1
|
Zhang H, Luo B, Liu J, Jin X, Zhang H, Zhong H, Li B, Hu H, Wang Y, Ali A, Riaz A, Sahito JH, Iqbal MZ, Zhang X, Liu D, Wu L, Gao D, Gao S, Su S, Gao S. Functional analysis of ZmG6PE reveals its role in responses to low-phosphorus stress and regulation of grain yield in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1286699. [PMID: 38023907 PMCID: PMC10666784 DOI: 10.3389/fpls.2023.1286699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
A previous metabolomic and genome-wide association analysis of maize screened a glucose-6-phosphate 1-epimerase (ZmG6PE) gene, which responds to low-phosphorus (LP) stress and regulates yield in maize's recombinant inbred lines (RILs). However, the relationship of ZmG6PE with phosphorus and yield remained elusive. This study aimed to elucidate the underlying response mechanism of the ZmG6PE gene to LP stress and its consequential impact on maize yield. The analysis indicated that ZmG6PE required the Aldose_epim conserved domain to maintain enzyme activity and localized in the nucleus and cell membrane. The zmg6pe mutants showed decreased biomass and sugar contents but had increased starch content in leaves under LP stress conditions. Combined transcriptome and metabolome analysis showed that LP stress activated plant immune regulation in response to the LP stress through carbon metabolism, amino acid metabolism, and fatty acid metabolism. Notably, LP stress significantly reduced the synthesis of glucose-1-phosphate, mannose-6-phosphate, and β-alanine-related metabolites and changed the expression of related genes. ZmG6PE regulates LP stress by mediating the expression of ZmSPX6 and ZmPHT1.13. Overall, this study revealed that ZmG6PE affected the number of grains per ear, ear thickness, and ear weight under LP stress, indicating that ZmG6PE participates in the phosphate signaling pathway and affects maize yield-related traits through balancing carbohydrates homeostasis.
Collapse
Affiliation(s)
- Hongkai Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Bowen Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Jin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Xinwu Jin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Haiying Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Haixu Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Binyang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Hongmei Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Yikai Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Asad Riaz
- Centre of Excellence for Plant Success in Nature and Agriculture, The Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Javed Hussain Sahito
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Muhammad Zafar Iqbal
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Dan Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Ling Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shunzong Su
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| |
Collapse
|
2
|
Shahbazi M, Tohidfar M, Azimzadeh Irani M, Moheb Seraj RG. Functional annotation and evaluation of hypothetical proteins in cyanobacterium Synechocystis sp. PCC 6803. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
3
|
Bearne SL. Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases. Chemistry 2020; 26:10367-10390. [DOI: 10.1002/chem.201905826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/09/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry & Molecular BiologyDepartment of ChemistryDalhousie University Halifax, Nova Scotia B3H 4R2 Canada
| |
Collapse
|
4
|
Watanabe Y, Watanabe S, Fukui Y, Nishiwaki H. Functional and structural characterization of a novel L-fucose mutarotase involved in non-phosphorylative pathway of L-fucose metabolism. Biochem Biophys Res Commun 2020; 528:21-27. [PMID: 32448506 DOI: 10.1016/j.bbrc.2020.05.094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/30/2022]
Abstract
Mutarotases catalyze the α-β anomeric conversion of monosaccharide, and play a key role in utilizing sugar as enzymes involved in sugar metabolism have specificity for the α- or β-anomer. In spite of the sequential similarity to l-rhamnose mutarotase protein superfamily (COG3254: RhaM), the ACAV_RS08160 gene in Acidovorax avenae ATCC 19860 (AaFucM) is located in a gene cluster related to non-phosphorylative l-fucose and l-galactose metabolism, and transcriptionally induced by these carbon sources; therefore, the physiological role remains unclear. Here, we report that AaFucM possesses mutarotation activity only toward l-fucose by saturation difference (SD) NMR experiments. Moreover, we determined the crystal structures of AaFucM in the apo form and in the l-fucose-bound form at resolutions of 2.21 and 1.75 Å, respectively. The overall structural folding was clearly similar to the RhaM members, differed from the known l-fucose mutarotase (COG4154: FucU), strongly indicating their convergent evolution. The structure-based mutational analyses suggest that Tyr18 is important for catalytic action, and that Gln87 and Trp99 are involved in the l-fucose-specific recognition.
