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Isogai S, Matsushita T, Imanishi H, Koonthongkaew J, Toyokawa Y, Nishimura A, Yi X, Kazlauskas R, Takagi H. High-Level Production of Lysine in the Yeast Saccharomyces cerevisiae by Rational Design of Homocitrate Synthase. Appl Environ Microbiol 2021; 87:e0060021. [PMID: 33990312 PMCID: PMC8276798 DOI: 10.1128/aem.00600-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes the aldol condensation of 2-oxoglutarate (2-OG) and acetyl coenzyme A (AcCoA) to form homocitrate, which is the first enzyme of the lysine biosynthetic pathway in the yeast Saccharomyces cerevisiae. The HCS activity is tightly regulated via feedback inhibition by the end product lysine. Here, we designed a feedback inhibition-insensitive HCS of S. cerevisiae (ScLys20) for high-level production of lysine in yeast cells. In silico docking of the substrate 2-OG and the inhibitor lysine to ScLys20 predicted that the substitution of serine with glutamate at position 385 would be more suitable for desensitization of the lysine feedback inhibition than the substitution from serine to phenylalanine in the already known Ser385Phe variant. Enzymatic analysis revealed that the Ser385Glu variant is far more insensitive to feedback inhibition than the Ser385Phe variant. We also found that the lysine contents in yeast cells expressing the Ser385Glu variant were 4.62- and 1.47-fold higher than those of cells expressing the wild-type HCS and Ser385Phe variant, respectively, due to the extreme desensitization to feedback inhibition. In this study, we obtained highly feedback inhibition-insensitive HCS using in silico docking and enzymatic analysis. Our results indicate that the rational engineering of HCS for feedback inhibition desensitization by lysine could be useful for constructing new yeast strains with higher lysine productivity. IMPORTANCE A traditional method for screening toxic analogue-resistant mutants has been established for the breeding of microbes that produce high levels of amino acids, including lysine. However, another efficient strategy is required to further improve their productivity. Homocitrate synthase (HCS) catalyzes the first step of lysine biosynthesis in the yeast Saccharomyces cerevisiae, and its activity is subject to feedback inhibition by lysine. Here, in silico design of a key enzyme that regulates the biosynthesis of lysine was utilized to increase the productivity of lysine. We designed HCS for the high-level production of lysine in yeast cells by in silico docking simulation. The engineered HCS exhibited much less sensitivity to lysine and conferred higher production of lysine than the already known variant obtained by traditional breeding. The combination of in silico design and experimental analysis of a key enzyme will contribute to advances in metabolic engineering for the construction of industrial microorganisms.
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Affiliation(s)
- Shota Isogai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tomonori Matsushita
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroyuki Imanishi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Jirasin Koonthongkaew
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yoichi Toyokawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Xiao Yi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- The BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, Minnesota, USA
- The BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Deering RW, Whalen KE, Alvarez I, Daffinee K, Beganovic M, LaPlante KL, Kishore S, Zhao S, Cezairliyan B, Yu S, Rosario M, Mincer TJ, Rowley DC. Identification of a bacteria-produced benzisoxazole with antibiotic activity against multi-drug resistant Acinetobacter baumannii. J Antibiot (Tokyo) 2021; 74:370-380. [PMID: 33580212 PMCID: PMC7879144 DOI: 10.1038/s41429-021-00412-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 01/05/2023]
Abstract
The emergence of multi-drug resistant pathogenic bacteria represents a serious and growing threat to national healthcare systems. Most pressing is an immediate need for the development of novel antibacterial agents to treat Gram-negative multi-drug resistant infections, including the opportunistic, hospital-derived pathogen, Acinetobacter baumannii. Herein we report a naturally occurring 1,2-benzisoxazole with minimum inhibitory concentrations as low as 6.25 μg ml-1 against clinical strains of multi-drug resistant A. baumannii and investigate its possible mechanisms of action. This molecule represents a new chemotype for antibacterial agents against A. baumannii and is easily accessed in two steps via de novo synthesis. In vitro testing of structural analogs suggest that the natural compound may already be optimized for activity against this pathogen. Our results demonstrate that supplementation of 4-hydroxybenzoate in minimal media was able to reverse 1,2-benzisoxazole's antibacterial effects in A. baumannii. A search of metabolic pathways involving 4-hydroxybenzoate coupled with molecular modeling studies implicates two enzymes, chorismate pyruvate-lyase and 4-hydroxybenzoate octaprenyltransferase, as promising leads for the target of 3,6-dihydroxy-1,2-benzisoxazole.
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Affiliation(s)
- Robert W Deering
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
| | | | - Ivan Alvarez
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
| | - Kathryn Daffinee
- Department of Pharmacy Practice, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
- Infectious Diseases Research Program, Providence Veterans Affairs Medical Center, Providence, RI, USA
| | - Maya Beganovic
- Department of Pharmacy Practice, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
- Infectious Diseases Research Program, Providence Veterans Affairs Medical Center, Providence, RI, USA
| | - Kerry L LaPlante
- Department of Pharmacy Practice, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
- Infectious Diseases Research Program, Providence Veterans Affairs Medical Center, Providence, RI, USA
| | - Shreya Kishore
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Sijing Zhao
- Department of Biology, Haverford College, Haverford, PA, USA
| | | | - Shen Yu
- Octagon Therapeutics, Inc., Cambridge, MA, USA
| | - Margaret Rosario
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
| | - Tracy J Mincer
- Wilkes Honors College and Harbor Branch Oceanographic Institute, Florida Atlantic University, Boca Raton, FL, USA.
| | - David C Rowley
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, USA.
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Bellés-Sancho P, Lardi M, Liu Y, Hug S, Pinto-Carbó MA, Zamboni N, Pessi G. Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions. Cells 2021; 10:cells10040952. [PMID: 33924023 PMCID: PMC8073898 DOI: 10.3390/cells10040952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/29/2022] Open
Abstract
Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N2) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. In contrast, non-nodulating free-living diazotrophs encode the homocitrate synthase (NifV) and reduce N2 in nitrogen-limiting free-living conditions. Paraburkholderia phymatum STM815 is a beta-rhizobial strain, which can enter symbiosis with a broad range of legumes, including papilionoids and mimosoids. In contrast to most alpha-rhizobia, which lack nifV, P. phymatum harbors a copy of nifV on its symbiotic plasmid. We show here that P. phymatum nifV is essential for nitrogenase activity both in root nodules of papilionoid plants and in free-living growth conditions. Notably, nifV was dispensable in nodules of Mimosa pudica despite the fact that the gene was highly expressed during symbiosis with all tested papilionoid and mimosoid plants. A metabolome analysis of papilionoid and mimosoid root nodules infected with the P. phymatum wild-type strain revealed that among the approximately 400 measured metabolites, homocitrate and other metabolites involved in lysine biosynthesis and degradation have accumulated in all plant nodules compared to uninfected roots, suggesting an important role of these metabolites during symbiosis.
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Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Sebastian Hug
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Marta Adriana Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, CH-8093 Zürich, Switzerland;
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
- Correspondence: ; Tel.: +41-44-63-52904
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Vieira AZ, Raittz RT, Faoro H. Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis. Microb Genom 2021; 7:000563. [PMID: 33848237 PMCID: PMC8208679 DOI: 10.1099/mgen.0.000563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/16/2021] [Indexed: 12/28/2022] Open
Abstract
Nonulosonic acids (NulOs) are a group of nine-carbon monosaccharides with different functions in nature. N-acetylneuraminic acid (Neu5Ac) is the most common NulO. It covers the membrane surface of all human cells and is a central molecule in the process of self-recognition via SIGLECS receptors. Some pathogenic bacteria escape the immune system by copying the sialylation of the host cell membrane. Neu5Ac production in these bacteria is catalysed by the enzyme NeuB. Some bacteria can also produce other NulOs named pseudaminic and legionaminic acids, through the NeuB homologues PseI and LegI, respectively. In Opisthokonta eukaryotes, the biosynthesis of Neu5Ac is catalysed by the enzyme NanS. In this study, we used publicly available data of sequences of NulOs synthases to investigate its distribution within the three domains of life and its relationship with pathogenic bacteria. We mined the KEGG database and found 425 NeuB sequences. Most NeuB sequences (58.74 %) from the KEGG orthology database were classified as from environmental bacteria; however, sequences from pathogenic bacteria showed higher conservation and prevalence of a specific domain named SAF. Using the HMM profile we identified 13 941 NulO synthase sequences in UniProt. Phylogenetic analysis of these sequences showed that the synthases were divided into three main groups that can be related to the lifestyle of these bacteria: (I) predominantly environmental, (II) intermediate and (III) predominantly pathogenic. NeuB was widely distributed in the groups. However, LegI and PseI were more concentrated in groups II and III, respectively. We also found that PseI appeared later in the evolutionary process, derived from NeuB. We use this same methodology to retrieve sialic acid synthase sequences from Archaea and Eukarya. A large-scale phylogenetic analysis showed that while the Archaea sequences are spread across the tree, the eukaryotic NanS sequences were grouped in a specific branch in group II. None of the bacterial NanS sequences grouped with the eukaryotic branch. The analysis of conserved residues showed that the synthases of Archaea and Eukarya present a mutation in one of the three catalytic residues, an E134D change, related to a Neisseria meningitidis reference sequence. We also found that the conservation profile is higher between NeuB of pathogenic bacteria and NanS of eukaryotes than between NeuB of environmental bacteria and NanS of eukaryotes. Our large-scale analysis brings new perspectives on the evolution of NulOs synthases, suggesting their presence in the last common universal ancestor.
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Affiliation(s)
- Alexandre Zanatta Vieira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz-PR, Algacyr Munhoz Mader street, 3775, Curitiba, Paraná, Brazil
- Graduation Program on Bioinformatics – Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, Brazil
| | - Roberto Tadeu Raittz
- Graduation Program on Bioinformatics – Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, Brazil
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz-PR, Algacyr Munhoz Mader street, 3775, Curitiba, Paraná, Brazil
- Graduation Program on Bioinformatics – Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, Brazil
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5
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Hu J, Jin K, He ZG, Zhang H. Citrate lyase CitE in Mycobacterium tuberculosis contributes to mycobacterial survival under hypoxic conditions. PLoS One 2020; 15:e0230786. [PMID: 32302313 PMCID: PMC7164622 DOI: 10.1371/journal.pone.0230786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/08/2020] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis and has evolved an ability to survive in hostile host environments. M. tuberculosis is thought to utilize the rTCA cycle to sustain its latent growth during infection, but the enzymatic characteristics and physiological function for the key citrate lyase of the rTCA cycle, MtbCitE, in the important pathogen remain unclear. In this study, we investigated the function of MtbCitE based on its structural properties and sequence comparisons with other bacterial citrate lyase subunits. We showed that several amino acid residues were important for the citrate cleavage activity of MtbCitE. Strikingly, the citrate cleavage activity of MtbCitE was inhibited by ATP, indicating that energy metabolism might couple with the regulation of MtbCitE activity, which differed from other CitEs. More interestingly, deletion of citE from Mycobacterium bovis BCG decreased the mycobacterial survival rate under hypoxic conditions, whereas complementation with citE restored the phenotype to wild-type levels. Consistently, three key rTCA cycle enzymes were positively regulated under hypoxic conditions in mycobacteria. Therefore, we characterized a unique citrate lyase MtbCitE from M. tuberculosis and found that the CitE protein significantly contributed to mycobacterial survival under hypoxic conditions.
