Michael R. Bubb

Upregulated miR-146a expression in peripheral blood mononuclear cells from rheumatoid arthritis patients

IntroductionMicroRNAs are small noncoding RNA molecules that negatively regulate gene expression via degradation or translational repression of their targeted mRNAs. It is known that aberrant microRNA expression can play important roles in cancer, but the role of microRNAs in autoimmune diseases is only beginning to emerge. In this study, the expression of selected microRNAs is examined in rheumatoid arthritis.MethodsTotal RNA was isolated from peripheral blood mononuclear cells obtained from patients with rheumatoid arthritis, and healthy and disease control individuals, and the expression of miR-146a, miR-155, miR-132, miR-16, and microRNA let-7a was analyzed using quantitative real-time PCR.ResultsRheumatoid arthritis peripheral blood mononuclear cells exhibited between 1.8-fold and 2.6-fold increases in miR-146a, miR-155, miR-132, and miR-16 expression, whereas let-7a expression was not significantly different compared with healthy control individuals. In addition, two targets of miR-146a, namely tumor necrosis factor receptor-associated factor 6 (TRAF6) and IL-1 receptor-associated kinase 1 (IRAK-1), were similarly expressed between rheumatoid arthritis patients and control individuals, despite increased expression of miR-146a in patients with rheumatoid arthritis. Repression of TRAF6 and/or IRAK-1 in THP-1 cells resulted in up to an 86% reduction in tumor necrosis factor-α production, implicating that normal miR-146a function is critical for the regulation of tumor necrosis factor-α production.ConclusionsRecent studies have shown that synovial tissue and synovial fibroblasts from patients with rheumatoid arthritis exhibit increased expression of certain microRNAs. Our data thus demonstrate that microRNA expression in rheumatoid arthritis peripheral blood mononuclear cells mimics that of synovial tissue/fibroblasts. The increased microRNA expression in rheumatoid arthritis patients is potentially useful as a marker for disease diagnosis, progression, or treatment efficacy, but this will require confirmation using a large and well defined cohort. Our data also suggest a possible mechanism contributing to rheumatoid arthritis pathogenesis, whereby miR-146a expression is increased but unable to properly function, leading to prolonged tumor necrosis factor-α production in patients with rheumatoid arthritis.

New anti-actin drugs in the study of the organization and function of the actin cytoskeleton.

The high degree of structural and molecular complexity of the actin‐based cytoskeleton, combined with its ability to reorganize rapidly and locally in response to stimuli, and its force‐generating properties, have made it difficult to assess how the different actin structures are assembled in cells, and how they regulate cell behavior. An obvious approach to study the relationships between actin organization, dynamics, and functions is the specific perturbation of actin structures using pharmacological means. Until recently there were only a few agents available that interfered with cellular activities by binding to actin and most of our knowledge concerning the involvement of actin in basic cellular processes was based on the extensive use of the cytochalasins. In recent years we have identified an increasing number of actin‐targeted marine natural products, including the latrunculins, jasplakinolides (jaspamides), swinholide A, misakinolide A, halichondramides, and pectenotoxin II, which are discussed in this article. All these marine‐sponge‐derived compounds are unusual macrolides and can be classified into several major families, each with its own distinct chemical structures. We describe the current state of knowledge concerning the actin‐binding properties of these compounds and show that each class of drugs alters the distribution patterns of actin in a unique way, and that even within a chemical class, structurally similar compounds can have different biochemical properties and cellular effects. We also discuss the effects of these new drugs on fenestrae formation in liver endothelial cells as an example of their usefulness as powerful tools to selectively unmask actin‐mediated dynamic processes. Microsc. Res. Tech. 47:18–37, 1999.

Vacuolar H+-ATPase Binding to Microfilaments REGULATION IN RESPONSE TO PHOSPHATIDYLINOSITOL 3-KINASE ACTIVITY AND DETAILED CHARACTERIZATION OF THE ACTIN-BINDING SITE IN SUBUNIT B

