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Essential amino acids

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https://www.readbyqxmd.com/read/28806503/identification-of-the-dimer-exchange-interface-of-the-bacterial-dna-damage-response-protein-umud
#1
David A Murison, Rebecca C Timson, Bilyana Koleva, Michael Ordazzo, Penny J Beuning
The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both non-mutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product, UmuD', together with UmuC, form the Y-family polymerase DNA Pol V (UmuD'2C) capable of performing TLS...
August 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28805808/constraints-and-consequences-of-the-emergence-of-amino-acid-repeats-in-eukaryotic-proteins
#2
Sreenivas Chavali, Pavithra L Chavali, Guilhem Chalancon, Natalia Sanchez de Groot, Rita Gemayel, Natasha S Latysheva, Elizabeth Ing-Simmons, Kevin J Verstrepen, Santhanam Balaji, M Madan Babu
Proteins with amino acid homorepeats have the potential to be detrimental to cells and are often associated with human diseases. Why, then, are homorepeats prevalent in eukaryotic proteomes? In yeast, homorepeats are enriched in proteins that are essential and pleiotropic and that buffer environmental insults. The presence of homorepeats increases the functional versatility of proteins by mediating protein interactions and facilitating spatial organization in a repeat-dependent manner. During evolution, homorepeats are preferentially retained in proteins with stringent proteostasis, which might minimize repeat-associated detrimental effects such as unregulated phase separation and protein aggregation...
August 14, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28805540/novel-approach-for-structural-identification-of-protein-family-glyoxalase-i
#3
Anton M Kargatov, Eugenia A Boshkova, Yuri N Chirgadze
Glyoxalase is one of two enzymes of the glyoxalase detoxification system against methylglyoxal and other aldehydes, the metabolites derived from glycolysis. The glyoxalase system is found almost in all living organisms: bacteria, protozoa, plants and animals, including humans, and is related to the class of "life essential proteins". The enzyme belongs to the expanded Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily. At present the GenBank contains about seven hundreds of amino acid sequences of this enzyme type, and the Protein Data Bank includes dozens of spatial structures...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28804797/bioactivities-of-alternative-protein-sources-and-their-potential-health-benefits
#4
REVIEW
A Pihlanto, P Mattila, S Mäkinen, A-M Pajari
Increasing the utilisation of plant proteins is needed to support the production of protein-rich foods that could replace animal proteins in the human diet so as to reduce the strain that intensive animal husbandry poses to the environment. Lupins, quinoa and hempseed are significant sources of energy, high quality proteins, fibre, vitamins and minerals. In addition, they contain compounds such as polyphenols and bioactive peptides that can increase the nutritional value of these plants. From the nutritional standpoint, the right combination of plant proteins can supply sufficient amounts of essential amino acids for human requirements...
August 14, 2017: Food & Function
https://www.readbyqxmd.com/read/28803959/thymosin-%C3%AE-4-is-involved-in-the-antimicrobial-immune-response-of-golden-pompano-trachinotus-ovatus
#5
Yun Sun, Xiaojuan Chen, Yue Xu, Qiaohong Liu, Xue Jiang, Shifeng Wang, Weiliang Guo, Yongcan Zhou
Thymosin beta belongs to the thymosin family, which consists of a series of highly conserved peptides involved in various biological processes. In teleosts, understanding of the immunological functions of thymosin beta is limited, particularly in vivo, which is essentially unknown. In the current study, we cloned and identified thymosin beta 4 from the teleost fish Golden pompano (Trachinotus ovatus), which we have named TroTβ4. We investigated the expression patterns and functions of TroTβ4 in both in vivo and in vitro assays...
