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Guo R, Zhang S, Chen J, Shen W, Zhang G, Wang J, Zhang F, Pan Q, Xie T, Ai D, Dong J, Suo J, Sun Y, Liu S. Comparison of gut microflora of donkeys in high and low altitude areas. Front Microbiol 2022; 13:964799. [PMID: 36225357 PMCID: PMC9549287 DOI: 10.3389/fmicb.2022.964799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Donkeys’ gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts—stomach, small intestine, cecum, and rectum—were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (p < 0.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (p < 0.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and Bacteroidales were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.
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Affiliation(s)
- Rong Guo
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, Shandong, China
| | - Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, Inner Mongolia, China
| | - Wei Shen
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Guoliang Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
| | - Junjie Wang
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Fali Zhang
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qingjie Pan
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Taifeng Xie
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Deqiang Ai
- Qinghai Sheep Breeding and Extension Service Center, Gangcha County, Haibei Prefecture, Qinghai, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, Shandong, China
| | - Jiajia Suo
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, Shandong, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- Vocational College of Dongying, Dongying, Shandong, China
- *Correspondence: Yujiang Sun,
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- Shuqin Liu,
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Wang F, Sun Z, Zhu M, Zhang Q, Sun Y, Sun W, Wu C, Li T, Zhao Y, Ma C, Zhang H, Zhao Y, Wang Z. Dissecting the Molecular Regulation of Natural Variation in Growth and Senescence of Two Eutrema salsugineum Ecotypes. Int J Mol Sci 2022; 23:ijms23116124. [PMID: 35682805 PMCID: PMC9181637 DOI: 10.3390/ijms23116124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/22/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
Salt cress (Eutrema salsugineum, aka Thellungiella salsuginea) is an extremophile and a close relative of Arabidopsis thaliana. To understand the mechanism of selection of complex traits under natural variation, we analyzed the physiological and proteomic differences between Shandong (SD) and Xinjiang (XJ) ecotypes. The SD ecotype has dark green leaves, short and flat leaves, and more conspicuous taproots, and the XJ ecotype had greater biomass and showed clear signs of senescence or leaf shedding with age. After 2-DE separation and ESI-MS/MS identification, between 25 and 28 differentially expressed protein spots were identified in shoots and roots, respectively. The proteins identified in shoots are mainly involved in cellular metabolic processes, stress responses, responses to abiotic stimuli, and aging responses, while those identified in roots are mainly involved in small-molecule metabolic processes, oxidation-reduction processes, and responses to abiotic stimuli. Our data revealed the evolutionary differences at the protein level between these two ecotypes. Namely, in the evolution of salt tolerance, the SD ecotype highly expressed some stress-related proteins to structurally adapt to the high salt environment in the Yellow River Delta, whereas the XJ ecotype utilizes the specialized energy metabolism to support this evolution of the short-lived xerophytes in the Xinjiang region.
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Affiliation(s)
- Fanhua Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Zhibin Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Min Zhu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Qikun Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Yufei Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Wei Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Chunxia Wu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Tongtong Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Yiwu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Hui Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
- Correspondence: (Y.Z.); (Z.W.)
| | - Zenglan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (F.W.); (Z.S.); (M.Z.); (Q.Z.); (Y.S.); (W.S.); (C.W.); (T.L.); (Y.Z.); (C.M.); (H.Z.)
- Correspondence: (Y.Z.); (Z.W.)