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Affiliation(s)
- Jialing Hu
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Kaixi Jin
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zheng-Guo He
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Hua Zhang
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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6
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Zhong R, Cui D, Richardson EA, Phillips DR, Azadi P, Lu G, Ye ZH. Cytosolic Acetyl-CoA Generated by ATP-Citrate Lyase Is Essential for Acetylation of Cell Wall Polysaccharides. Plant Cell Physiol 2020; 61:64-75. [PMID: 31503286 DOI: 10.1093/pcp/pcz178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 05/12/2023]
Abstract
Plant cell wall polysaccharides, including xylan, glucomannan, xyloglucan and pectin, are often acetylated. Although a number of acetyltransferases responsible for the acetylation of some of these polysaccharides have been biochemically characterized, little is known about the source of acetyl donors and how acetyl donors are translocated into the Golgi, where these polysaccharides are synthesized. In this report, we investigated roles of ATP-citrate lyase (ACL) that generates cytosolic acetyl-CoA in cell wall polysaccharide acetylation and effects of simultaneous mutations of four Reduced Wall Acetylation (RWA) genes on acetyl-CoA transport into the Golgi in Arabidopsis thaliana. Expression analyses of genes involved in the generation of acetyl-CoA in different subcellular compartments showed that the expression of several ACL genes responsible for cytosolic acetyl-CoA synthesis was elevated in interfascicular fiber cells and induced by secondary wall-associated transcriptional activators. Simultaneous downregulation of the expression of ACL genes was demonstrated to result in a substantial decrease in the degree of xylan acetylation and a severe alteration in secondary wall structure in xylem vessels. In addition, the degree of acetylation of other cell wall polysaccharides, including glucomannan, xyloglucan and pectin, was also reduced. Moreover, Golgi-enriched membrane vesicles isolated from the rwa1/2/3/4 quadruple mutant were found to exhibit a drastic reduction in acetyl-CoA transport activity compared with the wild type. These findings indicate that cytosolic acetyl-CoA generated by ACL is essential for cell wall polysaccharide acetylation and RWAs are required for its transport from the cytosol into the Golgi.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dongtao Cui
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | | | - Dennis R Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Grace Lu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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7
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Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proc Natl Acad Sci U S A 2019; 116:25287-25292. [PMID: 31767748 PMCID: PMC6911176 DOI: 10.1073/pnas.1909987116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evolution fine-tunes biological pathways to achieve a robust cellular physiology. Two and a half billion years ago, rapidly rising levels of oxygen as a byproduct of blooming cyanobacterial photosynthesis resulted in a redox upshift in microbial energetics. The appearance of higher-redox-potential respiratory quinone, ubiquinone (UQ), is believed to be an adaptive response to this environmental transition. However, the majority of bacterial species are still dependent on the ancient respiratory quinone, naphthoquinone (NQ). Gammaproteobacteria can biosynthesize both of these respiratory quinones, where UQ has been associated with aerobic lifestyle and NQ with anaerobic lifestyle. We engineered an obligate NQ-dependent γ-proteobacterium, Escherichia coli ΔubiC, and performed adaptive laboratory evolution to understand the selection against the use of NQ in an oxic environment and also the adaptation required to support the NQ-driven aerobic electron transport chain. A comparative systems-level analysis of pre- and postevolved NQ-dependent strains revealed a clear shift from fermentative to oxidative metabolism enabled by higher periplasmic superoxide defense. This metabolic shift was driven by the concerted activity of 3 transcriptional regulators (PdhR, RpoS, and Fur). Analysis of these findings using a genome-scale model suggested that resource allocation to reactive oxygen species (ROS) mitigation results in lower growth rates. These results provide a direct elucidation of a resource allocation tradeoff between growth rate and ROS mitigation costs associated with NQ usage under oxygen-replete condition.
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Affiliation(s)
- Amitesh Anand
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Ke Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Laurence Yang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Anand V Sastry
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Connor A Olson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Saugat Poudel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Yara Seif
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Patrick V Phaneuf
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093
| | - Sibei Xu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Adam M Feist
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens, Lyngby, Denmark
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8
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Abstract
3-methylglutaric (3MG) acid is a conspicuous C6 dicarboxylic organic acid classically associated with two distinct leucine pathway enzyme deficiencies. 3MG acid is excreted in urine of individuals harboring deficiencies in 3-hydroxy-3-methylglutaryl (HMG) CoA lyase (HMGCL) or 3-methylglutaconyl CoA hydratase (AUH). Whereas 3MG CoA is not part of the leucine catabolic pathway, it is likely formed via a side reaction involving reduction of the α-ß trans double bond in the leucine pathway intermediate, 3-methylglutaconyl CoA. While the metabolic basis for the accumulation of 3MG acid in subjects with deficiencies in HMGCL or AUH is apparent, the occurrence of 3MG aciduria in a host of unrelated inborn errors of metabolism associated with compromised mitochondrial energy metabolism is less clear. Herein, a novel mitochondrial biosynthetic pathway termed "the acetyl CoA diversion pathway", provides an explanation. The pathway is initiated by defective electron transport chain function which, ultimately, inhibits acetyl CoA entry into the TCA cycle. When this occurs, 3MG acid is synthesized in five steps from acetyl CoA via a novel reaction sequence, providing a metabolic rationale for the connection between 3MG aciduria and compromised mitochondrial energy metabolism.
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Affiliation(s)
- Dylan E Jones
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Leanne Perez
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Robert O Ryan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States.
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9
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Kumar R, Lee SG, Augustine R, Reichelt M, Vassão DG, Palavalli MH, Allen A, Gershenzon J, Jez JM, Bisht NC. Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates. Plant Cell 2019; 31:1633-1647. [PMID: 31023839 PMCID: PMC6635866 DOI: 10.1105/tpc.19.00046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/29/2019] [Accepted: 04/19/2019] [Indexed: 05/23/2023]
Abstract
The globally cultivated Brassica species possess diverse aliphatic glucosinolates, which are important for plant defense and animal nutrition. The committed step in the side chain elongation of methionine-derived aliphatic glucosinolates is catalyzed by methylthioalkylmalate synthase, which likely evolved from the isopropylmalate synthases of leucine biosynthesis. However, the molecular basis for the evolution of methylthioalkylmalate synthase and its generation of natural product diversity in Brassica is poorly understood. Here, we show that Brassica genomes encode multiple methylthioalkylmalate synthases that have differences in expression profiles and 2-oxo substrate preferences, which account for the diversity of aliphatic glucosinolates across Brassica accessions. Analysis of the 2.1 Å resolution x-ray crystal structure of Brassica juncea methylthioalkylmalate synthase identified key active site residues responsible for controlling the specificity for different 2-oxo substrates and the determinants of side chain length in aliphatic glucosinolates. Overall, these results provide the evolutionary and biochemical foundation for the diversification of glucosinolate profiles across globally cultivated Brassica species, which could be used with ongoing breeding strategies toward the manipulation of beneficial glucosinolate compounds for animal health and plant protection.
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Affiliation(s)
- Roshan Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Rehna Augustine
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Micheal Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Daniel G Vassão
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Manoj H Palavalli
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Aron Allen
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Naveen C Bisht
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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10
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Cai ZP, Conway LP, Huang YY, Wang WJ, Laborda P, Wang T, Lu AM, Yao HL, Huang K, Flitsch SL, Liu L, Voglmeir J. Enzymatic Synthesis of Trideuterated Sialosides. Molecules 2019; 24:molecules24071368. [PMID: 30965582 PMCID: PMC6479850 DOI: 10.3390/molecules24071368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/21/2022] Open
Abstract
Sialic acids are a family of acidic monosaccharides often found on the termini of cell surface proteins or lipid glycoconjugates of higher animals. Herein we describe the enzymatic synthesis of the two isotopically labeled sialic acid derivatives d3-X-Gal-α-2,3-Neu5Ac and d3-X-Gal-α-2,3-Neu5Gc. Using deuterium oxide as the reaction solvent, deuterium atoms could be successfully introduced during the enzymatic epimerization and aldol addition reactions when the sialosides were generated. NMR and mass spectrometric analyses confirmed that the resulting sialosides were indeed tri-deuterated. These compounds may be of interest as internal standards in liquid chromatography/mass spectrometric assays for biochemical or clinical studies of sialic acids. This was further exemplified by the use of this tri-deuterated sialosides as internal standards for the quantification of sialic acids in meat and egg samples.
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Affiliation(s)
- Zhi-P Cai
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Louis P Conway
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ying Y Huang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wen J Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Pedro Laborda
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ai M Lu
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hong L Yao
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kun Huang
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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11
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Kumar JP, Rao H, Nayak V, Ramaswamy S. Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum. Acta Crystallogr F Struct Biol Commun 2018; 74:725-732. [PMID: 30387778 PMCID: PMC6213981 DOI: 10.1107/s2053230x18012992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/13/2018] [Indexed: 12/18/2022] Open
Abstract
N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host-pathogen interactions. In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatum is a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterial N-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure-function relationship, the steady-state kinetic parameters of the enzyme are also reported.
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Affiliation(s)
- Jay Prakash Kumar
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
- School of Life Science, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, Karnataka 560 065, India
| | - Harshvardhan Rao
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Vinod Nayak
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - S. Ramaswamy
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India
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12
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Zhou Y, Memelink J, Linthorst HJM. An E. coli biosensor for screening of cDNA libraries for isochorismate pyruvate lyase-encoding cDNAs. Mol Genet Genomics 2018; 293:1181-1190. [PMID: 29796759 PMCID: PMC6153503 DOI: 10.1007/s00438-018-1450-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/17/2018] [Indexed: 01/24/2023]
Abstract
Salicylic acid (SA) is an essential hormone for development and induced defense against biotrophic pathogens in plants. The formation of SA mainly derives from chorismate via demonstrated isochorismate synthase (ICS) and presumed isochorismate pyruvate lyase (IPL)-mediated steps in Arabidopsis thaliana, but so far no plant enzyme displaying IPL activity has been identified. Here, we developed an E. coli SA biosensor to screen for IPL activity based on the SalR regulator/salA promoter combination from Acinetobacter sp ADP1, to control the expression of the reporter luxCDABE. The biosensor was responsive to micromolar concentrations of exogenous SA, and to endogenous SA produced after transformation with a plasmid permitting IPTG-inducible expression of bacterial IPL in this biosensor strain. After screening a cDNA library constructed from turnip crinkle virus (TCV)-infected Arabidopsis ecotype Di-17, we identified an enzyme, PRXR1, as a putative IPL that converts isochorismate into SA. Our results provide a new experimental approach to identify IPL and new insights into the SA biosynthesis pathway in Arabidopsis.