August 10, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28803324/decreased-serum-l-arginine-and-l-citrulline-levels-in-major-depression
#6
S Hess, G Baker, G Gyenes, R Tsuyuki, S Newman, Jean-Michel Le Melledo
RATIONALE: It has been suggested that endothelial dysfunction caused by a decreased endothelial production of nitric oxide (NO) may contribute to the consistently observed increased risk of developing cardiovascular disease (CVD) in physically healthy patients suffering from major depression (MD). NO is a gas synthesized from Larginine (a conditionally essential amino acid) and oxygen by endothelial nitric oxide synthase (eNOS). The end products of NO production include both NO and L-citrulline...
August 13, 2017: Psychopharmacology
https://www.readbyqxmd.com/read/28801717/vitamin-b6-is-essential-for-serine-de-novo-biosynthesis
#7
Rúben J Ramos, Mia L Pras-Raves, Johan Gerrits, Maria van der Ham, Marcel Willemsen, Hubertus Prinsen, Boudewijn Burgering, Judith J Jans, Nanda M Verhoeven-Duif
Pyridoxal 5'-phosphate (PLP), the metabolically active form of vitamin B6, plays an essential role in brain metabolism as a cofactor in numerous enzyme reactions. PLP deficiency in brain, either genetic or acquired, results in severe drug-resistant seizures that respond to vitamin B6 supplementation. The pathogenesis of vitamin B6 deficiency is largely unknown. To shed more light on the metabolic consequences of vitamin B6 deficiency in brain, we performed untargeted metabolomics in vitamin B6-deprived Neuro-2a cells...
August 11, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28801604/recombineering-using-recet-in-corynebacterium-glutamicum-atcc14067-via-a-self-excisable-cassette
#8
Yuanyuan Huang, Lu Li, Shan Xie, Nannan Zhao, Shuangyan Han, Ying Lin, Suiping Zheng
Gene manipulation is essential for metabolic engineering and synthetic biology, but the current general gene manipulation methods are not applicable to the non-model strain Corynebacterium glutamicum (C. glutamicum) ATCC14067, which is used for amino acid production. Here, we report an effective and sequential deletion method for C. glutamicum ATCC14067 using the exonuclease-recombinase pair RecE + RecT (RecET) for recombineering via a designed self-excisable linear double-strand DNA (dsDNA) cassette, which contains the Cre/loxP system, to accomplish markerless deletion...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28799778/how-important-is-tryptophan-in-human-health
#9
Joanna Kałużna-Czaplińska, Paulina Gątarek, Salvatore Chirumbolo, Max Stanley Chartrand, Geir Bjørklund
Tryptophan (Trp) is an amino acid and an essential component of the human diet. It plays a crucial role in many metabolic functions. Clinicians can use Trp levels in the course of diagnosing various metabolic disorders and the symptoms associated with those diseases. Furthermore, supplementation with this amino acid is considered in the treatment of depression and sleep disorders, mainly due to the Trp relationship with the synthesis of serotonin (5-HT) and melatonin. It is also used in helping to resolve cognitive disorders, anxiety, or neurodegenerative diseases...
August 11, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28799718/identification-and-elucidation-of-in-vivo-function-of-two-alanine-racemases-from-pseudomonas-putida-kt2440
#10
Estrella Duque, Abdelali Daddaoua, Baldo F Cordero, Jesús De la Torre, M Antonia Molina-Henares, Juan-Luis Ramos
The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate (PLP) binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine...
August 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28799697/methylmalonate-semialdehyde-dehydrogenase-mediated-metabolite-homeostasis-essentially-regulate-conidiation-polarized-germination-and-pathogenesis-in-magnaporthe-oryzae
#11
Justice Norvienyeku, Zhenhui Zhong, Lili Lin, Xie Dang, Meilian Chen, Xiaolian Lin, Honghong Zhang, Wilfred Mabeche Anjago, Lianyu Lin, Waheed Abdul, Zonghua Wang
Plants generate multitude of aldehydes under abiotic and biotic stress conditions. Ample demonstrations have shown that rice-derived aldehydes enhance the resistance of rice against the rice-blast fungus Magnaporthe oryzae. However, how the fungal pathogen nullifies the inhibitory effects of host aldehydes to establish compatible interaction remains unknown. Here we identified and evaluated the in vivo transcriptional activities of M. oryzae aldehyde dehydrogenase (ALDH) genes. Transcriptional analysis of M...
