1
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Kannan A, Chaurasiya DK, Naganathan AN. Conflicting Interfacial Electrostatic Interactions as a Design Principle to Modulate Long-Range Interdomain Communication. ACS BIO & MED CHEM AU 2024; 4:53-67. [PMID: 38404745 PMCID: PMC10885104 DOI: 10.1021/acsbiomedchemau.3c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 02/27/2024]
Abstract
The extent and molecular basis of interdomain communication in multidomain proteins, central to understanding allostery and function, is an open question. One simple evolutionary strategy could involve the selection of either conflicting or favorable electrostatic interactions across the interface of two closely spaced domains to tune the magnitude of interdomain connectivity. Here, we study a bilobed domain FF34 from the eukaryotic p190A RhoGAP protein to explore one such design principle that mediates interdomain communication. We find that while the individual structural units in wild-type FF34 are marginally coupled, they exhibit distinct intrinsic stabilities and low cooperativity, manifesting as slow folding. The FF3-FF4 interface harbors a frustrated network of highly conserved electrostatic interactions-a charge troika-that promotes the population of multiple, decoupled, and non-native structural modes on a rugged native landscape. Perturbing this network via a charge-reversal mutation not only enhances stability and cooperativity but also dampens the fluctuations globally and speeds up the folding rate by at least an order of magnitude. Our work highlights how a conserved but nonoptimal network of interfacial electrostatic interactions shapes the native ensemble of a bilobed protein, a feature that could be exploited in designing molecular systems with long-range connectivity and enhanced cooperativity.
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Affiliation(s)
- Adithi Kannan
- Department of Biotechnology,
Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology,
Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology,
Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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2
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Adhikari S, Mondal J. Machine Learning Subtle Conformational Change due to Phosphorylation in Intrinsically Disordered Proteins. J Phys Chem B 2023; 127:9433-9449. [PMID: 37905972 DOI: 10.1021/acs.jpcb.3c05136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Phosphorylation of intrinsically disordered proteins/regions (IDPs/IDRs) has a profound effect in biological functions such as cell signaling, protein folding or unfolding, and long-range allosteric effects. However, here we focus on two IDPs, namely 83-residue IDR transcription factor Ash1 and 92-residue long N-terminal region of CDK inhibitor Sic1 protein, found in Saccharomyces cerevisiae, for which experimental measurements of average conformational properties, namely, radius of gyration and structure factor, indicate negligible changes upon phosphorylation. Here, we show that a judicious dissection of conformational ensemble via combination of unsupervised machine learning and extensive molecular dynamics (MD) trajectories can highlight key differences and similarities among the phosphorylated and wild-type IDP. In particular, we develop Markov state model (MSM) using the latent-space dimensions of an autoencoder, trained using multi-microsecond long MD simulation trajectories. Examination of structural changes among the states, prior to and upon phosphorylation, captured several similarities and differences in their backbone contact maps, secondary structure, and torsion angles. Hydrogen bonding analysis revealed that phosphorylation not only increases the number of hydrogen bonds but also switches the pattern of hydrogen bonding between the backbone and side chain atoms with the phosphorylated residues. We also observe that although phosphorylation introduces salt bridges, there is a loss of the cation-π interaction. Phosphorylation also improved the probability for long-range hydrophobic contacts and also enhanced interaction with water molecules and improved the local structure of water as evident from the geometric order parameters. The observations on these machine-learnt states gave important insights, as it would otherwise be difficult to determine experimentally which is important, if we were to understand the role of phosphorylation of IDPs in their biological functions.
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3
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van Dijk MJ, de Wilde JRA, Bartels M, Kuo KHM, Glenthøj A, Rab MAE, van Beers EJ, van Wijk R. Activation of pyruvate kinase as therapeutic option for rare hemolytic anemias: Shedding new light on an old enzyme. Blood Rev 2023; 61:101103. [PMID: 37353463 DOI: 10.1016/j.blre.2023.101103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023]
Abstract
Novel developments in therapies for various hereditary hemolytic anemias reflect the pivotal role of pyruvate kinase (PK), a key enzyme of glycolysis, in red blood cell (RBC) health. Without PK catalyzing one of the final steps of the Embden-Meyerhof pathway, there is no net yield of adenosine triphosphate (ATP) during glycolysis, the sole source of energy production required for proper RBC function and survival. In hereditary hemolytic anemias, RBC health is compromised and therefore lifespan is shortened. Although our knowledge on glycolysis in general and PK function in particular is solid, recent advances in genetic, molecular, biochemical, and metabolic aspects of hereditary anemias have improved our understanding of these diseases. These advances provide a rationale for targeting PK as therapeutic option in hereditary hemolytic anemias other than PK deficiency. This review summarizes the knowledge, rationale, (pre)clinical trials, and future advances of PK activators for this important group of rare diseases.
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Affiliation(s)
- Myrthe J van Dijk
- Department of Central Diagnostic Laboratory - Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Benign Hematology, Thrombosis and Hemostasis - Van Creveldkliniek, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Jonathan R A de Wilde
- Department of Central Diagnostic Laboratory - Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marije Bartels
- Center for Benign Hematology, Thrombosis and Hemostasis - Van Creveldkliniek, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Kevin H M Kuo
- Division of Hematology, University of Toronto, Toronto, ON, Canada
| | - Andreas Glenthøj
- Danish Red Blood Center, Department of Hematology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Minke A E Rab
- Department of Central Diagnostic Laboratory - Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Hematology, Erasmus Medical Center Rotterdam, the Netherlands
| | - Eduard J van Beers
- Center for Benign Hematology, Thrombosis and Hemostasis - Van Creveldkliniek, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Richard van Wijk
- Department of Central Diagnostic Laboratory - Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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4
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Taguchi A, Nakashima R, Nishino K. Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance. J Biol Chem 2023:104892. [PMID: 37286036 PMCID: PMC10338316 DOI: 10.1016/j.jbc.2023.104892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
Glycolysis is the primary metabolic pathway in the strictly fermentative Streptococcus pneumoniae, which is a major human pathogen associated with antibiotic resistance. Pyruvate kinase (PYK) is the last enzyme in this pathway that catalyzes the production of pyruvate from phosphoenolpyruvate (PEP) and plays a crucial role in controlling carbon flux; however, while S. pneumoniae PYK (SpPYK) is indispensable for growth, surprisingly little is known about its functional properties. Here, we report that compromising mutations in SpPYK confer resistance to the antibiotic fosfomycin, which inhibits the peptidoglycan synthesis enzyme MurA, implying a direct link between PYK and cell wall biogenesis. The crystal structures of SpPYK in the apo and ligand-bound states reveal key interactions that contribute to its conformational change as well as residues responsible for the recognition of PEP and the allosteric activator fructose 1,6-bisphosphate (FBP). Strikingly, FBP binding was observed at a location distinct from previously reported PYK effector binding sites. Furthermore, we show that SpPYK could be engineered to become more responsive to glucose 6-phosphate instead of FBP by sequence and structure-guided mutagenesis of the effector binding site. Together, our work sheds light on the regulatory mechanism of SpPYK and lays the groundwork for antibiotic development that targets this essential enzyme.
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Affiliation(s)
- Atsushi Taguchi
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Ryosuke Nakashima
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
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5
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D'Rose V, Bhat SG. Whole genome sequence analysis enabled affirmation of the probiotic potential of marine sporulater Bacillus amyloliquefaciens BTSS3 isolated from Centroscyllium fabricii. Gene 2023; 864:147305. [PMID: 36813058 DOI: 10.1016/j.gene.2023.147305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/05/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023]
Abstract
Probiotics are microorganisms when administered in adequate amounts, confer health benefits on the host. Many probiotics find application in various industries however, probiotic bacteria linked to marine environments are less explored.Although Bifidobacteria, Lactobacilli, and Streptococcus thermophilus are the most frequently used probiotics, Bacillus spp. have acquired much acceptance in human functional foods due to their increased tolerance and enduring competence in harsh environments like the gastrointestinal (GI) tract. In this study, the 4 Mbp genome sequence of Bacillus amyloliquefaciens strain BTSS3, a marine spore former isolated from deep-sea shark Centroscyllium fabricii, with antimicrobial and probiotic properties was sequenced, assembled, and annotated. Analysis revealed the presence of numerous genes presenting probiotic traits like production of vitamins, secondary metabolites, amino acids, secretory proteins, enzymes and other proteins that allow survival in GI tract as well as adhesion to intestinal mucosa. Adhesion by colonization in the gut was studied in vivo in zebrafish (Danio rerio) using FITC labelled B.amyloliquefaciens BTSS3. Preliminary study revealed the ability of the marine Bacillus to attach to the intestinal mucosa of the fish gut. The genomic data and the in vivo experiment affirms that this marine spore former is a promising probiotic candidate with potential biotechnological applications.
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Affiliation(s)
- Venetia D'Rose
- Department of Biotechnology, Cochin University of Science and Technology, Cochin 22, India.
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Cochin 22, India; Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Cochin 22, Kerala, India.
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6
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Swint-Kruse L, Dougherty LL, Page B, Wu T, O’Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW. PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) 2023; 2023:baad030. [PMID: 37171062 PMCID: PMC10176505 DOI: 10.1093/database/baad030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Larissa L Dougherty
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Braelyn Page
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Tiffany Wu
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Pierce T O’Neil
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Cody Timmons
- Chemistry Department, Southwestern Oklahoma State University, 100 Campus Dr., Weatherford, OK 73096, USA
| | - Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Daniel J Parente
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Family Medicine and Community Health, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Shwetha Sreenivasan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Todd Holyoak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
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7
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Nain-Perez A, Nilsson O, Lulla A, Håversen L, Brear P, Liljenberg S, Hyvönen M, Borén J, Grøtli M. Tuning liver pyruvate kinase activity up or down with a new class of allosteric modulators. Eur J Med Chem 2023; 250:115177. [PMID: 36753880 DOI: 10.1016/j.ejmech.2023.115177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023]
Abstract
The liver isoform of pyruvate kinase (PKL) has gained interest due to its potential capacity to regulate fatty acid synthesis involved in the progression of non-alcoholic fatty liver disease (NAFLD). Here we describe a novel series of PKL modulators that can either activate or inhibit the enzyme allosterically, from a cryptic site at the interface of two protomers in the tetrameric enzyme. Starting from urolithin D, we designed and synthesised 42 new compounds. The effect of these compounds on PKL enzymatic activity was assessed after incubation with cell lysates obtained from a liver cell line. Pronounced activation of PKL activity, up to 3.8-fold, was observed for several compounds at 10 μM, while other compounds were prominent PKL inhibitors reducing its activity to 81% at best. A structure-activity relationship identified linear-shaped sulfone-sulfonamides as activators and non-linear compounds as inhibitors. Crystal structures revealed the conformations of these modulators, which were used as a reference for designing new modulators.
