioid receptor agonists, and galanin. This review focuses on the role of these neuropeptides in the pathophysiology of IBD and discusses the cell types and mechanisms involved in this process. The available evidence that neuropeptide blockade may be considered a therapeutic approach in both Crohn's disease and ulcerative colitis will also be discussed.

Essential roles of high-mobility group box 1 in the development of murine colitis and colitis-associated cancer

High-mobility group box 1 (HMGB1) is a nuclear factor released extracellularly as a proinflammatory cytokine. We measured the HMGB1 concentration in the sera of mice with chemically induced colitis (DSS; dextran sulfate sodium salt) and found a marked increase. Inhibition of HMGB1 by neutralizing anti-HMGB1 antibody resulted in reduced inflammation in DSS-treated colons. In macrophages, HMGB1 induces several proinflammatory cytokines, such as IL-6, which are regulated by NF-kappaB activation. Two putative sources of HMGB1 were explored: in one, bacterial factors induce HMGB1 secretion from macrophages and in the other, necrotic epithelial cells directly release HMGB1. LPS induced a small amount of HMGB1 in macrophages, but macrophages incubated with supernatant prepared from necrotic cells and containing large amounts of HMGB1 activated NF-kappaB and induced IL-6. Using the colitis-associated cancer model, we demonstrated that neutralizing anti-HMGB1 antibody decreases tumor incidence and size. These observations suggest that HMGB1 is a potentially useful target for IBD treatment and the prevention of colitis-associated cancer.