Growth Rate of Escherichia coli at Elevated Temperatures: Reversible Inhibition of Homoserine Trans-Succinylase

The preceding paper (10) showed that the growth of Escherichia coli is slowed, without killing, at 40 to 45 C, and that in the several strains tested the cause is a decrease in the activity of homoserine trans-succinylase. These temperatures are now shown to inhibit the enzyme directly, in crude extracts and after partial purification. The effect is rapid and is immediately reversible, unlike the progressive and slowly reversible changes of conventional denaturation.     

Epigenetics and migraine; complex mitochondrial interactions contributing to disease susceptibility

Migraine is a common neurological disorder classified by the World Health Organisation (WHO) as one of the top twenty most debilitating diseases in the developed world. Current therapies are only effective for a proportion of sufferers and new therapeutic targets are desperately needed to alleviate this burden. Recently the role of epigenetics in the development of many complex diseases including migraine has become an emerging topic. By understanding the importance of acetylation, methylation and other epigenetic modifications, it then follows that this modification process is a potential target to manipulate epigenetic status with the goal of treating disease. Bisulphite sequencing and methylated DNA immunoprecipitation have been used to demonstrate the presence of methylated cytosines in the human D-loop of mitochondrial DNA (mtDNA), proving that the mitochondrial genome is methylated. For the first time, it has been shown that there is a difference in mtDNA epigenetic status between healthy controls and those with disease, especially for neurodegenerative and age related conditions. Given co-morbidities with migraine and the suggestive link between mitochondrial dysfunction and the lowered threshold for triggering a migraine attack, mitochondrial methylation may be a new avenue to pursue. Creative thinking and new approaches are needed to solve complex problems and a systems biology approach, where multiple layers of information are integrated is becoming more important in complex disease modelling.     

DAP-kinase and autophagy

DAP-kinase (DAPK) is a Ca²⁺-calmodulin regulated kinase with various, diverse cellular activities, including regulation of apoptosis and caspase-independent death programs, cytoskeletal dynamics, and immune functions. Recently, DAPK has also been shown to be a critical regulator of autophagy, a catabolic process whereby the cell consumes cytoplasmic contents and organelles within specialized vesicles, called autophagosomes. Here we present the latest findings demonstrating how DAPK modulates autophagy. DAPK positively contributes to the induction stage of autophagosome nucleation by modulating the Vps34 class III phosphatidyl inositol 3-kinase complex by two independent mechanisms. The first involves a kinase cascade in which DAPK phosphorylates protein kinase D, which then phosphorylates and activates Vps34. In the second mechanism, DAPK directly phosphorylates Beclin 1, a necessary component of the Vps34 complex, thereby releasing it from its inhibitor, Bcl-2. In addition to these established pathways, we will discuss additional connections between DAPK and autophagy and potential mechanisms that still remain to be fully validated. These include myosin-dependent trafficking of Atg9-containing vesicles to the sites of autophagosome formation, membrane fusion events that contribute to expansion of the autophagosome membrane and maturation through the endocytic pathway, and trafficking to the lysosome on microtubules. Finally, we discuss how DAPK's participation in the autophagic process may be related to its function as a tumor suppressor protein, and its role in neurodegenerative diseases.     

A Substrate Trapping Approach Identifies Proteins Regulated by Reversible S-nitrosylation