Collapse
Affiliation(s)
- Yasunori Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Yasutaka Fukui
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Hisashi Nishiwaki
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| |
Collapse
|
5
|
Phithakrotchanakoon C, Phaonakrop N, Roytrakul S, Tanapongpipat S, Roongsawang N. Protein secretion in wild-type and Othac1 mutant strains of thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656. Mol Biol Rep 2019; 47:461-468. [DOI: 10.1007/s11033-019-05149-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
|
6
|
l-Arabinose induces d-galactose catabolism via the Leloir pathway in Aspergillus nidulans. Fungal Genet Biol 2018; 123:53-59. [PMID: 30496805 DOI: 10.1016/j.fgb.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/03/2018] [Accepted: 11/25/2018] [Indexed: 11/22/2022]
Abstract
l-Arabinose and d-galactose are the principal constituents of l-arabinogalactan, and also co-occur in other hemicelluloses and pectins. In this work we hypothesized that similar to the induction of relevant glycoside hydrolases by monomers liberated from these plant heteropolymers, their respective catabolisms in saprophytic and phytopathogenic fungi may respond to the presence of the other sugar to promote synergistic use of the complex growth substrate. We showed that these two sugars are indeed consumed simultaneously by Aspergillus nidulans, while l-arabinose is utilised faster in the presence than in the absence of d-galactose. Furthermore, the first two genes of the Leloir pathway for d-galactose catabolism - encoding d-galactose 1-epimerase and galactokinase - are induced more rapidly by l-arabinose than by d-galactose eventhough deletion mutants thereof grow as well as a wild type strain on the pentose. d-Galactose 1-epimerase is hyperinduced by l-arabinose, d-xylose and l-arabitol but not by xylitol. The results suggest that in A. nidulans, l-arabinose and d-xylose - both requiring NADPH for their catabolisation - actively promote the enzyme infrastructure necessary to convert β-d-galactopyranose via the Leloir pathway with its α-anomer specific enzymes, into β-d-glucose-6-phosphate (the starting substrate of the oxidative part of the pentose phosphate pathway) even in the absence of d-galactose.
Collapse
|
7
|
Discovery and characterization of a sulfoquinovose mutarotase using kinetic analysis at equilibrium by exchange spectroscopy. Biochem J 2018. [PMID: 29535276 PMCID: PMC5902678 DOI: 10.1042/bcj20170947] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacterial sulfoglycolytic pathways catabolize sulfoquinovose (SQ), or glycosides thereof, to generate a three-carbon metabolite for primary cellular metabolism and a three-carbon sulfonate that is expelled from the cell. Sulfoglycolytic operons encoding an Embden–Meyerhof–Parnas-like or Entner–Doudoroff (ED)-like pathway harbor an uncharacterized gene (yihR in Escherichia coli; PpSQ1_00415 in Pseudomonas putida) that is up-regulated in the presence of SQ, has been annotated as an aldose-1-epimerase and which may encode an SQ mutarotase. Our sequence analyses and structural modeling confirmed that these proteins possess mutarotase-like active sites with conserved catalytic residues. We overexpressed the homolog from the sulfo-ED operon of Herbaspirillum seropedicaea (HsSQM) and used it to demonstrate SQ mutarotase activity for the first time. This was accomplished using nuclear magnetic resonance exchange spectroscopy, a method that allows the chemical exchange of magnetization between the two SQ anomers at equilibrium. HsSQM also catalyzed the mutarotation of various aldohexoses with an equatorial 2-hydroxy group, including d-galactose, d-glucose, d-glucose-6-phosphate (Glc-6-P), and d-glucuronic acid, but not d-mannose. HsSQM displayed only 5-fold selectivity in terms of efficiency (kcat/KM) for SQ versus the glycolysis intermediate Glc-6-P; however, its proficiency [kuncat/(kcat/KM)] for SQ was 17 000-fold better than for Glc-6-P, revealing that HsSQM preferentially stabilizes the SQ transition state.
