• Title/Summary/Keyword: amino acid metabolism

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In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome

  • Shin, Donghyun;Oh, Jae-Don;Won, Kyeong-Hye;Song, Ki-Duk
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.8
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    • pp.1150-1159
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    • 2018
  • Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

An Investigation Into the Relationship Between Metabolic Responses and Energy Regulation in Antibody-Producing Cell

  • Sun, Ya-Ting;Zhao, Liang;Ye, Zhao-Yang;Fan, Li;Liu, Xu-Ping;Tan, Wen-Song
    • Journal of Microbiology and Biotechnology
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    • v.23 no.11
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    • pp.1586-1597
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    • 2013
  • Energy-efficient metabolic responses were often noted in high-productive cultures. To better understand these metabolic responses, an investigation into the relationship between metabolic responses and energy regulation was conducted via a comparative analysis among cultures with different energy source supplies. Both glycolysis and glutaminolysis were studied through the kinetic analyses of major extracellular metabolites concerning the fast and slow cell growth stages, respectively, as well as the time-course profiles of intracellular metabolites. In three cultures showing distinct antibody productivities, the amino acid metabolism and energy state were further examined. Both the transition of lactate from production to consumption and steady intracellular pools of pyruvate and lactate were observed to be correlated with efficient energy regulation. In addition, an efficient utilization of amino acids as the replenishment for the TCA cycle was also found in the cultures with upregulated energy metabolism. It was further revealed that the inefficient energy regulation would cause low cell productivity based on the comparative analysis of cell growth and productivity in cultures having distinct energy regulation.

The Effects of Copper Source and Concentration on Lipid Metabolism in Growing and Finishing Angus Steers

  • Johnson, L.R.;Engle, T.E.
    • Asian-Australasian Journal of Animal Sciences
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    • v.16 no.8
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    • pp.1131-1136
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    • 2003
  • Forty-eight individually fed Angus steers (body weight $220kg{\pm}9.1$) were utilized to investigate the effects of copper (Cu) source and concentration on lipid metabolism and carcass quality. Steers were stratified by body weight and initial liver Cu concentration and randomly assigned to one of five groups. Groups were then randomly assigned to treatments. Treatments consisted of: 1) control (no supplemental Cu); 2) 10 mg Cu/kg DM from $CuSO_4$; 3) 10 mg Cu/kg DM from a Cu amino acid complex (Availa Cu) 4) 20 mg Cu/kg DM from $CuSO_4$; and 5) 20 mg Cu/kg DM from Availa Cu. Steers were fed a corn-alfalfa-based growing diet for 56 d. Steers were then switched to a high concentrate finishing diet for 145 d. On day 74 of the finishing phase subcutaneous adipose tissue biopsies were obtained from three steers/treatment to determine basal and stimulated lipolytic rates in vitro. Steers were then slaughtered after receiving the finishing diet for 145 d. Control steers tended (p<0.12) to have lower ceruloplasmin (Cp) activity than Cu supplemented steers. Steers receiving 20 mg Cu/kg DM from Availa Cu had higher (p<0.03) Cp activity than steers receiving 20 mg Cu/kg DM from $CuSO_4$. Plasma non-esterified fatty acids were similar across treatments. Steers receiving 10 mg Cu/kg DM from Availa Cu had higher (p<0.02) total plasma cholesterol concentrations relative to steers receiving 10 mg Cu/kg DM from $CuSO_4$. Steers receiving 20 mg Cu/kg DM from Availa Cu had lower (p<0.03) plasma triglyceride concentrations than steers supplemented with 20 mg Cu/kg DM from $CuSO_4$. Fatty acid profile of longissimus muscle was similar across treatments. Backfat depth tended (p<0.18) to be lower in Cu supplemented steers relative to controls. Steers supplemented with 20 mg Cu/kg DM from Availa Cu had heavier (p<0.03) hot carcass weights and a greater (p<0.02) dressing percentage than steers supplemented with 20 mg Cu/kg DM from $CuSO_4$. Furthermore, in vitro basal (p<0.06) and epinephrine stimulated (p<0.04) lipolytic rates of subcutaneous adipose tissue were higher in Cu supplemented steers relative to controls. The results of this study suggest that Cu supplementation has minimal effects on blood and lean tissue lipid profile. However, it appears that Cu may play a role in lipid metabolism in subcutaneous adipose tissue.

