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amino acid starvation

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https://www.readbyqxmd.com/read/30221708/amino-acid-starvation-promotes-podocyte-autophagy-through-mammalian-target-of-rapamycin-inhibition-and-transcription-factor-eb-activation
#1
Yuanhan Chen, Xingchen Zhao, Jiaxin Li, Li Zhang, Ruizhao Li, Hong Zhang, Ruyi Liao, Shuangxin Liu, Wei Shi, Xinling Liang
Autophagy is important for maintaining normal physiological functions and podocyte cell homeostasis. Amino acid signaling is an important upstream signaling pathway for autophagy regulation. However, the function and the associated mechanism of amino acid signaling in podocyte autophagy is unclear. The present study used normal culture medium and amino acid deprivation medium to culture podocytes in vitro. Multiple methods were utilized to detect autophagic activity including western blot analysis to measure the levels of microtubule‑associated protein 1 light chain 3 (LC3) II and beclin1, reverse transcription‑quantitative polymerase chain reaction was performed to evaluate the levels of LC3 mRNA and transmission electron microscopy was conducted to observe autophagosomes...
September 3, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/30220080/optimization-of-parthenogenetic-activation-of-rabbit-oocytes-and-development-of-rabbit-embryo-by-somatic-cell-nuclear-transfer
#2
Shun Zhang, Xiang Shu, Jinji Yang, Jinyue Shi, Xiaomei Guan, Jianrong Jiang, Yingming Wei, Chan Luo, Deshun Shi, Fenghua Lu
The present study explored a suitable parthenogenetic activation (PA) procedure for rabbit oocytes and investigated the developmental potential of somatic cell nuclear transfer (SCNT) embryos using rabbit fetal fibroblasts (RFFs). The electrical activation had the optimal rate of blastocyst (14.06%) when oocytes were activated by three direct current (DC) pulses (40 V/mm, 20 μs each) followed by 6-dimethylaminopurine (6-DMAP) and cycloheximide (CHX) treatment; the blastocyst rate of ionomycin (ION)+6-DMAP+CHX (12...
September 16, 2018: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/30218327/intracellular-metabolic-changes-of-rhodococcus-sp-lh-during-the-biodegradation-of-diesel-oil
#3
Ze Chen, Zhou Zheng, Feng-Lian Wang, Yuan-Pu Niu, Jin-Lai Miao, Hao Li
In recent years, some marine microbes have been used to degrade diesel oil. However, the exact mechanisms underlying the biodegradation are still poorly understood. In this study, a hypothermophilous marine strain, which can degrade diesel oil in cold seawater was isolated from Antarctic floe-ice and identified and named as Rhodococcus sp. LH. To clarify the biodegradation mechanisms, a gas chromatography-mass spectrometry (GC-MS)-based metabolomics strategy was performed to determine the diesel biodegradation process-associated intracellular biochemical changes in Rhodococcus sp...
September 14, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/30212894/distinctive-structural-basis-for-dna-recognition-by-the-fission-yeast-zn2cys6-transcription-factor-pho7-and-its-role-in-phosphate-homeostasis
#4
Angad Garg, Yehuda Goldgur, Beate Schwer, Stewart Shuman
Pho7, a member of the Zn2Cys6 family of fungal transcription factors, is the key transcriptional activator underlying fission yeast phosphate homeostasis, a physiological response to phosphate starvation in which the pho1, pho84 and tgp1 genes are upregulated. Here, we delineated a minimized 61-amino-acid Pho7 DNA-binding domain (DBD) and determined the 1.7 Å crystal structure of the DBD at its target site in the tgp1 promoter. Two distinctive features of the Pho7 DBD are: it binds DNA as a monomer, unlike most other fungal zinc-cluster factors that bind as homodimers; and it makes extensive interactions with its asymmetric target sequence over a 14-bp footprint that entails hydrogen bonding to 13 individual bases within, and remote from, the CGG triplet typically recognized by other Zn2Cys6 DBDs...