August 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28798743/l-arginine-uptake-by-cationic-amino-acid-transporter-promotes-intra-macrophage-survival-of-leishmania-donovani-by-enhancing-arginase-mediated-polyamine-synthesis
#12
Abhishek Mandal, Sushmita Das, Ajay Kumar, Saptarshi Roy, Sudha Verma, Ayan Kumar Ghosh, Ruby Singh, Kumar Abhishek, Savita Saini, Abul Hasan Sardar, Bidyut Purkait, Ashish Kumar, Chitra Mandal, Pradeep Das
The survival of intracellular protozoan parasite, Leishmania donovani, the causative agent of Indian visceral leishmaniasis (VL), depends on the activation status of macrophages. l-Arginine, a semi-essential amino acid plays a crucial regulatory role for activation of macrophages. However, the role of l-arginine transport in VL still remains elusive. In this study, we demonstrated that intra-macrophage survival of L. donovani depends on the availability of extracellular l-arginine. Infection of THP-1-derived macrophage/human monocyte-derived macrophage (hMDM) with Leishmania, resulted in upregulation of l-arginine transport...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28797959/c-terminal-residues-of-rice-translin-are-essential-for-octamer-formation-and-nucleic-acid-binding
#13
Alka Gupta, Anuradha Nair, Anand Ballal, Rajani Kant Chittela
Translin is a DNA/RNA binding protein involved in DNA repair and RNA metabolism. Previously, we had shown that rice translin (221 amino acids) exhibits biochemical activities similar to that of the human translin protein. Here we report the role of the C-terminal random coil in rice translin function by analyzing truncation (after 215(th) residue, Tra - 215) and substitution mutant proteins (Ser216Ala, Lys217Ala, Gln218Ala, Glu219Ala). Circular Dichroism (CD) analysis of Tra-215 showed deviations in comparison to Tra-WT...
August 4, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28797955/stability-and-assessment-of-amino-acids-in-parenteral-nutrition-solutions
#14
REVIEW
Nina Unger, Ulrike Holzgrabe
Sterile amino acid solutions are applied in medical care as part of Total Parenteral Nutrition systems. Typical formulations consist of variable admixtures of essential and non-essential amino acids together with carbohydrates, electrolytes, vitamins, trace element solutions and lipid emulsions. The complexity of these formulations gives rise to stability and compatibility reflections. This review focuses on amino acid stability in pure amino acid solution and name methods of assessment. Incompatibilities of amino acids with the other ingredients are matter of concern in clinical practice and evaluated for relevance...
August 2, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28797638/a-novel-tnfaip8-gene-mediates-l-arginine-metabolism-in-apostichopus-japonicus
#15
Yina Shao, Huahui Chen, Miao Lv, Chenghua Li, Weiwei Zhang, Ye Li, Xuelin Zhao, Yongbo Bao
Tumor necrosis factor (TNF)-α-induced protein 8 (TNFAIP8) family is a newly identified protein with vital roles in maintaining immune homeostasis. In the current study, we first cloned and characterized a TNFAIP8 gene from the invertebrate sea cucumber Apostichopus japonicus. The gene was designated as AjTNFAIP8. The full-length cDNA of AjTNFAIP8 was 1455 bp long and encoded a matured protein of 201 amino acid residues. Structural analysis indicated that AjTNFAIP8 had a death effector domain (DED)-like domain and composed of six α-helices...
