Periplanetasin-4, a novel antimicrobial peptide from the cockroach, inhibits communications between mitochondria and vacuoles
In this study, we found a couple of cell death features, membrane damage, and apoptosis using antimicrobial peptide from American Cockroach. Periplanetasin-4 (LRHKVYGYCVLGP-NH2) is a 13-mer peptide derived from Periplaneta americana and exhibits phosphatidylserine exposure and caspase activation without DNA fragmentation. Apoptotic features without DNA damage provide evidence that this peptide did not interact with DNA directly and exhibited dysfunction of mitochondria and vacuoles. Superoxide radicals were generated from mitochondria and converted to hydrogen peroxide. Despite the enhancement of catalase and total glutath...
Source: Biochemical Journal - April 25, 2019 Category: Biochemistry Authors: Lee, H., Hwang, J. S., Lee, D. G. Tags: Research Articles Source Type: research
Regulation of differential proton-coupled folate transporter gene expression in human tumors: transactivation by KLF15 with NRF-1 and the role of Sp1
Tumors can be therapeutically targeted with novel antifolates (e.g. AGF94) that are selectively transported by the human proton-coupled folate transporter (hPCFT). Studies were performed to determine the transcription regulation of hPCFT in tumors and identify possible mechanisms that contribute to the highly disparate levels of hPCFT in HepG2 versus HT1080 tumor cells. Transfection of hPCFT-null HT1080 cells with hPCFT restored transport and sensitivity to AGF94. Progressive deletions of the hPCFT promoter construct (–2005 to +96) and reporter gene assays in HepG2 and HT1080 cells confirmed differences in hPCFT tran...
Source: Biochemical Journal - April 25, 2019 Category: Biochemistry Authors: Hou, Z., O'Connor, C., Frühauf, J., Orr, S., Kim, S., Gangjee, A., Matherly, L. H. Tags: Research Articles Source Type: research
The chemical diversity of RNA modifications
Nucleic acid modifications in DNA and RNA ubiquitously exist among all the three kingdoms of life. This trait significantly broadens the genome diversity and works as an important means of gene transcription regulation. Although mammalian systems have limited types of DNA modifications, over 150 different RNA modification types have been identified, with a wide variety of chemical diversities. Most modifications occur on transfer RNA and ribosomal RNA, however many of the modifications also occur on other types of RNA species including mammalian mRNA and small nuclear RNA, where they are essential for many biological roles...
Source: Biochemical Journal - April 25, 2019 Category: Biochemistry Authors: Ontiveros, R. J., Stoute, J., Liu, K. F. Tags: Review Articles Source Type: research
Correction: Phosphorylation of CK1{delta}: identification of Ser370 as the major phosphorylation site targeted by PKA in vitro and in vivo
(Source: Biochemical Journal)
Source: Biochemical Journal - April 17, 2019 Category: Biochemistry Authors: Giamas, G., Hirner, H., Shoshiashvili, L., Grothey, A., Gessert, S., Kühl, M., Henne-Bruns, D., Vorgias, C. E., Knippschild, U. Tags: Correction Source Type: research
Diacylglycerol kinase control of protein kinase C
The diacylglycerol kinases (DGK) are lipid kinases that transform diacylglycerol (DAG) into phosphatidic acid (PA) in a reaction that terminates DAG-based signals. DGK provide negative regulation to conventional and novel protein kinase C (PKC) enzymes, limiting local DAG availability in a tissue- and subcellular-restricted manner. Defects in the expression/activity of certain DGK isoforms contribute substantially to cognitive impairment and mental disorders. Abnormal DGK overexpression in tumors facilitates invasion and resistance to chemotherapy preventing tumor immune destruction by tumor-infiltrating lymphocytes. Effec...