The Diversity of Lysine-Acetylated Proteins in Escherichia coli

  • Yu, Byung-Jo;Kim, Jung-Ae;Moon, Jeong-Hee;Ryu, Seong-Eon;Pan, Jae-Gu
    • Journal of Microbiology and Biotechnology
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    • v.18 no.9
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    • pp.1529-1536
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    • 2008
  • Acetylation of lysine residues in proteins is a reversible and highly regulated posttranslational modification. However, it has not been systematically studied in prokaryotes. By affinity immunoseparation using an anti-acetyllysine antibody together with nano-HPLC/MS/MS, we identified 125 lysine-acetylated sites in 85 proteins among proteins derived from Escherichia coli. The lysine-acetylated proteins identified are involved in diverse cellular functions including protein synthesis, carbohydrate metabolism, the TCA cycle, nucleotide and amino acid metabolism, chaperones, and transcription. Interestingly, we found a higher level of acetylation during the stationary phase than in the exponential phase; proteins acetylated during the stationary phase were immediately deacetylated when the cells were transferred to fresh LB culture medium. These results demonstrate that lysine acetylation is abundant in E. coli and might be involved in modifying or regulating the activities of various enzymes involved in critical metabolic processes and the synthesis of building blocks in response to environmental changes.

Studies on Effects of Chloroform to the Tissue Lactic Dehydrogenase and Glutamic Dehydrogenase Activities of Rats (클로로포름이 백서장기(白鼠臟器)의 효소활성(酵素活性)에 관(關)한 연구(硏究))

  • Chun, Byung-Sam;Haw, Kum
    • Journal of Nutrition and Health
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    • v.4 no.1
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    • pp.21-28
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    • 1971
  • 1. The effects of chloroform to the tissue lactic dehydrogenase (LDH) activities and its isozymes and to the tissue glutamic dehydrogenase (GDH) activities and its isoaymes are studied using the experimental albino male adult rats in this paper. The tissues studies are liver, kidney, heart, and brain. Besides the control group, two experimental groups are studied providing succeedingly 4 days interpariental administrations of chloroform, 0.0025ml and 0.025ml per day respectively. The changes of body weights, weights of organs, activities of GDH and LDH and their isozymes of each tissues, are analysed. 2. The body weights of rats are decreased due to the chloroform administration. 3. There are no significant differences of weights of organs due to the chloroform administration. 4. The significant decreases of tissue GDH activities and the significant changes in percent distribution of the GDH isozymes are found due to the chloroform administration. This weight be interpretated that chloroform effects to the protein and amino acid metabolism of rats. 5. Due to the chloroform administration, the significant changes in tissue LDH activities and in percent distribution of tissue LDH isozymes indicating the decreases of $LDH_1$ which is the aerobic heart type and the increase of $LDH_5$ which is the anaerobic muscle type, are observed. This could be estimated that chloroform effects to the carbohydrate metabolism, particularly to the anaerobic glycolysis of rats.

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Oncogene-Driven Metabolic Alterations in Cancer

  • Min, Hye-Young;Lee, Ho-Young
    • Biomolecules & Therapeutics
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    • v.26 no.1
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    • pp.45-56
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    • 2018
  • Cancer is the leading cause of human deaths worldwide. Understanding the biology underlying the evolution of cancer is important for reducing the economic and social burden of cancer. In addition to genetic aberrations, recent studies demonstrate metabolic rewiring, such as aerobic glycolysis, glutamine dependency, accumulation of intermediates of glycolysis, and upregulation of lipid and amino acid synthesis, in several types of cancer to support their high demands on nutrients for building blocks and energy production. Moreover, oncogenic mutations are known to be associated with metabolic reprogramming in cancer, and these overall changes collectively influence tumor-microenvironment interactions and cancer progression. Accordingly, several agents targeting metabolic alterations in cancer have been extensively evaluated in preclinical and clinical settings. Additionally, metabolic reprogramming is considered a novel target to control cancers harboring un-targetable oncogenic alterations such as KRAS. Focusing on lung cancer, here, we highlight recent findings regarding metabolic rewiring in cancer, its association with oncogenic alterations, and therapeutic strategies to control deregulated metabolism in cancer.