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Affiliation(s)
- Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Oscar Nilsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Sara Liljenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden.
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8
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Dongerdiye R, Bokde M, More TA, Saptarshi A, Devendra R, Chiddarwar A, Warang P, Kedar P. Targeted next-generation sequencing identifies eighteen novel mutations expanding the molecular and clinical spectrum of PKLR gene disorders in the Indian population. Ann Hematol 2023; 102:1029-1036. [PMID: 36892591 DOI: 10.1007/s00277-023-05152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Pyruvate kinase deficiency (PKD) is an autosomal recessive condition, caused due to homozygous or compound heterozygous mutation in the PKLR gene resulting in non-spherocytic hereditary hemolytic anemia. Clinical manifestations in PKD patients vary from moderate to severe lifelong hemolytic anemia either requiring neonatal exchange transfusion or blood transfusion support. Measuring PK enzyme activity is the gold standard approach for diagnosis but residual activity must be related to the increased reticulocyte count. The confirmatory diagnosis is provided by PKLR gene sequencing by conventional as well as targeted next-generation sequencing involving genes associated with enzymopathies, membranopathies, hemoglobinopathies, and bone marrow failure disorders. In this study, we report the mutational landscape of 45 unrelated PK deficiency cases from India. The genetic sequencing of PKLR revealed 40 variants comprising 34 Missense Mutations (MM), 2 Nonsense Mutations (NM), 1 Splice site, 1 Intronic, 1 Insertion, and 1 Large Base Deletion. The 17 novel variants identified in this study are A115E, R116P, A423G, K313I, E315G, E318K, L327P, M377L, A423E, R449G, H507Q, E538K, G563S, c.507 + 1 G > C, c.801_802 ins A (p.Asp268ArgfsTer48), IVS9dsA-T + 3, and one large base deletion. In combination with previous reports on PK deficiency, we suggest c.880G > A, c.943G > A, c.994G > A, c.1456C > T, c.1529G > A are the most frequently observed mutations in India. This study expands the phenotypic and molecular spectrum of PKLR gene disorders and also emphasizes the importance of combining both targeted next-generation sequencing with bioinformatics analysis and detailed clinical evaluation to elaborate a more accurate diagnosis and correct diagnosis for transfusion dependant hemolytic anemia in a cohort of the Indian population.
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Affiliation(s)
- Rashmi Dongerdiye
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Meghana Bokde
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Tejashree Anil More
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Arati Saptarshi
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Rati Devendra
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Ashish Chiddarwar
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Prashant Warang
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India
| | - Prabhakar Kedar
- Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India.
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9
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Si-Hung L, Izumi Y, Bamba T. First proof-of-concept of UC/HILIC for extending the versatility of the current art of supercritical fluid separation. Anal Chim Acta 2023; 1240:340741. [PMID: 36641155 DOI: 10.1016/j.aca.2022.340741] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/04/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Supercritical Fluid Chromatography (SFC), a high-throughput separation technique, has been widely applied as a promising routine method in pharmaceutical, pesticides, and metabolome analysis in the same way as conventional liquid chromatography and gas chromatography. Unified chromatography (UC), an advanced version of SFC, which applied gradient elution with mobile phase changing continuously from supercritical to subcritical and to liquid states, can further extend the SFC applications. UC mostly applying the popular mobile phase of 95%:5%/Methanol:Water with additives allows to analyze many hydrophilic compounds. However, many of phosphorylated metabolites or multi carboxylic acids show very poor peak shapes or even can't be eluted under UC conditions, thus hampering the UC's metabolome coverage. In this study, we proposed the first proof-of-concept of UC/HILIC, a novel strategy to extend the current UC metabolome coverage by employing an aqueous gradient right after the UC gradient on a single packed column in a single measurement. The proposed method showed significant improvement regarding the chromatographic performance and metabolome coverage, while still maintaining the precision and high throughput in comparison with conventional UC methods.
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Affiliation(s)
- Le Si-Hung
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Japan.
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10
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Muralidhara P, Ewald JC. Protein-Metabolite Interactions Shape Cellular Metabolism and Physiology. Methods Mol Biol 2023; 2554:1-10. [PMID: 36178616 DOI: 10.1007/978-1-0716-2624-5_1] [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] [Indexed: 06/16/2023]
Abstract
Protein-metabolite interactions regulate many important cellular processes but still remain understudied. Recent technological advancements are gradually uncovering the complexity of the protein-metabolite interactome. Here, we highlight some classic and recent examples of how protein metabolite interactions regulate metabolism, both locally and globally, and how this contributes to cellular physiology. We also discuss the importance of these interactions in diseases such as cancer.
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Affiliation(s)
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
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11
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Dong H, Zhang J, Zhang H, Han Y, Lu C, Chen C, Tan X, Wang S, Bai X, Zhai G, Tian S, Zhang T, Cheng Z, Li E, Xu L, Zhang K. YiaC and CobB regulate lysine lactylation in Escherichia coli. Nat Commun 2022; 13:6628. [PMID: 36333310 PMCID: PMC9636275 DOI: 10.1038/s41467-022-34399-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Lysine lactylation (Kla) has recently been reported to participate in regulating transcription in human cells. However, the characterization, regulatory mechanism and functional consequence of Kla in prokaryotes remain unclear. Here, we report that YiaC functions as a lysine lactylase and that CobB serves as a lysine delactylase in the regulation of metabolism. We demonstrate that YiaC catalyzes the addition of Kla, while CobB erases this PTM both in vitro and intracellularly. Moreover, we show that YdiF can catalyze the formation of a lactyl-coenzyme A, which donates lactyl group for Kla. Quantitative proteomic analysis further reveals 446 endogenous Kla sites targeted by CobB and 79 candidates targeted by YiaC in Escherichia coli (E. coli). Furthermore, we present that Kla can influence the functions of metabolic enzymes. Interestingly, we demonstrate that CobB can specifically modulate the activity of PykF by regulating K382la, promoting glycolysis and bacterial growth. Our study identifies the regulatory enzymes and functional network of Kla and reveals a Kla-mediated molecular mechanism catalyzed by CobB for glycolysis regulation in E. coli.
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Affiliation(s)
- Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, 515041, Shantou, Guangdong, China
| | - Jianji Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Hui Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Yue Han
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Congcong Lu
- College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Chen Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xiaoxia Tan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Siyu Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Tao Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Zhongyi Cheng
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou, 310018, Zhejiang, China
| | - Enmin Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, 515041, Shantou, Guangdong, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 515041, Shantou, Guangdong, China
| | - Liyan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, 515041, Shantou, Guangdong, China.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin Medical University, 300070, Tianjin, China.
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, Medical University General Hospital, Tianjin Medical University, 300070, Tianjin, China.
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12
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Akunuri R, Unnissa T, Vadakattu M, Bujji S, Mahammad Ghouse S, Madhavi Yaddanapudi V, Chopra S, Nanduri S. Bacterial Pyruvate Kinase: A New Potential Target to Combat Drug‐Resistant
Staphylococcus aureus
Infections. ChemistrySelect 2022. [DOI: 10.1002/slct.202201403] [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]
Affiliation(s)
- Ravikumar Akunuri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Tanveer Unnissa
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Manasa Vadakattu
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sushmitha Bujji
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Shaik Mahammad Ghouse
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology CSIR-Central Drug Research Institute (CDRI) Sitapur Road, Sector 10, Janakipuram Extension Lucknow 226 031, Uttar Pradesh India
| | - Srinivas Nanduri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
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13
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Metabolic Reprogramming in Sickle Cell Diseases: Pathophysiology and Drug Discovery Opportunities. Int J Mol Sci 2022; 23:ijms23137448. [PMID: 35806451 PMCID: PMC9266828 DOI: 10.3390/ijms23137448] [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: 05/03/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 01/19/2023] Open
Abstract
Sickle cell disease (SCD) is a genetic disorder that affects millions of individuals worldwide. Chronic anemia, hemolysis, and vasculopathy are associated with SCD, and their role has been well characterized. These symptoms stem from hemoglobin (Hb) polymerization, which is the primary event in the molecular pathogenesis of SCD and contributes to erythrocyte or red blood cell (RBC) sickling, stiffness, and vaso-occlusion. The disease is caused by a mutation at the sixth position of the β-globin gene, coding for sickle Hb (HbS) instead of normal adult Hb (HbA), which under hypoxic conditions polymerizes into rigid fibers to distort the shapes of the RBCs. Only a few therapies are available, with the universal effectiveness of recently approved therapies still being monitored. In this review, we first focus on how sickle RBCs have altered metabolism and then highlight how this understanding reveals potential targets involved in the pathogenesis of the disease, which can be leveraged to create novel therapeutics for SCD.
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14
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Liang M, Ge X, Xua H, Ma K, Zhang W, Zan Y, Efferth T, Xue Z, Hua X. Phytochemicals with activity against methicillin-resistant Staphylococcus aureus. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 100:154073. [PMID: 35397285 DOI: 10.1016/j.phymed.2022.154073] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The evolution of resistance to antimicrobials is a ubiquitous phenomenon. The evolution of antibiotic resistance in Staphylococcus aureus suggests that there is no remedy with sustaining effectiveness against this pathogen. The limited number of antibacterial drug classes and the common occurrence of cross-resistant bacteria reinforce the urgent need to discover new compounds targeting novel cellular functions. Natural products are a potential source of novel antibacterial agents. Anti-MRSA (methicillin-resistant S. aureus) bioactive compounds from Streptomyces and the anti-MRSA activity of a series of plant extracts have been reviewed respectively. However, there has been no detailed review of the precise bioactive components from plants. PURPOSE The present review aimed to summarize the phytochemicals that have been reported with anti-MRSA activities, analyze their structure-activity relationship and novel anti-MRSA mechanisms. METHODS Data contained in this review article are compiled from the authoritative databases PubMed, Web of Science, Google Scholar, and so on. RESULTS This review summarizes 100 phytochemicals (27 flavonoids, 23 alkaloids, 17 terpenes and 33 others) that have been tested for their anti-MRSA activity. Among these phytochemicals, 39 compounds showed remarkable anti-MRSA activity with MIC values less than 10 μg/ml, 14 compounds with MIC ranges including values < 10 μg/ml, 5 compounds with MIC values less than 5 μM; 11 phytochemicals show synergism anti-MRSA effects in combination with antibiotics. Phytochemicals exerted anti-MRSA activities mainly by destroying the membrane structure and inhibiting the efflux pump. CONCLUSIONS The 58 compounds with excellent anti-MRSA activity the 11 compounds with synergistic anti-MRSA effect, especially cannabinoids, xanthones and fatty acids should be further studied in vitro. Novel targets, such as cell membrane and efflux pump could be promising alternatives to develop antibacterial drugs in the future in order to prevent drug resistance.