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Stryiński R, Mateos J, Carrera M, Jastrzębski JP, Bogacka I, Łopieńska-Biernat E. Tandem Mass Tagging (TMT) Reveals Tissue-Specific Proteome of L4 Larvae of Anisakis simplex s. s.: Enzymes of Energy and/or Carbohydrate Metabolism as Potential Drug Targets in Anisakiasis. Int J Mol Sci 2022; 23:ijms23084336. [PMID: 35457153 PMCID: PMC9027741 DOI: 10.3390/ijms23084336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Anisakis simplex s. s. is a parasitic nematode of marine mammals and causative agent of anisakiasis in humans. The cuticle and intestine of the larvae are the tissues most responsible for direct and indirect contact, respectively, of the parasite with the host. At the L4 larval stage, tissues, such as the cuticle and intestine, are fully developed and functional, in contrast to the L3 stage. As such, this work provides for the first time the tissue-specific proteome of A. simplex s. s. larvae in the L4 stage. Statistical analysis (FC ≥ 2; p-value ≤ 0.01) showed that 107 proteins were differentially regulated (DRPs) between the cuticle and the rest of the larval body. In the comparison between the intestine and the rest of the larval body at the L4 stage, 123 proteins were identified as DRPs. Comparison of the individual tissues examined revealed a total of 272 DRPs, with 133 proteins more abundant in the cuticle and 139 proteins more abundant in the intestine. Detailed functional analysis of the identified proteins was performed using bioinformatics tools. Glycolysis and the tricarboxylic acid cycle were the most enriched metabolic pathways by cuticular and intestinal proteins, respectively, in the L4 stage of A. simplex s. s. The presence of two proteins, folliculin (FLCN) and oxoglutarate dehydrogenase (OGDH), was confirmed by Western blot, and their tertiary structure was predicted and compared with other species. In addition, host–pathogen interactions were identified, and potential new allergens were predicted. The result of this manuscript shows the largest number of protein identifications to our knowledge using proteomics tools for different tissues of L4 larvae of A. simplex s. s. The identified tissue-specific proteins could serve as targets for new drugs against anisakiasis.
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Affiliation(s)
- Robert Stryiński
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
- Correspondence: (R.S.); (M.C.); (E.Ł.-B.)
| | - Jesús Mateos
- Clinical Pharmacology Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15-706 A Coruña, Spain;
| | - Mónica Carrera
- Department of Food Technology, Marine Research Institute (IIM), Spanish National Research Council (CSIC), 36-208 Vigo, Spain
- Correspondence: (R.S.); (M.C.); (E.Ł.-B.)
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Iwona Bogacka
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
- Correspondence: (R.S.); (M.C.); (E.Ł.-B.)
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de Sousa LO, Oliveira LN, Naves RB, Pereira ALA, Santiago Freitas E Silva K, de Almeida Soares CM, de Sousa Lima P. The dual role of SrbA from Paracoccidioides lutzii: a hypoxic regulator. Braz J Microbiol 2021; 52:1135-1149. [PMID: 34148216 PMCID: PMC8382145 DOI: 10.1007/s42770-021-00527-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022] Open
Abstract
The fungus Paracoccidioides lutzii is one of the species of the Paracoccidioides genus, responsible for a neglected human mycosis, endemic in Latin America, the paracoccidioidomycosis (PCM). In order to survive in the host, the fungus overcomes a hostile environment under low levels of oxygen (hypoxia) during the infectious process. The hypoxia adaptation mechanisms are variable among human pathogenic fungi and worthy to be investigated in Paracoccidoides spp. Previous proteomic results identified that P. lutzii responds to hypoxia and it has a functional homolog of the SrbA transcription factor, a well-described hypoxic regulator. However, the direct regulation of genes by SrbA and the biological processes it governs while performing protein interactions have not been revealed yet. The goal of this study was to demonstrate the potential of SrbA targets genes in P. lutzii. In addition, to show the SrbA three-dimensional aspects as well as a protein interaction map and important regions of interaction with predicted targets. The results show that SrbA-regulated genes were involved with several biological categories, such as metabolism, energy, basal processes for cell maintenance, fungal morphogenesis, defense, virulence, and signal transduction. Moreover, in order to investigate the SrbA's role as a protein, we performed a 3D simulation and also a protein-protein network linked to this hypoxic regulator. These in silico analyses revealed relevant aspects regarding the biology of this pathogen facing hypoxia and highlight the potential of SrbA as an antifungal target in the future.
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Affiliation(s)
- Lorena Ordones de Sousa
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - Lucas Nojosa Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Raphaela Barbosa Naves
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - André Luiz Araújo Pereira
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - Kleber Santiago Freitas E Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Patrícia de Sousa Lima
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil.
