Co-repressor, co-activator and general transcription factor: the many faces of the Sin3 histone deacetylase (HDAC) complex
At face value, the Sin3 histone deacetylase (HDAC) complex appears to be a prototypical co-repressor complex, that is, a multi-protein complex recruited to chromatin by DNA bound repressor proteins to facilitate local histone deacetylation and transcriptional repression. While this is almost certainly part of its role, Sin3 stubbornly refuses to be pigeon-holed in quite this way. Genome-wide mapping studies have found that Sin3 localises predominantly to the promoters of actively transcribed genes. While Sin3 knockout studies in various species result in a combination of both up- and down-regulated genes. Furthermore, gene...
Source: Biochemical Journal - December 14, 2018 Category: Biochemistry Authors: Adams, G. E., Chandru, A., Cowley, S. M. Tags: Review Articles Source Type: research
Piercing the lipid raft: the case of Vibrio cholerae cytolysin
In a recent issue of Biochemical Journal, Kathuria et al. [Biochem. J. (2018) 475, 3039–3055] report that membrane binding of the pore-forming toxin Vibrio cholerae cytolysin (VCC) is facilitated by the presence of cholesterol, and the presence of this sterol within the lipid bilayer is key for the formation of a functional pore. Yet, in the presence of accessory non-lipid components, VCC retains its membrane-binding capability likely through membrane lipid raft structures. In light of their results, the authors provide new insights into the roles of cholesterol and of membrane microstructures in the binding, the oli...
Source: Biochemical Journal - December 14, 2018 Category: Biochemistry Authors: Cyr, N. Tags: Commentaries Source Type: research
On mechanisms of colicin import: the outer membrane quandary
Discussion of channel-forming colicins focuses mainly on colicin E1 for which BtuB is receptor and the OM TolC protein the proposed translocator. The ability of TolC, part of a multidrug efflux pump, for which there is no precedent for an import function, to provide a trans-periplasmic import pathway for colicin E1, is questioned on the basis of an unfavorable hairpin conformation of colicin N-terminal peptides inserted into TolC. (Source: Biochemical Journal)
Source: Biochemical Journal - December 12, 2018 Category: Biochemistry Authors: Cramer, W. A., Sharma, O., Zakharov, S. D. Tags: Review Articles Source Type: research
Rational engineering of a malate dehydrogenase for microbial production of 2,4-dihydroxybutyric acid via homoserine pathway
A synthetic pathway for the production of 2,4-dihydroxybutyric acid from homoserine (HMS), composed of two consecutive enzymatic reaction steps has been recently reported. An important step in this pathway consists in the reduction in 2-keto-4-hydroxybutyrate (OHB) into (l)-dihydroxybutyrate (DHB), by an enzyme with OHB reductase activity. In the present study, we used a rational approach to engineer an OHB reductase by using the cytosolic (l)-malate dehydrogenase from Escherichia coli (Ec-Mdh) as the template enzyme. Structural analysis of (l)-malate dehydrogenase and (l)-lactate dehydrogenase enzymes acting on sterically...
Source: Biochemical Journal - December 12, 2018 Category: Biochemistry Authors: Frazao, C. J. R., Topham, C. M., Malbert, Y., Francois, J. M., Walther, T. Tags: Research Articles Source Type: research
Specificity and mechanism of carbohydrate demethylation by cytochrome P450 monooxygenases
Degradation of carbohydrates by bacteria represents a key step in energy metabolism that can be inhibited by methylated sugars. Removal of methyl groups, which is critical for further processing, poses a biocatalytic challenge because enzymes need to overcome a high energy barrier. Our structural and computational analysis revealed how a member of the cytochrome P450 family evolved to oxidize a carbohydrate ligand. Using structural biology, we ascertained the molecular determinants of substrate specificity and revealed a highly specialized active site complementary to the substrate chemistry. Invariance of the residues inv...