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Affiliation(s)
- Miaomiao Liang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala SE-75124, Sweden
| | - Hui Xua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Kaifeng Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Wei Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Yibo Zan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz 55128, Germany
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.
| | - Xin Hua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.
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15
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Dierolf JG, Hunter HLM, Watson AJ, Betts DH. Modulation of PKM1/2 levels by steric blocking morpholinos alters the metabolic and pluripotent state of murine pluripotent stem cells. Stem Cells Dev 2022; 31:278-295. [PMID: 35469439 DOI: 10.1089/scd.2021.0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cellular metabolism plays both an active and passive role in embryonic development, pluripotency, and cell-fate decisions. However, little is known regarding the role of metabolism in regulating the recently described "formative" pluripotent state. The pluripotent developmental continuum features a metabolic switch from a bivalent metabolism (both glycolysis and oxidative phosphorylation) in naïve cells, to predominantly glycolysis in primed cells. We investigated the role of pyruvate kinase muscle isoforms (PKM1/2) in naïve, formative, and primed mouse embryonic stem cells through modulation of PKM1/2 mRNA transcripts using steric blocking morpholinos that downregulate PKM2 and upregulate PKM1. We have examined these effects in naïve, formative, and primed cells by quantifying the effects of PKM1/2 modulation on pluripotent and metabolic transcripts and by measuring shifts in the population frequencies of cells expressing naïve and primed cell surface markers by flow cytometry. Our results demonstrate that modulating PKM1 and PKM2 levels alters the transition from the naïve state into a primed pluripotent state by enhancing the proportion of the affected cells seen in the "formative" state. Therefore, we conclude that PKM1/2 actively contributes to mechanisms that oversee early stem pluripotency and their progression towards a primed pluripotent state.
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Affiliation(s)
- Joshua George Dierolf
- University of Western Ontario Schulich School of Medicine and Dentistry, 70384, Physiology and Pharmacology, London, Ontario, Canada;
| | - Hailey L M Hunter
- University of Western Ontario Schulich School of Medicine and Dentistry, 70384, Physiology and Pharmacology, London, Ontario, Canada;
| | - Andrew John Watson
- University of Western Ontario Schulich School of Medicine and Dentistry, 70384, Physiology and Pharmacology, London, Ontario, Canada;
| | - Dean Harvey Betts
- University of Western Ontario Schulich School of Medicine and Dentistry, 70384, Physiology and Pharmacology, London, Ontario, Canada;
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16
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Ohba S, Tang Y, Johannessen TCA, Mukherjee J. PKM2 Interacts With the Cdk1-CyclinB Complex to Facilitate Cell Cycle Progression in Gliomas. Front Oncol 2022; 12:844861. [PMID: 35392228 PMCID: PMC8981990 DOI: 10.3389/fonc.2022.844861] [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: 12/28/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
PKM2 is a phosphotyrosine-binding glycolytic enzyme upregulated in many cancers, including glioma, and contributes to tumor growth by regulating cell cycle progression. We noted, however, that in multiple glioma cell lines, PKM2 knock-down resulted in an accumulation of cells in G2-M phase. Moreover, PKM2 knock-down decreased Cdk1 activity while introducing a constitutively active Cdk1 reversed the effects of PKM2 knock-down on cell cycle progression. The means by which PKM2 increases Cdk1 activity have not been described. Transient interaction of T14/Y15-phosphorylated Cdk1 with cyclin B allows Cdk7-mediated pT161 Cdk1 phosphorylation followed by cdc25C-mediated removal of pT14/Y15 and activation of Cdk1 in cycling cells. In the present course of investigation, PKM2 modulation did not influence Cdk7 activity, but phosphotyrosine binding forms of PKM2 co-immunoprecipitated with pY15-containing Cdk1-cyclinB and enhanced formation of active pT161 Cdk1-cyclin B complexes. Moreover, exogenous expression of phosphotyrosine binding forms of PKM2 reversed the effects of PKM2 knock-down on G2-M arrest. We here show that PKM2 binds and stabilize otherwise transient pY15-containing Cdk1-cyclinB complexes that in turn facilitate Cdk1-cyclin B activation and entry of cells into mitosis. These results, therefore, establish metabolic enzyme PKM2 as a direct interactor and activator of Cdk1-cyclin B complex and thereby directly controls mitotic progression and the growth of brain tumor cells.
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Affiliation(s)
- Shigeo Ohba
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurosurgery, Fujita Health University, Toyoake, Japan
| | - Yongjian Tang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Tor-Christian Aase Johannessen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- The Kristian Gerhard Jebsen Brain Tumor Research Centre, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Joydeep Mukherjee
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Joydeep Mukherjee,
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17
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Yuce M, Sarica Z, Ates B, Kurkcuoglu O. Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow. J Biomol Struct Dyn 2022; 41:3496-3510. [PMID: 35302925 DOI: 10.1080/07391102.2022.2051743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Experimental evidence indicated that bacterial pyruvate kinase of glycolysis can be evaluated as an alternative target to eliminate infections, while antibiotic resistance poses a global threat. Here, we use a computational workflow to reveal and investigate the potential allosteric sites of methicillin-resistant S. aureus PK, which can help in designing species-specific drugs to inhibit activity of this organism. Residue interaction networks point to a known allosteric site at the small C-C interface, a potential allosteric site near the small interface (site #1), and a second potential allosteric site at the large interface (site #2). 2 µs-long molecular dynamics (MD) simulations with AMBER16 generate different conformations of one narrow target site. Known and potential allosteric sites on the selected conformers are investigated using ensemble docking with AutoDock Vina and a library of 2447 FDA-approved drugs. We determine 18 hits, comprising ergot-alkaloids, anti-cancer-agents, antivirals, analgesics, cardiac glycosides, all with a high docking z-score for three sites. 5 selected compounds with high, average and low z-scores are subjected to 50 ns-long MD simulations for MM-GBSA calculations. ΔGbind values up to -49.3 kcal/mol at the C-C interface, up to -32.7 kcal/mol at site #1, and up to -53.3 kcal/mol at site #2 support the docking calculations. We investigate mitapivat and TT-232 as reference compounds under clinical trial, targeting human PK isomers. We suggest 18 FDA-approved hits from the docking calculations and TT-232 as potential inhibitors with multiple target sites on S. aureus PK. This study also proposes pharmacophores models for de novo drug design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Merve Yuce
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Zehra Sarica
- Computational Science and Engineering Division, Informatics Institute, Istanbul Technical University, Istanbul, Turkey
| | - Beril Ates
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
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18
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Arora S, Joshi G, Chaturvedi A, Heuser M, Patil S, Kumar R. A Perspective on Medicinal Chemistry Approaches for Targeting Pyruvate Kinase M2. J Med Chem 2022; 65:1171-1205. [PMID: 34726055 DOI: 10.1021/acs.jmedchem.1c00981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The allosteric regulation of pyruvate kinase M2 (PKM2) affects the switching of the PKM2 protein between the high-activity and low-activity states that allow ATP and lactate production, respectively. PKM2, in its low catalytic state (dimeric form), is chiefly active in metabolically energetic cells, including cancer cells. More recently, PKM2 has emerged as an attractive target due to its role in metabolic dysfunction and other interrelated conditions. PKM2 (dimer) activity can be inhibited by modulating PKM2 dimer-tetramer dynamics using either PKM2 inhibitors that bind at the ATP binding active site of PKM2 (dimer) or PKM2 activators that bind at the allosteric site of PKM2, thus activating PKM2 from the dimer formation to the tetrameric formation. The present perspective focuses on medicinal chemistry approaches to design and discover PKM2 inhibitors and activators and further provides a scope for the future design of compounds targeting PKM2 with better efficacy and selectivity.
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Affiliation(s)
- Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
- School of Pharmacy, Graphic Era Hill University, Dehradun, Uttarakhand 248171, India
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | - Santoshkumar Patil
- Discovery Services, Syngene International Ltd., Biocon Park, SEZ, Bommasandra Industrial Area-Phase-IV, Bommasandra-Jigani Link Road, Bengaluru, Karnataka 560099, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
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19
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Sørensen PE, Baig S, Stegger M, Ingmer H, Garmyn A, Butaye P. Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. Front Microbiol 2021; 12:782757. [PMID: 34966369 PMCID: PMC8711792 DOI: 10.3389/fmicb.2021.782757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/23/2021] [Indexed: 01/19/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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20
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Herkenhoff ME, Bovolenta LA, Broedel O, Dos Santos LD, de Oliveira AC, Chuffa LGA, Ribeiro ADO, Lupi LA, Dias MAD, Hilsdorf AWS, Frohme M, Pinhal D. Variant expression signatures of microRNAs and protein related to growth in a crossbreed between two strains of Nile tilapia (Oreochromis niloticus). Genomics 2021; 113:4303-4312. [PMID: 34774982 DOI: 10.1016/j.ygeno.2021.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/05/2021] [Accepted: 11/07/2021] [Indexed: 11/24/2022]
Abstract
Nile tilapia (Oreochromis niloticus) is a species of worldwide importance for aquaculture. A crossbred lineage was developed through introgressive backcross breeding techniques and combines the high growth performance of the Chitralada (CHIT) lwith attractive reddish color of the Red Stirling (REDS) strains. Since the crossbreed has an unknown genetically improved background, the objective of this work was to characterize expression signatures that portray the advantageous phenotype of the crossbreeds. We characterized the microRNA transcriptome by high throughput sequencing (RNA-seq) and the proteome through mass spectrometry (ESI-Q-TOF-MS) and applied bioinformatics for the comparative analysis of such molecular data on the three strains. Crossbreed expressed a distinct set of miRNAs and proteins compared to the parents. They comprised several microRNAs regulate traits of economic interest. Proteomic profiles revealed differences between parental and crossbreed in expression of proteins associated with glycolisis. Distinctive miRNA and protein signatures contribute to the phenotype of crossbreed.