September 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30196486/boric-acid-activation-of-eif2%C3%AE-and-nrf2-is-perk-dependent-a-mechanism-that-explains-how-boron-prevents-dna-damage-and-enhances-antioxidant-status
#5
Kristin E Yamada, Curtis D Eckhert
Boron is abundant in vegetables, nuts, legumes, and fruit and intake is associated with reduced risk of cancer and DNA damage and increased antioxidant status. Blood boric acid (BA) levels are approximately 10 μM BA in men at the mean US boron intake. Treatment of DU-145 human prostate cancer cells with 10 μM BA stimulates phosphorylation of elongation initiation factor 2α (eIF2α) at Ser51 leading to activation of the eIF2α/ATF4 pathway which activates the DNA damage-inducible protein GADD34. In the present study, we used MEF WT and MEF PERK (±) cells to test the hypothesis that BA-activated eIF2α phosphorylation requires protein kinase RNA-like endoplasmic reticulum kinase (PERK) and activates Nrf2 and the antioxidant response element (ARE)...
September 8, 2018: Biological Trace Element Research
https://www.readbyqxmd.com/read/30196429/an-integrated-analysis-of-mrna-and-srna-transcriptional-profiles-in-coffea-arabica-l-roots-insights-on-nitrogen-starvation-responses
#6
Tiago Benedito Dos Santos, João D M Soares, Joni E Lima, Juliana C Silva, Suzana T Ivamoto, Viviane Y Baba, Silvia G H Souza, Alan P R Lorenzetti, Alexandre R Paschoal, Anderson R Meda, Milton Y Nishiyama Júnior, Úrsula C de Oliveira, João B Mokochinski, Romain Guyot, Inácio L M Junqueira-de-Azevedo, Antônio V O Figueira, Paulo Mazzafera, Osvaldo R Júnior, Luiz G E Vieira, Luiz F P Pereira, Douglas S Domingues
Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots...
September 8, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/30190534/utilization-of-rare-codon-rich-markers-for-screening-amino-acid-overproducers
#7
Bo Zheng, Xiaoyan Ma, Ning Wang, Tingting Ding, Liwei Guo, Xiaorong Zhang, Yu Yang, Chun Li, Yi-Xin Huo
The translation of rare codons relies on their corresponding rare tRNAs, which could not be fully charged under amino acid starvation. Theoretically, disrupted or retarded translation caused by the lack of charged rare tRNAs can be partially restored by feeding or intracellular synthesis of the corresponding amino acids. Inspired by this assumption, we develop a screening or selection system for obtaining overproducers of a target amino acid by replacing its common codons with the corresponding synonymous rare alternative in the coding sequence of selected reporter proteins or antibiotic-resistant markers...
September 6, 2018: Nature Communications
https://www.readbyqxmd.com/read/30186274/metabolic-reprogramming-of-clostridioides-difficile-during-the-stationary-phase-with-the-induction-of-toxin-production
#8
Julia D Hofmann, Andreas Otto, Mareike Berges, Rebekka Biedendieck, Annika-Marisa Michel, Dörte Becher, Dieter Jahn, Meina Neumann-Schaal
The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium difficile ) causes nosocomial and community acquired diarrhea often associated with antibiotic therapy. Major virulence factors of the bacterium are the two large clostridial toxins TcdA and TcdB. The production of both toxins was found strongly connected to the metabolism and the nutritional status of the growth environment. Here, we systematically investigated the changes of the gene regulatory, proteomic and metabolic networks of C...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30181248/branching-out-alterations-in-bacterial-physiology-and-virulence-due-to-branched-chain-amino-acid-deprivation
#9
REVIEW
Julienne C Kaiser, David E Heinrichs
The branched-chain amino acids (BCAAs [Ile, Leu, and Val]) represent important nutrients in bacterial physiology, with roles that range from supporting protein synthesis to signaling and fine-tuning the adaptation to amino acid starvation. In some pathogenic bacteria, the adaptation to amino acid starvation includes induction of virulence gene expression: thus, BCAAs support not only proliferation during infection, but also the evasion of host defenses. A body of research has accumulated over the years to describe the multifaceted physiological roles of BCAAs and the mechanisms bacteria use to maintain their intracellular levels...
September 4, 2018: MBio
https://www.readbyqxmd.com/read/30176893/fecal-microbiota-and-bile-acid-interactions-with-systemic-and-adipose-tissue-metabolism-in-diet-induced-weight-loss-of-obese-postmenopausal-women
#10
José O Alemán, Nicholas A Bokulich, Jonathan R Swann, Jeanne M Walker, Joel Correa De Rosa, Thomas Battaglia, Adele Costabile, Alexandros Pechlivanis, Yupu Liang, Jan L Breslow, Martin J Blaser, Peter R Holt
BACKGROUND: Microbiota and bile acids in the gastrointestinal tract profoundly alter systemic metabolic processes. In obese subjects, gradual weight loss ameliorates adipose tissue inflammation and related systemic changes. We assessed how rapid weight loss due to a very low calorie diet (VLCD) affects the fecal microbiome and fecal bile acid composition, and their interactions with the plasma metabolome and subcutaneous adipose tissue inflammation in obesity. METHODS: We performed a prospective cohort study of VLCD-induced weight loss of 10% in ten grades 2-3 obese postmenopausal women in a metabolic unit...