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Affiliation(s)
- Yingjie Zhou
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Johan Memelink
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Huub J M Linthorst
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
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13
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Wang Z, Zhuang W, Cheng J, Sun W, Wu J, Chen Y, Ying H. In Vivo Multienzyme Complex Coconstruction of N-Acetylneuraminic Acid Lyase and N-Acetylglucosamine-2-epimerase for Biosynthesis of N-Acetylneuraminic Acid. J Agric Food Chem 2017; 65:7467-7475. [PMID: 28791861 DOI: 10.1021/acs.jafc.7b02708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Metabolic channeling enables efficient transfer of the intermediates by forming a multienzyme complex. To leverage the metabolic channeling for improved biosynthesis, we coexpressed N-acetylneuraminic acid lyase from C. glutamicum ATCC 13032 (CgNal) and N-acetylglucosamine-2-epimerase from Anabaena sp. CH1 (anAGE) in Escherichia coli and used the whole cell to synthesize N-acetylneuraminic acid (Neu5Ac) from N-acetylglucosamine (GlcNAc) and pyruvate. To get the multienzyme complex, polycistronic plasmid with high levels of CgNal and anAGE expression was constructed by tuning the orders of the genes. The Shine-Dalgarno (SD) sequence and aligned spacing (AS) distance were optimized. The E. coli Rosetta harboring the polycistronic plasmid pET-28a-SD2-AS1-CgNal-SD-AS-anAGE increased the production of Neu5Ac by 58.7% to 92.5 g/L in 36 h by whole-cell catalysis and by 21.9% up to 112.8 g/L in 24 h with the addition of Triton X-100.
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Affiliation(s)
- Zhenfu Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Wei Zhuang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Jian Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Wujin Sun
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jinglan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
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14
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González JM, Marti-Arbona R, Chen JCH, Unkefer CJ. Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift. Acta Crystallogr F Struct Biol Commun 2017; 73:79-85. [PMID: 28177317 PMCID: PMC5297927 DOI: 10.1107/s2053230x17001029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/19/2017] [Indexed: 11/10/2022] Open
Abstract
Malyl-CoA lyase (MCL) is an Mg2+-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg2+ is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg2+, oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding. Alignment of the structures shows that a simple hinge motion centered on the conserved residues Phe268 and Thr269 moves the C-terminal domain by about 30° relative to the rest of the molecule. This domain motion positions a conserved aspartate residue located in the C-terminal domain in the active site of the adjacent monomer, which may serve as a general acid/base in the catalytic mechanism.
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Affiliation(s)
- Javier M. González
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Julian C.-H. Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Clifford J. Unkefer
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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15
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Mazurkewich S, Seah SYK. Investigation into the Mode of Phosphate Activation in the 4-Hydroxy-4-Methyl-2-Oxoglutarate/4-Carboxy-4-Hydroxy-2-Oxoadipate Aldolase from Pseudomonas putida F1. PLoS One 2016; 11:e0164556. [PMID: 27741265 PMCID: PMC5065237 DOI: 10.1371/journal.pone.0164556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/03/2016] [Indexed: 11/18/2022] Open
Abstract
The 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy-4-hydroxy-2-oxoadipate (CHA) aldolase is the last enzyme of both the gallate and protocatechuate 4,5-cleavage pathways which links aromatic catabolism to central cellular metabolism. The enzyme is a class II, divalent metal dependent, aldolase which is activated in the presence of inorganic phosphate (Pi), increasing its turnover rate >10-fold. This phosphate activation is unique for a class II aldolase. The aldolase pyruvate methyl proton exchange rate, a probe of the general acid half reaction, was increased 300-fold in the presence of 1 mM Pi and the rate enhancement followed saturation kinetics giving rise to a KM of 397 ± 30 μM. Docking studies revealed a potential Pi binding site close to, or overlapping with, the proposed general acid water site. Putative Pi binding residues were substituted by site-directed mutagenesis which resulted in reductions of Pi activation. Significantly, the active site residue Arg-123, known to be critical for the catalytic mechanism of the enzyme, was also implicated in supporting Pi mediated activation.
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Affiliation(s)
- Scott Mazurkewich
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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16
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Upadhyaya P, Tyagi K, Sarma S, Tamboli V, Sreelakshmi Y, Sharma R. Natural variation in folate levels among tomato (Solanum lycopersicum) accessions. Food Chem 2016; 217:610-619. [PMID: 27664678 DOI: 10.1016/j.foodchem.2016.09.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 06/02/2016] [Accepted: 09/05/2016] [Indexed: 11/17/2022]
Abstract
Folate content was estimated in tomato (Solanum lycopersicum) accessions using microbiological assay (MA) and by LC-MS. The MA revealed that in red-ripe fruits folate levels ranged from 4 to 60μg/100g fresh weight. The LC-MS estimation of red-ripe fruits detected three folate forms, 5-CH3-THF, 5-CHO-THF, 5,10-CH(+)THF and folate levels ranged from 14 to 46μg/100g fresh weight. In mature green and red ripe fruit, 5-CH3-THF was the most abundant folate form. Comparison of LC-MS with MA revealed that MA inaccurately estimates folate levels. The accumulation of folate forms and their distribution varied among accessions. The single nucleotide polymorphism was examined in the key genes of the folate pathway to understand its linkage with folate levels. Despite the significant variation in folate levels among tomato accessions, little polymorphism was found in folate biosynthesis genes. Our results indicate that variation in folate level is governed by a more complex regulation at cellular homeostasis level.
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Affiliation(s)
- Pallawi Upadhyaya
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Vajir Tamboli
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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17
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Jiao Y, Zhang J, Lu L, Xu J, Qin L. The Fto Gene Regulates the Proliferation and Differentiation of Pre-Adipocytes in Vitro. Nutrients 2016; 8:102. [PMID: 26907332 PMCID: PMC4772064 DOI: 10.3390/nu8020102] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/22/2016] [Accepted: 02/15/2016] [Indexed: 12/17/2022] Open
Abstract
The highly regulated differentiation and proliferation of pre-adipocytes play a key role in the initiation of obesity. Fat mass and obesity associated (FTO) is a novel gene strongly associated with the risk of obesity. A deficiency of FTO may cause growth retardation in addition to fat mass and adipocyte size reduction in vivo. To investigate the potential role of Fto gene on the proliferation and differentiation of pre-adipocytes, we generated Fto-knockdown and overexpressed 3T3-L1 cells. Using numerous proliferation assays our results suggest that Fto knockdown leads to suppression of proliferation, lower mitochondrial membrane potential, less cellular ATP, and decreased and smaller intracellular lipid droplets compared with controls (p < 0.05). Western blot analysis demonstrated that Fto knockdown can significantly suppress peroxisome proliferator-activated receptor gamma (PPARγ) and glucose transporter type 4 (GLUT4) expression and inhibit Akt phosphorylation. By contrast, overexpression of Fto had the opposing effect on proliferation, mitochondrial membrane potential, ATP generation, in vitro differentiation, Akt phosphorylation, and PPARγ and GLUT4 expression. Moreover, we demonstrated that Wortmannin, a phosphoinositide 3-kinase (PI3K) inhibitor, could inhibit phospho-Akt in Fto overexpressed 3T3-L1 cells. Taken together, the results suggest that Fto regulates the proliferation and differentiation of 3T3-L1 cells via multiple mechanisms, including PPARγ and PI3K/Akt signaling.
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Affiliation(s)
- Yang Jiao
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Medical College of Soochow University, Suzhou 215123, China.
- Department of Radiation Genetics, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China.
| | - Jingying Zhang
- Department of Radiation Genetics, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China.
| | - Lunjie Lu
- Department of Radiation Genetics, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China.
| | - Jiaying Xu
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Medical College of Soochow University, Suzhou 215123, China.
| | - Liqiang Qin
- Department of Nutrition and Food Hygiene, School of Public Health, Medical College of Soochow University, Suzhou 215123, China.
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Stockwell J, Daniels AD, Windle CL, Harman TA, Woodhall T, Lebl T, Trinh CH, Mulholland K, Pearson AR, Berry A, Nelson A. Evaluation of fluoropyruvate as nucleophile in reactions catalysed by N-acetyl neuraminic acid lyase variants: scope, limitations and stereoselectivity. Org Biomol Chem 2016; 14:105-12. [PMID: 26537532 PMCID: PMC4717870 DOI: 10.1039/c5ob02037a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/30/2015] [Indexed: 12/25/2022]
Abstract
The catalysis of reactions involving fluoropyruvate as donor by N-acetyl neuraminic acid lyase (NAL) variants was investigated. Under kinetic control, the wild-type enzyme catalysed the reaction between fluoropyruvate and N-acetyl mannosamine to give a 90 : 10 ratio of the (3R,4R)- and (3S,4R)-configured products; after extended reaction times, equilibration occurred to give a 30 : 70 mixture of these products. The efficiency and stereoselectivity of reactions of a range of substrates catalysed by the E192N, E192N/T167V/S208V and E192N/T167G NAL variants were also studied. Using fluoropyruvate and (2R,3S)- or (2S,3R)-2,3-dihydroxy-4-oxo-N,N-dipropylbutanamide as substrates, it was possible to obtain three of the four possible diastereomeric products; for each product, the ratio of anomeric and pyranose/furanose forms was determined. The crystal structure of S. aureus NAL in complex with fluoropyruvate was determined, assisting rationalisation of the stereochemical outcome of C-C bond formation.
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Affiliation(s)
- Jennifer Stockwell
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
| | - Adam D. Daniels
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Claire L. Windle
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Thomas A. Harman
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
| | - Thomas Woodhall
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
| | - Tomas Lebl
- School of Chemistry , University of St Andrews , St Andrews , KY16 9ST , UK
| | - Chi H. Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Keith Mulholland
- Chemical Development , AstraZeneca , Silk Road Business Park , Macclesfield , Cheshire , SK10 2NA , UK
| | - Arwen R. Pearson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Adam Nelson
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
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Abstract
In this issue Kang et al. (2015) show that oncogenic BRAF(V600E) stimulates expression of ketogenic enzyme 3-hydroxy-3-methylglutaryl-CoA lyase and promotes the formation of the ketone body acetoacetate, which subsequently enhances BRAF(V600E)/MEK/ERK signaling.
