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Sanit Piyapattanakorn - One of the best experts on this subject based on the ideXlab platform.
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Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp (Marsupenaeus japonicus) acclimated at different salinities.
The Journal of experimental biology, 2018Co-Authors: Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit PiyapattanakornAbstract:Shrimps inhabiting coastal waters can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp (Marsupenaeus japonicus) at 1.7%, 3.4% and 4.0% salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA sequencing analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after 24 h of acclimation. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. In particular, the increase of the expression level of the gene encoding Glutamate-Ammonia Ligase, which functions in glutamine metabolism, appeared to be associated with the increased glutamine concentration at high salinity. Furthermore, the increased alanine concentration at high salinity was likely associated with the decrease in the expression levels of the the gene encoding alanine-glyoxylate transaminase. Thus, there is a possibility that changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are regulated by changes in the expression levels of genes related to amino acid metabolism.
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Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp (Marsupenaeus japonicus) acclimated at different salinities.
The Journal of Experimental Biology, 2018Co-Authors: Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit PiyapattanakornAbstract:Shrimps inhabiting the coastal water can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after acclimating for 24 h. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. In particular, the increase of the expression level of the gene encoding Glutamate-Ammonia Ligase which functions in the glutamine metabolism appeared to be relevant to the increased glutamine concentration at high salinity. Furthermore, the alanine concentration increased at high salinity was likely to be associated with the decrease in the expression levels of the alanine-glyoxylate transaminase gene. Thus, there is a possibility that changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are regulated by changes in the expression levels of genes related to amino acid metabolism.
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Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp Marsupenaeus japonicus reared at different salinity
2017Co-Authors: Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit PiyapattanakornAbstract:Shrimps inhabiting around the coastal area can survive in a wide range of salinity. However, the molecular mechanisms involved in their adaptation to different environmental salinity have remained largely unknown. In the present study, we reared kuruma shrimp Marsupenaeus japonicus at 1.7%, 3.4% and 4.0% salinity. After rearing for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after rearing for 24 h. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. Notably, the increased glutamine content at high salinity appeared to be relevant to the increase of the expression level of the gene encoding Glutamate-Ammonia Ligase which functions in the glutamine metabolism. Furthermore, the alanine content increased at high salinity was likely to be associated with the decrease in the expression levels of the alanine-glyoxylate transaminase gene. Thus, the changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are considered to be regulated by the changes in the expression levels of genes related to amino acid metabolism.
Yl Ramachandra - One of the best experts on this subject based on the ideXlab platform.
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Quantitative proteomics for identifying biomarkers for Rabies
Clinical proteomics, 2013Co-Authors: Abhilash K Venugopal, S Sameer Kumar Ghantasala, Lakshmi Dhevi N Selvan, Santosh Renuse, Nandini A Sahasrabhuddhe, Mooriyath S Suja, Anita Mahadevan, Harsh Pawar, Praveen Kumar, Yl RamachandraAbstract:Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into encephalitic (furious) or paralytic (numb) rabies. Early diagnosis of this disease is particularly important as rabies is invariably fatal if adequate post exposure prophylaxis is not administered immediately following the bite. In this study, we carried out a quantitative proteomic analysis of the human brain tissue from cases of encephalitic and paralytic rabies along with normal human brain tissues using an 8-plex isobaric tags for relative and absolute quantification (iTRAQ) strategy. We identified 402 proteins, of which a number of proteins were differentially expressed between encephalitic and paralytic rabies, including several novel proteins. The differentially expressed molecules included karyopherin alpha 4 (KPNA4), which was overexpressed only in paralytic rabies, calcium calmodulin dependent kinase 2 alpha (CAMK2A), which was upregulated in paralytic rabies group and Glutamate Ammonia Ligase (GLUL), which was overexpressed in paralytic as well as encephalitic rabies. We validated two of the upregulated molecules, GLUL and CAMK2A, by dot blot assays and further validated CAMK2A by immunohistochemistry. These molecules need to be further investigated in body fluids such as cerebrospinal fluid in a larger cohort of rabies cases to determine their potential use as antemortem diagnostic biomarkers in rabies. This is the first study to systematically profile clinical subtypes of human rabies using an iTRAQ quantitative proteomics approach.