Source: Biochemical Journal - April 17, 2019 Category: Biochemistry Authors: Merida, I., Arranz-Nicolas, J., Rodriguez-Rodriguez, C., Avila-Flores, A. Tags: Review Articles Source Type: research
Plant glutathione biosynthesis revisited: redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization
Plant -glutamylcysteine ligase (GCL), catalyzing the first and tightly regulated step of glutathione (GSH) biosynthesis, is redox-activated via formation of an intramolecular disulfide bond. In vitro, redox-activation of recombinant GCL protein causes formation of homo-dimers. Here, we have investigated whether dimerization occurs in vivo and if so whether it contributes to redox-activation. FPLC analysis indicated that recombinant redox-activated WT (wild type) AtGCL dissociates into monomers at concentrations below 10–6 M, i.e. below the endogenous AtGCL concentration in plastids, which was estimated to be in ...
Source: Biochemical Journal - April 14, 2019 Category: Biochemistry Authors: Yang, Y., Lenherr, E. D., Gromes, R., Wang, S., Wirtz, M., Hell, R., Peskan-Berghöfer, T., Scheffzek, K., Rausch, T. Tags: Research Articles Source Type: research
Molecular dynamics of C99-bound {gamma}-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for A{beta} production
We report here an essentially complete atomic model of C99 within wild-type -secretase that respects all the experimental constraints and additionally describes loop, helix, and C99 substrate dynamics in a realistic all-atom membrane. Our model represents the matured auto-cleaved state required for catalysis. From two independent 500-ns molecular dynamic simulations, we identify two conformation states of C99 in equilibrium, a compact and a loose state. Our simulations provide a basis for C99 processing and Aβ formation and explain the production of longer and shorter Aβ, as the compact state retains C99 for long...
Source: Biochemical Journal - April 14, 2019 Category: Biochemistry Authors: Dehury, B., Tang, N., Kepp, K. P. Tags: Research Articles Source Type: research
Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants
Photosynthesis is a highly regulated process in photoautotrophic cells. The main goal of the regulation is to keep the basic photosynthetic reactions, i.e. capturing light energy, conversion into chemical energy and production of carbohydrates, in balance. The rationale behind the evolution of strong regulation mechanisms is to keep photosynthesis functional under all conditions encountered by sessile plants during their lifetimes. The regulatory mechanisms may, however, also impair photosynthetic efficiency by overriding the photosynthetic reactions in controlled environments like crop fields or bioreactors, where light e...
Source: Biochemical Journal - April 14, 2019 Category: Biochemistry Authors: Nikkanen, L., Rintamäki, E. Tags: Review Articles Source Type: research
Stem cell models as an in vitro model for predictive toxicology
Adverse drug reactions (ADRs) are the unintended side effects of drugs. They are categorised as either predictable or unpredictable drug-induced injury and may be exhibited after a single or prolonged exposure to one or multiple compounds. Historically, toxicology studies rely heavily on animal models to understand and characterise the toxicity of novel compounds. However, animal models are imperfect proxies for human toxicity and there have been several high-profile cases of failure of animal models to predict human toxicity e.g. fialuridine, TGN1412 which highlight the need for improved predictive models of human toxicit...
Source: Biochemical Journal - April 14, 2019 Category: Biochemistry Authors: Lynch, S., Pridgeon, C. S., Duckworth, C. A., Sharma, P., Park, B. K., Goldring, C. E. P. Tags: Review Articles Source Type: research
Calcium-calmodulin gating of a pH-insensitive isoform of connexin43 gap junctions
Intracellular protons and calcium ions are two major chemical factors that regulate connexin43 (Cx43) gap junction communication and the synergism or antagonism between pH and Ca2+ has been questioned for decades. To assess the ability of Ca2+ ions to modulate Cx43 junctional conductance (gj) in the absence of pH-sensitivity, patch clamp experiments were performed on Neuroblastoma-2a (N2a) cells or neonatal mouse ventricular myocytes (NMVMs) expressing either full-length Cx43 or the Cx43-M257 (Cx43K258stop) mutant protein, a carboxyl-terminus (CT) truncated version of Cx43 lacking pH-sensitivity. The addition of 1 &mu...
