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amino acid starvation

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https://www.readbyqxmd.com/read/29348240/snf1-related-kinase1-controlled-c-s1-bzip-signaling-activates-alternative-mitochondrial-metabolic-pathways-to-ensure-plant-survival-in-extended-darkness
#1
Lorenzo Pedrotti, Christoph Weiste, Thomas Nägele, Elmar Wolf, Francesca Lorenzin, Katrin Dietrich, Andrea Mair, Wolfram Weckwerth, Markus Teige, Elena Baena-González, Wolfgang Dröge-Laser
Sustaining energy homeostasis is of pivotal importance for all living organisms. In Arabidopsis thaliana, evolutionarily conserved SnRK1 kinases (Snf1-RELATED KINASE1) control metabolic adaptation during low energy stress. To unravel starvation-induced transcriptional mechanisms, we performed transcriptome studies of inducible knock-down lines and found that S1-basic leucine Zipper transcription factors (S1-bZIPs) control a defined subset of genes downstream of SnRK1. For example, S1-bZIPs coordinate the expression of genes involved in branched-chain amino acid catabolism, which constitutes an alternative mitochondrial respiratory pathway that is crucial for plant survival during starvation...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29346516/deletion-of-nrip1-extends-female-mice-longevity-increases-autophagy-and-delays-cell-senescence
#2
Jinyu Wang, Xundi Chen, Jared Osland, D Skyler Gerber, Chao Luan, Kristin Delfino, Leslie Goodwin, Rong Yuan
Using age of female sexual maturation as a biomarker, we previously identified nuclear receptor interacting protein 1 (Nrip1) as a candidate gene that may regulate aging and longevity. In the current report, we found that the deletion of Nrip1 can significantly extend longevity of female mice (log rank test, P=0.0004). We also found that Nrip1 expression is altered differently in various tissues during aging and under diet restriction. Remarkably, Nrip1 expression is elevated with aging in visceral white adipose tissue (WAT), but significantly reduced after four months of diet restriction...
January 13, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29343716/expression-of-the-methionine-sulfoxide-reductase-lost-during-evolution-extends-drosophila-lifespan-in-a-methionine-dependent-manner
#3
Byung Cheon Lee, Hae Min Lee, Sorah Kim, Andrei S Avanesov, Aro Lee, Bok-Hwan Chun, Gerd Vorbruggen, Vadim N Gladyshev
Accumulation of oxidized amino acids, including methionine, has been implicated in aging. The ability to reduce one of the products of methionine oxidation, free methionine-R-sulfoxide (Met-R-SO), is widespread in microorganisms, but during evolution this function, conferred by the enzyme fRMsr, was lost in metazoa. We examined whether restoration of the fRMsr function in an animal can alleviate the consequences of methionine oxidation. Ectopic expression of yeast fRMsr supported the ability of Drosophila to catalyze free Met-R-SO reduction without affecting fecundity, food consumption, and response to starvation...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29326162/structural-basis-for-p-ppgpp-synthesis-by-the-staphylococcus-aureus-small-alarmone-synthetase-relp
#4
Melek Cemre Manav, Jelena Beljantseva, Martin Saxtorph Bojer, Tanel Tenson, Hanne Ingmer, Vasili Hauryliuk, Ditlev Egeskov Brodersen
The stringent response is a global reprogramming of bacterial physiology that renders cells more tolerant to antibiotics and induces virulence gene expression in pathogens in response to stress. This process is driven by accumulation of the intracellular alarmone guanosine-5'-di(tri)phosphate-3'-diphosphate ([p]ppGpp), which is produced by enzymes of the RelA SpoT homologue (RSH) family. The Gram-positive Firmicute pathogen, Staphylococcus aureus, encodes three RSH enzymes: a multi-domain RSH (Rel) that senses amino acid starvation on the ribosome and two small alarmone synthetase (SAS) enzymes, RelQ (SAS1) and RelP (SAS2)...
January 11, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29317496/a-functional-link-between-nad-homeostasis-and-n-terminal-protein-acetylation-in-saccharomyces-cerevisiae
#5
Trevor Croft, Christol James Theoga Raj, Michelle Salemi, Brett S Phinney, Su-Ju Lin
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite participating in cellular redox chemistry and signaling, and the complex regulation of NAD+ metabolism is not yet fully understood. To investigate this, we established a NAD+-intermediate specific reporter system to identify factors required for salvage of metabolically-linked nicotinamide (NAM) and nicotinic acid (NA). Mutants lacking components of the NatB complex, NAT3 and MDM20, appeared as hits in this screen. NatB is an Nα-terminal-acetyltransferase responsible for acetylation of the amino terminus of specific Met-retained peptides...