Protein S-nitrosylation, the nitric oxide-mediated posttranslational modification of cysteine residues, has emerged as an important regulatory mechanism in diverse cellular processes. Yet, knowledge about the S-nitrosoproteome in different cell types and cellular contexts is still limited and many questions remain regarding the precise roles of protein S-nitrosylation and denitrosylation. Here we present a novel strategy to identify reversibly nitrosylated proteins. Our approach is based on nitrosothiol capture and enrichment using a thioredoxin trap mutant, followed by protein identification by mass spectrometry. Employing this approach, we identified more than 400 putative nitroso-proteins in S-nitrosocysteine-treated human monocytes and about 200 nitrosylation substrates in endotoxin and cytokine-stimulated mouse macrophages. The large majority of these represent novel nitrosylation targets and they include many proteins with key functions in cellular homeostasis and signaling. Biochemical and functional experiments in vitro and in cells validated the proteomic results and further suggested a role for thioredoxin in the denitrosylation and activation of inducible nitric oxide synthase and the protein kinase MEK1. Our findings contribute to a better understanding of the macrophage S-nitrosoproteome and the role of thioredoxin-mediated denitrosylation in nitric oxide signaling. The approach described here may prove generally useful for the identification and exploration of nitroso-proteomes under various physiological and pathophysiological conditions.Protein S-nitrosylation, the covalent addition of a nitric oxide (NO)¹ group to a cysteine thiol, constitutes a widespread regulatory mechanism involved in various biological processes, such as control of cell growth, metabolism, differentiation, and apoptosis (1–4). S-nitrosylation is known to modulate the functional properties of a large number of proteins and thereby influence normal cell function and emerging evidence implicates aberrant protein S-nitrosylation in multiple pathological conditions, including cardiovascular disease, neurodegeneration, and cancer (5, 6). Although significant advances have been made in the field of S-nitrosylation, there is still limited knowledge regarding the constituents of the proteome that become nitrosylated (that is, the nitrosoproteome) across different cell types and conditions. Therefore, much remains unknown about the specific roles and functional significance of S-nitrosylation in cellular function and disease. In addition, there is a need to better understand the mechanisms and consequences of denitrosylation, both for individual proteins and on a systems level.Protein denitrosylation is substantially mediated by two cellular denitrosylating systems, namely the glutathione and S-nitrosoglutathione reductase (GSH/GSNOR) and the thioredoxin and thioredoxin reductase (Trx/TrxR) systems, with the latter representing a direct mechanism of protein denitrosylation (7–11). Trx/TrxR-mediated denitrosylation has been specifically linked to several cellular processes, including apoptosis (7), cell adhesion (12), exocytosis (13) and heme protein maturation (14). Despite recent progress in characterizing protein nitrosylation and denitrosylation, the dynamic cellular nitrosoproteome remains relatively unexplored, particularly under physiologically relevant conditions. This may be in part because of methodological challenges inherent to the proteomic analysis of S-nitrosylation and denitrosylation (See Discussion and (15–17)).The disulfide and nitrosothiol (SNO) reductase activities of Trx depend on a highly conserved Cys-Gly-Pro-Cys active site (8, 18). Recent evidence suggests that, similar to reduction of disulfides, SNO reduction occurs in a two-step mechanism (7, 8). First, the more N-terminal cysteine (Cys32 in human Trx1) attacks the sulfur atom on the SNO moiety of the substrate protein, thereby displacing NO (formally, NO⁻) and generating an intermolecular disulfide between Trx and the substrate. The second step entails an intramolecular attack by the second active site cysteine (Cys35, known as the “resolving cysteine”) on the mixed disulfide intermediate, thus releasing the reduced target protein and the oxidized Trx. The normally transient disulfide intermediate formed in the first step is stabilized in a reaction that involves a Trx mutant that lacks the resolving cysteine. This so-called “trap mutant” has been employed in the identification of disulfide targets of Trx in several cell systems (19–22). However, the utility and value of such a trapping approach in the context of nitrosylation proteomics has not been evaluated.In this study we adapted the Trx trapping strategy for global profiling of cellular nitrosylation and denitrosylation processes. Using this approach, we report the identification of hundreds of potential new nitrosylated targets in monoctyes and macrophages, followed by validation using biochemical and functional assays. The findings presented herein greatly expand our knowledge of the monocyte and macrophage nitrosoproteome and suggest multiple roles for nitrosylation and denitrosylation in macrophage activation and function. The approach employed in this study may be applied to exploring nitrosoproteomes in different cells and under various physiological and pathological conditions.     

The Butyrylcholinesterase K Variant Confers Structurally Derived Risks for Alzheimer Pathology?