Francisco M. Cánovas - One of the best experts on this subject based on the ideXlab platform.
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Redundancy and metabolic function of the glutamine synthetase gene family in poplar
BMC plant biology, 2015Co-Authors: Vanessa Castro-rodríguez, Angel García-gutiérrez, Concepción Avila, Rafael A. Cañas, Mª Belén Pascual, Francisco M. CánovasAbstract:Glutamine synthetase (GS; EC: 6.3.1.2, L-Glutamate: Ammonia Ligase ADP-forming) is a key enzyme in ammonium assimilation and metabolism in higher plants. In poplar, the GS family is organized in 4 groups of duplicated genes, 3 of which code for cytosolic GS isoforms (GS1.1, GS1.2 and GS1.3) and one group that codes for the choroplastic GS isoform (GS2). Our previous work suggested that GS duplicates may have been retained to increase the amount of enzyme in a particular cell type. The current study was conducted to test this hypothesis by developing a more comprehensive understanding of the molecular and biochemical characteristics of the poplar GS isoenzymes and by determinating their kinetic parameters. To obtain further insights into the function of the poplar GS genes, in situ hybridization and laser capture microdissections were conducted in different tissues, and the precise GS gene spatial expression patterns were determined in specific cell/tissue types of the leaves, stems and roots. The molecular and functional analysis of the poplar GS family and the precise localization of the corresponding mRNA in different cell types strongly suggest that the GS isoforms play non-redundant roles in poplar tree biology. Furthermore, our results support the proposal that a function of the duplicated genes in specific cell/tissue types is to increase the abundance of the enzymes. Taken together, our results reveal that there is no redundancy in the poplar GS family at the whole plant level but it exists in specific cell types where the two duplicated genes are expressed and their gene expression products have similar metabolic roles. Gene redundancy may contribute to the homeostasis of nitrogen metabolism in functions associated with changes in environmental conditions and developmental stages.
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RESEARCH ARTICLE Open Access The glutamine synthetase gene family in Populus
2013Co-Authors: Vanessa Castro-rodríguez, Angel García-gutiérrez, Javier Canales, Concepción Avila, Edward G. Kirby, Francisco M. CánovasAbstract:Background: Glutamine synthetase (GS; EC: 6.3.1.2, L-Glutamate: Ammonia Ligase ADP-forming) is a key enzyme in ammonium assimilation and metabolism of higher plants. The current work was undertaken to develop a more comprehensive understanding of molecular and biochemical features of GS gene family in poplar, and to characterize the developmental regulation of GS expression in various tissues and at various times during the poplar perennial growth. Results: The GS gene family consists of 8 different genes exhibiting all structural and regulatory elements consistent with their roles as functional genes. Our results indicate that the family members are organized in 4 groups of duplicated genes, 3 of which code for cytosolic GS isoforms (GS1) and 1 which codes for the choroplastic GS isoform (GS2). Our analysis shows that Populus trichocarpa is the first plant species in which it was observed the complete GS family duplicated. Detailed expression analyses have revealed specific spatial and seasonal patterns of GS expression in poplar. These data provide insights into the metabolic function of GS isoforms in poplar and pave the way for future functional studies. Conclusions: Our data suggest that GS duplicates could have been retained in order to increase the amount of enzyme in a particular cell type. This possibility could contribute to the homeostasis of nitrogen metabolism in functions associated to changes in glutamine-derived metabolic products. The presence of duplicated GS genes in poplar could also contribute to diversification of the enzymatic properties for a particular GS isoform through the assembly of GS polypeptides into homo oligomeric and/or hetero oligomeric holoenzymes in specific cell types
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The glutamine synthetase gene family in Populus.