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Ateya AI, Hendam BM, Radwan HA, Abo Elfadl EA, Al-Sharif MM. Using Linear Discriminant Analysis to Characterize Novel Single Nucleotide Polymorphisms and Expression Profile Changes in Genes of Three Breeds of Rabbit ( Oryctolagus cuniculus). Comp Med 2021; 71:222-234. [PMID: 34034856 DOI: 10.30802/aalas-cm-20-000103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The objectives of this study were to investigate polymorphisms and changes in expression patterns of the genes FGF5, PGAM2, TLR2 and IL10 in V-line, Baladi Black and Baladi Red rabbits. Blood samples were collected from 180 healthy rabbits (n = 60 for each breed) for DNA extraction and DNA sequencing. At 3 mo of age, 20 randomly selected females from each breed were euthanized for gene expression quantification in muscle and spleen samples. PCR-DNA sequencing revealed single nucleotide polymorphisms (SNPs) among the 3 breeds that provided a monomorphic pattern for 3 of the 4 genes analyzed. Linear discriminant analysis (LDA) was used to classify the SNPs of these genes in the 3 breeds. The overall percentage of correctly classified cases for the model was 75%, with percentages of 100% for FGF5, 63% for IL10, and 100% for TLR2. Breed was a significant predictor for gene classification with estimation (1.00). Expression profiles of the genes were higher in V-line as compared with Baladi Black or Baladi Red. The LDA discriminated the 3 breeds using results of the gene expression profile as predictors for classification. Overall, 73% of the cases were correctly classified by gene expression. The identified SNPs, along with changes in mRNA levels of FGF5, PGAM2, TLR2, and IL10, could provide a biomarker for efficient characterization of rabbit breeds and could thus help develop marker assisted selection for growth and immune traits in rabbits.
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Affiliation(s)
- Ahmed I Ateya
- Department of Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Gomhoria St., Mansoura, Mansoura, Egypt;,
| | - Basma M Hendam
- Department of Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Gomhoria St., Mansoura, Mansoura, Egypt
| | - Hend A Radwan
- Department of Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Gomhoria St., Mansoura, Mansoura, Egypt
| | - Eman A Abo Elfadl
- Department of Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Gomhoria St., Mansoura, Mansoura, Egypt
| | - Mona M Al-Sharif
- Department of Biology, College of Science, Jeddah University, Jeddah, Saudi Arabia
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Chowdhury S, Hepper S, Lodi MK, Saier MH, Uetz P. The Protein Interactome of Glycolysis in Escherichia coli. Proteomes 2021; 9:proteomes9020016. [PMID: 33917325 PMCID: PMC8167557 DOI: 10.3390/proteomes9020016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 11/16/2022] Open
Abstract
Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.
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Affiliation(s)
- Shomeek Chowdhury
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Cary Street, Richmond, VA 23284, USA; or
| | - Stephen Hepper
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA; (S.H.); (M.K.L.)
| | - Mudassir K. Lodi
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA; (S.H.); (M.K.L.)
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA;
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA; (S.H.); (M.K.L.)
- Correspondence:
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Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii. J Bacteriol 2021; 203:JB.00690-20. [PMID: 33558390 DOI: 10.1128/jb.00690-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/28/2021] [Indexed: 12/19/2022] Open
Abstract
The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.