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Affiliation(s)
- Marcos Edgar Herkenhoff
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Luiz A Bovolenta
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Oliver Broedel
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany.
| | - Lucilene D Dos Santos
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Arthur C de Oliveira
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Luiz G A Chuffa
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Amanda de O Ribeiro
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Luiz A Lupi
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Marco A D Dias
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil; Department of Animal Sciences, Federal University of Lavras, Lavras, MG, Brazil
| | - Alexandre W S Hilsdorf
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil; Department of Animal Sciences, Federal University of Lavras, Lavras, MG, Brazil.
| | - Marcus Frohme
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany.
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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21
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Badruna L, Burlat V, Roblin P, Enjalbert T, Lippens G, Venditto I, O'Donohue MJ, Montanier CY. The Jo-In protein welding system is a relevant tool to create CBM-containing plant cell wall degrading enzymes. N Biotechnol 2021; 65:31-41. [PMID: 34352412 DOI: 10.1016/j.nbt.2021.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022]
Abstract
Irrespective of their biological origin, most proteins are composed of several elementary domains connected by linkers. These domains are either functionally independent units, or part of larger multidomain structures whose functions are defined by their spatial proximity. Carbohydrate-degrading enzymes provide examples of a range of multidomain structures, in which catalytic protein domains are frequently appended to one or more non-catalytic carbohydrate-binding modules which specifically bind to carbohydrate motifs. While the carbohydrate-binding specificity of these modules is clear, their function is not fully elucidated. Herein, an original approach to tackle the study of carbohydrate-binding modules using the Jo-In biomolecular welding protein pair is presented. To provide a proof of concept, recombinant xylanases appended to two different carbohydrate-binding modules have been created and produced. The data reveal the biochemical properties of four xylanase variants and provide the basis for correlating enzyme activity to structural properties and to the nature of the substrate and the ligand specificity of the appended carbohydrate-binding module. It reveals that specific spatial arrangements favour activity on soluble polymeric substrates and that activity on such substrates does not predict the behaviour of multimodular enzymes on insoluble plant cell wall samples. The results highlight that the Jo-In protein welding system is extremely useful to design multimodular enzyme systems, especially to create rigid conformations that decrease the risk of intermodular interference. Further work on Jo-In will target the introduction of varying degrees of flexibility, providing the means to study this property and the way it may influence multimodular enzyme functions.
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Affiliation(s)
- Louise Badruna
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 24 chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Pierre Roblin
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Thomas Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Guy Lippens
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Immacolata Venditto
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021; 60:11448-11456. [PMID: 33687787 PMCID: PMC8252522 DOI: 10.1002/anie.202101642] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 11/06/2022]
Abstract
Biocatalysis for the synthesis of fine chemicals is highly attractive but usually requires organic (co-)solvents (OSs). However, native enzymes often have low activity and resistance in OSs and at elevated temperatures. Herein, we report a smart salt bridge design strategy for simultaneously improving OS resistance and thermostability of the model enzyme, Bacillus subtilits Lipase A (BSLA). We combined comprehensive experimental studies of 3450 BSLA variants and molecular dynamics simulations of 36 systems. Iterative recombination of four beneficial substitutions yielded superior resistant variants with up to 7.6-fold (D64K/D144K) improved resistance toward three OSs while exhibiting significant thermostability (thermal resistance up to 137-fold, and half-life up to 3.3-fold). Molecular dynamics simulations revealed that locally refined flexibility and strengthened hydration jointly govern the highly increased resistance in OSs and at 50-100 °C. The salt bridge redesign provides protein engineers with a powerful and likely general approach to design OSs- and/or thermal-resistant lipases and other α/β-hydrolases.
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Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| | - Lobna Eltoukhy
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Lingling Zhang
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th Avenue 32, Tianjin Airport Economic Area300308TianjinChina
| | - Ulrich Markel
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfWilhelm Johnen Strasse52426JülichGermany
- Institute of Bio-and Geosciences IBG 1: BiotechnologyForschungszentrum Jülich GmbHWilhelm Johnen Strasse52426JülichGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
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23
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Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | - Lobna Eltoukhy
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Lingling Zhang
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue 32, Tianjin Airport Economic Area 300308 Tianjin China
| | - Ulrich Markel
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf Wilhelm Johnen Strasse 52426 Jülich Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology Forschungszentrum Jülich GmbH Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Mehdi D. Davari
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
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24
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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25
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Puccio T, Misra BB, Kitten T. Time-course analysis of Streptococcus sanguinis after manganese depletion reveals changes in glycolytic and nucleic acid metabolites. Metabolomics 2021; 17:44. [PMID: 33893555 PMCID: PMC8064989 DOI: 10.1007/s11306-021-01795-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/13/2021] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Manganese is important for the endocarditis pathogen Streptococcus sanguinis. Little is known about why manganese is required for virulence or how it impacts the metabolome of streptococci. OBJECTIVES We applied untargeted metabolomics to cells and media to understand temporal changes resulting from manganese depletion. METHODS EDTA was added to a S. sanguinis manganese-transporter mutant in aerobic fermentor conditions. Cell and media samples were collected pre- and post-EDTA treatment. Metabolomics data were generated using positive and negative modes of data acquisition on an LC-MS/MS system. Data were subjected to statistical processing using MetaboAnalyst and time-course analysis using Short Time series Expression Miner (STEM). Recombinant enzymes were assayed for metal dependence. RESULTS We observed quantitative changes in 534 and 422 metabolites in cells and media, respectively, after EDTA addition. The 173 cellular metabolites identified as significantly different indicated enrichment of purine and pyrimidine metabolism. Further multivariate analysis revealed that the top 15 cellular metabolites belonged primarily to lipids and redox metabolites. The STEM analysis revealed global changes in cells and media in comparable metabolic pathways. Glycolytic intermediates such as fructose-1,6-bisphosphate increased, suggesting that enzymes that utilize them require manganese for activity or expression. Recombinant enzymes were confirmed to utilize manganese in vitro. Nucleosides accumulated, possibly due to a blockage in conversion to nucleobases resulting from manganese-dependent regulation. CONCLUSION Differential analysis of metabolites revealed the activation of a number of metabolic pathways in response to manganese depletion, many of which are connected to carbon catabolite repression.
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Affiliation(s)
- Tanya Puccio
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, VA, 23298, USA
| | - Biswapriya B Misra
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA
| | - Todd Kitten
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, VA, 23298, USA.
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Liu J, Zhu XY, Deng LB, Liu HF, Li J, Zhou XR, Wang HZ, Hua W. Nitric oxide affects seed oil accumulation and fatty acid composition through protein S-nitrosation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:385-397. [PMID: 33045083 DOI: 10.1093/jxb/eraa456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Nitric oxide (NO) is a key signaling molecule regulating several plant developmental and stress responses. Here, we report that NO plays an important role in seed oil content and fatty acid composition. RNAi silencing of Arabidopsis S-nitrosoglutathione reductase 1 (GSNOR1) led to reduced seed oil content. In contrast, nitrate reductase double mutant nia1nia2 had increased seed oil content, compared with wild-type plants. Moreover, the concentrations of palmitic acid (C16:0), linoleic acid (C18:2), and linolenic acid (C18:3) were higher, whereas those of stearic acid (C18:0), oleic acid (C18:1), and arachidonic acid (C20:1) were lower, in seeds of GSNOR1 RNAi lines. Similar results were obtained with rapeseed embryos cultured in vitro with the NO donor sodium nitroprusside (SNP), and the NO inhibitor NG-Nitro-L-arginine Methyl Ester (L-NAME). Compared with non-treated embryos, the oil content decreased in SNP-treated embryos, and increased in L-NAME-treated embryos. Relative concentrations of C16:0, C18:2 and C18:3 were higher, whereas C18:1 concentration decreased in rapeseed embryos treated with SNP. Proteomics and transcriptome analysis revealed that three S-nitrosated proteins and some key genes involved in oil synthesis, were differentially regulated in SNP-treated embryos. Therefore, regulating NO content could be a novel approach to increasing seed oil content in cultivated oil crops.
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Affiliation(s)
- Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Xiao-Yi Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Lin-Bin Deng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Hong-Fang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Jun Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Xue-Rong Zhou
- Agriculture and Food Commonwealth Scientific and Industrial Research Organization, Canberra, ACT 2601, Australia
| | - Han-Zhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
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Kok ADX, Mohd Yusoff NF, Sekeli R, Wee CY, Lamasudin DU, Ong-Abdullah J, Lai KS. Pluronic F-68 Improves Callus Proliferation of Recalcitrant Rice Cultivar via Enhanced Carbon and Nitrogen Metabolism and Nutrients Uptake. FRONTIERS IN PLANT SCIENCE 2021; 12:667434. [PMID: 34149763 PMCID: PMC8207202 DOI: 10.3389/fpls.2021.667434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/27/2021] [Indexed: 05/12/2023]
Abstract
Pluronic F-68 (PF-68) is a non-ionic surfactant used in plant tissue culture as a growth additive. Despite its usage as a plant growth enhancer, the mechanism underlying the growth-promoting effects of PF-68 remains largely unknown. Hence, this study was undertaken to elucidate the growth-promoting mechanism of PF-68 using recalcitrant MR 219 callus as a model. Supplementation of 0.04% PF-68 (optimum concentration) was shown to enhance callus proliferation. The treated callus recorded enhanced sugar content, protein content, and glutamate synthase activity as exemplified in the comparative proteome analysis, showing protein abundance involved in carbohydrate metabolism (alpha amylase), protein biosynthesis (ribosomal proteins), and nitrogen metabolism (glutamate synthase), which are crucial to plant growth and development. Moreover, an increase in nutrients uptake was also noted with potassium topping the list, suggesting a vital role of K in governing plant growth. In contrast, 0.10% PF-68 (high concentration) induced stress response in the callus, revealing an increment in phenylalanine ammonia lyase activity, malondialdehyde content, and peroxidase activity, which were consistent with high abundance of phenylalanine ammonia lyase, peroxidase, and peroxiredoxin proteins detected and concomitant with a reduced level of esterase activity. The data highlighted that incorporation of PF-68 at optimum concentration improved callus proliferation of recalcitrant MR 219 through enhanced carbohydrate metabolism, nitrogen metabolism, and nutrient uptake. However, growth-promoting effects of PF-68 are concentration dependent.