January 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29313410/ulk1-phosphorylates-ser30-of-becn1-in-association-with-atg14-to-stimulate-autophagy-induction
#6
Ji-Man Park, Minchul Seo, Chang Hwa Jung, Douglas Grunwald, Matthew Stone, Neil Michael Otto, Erik Toso, Yeseul Ahn, Michael Kyba, Timothy J Griffin, LeeAnn Higgins, Do-Hyung Kim
ULK1 (unc51-like autophagy activating kinase 1) is a serine/threonine kinase that plays a key role in regulating macroautophagy/autophagy induction in response to amino acid starvation. Despite the recent progress in understanding ULK1 functions, the molecular mechanism by which ULK1 regulates the induction of autophagy remains elusive. In this study, we determined that ULK1 phosphorylates Ser30 of BECN1 (beclin 1) in association with ATG14 (autophagy related 14) but not with UVRAG (UV radiation resistance associated)...
January 9, 2018: Autophagy
https://www.readbyqxmd.com/read/29311600/depdc5-deficiency-contributes-to-resistance-to-leucine-starvation-via-p62-accumulation-in-hepatocellular-carcinoma
#7
Yuki Mizuno, Shu Shimada, Yoshimitsu Akiyama, Shuichi Watanabe, Tomomi Aida, Kosuke Ogawa, Hiroaki Ono, Yusuke Mitsunori, Daisuke Ban, Atsushi Kudo, Shigeki Arii, Shoji Yamaoka, Minoru Tanabe, Shinji Tanaka
Decrease in blood concentration of branched-chain amino acids, especially leucine, is known to promote liver carcinogenesis in patients with chronic liver disease, but the mechanism is unclear. We herein established hepatocellular carcinoma (HCC) cells knocked out for DEPDC5 by using the CRISPR/Cas9 system, and elucidated that cell viability of the DEPDC5 knockout (DEPDC5-KO) cells was higher than that of the DEPDC5 wild-type (DEPDC5-WT) under leucine starvation. Considering that autophagy deficiency might be involved in acquired resistance to leucine deprivation, we observed reduction of LC3-II followed by accumulation of p62 in the DEPDC5-KO, which induced reactive oxygen species (ROS) tolerance...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29261652/proteolytic-systems-expression-during-myogenesis-and-transcriptional-regulation-by-amino-acids-in-gilthead-sea-bream-cultured-muscle-cells
#8
Emilio J Vélez, Sheida Azizi, Dorothy Verheyden, Cristina Salmerón, Esmail Lutfi, Albert Sánchez-Moya, Isabel Navarro, Joaquim Gutiérrez, Encarnación Capilla
Proteolytic systems exert an important role in vertebrate muscle controlling protein turnover, recycling of amino acids (AA) or its use for energy production, as well as other functions like myogenesis. In fish, proteolytic systems are crucial for the relatively high muscle somatic index they possess, and because protein is the most important dietary component. Thus in this study, the molecular profile of proteolytic markers (calpains, cathepsins and ubiquitin-proteasome system (UbP) members) were analyzed during gilthead sea bream (Sparus aurata) myogenesis in vitro and under different AA treatments...
2017: PloS One
https://www.readbyqxmd.com/read/29247800/de-novo-rna-seq-based-transcriptome-analysis-of-papiliotrema-laurentii-strain-ry1-under-nitrogen-starvation
#9
Soumyadev Sarkar, Somnath Chakravorty, Avishek Mukherjee, Debanjana Bhattacharya, Semantee Bhattacharya, Ratan Gachhui
Nitrogen is a key nutrient for all cell forms. Most organisms respond to nitrogen scarcity by slowing down their growth rate. On the contrary, our previous studies have shown that Papiliotrema laurentii strain RY1 has a robust growth under nitrogen starvation. To understand the global regulation that leads to such an extraordinary response, we undertook a de novo approach for transcriptome analysis of the yeast. Close to 33 million sequence reads of high quality for nitrogen limited and enriched condition were generated using Illumina NextSeq500...