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Lin D, Zhang L, Mei J, Chen J, Piao Z, Lee G, Dong Y. Mutation of the rice TCM12 gene encoding 2,3-bisphosphoglycerate-independent phosphoglycerate mutase affects chlorophyll synthesis, photosynthesis and chloroplast development at seedling stage at low temperatures. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:585-594. [PMID: 30803106 DOI: 10.1111/plb.12978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Glycolysis is a central metabolic pathway that provides energy and products of primary metabolites. 2,3-Biphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is a key enzyme that catalyses the reversible interconversion of 3-phosphoglycerate (3-PGA) to 2-phosphoglycerate (2-PGA) in glycolysis. Low temperature is a common abiotic stress in rice production. However, the mechanism for rice iPGAM genes is not fully understood at low temperature. In this study, the rice mutant tcm12, with chlorosis, malformed chloroplasts and impaired photosynthesis, was grown at a low temperature (<20 °C) to the three-leaf stage, while the normal phenotype at 32 °C was used. Chlorophyll fluorescence analysis and transmission electron microscopy were used to examine features of the tcm12 mutant. The inheritance behaviour and function of TCM12 were then analysed thorough map-based cloning, transgenic complementation and subcellular localisation. The thermo-sensitive chlorosis phenotype was caused by a single nucleotide mutation (T→C) on the fifth exon of TCM12 (LOC_Os12g35040) encoding iPGAM, localised to both nucleus and membranes. In addition, TCM12 was constitutively expressed, and its disruption resulted in down-regulation of some genes associated with chlorophyll biosynthesis and photosynthesis at low temperatures (20 °C). This is the first report of the involvement of rice iPGAM gene in chlorophyll synthesis, photosynthesis and chloroplast development, providing new insights into the mechanisms underlying early growth of rice at low temperatures.
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Affiliation(s)
- D Lin
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - L Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - J Mei
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - J Chen
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Z Piao
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Fengxian District, Shanghai 3, China
| | - G Lee
- National Institute of Agricultural Science, Jeon Ju, Korea
| | - Y Dong
- College of Life Sciences, Shanghai Normal University, Shanghai, China
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Gao L, Sun Y, Wu M, Wang D, Wei J, Wu B, Wang G, Wu W, Jin X, Wang X, He P. Physiological and Proteomic Analyses of Molybdenum- and Ethylene-Responsive Mechanisms in Rubber Latex. FRONTIERS IN PLANT SCIENCE 2018; 9:621. [PMID: 29868077 PMCID: PMC5962772 DOI: 10.3389/fpls.2018.00621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Molybdenum (Mo) is an essential micronutrient in many plants. In the rubber tree Hevea brasiliensis, Mo application can reduce the shrinkage of the tapping line, decrease tapping panel dryness, and finally increase rubber latex yield. After combined Mo with ethylene (Eth), these effects become more obvious. However, the molecular mechanism remains unclear. Here, we compared the changed patterns of physiological parameters and protein accumulation in rubber latex after treated with Mo and/or Eth. Our results demonstrated that both Eth and Mo can improve the contents of thiol, sucrose, and dry yield in rubber latex. However, lutoid bursting is significantly inhibited by Mo. Comparative proteomics identified 169 differentially expressed proteins, including 114 unique proteins, which are mainly involved in posttranslational modification, carbohydrate metabolism, and energy production. The abundances of several proteins involved in rubber particle aggregation are decreased upon Mo stimulation, while many enzymes related to natural rubber biosynthesis are increased. Comparison of the accumulation patterns of 25 proteins revealed that a large portion of proteins have different changed patterns with their gene expression levels. Activity assays of six enzymes revealed that Mo stimulation can increase latex yield by improving the activity of some Mo-responsive enzymes. These results not only deepen our understanding of the rubber latex proteome but also provide new insights into the molecular mechanism of Mo-stimulated rubber latex yield.
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Affiliation(s)
- Le Gao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
| | - Yong Sun
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
| | - Min Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashao Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bingsun Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Guihua Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenguan Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiang Jin
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuchu Wang
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Peng He
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
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10
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Manzella MP, Holmes DE, Rocheleau JM, Chung A, Reguera G, Kashefi K. The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T). Stand Genomic Sci 2015; 10:77. [PMID: 26457129 PMCID: PMC4600277 DOI: 10.1186/s40793-015-0035-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022] Open
Abstract
“Geoglobus ahangari” strain 234T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal system. It grows optimally at 88 °C by coupling the reduction of Fe(III) oxides to the oxidation of a wide range of compounds, including long-chain fatty acids, and also grows autotrophically with hydrogen and Fe(III). It is the first archaeon reported to use a direct contact mechanism for Fe(III) oxide reduction, relying on a single archaellum for locomotion, numerous curled extracellular appendages for attachment, and outer-surface heme-containing proteins for electron transfer to the insoluble Fe(III) oxides. Here we describe the annotation of the genome of “G. ahangari” strain 234T and identify components critical to its versatility in electron donor utilization and obligate Fe(III) respiratory metabolism at high temperatures. The genome comprises a single, circular chromosome of 1,770,093 base pairs containing 2034 protein-coding genes and 52 RNA genes. In addition, emended descriptions of the genus “Geoglobus” and species “G. ahangari” are described.