BMC plant biology, 2011Co-Authors: Vanessa Castro-rodríguez, Angel García-gutiérrez, Javier Canales, Concepción Avila, Edward G. Kirby, Francisco M. CánovasAbstract:Glutamine synthetase (GS; EC: 6.3.1.2, L-Glutamate: Ammonia Ligase ADP-forming) is a key enzyme in ammonium assimilation and metabolism of higher plants. The current work was undertaken to develop a more comprehensive understanding of molecular and biochemical features of GS gene family in poplar, and to characterize the developmental regulation of GS expression in various tissues and at various times during the poplar perennial growth. The GS gene family consists of 8 different genes exhibiting all structural and regulatory elements consistent with their roles as functional genes. Our results indicate that the family members are organized in 4 groups of duplicated genes, 3 of which code for cytosolic GS isoforms (GS1) and 1 which codes for the choroplastic GS isoform (GS2). Our analysis shows that Populus trichocarpa is the first plant species in which it was observed the complete GS family duplicated. Detailed expression analyses have revealed specific spatial and seasonal patterns of GS expression in poplar. These data provide insights into the metabolic function of GS isoforms in poplar and pave the way for future functional studies. Our data suggest that GS duplicates could have been retained in order to increase the amount of enzyme in a particular cell type. This possibility could contribute to the homeostasis of nitrogen metabolism in functions associated to changes in glutamine-derived metabolic products. The presence of duplicated GS genes in poplar could also contribute to diversification of the enzymatic properties for a particular GS isoform through the assembly of GS polypeptides into homo oligomeric and/or hetero oligomeric holoenzymes in specific cell types.
Hiroki Koyama - One of the best experts on this subject based on the ideXlab platform.
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Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp (Marsupenaeus japonicus) acclimated at different salinities.
The Journal of experimental biology, 2018Co-Authors: Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit PiyapattanakornAbstract:Shrimps inhabiting coastal waters can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp (Marsupenaeus japonicus) at 1.7%, 3.4% and 4.0% salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA sequencing analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after 24 h of acclimation. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. In particular, the increase of the expression level of the gene encoding Glutamate-Ammonia Ligase, which functions in glutamine metabolism, appeared to be associated with the increased glutamine concentration at high salinity. Furthermore, the increased alanine concentration at high salinity was likely associated with the decrease in the expression levels of the the gene encoding alanine-glyoxylate transaminase. Thus, there is a possibility that changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are regulated by changes in the expression levels of genes related to amino acid metabolism.
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Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp (Marsupenaeus japonicus) acclimated at different salinities.
The Journal of Experimental Biology, 2018Co-Authors: Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit PiyapattanakornAbstract:Shrimps inhabiting the coastal water can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after acclimating for 24 h. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. In particular, the increase of the expression level of the gene encoding Glutamate-Ammonia Ligase which functions in the glutamine metabolism appeared to be relevant to the increased glutamine concentration at high salinity. Furthermore, the alanine concentration increased at high salinity was likely to be associated with the decrease in the expression levels of the alanine-glyoxylate transaminase gene. Thus, there is a possibility that changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are regulated by changes in the expression levels of genes related to amino acid metabolism.
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Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp Marsupenaeus japonicus reared at different salinity
2017Co-Authors: Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit PiyapattanakornAbstract:Shrimps inhabiting around the coastal area can survive in a wide range of salinity. However, the molecular mechanisms involved in their adaptation to different environmental salinity have remained largely unknown. In the present study, we reared kuruma shrimp Marsupenaeus japonicus at 1.7%, 3.4% and 4.0% salinity. After rearing for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after rearing for 24 h. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. Notably, the increased glutamine content at high salinity appeared to be relevant to the increase of the expression level of the gene encoding Glutamate-Ammonia Ligase which functions in the glutamine metabolism. Furthermore, the alanine content increased at high salinity was likely to be associated with the decrease in the expression levels of the alanine-glyoxylate transaminase gene. Thus, the changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are considered to be regulated by the changes in the expression levels of genes related to amino acid metabolism.
