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Koyama H, Yamashita K, Narita H, Hiraoka H, Sasaki Y, Kamiya K, Yamakawa R, Kuniyoshi H, Piyapattanakorn S, Watabe S. Cloning and expression profile of the alanine aminotransferase gene from kuruma shrimp Penaeus japonicus exposed to different salinities. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:615-626. [PMID: 38529846 DOI: 10.1002/jez.2811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
Several crustaceans including shrimps change the amount of specific free amino acids to regulate the osmotic pressure in their bodies. Kuruma shrimp Penaeus japonicus also increases the concentration of alanine (Ala) in the abdominal muscle following the increase of environmental salinity. In the present study, to elucidate the mechanisms of changes in Ala accumulation of kuruma shrimp depending on salinity, we cloned the gene encoding alanine aminotransferase (ALT), an enzyme involved in Ala biosynthesis, and examined its expression profile. It was found that the full-length kuruma shrimp ALT1 cDNA consisted of 3,301 bp, encoding 514 amino acids, and that all amino acid residues important for ALT activity were conserved. Phylogenetic analysis also indicated that the ALT gene cloned in this study was classified as ALT1. Moreover, we examined the expression levels of the ALT1 gene in the abdominal muscle and the hepatopancreas of kuruma shrimp acclimated at 17‰, 34‰, and 40‰ salinities, resulting that the mRNA levels of the ALT1 genes in both tissues of the shrimp acclimated at 40‰ were significantly higher than those at 17‰ for 12 h (p < 0.05). The mRNA levels of the ALT1 gene in the abdominal muscle of the shrimp acclimated for more than 24 h tended to increase following the increase of environmental salinity. These results indicate that ALT1 is responsible for the increase of free Ala concentration in the abdominal muscle of kuruma shrimp to regulate osmotic pressure at high salinity.
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Affiliation(s)
- Hiroki Koyama
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Kyoko Yamashita
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hinano Narita
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Haruki Hiraoka
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yuka Sasaki
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kanna Kamiya
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Rin Yamakawa
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisato Kuniyoshi
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Sanit Piyapattanakorn
- Department of Marine Science, Center of Excellence for Marine Biotechnology, Chulalongkorn University, Bangkok, Thailand
| | - Shugo Watabe
- Department of Marine Biochemistry, School of Marine Biosciences, Kitasato University, Kanagawa, Japan
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2
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Göttlinger T, Lohaus G. Origin and Function of Amino Acids in Nectar and Nectaries of Pitcairnia Species with Particular Emphasis on Alanine and Glutamine. PLANTS (BASEL, SWITZERLAND) 2023; 13:23. [PMID: 38202331 PMCID: PMC10780904 DOI: 10.3390/plants13010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Floral nectar contains sugars and numerous other compounds, including amino acids, but little is known about their function and origin in nectar. Therefore, the amino acid, sugar, and inorganic ion concentrations, as well as the activity of alanine aminotransferase (AlaAT) and glutamine synthetase (GS) in nectar, nectaries, and leaves were analyzed in 30 Pitcairnia species. These data were compared with various floral traits, the pollinator type, and the phylogenetic relationships of the species to find possible causes for the high amino acid concentrations in the nectar of some species. The highest concentrations of amino acids (especially alanine) in nectar were found in species with reddish flowers. Furthermore, the concentration of amino acids in nectar and nectaries is determined through analyzing flower color/pollination type rather than phylogenetic relations. This study provides new insights into the origin of amino acids in nectar. The presence of almost all amino acids in nectar is mainly due to their transport in the phloem to the nectaries, with the exception of alanine, which is partially produced in nectaries. In addition, active regulatory mechanisms are required in nectaries that retain most of the amino acids and allow the selective secretion of specific amino acids, such as alanine.
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Affiliation(s)
- Thomas Göttlinger
- Molecular Plant Science and Plant Biochemistry, University of Wuppertal, 42119 Wuppertal, Germany;
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3
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Bakunova AK, Matyuta IO, Nikolaeva AY, Boyko KM, Popov VO, Bezsudnova EY. Mechanism of D-Cycloserine Inhibition of D-Amino Acid Transaminase from Haliscomenobacter hydrossis. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:687-697. [PMID: 37331714 DOI: 10.1134/s0006297923050115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 06/20/2023]
Abstract
D-cycloserine inhibits pyridoxal-5'-phosphate (PLP)-dependent enzymes. Inhibition effect depend on organization of the active site and mechanism of the catalyzed reaction. D-cycloserine interacts with the PLP form of the enzyme similarly to the substrate (amino acid), and this interaction is predominantly reversible. Several products of the interaction of PLP with D-cycloserine are known. For some enzymes formation of a stable aromatic product - hydroxyisoxazole-pyridoxamine-5'-phosphate at certain pH - leads to irreversible inhibition. The aim of this work was to study the mechanism of D-cycloserine inhibition of the PLP-dependent D-amino acid transaminase from Haliscomenobacter hydrossis. Spectral methods revealed several products of interaction of D-cycloserine with PLP in the active site of transaminase: oxime between PLP and β-aminooxy-D-alanine, ketimine between pyridoxamine-5'-phosphate and cyclic form of D-cycloserine, and pyridoxamine-5'-phosphate. Formation of hydroxyisoxazole-pyridoxamine-5'-phosphate was not observed. 3D structure of the complex with D-cycloserine was obtained using X-ray diffraction analysis. In the active site of transaminase, a ketimine adduct between pyridoxamine-5'-phosphate and D-cycloserine in the cyclic form was found. Ketimine occupied two positions interacting with different active site residues via hydrogen bonds. Using kinetic and spectral methods we have shown that D-cycloserine inhibition is reversible, and activity of the inhibited transaminase from H. hydrossis could be restored by adding excess of keto substrate or excess of cofactor. The obtained results confirm reversibility of the inhibition by D-cycloserine and interconversion of various adducts of D-cycloserine and PLP.