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Affiliation(s)
- Michael P Manzella
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Jessica M Rocheleau
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Amanda Chung
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
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11
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Ali B, Gill RA, Yang S, Gill MB, Farooq MA, Liu D, Daud MK, Ali S, Zhou W. Regulation of Cadmium-Induced Proteomic and Metabolic Changes by 5-Aminolevulinic Acid in Leaves of Brassica napus L. PLoS One 2015; 10:e0123328. [PMID: 25909456 PMCID: PMC4409391 DOI: 10.1371/journal.pone.0123328] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/03/2015] [Indexed: 01/17/2023] Open
Abstract
It is evident from previous reports that 5-aminolevulinic acid (ALA), like other known plant growth regulators, is effective in countering the injurious effects of heavy metal-stress in oilseed rape (Brassica napus L.). The present study was carried out to explore the capability of ALA to improve cadmium (Cd2+) tolerance in B. napus through physiological, molecular, and proteomic analytical approaches. Results showed that application of ALA helped the plants to adjust Cd2+-induced metabolic and photosynthetic fluorescence changes in the leaves of B. napus under Cd2+ stress. The data revealed that ALA treatment enhanced the gene expressions of antioxidant enzyme activities substantially and could increase the expression to a certain degree under Cd2+ stress conditions. In the present study, 34 protein spots were identified that differentially regulated due to Cd2+ and/or ALA treatments. Among them, 18 proteins were significantly regulated by ALA, including the proteins associated with stress related, carbohydrate metabolism, catalysis, dehydration of damaged protein, CO2 assimilation/photosynthesis and protein synthesis/regulation. From these 18 ALA-regulated proteins, 12 proteins were significantly down-regulated and 6 proteins were up-regulated. Interestingly, it was observed that ALA-induced the up-regulation of dihydrolipoyl dehydrogenase, light harvesting complex photo-system II subunit 6 and 30S ribosomal proteins in the presence of Cd2+ stress. In addition, it was also observed that ALA-induced the down-regulation in thioredoxin-like protein, 2, 3-bisphosphoglycerate, proteasome and thiamine thiazole synthase proteins under Cd2+ stress. Taken together, the present study sheds light on molecular mechanisms involved in ALA-induced Cd2+ tolerance in B. napus leaves and suggests a more active involvement of ALA in plant physiological processes than previously proposed.
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Affiliation(s)
- Basharat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Rafaqat A. Gill
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Su Yang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Muhammad B. Gill
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Muhammad A. Farooq
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Dan Liu
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Muhammad K. Daud
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad 38000, Pakistan
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- * E-mail:
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12
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Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics. J Proteomics 2014; 109:276-89. [DOI: 10.1016/j.jprot.2014.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 12/16/2022]
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13
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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Cofactor independent phosphoglycerate mutase of Brugia malayi induces a mixed Th1/Th2 type immune response and inhibits larval development in the host. BIOMED RESEARCH INTERNATIONAL 2014; 2014:590281. [PMID: 25061608 PMCID: PMC4100390 DOI: 10.1155/2014/590281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/06/2014] [Accepted: 05/20/2014] [Indexed: 01/24/2023]
Abstract
Lymphatic filariasis is a major debilitating disease, endemic in 72 countries putting more than 1.39 billion people at risk and 120 million are already infected. Despite the significant progress in chemotherapeutic advancements, there is still need for other measures like development of an effective vaccine or discovery of novel drug targets. In this study, structural and immunological characterization of independent phosphoglycerate mutase of filarial parasite Brugia malayi was carried out. Protein was found to be expressed in all major parasite life stages and as an excretory secretory product of adult parasites. Bm-iPGM also reacted to all the categories of human bancroftian patient's sera including endemic normals. In vivo immunological behaviour of protein was determined in immunized BALB/c mice followed by prophylactic analysis in BALB/c mice and Mastomys coucha. Immunization with Bm-iPGM led to generation of a mixed Th1/Th2 type immune response offering 58.2% protection against larval challenge in BALB/c and 65–68% protection in M. coucha. In vitro studies confirmed participation of anti-Bm-iPGM antibodies in killing of B. malayi infective larvae and microfilariae through ADCC mechanism. The present findings reveal potential immunoprotective nature of Bm-iPGM advocating its worth as an antifilarial vaccine candidate.