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Affiliation(s)
- Sebastian Trousil
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bin Zheng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Wang CY, Shie SS, Hsieh IC, Tsai ML, Wen MS. FTO modulates circadian rhythms and inhibits the CLOCK-BMAL1-induced transcription. Biochem Biophys Res Commun 2015; 464:826-32. [PMID: 26188089 DOI: 10.1016/j.bbrc.2015.07.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022]
Abstract
Variations in the human fat mass and obesity-associated gene, which encodes FTO, an 2-oxoglutarate-dependent nucleic acid demethylase, are associated with increased risk of obesity. These FTO variations were recently shown to affect IRX3 and the exact function of FTO is still controversial. Obesity is closely linked to circadian rhythm. To understand the role of FTO in circadian rhythm, we analyzed the circadian rhythm of FTO deficient mice. FTO deficient mice had robust circadian locomotor activity rhythms with prolonged periods. The light-induced phase shifts of circadian rhythms were also significantly affected in FTO deficient mice. Tissue explants of FTO deficient mice maintained robust peripheral rhythms with prolonged period. Overexpress of FTO represses the transcriptional activation by CLOCK and BMAL1. Core clock genes expression of mRNA and protein were also altered in FTO deficient mice. Furthermore, FTO co-immunoprecipitated with CRY1/2 in a circadian manner. These results indicate a fundamental link between the circadian rhythm and FTO and extend the function of FTO to the core clockwork machinery.
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Affiliation(s)
- Chao-Yung Wang
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan.
| | - Shian-Sen Shie
- Department of Infectious Diseases, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - I-Chang Hsieh
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Ming-Lung Tsai
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Ming-Shien Wen
- Department of Cardiology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
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22
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Fan HQ, He W, Xu KF, Wang ZX, Xu XY, Chen H. FTO Inhibits Insulin Secretion and Promotes NF-κB Activation through Positively Regulating ROS Production in Pancreatic β cells. PLoS One 2015; 10:e0127705. [PMID: 26018652 PMCID: PMC4446323 DOI: 10.1371/journal.pone.0127705] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/17/2015] [Indexed: 11/25/2022] Open
Abstract
FTO (Fat mass and obesity-associated) is associated with increased risk of obesity and type 2 diabetes incurrence. Pancreas islet β cells dysfunction and insulin resistance are major causes of type 2 diabetes. However, whether FTO plays an important functional role in pancreatic β cells as well as the related molecular mechanism is still unclear. In the present study, the tissue expression profile of FTO was firstly determined using quantitative PCR and western blot. FTO is widely expressed in various tissues and presented with relative high expression in pancreas tissue, especially in endocrine pancreas. FTO overexpression in MIN6 cells achieved by lentivirus delivery significantly inhibits insulin secretion in the presence of glucose stimulus as well as KCl. FTO silence has no effect on insulin secretion of MIN6 cells. However, FTO overexpression doesn’t affect the transcription of insulin gene. Furthermore, reactive oxygen species (ROS) production and NF-κB activation are significantly promoted by FTO overexpression. Inhibition of intracellular ROS production by N-acetyl-L-cysteine (NAC) can alleviate NF-κB activation and restore the insulin secretion mediated by FTO overexpression. A whole transcript-microarray is employed to analyze the differential gene expression mediated by FTO overexpression. The genes which are modulated by FTO are involved in many important biological pathways such as G-protein coupled receptor signaling and NF-κB signaling. Therefore, our study indicates that FTO may contribute to pancreas islet β cells dysfunction and the inhibition of FTO activity is a potential target for the treatment of diabetes.
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Affiliation(s)
- Hong-Qi Fan
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- * E-mail:
| | - Wei He
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kuan-Feng Xu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi-Xiao Wang
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin-Yu Xu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Heng Chen
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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23
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McMurray F, Demetriades M, Aik W, Merkestein M, Kramer H, Andrew DS, Scudamore CL, Hough TA, Wells S, Ashcroft FM, McDonough MA, Schofield CJ, Cox RD. Pharmacological inhibition of FTO. PLoS One 2015; 10:e0121829. [PMID: 25830347 PMCID: PMC4382163 DOI: 10.1371/journal.pone.0121829] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/04/2015] [Indexed: 11/24/2022] Open
Abstract
In 2007, a genome wide association study identified a SNP in intron one of the gene encoding human FTO that was associated with increased body mass index. Homozygous risk allele carriers are on average three kg heavier than those homozygous for the protective allele. FTO is a DNA/RNA demethylase, however, how this function affects body weight, if at all, is unknown. Here we aimed to pharmacologically inhibit FTO to examine the effect of its demethylase function in vitro and in vivo as a first step in evaluating the therapeutic potential of FTO. We showed that IOX3, a known inhibitor of the HIF prolyl hydroxylases, decreased protein expression of FTO (in C2C12 cells) and reduced maximal respiration rate in vitro. However, FTO protein levels were not significantly altered by treatment of mice with IOX3 at 60 mg/kg every two days. This treatment did not affect body weight, or RER, but did significantly reduce bone mineral density and content and alter adipose tissue distribution. Future compounds designed to selectively inhibit FTO’s demethylase activity could be therapeutically useful for the treatment of obesity.
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Affiliation(s)
- Fiona McMurray
- MRC Harwell, Harwell Oxford Campus, Oxfordshire, Oxford, OX11 0RD, United Kingdom
- * E-mail:
| | - Marina Demetriades
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - WeiShen Aik
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Myrte Merkestein
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, United Kingdom
| | - Holger Kramer
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, United Kingdom
| | - Daniel S. Andrew
- MRC Harwell, Harwell Oxford Campus, Oxfordshire, Oxford, OX11 0RD, United Kingdom
| | - Cheryl L. Scudamore
- MRC Harwell, Harwell Oxford Campus, Oxfordshire, Oxford, OX11 0RD, United Kingdom
| | - Tertius A. Hough
- MRC Harwell, Harwell Oxford Campus, Oxfordshire, Oxford, OX11 0RD, United Kingdom
| | - Sara Wells
- MRC Harwell, Harwell Oxford Campus, Oxfordshire, Oxford, OX11 0RD, United Kingdom
| | - Frances M. Ashcroft
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, United Kingdom
| | - Michael A. McDonough
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Roger D. Cox
- MRC Harwell, Harwell Oxford Campus, Oxfordshire, Oxford, OX11 0RD, United Kingdom
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24
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Choi YG, Park CJ, Kim HE, Seo YJ, Lee AR, Choi SR, Lee SS, Lee JH. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase. J Biomol NMR 2015; 61:137-150. [PMID: 25575834 DOI: 10.1007/s10858-014-9895-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3(10)-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.
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Affiliation(s)
- Yong-Geun Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam, 660-701, Republic of Korea
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25
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Merkestein M, McTaggart JS, Lee S, Kramer HB, McMurray F, Lafond M, Boutens L, Cox R, Ashcroft FM. Changes in gene expression associated with FTO overexpression in mice. PLoS One 2014; 9:e97162. [PMID: 24842286 PMCID: PMC4026227 DOI: 10.1371/journal.pone.0097162] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/14/2014] [Indexed: 01/24/2023] Open
Abstract
Single nucleotide polymorphisms in the first intron of the fat-mass-and-obesity-related gene FTO are associated with increased body weight and adiposity. Increased expression of FTO is likely underlying this obesity phenotype, as mice with two additional copies of Fto (FTO-4 mice) exhibit increased adiposity and are hyperphagic. FTO is a demethylase of single stranded DNA and RNA, and one of its targets is the m6A modification in RNA, which might play a role in the regulation of gene expression. In this study, we aimed to examine the changes in gene expression that occur in FTO-4 mice in order to gain more insight into the underlying mechanisms by which FTO influences body weight and adiposity. Our results indicate an upregulation of anabolic pathways and a downregulation of catabolic pathways in FTO-4 mice. Interestingly, although genes involved in methylation were differentially regulated in skeletal muscle of FTO-4 mice, no effect of FTO overexpression on m6A methylation of total mRNA was detected.
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Affiliation(s)
- Myrte Merkestein
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - James S. McTaggart
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Sheena Lee
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Holger B. Kramer
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Fiona McMurray
- Medical Research Council Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxford, United Kingdom
| | - Mathilde Lafond
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Lily Boutens
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Roger Cox
- Medical Research Council Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxford, United Kingdom
| | - Frances M. Ashcroft
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
- * E-mail:
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26
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Xiao S, Li R, Diao H, Zhao F, Ye X. Progesterone receptor-mediated regulation of N-acetylneuraminate pyruvate lyase (NPL) in mouse uterine luminal epithelium and nonessential role of NPL in uterine function. PLoS One 2013; 8:e65607. [PMID: 23741500 PMCID: PMC3669229 DOI: 10.1371/journal.pone.0065607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 04/30/2013] [Indexed: 11/26/2022] Open
Abstract
N-acetylneuraminate pyruvate lyase (NPL) catalyzes N-acetylneuraminic acid, the predominant sialic acid. Microarray analysis of the periimplantation mouse uterine luminal epithelium (LE) revealed Npl being the most downregulated (35×) gene in the LE upon embryo implantation. In natural pregnant mouse uterus, Npl expression increased 56× from gestation day 0.5 (D0.5) to D2.5. In ovariectomized mouse uterus, Npl was significantly upregulated by progesterone (P4) but downregulated by 17β-estradiol (E2). Progesterone receptor (PR) antagonist RU486 blocked the upregulation of Npl in both preimplantation uterus and P4-treated ovariectomized uterus. Npl was specifically localized in the preimplantation D2.5 and D3.5 uterine LE. Since LE is essential for establishing uterine receptivity, it was hypothesized that NPL might play a critical role in uterine function, especially during embryo implantation. This hypothesis was tested in the Npl(−/−) mice. No significant differences were observed in the numbers of implantation sites on D4.5, gestation periods, litter sizes, and postnatal offspring growth between wild type (WT) and Npl(−/−) females from mating with WT males. Npl(−/−)xNpl(−/−) crosses produced comparable little sizes as that from WTxWT crosses. Comparable mRNA expression levels of several genes involved in sialic acid metabolism were observed in D3.5 uterus and uterine LE between WT and Npl(−/−), indicating no compensatory upregulation in the D3.5 Npl(−/−) uterus and LE. This study demonstrates PR-mediated dynamic expression of Npl in the periimplantation uterus and dispensable role of Npl in uterine function and embryo development.