J Rothuizen - One of the best experts on this subject based on the ideXlab platform.
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Aberrant Expression and Distribution of Enzymes of the Urea Cycle and Other Ammonia Metabolizing Pathways in Dogs with Congenital Portosystemic Shunts
2016Co-Authors: Giora Van Straten, Frank G Van Steenbeek, Guy C M Grinwis, Robert P Favier, Anne Kummeling, Hille Fieten, Marian Groot J A Koerkamp, Frank C P Holstege, Ingrid H. Van Gils, J RothuizenAbstract:The detoxification of Ammonia occurs mainly through conversion of Ammonia to urea in the liver via the urea cycle and glutamine synthesis. Congenital portosystemic shunts (CPSS) in dogs cause hyperammonemia eventually leading to hepatic encephalopathy. In this study, the gene expression of urea cycle enzymes (carbamoylphosphate synthetase (CPS1), ornithine carbamoyltransferase (OTC), argininosuccinate synthetase (ASS1), argininosuccinate lyase (ASL), and arginase (ARG1)), N-acetylGlutamate synthase (NAGS), Glutamate dehydrogenase (GLUD1), and Glutamate-Ammonia Ligase (GLUL) was evaluated in dogs with CPSS before and after surgical closure of the shunt. Additionally, immunohistochemistry was performed on urea cycle enzymes and GLUL on liver samples of healthy dogs and dogs with CPSS to investigate a possible zonal distribution of these enzymes within the liver lobule and to investigate possible differences in distribution in dogs with CPSS compared to healthy dogs. Furthermore, the effect of increasing Ammonia concentrations on the expression of the urea cycle enzymes was investigated in primary hepatocytes in vitro. Gene-expression of CPS1, OTC, ASL, GLUD1 and NAGS was down regulated in dogs with CPSS and did not normalize after surgical closure of the shunt. In all dogs GLUL distribution was localized pericentrally. CPS1, OTC and ASS1 were localized periportally in healthy dogs, whereas in CPSS dogs, these enzymes lacked a clear zonal distribution. In primary hepatocytes higher Ammonia concentrations induced mRNA levels of CPS1. We hypothesize that the reduction in expression of urea cycle enzymes, NAGS and GLUD1 as well a
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aberrant expression and distribution of enzymes of the urea cycle and other Ammonia metabolizing pathways in dogs with congenital portosystemic shunts
PLOS ONE, 2014Co-Authors: Giora Van Straten, Frank G Van Steenbeek, Guy C M Grinwis, Robert P Favier, Anne Kummeling, Ingrid H M Van Gils, Hille Fieten, Marian Groot J A Koerkamp, Frank C P Holstege, J RothuizenAbstract:The detoxification of Ammonia occurs mainly through conversion of Ammonia to urea in the liver via the urea cycle and glutamine synthesis. Congenital portosystemic shunts (CPSS) in dogs cause hyperammonemia eventually leading to hepatic encephalopathy. In this study, the gene expression of urea cycle enzymes (carbamoylphosphate synthetase (CPS1), ornithine carbamoyltransferase (OTC), argininosuccinate synthetase (ASS1), argininosuccinate lyase (ASL), and arginase (ARG1)), N-acetylGlutamate synthase (NAGS), Glutamate dehydrogenase (GLUD1), and Glutamate-Ammonia Ligase (GLUL) was evaluated in dogs with CPSS before and after surgical closure of the shunt. Additionally, immunohistochemistry was performed on urea cycle enzymes and GLUL on liver samples of healthy dogs and dogs with CPSS to investigate a possible zonal distribution of these enzymes within the liver lobule and to investigate possible differences in distribution in dogs with CPSS compared to healthy dogs. Furthermore, the effect of increasing Ammonia concentrations on the expression of the urea cycle enzymes was investigated in primary hepatocytes in vitro. Gene-expression of CPS1, OTC, ASL, GLUD1 and NAGS was down regulated in dogs with CPSS and did not normalize after surgical closure of the shunt. In all dogs GLUL distribution was localized pericentrally. CPS1, OTC and ASS1 were localized periportally in healthy dogs, whereas in CPSS dogs, these enzymes lacked a clear zonal distribution. In primary hepatocytes higher Ammonia concentrations induced mRNA levels of CPS1. We hypothesize that the reduction in expression of urea cycle enzymes, NAGS and GLUD1 as well as the alterations in zonal distribution in dogs with CPSS may be caused by a developmental arrest of these enzymes during the embryonic or early postnatal phase.