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Affiliation(s)
- Andrew De-Xian Kok
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nur Fatihah Mohd Yusoff
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Rogayah Sekeli
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Kuala Lumpur, Malaysia
| | - Chien-Yeong Wee
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Kuala Lumpur, Malaysia
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Janna Ong-Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- *Correspondence: Janna Ong-Abdullah
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
- Kok-Song Lai
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28
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Usman B, Nawaz G, Zhao N, Liao S, Qin B, Liu F, Liu Y, Li R. Programmed Editing of Rice ( Oryza sativa L.) OsSPL16 Gene Using CRISPR/Cas9 Improves Grain Yield by Modulating the Expression of Pyruvate Enzymes and Cell Cycle Proteins. Int J Mol Sci 2020; 22:E249. [PMID: 33383688 PMCID: PMC7795130 DOI: 10.3390/ijms22010249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/17/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the major crops in the world and significant increase in grain yield is constant demand for breeders to meet the needs of a rapidly growing population. The size of grains is one of major components determining rice yield and a vital trait for domestication and breeding. To increase the grain size in rice, OsSPL16/qGW8 was mutagenized through CRISPR/Cas9, and proteomic analysis was performed to reveal variations triggered by mutations. More specifically, mutants were generated with two separate guide RNAs targeting recognition sites on opposite strands and genomic insertions and deletions were characterized. Mutations followed Mendelian inheritance and homozygous and heterozygous mutants lacking any T-DNA and off-target effects were screened. The mutant lines showed a significant increase in grain yield without any change in other agronomic traits in T0, T1, and T2 generations. Proteomic screening found a total of 44 differentially expressed proteins (DEPs), out of which 33 and 11 were up and downregulated, respectively. Most of the DEPs related to pyruvate kinase, pyruvate dehydrogenase, and cell division and proliferation were upregulated in the mutant plants. Pathway analysis revealed that DEPs were enriched in the biosynthesis of secondary metabolites, pyruvate metabolism, glycolysis/gluconeogenesis, carbon metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and citrate cycle. Gene Ontology (GO) analysis presented that most of the DEPs were involved in the pyruvate metabolic process and pyruvate dehydrogenase complex. Proteins related to pyruvate dehydrogenase E1 component subunit alpha-1 displayed higher interaction in the protein-protein interaction (PPI) network. Thus, the overall results revealed that CRISPR/Cas9-guided OsSPL16 mutations have the potential to boost the grain yield of rice. Additionally, global proteome analysis has broad applications for discovering molecular components and dynamic regulation underlying the targeted gene mutations.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Shanyue Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
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29
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Grotegut P, Perumal N, Kuehn S, Smit A, Dick HB, Grus FH, Joachim SC. Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model. J Neuroinflammation 2020; 17:375. [PMID: 33317557 PMCID: PMC7737388 DOI: 10.1186/s12974-020-02012-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Previous studies noted that intravitreal injection of S100B triggered a glaucoma-like degeneration of retina and optic nerve as well as microglia activation after 14 days. The precise role of microglia in our intravitreal S100B model is still unclear. Hence, microglia were inhibited through minocycline. The aim is to investigate whether microglia have a significant influence on the degeneration process or whether they are only a side effect in the model studied here. METHODS Minocycline was applied daily in rats by intraperitoneal injection using two different concentrations (13.5 mg/kg body weight, 25 mg/kg body weight). One day after treatment start, S100B or PBS was intravitreally injected in one eye per rat. The naïve groups received no injections. This resulted in a total of five groups (naïve n = 14, PBS n = 14, S100B n = 13, 13.5 mg/kg mino n = 15, 25 mg/kg mino n = 15). At day 14, electroretinogram measurements were performed, followed by immunofluorescence and label-free quantitative proteomics analysis. The focus of these investigations was on the survival of RGCs as well as their axons, the response of the microglia, and the identification of further pathological modes of action of S100B. RESULTS The best signal transmission was detected via ERG in the 13.5 mg/kg mino group. The inhibition of the microglia protected optic nerve neurofilaments and decreased the negative impact of S100B on RGCs. However, the minocycline treatment could not trigger complete protection of RGCs. Furthermore, in retina and optic nerve, the minocycline treatment reduced the number and activity of S100B-triggered microglia in a concentration-dependent manner. Proteomics analysis showed that S100B application led to numerous metabolic functions and cellular stress, mainly an increased inflammatory response, glycolysis, and mitochondrial dysfunction, which caused oxidative stress in the retina. Importantly, the protective capability of lower dose of minocycline was unraveled by suppressing the apoptotic, inflammatory, and the altered metabolic processes caused by S100B insult in the retina. CONCLUSION Intravitreally injected S100B not only led to a pro-inflammatory microglial reaction, but also a mitochondrial and metabolic dysfunction. Also, these results suggest that an excessive microglial response may be a significant degenerative factor, but not the only trigger for increased cell death.
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Affiliation(s)
- Pia Grotegut
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sandra Kuehn
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Andreas Smit
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - H Burkhard Dick
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Franz H Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stephanie C Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany.
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Kitamura S, Shimizu H, Toya Y. Identification of a rate-limiting step in a metabolic pathway using the kinetic model and in vitro experiment. J Biosci Bioeng 2020; 131:271-276. [PMID: 33168471 DOI: 10.1016/j.jbiosc.2020.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022]
Abstract
Identification of the rate-limiting step in a metabolic pathway is an important challenge in metabolic engineering for enhancing pathway flow. Although specific enzyme activities (Vmax) provide valuable clues for the identification, it is time-consuming and difficult to measure multiple enzymes in the pathway because different assay protocols are required for each enzyme. In the present study, we propose a method to simultaneously determine the Vmax values of multiple enzymes using a kinetic model with a time course of the intermediate concentrations through an in vitro experiment. To demonstrate this method, nine glycolysis reactions for converting glucose-6-phosphate (G6P) to pyruvate in Escherichia coli were considered. In a reaction mixture containing G6P and cofactors, glycolysis was initiated by adding a crude cell extract obtained from stationary phase cells. The Vmax values were optimized to minimize the difference between the measured and simulated time-courses using a kinetic model. Metabolic control analysis using the kinetic model with the estimated Vmax values revealed that fructose bisphosphate aldolase (FBA) was the rate-limiting step in the upper part of glycolysis. The addition of FBA in the reaction mixture successfully increased the glycolytic flux in vitro. Furthermore, in vivo, the specific glucose consumption rate of an FBA overexpression strain was 1.4 times higher than that of the control strain during the stationary phase. These results confirmed that FBA was the rate-limiting step in glycolysis under the stationary phase. This approach provides Vmax values of multiple enzymes in a pathway for metabolic control analysis with a kinetic model.
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Affiliation(s)
- Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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31
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Sugrue E, Coombes D, Wood D, Zhu T, Donovan KA, Dobson RCJ. The lid domain is important, but not essential, for catalysis of Escherichia coli pyruvate kinase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:761-772. [PMID: 32978636 DOI: 10.1007/s00249-020-01466-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/24/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022]
Abstract
Pyruvate kinase catalyses the final step of the glycolytic pathway in central energy metabolism. The monomeric structure comprises three domains: a catalytic TIM-barrel, a regulatory domain involved in allosteric activation, and a lid domain that encloses the substrates. The lid domain is thought to close over the TIM-barrel domain forming contacts with the substrates to promote catalysis and may be involved in stabilising the activated state when the allosteric activator is bound. However, it remains unknown whether the lid domain is essential for pyruvate kinase catalytic or regulatory function. To address this, we removed the lid domain of Escherichia coli pyruvate kinase type 1 (PKTIM+Reg) using protein engineering. Biochemical analyses demonstrate that, despite the absence of key catalytic residues in the lid domain, PKTIM+Reg retains a low level of catalytic activity and has a reduced binding affinity for the substrate phosphoenolpyruvate. The enzyme retains allosteric activation, but the regulatory profile of the enzyme is changed relative to the wild-type enzyme. Analytical ultracentrifugation and small-angle X-ray scattering data show that, beyond the loss of the lid domain, the PKTIM+Reg structure is not significantly altered and is consistent with the wild-type tetramer that is assembled through interactions at the TIM and regulatory domains. Our results highlight the contribution of the lid domain for facilitating pyruvate kinase catalysis and regulation, which could aid in the development of small molecule inhibitors for pyruvate kinase and related lid-regulated enzymes.
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Affiliation(s)
- Elena Sugrue
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - David Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Tong Zhu
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Katherine A Donovan
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
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Bianchi P, Fermo E. Molecular heterogeneity of pyruvate kinase deficiency. Haematologica 2020; 105:2218-2228. [PMID: 33054047 PMCID: PMC7556514 DOI: 10.3324/haematol.2019.241141] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/03/2020] [Indexed: 01/19/2023] Open
Abstract
Red cell pyruvate kinase (PK) deficiency is the most common glycolytic defect associated with congenital non-spherocytic hemolytic anemia. The disease, transmitted as an autosomal recessive trait, is caused by mutations in the PKLR gene and is characterized by molecular and clinical heterogeneity; anemia ranges from mild or fully compensated hemolysis to life-threatening forms necessitating neonatal exchange transfusions and/or subsequent regular transfusion support; complications include gallstones, pulmonary hypertension, extramedullary hematopoiesis and iron overload. Since identification of the first pathogenic variants responsible for PK deficiency in 1991, more than 300 different variants have been reported, and the study of molecular mechanisms and the existence of genotype-phenotype correlations have been investigated in-depth. In recent years, during which progress in genetic analysis, next-generation sequencing technologies and personalized medicine have opened up important landscapes for diagnosis and study of molecular mechanisms of congenital hemolytic anemias, genotyping has become a prerequisite for accessing new treatments and for evaluating disease state and progression. This review examines the extensive molecular heterogeneity of PK deficiency, focusing on the diagnostic impact of genotypes and new acquisitions on pathogenic non-canonical variants. The recent progress and the weakness in understanding the genotype-phenotype correlation, and its practical usefulness in light of new therapeutic opportunities for PK deficiency are also discussed.