The K variant of butyrylcholinesterase (BChE-K, 20% incidence) is a long debated risk factor for Alzheimer disease (AD). The A539T substitution in BChE-K is located at the C terminus, which is essential both for BChE tetramerization and for its capacity to attenuate β-amyloid (Aβ) fibril formation. Here, we report that BChE-K is inherently unstable as compared with the “usual” BChE (BChE-U), resulting in reduced hydrolytic activity and predicting prolonged acetylcholine maintenance and protection from AD. A synthetic peptide derived from the C terminus of BChE-K (BSP-K), which displayed impaired intermolecular interactions, was less potent in suppressing Aβ oligomerization than its BSP-U counterpart. Correspondingly, highly purified recombinant human rBChE-U monomers suppressed β-amyloid fibril formation less effectively than dimers, which also protected cultured neuroblastoma cells from Aβ neurotoxicity. Dual activity structurally derived changes due to the A539T substitution can thus account for both neuroprotective characteristics caused by sustained acetylcholine levels and elevated AD risk due to inefficient interference with amyloidogenic processes.Butyrylcholinesterase (BChE),³ the secondary acetylcholine (ACh)-hydrolyzing enzyme, is associated with the neurofibrillary tangles and amyloid plaques characteristic of Alzheimer disease (AD) (1), which suggests that it functions as a potential AD modulator. BChE activity increases in the AD brain (2–4), where it co-localizes with β-amyloid (Aβ) fibrils (5, 6). Aβ is a 39–42-amino-acid amphiphilic peptide, derived from the transmembrane domain and extracellular region of the Aβ precursor protein (7). At high concentrations, Aβ acquires a β-sheet structure, becomes insoluble, and accumulates in neurotoxic oligomers and fibrils (8) to become the main constituent of plaques in the brain of AD patients. Recent hypotheses attribute causal roles in AD to presenilin (9), oxidative stress (10), metals (11), double hit origin (12), or mitochondrial damage (13). The alternative theories state that Aβ represents a bystander or even a protector rather than the causative factor of disease and that Aβ amyloidogenesis is secondary to other pathogenic events (14). Nevertheless, a wealth of evidence demonstrates a pivotal role for Aβ in the pathogenesis of AD, yielding the amyloid cascade hypothesis (15). According to this hypothesis, the pathological accumulation of Aβ in the brain leads to oxidative stress, neuronal destruction, and finally, the clinical syndrome of AD. It is within this context that we have studied the interactions of the Kalow variant (BChE-K) with Aβ.The C terminus of BChE functions as a tetramerization domain (16, 17) and is responsible for its quaternary organization. Four BChE monomers are held together by the aromatic interactions of seven highly conserved aromatic residues, termed the tryptophan amphiphilic tetramerization domain (WAT) (16, 17). The WAT domain interacts with proline-rich attachment domains, either via proline-rich membrane anchor in brain neurons (18) or, in neuromuscular junctions, with cholinesterase-associated collagen Q (19). In the serum, BChE tetramerization is supported by an analogous 17-mer proline-rich peptide derived from lamellipodin (20).Analyzing the quaternary organization of cholinesterases is a complicated task. To date, all biologically relevant crystal structures of cholinesterases have been truncated forms that lack the C terminus of the protein (21), apart from a more recent study of full-length BChE that yielded crystal packing, which did not allow C-terminal interactions among subunits and lacked electron densities in the C terminus region, indicating structural disorder Protein Data Bank (PDB) code 1VZJ (22). Of note, the crystal structure of the homologous C terminus of tetrameric synaptic acetylcholinesterase (AChE-S) could only be determined based on synthetic peptides derived from the sequence of the AChE-S tail and stabilized with a proline-rich attachment domain (23).In addition to the “usual” (BChE-U) form, BChE has nearly 40 genomic variants. The most common is BChE-K, with allelic frequencies of 0.13–0.21. BChE-K includes a single nucleotide polymorphism at position 1699 (single nucleotide polymorphism data base (dbSNP) ID: rs1803274; alleles, A/G). This leads to an alanine-to-threonine substitution at position 539, 36 residues upstream to the C terminus of BChE (24), within the tetramerization domain that we previously found to attenuate amyloid fibril formation (25).Ample evidence supports the importance of alanine-to-threonine substitutions and their relevance to amyloidogenic processes, protein stability, and quaternary organization (supplemental Table ST1). Point mutations at the dimer interface of light chain immunoglobulins decrease their stability so that the A34T polymorphism in this protein leads to systemic amyloidosis (26). An A25T mutant of the tetrameric human protein Transthyretin (TTR), associated with central nervous system amyloidosis, is prone to aggregation and exhibits drastically reduced tertiary and quaternary structural stabilities (27). The thermodynamic stability profile of the A25T TTR mutant shows that both monomers and tetramers of this variant are highly destabilized. In addition, A25T TTR tetramers dissociate very rapidly (about 1200-fold faster than the dissociation of wild-type TTR), reflecting a high degree of kinetic destabilization of their quaternary structure. These factors together probably contribute to the high propensity of A25T TTR to aggregate in vitro.The capacity of serum BChE-K to hydrolyze butyrylthiocholine was reported to be reduced by 30% relative to BChE-U, for yet unclear reasons (24). The reduced hydrolytic activity of BChE-K predicts that BChE-K carriers would potentially sustain improved cholinergic transmission as compared with BChE-U carriers and has been shown to correlate with preserved performance of attention and reduced rates of cognitive decline (28). However, BChE-K carriers are refractory to cholinesterase inhibitor therapy, the current leading treatment of AD (29). This raised the question whether BChE-K functions as an AD risk or protection factor. Genotype studies are controversial, with some showing increased risk of AD for homozygote BChE-K carriers (e.g. Ref. 30), whereas others suggest a protective effect (e.g. Ref. 31). A recent meta-analysis concluded that on average, BChE-K is neither a risk factor nor a protection factor for AD (32). Based on our previous findings of the arrest of Aβ fibril formation by BChE and considering the accumulation of monomeric BChE in the most severe AD cases (33), we used a variety of chemical techniques to study the effect of the A539T substitution on BChE stability and tetramerization on the one hand and on its potency in attenuating Aβ oligomerization and fibril formation on the other.     