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Affiliation(s)
- Alina K Bakunova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Ilya O Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alena Yu Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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4
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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Chaves GL, Batista RS, Cunha JDS, Oliveira DB, da Silva MR, Pisani GFD, Selistre-de-Araújo HS, Zangirolami TC, da Silva AJ. Improving 3-hydroxypropionic acid production in E. coli by in silico prediction of new metabolic targets. N Biotechnol 2022; 72:80-88. [PMID: 36272546 DOI: 10.1016/j.nbt.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
3-Hydroxypropionic acid (3-HP) production from renewable feedstocks is of great interest in efforts to develop greener processes for obtaining this chemical platform. Here we report an engineered E. coli strain for 3-HP production through the β-alanine pathway. To obtain a new strain capable of producing 3-HP, the pathway was established by overexpressing the enzymes pyruvate aminotransferase, 3-hydroxyacid dehydrogenase, and L-aspartate-1-decarboxylase. Further increase of the 3-HP titer was achieved using evolutionary optimizations of a genome-scale metabolic model of E. coli containing the adopted pathway. From these optimizations, three non-intuitive targets for in vivo assessment were identified: L-alanine aminotransferase and alanine racemase overexpression, and L-valine transaminase knock-out. The implementation of these targets in the production strain resulted in a 40% increase in 3-HP titer. The strain was further engineered to overexpress phosphoenolpyruvate carboxylase, reaching 0.79 ± 0.02 g/L of 3-HP when grown using glucose. Surprisingly, this strain produced 63% more of the desired product when grown using a mixture of glucose and xylose (1:1, C-mol), and gene expression analysis showed that the cellular adjustment to consume xylose had a positive impact on 3-HP accumulation. Fed-batch culture with xylose feeding led to a final titer of 29.1 g/L. These results reinforce the value of computational methods in strain engineering, enabling the design of more efficient strategies to be assessed. Moreover, higher production of 3-HP under a sugar mixture condition points towards the development of bioprocesses based on renewable resources, such as hemicellulose hydrolysates.
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Affiliation(s)
- Gabriel Luz Chaves
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Raquel Salgado Batista
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Josivan de Sousa Cunha
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Davi Benedito Oliveira
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Mateus Ribeiro da Silva
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil
| | - Graziéle Fernanda Deriggi Pisani
- Department of Physiological Sciences, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | | | - Teresa Cristina Zangirolami
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Adilson José da Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil.
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6
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Le XH, Lee CP, Millar AH. The mitochondrial pyruvate carrier (MPC) complex mediates one of three pyruvate-supplying pathways that sustain Arabidopsis respiratory metabolism. THE PLANT CELL 2021; 33:2776-2793. [PMID: 34137858 PMCID: PMC8408480 DOI: 10.1093/plcell/koab148] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/19/2021] [Indexed: 05/03/2023]
Abstract
Malate oxidation by plant mitochondria enables the generation of both oxaloacetate and pyruvate for tricarboxylic acid (TCA) cycle function, potentially eliminating the need for pyruvate transport into mitochondria in plants. Here, we show that the absence of the mitochondrial pyruvate carrier 1 (MPC1) causes the co-commitment loss of its putative orthologs, MPC3/MPC4, and eliminates pyruvate transport into Arabidopsis thaliana mitochondria, proving it is essential for MPC complex function. While the loss of either MPC or mitochondrial pyruvate-generating NAD-malic enzyme (NAD-ME) did not cause vegetative phenotypes, the lack of both reduced plant growth and caused an increase in cellular pyruvate levels, indicating a block in respiratory metabolism, and elevated the levels of branched-chain amino acids at night, a sign of alterative substrate provision for respiration. 13C-pyruvate feeding of leaves lacking MPC showed metabolic homeostasis was largely maintained except for alanine and glutamate, indicating that transamination contributes to the restoration of the metabolic network to an operating equilibrium by delivering pyruvate independently of MPC into the matrix. Inhibition of alanine aminotransferases when MPC1 is absent resulted in extremely retarded phenotypes in Arabidopsis, suggesting all pyruvate-supplying enzymes work synergistically to support the TCA cycle for sustained plant growth.