Source: Biochemical Journal - December 12, 2018 Category: Biochemistry Authors: Robb, C. S., Reisky, L., Bornscheuer, U. T., Hehemann, J.-H. Tags: Research Articles Source Type: research
Characterization of TCDD-inducible poly-ADP-ribose polymerase (TIPARP/ARTD14) catalytic activity
Here, we report the biochemical characterization of the mono-ADP-ribosyltransferase 2,3,7,8-tetrachlorodibenzo-p-dioxin poly-ADP-ribose polymerase (TIPARP/ARTD14/PARP7), which is known to repress aryl hydrocarbon receptor (AHR)-dependent transcription. We found that the nuclear localization of TIPARP was dependent on a short N-terminal sequence and its zinc finger domain. Deletion and in vitro ADP-ribosylation studies identified amino acids 400–657 as the minimum catalytically active region, which retained its ability to mono-ADP-ribosylate AHR. However, the ability of TIPARP to ADP-ribosylate and repress AHR in cell...
Source: Biochemical Journal - December 11, 2018 Category: Biochemistry Authors: Gomez, A., Bindesboll, C., Satheesh, S. V., Grimaldi, G., Hutin, D., MacPherson, L., Ahmed, S., Tamblyn, L., Cho, T., Nebb, H. I., Moen, A., Anonsen, J. H., Grant, D. M., Matthews, J. Tags: Research Articles Source Type: research
Identification of active site residues implies a two-step catalytic mechanism for acyl-ACP thioesterase
In plants and bacteria that use a Type II fatty acid synthase, isozymes of acyl-acyl carrier protein (ACP) thioesterase (TE) hydrolyze the thioester bond of acyl-ACPs, terminating the process of fatty acid biosynthesis. These TEs are therefore critical in determining the fatty acid profiles produced by these organisms. Past characterizations of a limited number of plant-sourced acyl-ACP TEs have suggested a thiol-based, papain-like catalytic mechanism, involving a triad of Cys, His, and Asn residues. In the present study, the sequence alignment of 1019 plant and bacterial acyl-ACP TEs revealed that the previously proposed ...
Source: Biochemical Journal - December 10, 2018 Category: Biochemistry Authors: Jing, F., Yandeau-Nelson, M. D., Nikolau, B. J. Tags: Research Articles Source Type: research
DNA-linked inhibitor antibody assay (DIANA) as a new method for screening influenza neuraminidase inhibitors
Influenza neuraminidase is responsible for the escape of new viral particles from the infected cell surface. Several neuraminidase inhibitors are used clinically to treat patients or stockpiled for emergencies. However, the increasing development of viral resistance against approved inhibitors has underscored the need for the development of new antivirals effective against resistant influenza strains. A facile, sensitive, and inexpensive screening method would help achieve this goal. Recently, we described a multiwell plate-based DNA-linked inhibitor antibody assay (DIANA). This highly sensitive method can quantify femtomo...
Source: Biochemical Journal - December 10, 2018 Category: Biochemistry Authors: Kozisek, M., Navratil, V., Rojikova, K., Pokorna, J., Berenguer Albinana, C., Pachl, P., Zemanova, J., Machara, A., Sacha, P., Hudlicky, J., Cisarova, I., Rezacova, P., Konvalinka, J. Tags: Research Articles Source Type: research
GPCR structure and function relationship: identification of a biased apelin receptor mutant
Biased ligands of G protein-coupled receptors (GPCRs) may have improved therapeutic benefits and safety profiles. However, the molecular mechanism of GPCR biased signaling remains largely unknown. Using apelin receptor (APJ) as a model, we systematically investigated the potential effects of amino acid residues around the orthosteric binding site on biased signaling. We discovered that a single residue mutation I109A (I1093.32) in the transmembrane domain 3 (TM3) located in the deep ligand-binding pocket was sufficient to convert a balanced APJ into a G protein signaling biased receptor. APJ I109A mutant receptor retained ...
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Ban, T., Li, X., Ma, X., Yang, H., Song, Y., Sun, Y., Shen, M., Li, N., Zhang, M.-Y., Ma, Y., Zhong, W., Zhang, M., Hu, L. A. Tags: Research Articles Source Type: research
Polyamines stimulate the CHSY1 synthesis through the unfolding of the RNA G-quadruplex at the 5'-untraslated region
Glycosaminoglycans (GAGs), a group of structurally related acidic polysaccharides, are primarily found as glycan moieties of proteoglycans (PGs). Among these, chondroitin sulfate (CS) and dermatan sulfate, side chains of PGs, are widely distributed in animal kingdom and show structural variations, such as sulfation patterns and degree of epimerization, which are responsible for their physiological functions through interactions with growth factors, chemokines and adhesion molecules. However, structural changes in CS, particularly the ratio of 4-O-sulfation to 6-O-sulfation (4S/6S) and CS chain length that occur during the ...