August 7, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28797105/regulation-of-hepatic-stellate-cell-proliferation-and-activation-by-glutamine-metabolism
#16
Jiang Li, Mohammed Ghazwani, Ke Liu, Yixian Huang, Na Chang, Jie Fan, Fengtian He, Liying Li, Shizhong Bu, Wen Xie, Xiaochao Ma, Song Li
Liver fibrosis is the excessive accumulation of extracellular matrix proteins, which is mainly caused by accumulation of activated hepatic stellate cells (HSCs). The mechanisms of activation and proliferation of HSCs, two key events after liver damage, have been studied for many years. Here we report a novel pathway to control HSCs by regulating glutamine metabolism. We demonstrated that the proliferation of HSCs is critically dependent on glutamine that is used to generate α-ketoglutarate (α-KG) and non-essential amino acid (NEAA)...
2017: PloS One
https://www.readbyqxmd.com/read/28795459/dissecting-the-behaviour-of-%C3%AE-amyloid-peptide-variants-during-oligomerization-and-fibrillation
#17
Jing-Ming Shi, Lin Zhang, En-Qi Liu
The oligomerization and fibrillation of β-amyloid (Aβ) peptides are important events in the pathogenesis of Alzheimer's disease. However, the motifs within the Aβ sequence that contribute to oligomerization and fibrillation and the complex interplay among these short motifs are unclear. In this study, the oligomerization and fibrillation abilities of the Aβ variants Aβ1-28, Aβ1-36, Aβ11-42, Aβ17-42, Aβ1-40 and Aβ1-42 were examined by thioflavin T fluorescence, western blotting and transmission electron microscopy...
August 10, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28794925/expression-of-codon-optimized-tgmic16-in-three-escherichia-coli-strains
#18
Hui Sun, Jin Li, Gong-Zhen Liu, Kun Yin, Yong Cui, Ting Xiao, Chao Xu, Bing-Cheng Huang, Qing-Kuan Wei
In a previous study, we found that rabbit anti-Toxoplasma gondii serum was capable of recognizing truncated T. gondii microneme protein 16 (TgMIC16), indicating that TgMIC16 is an essential antigenic T. gondii protein. However, the broad application of this recombinant protein is limited by its low expression level. In this study, we performed codon optimization of TgMIC16 by changing the codon-adaptation index from 0.22 to 1.0 without altering the amino acid sequence and expressed the optimized gene in three different Escherichia coli strains, followed by comparison of soluble recombinant-protein expression and yield...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28794274/stable-isotope-analyses-of-feather-amino-acids-identify-penguin-migration-strategies-at-ocean-basin-scales
#19
Michael J Polito, Jefferson T Hinke, Tom Hart, Mercedes Santos, Leah A Houghton, Simon R Thorrold
Identifying the at-sea distribution of wide-ranging marine predators is critical to understanding their ecology. Advances in electronic tracking devices and intrinsic biogeochemical markers have greatly improved our ability to track animal movements on ocean-wide scales. Here, we show that, in combination with direct tracking, stable carbon isotope analysis of essential amino acids in tail feathers provides the ability to track the movement patterns of two, wide-ranging penguin species over ocean basin scales...
August 2017: Biology Letters
https://www.readbyqxmd.com/read/28792588/immunosuppressive-enzymes-in-the-tumor-microenvironement
#20
REVIEW
Valérie Molinier-Frenkel, Flavia Castellano
Antigen encounter by T lymphocytes induces important metabolic changes. Anti-tumor T lymphocytes enter in a metabolic competition with tumors, which divert feedback mechanisms of the immune response. Immunosuppressive enzymes, modifying the nutrient availability and leading to the production of toxic catabolites, represent one of these mechanisms, contributing to the metabolic halo in which T lymphocytes evolve during immune responses. Two classes of immunosuppressive enzymes, expressed by the tumor cells or by cells of the microenvironment, have been described: those catabolizing essential or semi-essential amino acids, tryptophan, arginine and phenylalanine and the ectoenzymes, which degrade the ATP to produce adenosine...
August 9, 2017: FEBS Letters
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