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Affiliation(s)
- Xuyen H. Le
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Chun-Pong Lee
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - A. Harvey Millar
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
- Author for correspondence:
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7
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Solhaug EM, Roy R, Venterea RT, Carter CJ. The role of alanine synthesis and nitrate-induced nitric oxide production during hypoxia stress in Cucurbita pepo nectaries. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:580-599. [PMID: 33119149 DOI: 10.1111/tpj.15055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/09/2020] [Accepted: 10/21/2020] [Indexed: 05/19/2023]
Abstract
Floral nectar is a sugary solution produced by nectaries to attract and reward pollinators. Nectar metabolites, such as sugars, are synthesized within the nectary during secretion from both pre-stored and direct phloem-derived precursors. In addition to sugars, nectars contain nitrogenous compounds such as amino acids; however, little is known about the role(s) of nitrogen (N) compounds in nectary function. In this study, we investigated N metabolism in Cucurbita pepo (squash) floral nectaries in order to understand how various N-containing compounds are produced and determine the role of N metabolism in nectar secretion. The expression and activity of key enzymes involved in primary N assimilation, including nitrate reductase (NR) and alanine aminotransferase (AlaAT), were induced during secretion in C. pepo nectaries. Alanine (Ala) accumulated to about 35% of total amino acids in nectaries and nectar during peak secretion; however, alteration of vascular nitrate supply had no impact on Ala accumulation during secretion, suggesting that nectar(y) amino acids are produced by precursors other than nitrate. In addition, nitric oxide (NO) is produced from nitrate and nitrite, at least partially by NR, in nectaries and nectar. Hypoxia-related processes are induced in nectaries during secretion, including lactic acid and ethanolic fermentation. Finally, treatments that alter nitrate supply affect levels of hypoxic metabolites, nectar volume and nectar sugar composition. The induction of N metabolism in C. pepo nectaries thus plays an important role in the synthesis and secretion of nectar sugar.
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Affiliation(s)
- Erik M Solhaug
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Rahul Roy
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Rodney T Venterea
- Soil and Water Management Research Unit, Agricultural Research Service, USDA, St Paul, MN, 55108, USA
| | - Clay J Carter
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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8
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Osire T, Yang T, Xu M, Zhang X, Long M, Ngon NKA, Rao Z. Integrated gene engineering synergistically improved substrate-product transport, cofactor generation and gene translation for cadaverine biosynthesis in E. coli. Int J Biol Macromol 2020; 169:8-17. [PMID: 33301846 DOI: 10.1016/j.ijbiomac.2020.12.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022]
Abstract
Several approaches for efficient production of cadaverine, a bio-based diamine with broad industrial applications have been explored. Here, Serratia marcescens lysine decarboxylase (SmcadA) was expressed in E. coli; mild surfactants added in biotransformation reactions; the E. coli native lysine/cadaverine antiporter cadB, E. coli pyridoxal kinases pdxK and pdxY overexpressed and synthetic RBS libraries screened. Addition of mild surfactants and overexpression of antiporter cadB increased cadaverine biosynthesis of SmcadA. Moreover, expression of pdxY gene yielded 19.82 g/L in a reaction mixture containing added cofactor precursor pyridoxal (PL), without adding exogenous PLP. The screened synthetic RBS1, applied to fully exploit pdxY gene expression, ultimately resulted in PLP self-sufficiency, producing 27.02 g/L cadaverine using strain T7R1_PL. To boost SmcadA catalytic activity, the designed mutants Arg595Lys and Ser512Ala had significantly improved cumulative cadaverine production of 219.54 and 201.79 g/L respectively compared to the wild-type WT (181.62 g/L), after 20 h reaction. Finally, molecular dynamics simulations for WT and variants indicated that increased flexibility at the binding sites of the protein enhanced residue-ligand interactions, contributing to high cadaverine synthesis. This work demonstrates potential of harnessing different pull factors through integrated gene engineering of efficient biocatalysts and gaining insight into the mechanisms involved through MD simulations.
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Affiliation(s)
- Tolbert Osire
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China
| | - Noelle Kewang A Ngon
- National Engineering Laboratory for Cereal Fermentation Technology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 LiHu Boulevard, Wuxi 214122, Jiangsu, China.
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9
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Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Nat Commun 2020; 11:1960. [PMID: 32327655 PMCID: PMC7181641 DOI: 10.1038/s41467-020-15876-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.