Collapse
|
8
|
Li G, Huang J, Yang J, He D, Wang C, Qi X, Taylor IA, Liu J, Peng YL. Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3. Sci Rep 2018; 8:3952. [PMID: 29500373 PMCID: PMC5834530 DOI: 10.1038/s41598-018-21667-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/07/2018] [Indexed: 11/09/2022] Open
Abstract
Magnaporthe oryzae is a model fungal plant pathogen employed for studying plant-fungi interactions. Whole genome sequencing and bioinformatics analyses revealed that this fungal pathogen has more than 12,000 protein-coding genes with 65% of the genes remaining functionally un-annotated. Here, we determine the structure of the hypothetical protein, MGG_01005 and show that it is the Magnaporthe oryzae Dynein light chain Tctex-type 1 (dynlt1/3), demonstrated by its structural similarity to other orthologous dynlt1 proteins and its conserved interaction with the N-terminus of the Magnaporthe oryzae dynein intermediate chain, MoDyn1I2. In addition, we present the structure of the MGG_01005-MoDyn1I2 complex together with mutagenesis studies that reveals a di-histidine motif interaction with a glutamate residue in the dynein intermediate chain within a conserved molecular interface. These results demonstrate the utility of structure-based annotation and validate it as a viable approach for the molecular assignment of hypothetic proteins from phyto-pathogenic fungi.
Collapse
Affiliation(s)
- Guorui Li
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.,College of life science, Inner Mongolia University for Nationalities, No. 996 Xilamulun Street, Tongliao, 028043, China
| | - Jinguang Huang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.,State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.,College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Jun Yang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.,State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China
| | - Dan He
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.,State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China
| | - Chao Wang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China
| | - Xiaoxuan Qi
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Junfeng Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.
| | - You-Liang Peng
- MOA Key Laboratory of Plant Pathology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China. .,State key Laboratory of Agrobiotechnology, China Agricultural University, No2 Yunamingyuanxilu, Beijing, 100193, China.
| |
Collapse
|
9
|
Kulcsár L, Flipphi M, Jónás Á, Sándor E, Fekete E, Karaffa L. Identification of a mutarotase gene involved in D-galactose utilization in Aspergillus nidulans. FEMS Microbiol Lett 2017; 364:4222790. [PMID: 29029189 DOI: 10.1093/femsle/fnx202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/22/2017] [Indexed: 11/14/2022] Open
Abstract
Aldose 1-epimerases or mutarotases (EC 5.1.3.3) are catalyzing the interconversion of α- and β-anomers of hemiacetals of aldose sugars such as D-glucose and D-galactose, and are presumed to play an auxiliary role in carbohydrate metabolism as mutarotation occurs spontaneously in watery solutions. The first step in the Leloir pathway of D-galactose breakdown is preceded by accelerated conversion of β-D-galactopyranose into the α-anomer, the substrate of the anomer-specific D-galactose 1-kinase. Here, we identified two putative aldose-1-epimerase genes (galmA and galmB) in the model organism Aspergillus nidulans, and characterized them upon generation of single- and double deletion mutant strains, as well as overexpressing mutants carrying multiple copies of either. Assaying cell-free extracts from the galmB single- and galm double mutants, we observed that the mutarotation hardly exceeded spontaneous anomer conversion, while galmB multicopy strains displayed higher activities than the wild type, increasing with the copy number. When grown on D-galactose in submerged cultures, biomass formation and D-galactose uptake rates in mutants lacking galmB were considerably reduced. None such effects were observed studying galmA deletion mutants, which consistently behave like the wild type. We conclude that GalmB is the physiologically relevant mutarotase for the utilization of D-galactose in A. nidulans.