December 13, 2017: Gene
https://www.readbyqxmd.com/read/29240272/amino-acid-deprivation-and-central-carbon-metabolism-regulate-the-production-of-outer-membrane-vesicles-and-tubes-by-francisella
#10
Vinaya Sampath, William D McCaig, David G Thanassi
Francisella tularensis is a highly virulent Gram-negative bacterial pathogen that causes the zoonotic disease tularemia. F. novicida, a model tularemia strain, produces spherical outer membrane vesicles (OMV), as well as novel tubular vesicles and extensions of the cell surface. These OMV and tubes (OMV/T) are produced in a regulated manner and contain known virulence factors. Mechanisms by which bacterial vesicles are produced and regulated are not well understood. We performed a genetic screen in F. novicida to decipher the molecular basis for regulated OMV/T formation, and identified both hypo- and hyper-vesiculating mutants...
December 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29237832/the-partitivirus-hetpv13-an1-mediates-severe-growth-debilitation-and-major-alterations-in-the-gene-expression-of-a-fungal-forest-pathogen
#11
Eeva J Vainio, Jaana Jurvansuu, Rafiqul Hyder, Muhammad Kashif, Tuula Piri, Tero Tuomivirta, Anna Poimala, Ping Xu, Salla Mäkelä, Dina Nitisa, Jarkko Hantula
The fungal genus Heterobasidion includes some of the most devastating conifer pathogens in the Boreal forest region. In this study we showed that the alphapartitivirus Heterobasidion partitivirus 13 from H. annosum (HetPV13-an1) is the main causal agent of severe phenotypic debilitation in the host fungus. Based on RNA sequencing using isogenic virus-infected and cured fungal strains, HetPV13-an1 affected the transcription of 683 genes, from which 60% were downregulated and 40% upregulated. Alterations observed in carbohydrate and amino acid metabolism suggest that the virus causes a state of starvation, which is compensated for by alternative synthesis routes...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29237556/ubiquitination-regulates-the-proteasomal-degradation-and-nuclear-translocation-of-the-fat-mass-and-obesity-associated-fto-protein
#12
Tianyi Zhu, Xuan Ling Hilary Yong, Xia Di, Jocelyn Widagdo, Victor Anggono
Genetic polymorphisms in the fat mass and obesity-associated (FTO) gene have been strongly associated with obesity in humans. The cellular level of FTO is tightly regulated, with alterations in its expression influencing energy metabolism, food intake and body weight. Although the proteasome system is involved, the cellular mechanism underlying FTO protein turnover remains unknown. Here, we report that FTO undergoes post-translational ubiquitination on Lys-216. Knock-in HeLa cells harboring the ubiquitin-deficient K216R mutation displayed a slower rate of FTO turnover, resulting in an increase in the level of FTO as well as enhanced phosphorylation of the ribosomal S6 kinase...
December 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29234200/nutrition-and-muscle-in-cirrhosis
#13
REVIEW
Anil C Anand
As the cirrhosis progresses, development of complication like ascites, hepatic encephalopathy, variceal bleeding, kidney dysfunction, and hepatocellular carcinoma signify increasing risk of short term mortality. Malnutrition and muscle wasting (sarcopenia) is yet other complications that negatively impact survival, quality of life, and response to stressors, such as infection and surgery in patients with cirrhosis. Conventionally, these are not routinely looked for, because nutritional assessment can be a difficult especially if there is associated fluid retention and/or obesity...
December 2017: Journal of Clinical and Experimental Hepatology
https://www.readbyqxmd.com/read/29233878/host-pathogen-interactions-and-subversion-of-autophagy
#14
REVIEW
David G McEwan
Macroautophagy ('autophagy'), is the process by which cells can form a double-membraned vesicle that encapsulates material to be degraded by the lysosome. This can include complex structures such as damaged mitochondria, peroxisomes, protein aggregates and large swathes of cytoplasm that can not be processed efficiently by other means of degradation. Recycling of amino acids and lipids through autophagy allows the cell to form intracellular pools that aid survival during periods of stress, including growth factor deprivation, amino acid starvation or a depleted oxygen supply...
December 12, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/29198169/stress-response-transcription-factors-msn2-and-msn4-couple-torc2-ypk1-signaling-and-mitochondrial-respiration-to-atg8-gene-expression-and-autophagy
#15
Ariadne Vlahakis, Nerea Lopez Muniozguren, Ted Powers
Macroautophagy/autophagy is a starvation and stress-induced catabolic process critical for cellular homeostasis and adaptation. Several Atg proteins are involved in the formation of the autophagosome and subsequent degradation of cytoplasmic components, a process termed autophagy flux. Additionally, the expression of several Atg proteins, in particular Atg8, is modulated transcriptionally, yet the regulatory mechanisms involved remain poorly understood. Here we demonstrate that the AGC kinase Ypk1, target of the rapamycin-insensitive TORC2 signaling pathway, controls ATG8 expression by repressing the heterodimeric Zinc-finger transcription factors Msn2 and Msn4...