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10
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Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
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Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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11
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Blätke MA, Bräutigam A. Evolution of C4 photosynthesis predicted by constraint-based modelling. eLife 2019; 8:e49305. [PMID: 31799932 PMCID: PMC6905489 DOI: 10.7554/elife.49305] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/08/2019] [Indexed: 01/03/2023] Open
Abstract
Constraint-based modelling (CBM) is a powerful tool for the analysis of evolutionary trajectories. Evolution, especially evolution in the distant past, is not easily accessible to laboratory experimentation. Modelling can provide a window into evolutionary processes by allowing the examination of selective pressures which lead to particular optimal solutions in the model. To study the evolution of C4 photosynthesis from a ground state of C3 photosynthesis, we initially construct a C3 model. After duplication into two cells to reflect typical C4 leaf architecture, we allow the model to predict the optimal metabolic solution under various conditions. The model thus identifies resource limitation in conjunction with high photorespiratory flux as a selective pressure relevant to the evolution of C4. It also predicts that light availability and distribution play a role in guiding the evolutionary choice of possible decarboxylation enzymes. The data shows evolutionary CBM in eukaryotes predicts molecular evolution with precision.
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Affiliation(s)
- Mary-Ann Blätke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Andrea Bräutigam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Computational Biology, Faculty of Biology, Bielefeld University, UniversitätsstraßeBielefeldGermany
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12
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Abstract
Stereospecific generation of α-amino ketones from common α-amino acids is difficult to achieve, often employing superstoichiometric alkylating reagents and requiring multiple protecting group manipulations. In contrast, the α-oxoamine synthase protein family performs this transformation stereospecifically in a single step without the need for protecting groups. Herein, we detail the characterization of the 8-amino-7-oxononanoate synthase (AONS) domain of the four-domain polyketide-like synthase SxtA, which natively mediates the formation of the ethyl ketone derivative of arginine. The function of each of the four domains is elucidated, leading to a revised proposal for the initiation of saxitoxin biosynthesis, a potent neurotoxin. We also demonstrate the synthetic potential of SxtA AONS, which is applied to the synthesis of a panel of novel α-amino ketones.
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Affiliation(s)
- Stephanie W Chun
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA.,Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA.,Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
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13
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Liang J, Han Q, Tan Y, Ding H, Li J. Current Advances on Structure-Function Relationships of Pyridoxal 5'-Phosphate-Dependent Enzymes. Front Mol Biosci 2019; 6:4. [PMID: 30891451 PMCID: PMC6411801 DOI: 10.3389/fmolb.2019.00004] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 01/25/2019] [Indexed: 12/23/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP) functions as a coenzyme in many enzymatic processes, including decarboxylation, deamination, transamination, racemization, and others. Enzymes, requiring PLP, are commonly termed PLP-dependent enzymes, and they are widely involved in crucial cellular metabolic pathways in most of (if not all) living organisms. The chemical mechanisms for PLP-mediated reactions have been well elaborated and accepted with an emphasis on the pure chemical steps, but how the chemical steps are processed by enzymes, especially by functions of active site residues, are not fully elucidated. Furthermore, the specific mechanism of an enzyme in relation to the one for a similar class of enzymes seems scarcely described or discussed. This discussion aims to link the specific mechanism described for the individual enzyme to the same types of enzymes from different species with aminotransferases, decarboxylases, racemase, aldolase, cystathionine β-synthase, aromatic phenylacetaldehyde synthase, et al. as models. The structural factors that contribute to the reaction mechanisms, particularly active site residues critical for dictating the reaction specificity, are summarized in this review.
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Affiliation(s)
- Jing Liang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Institute of Agriculture and Forestry, Hainan University, Haikou, China
| | - Yang Tan
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haizhen Ding
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jianyong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Pala ZR, Saxena V, Saggu GS, Mani SK, Pareek RP, Kochar SK, Kochar DK, Garg S. Functional analysis of iron-sulfur cluster biogenesis (SUF pathway) from Plasmodium vivax clinical isolates. Exp Parasitol 2019; 198:53-62. [PMID: 30721667 DOI: 10.1016/j.exppara.2019.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/29/2018] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
Abstract
Iron-sulfur (Fe-S) clusters are critical metallo-cofactors required for cell function. Assembly of these cofactors is a carefully controlled process in cells to avoid toxicity from free iron and sulfide. In Plasmodium, two pathways for these Fe-S cluster biogenesis have been reported; ISC pathway in the mitochondria and SUF pathway functional in the apicoplast. Amongst these, SUF pathway is reported essential for the apicoplast maintenance and parasite survival. Many of its components have been studied from P. falciparum and P. berghei in recent years, still few queries remain to be addressed; one of them being the assembly and transfer of Fe-S clusters. In this study, using P. vivax clinical isolates, we have shown the in vitro interaction of SUF pathway proteins SufS and SufE responsible for sulfur mobilization in the apicoplast. The sulfur mobilized by the SufSE complex assembles on the scaffold protein PvSufA along with iron provided by the external source. Here, we demonstrate in vitro transfer of these labile Fe-S clusters from the scaffold protein on to an apo-protein, PvIspG (a protein involved in penultimate step of Isoprenoids biosynthesis pathway) in order to provide an insight into the interaction of different components for the biosynthesis and transfer of Fe-S clusters. Our analysis indicate that inspite of the presence of variations in pathway proteins, the overall pathway remains well conserved in the clinical isolates when compared to that reported in lab strains.