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Affiliation(s)
- Shuo Xiao
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, United States of America
| | - Rong Li
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, United States of America
| | - Honglu Diao
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Reproductive Medical Center, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Fei Zhao
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, United States of America
| | - Xiaoqin Ye
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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27
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Sun Y, Song H, Li J, Li Y, Jiang M, Zhou J, Guo Z. Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily. PLoS One 2013; 8:e63095. [PMID: 23658663 PMCID: PMC3637252 DOI: 10.1371/journal.pone.0063095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 03/28/2013] [Indexed: 01/25/2023] Open
Abstract
1, 4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase is a typical crotonase fold enzyme with an implicated role of conformational changes in catalysis. We have identified these conformational changes by determining the structures of its Escherichia coli and Synechocystis sp. PCC6803 orthologues in complex with a product analog. The structural changes include the folding of an active-site loop into a β-hairpin and significant reorientation of a helix at the carboxy terminus. Interestingly, a new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand. Site-directed mutation of the amino acid residues involved in these ligand-induced interactions significantly diminishes the enzyme activity. These results suggest a catalytically essential induced-fit that is likely initiated by the enzyme-ligand interactions at the active site.
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Affiliation(s)
- Yueru Sun
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Haigang Song
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jie Li
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yan Li
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Ming Jiang
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (ZG); (JZ)
| | - Zhihong Guo
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- * E-mail: (ZG); (JZ)
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28
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Zhou C, Chen X, Feng J, Xiao D, Wuz Q, Zhu D. [Molecular cloning and characterization of a N-acetylneuraminate lyase gene from Staphylococcus hominis]. Sheng Wu Gong Cheng Xue Bao 2013; 29:480-489. [PMID: 23894821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A N-acetylneuraminate lyase gene (shnal) from Staphylococcus hominis was cloned into pET-28a and expressed in Escherichia coli BL21 (DE3) host cells. The recombinant enzyme was purified and characterized. It is a homotetrameric enzyme with the optimum pH at 8.0 for the cleavage direction and the optimum pH and temperature were 7.5 and 45 degrees C for the synthetic direction. The activity of ShNAL is stable when incubated at 45 degrees C for 2 h but decreased rapidly over 50 degrees C. ShNAL showed high stability in a wide range pH from 5.0 to 10.0 with the residual activity being > 70% when the enzyme was incubated in different buffers at 4 degrees C for 24 h. Its K(m) towards N-acetylneuraminic acid, pyruvate and ManNAc were (4.0 +/- 0.2) mmol/L, (35.1 +/- 3.2) mmol/L and (131.7 +/- 12.1) mmol/L, respectively. The k(cat)/K(m) value of Neu5Ac, ManNAc, and Pyr for ShNAL were 1.9 L/(mmol x s), 0.08 L/(mmol x s) and 0.08 L/(mmol x s), respectively.
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Affiliation(s)
- Chuanhua Zhou
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin 300457, China
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29
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Timms N, Windle CL, Polyakova A, Ault JR, Trinh CH, Pearson AR, Nelson A, Berry A. Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy. Chembiochem 2013; 14:474-81. [PMID: 23418011 PMCID: PMC3792637 DOI: 10.1002/cbic.201200714] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/29/2022]
Abstract
Chemical modification has been used to introduce the unnatural amino acid γ-thialysine in place of the catalytically important Lys165 in the enzyme N-acetylneuraminic acid lyase (NAL). The Staphylococcus aureus nanA gene, encoding NAL, was cloned and expressed in E. coli. The protein, purified in high yield, has all the properties expected of a class I NAL. The S. aureus NAL which contains no natural cysteine residues was subjected to site-directed mutagenesis to introduce a cysteine in place of Lys165 in the enzyme active site. Subsequently chemical mutagenesis completely converted the cysteine into γ-thialysine through dehydroalanine (Dha) as demonstrated by ESI-MS. Initial kinetic characterisation showed that the protein containing γ-thialysine regained 17 % of the wild-type activity. To understand the reason for this lower activity, we solved X-ray crystal structures of the wild-type S. aureus NAL, both in the absence of, and in complex with, pyruvate. We also report the structures of the K165C variant, and the K165-γ-thialysine enzyme in the presence, or absence, of pyruvate. These structures reveal that γ-thialysine in NAL is an excellent structural mimic of lysine. Measurement of the pH-activity profile of the thialysine modified enzyme revealed that its pH optimum is shifted from 7.4 to 6.8. At its optimum pH, the thialysine-containing enzyme showed almost 30 % of the activity of the wild-type enzyme at its pH optimum. The lowered activity and altered pH profile of the unnatural amino acid-containing enzyme can be rationalised by imbalances of the ionisation states of residues within the active site when the pK(a) of the residue at position 165 is perturbed by replacement with γ-thialysine. The results reveal the utility of chemical mutagenesis for the modification of enzyme active sites and the exquisite sensitivity of catalysis to the local structural and electrostatic environment in NAL.
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Affiliation(s)
- Nicole Timms
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Claire L Windle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Anna Polyakova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Chemistry, University of LeedsLeeds, LS2 9JT (UK)
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
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30
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North RA, Kessans SA, Atkinson SC, Suzuki H, Watson AJA, Burgess BR, Angley LM, Hudson AO, Varsani A, Griffin MDW, Fairbanks AJ, Dobson RCJ. Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:306-12. [PMID: 23519810 PMCID: PMC3606580 DOI: 10.1107/s1744309113003060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/30/2013] [Indexed: 01/13/2023]
Abstract
The enzyme N-acetylneuraminate lyase (EC 4.1.3.3) is involved in the metabolism of sialic acids. Specifically, the enzyme catalyzes the retro-aldol cleavage of N-acetylneuraminic acid to form N-acetyl-D-mannosamine and pyruvate. Sialic acids comprise a large family of nine-carbon amino sugars, all of which are derived from the parent compound N-acetylneuraminic acid. In recent years, N-acetylneuraminate lyase has received considerable attention from both mechanistic and structural viewpoints and has been recognized as a potential antimicrobial drug target. The N-acetylneuraminate lyase gene was cloned from methicillin-resistant Staphylococcus aureus genomic DNA, and recombinant protein was expressed and purified from Escherichia coli BL21 (DE3). The enzyme crystallized in a number of crystal forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.70 Å resolution in space group P2₁. Molecular replacement indicates the presence of eight monomers per asymmetric unit. Understanding the structural biology of N-acetylneuraminate lyase in pathogenic bacteria, such as methicillin-resistant S. aureus, will provide insights for the development of future antimicrobials.
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Affiliation(s)
- Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Andrew J. A. Watson
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Benjamin R. Burgess
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Lauren M. Angley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Arvind Varsani
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Antony J. Fairbanks
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
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31
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Sun W, Ji W, Li N, Tong P, Cheng J, He Y, Chen Y, Chen X, Wu J, Ouyang P, Xie J, Ying H. Construction and expression of a polycistronic plasmid encoding N-acetylglucosamine 2-epimerase and N-acetylneuraminic acid lyase simultaneously for production of N-acetylneuraminic acid. Bioresour Technol 2013; 130:23-9. [PMID: 23280182 DOI: 10.1016/j.biortech.2012.12.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 12/04/2012] [Accepted: 12/07/2012] [Indexed: 05/21/2023]
Abstract
Synthesis of N-acetylneuraminic acid (Neu5Ac) from N-acetylglucosamine (GlcNAc) and pyruvate was carried out by constructing and expressing a polycistronic plasmid encoding an N-acetylglucosamine 2-epimerase (AGE) gene and an N-acetylneuraminic acid lyase (Nal) gene simultaneously. Nal from Escherichia coli K12 and AGEs from Synechocystis sp. PCC 6803 (snAGE) and Anabaena sp. CH1 (anAGE) were used. And four polycistronic plasmids were constructed in which the positions of AGE gene differed with respect to Nal gene. Among these plasmids, pET-28a-Nal-anAGE with anAGE gene located next to Nal gene caused the production of the highest amount of Neu5Ac, generating 61.3g/L in 60h by whole-cell catalysis without the addition of ATP as AGE activator. And pET-28a-Nal-anAGE lowered anAGE's expression level, allowing it to fold properly. Thus, an inclusion-body-free E. coli strain capable of producing Neu5Ac by whole-cell catalysis with high yield and low cost was constructed in the present study.
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Affiliation(s)
- Wujin Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
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Riedel TJ, Knight J, Murray MS, Milliner DS, Holmes RP, Lowther WT. 4-Hydroxy-2-oxoglutarate aldolase inactivity in primary hyperoxaluria type 3 and glyoxylate reductase inhibition. Biochim Biophys Acta 2012; 1822:1544-52. [PMID: 22771891 PMCID: PMC3418427 DOI: 10.1016/j.bbadis.2012.06.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 01/25/2023]
Abstract
Mutations in the gene encoding for 4-hydroxy-2-oxoglutarate aldolase (HOGA) are associated with an excessive production of oxalate in Primary Hyperoxaluria type 3 (PH3). This enzyme is the final step of the hydroxyproline degradation pathway within the mitochondria and catalyzes the cleavage of 4-hydroxy-2-oxoglutarate (HOG) to pyruvate and glyoxylate. No analyses have been performed to assess the consequences of the mutations identified, particularly for those variants that produce either full-length or nearly full-length proteins. In this study, the expression, stability, and activity of nine PH3 human HOGA variants were examined. Using recombinant protein produced in Escherichia coli as well as transfected Chinese hamster ovary (CHO) cells, it was found that all nine PH3 variants are quite unstable, have a tendency to aggregate, and retain no measurable activity. A buildup of HOG was confirmed in the urine, sera and liver samples from PH3 patients. To determine how HOG is cleaved in the absence of HOGA activity, the ability of N-acetylneuraminate aldolase (NAL) to cleave HOG was evaluated. NAL showed minimal activity towards HOG. Whether the expected buildup of HOG in mitochondria could inhibit glyoxylate reductase (GR), the enzyme mutated in PH2, was also evaluated. GR was inhibited by HOG but not by 2-hydroxyglutarate or 2-oxoglutarate. Thus, one hypothetical component of the molecular basis for the excessive oxalate production in PH3 appears to be the inhibition of GR by HOG, resulting in a phenotype similar to PH2.