Collapse
Affiliation(s)
- László Kulcsár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1., Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1., Debrecen, Hungary
| | - Ágota Jónás
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1., Debrecen, Hungary
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, H-4032, Böszörményi út 138., Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1., Debrecen, Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032, Egyetem tér 1., Debrecen, Hungary
| |
Collapse
|
10
|
Trz1, the long form RNase Z from yeast, forms a stable heterohexamer with endonuclease Nuc1 and mutarotase. Biochem J 2017; 474:3599-3613. [PMID: 28899942 DOI: 10.1042/bcj20170435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022]
Abstract
Proteomic studies have established that Trz1, Nuc1 and mutarotase form a complex in yeast. Trz1 is a β-lactamase-type RNase composed of two β-lactamase-type domains connected by a long linker that is responsible for the endonucleolytic cleavage at the 3'-end of tRNAs during the maturation process (RNase Z activity); Nuc1 is a dimeric mitochondrial nuclease involved in apoptosis, while mutarotase (encoded by YMR099C) catalyzes the conversion between the α- and β-configuration of glucose-6-phosphate. Using gel filtration, small angle X-ray scattering and electron microscopy, we demonstrated that Trz1, Nuc1 and mutarotase form a very stable heterohexamer, composed of two copies of each of the three subunits. A Nuc1 homodimer is at the center of the complex, creating a two-fold symmetry and interacting with both Trz1 and mutarotase. Enzymatic characterization of the ternary complex revealed that the activities of Trz1 and mutarotase are not affected by complex formation, but that the Nuc1 activity is completely inhibited by mutarotase and partially by Trz1. This suggests that mutarotase and Trz1 might be regulators of the Nuc1 apoptotic nuclease activity.
Collapse
|
11
|
Becker E, Com E, Lavigne R, Guilleux MH, Evrard B, Pineau C, Primig M. The protein expression landscape of mitosis and meiosis in diploid budding yeast. J Proteomics 2017; 156:5-19. [DOI: 10.1016/j.jprot.2016.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/26/2016] [Indexed: 12/12/2022]
|
12
|
Van Overtveldt S, Verhaeghe T, Joosten HJ, van den Bergh T, Beerens K, Desmet T. A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications. Biotechnol Adv 2015; 33:1814-28. [DOI: 10.1016/j.biotechadv.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/15/2015] [Accepted: 10/22/2015] [Indexed: 12/26/2022]
|
13
|
Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae. 3 Biotech 2015; 5:741-763. [PMID: 28324524 PMCID: PMC4569619 DOI: 10.1007/s13205-014-0274-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 12/18/2014] [Indexed: 01/09/2023] Open
Abstract
Haemophilus influenzae, a Gram-negative bacterium and a member of the family Pasteurellaceae, causes chronic bronchitis, bacteremia, meningitis, etc. The H. influenzae is the first organism whose genome was completely sequenced and annotated. Here, we have extensively analyzed the genome of H. influenzae using available proteins structure and function analysis tools. The objective of this analysis is to assign a precise function to hypothetical proteins (HPs) whose functions are not determined so far. Function prediction of these proteins is helpful in precise understanding of mechanisms of pathogenesis and biochemical pathways important for selecting novel therapeutic target. After an extensive analysis of H. Influenzae genome we have found 13 HPs showing high level of sequence and structural similarity to the enzyme isomerase. Consequently, the structures of HPs have been modeled and analyzed to determine their precise functions. We found these HPs are alanine racemase, lysine 2, 3-aminomutase, topoisomerase DNA-binding C4 zinc finger, pseudouridine synthase B, C and E (Rlu B, C and E), hydroxypyruvate isomerase, nucleoside-diphosphate-sugar epimerase, amidophosphoribosyltransferase, aldose-1-epimerase, tautomerase/MIF, Xylose isomerase-like, have TIM barrel domain and sedoheptulose-7-phosphate isomerase like activity, signifying their corresponding functions in the H. influenzae. This work provides a better understanding of the role HPs with isomerase activities in the survival and pathogenesis of H. influenzae.