Vacuolar H+-ATPase (V-ATPase) binds microfilaments, and that interaction may be mediated by an actin binding domain in subunit B of the enzyme. To test for possible physiologic functions of the actin binding activity of V-ATPase, early responses of resorbing osteoclasts to inhibition of phosphatidylinositol 3-kinase activity by wortmannin and LY294002 were examined. Rapid co-localization between V-ATPase and F-actin was demonstrated by immunocytochemistry, and corresponding association between V-ATPase and F-actin in immunoprecipitations and pelleting assays was detected. This response was reversed as osteoclasts recovered resorptive activity after inhibitors were removed. By expressing and characterizing fusion proteins containing segments of the actin-binding amino-terminal regions of the B subunits of V-ATPase, we mapped the actin-binding site to a 44-amino acid domain. An 11-amino acid segment with a sequence similar to the actin-binding site of human profilin I was detected within this region. 13-Mers containing these profilin-like segments bound actin in fluorescent anisotropy studies and competed with profilin for binding to actin. Using site-directed mutagenesis, the 11-amino acid profilin-like actin-binding motifs (amino acids 49–59 of B1 and 55–65 of B2) were replaced with an 11-amino acid spacer with a sequence based on the homologous sequence from subunit B of Pyrococcus horikoshii, an organism that lacks an actin cytoskeleton. These substitutions eliminated the actin-binding activity of the B subunit fusion proteins. In summary, binding between V-ATPase and F-actin in osteoclasts occurs in response to blocking phosphatidylinositol 3-kinase activity. This response was fully reversible. The actin binding activities of the B subunits of V-ATPase required 11-amino acid actin-binding motifs that are similar in sequence to the actin-binding site of mammalian profilin I.

Control of actin dynamics by proteins made of β-thymosin repeats: The actobindin family

Actobindin is an actin-binding protein from amoeba, which consists of two β-thymosin repeats and has been shown to inhibit actin polymerization by sequestering G-actin and by stabilizing actin dimers. Here we show that actobindin has the same biochemical properties as the Drosophila orCaenorhabditis elegans homologous protein that consists of three β-thymosin repeats. These proteins define a new family of actin-binding proteins. They bind G-actin in a 1:1 complex with thermodynamic and kinetic parameters similar to β-thymosins. Like β-thymosins, they slow down nucleotide exchange on G-actin and make a ternary complex with G-actin and Latrunculin A. On the other hand, they behave as functional homologs of profilin because their complex with MgATP-G-actin, unlike β-thymosin-actin, participates in filament barbed end growth, like profilin-actin complex. Therefore these proteins play an active role in actin-based motility processes. In addition, proteins of the actobindin family interact with the pointed end of actin filaments and inhibit pointed end growth, maybe via the interaction of the β-thymosin repeats with two terminal subunits.

Polylysine Induces an Antiparallel Actin Dimer That Nucleates Filament Assembly CRYSTAL STRUCTURE AT 3.5-Å RESOLUTION

An antiparallel actin dimer has been proposed to be an intermediate species during actin filament nucleation. We now show that latrunculin A, a marine natural product that inhibits actin polymerization, arrests polylysine-induced nucleation at the level of an antiparallel dimer, resulting in its accumulation. These dimers, when composed of pyrene-labeled actin subunits, give rise to a fluorescent excimer, permitting detection during polymerizationin vitro. We report the crystallographic structure of the polylysine-actin-latrunculin A complex at 3.5-Å resolution. The non-crystallographic contact is consistent with a dimeric structure and confirms the antiparallel orientation of its subunits. The crystallographic contacts reveal that the mobile DNase I binding loop of one subunit of a symmetry-related antiparallel actin dimer is partially stabilized in the interface between the two subunits of a second antiparallel dimer. These results provide a potential explanation for the paradoxical nucleation of actin filaments that have exclusively parallel subunits by a dimer containing antiparallel subunits.

Lengthening the Second Stalk of F1F0 ATP Synthase in Escherichia coli

In Escherichia coliF1F0 ATP synthase, the two bsubunits dimerize forming the peripheral second stalk linking the membrane F0 sector to F1. Previously, we have demonstrated that the enzyme could accommodate relatively large deletions in the b subunits while retaining function (Sorgen, P. L., Caviston, T. L., Perry, R. C., and Cain, B. D. (1998) J. Biol. Chem. 273, 27873–27878). The manipulations of b subunit length have been extended by construction of insertion mutations into the uncF(b) gene adding amino acids to the second stalk. Mutants with insertions of seven amino acids were essentially identical to wild type strains, and mutants with insertions of up to 14 amino acids retained biologically significant levels of activity. Membranes prepared from these strains had readily detectable levels of F1F0-ATPase activity and proton pumping activity. However, the larger insertions resulted in decreasing levels of activity, and immunoblot analysis indicated that these reductions in activity correlated with reduced levels of b subunit in the membranes. Addition of 18 amino acids was sufficient to result in the loss of F1F0 ATP synthase function. Assuming the predicted α-helical structure for this area of the bsubunit, the 14-amino acid insertion would result in the addition of enough material to lengthen the b subunit by as much as 20 Å. The results of both insertion and deletion experiments support a model in which the second stalk is a flexible feature of the enzyme rather than a rigid rod-like structure.