Source: Biochemical Journal - April 9, 2019 Category: Biochemistry Authors: Wei, S., Cassara, C., Lin, X., Veenstra, R. D. Tags: Research Articles Source Type: research
Preferential adsorption to air-water interfaces: a novel cryoprotective mechanism for LEA proteins
Late embryogenesis abundant (LEA) proteins comprise a diverse family whose members play a key role in abiotic stress tolerance. As intrinsically disordered proteins, LEA proteins are highly hydrophilic and inherently stress tolerant. They have been shown to stabilise multiple client proteins under a variety of stresses, but current hypotheses do not fully explain how such broad range stabilisation is achieved. Here, using neutron reflection and surface tension experiments, we examine in detail the mechanism by which model LEA proteins, AavLEA1 and ERD10, protect the enzyme citrate synthase (CS) from aggregation during free...
Source: Biochemical Journal - April 9, 2019 Category: Biochemistry Authors: Yuen, F., Watson, M., Barker, R., Grillo, I., Heenan, R. K., Tunnacliffe, A., Routh, A. F. Tags: Research Articles Source Type: research
Investigating the active site of human trimethyllysine hydroxylase
The biologically important carnitine biosynthesis pathway in humans proceeds via four enzymatic steps. The first step in carnitine biosynthesis is catalyzed by trimethyllysine hydroxylase (TMLH), a non-heme Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenase, which catalyzes the stereospecific hydroxylation of (2S)-N-trimethyllysine to (2S,3S)-3-hydroxy-N-trimethyllysine. Here, we report biocatalytic studies on human TMLH and its 19 variants introduced through site-directed mutagenesis. Amino acid substitutions at the sites involved in binding of the Fe(II) cofactor, 2OG cosubstrate and (2S)-N-trimethyllysine substrate pro...
Source: Biochemical Journal - April 9, 2019 Category: Biochemistry Authors: Wang, Y., Reddy, Y. V., Al Temimi, A. H. K., Venselaar, H., Nelissen, F. H. T., Lenstra, D. C., Mecinovic, J. Tags: Research Articles Source Type: research
Plant nitrilase: a new job for an old enzyme
Nitrilases are versatile enzymes that hydrolyze nitriles to carboxylic acids and ammonia, but many members of this family lack defined biological functions. In plants, nitrilases have been associated with detoxification of cyanide-containing compounds and auxin biosynthesis; however, recent work suggests that the chemical versatility of these proteins contributes to metabolite repair. In this issue of the Biochemical Journal, Niehaus et al. demonstrate that the Nit1 nitrilase from Arabidopsis thaliana functions as a metabolite repair enzyme that removes deaminated glutathione from the cytoplasm and plastids. (Source: Biochemical Journal)
Source: Biochemical Journal - April 9, 2019 Category: Biochemistry Authors: Jez, J. M. Tags: Commentaries Source Type: research
lncRedibly versatile: biochemical and biological functions of long noncoding RNAs
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein–protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide in...
Source: Biochemical Journal - April 9, 2019 Category: Biochemistry Authors: Shields, E. J., Petracovici, A. F., Bonasio, R. Tags: Review Articles Source Type: research
Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on the Saccharomyces cerevisiae proteome and metabolism under glucose-rich conditions. We show for the first time that RNAP III is tightly coupled to the glycolytic system at the molecular systems level. Decreased RNAP III activity or the absence of the RNAP III negative regulator, ...
Source: Biochemical Journal - April 3, 2019 Category: Biochemistry Authors: Szatkowska, R., Garcia-Albornoz, M., Roszkowska, K., Holman, S. W., Furmanek, E., Hubbard, S. J., Beynon, R. J., Adamczyk, M. Tags: Research Articles Source Type: research