Collapse
|
14
|
Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry 2012; 51:1762-73. [PMID: 22313111 PMCID: PMC3298459 DOI: 10.1021/bi201838b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two enzymes of unknown function from the cog1735 subset of the amidohydrolase superfamily (AHS), LMOf2365_2620 (Lmo2620) from Listeria monocytogenes str. 4b F2365 and Bh0225 from Bacillus halodurans C-125, were cloned, expressed, and purified to homogeneity. The catalytic functions of these two enzymes were interrogated by an integrated strategy encompassing bioinformatics, computational docking to three-dimensional crystal structures, and library screening. The three-dimensional structure of Lmo2620 was determined at a resolution of 1.6 Å with two phosphates and a binuclear zinc center in the active site. The proximal phosphate bridges the binuclear metal center and is 7.1 Å from the distal phosphate. The distal phosphate hydrogen bonds with Lys-242, Lys-244, Arg-275, and Tyr-278. Enzymes within cog1735 of the AHS have previously been shown to catalyze the hydrolysis of substituted lactones. Computational docking of the high-energy intermediate form of the KEGG database to the three-dimensional structure of Lmo2620 highly enriched anionic lactones versus other candidate substrates. The active site structure and the computational docking results suggested that probable substrates would likely include phosphorylated sugar lactones. A small library of diacid sugar lactones and phosphorylated sugar lactones was synthesized and tested for substrate activity with Lmo2620 and Bh0225. Two substrates were identified for these enzymes, D-lyxono-1,4-lactone-5-phosphate and l-ribono-1,4-lactone-5-phosphate. The k(cat)/K(m) values for the cobalt-substituted enzymes with these substrates are ~10(5) M(-1) s(-1).
Collapse
Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330
| | - Alexander A. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Chengfu Xu
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Elena V. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Tamari Narindoshivili
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Howard J. Williams
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| |
Collapse
|
15
|
Rispal D, Henri J, van Tilbeurgh H, Graille M, Séraphin B. Structural and functional analysis of Nro1/Ett1: a protein involved in translation termination in S. cerevisiae and in O2-mediated gene control in S. pombe. RNA (NEW YORK, N.Y.) 2011; 17:1213-1224. [PMID: 21610214 PMCID: PMC3138559 DOI: 10.1261/rna.2697111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 04/01/2011] [Indexed: 05/30/2023]
Abstract
In Saccharomyces cerevisiae, the putative 2-OG-Fe(II) dioxygenase Tpa1 and its partner Ett1 have been shown to impact mRNA decay and translation. Hence, inactivation of these factors was shown to influence stop codon read-though. In addition, Tpa1 represses, by an unknown mechanism, genes regulated by Hap1, a transcription factor involved in the response to levels of heme and O(2). The Schizosaccharomyces pombe orthologs of Tpa1 and Ett1, Ofd1, and its partner Nro1, respectively, have been shown to regulate the stability of the Sre1 transcription factor in response to oxygen levels. To gain insight into the function of Nro1/Ett1, we have solved the crystal structure of the S. pombe Nro1 protein deleted of its 54 N-terminal residues. Nro1 unexpectedly adopts a Tetratrico Peptide Repeat (TPR) fold, a motif often responsible for protein or peptide binding. Two ligands, a sulfate ion and an unknown molecule, interact with a cluster of highly conserved amino acids on the protein surface. Mutation of these residues demonstrates that these ligand binding sites are essential for Ett1 function in S. cerevisiae, as investigated by assaying for efficient translation termination.
Collapse
Affiliation(s)
- Delphine Rispal
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, Inserm U964, and Université de Strasbourg, Strasbourg, Illkirch F-67000, France
- Centre de Génétique Moléculaire (CGM), CNRS, F-91198 Gif-sur-Yvette Cedex, France
| | - Julien Henri
- Equipe “Fonction et Architecture des Assemblages Macromoléculaires”, IBBMC (Institut de Biochimie et Biophysique Moléculaire et Cellulaire), CNRS, UMR8619, Bat 430, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Herman van Tilbeurgh
- Equipe “Fonction et Architecture des Assemblages Macromoléculaires”, IBBMC (Institut de Biochimie et Biophysique Moléculaire et Cellulaire), CNRS, UMR8619, Bat 430, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Marc Graille
- Equipe “Fonction et Architecture des Assemblages Macromoléculaires”, IBBMC (Institut de Biochimie et Biophysique Moléculaire et Cellulaire), CNRS, UMR8619, Bat 430, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, Inserm U964, and Université de Strasbourg, Strasbourg, Illkirch F-67000, France
- Centre de Génétique Moléculaire (CGM), CNRS, F-91198 Gif-sur-Yvette Cedex, France
| |
Collapse
|
16
|
Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HWM, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FCP, Kemmeren P. A consensus of core protein complex compositions for Saccharomyces cerevisiae. Mol Cell 2010; 38:916-28. [PMID: 20620961 DOI: 10.1016/j.molcel.2010.06.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 04/02/2010] [Accepted: 05/16/2010] [Indexed: 11/28/2022]
Abstract
Analyses of biological processes would benefit from accurate definitions of protein complexes. High-throughput mass spectrometry data offer the possibility of systematically defining protein complexes; however, the predicted compositions vary substantially depending on the algorithm applied. We determine consensus compositions for 409 core protein complexes from Saccharomyces cerevisiae by merging previous predictions with a new approach. Various analyses indicate that the consensus is comprehensive and of high quality. For 85 out of 259 complexes not recorded in GO, literature search revealed strong support in the form of coprecipitation. New complexes were verified by an independent interaction assay and by gene expression profiling of strains with deleted subunits, often revealing which cellular processes are affected. The consensus complexes are available in various formats, including a merge with GO, resulting in 518 protein complex compositions. The utility is further demonstrated by comparison with binary interaction data to reveal interactions between core complexes.