December 4, 2017: Autophagy
https://www.readbyqxmd.com/read/29193752/the-proteomic-response-of-b-%C3%A2-pumilus-cells-to-glucose-starvation
#16
Stefan Handtke, Dirk Albrecht, Andreas Otto, Dörte Becher, Michael Hecker, Birgit Voigt
Since starvation for carbon sources is a common condition for bacteria in nature and can also occur in industrial fermentation processes due to mixing zones, knowledge about the response of cells to carbon starvation is beneficial. The preferred carbon source for bacilli is glucose. We analysed the response of B. pumilus cells to glucose starvation using metabolic labelling and quantitative proteomics. Glucose starvation led to an extensive reprogramming of the protein expression pattern in B. pumilus. The amounts of proteins of the central carbon metabolic pathways (glycolysis and TCC) remained stable in starving cells...
November 30, 2017: Proteomics
https://www.readbyqxmd.com/read/29186773/metabolic-perturbations-in-a-bacillus-subtilis-clpp-mutant-during-glucose-starvation
#17
(no author information available yet)
Proteolysis is essential for all living organisms to maintain the protein homeostasis and to adapt to changing environmental conditions. ClpP is the main protease in Bacillus subtilis, and forms complexes with different Clp ATPases. These complexes play crucial roles during heat stress, but also in sporulation or cell morphology. Especially enzymes of cell wall-, amino acid-, and nucleic acid biosynthesis are known substrates of the protease ClpP during glucose starvation. The aim of this study was to analyze the influence of a clpP mutation on the metabolism in different growth phases and to search for putative new ClpP substrates...
November 24, 2017: Metabolites
https://www.readbyqxmd.com/read/29173006/systematic-analysis-of-atg13-domain-requirements-for-autophagy-induction
#18
Nora Wallot-Hieke, Neha Verma, David Schlütermann, Niklas Berleth, Jana Deitersen, Philip Böhler, Fabian Stuhldreier, Wenxian Wu, Sabine Seggewiß, Christoph Peter, Holger Gohlke, Noboru Mizushima, Björn Stork
Macroautophagy/autophagy is an evolutionarily conserved cellular process whose induction is regulated by the ULK1 protein kinase complex. The subunit ATG13 functions as an adaptor protein by recruiting ULK1, RB1CC1 and ATG101 to a core ULK1 complex. Furthermore, ATG13 directly binds both phospholipids and members of the Atg8 family. The central involvement of ATG13 in complex formation makes it an attractive target for autophagy regulation. Here, we analyzed known interactions of ATG13 with proteins and lipids for their potential modulation of ULK1 complex formation and autophagy induction...
November 26, 2017: Autophagy
https://www.readbyqxmd.com/read/29167675/boron-deficiency-in-trifoliate-orange-induces-changes-in-pectin-composition-and-architecture-of-components-in-root-cell-walls
#19
Xiuwen Wu, Muhammad Riaz, Lei Yan, Chenqing Du, Yalin Liu, Cuncang Jiang
Boron (B) is a micronutrient indispensable for citrus and B deficiency causes a considerable loss of productivity and quality in China. However, studies on pectin composition and architecture of cell wall components in trifoliate orange roots under B deficiency condition are not sufficient. In this study, we investigated the alteration in pectin characteristics and the architecture of cell wall components in trifoliate orange [Poncirus trifoliata (L.) Raf.] roots under B starvation. The results showed that B-deficient roots resulted in a significant enlargement of root tips and an obvious decrease in cell wall B and uronic acid content in Na2CO3-soluble pectin compared with B-adequate roots...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163028/the-neuronal-and-peripheral-expressed-membrane-bound-unc93a-respond-to-nutrient-availability-in-mice
#20
Mikaela M Ceder, Emilia Lekholm, Sofie V Hellsten, Emelie Perland, Robert Fredriksson
Many transporters such as the solute carriers belonging to the Major facilitator superfamily Pfam clan are orphans in that their tissue and cellular localization as well as substrate profile and function are still unknown. Here we have characterized the putative solute carrier UNC93A. We aimed to investigate the expression profile on both protein and mRNA level of UNC93A in mouse since it has not been clarified. UNC93A staining was found in cortex, hippocampus and cerebellum. It was found to be expressed in many neurons, but not all, with staining located in close proximity to the plasma membrane...
2017: Frontiers in Molecular Neuroscience
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