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Affiliation(s)
- Travis J. Riedel
- Center for Structural Biology and Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - John Knight
- Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Michael S. Murray
- Center for Structural Biology and Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Dawn S. Milliner
- Mayo Clinic Hyperoxaluria Center, Divisions of Nephrology and Hypertension, and Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | - Ross P. Holmes
- Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - W. Todd Lowther
- Center for Structural Biology and Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Jin RP, Hu YH, Sun BG, Zhang XH, Sun L. Edwardsiella tarda sialidase: pathogenicity involvement and vaccine potential. Fish Shellfish Immunol 2012; 33:514-521. [PMID: 22705341 DOI: 10.1016/j.fsi.2012.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 06/04/2012] [Accepted: 06/04/2012] [Indexed: 06/01/2023]
Abstract
Bacterial sialidases are a group of glycohydrolases that are known to play an important role in invasion of host cells and tissues. In this study, we examined in a model of Japanese flounder (Paralichthys olivaceus) the potential function of NanA, a sialidase from the fish pathogen Edwardsiella tarda. NanA is composed of 670 residues and shares low sequence identities with known bacterial sialidases. In silico analysis indicated that NanA possesses a sialidase domain and an autotransporter domain, the former containing five Asp-boxes, a RIP motif, and the conserved catalytic site of bacterial sialidases. Purified recombinant NanA (rNanA) corresponding to the sialidase domain exhibited glycohydrolase activity against sialic acid substrate in a manner that is pH and temperature dependent. Immunofluorescence microscopy showed binding of anti-rNanA antibodies to E. tarda, suggesting that NanA was localized on cell surface. Mutation of nanA caused drastic attenuation in the ability of E. tarda to disseminate into and colonize fish tissues and to induce mortality in infected fish. Likewise, cellular study showed that the nanA mutant was significantly impaired in the infectivity against cultured flounder cells. Immunoprotective analysis showed that rNanA in the form of a subunit vaccine conferred effective protection upon flounder against lethal E. tarda challenge. rNanA vaccination induced the production of specific serum antibodies, which enhanced complement-mediated bactericidal activity and reduced infection of E. tarda into flounder cells. Together these results indicate that NanA plays an important role in the pathogenesis of E. tarda and may be exploited for the control of E. tarda infection in aquaculture.
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Affiliation(s)
- Ren-ping Jin
- Department of Marine Biology, Ocean University of China, Qingdao, China
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García García MI, Sola Carvajal A, García Carmona F, Sánchez Ferrer Á. Characterization of a novel N-acetylneuraminate lyase from Staphylococcus carnosus TM300 and its application to N-acetylneuraminic acid production. J Agric Food Chem 2012; 60:7450-7456. [PMID: 22803763 DOI: 10.1021/jf3014102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The possibility of incorporating N-acetylneuraminic acid (Neu5Ac) in infant formulas and other functional foods has opened up the need to synthesize N-acetylneuraminic acid using N-acetylneuraminate lyases (NALs) by reversible aldol condensation of pyruvate and N-acetyl-d-mannosamine. Until now, NALs have been cloned from pathogenic microorganisms; however, this Article describes the expression and characterization of an N-acetylneuraminate lyase from the Staphylococcus carnosus TM300, a GRAS microorganism used in fermented meat. ScNAL showed a high level of expression in E. coli (403 mg L(-1) culture). This, combined with its simple two-step purification procedure, the highest recovery described to date (86%), its kinetic parameters, which are in the same order of magnitude as best reported NALs, and its optimum pH and temperature, make ScNAL a promising and cheap biocatalyst. To confirm its biotechnological potential, the Neu5Ac was synthesized in 3 h in simple industrial working conditions with a high degree of conversion (94%).
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Affiliation(s)
- María Inmaculada García García
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia , Campus Espinardo, E-30100 Murcia, Spain
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Pitman RT, Fong JT, Billman P, Puri N. Knockdown of the fat mass and obesity gene disrupts cellular energy balance in a cell-type specific manner. PLoS One 2012; 7:e38444. [PMID: 22675562 PMCID: PMC3367022 DOI: 10.1371/journal.pone.0038444] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 05/08/2012] [Indexed: 11/19/2022] Open
Abstract
Recent studies suggest that FTO variants strongly correlate with obesity and mainly influence energy intake with little effect on the basal metabolic rate. We suggest that FTO influences eating behavior by modulating intracellular energy levels and downstream signaling mechanisms which control energy intake and metabolism. Since FTO plays a particularly important role in adipocytes and in hypothalamic neurons, SH-SY5Y neuronal cells and 3T3-L1 adipocytes were used to understand how siRNA mediated knockdown of FTO expression alters cellular energy homeostasis. Cellular energy status was evaluated by measuring ATP levels using a luminescence assay and uptake of fluorescent glucose. FTO siRNA in SH-SY5Y cells mediated mRNA knockdown (−82%), increased ATP concentrations by up to 46% (P = 0.013) compared to controls, and decreased phosphorylation of AMPk and Akt in SH-SY5Y by −52% and −46% respectively as seen by immunoblotting. In contrast, FTO siRNA in 3T3-L1 cells decreased ATP concentration by −93% (p<0.0005), and increased AMPk and Akt phosphorylation by 204% and 70%, respectively suggesting that FTO mediates control of energy levels in a cell-type specific manner. Furthermore, glucose uptake was decreased in both SH-SY5Y (−51% p = 0.015) and 3T3-L1 cells (−30%, p = 0.0002). We also show that FTO knockdown decreases NPY mRNA expression in SH-SY5Y cells (−21%) through upregulation of pSTAT3 (118%). These results provide important evidence that FTO-variant linked obesity may be associated with altered metabolic functions through activation of downstream metabolic mediators including AMPk.
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Affiliation(s)
- Ryan T. Pitman
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, Illinois, United States of America
| | - Jason T. Fong
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, Illinois, United States of America
| | - Penny Billman
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, Illinois, United States of America
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford, Illinois, United States of America
- * E-mail:
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Redovniković IR, Textor S, Lisnić B, Gershenzon J. Expression pattern of the glucosinolate side chain biosynthetic genes MAM1 and MAM3 of Arabidopsis thaliana in different organs and developmental stages. Plant Physiol Biochem 2012; 53:77-83. [PMID: 22336876 DOI: 10.1016/j.plaphy.2012.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/20/2012] [Indexed: 05/26/2023]
Abstract
Aliphatic glucosinolates, secondary metabolites known to be involved in plant defence, make up the majority of the glucosinolate content of Arabidopsis thaliana, and their structural diversity arises in part from chain elongations of methionine before the formation of the glucosinolate core structure. The key enzymatic step in determining the length of the chain is the condensation of acetyl-coenzyme A with a series of ω-methylthio-2-oxoalkanoic acids, catalyzed by methylthioalkylmalate (MAM) synthases. The existence of two MAM synthases has been previously reported in A. thaliana, ecotype Columbia-0. MAM1 catalyses the condensation step of the first three elongation cycles while MAM3 catalyzes the condensation step of all six elongation cycles. We studied the expression patterns of MAM1 and MAM3 genes in different organs and developmental stages using promoter-GUS fusion lines and qRT-PCR. The promoter-GUS lines revealed MAM1 and MAM3 expression in varying degrees in all organs, but this was generally restricted to the phloem, except in wounded tissue where expression was general. No difference was found between the two genes. The qRT-PCR measurements showed that expression was generally highest in seedlings and vegetative parts at the reproductive phase, but low in flowers and fruits. Since high amounts of glucosinolates accumulate in flowers and fruits, these data indicate possible transport from vegetative to reproductive organs. The expression of MAM1 was different than that of MAM3 with MAM3 having relative more expression in seedlings and roots than MAM1.
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McTaggart JS, Lee S, Iberl M, Church C, Cox RD, Ashcroft FM. FTO is expressed in neurones throughout the brain and its expression is unaltered by fasting. PLoS One 2011; 6:e27968. [PMID: 22140494 PMCID: PMC3227617 DOI: 10.1371/journal.pone.0027968] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 10/28/2011] [Indexed: 11/20/2022] Open
Abstract
Single-nucleotide polymorphisms in the first intron of the ubiquitously expressed FTO gene are associated with obesity. Although the physiological functions of FTO remain unclear, food intake is often altered when Fto expression levels are manipulated. Furthermore, deletion of FTO from neurones alone has a similar effect on food intake to deletion of FTO in all tissues. These results indicate that FTO expression in the brain is particularly important. Considerable focus has been placed on the dynamic regulation of Fto mRNA expression in the hypothalamus after short-term (16–48 hour) fasting, but results have been controversial. There are no studies that quantify FTO protein levels across the brain, and assess its alteration following short-term fasting. Using immunohistochemistry, we found that FTO protein is widely expressed in mouse brain, and present in the majority of neurones. Using quantitative Western blotting and RT-qPCR we show that FTO protein and mRNA levels in the hypothalamus, cerebellum and rostral brain are relatively uniform, and levels in the brain are higher than in skeletal muscles of the lower limbs. Fasting for 18 hours does not alter the expression pattern, or levels, of FTO protein and mRNA. We further show that the majority of POMC neurones, which are critically involved in food intake regulation, also express FTO, but that the percentage of FTO-positive POMC neurones is not altered by fasting. In summary, we find no evidence that Fto/FTO expression is regulated by short-term (18-hour) fasting. Thus, it is unlikely that the hunger and increased post-fasting food intake caused by such food deprivation is driven by alterations in Fto/FTO expression. The widespread expression of FTO in neurones also suggests that physiological studies of this protein should not be limited to the hypothalamus.
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Affiliation(s)
- James S. McTaggart
- Department of Physiology, Anatomy and Genetics, OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
| | - Sheena Lee
- Department of Physiology, Anatomy and Genetics, OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
| | - Michaela Iberl
- Department of Physiology, Anatomy and Genetics, OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
| | - Chris Church
- OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- MRC Harwell, Metabolism and Inflammation, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Roger D. Cox
- OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- MRC Harwell, Metabolism and Inflammation, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Frances M. Ashcroft
- Department of Physiology, Anatomy and Genetics, OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- OXION Centre for Ion Channel Studies, Henry Wellcome Centre for Gene Function, Oxford, United Kingdom
- * E-mail:
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Bellinzoni M, Bastard K, Perret A, Zaparucha A, Perchat N, Vergne C, Wagner T, de Melo-Minardi RC, Artiguenave F, Cohen GN, Weissenbach J, Salanoubat M, Alzari PM. 3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation. J Biol Chem 2011; 286:27399-405. [PMID: 21632536 PMCID: PMC3149333 DOI: 10.1074/jbc.m111.253260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 05/17/2011] [Indexed: 11/06/2022] Open
Abstract
The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn(2+) cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the "domain of unknown function" DUF849.