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MESH Headings
- Anemia, Hemolytic, Congenital/diagnosis
- Anemia, Hemolytic, Congenital/genetics
- Anemia, Hemolytic, Congenital/therapy
- Anemia, Hemolytic, Congenital Nonspherocytic/diagnosis
- Anemia, Hemolytic, Congenital Nonspherocytic/genetics
- Humans
- Mutation
- Pyruvate Kinase/deficiency
- Pyruvate Kinase/genetics
- Pyruvate Metabolism, Inborn Errors/diagnosis
- Pyruvate Metabolism, Inborn Errors/genetics
- Pyruvate Metabolism, Inborn Errors/therapy
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Affiliation(s)
- Paola Bianchi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, UOC Ematologia, UOS Fisiopatologia delle Anemie, Milan, Italy.
| | - Elisa Fermo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, UOC Ematologia, UOS Fisiopatologia delle Anemie, Milan, Italy
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Tsujii T, Kawada-Matsuo M, Migita H, Ohta K, Oogai Y, Yamasaki Y, Komatsuzawa H. Antibacterial activity of phellodendron bark against Streptococcus mutans. Microbiol Immunol 2020; 64:424-434. [PMID: 32196736 DOI: 10.1111/1348-0421.12787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 01/01/2023]
Abstract
Streptococcus mutans is a major cause of tooth decay due to its promotion of biofilm formation and acid production. Several plant extracts have been reported to have multiple biological activities such as anti-inflammation and antibacterial effects. This study investigated the antibacterial activity of three plant extracts, phellodendron bark (PB), yucca, and black ginger, and found that PB had a stronger effect than the other extracts. Then, the minimum inhibitory concentration (MIC) of PB against 100 S. mutans strains was investigated. The MIC range of PB was 9.8-312.5 µg/mL. PB suppressed the growth kinetics of S. mutans in a dose-dependent manner, even at sub-MICs of PB. Then, we investigated the effect of PB on S. mutans virulence. The PB suppressed biofilm formation at high concentrations, although PB did not affect the expression of glucosyltransferase genes. Additionally, PB suppressed the decrease in pH from adding an excess of glucose. The expression of genes responsible for acid production was increased by the addition of excess glucose without PB, whereas their expression levels were not increased in the presence of 1× and 2× MIC of PB. Although PB showed a bacteriostatic effect on planktonic S. mutans cells, it was found that more than 2× MIC of PB showed a partial bactericidal effect on biofilm cells. In conclusion, PB not only showed antibacterial activity against S. mutans but also decreased the cariogenic activity in S. mutans.
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Affiliation(s)
- Toshiya Tsujii
- Department of Pediatric Dentistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Miki Kawada-Matsuo
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hirono Migita
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kouji Ohta
- Department of Public Oral Health, Program of Oral Health Sciences, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Youichi Yamasaki
- Department of Pediatric Dentistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
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34
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Ates-Alagoz Z, Kisla MM, Goker H, Yildiz S. Synthesis, Molecular Docking Studies and Antibacterial Activities of Novel Monocationic Indole-benzimidazole Derivatives. Med Chem 2020; 17:699-706. [PMID: 32310051 DOI: 10.2174/1573406416666200420080459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/18/2020] [Accepted: 04/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Finding efficient therapy against hospital-acquired MRSA infections has become rather important in the last decade. To this end, inhibition of the enzyme pyruvate kinase (PK) is being investigated for antibacterial activity, since this enzyme controls energy generation and metabolic flux distribution. Our main scaffold consists of benzimidazole and indole rings fused together. Both rings are famous for antibacterial properties and promising anti-MRSA compounds including indole ring. METHODS Several 1-substituted-2-(1H-indol-3-yl)-N-substituted-1H-benzimidazole-5-carboxamidine analogues were developed, synthesized and their antibacterial activities were evaluated against Staphylococcus aureus (ATCC 25923), Methicillin resistant Staphylococcus aureus (MRSA) (ATCC 43300), and Staphylococcus epidermidis (ATCC 12228) by using tube dilution method. Molecular docking analysis with a characteristic protein called MRSA- Pyruvate Kinase has been conducted for the assessment of the activities of our compounds against Methicillinresistant S. aureus (MRSA). RESULTS Among all the tested compounds, the most potent compound 36 had MIC values as 3.12, 3.12 and 6.25 μg/mL against S. aureus, Methicillin-resistant S. aureus (MRSA), and S. epidermidis, respectively. This compound had much better docking energy value than standard ampicillin and also created the link between two residues in different monomers of PK. DISCUSSION This approach of using indol-amidine conjugate systems as anti-MRSA agents may include MRSA-PK as potential target. To further increase the affinity, some other H-bonding parts may be added. By doing so, another bridge with Ile361 residues on both sides can be created. Our compounds tend to violate log P limit of Lipinski, therefore some optimizations with formulation can be made. CONCLUSION This study mainly includes the design, synthesis and optimization of indolebenzimidazole- amidine derivatives. Docking studies confirmed our results, since our most potent hit compound 36 created the necessary interactions between two chains of MRSA-PK. Further optimization can be considered to increase drug ability.
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Affiliation(s)
- Zeynep Ates-Alagoz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Mehmet Murat Kisla
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Hakan Goker
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Sulhiye Yildiz
- Department of Microbiology, Faculty of Pharmacy, Ankara University, Ankara, Turkey
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Ding Y, Xue Q, Liu S, Hu K, Wang D, Wang T, Li Y, Guo H, Hao X, Ge W, Zhang Y, Li A, Li J, Chen Y, Zhang Q. Identification of Parthenolide Dimers as Activators of Pyruvate Kinase M2 in Xenografts of Glioblastoma Multiforme in Vivo. J Med Chem 2020; 63:1597-1611. [DOI: 10.1021/acs.jmedchem.9b01328] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yahui Ding
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Qingqing Xue
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Shuo Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Kai Hu
- College of Medicine, Nankai University, 94 Weijin Road, Tianjin 3000710, People’s Republic of China
| | - Da Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Tianpeng Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Ye Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Hongyu Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Xin Hao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Weizhi Ge
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Yan Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Ang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Jing Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Yue Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Quan Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
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36
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Experimental infection by Neospora caninum in gerbil reduces activity of enzymes involved in energy metabolism. Exp Parasitol 2019; 208:107790. [PMID: 31697939 DOI: 10.1016/j.exppara.2019.107790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/24/2019] [Accepted: 11/02/2019] [Indexed: 11/24/2022]
Abstract
Neospora caninum is a protozoan that has tropism for the central nervous system. The aim of this study was to determine whether experimental infection of gerbils would interfere with activity of enzymes associated with energy metabolism. We randomized 20 gerbils into two groups (ten animals per group): the control group (healthy animals; uninfected) and the infected group (experimentally infected with dose 7.8 × 102 tachyzoites of N. caninum per gerbil). On day six and twelve post-infection (PI), brain and spleen tissues were collected for biochemical and histopathological analyses. No histopathological lesions were observed in the brains of infected animals; however, inflammatory infiltrates were found in the spleen. Significantly greater levels of reactive oxygen species (ROS) were observed in the brain and spleen of infected gerbils than in the control group at 12 days PI. Cytosolic creatine kinase (CK-CYT), mitochondrial creatine kinase (CK-MIT), and pyruvate kinase (PK) activities were lower in the brains of infected gerbils than in those of the control group on day 12 PI. There was significantly less CK-CYT activity in the spleens of infected gerbils on day 6 and 12 PI. Finally, there was significantly less sodium-potassium ion pump (Na+/K+ ATPase) activity in the brains and spleens of infected gerbils on day 12 PI. These data suggest that experimental infection with N. caninum interfered with energy metabolism associated with ATP homeostasis in the brain and spleen, directly or indirectly, apparently mediated by ROS overproduction, contributing to inhibition of Na+/K+ ATPase activity.
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Biochemical and biophysical characterization of the smallest pyruvate kinase from Entamoeba histolytica. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140296. [PMID: 31676451 DOI: 10.1016/j.bbapap.2019.140296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/07/2023]
Abstract
Entamoeba histolytica infection is highly prevalent in developing countries across the globe. The ATP synthesis in this pathogen is solely dependent on the glycolysis pathway where pyruvate kinase (Pyk) catalyzes the final reaction. Here, we have cloned, overexpressed and purified the pyruvate kinase (EhPyk) from E. histolytica. EhPyk is the shortest currently known Pyk till date as it contains only two of the three characterized domains when compared to the other homologues and our phylogenetic analysis places it on a distinct branch from the known type I/II Pyks. Our purification results suggested that it exists as a homodimer in solution. The kinetic characterization showed that EhPyk has maximum activity at pH 7.5 where it exhibited Michaelis-Menten's kinetics for phosphoenolpyruvate with a Km of 0.23 mM, and it lost its activity at both the acidic pH 4.0 and basic pH 10.0. We also determined the key secondary structural elements of EhPyk at different pH values. MD simulation of EhPyk structure at different pH values suggested that it is most stable at pH 7.0, while least stable at pH 10.0 followed by pH 4.0. Together, our computational simulations correlate well with the experimental studies. In summary, this study expands the current understanding of the EhPyk identified earlier in the amoebic genome and provides the first characterization of this bacterially expressed protein.
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Gaviraghi A, Correa Soares JBR, Mignaco JA, Fontes CFL, Oliveira MF. Mitochondrial glycerol phosphate oxidation is modulated by adenylates through allosteric regulation of cytochrome c oxidase activity in mosquito flight muscle. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 114:103226. [PMID: 31446033 DOI: 10.1016/j.ibmb.2019.103226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/20/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
The huge energy demand posed by insect flight activity is met by an efficient oxidative phosphorylation process that takes place within flight muscle mitochondria. In the major arbovirus vector Aedes aegypti, mitochondrial oxidation of pyruvate, proline and glycerol 3-phosphate (G3P) represent the major energy sources of ATP to sustain flight muscle energy demand. Although adenylates exert critical regulatory effects on several mitochondrial enzyme activities, the potential consequences of altered adenylate levels to G3P oxidation remains to be determined. Here, we report that mitochondrial G3P oxidation is controlled by adenylates through allosteric regulation of cytochrome c oxidase (COX) activity in A. aegypti flight muscle. We observed that ADP significantly activated respiratory rates linked to G3P oxidation, in a protonmotive force-independent manner. Kinetic analyses revealed that ADP activates respiration through a slightly cooperative mechanism. Despite adenylates caused no effects on G3P-cytochrome c oxidoreductase activity, COX activity was allosterically activated by ADP. Conversely, ATP exerted powerful inhibitory effects on respiratory rates linked to G3P oxidation and on COX activity. We also observed that high energy phosphate recycling mechanisms did not contribute to the regulatory effects of adenylates on COX activity or G3P oxidation. We conclude that mitochondrial G3P oxidation in A. aegypti flight muscle is regulated by adenylates through the allosteric modulation of COX activity, underscoring the bioenergetic relevance of this novel mechanism and the potential consequences for mosquito dispersal.