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Affiliation(s)
- Zarna Rajeshkumar Pala
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India.
| | - Gagandeep Singh Saggu
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Satish Kailasam Mani
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Rajendra Prasad Pareek
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Sanjay Kumar Kochar
- Department of Medicine, Sardar Patel Medical College, Bikaner, Rajasthan, India
| | - Dhanpat Kumar Kochar
- Department of Medicine, Rajasthan University of Health Sciences, Jaipur, Rajasthan, India
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India.
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15
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Nakamura S. Grain dormancy genes responsible for preventing pre-harvest sprouting in barley and wheat. BREEDING SCIENCE 2018; 68:295-304. [PMID: 30100796 PMCID: PMC6081298 DOI: 10.1270/jsbbs.17138] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/31/2018] [Indexed: 05/04/2023]
Abstract
Pre-harvest sprouting (PHS) remains a long-standing problem for the production of barley (Hordeum vulgare) and wheat (Triticum aestivum) worldwide. Grain dormancy, a key trait for the prevention of PHS, controls the timing of germination. Discovery of the causal sequence polymorphisms (CSPs) that produce naturally occurring variation in dormancy will help improve PHS tolerance. The identification of CSPs for dormancy remains difficult, especially for barley and wheat, because they are the last major cereals to have their genomes sequenced. However, recent work has identified several important CSPs that play pivotal roles in fine-tuning the dormancy levels in barley and wheat cultivars. This review summarizes these recent advances, which can be directly applied in breeding programs to improve PHS tolerance. These recent findings indicate the possibility that barley and wheat cultivars grown in East Asia, where much rain falls during the harvest season, will be rich sources of alleles that confer strong dormancy, since these cultivars have been selected to cope with the regional climate. The newly discovered dormant alleles will be useful for improving PHS tolerance around the world, just as Reduced-height (Rht) alleles from Japanese wheat varieties contributed to yield increases for the Green Revolution.
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16
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Rojas-Ortega E, Aguirre-López B, Reyes-Vivas H, González-Andrade M, Campero-Basaldúa JC, Pardo JP, González A. Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions. Front Microbiol 2018; 9:944. [PMID: 29867852 PMCID: PMC5960717 DOI: 10.3389/fmicb.2018.00944] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/23/2018] [Indexed: 12/16/2022] Open
Abstract
Saccharomyces cerevisiae arose from an interspecies hybridization (allopolyploidiza-tion), followed by Whole Genome Duplication. Diversification analysis of ScAlt1/ScAlt2 indicated that while ScAlt1 is an alanine transaminase, ScAlt2 lost this activity, constituting an example in which one of the members of the gene pair lacks the apparent ancestral physiological role. This paper analyzes structural organization and pyridoxal phosphate (PLP) binding properties of ScAlt1 and ScAlt2 indicating functional diversification could have determined loss of ScAlt2 alanine transaminase activity and thus its role in alanine metabolism. It was found that ScAlt1 and ScAlt2 are dimeric enzymes harboring 67% identity and intact conservation of the catalytic residues, with very similar structures. However, tertiary structure analysis indicated that ScAlt2 has a more open conformation than that of ScAlt1 so that under physiological conditions, while PLP interaction with ScAlt1 allows the formation of two tautomeric PLP isomers (enolimine and ketoenamine) ScAlt2 preferentially forms the ketoenamine PLP tautomer, indicating a modified polarity of the active sites which affect the interaction of PLP with these proteins, that could result in lack of alanine transaminase activity in ScAlt2. The fact that ScAlt2 forms a catalytically active Schiff base with PLP and its position in an independent clade in "sensu strictu" yeasts suggests this protein has a yet undiscovered physiological function.