Expression of endo-1,4-β-glucanase (cel1) in Arabidopsis thaliana is associated with plant growth, xylem development and cell wall thickening

Arabidopsis thaliana CEL1 protein was detected in young expanding tissues. Immunostaining revealed that CEL1 accumulated mostly in xylem cells. The primary, as well as the secondary xylem showed considerable CEL1 staining. CEL1 was also observed in young epidermal cells, in which the thicker lateral and tangential walls stained more intensely than the inner walls. In newly formed cell walls, the lateral tangential walls were labeled more intensively than the inner walls. Cellulase activity was found to be significantly higher in growing tissue compared to mature parts of the plant. Cel1 expression concurrently with cellulase activity could be restored in detached matured leaves by sucrose treatment after 48 h in the culture medium.     

Carbohydrate binding modules: biochemical properties and novel applications.

Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular "Velcro" for diverse and unusual applications. In this article, we review recent progress in the field of CBMs and provide an up-to-date summary of the latest developments in CBM applications.     

Combinatorial Method for Overexpression of Membrane Proteins in Escherichia coli

Membrane proteins constitute 20–30% of all proteins encoded by the genome of various organisms. Large amounts of purified proteins are required for activity and crystallization attempts. Thus, there is an unmet need for a heterologous membrane protein overexpression system for purification, crystallization, and activity determination. We developed a combinatorial method for overexpressing and purifying membrane proteins using Escherichia coli. This method utilizes short hydrophilic bacterial proteins, YaiN and YbeL, fused to the ends of the membrane proteins to serve as facilitating factors for expression and purification. Fourteen prokaryotic and mammalian membrane proteins were expressed using this system. Moderate to high expression was obtained for most proteins, and detergent solubilization combined with a short purification process produced stable, monodispersed membrane proteins. Five of the mammalian membrane proteins, overexpressed using our system, were reconstituted into liposomes and exhibited transport activity comparable with the native transporters.