September 3, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/30145926/tfeb-driven-endocytosis-coordinates-mtorc1-signaling-and-autophagy
#11
Israel C Nnah, Biao Wang, Chaitali Saqcena, Gregory F Weber, Edward M Bonder, Dustin Bagley, Rossella De Cegli, Gennaro Napolitano, Diego L Medina, Andrea Ballabio, Radek Dobrowolski
The mechanistic target of rapamycin kinase complex 1 (MTORC1) is a central cellular kinase that integrates major signaling pathways, allowing for regulation of anabolic and catabolic processes including macroautophagy/autophagy and lysosomal biogenesis. Essential to these processes is the regulatory activity of TFEB (transcription factor EB). In a regulatory feedback loop modulating transcriptional levels of RRAG/Rag GTPases, TFEB controls MTORC1 tethering to membranes and induction of anabolic processes upon nutrient replenishment...
September 10, 2018: Autophagy
https://www.readbyqxmd.com/read/30143990/synthesis-versus-degradation-directions-of-amino-acid-metabolism-during-arabidopsis-abiotic-stress-response
#12
Tatjana M Hildebrandt
During abiotic stress low abundant amino acids are not synthesized but they accumulate due to increased protein turnover under conditions inducing carbohydrate starvation (dehydration, salt stress, darkness) and are degraded. Metabolic adaptation is crucial for abiotic stress resistance in plants, and accumulation of specific amino acids as well as secondary metabolites derived from amino acid metabolism has been implicated in increased tolerance to adverse environmental conditions. The role of proline, which is synthesized during Arabidopsis stress response to act as a compatible osmolyte, has been well established...
August 24, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/30135481/fitness-loss-under-amino-acid-starvation-in-artemisinin-resistant-plasmodium-falciparum-isolates-from-cambodia
#13
Duangkamon Bunditvorapoom, Theerarat Kochakarn, Namfon Kotanan, Charin Modchang, Krittikorn Kümpornsin, Duangkamon Loesbanluechai, Thanyaluk Krasae, Liwang Cui, Kesinee Chotivanich, Nicholas J White, Prapon Wilairat, Olivo Miotto, Thanat Chookajorn
Artemisinin is the most rapidly effective drug for Plasmodium falciparum malaria treatment currently in clinical use. Emerging artemisinin-resistant parasites pose a great global health risk. At present, the level of artemisinin resistance is still relatively low with evidence pointing towards a trade-off between artemisinin resistance and fitness loss. Here we show that artemisinin-resistant P. falciparum isolates from Cambodia manifested fitness loss, showing fewer progenies during the intra-erythrocytic developmental cycle...
August 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30135314/the-circulating-metabolome-of-human-starvation
#14
Matthew L Steinhauser, Benjamin A Olenchock, John O'Keefe, Mingyue Lun, Kerry A Pierce, Hang Lee, Lorena Pantano, Anne Klibanski, Gerald I Shulman, Clary B Clish, Pouneh K Fazeli
The human adaptive starvation response allows for survival during long-term caloric deprivation. Whether the physiology of starvation is adaptive or maladaptive is context dependent: activation of pathways by caloric restriction may promote longevity, yet in the context of caloric excess, the same pathways may contribute to obesity. Here, we performed plasma metabolite profiling of longitudinally collected samples during a 10-day, 0-calorie fast in humans. We identify classical milestones in adaptive starvation, including the early consumption of gluconeogenic amino acids and the subsequent surge in plasma nonesterified fatty acids that marks the shift from carbohydrate to lipid metabolism, and demonstrate findings, including (a) the preferential release of unsaturated fatty acids and an associated shift in plasma lipid species with high degrees of unsaturation and (b) evidence that acute, starvation-mediated hypoleptinemia may be a driver of the transition from glucose to lipid metabolism in humans...