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Affiliation(s)
- Alessandro Gaviraghi
- Laboratório de Bioquímica de Resposta ao Estresse, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil.
| | - Juliana B R Correa Soares
- Laboratório de Bioquímica de Resposta ao Estresse, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil
| | - Julio A Mignaco
- Laboratório de Estrutura e Regulação de Proteínas e ATPases, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Carlos Frederico L Fontes
- Laboratório de Estrutura e Regulação de Proteínas e ATPases, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Marcus F Oliveira
- Laboratório de Bioquímica de Resposta ao Estresse, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil.
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Alquraishi M, Puckett DL, Alani DS, Humidat AS, Frankel VD, Donohoe DR, Whelan J, Bettaieb A. Pyruvate kinase M2: A simple molecule with complex functions. Free Radic Biol Med 2019; 143:176-192. [PMID: 31401304 PMCID: PMC6848794 DOI: 10.1016/j.freeradbiomed.2019.08.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/29/2019] [Accepted: 08/07/2019] [Indexed: 12/31/2022]
Abstract
Pyruvate kinase M2 is a critical enzyme that regulates cell metabolism and growth under different physiological conditions. In its metabolic role, pyruvate kinase M2 catalyzes the last glycolytic step which converts phosphoenolpyruvate to pyruvate with the generation of ATP. Beyond this metabolic role in glycolysis, PKM2 regulates gene expression in the nucleus, phosphorylates several essential proteins that regulate major cell signaling pathways, and contribute to the redox homeostasis of cancer cells. The expression of PKM2 has been demonstrated to be significantly elevated in several types of cancer, and the overall inflammatory response. The unusual pattern of PKM2 expression inspired scientists to investigate the unrevealed functions of PKM2 and the therapeutic potential of targeting PKM2 in cancer and other disorders. Therefore, the purpose of this review is to discuss the mechanistic and therapeutic potential of targeting PKM2 with the focus on cancer metabolism, redox homeostasis, inflammation, and metabolic disorders. This review highlights and provides insight into the metabolic and non-metabolic functions of PKM2 and its relevant association with health and disease.
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Affiliation(s)
- Mohammed Alquraishi
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Dexter L Puckett
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Dina S Alani
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Amal S Humidat
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Victoria D Frankel
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Dallas R Donohoe
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Jay Whelan
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA
| | - Ahmed Bettaieb
- Department of Nutrition, University of Tennessee Knoxville, Knoxville, TN, 37996-0840, USA; Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996-0840, USA.
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Schormann N, Hayden KL, Lee P, Banerjee S, Chattopadhyay D. An overview of structure, function, and regulation of pyruvate kinases. Protein Sci 2019; 28:1771-1784. [PMID: 31342570 DOI: 10.1002/pro.3691] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/24/2022]
Abstract
In the last step of glycolysis Pyruvate kinase catalyzes the irreversible conversion of ADP and phosphoenolpyruvate to ATP and pyruvic acid, both crucial for cellular metabolism. Thus pyruvate kinase plays a key role in controlling the metabolic flux and ATP production. The hallmark of the activity of different pyruvate kinases is their tight modulation by a variety of mechanisms including the use of a large number of physiological allosteric effectors in addition to their homotropic regulation by phosphoenolpyruvate. Binding of effectors signals precise and orchestrated movements in selected areas of the protein structure that alter the catalytic action of these evolutionarily conserved enzymes with remarkably conserved architecture and sequences. While the diverse nature of the allosteric effectors has been discussed in the literature, the structural basis of their regulatory effects is still not well understood because of the lack of data representing conformations in various activation states. Results of recent studies on pyruvate kinases of different families suggest that members of evolutionarily related families follow somewhat conserved allosteric strategies but evolutionarily distant members adopt different strategies. Here we review the structure and allosteric properties of pyruvate kinases of different families for which structural data are available.
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Affiliation(s)
- Norbert Schormann
- Department of Biochemistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katherine L Hayden
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama
| | - Paul Lee
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois
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Flexible Metabolism and Suppression of Latent Enzymes Are Important for Escherichia coli Adaptation to Diverse Environments within the Host. J Bacteriol 2019; 201:JB.00181-19. [PMID: 31160397 DOI: 10.1128/jb.00181-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/27/2019] [Indexed: 12/13/2022] Open
Abstract
Bacterial metabolism is necessary for adaptation to the host microenvironment. Flexible metabolic pathways allow uropathogenic Escherichia coli (UPEC) to harmlessly reside in the human intestinal tract and cause disease upon extraintestinal colonization. E. coli intestinal colonization requires carbohydrates as a carbon source, while UPEC extraintestinal colonization requires gluconeogenesis and the tricarboxylic acid cycle. UPEC containing disruptions in two irreversible glycolytic steps involving 6-carbon (6-phosphofructokinase; pfkA) and 3-carbon (pyruvate kinase; pykA) substrates have no fitness defect during urinary tract infection (UTI); however, both reactions are catalyzed by isozymes: 6-phosphofructokinases Pfk1 and Pfk2, encoded by pfkA and pfkB, and pyruvate kinases Pyk II and Pyk I, encoded by pykA and pykF UPEC strains lacking one or both phosphofructokinase-encoding genes (pfkB and pfkA pfkB) and strains lacking one or both pyruvate kinase genes (pykF and pykA pykF) were investigated to determine their regulatory roles in carbon flow during glycolysis by examining their fitness during UTI and in vitro growth requirements. Loss of a single phosphofructokinase-encoding gene has no effect on fitness, while the pfkA pfkB double mutant outcompeted the parental strain in the bladder. A defect in bladder and kidney colonization was observed with loss of pykF, while loss of pykA resulted in a fitness advantage. The pykA pykF mutant was indistinguishable from wild-type in vivo, suggesting that the presence of Pyk II rather than the loss of Pyk I itself is responsible for the fitness defect in the pykF mutant. These findings suggest that E. coli suppresses latent enzymes to survive in the host urinary tract.IMPORTANCE Urinary tract infections are the most frequently diagnosed urologic disease, with uropathogenic Escherichia coli (UPEC) infections placing a significant financial burden on the health care system by generating more than two billion dollars in annual costs. This, in combination with steadily increasing antibiotic resistances to present day treatments, necessitates the discovery of new antimicrobial agents to combat these infections. By broadening our scope beyond the study of virulence properties and investigating bacterial physiology and metabolism, we gain a better understanding of how pathogens use nutrients and compete within host microenvironments, enabling us to cultivate new therapeutics to exploit and target pathogen growth requirements in a specific host environment.
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Chen P, Shi Q, Liang Z, Lu H, Li R. Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line. Genome 2019; 62:455-466. [DOI: 10.1139/gen-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.
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Affiliation(s)
- Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Qiqi Shi
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhichen Liang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
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Yamashita T, Kawada-Matsuo M, Katsumata T, Watanabe A, Oogai Y, Nishitani Y, Miyawaki S, Komatsuzawa H. Antibacterial activity of disodium succinoyl glycyrrhetinate, a derivative of glycyrrhetinic acid against Streptococcus mutans. Microbiol Immunol 2019; 63:251-260. [PMID: 31166029 DOI: 10.1111/1348-0421.12717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/09/2019] [Accepted: 05/23/2019] [Indexed: 11/28/2022]
Abstract
Streptococcus mutans is a cariogenic bacterium that localizes in the oral cavity. Glycyrrhetinic acid (GRA) is a major component of licorice extract. GRA and several derivatives, including disodium succinoyl glycyrrhetinate (GR-SU), are known to have anti-inflammatory effects in humans. In this study, the antimicrobial effect of GRA and its derivatives against the S. mutans UA159 strain were investigated. Minimum inhibitory concentrations (MICs) of GRA and GR-SU showed antibacterial activity against the S. mutans strain, whereas other tested derivatives did not. Because GR-SU is more soluble than GRA, GR-SU was used for further experiments. The antibacterial activity of GR-SU against 100 S. mutans strains was evaluated and it was found that all strains are susceptible to GR-SU, with MIC values below 256 µg/mL. A cell viability assay showed that GR-SU has a bacteriostatic effect on S. mutans cells. As to growth kinetics, sub-MICs of GR-SU inhibited growth. The effect of GR-SU on S. mutans virulence was then investigated. GR-SU at sub-MICs suppresses biofilm formation. Additionally, GR-SU greatly suppresses the pH drop caused by the addition of glucose and glucose-induced expression of the genes responsible for acid production (ldh and pykF) and tolerance (aguD and atpD). Additionally, expression of enolase, which is responsible for the carbohydrate phosphotransferase system, was not increased in the presence of GR-SU, indicating that GR-SU suppresses incorporation of sugars into S. mutans. In conclusion, GR-SU has antibacterial activity against S. mutans and also decreases S. mutans virulence.