Collapse
Affiliation(s)
- Joris J Benschop
- Department of Physiological Chemistry, University Medical Centre Utrecht, 3584 CG Utrecht, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Fukasawa T, Sakurai H, Nogi Y, Baruffini E. Galactose transporters discriminate steric anomers at the cell surface in yeast. FEMS Yeast Res 2009; 9:723-31. [DOI: 10.1111/j.1567-1364.2009.00517.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
18
|
Crystal structures and enzyme mechanisms of a dual fucose mutarotase/ribose pyranase. J Mol Biol 2009; 391:178-91. [PMID: 19524593 DOI: 10.1016/j.jmb.2009.06.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 06/03/2009] [Accepted: 06/08/2009] [Indexed: 11/24/2022]
Abstract
Escherichia coli FucU (Fucose Unknown) is a dual fucose mutarotase and ribose pyranase, which shares 44% sequence identity with its human counterpart. Herein, we report the structures of E. coli FucU and mouse FucU bound to L-fucose and delineate the catalytic mechanisms underlying the interconversion between stereoisomers of fucose and ribose. E. coli FucU forms a decameric toroid with each active site formed by two adjacent subunits. While one subunit provides most of the fucose-interacting residues including a catalytic tyrosine residue, the other subunit provides a catalytic His-Asp dyad. This active-site feature is critical not only for the mutarotase activity toward L-fucose but also for the pyranase activity toward D-ribose. Structural and biochemical analyses pointed that mouse FucU assembles into four different oligomeric forms, among which the smallest homodimeric form is most abundant and would be the predominant species under physiological conditions. This homodimer has two fucose-binding sites that are devoid of the His-Asp dyad and catalytically inactive, indicating that the mutarotase and the pyranase activities appear dispensable in vertebrates. The defective assembly of the mouse FucU homodimer into the decameric form is due to an insertion of two residues at the N-terminal extreme, which is a common aspect of all the known vertebrate FucU proteins. Therefore, vertebrate FucU appears to serve for as yet unknown function through the quaternary structural alteration.
Collapse
|
19
|
Mukherjee S, Zhang Y. MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Res 2009; 37:e83. [PMID: 19443443 PMCID: PMC2699532 DOI: 10.1093/nar/gkp318] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Structural comparison of multiple-chain protein complexes is essential in many studies of protein-protein interactions. We develop a new algorithm, MM-align, for sequence-independent alignment of protein complex structures. The algorithm is built on a heuristic iteration of a modified Needleman-Wunsch dynamic programming (DP) algorithm, with the alignment score specified by the inter-complex residue distances. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. The alignments of interface residues are enhanced by an interface-specific weighting factor. MM-align is tested on a large-scale benchmark set of 205 x 3897 non-homologous multiple-chain complex pairs. Compared with a naïve extension of the monomer alignment program of TM-align, the alignment accuracy of MM-align is significantly higher as judged by the average TM-score of the physically-aligned residues. MM-align is about two times faster than TM-align because of omitting the cross-alignment zone of the DP matrix. It also shows that the enhanced alignment of the interfaces helps in identifying biologically relevant protein complex pairs.