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Affiliation(s)
- Erendira Rojas-Ortega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City, Mexico
| | - Martín González-Andrade
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jose C Campero-Basaldúa
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan P Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Liu H, Han Y, Li J, Qin M, Fu Q, Wang C, Liu Z. 18F-Alanine Derivative Serves as an ASCT2 Marker for Cancer Imaging. Mol Pharm 2018; 15:947-954. [DOI: 10.1021/acs.molpharmaceut.7b00884] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hui Liu
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yuxiang Han
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiyuan Li
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ming Qin
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qunfeng Fu
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunhong Wang
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhibo Liu
- Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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18
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Sekula B, Ruszkowski M, Dauter Z. Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:876. [PMID: 30034403 PMCID: PMC6043687 DOI: 10.3389/fpls.2018.00876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/05/2018] [Indexed: 05/17/2023]
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 3-phosphohydroxypyruvate (3-PHP) to 3-phosphoserine (PSer) in an L-glutamate (Glu)-linked reversible transamination reaction. This process proceeds through a bimolecular ping-pong mechanism and in plants takes place in plastids. It is a part of the phosphorylated pathway of serine biosynthesis, one of three routes recognized in plant organisms that yield serine. In this three-step biotransformation, 3-phosphoglycerate (3-PGA) delivered from plastidial glycolysis and Calvin cycle is oxidized by 3-PGA dehydrogenase. Then, 3-PHP is subjected to transamination with Glu to yield PSer and α-ketoglutarate (AKG). In the last step of the pathway, serine is produced by the action of phosphoserine phosphatase. Here we present the structural characterization of PSAT isoform 1 from Arabidopsis thaliana (AtPSAT1), a dimeric S-shaped protein that truncated of its 71-residue-long chloroplast-targeting signal peptide. Three crystal structures of AtPSAT1 captured at different stages of the reaction: (i) internal aldimine state with PLP covalently bound to the catalytic K265, (ii) holoenzyme in complex with pyridoxamine-5'-phosphate (PMP) after transfer of the amino group from glutamate and (iii) the geminal diamine intermediate state wherein the cofactor is covalently bound to both, K265 and PSer. These snapshots over the course of the reaction present detailed architecture of AtPSAT1 and allow for the comparison of this plant enzyme with other PSATs. Conformational changes of the protein during the catalytic event concern (i) the neighborhood of K265 when the amino group is transferred to the cofactor to form PMP and (ii) movement of the gate-keeping loop (residues 391-401) upon binding of 3-PHP and PSer. The latter conformational change of the loop may likely be one of key elements that regulate catalytic activity of PSATs.
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19
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Peña PA, Quach T, Sato S, Ge Z, Nersesian N, Dweikat IM, Soundararajan M, Clemente T. Molecular and phenotypic characterization of transgenic wheat and sorghum events expressing the barley alanine aminotransferase. PLANTA 2017; 246:1097-1107. [PMID: 28801748 DOI: 10.1007/s00425-017-2753-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/02/2017] [Indexed: 05/03/2023]
Abstract
The expression of a barley alanine aminotransferase gene impacts agronomic outcomes in a C3 crop, wheat. The use of nitrogen-based fertilizers has become one of the major agronomic inputs in crop production systems. Strategies to enhance nitrogen assimilation and flux in planta are being pursued through the introduction of novel genetic alleles. Here an Agrobacterium-mediated approach was employed to introduce the alanine aminotransferase from barley (Hordeum vulgare), HvAlaAT, into wheat (Triticum aestivum) and sorghum (Sorghum bicolor), regulated by either constitutive or root preferred promoter elements. Plants harboring the transgenic HvAlaAT alleles displayed increased alanine aminotransferase (alt) activity. The enhanced alt activity impacted height, tillering and significantly boosted vegetative biomass relative to controls in wheat evaluated under hydroponic conditions, where the phenotypic outcome across these parameters varied relative to time of year study was conducted. Constitutive expression of HvAlaAT translated to elevation in wheat grain yield under field conditions. In sorghum, expression of HvAlaAT enhanced enzymatic activity, but no changes in phenotypic outcomes were observed. Taken together these results suggest that positive agronomic outcomes can be achieved through enhanced alt activity in a C3 crop, wheat. However, the variability observed across experiments under greenhouse conditions implies the phenotypic outcomes imparted by the HvAlaAT allele in wheat may be impacted by environment.
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Affiliation(s)
- Pamela A Peña
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Truyen Quach
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Shirley Sato
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Zhengxiang Ge
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Natalya Nersesian
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | | | - Tom Clemente
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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20
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Bouzon M, Perret A, Loreau O, Delmas V, Perchat N, Weissenbach J, Taran F, Marlière P. A Synthetic Alternative to Canonical One-Carbon Metabolism. ACS Synth Biol 2017; 6:1520-1533. [PMID: 28467058 DOI: 10.1021/acssynbio.7b00029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One-carbon metabolism is an ubiquitous metabolic pathway that encompasses the reactions transferring formyl-, hydroxymethyl- and methyl-groups bound to tetrahydrofolate for the synthesis of purine nucleotides, thymidylate, methionine and dehydropantoate, the precursor of coenzyme A. An alternative cyclic pathway was designed that substitutes 4-hydroxy-2-oxobutanoic acid (HOB), a compound absent from known metabolism, for the amino acids serine and glycine as one-carbon donors. It involves two novel reactions, the transamination of l-homoserine and the transfer of a one-carbon unit from HOB to tetrahydrofolate releasing pyruvate as coproduct. Since canonical reactions regenerate l-homoserine from pyruvate by carboxylation and subsequent reduction, every one-carbon moiety made available for anabolic reactions originates from CO2. The HOB-dependent pathway was established in an Escherichia coli auxotroph selected for prototrophy using long-term cultivation protocols. Genetic, metabolic and biochemical evidence support the emergence of a functional HOB-dependent one-carbon pathway achieved with the recruitment of the two enzymes l-homoserine transaminase and HOB-hydroxymethyltransferase and of HOB as an essential metabolic intermediate. Escherichia coli biochemical reprogramming was achieved by minimally altering canonical metabolism and leveraging on natural selection mechanisms, thereby launching the resulting strain on an evolutionary trajectory diverging from all known extant species.