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15
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Yip SHC, Matsumura I. Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem. Mol Biol Evol 2013; 30:2001-12. [PMID: 23728795 DOI: 10.1093/molbev/mst105] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many enzymes exhibit some catalytic promiscuity or substrate ambiguity. These weak activities do not affect the fitness of the organism under ordinary circumstances, but can serve as potential evolutionary precursors of new catalytic functions. We wondered whether different proteins with the same substrate ambiguous activity evolve differently under identical selection conditions. Patrick et al. (Patrick WM, Quandt EM, Swartzlander DB, Matsumura I. 2007. Multicopy suppression underpins metabolic evolvability. Mol Biol Evol. 24:2716-2722.) previously showed that three multicopy suppressors, gph, hisB, and ytjC, rescue ΔserB Escherichia coli cells from starvation on minimal media. We directed the evolution of variants of Gph, histidinol phosphatase (HisB), and YtjC that complemented ΔserB more efficiently, and characterized the effects of the amino acid changes, alone and in combination, upon the evolved phosphoserine phosphatase (PSP) activity. Gph and HisB are members of the HAD superfamily of hydrolases, but they adapted through different, kinetically distinguishable, biochemical mechanisms. All of the selected mutations, except N102T in YtjC, proved to be beneficial in isolation. They exhibited a pattern of antagonistic epistasis, as their effects in combination upon the kinetic parameters of the three proteins in reactions with phosphoserine were nonmultiplicative. The N102T mutation exhibited sign epistasis, as it was deleterious in isolation but beneficial in the context of other mutations. We also showed that the D57N mutation in the chromosomal copy of hisB is sufficient to suppress the ΔserB deletion. These results in combination show that proteomes can offer multiple mechanistic solutions to a molecular recognition problem.
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Affiliation(s)
- Sylvia Hsu-Chen Yip
- Department of Biochemistry, Center for Fundamental and Applied Molecular Evolution, Rollins Research Center, Emory University School of Medicine, USA
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16
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Ye X, Honda K, Sakai T, Okano K, Omasa T, Hirota R, Kuroda A, Ohtake H. Synthetic metabolic engineering-a novel, simple technology for designing a chimeric metabolic pathway. Microb Cell Fact 2012; 11:120. [PMID: 22950411 PMCID: PMC3512521 DOI: 10.1186/1475-2859-11-120] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/31/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The integration of biotechnology into chemical manufacturing has been recognized as a key technology to build a sustainable society. However, the practical applications of biocatalytic chemical conversions are often restricted due to their complexities involving the unpredictability of product yield and the troublesome controls in fermentation processes. One of the possible strategies to overcome these limitations is to eliminate the use of living microorganisms and to use only enzymes involved in the metabolic pathway. Use of recombinant mesophiles producing thermophilic enzymes at high temperature results in denaturation of indigenous proteins and elimination of undesired side reactions; consequently, highly selective and stable biocatalytic modules can be readily prepared. By rationally combining those modules together, artificial synthetic pathways specialized for chemical manufacturing could be designed and constructed. RESULTS A chimeric Embden-Meyerhof (EM) pathway with balanced consumption and regeneration of ATP and ADP was constructed by using nine recombinant E. coli strains overproducing either one of the seven glycolytic enzymes of Thermus thermophilus, the cofactor-independent phosphoglycerate mutase of Pyrococcus horikoshii, or the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase of Thermococcus kodakarensis. By coupling this pathway with the Thermus malate/lactate dehydrogenase, a stoichiometric amount of lactate was produced from glucose with an overall ATP turnover number of 31. CONCLUSIONS In this study, a novel and simple technology for flexible design of a bespoke metabolic pathway was developed. The concept has been testified via a non-ATP-forming chimeric EM pathway. We designated this technology as "synthetic metabolic engineering". Our technology is, in principle, applicable to all thermophilic enzymes as long as they can be functionally expressed in the host, and thus would be potentially applicable to the biocatalytic manufacture of any chemicals or materials on demand.