August 23, 2018: JCI Insight
https://www.readbyqxmd.com/read/30120602/genome-wide-analysis-of-oligopeptide-transporters-and-detailed-characterization-of-yellow-stripe-transporter-genes-in-hexaploid-wheat
#15
Anil Kumar, Gazaldeep Kaur, Parul Goel, Kaushal Kumar Bhati, Mandeep Kaur, Vishnu Shukla, Ajay Kumar Pandey
Oligopeptide transporters (OPT) are integral cell membrane proteins that play a critical role in the transport of small peptides, secondary amino acids, glutathione conjugates, and mineral uptake. In the present study, 67 putative wheat yellow stripe-like transporter (YSL) proteins belonging to the subfamily of OPT transporters were identified. Phylogeny analysis resulted in the distribution of wheat YSLs into four discrete clades. The highest number of YSLs was present on the A genome and the chromosome 2 of hexaploid wheat...
August 17, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/30111825/early-molecular-events-associated-with-nitrogen-deficiency-in-rice-seedling-roots
#16
Ping-Han Hsieh, Chia-Cheng Kan, Hsin-Yu Wu, Hsiu-Chun Yang, Ming-Hsiun Hsieh
Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (-N, 1 h), focusing on amino acid analysis and identification of -N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of -N treatment, indicating that part of the N-deficient signals could be mediated by glutamine...
August 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30103455/nitrogen-supply-and-leaf-age-affect-the-expression-of-tags1-or-tags2-driven-by-a-constitutive-promoter-in-transgenic-tobacco
#17
Yihao Wei, Aibo Shi, Xiting Jia, Zhiyong Zhang, Xinming Ma, Mingxin Gu, Xiaodan Meng, Xiaochun Wang
Glutamine synthetase (GS) plays a key role in nitrogen metabolism. Here, two types of tobacco transformants, overexpressing Triticum aestivum GS1 (TaGS1) or GS2 (TaGS2), were analysed. Four independent transformed lines, GS1-TR1, GS1-TR2, GS2-TR1 and GS2-TR2, were used for the nitrogen treatment. Under nitrogen-sufficient conditions, the leaves of GS2-TR showed high accumulation of the TaGS2 transcript, while those of GS1-TR showed a low TaGS1 transcript levels. However, compared with nitrogen-sufficient conditions, the TaGS1 transcript level increased in the leaves under nitrogen starvation, but the TaGS2 transcript level decreased...
August 10, 2018: Genes
https://www.readbyqxmd.com/read/30097557/ivy1-is-a-negative-regulator-of-gtr-dependent-torc1-activation
#18
Natalia V Varlakhanova, Bryan A Tornabene, Marijn G J Ford
The highly conserved TORC1 complex controls cell growth in response to nutrients, especially amino acids. The EGO complex activates TORC1 in response to glutamine and leucine. Here, we demonstrate that the I-BAR domain-containing protein Ivy1 colocalizes with Gtr1 and Gtr2, a heterodimer of small GTPases that are part of the EGO complex. Ivy1 is a negative regulator of Gtr-induced TORC1 activation, and is contained within puncta associated with the vacuolar membrane in cells grown in nutrient-rich medium or after brief nitrogen starvation...
September 7, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/30095066/efficient-analysis-of-mammalian-polysomes-in-cells-and-tissues-using-ribo-mega-sec
#19
Harunori Yoshikawa, Mark Larance, Dylan J Harney, Ramasubramanian Sundaramoorthy, Tony Ly, Tom Owen-Hughes, Angus I Lamond
We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC. Using extracts from either cells, or tissues, polysomes can be separated within 15 min from sample injection to fraction collection. Ribo Mega-SEC shows translating ribosomes exist predominantly in polysome complexes in human cell lines and mouse liver tissue. Changes in polysomes are easily quantified between treatments, such as the cellular response to amino acid starvation...
August 10, 2018: ELife
https://www.readbyqxmd.com/read/30092103/extended-darkness-induces-internal-turnover-of-glucosinolates-in-arabidopsis-thaliana-leaves
#20
Saskia Brandt, Sara Fachinger, Takayuki Tohge, Alisdair R Fernie, Hans-Peter Braun, Tatjana M Hildebrandt
Prolonged darkness leads to carbohydrate starvation, and as a consequence plants degrade proteins and lipids to oxidize amino acids and fatty acids as alternative substrates for mitochondrial ATP production. We investigated, whether the internal breakdown of glucosinolates, a major class of sulfur-containing secondary metabolites, might be an additional component of the carbohydrate starvation response in Arabidopsis thaliana (A. thaliana). The glucosinolate content of A. thaliana leaves was strongly reduced after seven days of darkness...
2018: PloS One
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