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Affiliation(s)
- Madeleine Bouzon
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Alain Perret
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | | | - Valérie Delmas
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Nadia Perchat
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Jean Weissenbach
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | | | - Philippe Marlière
- Institute of Systems and Synthetic Biology, Génopole, 5 rue Desbruères, 91030 Evry Cedex, France
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Onishi K, Yamane M, Yamaji N, Tokui M, Kanamori H, Wu J, Komatsuda T, Sato K. Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes. BMC Genomics 2017; 18:497. [PMID: 28662630 PMCID: PMC5492916 DOI: 10.1186/s12864-017-3880-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS We identified orthologous sequences of the major Hordeum vulgare (barley) seed dormancy gene Qsd1 in hexaploid wheat cv. Chinese Spring by performing genomic clone sequencing, followed by transcript sequencing. We detected 13 non-synonymous amino acid substitutions among the three sub-genomes of wheat and found that the Qsd1 sequence in the B sub-genome is most similar to that in barley. The Qsd1 sequence in A genome diploid wheat is highly similar to that in the hexaploid A sub-genome. Wheat orthologs of Qsd1 showed closer similarities to barley Qsd1 than did those of other accessions in the DNA database. Like barley Qsd1, all three wheat Qsd1s showed embryo-specific gene expression patterns, indicating that barley and wheat Qsd1 share an orthologous origin. The alignment of four hexaploid wheat cultivars indicated that the amino acid sequences of three spring cultivars, Chinese Spring, Haruyo Koi, and Fielder, are exactly the same in each sub-genome. Only Kitahonami has three amino acid substitutions at the B sub-genome. CONCLUSIONS Kitahonami has a longer seed dormancy period than does Chinese Spring. Sequence polymorphisms between Chiniese Spring and Kitahonami in the B sub-genome may underlie the phenotypic differences in seed dormancy between these hexaploid wheat cultivars.
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Affiliation(s)
- Kazumitsu Onishi
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Miki Yamane
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nami Yamaji
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Mayumi Tokui
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8634, Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8634, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8634, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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A Homozygous Mutation in GPT2 Associated with Nonsyndromic Intellectual Disability in a Consanguineous Family from Costa Rica. JIMD Rep 2017. [PMID: 28130718 DOI: 10.1007/8904_2016_40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Intellectual disability is a highly heterogeneous disease that affects the central nervous system and impairs patients' ability to function independently. Despite multiples genes involved in the etiology of disease, most of the genetic background is yet to be discovered. We used runs of homozygosity and exome sequencing to study a large Costa Rican family with four individuals affected with severe intellectual disability and found a novel homozygous missense mutation, p. 96G>R, c. 286G>A, in all affected individuals. This gene encodes for a pyridoxal enzyme involved in the production of the neurotransmitter glutamate and is highly expressed in the white matter of brain and cerebellum. Protein modeling of GPT2 predicted that the mutation is located in a loop where the substrate binds to the active site of the enzyme, therefore, suggesting that the catalytic activity is impaired. With our report of a second mutation we fortify the importance of GPT2 as a novel cause of autosomal recessive nonsyndromic intellectual disability and support the premise that GPT2 is highly important for the neurodevelopment of the central nervous system. SYNOPSIS The mutation p. 96G>R c. 286G>A in GPT2, located in a loop where the substrate binds to the active site of the enzyme, fortifies the importance of GPT2 in the pathogenesis of nonsyndromic intellectual disability.
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23
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Sato K, Yamane M, Yamaji N, Kanamori H, Tagiri A, Schwerdt JG, Fincher GB, Matsumoto T, Takeda K, Komatsuda T. Alanine aminotransferase controls seed dormancy in barley. Nat Commun 2016; 7:11625. [PMID: 27188711 PMCID: PMC4873977 DOI: 10.1038/ncomms11625] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/13/2016] [Indexed: 01/08/2023] Open
Abstract
Dormancy allows wild barley grains to survive dry summers in the Near East. After domestication, barley was selected for shorter dormancy periods. Here we isolate the major seed dormancy gene qsd1 from wild barley, which encodes an alanine aminotransferase (AlaAT). The seed dormancy gene is expressed specifically in the embryo. The AlaAT isoenzymes encoded by the long and short dormancy alleles differ in a single amino acid residue. The reduced dormancy allele Qsd1 evolved from barleys that were first domesticated in the southern Levant and had the long dormancy qsd1 allele that can be traced back to wild barleys. The reduced dormancy mutation likely contributed to the enhanced performance of barley in industrial applications such as beer and whisky production, which involve controlled germination. In contrast, the long dormancy allele might be used to control pre-harvest sprouting in higher rainfall areas to enhance global adaptation of barley. Seed dormancy allows wild barley grains to survive dry summers in the Near East but has been selected against for industrial applications such as beer and whisky production that require quicker germination. Here Sato et al. show that Qsd1 is a major seed dormancy gene in barley and encodes an alanine aminotransferase.