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Antibody characteristics, manufacturers, dilutions and protocol specifications for immunohistochemistry.
2014Co-Authors: Giora Van Straten, Frank G Van Steenbeek, Guy C M Grinwis, Robert P Favier, Anne Kummeling, Hille Fieten, Marian Groot J A Koerkamp, Frank C P Holstege, Ingrid H. Van Gils, J RothuizenAbstract:CPS1, carbamoyl phosphate synthetase 1; OTC, ornithine carbamoyltransferase; ASS1, argininosuccinate synthetase; ASL, argininosuccinate lyase; ARG1, arginase; GLUL, Glutamate–Ammonia Ligase; ABD, antibody diluent (DAKO); PBS, Phosphate-buffered saline; BSA, Bovine serum albumin; TE, Tris-Ethylenediaminetetraacetic acid.
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Primers used for qPCR.
2014Co-Authors: Giora Van Straten, Frank G Van Steenbeek, Guy C M Grinwis, Robert P Favier, Anne Kummeling, Hille Fieten, Marian Groot J A Koerkamp, Frank C P Holstege, Ingrid H. Van Gils, J RothuizenAbstract:CPS1, carbamoyl phosphate synthetase 1; OTC, ornithine carbamoyltransferase; ASS1, argininosuccinate synthetase; ASL, argininosuccinate lyase; ARG1, arginase; NAGS, N-acetylGlutamate synthase; GLUL, Glutamate–Ammonia Ligase; GLUD1, Glutamate dehydrogenase; GAPDH, Glyceraldehyde-3-phosphatedehdrogenase; B2M, b-2-Microglobulin; RPS5, Ribosomal protein S5; RPL8, ribosomal protein L8.
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The two major pathways metabolizing Ammonia: the urea cycle (periportal), and glutamine synthesis (pericentral).
2014Co-Authors: Giora Van Straten, Frank G Van Steenbeek, Guy C M Grinwis, Robert P Favier, Anne Kummeling, Hille Fieten, Marian Groot J A Koerkamp, Frank C P Holstege, Ingrid H. Van Gils, J RothuizenAbstract:In the urea cycle: Ammonia and bicarbonate form carbamoylphosphate via carbamoyl phosphate synthetase1 (CPS1). This reaction requires N-acetylGlutamate (acquired via a reaction catalysed by N-acetylGlutamate synthase (NAGS)), Mg2+ and MgATP. Carbamoylphosphate combines with ornithine in a reaction catalysed by ornithine carbamoyltransferase (OTC) to form citrulline. Citrulline is transported to the cytosol and combines with aspartate to form argininosuccinate (reaction catalysed by argininosuccinate synthetase (ASS1)). Argininosuccinate is then cleaved by argininosuccinate lyase (ASL) yielding fumarate and arginine. Arginase (ARG1) cleaves arginine, producing urea and ornithine. Urea is excreted as waste and ornithine is transported back to the mitochondria to be used in subsequent cycles of urea synthesis. In the pericentral hepatocytes, Ammonia ‘escaping’ the urea cycle is metabolized to glutamine (reaction catalysed by Glutamate–Ammonia Ligase (GLUL).