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Affiliation(s)
- Xiaoting Ye
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers. PLoS One 2010; 5:e13576. [PMID: 21187861 PMCID: PMC2964296 DOI: 10.1371/journal.pone.0013576] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/27/2010] [Indexed: 11/28/2022] Open
Abstract
Background The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE) having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms. Methods/Principal Findings To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM null mutants in E. coli and discovered the ΔdPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect. Conclusions/Significance Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.
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Foster JM, Raverdy S, Ganatra MB, Colussi PA, Taron CH, Carlow CKS. The Wolbachia endosymbiont of Brugia malayi has an active phosphoglycerate mutase: a candidate target for anti-filarial therapies. Parasitol Res 2008; 104:1047-52. [PMID: 19043737 DOI: 10.1007/s00436-008-1287-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 11/11/2008] [Indexed: 11/25/2022]
Abstract
Phosphoglycerate mutases (PGM) interconvert 2- and 3-phosphoglycerate in the glycolytic and gluconeogenic pathways. A putative cofactor-independent phosphoglycerate mutase gene (iPGM) was identified in the genome sequence of the Wolbachia endosymbiont from the filarial nematode, Brugia malayi (wBm). Since iPGM has no sequence or structural similarity to the cofactor-dependent phosphoglycerate mutase (dPGM) found in mammals, it may represent an attractive Wolbachia drug target. In the present study, wBm-iPGM cloned and expressed in Escherichia coli was mostly insoluble and inactive. However, the protein was successfully produced in the yeast Kluyveromyces lactis and the purified recombinant wBm-iPGM showed typical PGM activity. Our results provide a foundation for further development of wBm-iPGM as a promising new drug target for novel anti-filarial therapies that selectively target the endosymbiont.
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Affiliation(s)
- Jeremy M Foster
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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19
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Reher M, Gebhard S, Schönheit P. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) and nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), key enzymes of the respective modified Embden-Meyerhof pathways in the hyperthermophilic crenarchaeota Pyrobaculum aerophilum and Aeropyrum pernix. FEMS Microbiol Lett 2007; 273:196-205. [PMID: 17559573 DOI: 10.1111/j.1574-6968.2007.00787.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The growth of Pyrobaculum aerophilum on yeast extract and nitrate was stimulated by the addition of maltose. Extracts of maltose/yeast extract/nitrate-grown cells contained all enzyme activities of a modified Embden-Meyerhof (EM) pathway, including ATP-dependent glucokinase, phosphoglucose isomerase, ATP-dependent 6-phosphofructokinase, fructose-1,6-phosphate aldolase, triose-phosphate isomerase, GAPOR, phosphoglycerate mutase, enolase and pyruvate kinase. The activity of GAPOR was stimulated about fourfold by maltose, indicating a role in sugar degradation. GAPOR was purified 200-fold to homogeneity and characterized as a 67 kDa monomeric, extremely thermostable protein. The enzyme showed high specificity for glyceraldehyde-3-phosphate and did not use glyceraldehyde, acetaldehyde or formaldehyde as substrates. By matrix-assisted laser desorption/ionization-time of flight analysis of the purified enzyme, ORF PA1029 was identified as a coding gene, gapor, in the sequenced genome of Pyrobaculum aerophilum. The data indicate that the (micro)aerophilic Pyrobaculum aerophilum contains a functional GAPOR as part of a modified EM pathway. Cells of the strictly aerobic crenarchaeon Aeropyrum pernix also contain enzyme activities of a modified EM pathway similar to that of Pyrobaculum aerophilum, except that a GAPN activity replaces GAPOR activity.
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Affiliation(s)
- Matthias Reher
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
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