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Yamaguchi, K., Asakura, K., Imamura, M., Kawai, G., Sakamoto, T., Furihata, T., Linhardt, R. J., Igarashi, K., Toida, T., Higashi, K. Tags: Research Articles Source Type: research
Rhodobacter sphaeroides methionine sulfoxide reductase P reduces R- and S-diastereomers of methionine sulfoxide from a broad-spectrum of protein substrates
Methionine (Met) is prone to oxidation and can be converted to Met sulfoxide (MetO), which exists as R- and S-diastereomers. MetO can be reduced back to Met by the ubiquitous methionine sulfoxide reductase (Msr) enzymes. Canonical MsrA and MsrB were shown to be absolutely stereospecific for the reduction of S-diastereomer and R-diastereomer, respectively. Recently, a new enzymatic system, MsrQ/MsrP which is conserved in all gram-negative bacteria, was identified as a key actor for the reduction of oxidized periplasmic proteins. The haem-binding membrane protein MsrQ transmits reducing power from the electron transport chai...
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Tarrago, L., Grosse, S., Siponen, M. I., Lemaire, D., Alonso, B., Miotello, G., Armengaud, J., Arnoux, P., Pignol, D., Sabaty, M. Tags: Research Articles Source Type: research
Solution structure of TbCentrin4 from Trypanosoma brucei and its interactions with Ca2+ and other centrins
Centrin is a conserved calcium-binding protein that plays an important role in diverse cellular biological processes such as ciliogenesis, gene expression, DNA repair and signal transduction. In Trypanosoma brucei, TbCentrin4 is mainly localized in basal bodies and bi-lobe structure, and is involved in the processes coordinating karyokinesis and cytokinesis. In the present study, we solved the solution structure of TbCentrin4 using NMR (nuclear magnetic resonance) spectroscopy. TbCentrin4 contains four EF-hand motifs consisting of eight α-helices. Isothermal titration calorimetry experiment showed that TbCentrin4 has...
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Shan, F., Ye, K., Zhang, J., Liao, S., Zhang, X., Xu, C., Tu, X. Tags: Research Articles Source Type: research
LIMK2-1, a new isoform of human LIMK2, regulates actin cytoskeleton remodeling via a different signaling pathway than that of its two homologs, LIMK2a and LIMK2b
LIMK1 and LIMK2 (LIMKs, LIM kinases) are kinases that play a crucial role in cytoskeleton dynamics by independently regulating both actin filament and microtubule remodeling. LIMK1 and, more recently, LIMK2 have been shown to be involved in cancer development and metastasis, resistance of cancer cells to microtubule-targeted treatments, neurological diseases, and viral infection. LIMKs have thus recently emerged as new therapeutic targets. Databanks describe three isoforms of human LIMK2: LIMK2a, LIMK2b, and LIMK2-1. Evidence suggests that they may not have completely overlapping functions. We biochemically characterized t...
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Vallee, B., Cuberos, H., Doudeau, M., Godin, F., Gosset, D., Vourc'h, P., Andres, C. R., Benedetti, H. Tags: Research Articles Source Type: research
Redox poise and metabolite changes in bread wheat seeds are advanced by priming with hot steam
In conclusion, the priming effect of the hot steam treatment advanced the onset of seed metabolism, including redox shifts associated with germination and seedling growth. (Source: Biochemical Journal)
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Gerna, D., Roach, T., Arc, E., Stöggl, W., Limonta, M., Vaccino, P., Kranner, I. Tags: Research Articles Source Type: research
The split protein phosphatase system
Reversible phosphorylation of proteins is a post-translational modification that regulates all aspect of life through the antagonistic action of kinases and phosphatases. Protein kinases are well characterized, but protein phosphatases have been relatively neglected. Protein phosphatase 1 (PP1) catalyzes the dephosphorylation of a major fraction of phospho-serines and phospho-threonines in cells and thereby controls a broad range of cellular processes. In this review, I will discuss how phosphatases were discovered, how the view that they were unselective emerged and how recent findings have revealed their exquisite select...
Source: Biochemical Journal - December 6, 2018 Category: Biochemistry Authors: Bertolotti, A. Tags: Review Articles Source Type: research