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Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Miki Yamane
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Nami Yamaji
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Julian G Schwerdt
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Kazuyoshi Takeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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24
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McAllister CH, Good AG. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana. PLoS One 2015; 10:e0121830. [PMID: 25830496 PMCID: PMC4382294 DOI: 10.1371/journal.pone.0121830] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/04/2015] [Indexed: 01/08/2023] Open
Abstract
Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.
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Affiliation(s)
- Chandra H. McAllister
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- * E-mail:
| | - Allen G. Good
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Peña-Soler E, Fernandez FJ, López-Estepa M, Garces F, Richardson AJ, Quintana JF, Rudd KE, Coll M, Vega MC. Structural analysis and mutant growth properties reveal distinctive enzymatic and cellular roles for the three major L-alanine transaminases of Escherichia coli. PLoS One 2014; 9:e102139. [PMID: 25014014 PMCID: PMC4094517 DOI: 10.1371/journal.pone.0102139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
In order to maintain proper cellular function, the metabolism of the bacterial microbiota presents several mechanisms oriented to keep a correctly balanced amino acid pool. Central components of these mechanisms are enzymes with alanine transaminase activity, pyridoxal 5′-phosphate-dependent enzymes that interconvert alanine and pyruvate, thereby allowing the precise control of alanine and glutamate concentrations, two of the most abundant amino acids in the cellular amino acid pool. Here we report the 2.11-Å crystal structure of full-length AlaA from the model organism Escherichia coli, a major bacterial alanine aminotransferase, and compare its overall structure and active site composition with detailed atomic models of two other bacterial enzymes capable of catalyzing this reaction in vivo, AlaC and valine-pyruvate aminotransferase (AvtA). Apart from a narrow entry channel to the active site, a feature of this new crystal structure is the role of an active site loop that closes in upon binding of substrate-mimicking molecules, and which has only been previously reported in a plant enzyme. Comparison of the available structures indicates that beyond superficial differences, alanine aminotransferases of diverse phylogenetic origins share a universal reaction mechanism that depends on an array of highly conserved amino acid residues and is similarly regulated by various unrelated motifs. Despite this unifying mechanism and regulation, growth competition experiments demonstrate that AlaA, AlaC and AvtA are not freely exchangeable in vivo, suggesting that their functional repertoire is not completely redundant thus providing an explanation for their independent evolutionary conservation.
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Affiliation(s)
- Esther Peña-Soler
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Francisco J. Fernandez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
| | - Miguel López-Estepa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Andrew J. Richardson
- University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Juan F. Quintana
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
| | - Kenneth E. Rudd
- University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
- * E-mail:
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McAllister CH, Facette M, Holt A, Good AG. Analysis of the enzymatic properties of a broad family of alanine aminotransferases. PLoS One 2013; 8:e55032. [PMID: 23408955 PMCID: PMC3567105 DOI: 10.1371/journal.pone.0055032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 12/17/2012] [Indexed: 01/04/2023] Open
Abstract
Alanine aminotransferase (AlaAT) has been studied in a variety of organisms due to the involvement of this enzyme in mammalian processes such as non-alcoholic hepatocellular damage, and in plant processes such as C4 photosynthesis, post-hypoxic stress response and nitrogen use efficiency. To date, very few studies have made direct comparisons of AlaAT enzymes and fewer still have made direct comparisons of this enzyme across a broad spectrum of organisms. In this study we present a direct kinetic comparison of glutamate:pyruvate aminotransferase (GPAT) activity for seven AlaATs and two glutamate:glyoxylate aminotransferases (GGAT), measuring the KM values for the enzymes analyzed. We also demonstrate that recombinant expression of AlaAT enzymes in Eschericia coli results in differences in bacterial growth inhibition, supporting previous reports of AlaAT possessing bactericidal properties, attributed to lipopolysaccharide endotoxin recognition and binding. A probable lipopolysaccharide binding region within the AlaAT enzymes, homologous to a region of a lipopolysaccharide binding protein (LBP) in humans, was also identified in this study. The AlaAT enzyme differences identified here indicate that AlaAT homologues have differentiated significantly and the roles these homologues play in vivo may also have diverged significantly. Specifically, the differing kinetics of AlaAT enzymes and how this may alter the nitrogen use efficiency in plants is discussed.
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