Tropomodulin 3 binds to actin monomers.

Regulation of the actin cytoskeleton by filament capping proteins is critical to myriad dynamic cellular functions. The ability of these proteins to bind both filaments as well as monomers is often central to their cellular functions. The ubiquitous pointed end capping protein Tmod3 (tropomodulin 3) acts as a negative regulator of cell migration, yet mechanisms behind its cellular functions are not understood. Analysis of Tmod3 effects on kinetics of actin polymerization and steady state monomer levels revealed that Tmod3, unlike previously characterized tropomodulins, sequesters actin monomers with an affinity similar to its affinity for capping pointed ends. Furthermore, Tmod3 is found bound to actin in high speed supernatant cytosolic extracts, suggesting that Tmod3 can bind to monomers in the context of other cytosolic monomer binding proteins. The Tmod3-actin complex can be efficiently cross-linked with 1-ethyl-3-(dimethylaminopropyl)carbodiimide/N-hydroxylsulfosuccinimide in a 1:1 complex. Subsequent tryptic digestion and liquid chromatography/tandem mass spectrometry revealed two binding interfaces on actin, one distinct from other actin monomer binding proteins, and two potential binding sites in Tmod3, which are independent of the previously characterized leucine-rich repeat structure involved in pointed end capping. These data suggest that the Tmod3 isoform may regulate actin dynamics differently in cells than the previously described tropomodulin isoforms.

How depolymerization can promote polymerization: the case of actin and profilin

Rapid polymerization and depolymerization of actin filaments in response to extracellular stimuli is required for normal cell motility and development. Profilin is one of the most important actin‐binding proteins; it regulates actin polymerization and interacts with many cytoskeletal proteins that link actin to extracellular membrane. The molecular mechanism of profilin has been extensively considered and debated in the literature for over two decades. Here we discuss several accepted hypotheses regarding the mechanism of profilin function as well as new recently emerged possibilities. Thermal noise is routine in molecular world and unsurprisingly, nature has found a way to utilize it. An increasing amount of theoretical and experimental research suggests that fluctuation‐based processes play important roles in many cell events. Here we show how a fluctuation‐based process of exchange diffusion is involved in the regulation of actin polymerization.

Misakinolide A Is a Marine Macrolide That Caps but Does Not Sever Filamentous Actin

We have investigated the biochemical properties of the marine natural product, misakinolide A, a 40-membered dimeric lactone macrolide that differs from swinholide A only in the size of the macrolide ring. Analytical ultracentrifugation and steady-state fluorescence experiments show that misakinolide A binds simultaneously to two actin subunits with virtually the same affinity as swinholide A, suggesting that the modification in the ring size does not change the actin-binding site. Sedimentation equilibrium experiments suggest that binding is independent at each binding site, with a Kd of approximately 50 nM. Remarkably, misakinolide A does not sever actin filaments like swinholide A; rather, it caps the barbed end of F-actin. When capped by misakinolide A, the elongation rate constant at the barbed end is reduced to zero; pointed end growth was affected only to the extent that the compound sequesters unpolymerized actin. Misakinolide A has essentially no effect on the off-rate of actin subunits leaving the barbed end. Energy-minimized models of misakinolide A and swinholide A are consistent with conservation of identical binding sites in both molecules, but a difference in orientation of one binding site relative to the other may explain why swinholide A has severing activity whereas misakinolide A only has capping activity.

Phosphorylation-dependent conformational changes induce a switch in the actin-binding function of MARCKS.

Phosphorylation of myristoylated alanine-rich protein kinase C substrate (MARCKS) by protein kinase C eliminates actin filament cross-linking activity, but residual filament binding activity docks phosphorylated MARCKS on filamentous actin. The postulated actin-binding region of MARCKS, which includes a Ca2+-calmodulin-binding site, has been portrayed with α-helical structure, analogous to other calmodulin-binding domains. Previous speculation suggested that MARCKS may dimerize to form the two functional actin-binding sites requisite for cross-linking activity. Contrary to these hypotheses, we show that MARCKS peptide with actin-cross-linking activity has an extended structure in aqueous solution but assumes a more compact structure upon phosphorylation. We hypothesize that structural changes in the MARCKS peptide induced by phosphorylation create a dynamic structure that, on average, has only one actin-binding site. Moreover, independent of the state of phosphorylation, this peptide is monomeric rather than dimeric, implying that two distinct actin-binding sites are responsible for the actin-cross-linking activity of unphosphorylated MARCKS. These studies uniquely elucidate the mechanism by which phosphorylation of MARCKS induces structural changes and suggest how these structural changes determine biological activity.