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Affiliation(s)
- Marco Bellinzoni
- From the Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15
| | - Karine Bastard
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Alain Perret
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Anne Zaparucha
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Nadia Perchat
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Carine Vergne
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Tristan Wagner
- From the Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15
| | - Raquel C. de Melo-Minardi
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - François Artiguenave
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Georges N. Cohen
- the Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Jean Weissenbach
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Marcel Salanoubat
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Pedro M. Alzari
- From the Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15
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Olszewski PK, Fredriksson R, Eriksson JD, Mitra A, Radomska KJ, Gosnell BA, Solvang MN, Levine AS, Schiöth HB. Fto colocalizes with a satiety mediator oxytocin in the brain and upregulates oxytocin gene expression. Biochem Biophys Res Commun 2011; 408:422-6. [PMID: 21514276 DOI: 10.1016/j.bbrc.2011.04.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 04/07/2011] [Indexed: 12/31/2022]
Abstract
Single nucleotide polymorphisms in the fat mass and obesity-associated (FTO) gene have been associated with obesity in humans. Alterations in Fto expression in transgenic animals affect body weight, energy expenditure and food intake. Fto, a nuclear protein and proposed transcription co-factor, has been speculated to affect energy balance through a functional relationship with specific genes encoding feeding-related peptides. Herein, we employed double immunohistochemistry and showed that the majority of neurons synthesizing a satiety mediator, oxytocin, coexpress Fto in the brain of male and female mice. We then overexpressed Fto in a murine hypothalamic cell line and, using qPCR, detected a 50% increase in the level of oxytocin mRNA. Expression levels of several other feeding-related genes, including neuropeptide Y (NPY) and Agouti-related protein (AgRP), were unaffected by the FTO transfection. Addition of 10 and 100 nmol oxytocin to the cell culture medium did not affect Fto expression in hypothalamic cells. We conclude that Fto, a proposed transcription co-factor, influences expression of the gene encoding a satiety mediator, oxytocin.
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Affiliation(s)
- Pawel K Olszewski
- Department of Neuroscience, Functional Pharmacology, Uppsala University, 75124 Uppsala, Sweden.
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Montgomery C, Miziorko HM. Influence of multiple cysteines on human 3-hydroxy-3-methylglutaryl-CoA lyase activity and formation of inter-subunit adducts. Arch Biochem Biophys 2011; 511:48-55. [PMID: 21514269 DOI: 10.1016/j.abb.2011.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 04/05/2011] [Accepted: 04/07/2011] [Indexed: 11/18/2022]
Abstract
Human 3-hydroxy-3-methylglutaryl-CoA lyase catalyzes formation of acetyl-CoA and acetoacetate in a reaction that requires divalent cation and is stimulated by sulfhydryl protective reagents. The enzyme is a homodimer and inter-subunit adducts form in the absence of reducing agents or upon treatment with cysteine selective crosslinking agents. To address the influence of cysteines on enzyme activity and formation of inter-subunit and intra-subunit adducts, single serine substitutions have been engineered for each enzyme cysteine. Enzyme activity varies for each cysteine→serine mutant protein and different mutations have widely different effects on recovery of activity upon DTT treatment of non-reduced enzyme. These levels of enzyme activity do not strongly correlate with formation of inter-subunit adducts by these HMGCL mutants. C170S, C266S, and C323S proteins do not form inter-subunit disulfide adducts but such an adduct is restored in the C170S/C174S double mutant. Coexpression of HMGCL proteins encoded by C266S and C323S expression plasmids supports formation of a C266S/C323S heterodimer which does form a covalent inter-subunit adduct. These observations are interpreted in the context of competition between cysteines in formation of intra-subunit and inter-subunit heterodisulfide adducts.
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Affiliation(s)
- Christa Montgomery
- Division of Molecular Biology and Biochemistry, University of Missouri, Kansas City, MO 64110, United States
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41
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Bulfer SL, McQuade TJ, Larsen MJ, Trievel RC. Application of a high-throughput fluorescent acetyltransferase assay to identify inhibitors of homocitrate synthase. Anal Biochem 2011; 410:133-40. [PMID: 21073853 PMCID: PMC3115995 DOI: 10.1016/j.ab.2010.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 01/06/2023]
Abstract
Homocitrate synthase (HCS) catalyzes the first step of l-lysine biosynthesis in fungi by condensing acetyl-coenzyme A and 2-oxoglutarate to form 3R-homocitrate and coenzyme A. Due to its conservation in pathogenic fungi, HCS has been proposed as a candidate for antifungal drug design. Here we report the development and validation of a robust fluorescent assay for HCS that is amenable to high-throughput screening for inhibitors in vitro. Using this assay, Schizosaccharomyces pombe HCS was screened against a diverse library of approximately 41,000 small molecules. Following confirmation, counter screens, and dose-response analysis, we prioritized more than 100 compounds for further in vitro and in vivo analysis. This assay can be readily adapted to screen for small molecule modulators of other acyl-CoA-dependent acyltransferases or enzymes that generate a product with a free sulfhydryl group, including histone acetyltransferases, aminoglycoside N-acetyltransferases, thioesterases, and enzymes involved in lipid metabolism.
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Affiliation(s)
- Stacie L Bulfer
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Di Lorenzo M, Stork M, Crosa JH. Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrio anguillarum strain 775. Biometals 2011; 24:629-43. [PMID: 21286786 PMCID: PMC3123441 DOI: 10.1007/s10534-011-9416-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 01/10/2011] [Indexed: 11/30/2022]
Abstract
Anguibactin, the siderophore produced by Vibrioanguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. In this work we report the identification of a homologue of the plasmid-encoded angB on the chromosome of strain 775. The product of both genes harbor an isochorismate lyase (ICL) domain that converts isochorismic acid to 2,3-dihydro-2,3-dihydroxybenzoic acid, one of the steps of DHBA synthesis. We show in this work that both ICL domains are functional in the production of DHBA in V. anguillarum as well as in E. coli. Substitution by alanine of the aspartic acid residue in the active site of both ICL domains completely abolishes their isochorismate lyase activity in vivo. The two proteins also carry an aryl carrier protein (ArCP) domain. In contrast with the ICL domains only the plasmid encoded ArCP can participate in anguibactin production as determined by complementation analyses and site-directed mutagenesis in the active site of the plasmid encoded protein, S248A. The site-directed mutants, D37A in the ICL domain and S248A in the ArCP domain of the plasmid encoded AngB were also tested in vitro and clearly show the importance of each residue for the domain function and that each domain operates independently.
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Affiliation(s)
- Manuela Di Lorenzo
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageninegen, The Netherlands.
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de Kraker JW, Gershenzon J. From amino acid to glucosinolate biosynthesis: protein sequence changes in the evolution of methylthioalkylmalate synthase in Arabidopsis. Plant Cell 2011; 23:38-53. [PMID: 21205930 PMCID: PMC3051243 DOI: 10.1105/tpc.110.079269] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 12/02/2010] [Accepted: 12/16/2010] [Indexed: 05/18/2023]
Abstract
Methylthioalkylmalate synthase (MAM) catalyzes the committed step in the side chain elongation of Met, yielding important precursors for glucosinolate biosynthesis in Arabidopsis thaliana and other Brassicaceae species. MAM is believed to have evolved from isopropylmalate synthase (IPMS), an enzyme involved in Leu biosynthesis, based on phylogenetic analyses and an overlap of catalytic abilities. Here, we investigated the changes in protein structure that have occurred during the recruitment of IPMS from amino acid to glucosinolate metabolism. The major sequence difference between IPMS and MAM is the absence of 120 amino acids at the C-terminal end of MAM that constitute a regulatory domain for Leu-mediated feedback inhibition. Truncation of this domain in Arabidopsis IPMS2 results in loss of Leu feedback inhibition and quaternary structure, two features common to MAM enzymes, plus an 8.4-fold increase in the k(cat)/K(m) for a MAM substrate. Additional exchange of two amino acids in the active site resulted in a MAM-like enzyme that had little residual IPMS activity. Hence, combination of the loss of the regulatory domain and a few additional amino acid exchanges can explain the evolution of MAM from IPMS during its recruitment from primary to secondary metabolism.
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Bielohuby M, Menhofer D, Kirchner H, Stoehr BJM, Müller TD, Stock P, Hempel M, Stemmer K, Pfluger PT, Kienzle E, Christ B, Tschöp MH, Bidlingmaier M. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein. Am J Physiol Endocrinol Metab 2011; 300:E65-76. [PMID: 20943751 DOI: 10.1152/ajpendo.00478.2010] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, which only differed in the relative abundance of fat and protein (percentages of fat/protein in dry matter: LC-75/10; LC-65/20; LC-55/30). We subsequently measured body composition by nuclear magnetic resonance (NMR), analyzed blood chemistry and urine acetone content, evaluated gene expression changes of key ketogenic and gluconeogenic genes, and measured energy expenditure (EE) and locomotor activity (LA) during the first 4 days and after 3 wk on the respective diets. Compared with chow, rats fed with LC-75/10, LC-65/20, and LC-55/30 gained significantly less body weight. Reductions in body weight were mainly due to lower lean body mass and paralleled by significantly increased fat mass. Levels of β-hydroxybutyate were significantly elevated feeding LC-75/10 and LC-65/20 but decreased in parallel to reductions in dietary fat. Acetone was about 16-fold higher with LC-75/10 only (P < 0.001). In contrast, rats fed with LC-55/30 were not ketotic. Serum fibroblast growth factor-21, hepatic mRNA expression of hydroxymethylglutaryl-CoA-lyase, peroxisome proliferator-activated receptor-γ coactivator-1α, and peroxisome proliferator-activated receptor-γ coactivator-1β were increased with LC-75/10 only. Expression of phosphoenolpyruvate carboxykinase and glucose-6-phosphatase was downregulated by 50-70% in LC-HF groups. Furthermore, EE and LA were significantly decreased in all groups fed with LC-HFDs after 3 wk on the diets. In rats, the absence of dietary carbohydrates per se does not induce ketosis. LC-HFDs must be high in fat, but also low in protein contents to be clearly ketogenic. Independent of the macronutrient composition, LC-HFD-induced weight loss is not due to increased EE and LA.
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Affiliation(s)
- Maximilian Bielohuby
- Ludwig-Maximilians-University, Endocrine Research Unit, Ziemssenstrasse 1 80336, Munich, Germany.
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Abstract
Previous genome-wide association studies have identified a strong association between FTO and human obesity, although the mechanism by which FTO affects obesity remains unknown. Anew study suggests that the obesity risk alleles are gain-of-function.