A Rare Cause of Recurrent Acute Pancreatitis in a Child: Isovaleric Acidemia with Novel Mutation

  • Sag, Elif;Cebi, Alper Han;Kaya, Gulay;Karaguzel, Gulay;Cakir, Murat
    • Pediatric Gastroenterology, Hepatology & Nutrition
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    • v.20 no.1
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    • pp.61-64
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    • 2017
  • Recurrent acute pancreatic attacks is a rare clinical condition (2-5% of all acute pancreatis) in children and is mainly idiopathic in most cases. Sometimes it may be associated with congenital anomalies, metabolic diseases or hereditary conditions. Isovaleric acidemia (IVA) is a rare autosomal recessive amino acid metabolism disorder associated with isovaleryl coenzyme A dehydrogenase deficiency presenting the clinical findings such metabolic acidosis with increased anion gap, hyperammonemia, ketonemia, hypoglycemia, "the odor of sweaty feet," abdominal pain, vomiting, feeding intolerance, shock and coma. Recurrent acute pancreatitis associated with IVA have been rarely reported. Herein; we report a child who admitted with recurrent acute pancreatic attacks and had the final diagnosis of IVA. Mutation analysis revealed a novel homozygous mutation of (p.E117K [c.349G>A]) in the IVA gene. Organic acidemias must kept in mind in the differential diagnosis of recurrent acute pancreatic attacks in children.

Cloning and Nucleotide Sequencing of a Partial Glutamate Decarboxylase Gene from Arabidopsis thaliana cDNA Library (애기장대 cDNA library로부터 Glutamate Decarboxylase 유전자의 부분 클로닝 및 서열분석)

  • 오석흥;최원규;최동성
    • KSBB Journal
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    • v.16 no.1
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    • pp.36-40
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    • 2001
  • In order to study the molecular mechanism of $\gamma$-aminobutyric acid (GABA) production in plants, we cloned and sequenced a partial glutamate decarboxylase (GAD) cDNA from the Arabidopsis thaliana cDNA library, using primers targeted at highly conserved sequences of the petunia GAD gene. The cDNA fragment was inserted into TA cloning vector with T7 promoter and the recombinant plasmid obtained was used to transform E. coli. The plasmid DNA purified from the transformed E. coli was digested with EcoRI and the presence of the insert was confirmed. Nucleotide sequence analysis showed that the fragment is a partial Arabidopsis thaliana GAD gene and that the sequence showed 98% and 78% identity to the region of the putative Arabidopsis thaliana GAD sequences deposited in GenBank, Accession nos: U46665 and U10034, respectively. The amino acid sequence deduced from the partial Arabidopsis thaliana GAD gene showed 99% and 91% identities to the GAD sequences deduced from the genes of the U46665 and U10034, respectively. The partial cDNA sequence determined may facilitate the study of the molecular mechanism of GABA metabolism in plants.

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Amino Acid Biosynthesis and Gene Regulation in Seed (종자내 아미노산 합성 조절 유전자에 관한 연구)

  • ;;;;;Fumio Takaiwa
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Isolation and characterization of BrMDR1 a novel MDR-type ATP-binding cassette (ABC) transporter in Brassica rapa L.

  • Lee, Sun-Yong;Jung, Yu-Jin;Kang, Kwon-Kyoo
    • Korean Journal of Plant Resources
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    • v.22 no.3
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    • pp.273-280
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    • 2009
  • A cDNA clone encoding a MDR-like ABC transporter protein was isolated from Brassica rapa seedlings, through rapid amplification of cDNA ends (RACE). This gene (named as Brmdr 1; GenBank accession no.: DQ296184 ) had a total length of 4222 bp with an open reading frame of 3900 bp, and encoded a predicted polypeptide of 1300 amino acids with a molecular weight of 143.1 kDa. The BrMDR1 protein shared 71.0, 62.5, 60.0 and 58.2% identity with other MDR proteins isolated from Arabidopsis thaliana (AAN28720), Coptis japonica (CjMDR), Gossypium hirsutum (GhMDR) and Triticum aestivum (TaMDR) at amino acid level, respectively. Southern blot analysis showed that Brmdr1 was a low-copy gene. Expression pattern analysis revealed that Brmdr1 constitutively expressed in the root, stem petals and stamens, but with lower expression in leaves and open flowers. The domains analysis showed that BrMDR1 protein possessed two transmembrane domains (TMDs) and two nucleotide binding domains (NBDs) arranging in "TMD1-NBD1-TMD2-NBD2" direction, which is consistent with other MDR transporters. Within NBDs three characteristic motifs common to all ABC transporters, "Walker A", "Walker B" and C motif, were found. These results indicate that BrMDR1 is a MDR-like ABC transporter protein that may be involved in the transport and accumulation of secondary metabolites.