Collapse
Affiliation(s)
- Srayanta Mukherjee
- Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
| | | |
Collapse
|
20
|
Severi E, Müller A, Potts JR, Leech A, Williamson D, Wilson KS, Thomas GH. Sialic acid mutarotation is catalyzed by the Escherichia coli beta-propeller protein YjhT. J Biol Chem 2007; 283:4841-9. [PMID: 18063573 DOI: 10.1074/jbc.m707822200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The acquisition of host-derived sialic acid is an important virulence factor for some bacterial pathogens, but in vivo this sugar acid is sequestered in sialoconjugates as the alpha-anomer. In solution, however, sialic acid is present mainly as the beta-anomer, formed by a slow spontaneous mutarotation. We studied the Escherichia coli protein YjhT as a member of a family of uncharacterized proteins present in many sialic acid-utilizing pathogens. This protein is able to accelerate the equilibration of the alpha- and beta-anomers of the sialic acid N-acetylneuraminic acid, thus describing a novel sialic acid mutarotase activity. The structure of this periplasmic protein, solved to 1.5A resolution, reveals a dimeric 6-bladed unclosed beta-propeller, the first of a bacterial Kelch domain protein. Mutagenesis of conserved residues in YjhT demonstrated an important role for Glu-209 and Arg-215 in mutarotase activity. We also present data suggesting that the ability to utilize alpha-N-acetylneuraminic acid released from complex sialoconjugates in vivo provides a physiological advantage to bacteria containing YjhT.
Collapse
Affiliation(s)
- Emmanuele Severi
- Department of Biology (Area 10), York Structural Biology Laboratory, University of York, York YO10 5YW, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
21
|
Cordeiro AT, Cáceres AJ, Vertommen D, Concepción JL, Michels PAM, Versées W. The crystal structure of Trypanosoma cruzi glucokinase reveals features determining oligomerization and anomer specificity of hexose-phosphorylating enzymes. J Mol Biol 2007; 372:1215-26. [PMID: 17761195 DOI: 10.1016/j.jmb.2007.07.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 07/06/2007] [Accepted: 07/11/2007] [Indexed: 11/30/2022]
Abstract
Glucose is an essential substrate for Trypanosoma cruzi, the protozoan organism responsible for Chagas' disease. The glucose is intracellularly phosphorylated to glucose 6-phosphate. Previously, a hexokinase responsible for this phosphorylation has been characterized. Recently, we identified an ATP-dependent glucokinase in T. cruzi exhibiting a tenfold lower substrate affinity compared to the hexokinase. Both enzymes, which belong to very different groups of the same family, are located inside glycosomes, the peroxisome-like organelles of Kinetoplastida that are known to contain the first seven glycolytic steps as well as enzymes of the oxidative branch of the pentose phosphate pathway. Here, we present the crystallographic structure of T. cruzi glucokinase, in complex with glucose and ADP. The structure suggests a loose tetrameric assembly formed by the association of two tight dimers. TcGlcK was previously reported to exist in a concentration-dependent equilibrium of monomeric and dimeric states. Here, we used mass spectrometry analysis to confirm the existence of TcGlcK monomeric and dimeric states. The analysis of subunit interactions and comparison with the bacterial glucokinases give insights into the forces promoting the stability of the different oligomeric states. Each T. cruzi glucokinase monomer contains one glucose and one ADP molecule. In contrast to hexokinases, which show a moderate preference for the alpha anomer of glucose, the electron density clearly shows the d-glucose bound in the beta configuration in the T.cruzi glucokinase. Kinetic assays with alpha and beta-d-glucose further confirm a moderate preference of the T. cruzi glucokinase for the beta anomer. Structural comparison of the glucokinase and hexokinases permits the identification of a possible mechanism for anomer selectivity in these hexose-phosphorylating enzymes. The preference for distinct anomers suggests that in T. cruzi hexokinase and glucokinase are not directly competing for the same substrate and are probably both present because they exert distinct physiological functions.
Collapse
Affiliation(s)
- Artur T Cordeiro
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | | | | | | | | | | |
Collapse
|
22
|
Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|