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Peplinski K, Ehrenreich A, Döring C, Bömeke M, Steinbüchel A. Investigations on the microbial catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha H16 employing DNA microarrays. Appl Microbiol Biotechnol 2010; 88:1145-59. [PMID: 20924576 PMCID: PMC3128720 DOI: 10.1007/s00253-010-2915-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/05/2010] [Accepted: 09/08/2010] [Indexed: 11/27/2022]
Abstract
In this study, we have investigated the transcriptome of Ralstonia eutropha H16 during cultivation with gluconate in presence of 3,3′-thiodipropionic acid (TDP) or 3,3′-dithiodipropionic acid (DTDP) during biosynthesis of poly(3-hydroxybutyrate-co-3-mercaptopropionate). Genome-wide transcriptome analyses revealed several genes which were upregulated during cultivation in presence of the above-mentioned compounds. Obtained data strongly suggest that two ABC-type transport system and three probable extracytoplasmic solute receptors mediate the uptake of TDP and DTDP, respectively. In addition, genes encoding the hydrolase S-adenosylhomocysteinase AhcY and the thiol-disulfide interchange proteins DsbA, DsbD, and FrnE were upregulated during cultivation on DTDP and, in case of AhcY and FrnE, on TDP as well. It is assumed that the corresponding enzymes are involved in the cleavage of TDP and DTDP. Several genes of the fatty acid metabolism exhibited increased expression levels: genes encoding two acetyltransferases, a predicted acyltransferase, the acetoacetyl-CoA reductase phaB3, an enoyl-CoA hydratase as well as an acyl dehydratase, an acetyl-CoA synthetase, two acyl-CoA dehydrogenases, the methylmalonyl-CoA mutase encoded by sbm1 and sbm2 and phaY1 were detected. Furthermore, ORF H16_A0217 encoding a hypothetical protein and exhibiting 54% amino acids identical to an acyl-CoA thioesterase from Saccharomonospora viridis was found to be highly upregulated. As the 2-methylcitrate synthase PrpC exhibited a three- to fourfold increased activity in cells grown in presence of TDP or DTDP as compared to gluconate, metabolization of the cleavage products 3MP and 3-hydroxypropionate to propionyl-CoA is proposed.
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Affiliation(s)
- Katja Peplinski
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Armin Ehrenreich
- Institut für Mikrobiologie, Technische Universität München, Am Hochanger 4, 85354 Freising, Germany
| | - Christina Döring
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Mechthild Bömeke
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149 Münster, Germany
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Puisac B, Arnedo M, Casale CH, Ribate MP, Castiella T, Ramos FJ, Ribes A, Pérez-Cerdá C, Casals N, Hegardt FG, Pié J. Differential HMG-CoA lyase expression in human tissues provides clues about 3-hydroxy-3-methylglutaric aciduria. J Inherit Metab Dis 2010; 33:405-10. [PMID: 20532825 PMCID: PMC2903694 DOI: 10.1007/s10545-010-9097-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 03/30/2010] [Accepted: 04/01/2010] [Indexed: 12/31/2022]
Abstract
3-Hydroxy-3-methylglutaric aciduria is a rare human autosomal recessive disorder caused by deficiency of 3-hydroxy-3-methylglutaryl CoA lyase (HL). This mitochondrial enzyme catalyzes the common final step of leucine degradation and ketogenesis. Acute symptoms include vomiting, seizures and lethargy, accompanied by metabolic acidosis and hypoketotic hypoglycaemia. Such organs as the liver, brain, pancreas, and heart can also be involved. However, the pathophysiology of this disease is only partially understood. We measured mRNA levels, protein expression and enzyme activity of human HMG-CoA lyase from liver, kidney, pancreas, testis, heart, skeletal muscle, and brain. Surprisingly, the pancreas is, after the liver, the tissue with most HL activity. However, in heart and adult brain, HL activity was not detected in the mitochondrial fraction. These findings contribute to our understanding of the enzyme function and the consequences of its deficiency and suggest the need for assessment of pancreatic damage in these patients.
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Affiliation(s)
- Beatriz Puisac
- Laboratory of Clinical Genetics and Functional Genomics, Department of Pharmacology and Physiology, School of Medicine, University of Zaragoza, C/ Domingo Miral s/n, 50009 Zaragoza, Spain
| | - María Arnedo
- Laboratory of Clinical Genetics and Functional Genomics, Department of Pharmacology and Physiology, School of Medicine, University of Zaragoza, C/ Domingo Miral s/n, 50009 Zaragoza, Spain
| | - Cesar H. Casale
- Department of Molecular Biology, National University of Rio Cuarto, 5800 Rio Cuarto, Cordoba Argentina
| | - María Pilar Ribate
- Laboratory of Clinical Genetics and Functional Genomics, Department of Pharmacology and Physiology, School of Medicine, University of Zaragoza, C/ Domingo Miral s/n, 50009 Zaragoza, Spain
| | - Tomás Castiella
- Department of Pathology, School of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
| | - Feliciano J. Ramos
- Laboratory of Clinical Genetics and Functional Genomics, Department of Pharmacology and Physiology, School of Medicine, University of Zaragoza, C/ Domingo Miral s/n, 50009 Zaragoza, Spain
| | - Antonia Ribes
- Division of Inborn Errors of Metabolism (IBC), Department of Biochemistry and Molecular Genetics, Hospital Clinic and CIBERER, 08036 Barcelona, Spain
| | - Celia Pérez-Cerdá
- Department of Molecular Biology, Molecular Biological Center Severo Ochoa CSIC-UAM, University Autonoma of Madrid, CIBERER, 28049 Madrid, Spain
| | - Nuria Casals
- Department of Biochemistry and Molecular Biology, School of Health Sciences, International University of Catalonia, 08190 Sant Cugat, Barcelona Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de la Salud Carlos III, 28029 Madrid, Spain
| | - Fausto G. Hegardt
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de la Salud Carlos III, 28029 Madrid, Spain
| | - Juan Pié
- Laboratory of Clinical Genetics and Functional Genomics, Department of Pharmacology and Physiology, School of Medicine, University of Zaragoza, C/ Domingo Miral s/n, 50009 Zaragoza, Spain
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Bulfer SL, Scott EM, Pillus L, Trievel RC. Structural basis for L-lysine feedback inhibition of homocitrate synthase. J Biol Chem 2010; 285:10446-53. [PMID: 20089861 PMCID: PMC2856251 DOI: 10.1074/jbc.m109.094383] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 01/12/2010] [Indexed: 11/06/2022] Open
Abstract
The alpha-aminoadipate pathway of lysine biosynthesis is modulated at the transcriptional and biochemical levels by feedback inhibition. The first enzyme in the alpha-aminoadipate pathway, homocitrate synthase (HCS), is the target of the feedback regulation and is strongly inhibited by l-lysine. Here we report the structure of Schizosaccharomyces pombe HCS (SpHCS) in complex with l-lysine. The structure illustrates that the amino acid directly competes with the substrate 2-oxoglutarate for binding within the active site of HCS. Differential recognition of the substrate and inhibitor is achieved via a switch position within the (alpha/beta)(8) TIM barrel of the enzyme that can distinguish between the C5-carboxylate group of 2-oxoglutarate and the epsilon-ammonium group of l-lysine. In vitro and in vivo assays demonstrate that mutations of the switch residues, which interact with the l-lysine epsilon-ammonium group, abrogate feedback inhibition, as do substitutions of residues within the C-terminal domain that were identified in a previous study of l-lysine-insensitive HCS mutants in Saccharomyces cerevisiae. Together, these results yield new insights into the mechanism of feedback regulation of an enzyme central to lysine biosynthesis.
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Affiliation(s)
- Stacie L. Bulfer
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Erin M. Scott
- the Division of Biological Sciences and Moores UCSD Cancer Center, University of California San Diego, La Jolla, California 92093-0347
| | - Lorraine Pillus
- the Division of Biological Sciences and Moores UCSD Cancer Center, University of California San Diego, La Jolla, California 92093-0347
| | - Raymond C. Trievel
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
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Okada T, Tomita T, Wulandari AP, Kuzuyama T, Nishiyama M. Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus. J Biol Chem 2010; 285:4195-4205. [PMID: 19996101 PMCID: PMC2823558 DOI: 10.1074/jbc.m109.086330] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Indexed: 11/06/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes aldol-type condensation of acetyl coenzyme A (acetyl-CoA) and alpha-ketoglutarate (alpha-KG) to synthesize homocitrate (HC), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. As known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, HCS is regulated via feedback inhibition by the end product, lysine. Here, we determined the crystal structures of HCS from Thermus thermophilus complexed with alpha-KG, HC, or lysine. In the HC complex, the C1-carboxyl group of HC, which is derived from acetyl-CoA, is hydrogen-bonded with His-292* from another subunit (indicated by the asterisk), indicating direct involvement of this residue in the catalytic mechanism of HCS. The crystal structure of HCS complexed with lysine showed that lysine is bound to the active site with rearrangement of amino acid residues in the substrate-binding site, which accounts for the competitive inhibition by lysine with alpha-KG. Comparison between the structures suggests that His-72, which is conserved in lysine-sensitive HCSs and binds the C5-carboxyl group of alpha-KG, serves as a switch for the conformational change. Replacement of His-72 by leucine made HCS resistant to lysine inhibition, demonstrating the regulatory role of this conserved residue.
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Affiliation(s)
- Takuya Okada
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Takeo Tomita
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Asri P Wulandari
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and
| | - Makoto Nishiyama
- From the Biotechnology Research Center, University of Tokyo, Tokyo 113-8657 and; the RIKEN SPring-8 Center, Hyogo 679-5148, Japan.
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Yang WL, Rao R, Shen J, Feng L. [Cloning and expression of N-acetyl-D-neuraminic acid aldolase in Escherichia coli]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2010; 39:57-63. [PMID: 20175237 DOI: 10.3785/j.issn.1008-9292.2010.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To obtain the Escherichia coli strains expressing N-Acetyl-D-neuraminic acid aldolase (Neu5Ac aldolase). METHODS The gene (nanA) coding Neu5Ac aldolase was cloned from Escherichia coli C600, and the recombinant plasmid was sequenced and expressed in Escherichia coli. RESULTS Sequencing data revealed that the open reading frame was 894 bp and predicted to encode a protein consisting of 298 amino acids. The patterns of SDS-PAGE showed that the purified enzyme protein as a single protein band with a molecular weight of 33 kD, which was consistent with those reported in the reference. In the recombinant plasmid pRY1, the expression of nanA gene was controlled by the lac promoter with the induction of IPTG or lactose. The plasmid pRY3 was constructed, in which the nanA gene ws controlled by the tac promoter. The protein of Neu5Ac aldolase was constitutively expressed using the recombinant strain, E.coli DH5 alpha/pRY3 without induction of IPTG or lactose. The crystal was finally obtained with the efficiency of 90.2% of Neu5Ac. The HPLC indicated that the Neu5Ac crystal prepared in this experiment was same as Simga product. CONCLUSION The protein products expressed by two recombinant strains E.coli BL21(DE3)/pRY1 and DH5 alpha/pRY3 has the characteristics of Neu5Ac.
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Affiliation(s)
- Wen-liu Yang
- Shanghai Institute of Plant Physiology, Chinese Academy of Sciences, Shanghai, China
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