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Affiliation(s)
- Takahito Yamashita
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Miki Kawada-Matsuo
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Tamaki Katsumata
- Department of Restorative Dentistry and Endodontology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Atsuko Watanabe
- Department of Orthodontics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yoshihiro Nishitani
- Department of Restorative Dentistry and Endodontology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shouichi Miyawaki
- Department of Orthodontics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
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Stella RG, Wiechert J, Noack S, Frunzke J. Evolutionary engineering of
Corynebacterium glutamicum. Biotechnol J 2019; 14:e1800444. [DOI: 10.1002/biot.201800444] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/23/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Roberto G. Stella
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Johanna Wiechert
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Stephan Noack
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Julia Frunzke
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
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Sultana MM, Dutta AK, Tanaka Y, Aboulela M, Nishimura K, Sugiura S, Niwa T, Maeo K, Goto-Yamada S, Kimura T, Ishiguro S, Mano S, Nakagawa T. Gateway binary vectors with organelle-targeted fluorescent proteins for highly sensitive reporter assay in gene expression analysis of plants. J Biotechnol 2019; 297:19-27. [PMID: 30902643 DOI: 10.1016/j.jbiotec.2019.03.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 11/18/2022]
Abstract
Fluorescent proteins are valuable tools in the bioscience field especially in subcellular localization analysis of proteins and expression analysis of genes. Fusion with organelle-targeting signal accumulates fluorescent proteins in specific organelles, increases local brightness, and highlights the signal of fluorescent proteins even in tissues emitting a high background of autofluorescence. For these advantages, organelle-targeted fluorescent proteins are preferably used for promoter:reporter assay to define organ-, tissue-, or cell-specific expression pattern of genes in detail. In this study, we have developed a new series of Gateway cloning technology-compatible binary vectors, pGWBs (attR1-attR2 acceptor sites) and R4L1pGWB (attR4-attL1 acceptor sites), carrying organelle-targeted synthetic green fluorescent protein with S65T mutation (sGFP) (ER-, nucleus-, peroxisome-, and mitochondria-targeted sGFP) and organelle-targeted tag red fluorescent protein (TagRFP) (nucleus-, peroxisome-, and mitochondria-targeted TagRFP). These are available for preparation of promoter:reporter constructs by an LR reaction with a promoter entry clone attL1-promoter-attL2 (for pGWBs) or attL4-promoter-attR1 (for R4L1pGWBs), respectively. A transient expression experiment with particle bombardment using cauliflower mosaic virus 35S promoter-driven constructs has confirmed the correct localization of newly developed organelle-targeted TagRFPs by a co-localization analysis with the previously established organelle-targeted sGFPs. More intense and apparent fluorescence signals were detected by the nucleus- and peroxisome-targeted sGFPs than by the normal sGFPs in the promoter assay using transgenic Arabidopsis thaliana. The new pGWBs and R4L1pGWBs developed here are highly efficient and may serve as useful platforms for more accurate observation of GFP and RFP signals in gene expression analyses of plants.
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Affiliation(s)
- Mst Momtaz Sultana
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan; Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan; Department of Agricultural Extension (DAE), Ministry of Agriculture, Khamarbari, Dhaka, Bangladesh
| | - Amit Kumar Dutta
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan; Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan; Department of Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Yuji Tanaka
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan
| | - Mostafa Aboulela
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan; Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Kohji Nishimura
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan; Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Sayaka Sugiura
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomoko Niwa
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenichiro Maeo
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Tetsuya Kimura
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Sumie Ishiguro
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Tsuyoshi Nakagawa
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan; Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan.
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Johnsen U, Reinhardt A, Landan G, Tria FDK, Turner JM, Davies C, Schönheit P. New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases. FEBS J 2019; 286:2471-2489. [PMID: 30945446 DOI: 10.1111/febs.14837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/01/2019] [Accepted: 04/02/2019] [Indexed: 11/28/2022]
Abstract
Pyruvate kinases (PKs) synthesize ATP as the final step of glycolysis in the three domains of life. PKs from most bacteria and eukarya are allosteric enzymes that are activated by sugar phosphates; for example, the feed-forward regulator fructose-1,6-bisphosphate, or AMP as a sensor of energy charge. Archaea utilize unusual glycolytic pathways, but the allosteric properties of PKs from these species are largely unknown. Here, we present an analysis of 24 PKs from most archaeal clades with respect to allosteric properties, together with phylogenetic analyses constructed using a novel mode of rooting protein trees. We find that PKs from many Thermoproteales, an order of crenarchaeota, are allosterically activated by 3-phosphoglycerate (3PG). We also identify five conserved amino acids that form the binding pocket for 3PG. 3PG is generated via an irreversible reaction in the modified glycolytic pathway of these archaea and therefore functions as a feed-forward regulator. We also show that PKs from hyperthermophilic Methanococcales, an order of euryarchaeota, are activated by AMP. Phylogenetic analyses indicate that 3PG-activated PKs form an evolutionary lineage that is distinct from that of sugar-phosphate activated PKs, and that sugar phosphate-activated PKs originated as AMP-regulated PKs in hyperthermophilic Methanococcales. Since the phospho group of sugar phosphates and 3PG overlap in the allosteric site, our data indicate that the allostery in PKs first started from a progenitor phosphate-binding site that evolved in two spatially distinct directions: one direction generated the canonical site that responds to sugar phosphates and the other gave rise to the 3PG site present in Thermoproteales. Overall, our data suggest an intimate connection between the allosteric properties and evolution of PKs.
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Affiliation(s)
- Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
| | - Andreas Reinhardt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
| | - Giddy Landan
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
| | - Fernando D K Tria
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
| | - Jonathan M Turner
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Christopher Davies
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
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47
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Bianchi P, Fermo E, Glader B, Kanno H, Agarwal A, Barcellini W, Eber S, Hoyer JD, Kuter DJ, Maia TM, Mañu-Pereira MDM, Kalfa TA, Pissard S, Segovia JC, van Beers E, Gallagher PG, Rees DC, van Wijk R. Addressing the diagnostic gaps in pyruvate kinase deficiency: Consensus recommendations on the diagnosis of pyruvate kinase deficiency. Am J Hematol 2019; 94:149-161. [PMID: 30358897 DOI: 10.1002/ajh.25325] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 01/19/2023]
Abstract
Pyruvate kinase deficiency (PKD) is the most common enzyme defect of glycolysis and an important cause of hereditary, nonspherocytic hemolytic anemia. The disease has a worldwide geographical distribution but there are no verified data regarding its frequency. Difficulties in the diagnostic workflow and interpretation of PK enzyme assay likely play a role. By the creation of a global PKD International Working Group in 2016, involving 24 experts from 20 Centers of Expertise we studied the current gaps in the diagnosis of PKD in order to establish diagnostic guidelines. By means of a detailed survey and subsequent discussions, multiple aspects of the diagnosis of PKD were evaluated and discussed by members of Expert Centers from Europe, USA, and Asia directly involved in diagnosis. Broad consensus was reached among the Centers on many clinical and technical aspects of the diagnosis of PKD. The results of this study are here presented as recommendations for the diagnosis of PKD and used to prepare a diagnostic algorithm. This information might be helpful for other Centers to deliver timely and appropriate diagnosis and to increase awareness in PKD.
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Affiliation(s)
- Paola Bianchi
- UOC Ematologia, Fisiopatologia delle Anemie; Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico; Milan Italy
| | - Elisa Fermo
- UOC Ematologia, Fisiopatologia delle Anemie; Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico; Milan Italy
| | - Bertil Glader
- Lucile Packard Children's Hospital; Stanford University School of Medicine; Palo Alto California
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing; Faculty of Medicine, Tokyo Women's Medical University; Tokyo Japan
| | | | - Wilma Barcellini
- UOC Ematologia, Fisiopatologia delle Anemie; Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico; Milan Italy
| | - Stefan Eber
- Special Praxis for Pediatric Hematology and Childrens’ Hospital; Technical University; Munich Germany
| | - James D. Hoyer
- Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - David J. Kuter
- Hematology Division; Massachusetts General Hospital; Boston Massachusetts
| | | | | | - Theodosia A. Kalfa
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and Department of Pediatrics; University of Cincinnati, College of Medicine; Cincinnati Ohio
| | - Serge Pissard
- APHP-University Hospital Henri Mondor and Inserm IMRB U955eq2; Creteil France
| | - José-Carlos Segovia
- Differentiation and Cytometry Unit. Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas; Medioambientales y Tecnológicas (CIEMAT) - Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER); Madrid Spain
- Advance Therapies Mixed Unit; Instituto de Investigación Sanitaria-Fundación Jimenez Díaz (IIS-FJD); Madrid Spain
| | - Eduard van Beers
- Van Creveldkliniek, University Medical Center Utrecht; University of Utrecht; Utrecht The Netherlands
| | - Patrick G. Gallagher
- Departments of Pediatrics, Pathology and Genetics; Yale University School of Medicine; New Haven Connecticut
| | - David C. Rees
- Department of Paediatric Haematology; King's College Hospital; London United Kingdom
| | - Richard van Wijk
- Department of Clinical Chemistry and Haematology, Division Laboratories, Pharmacy and Biomedical Genetics; University Medical Center Utrecht, Utrecht University; Utrecht The Netherlands
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48
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Liao Y, Yang J, Brandt BW, Li J, Crielaard W, van Loveren C, Deng DM. Genetic Loci Associated With Fluoride Resistance in Streptococcus mutans. Front Microbiol 2018; 9:3093. [PMID: 30619172 PMCID: PMC6297193 DOI: 10.3389/fmicb.2018.03093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/29/2018] [Indexed: 12/03/2022] Open
Abstract
The prolonged exposure of the cariogenic bacterial species Streptococcus mutans to high concentrations of fluoride leads to the development of fluoride resistance in this species. Previous studies confirmed the involvement of a mutation in a single chromosomal region in the occurrence of fluoride resistance. The involvement of multiple genomic mutations has not been verified. The aim of this study is to identify multiple genetic loci associated with fluoride resistance in S. mutans. The previously published whole genome sequences of two fluoride-resistant S. mutans strains (UA159-FR and C180-2FR) and their corresponding wild-type strains (UA159 and C180-2) were analyzed to locate shared chromosomal mutations in fluoride-resistant strains. Both fluoride-resistant strains were isolated in laboratory by culturing their mother strains in media with high concentrations of fluoride. The corresponding gene expression and enzyme activities were accordingly validated. Mutations were identified in two glycolytic enzymes, namely pyruvate kinase and enolase. Pyruvate kinase was deactivated in fluoride-resistant strain C180-2FR. Enolase was less inhibited by fluoride in fluoride-resistant strain UA159-FR than in its wild-type strain. Mutations in the promoter mutp constitutively increased the promoter activity and up-regulated the expression of the downstream fluoride antiporters in fluoride-resistant strains. Mutations in the intergenic region glpFp led to lower expression of glpF, encoding a glycerol uptake facilitator protein, in fluoride-resistant strains than in wild-type strains. Our results revealed that there is overlap of chromosomal regions with mutations among different fluoride-resistant S. mutans strains. They provide novel candidates for the study of the mechanisms of fluoride resistance.
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Affiliation(s)
- Ying Liao
- West China College of Stomatology, Sichuan University, Chengdu, China.,Nanjing Stomatological Hospital, Nanjing University Medical School, Nanjing, China.,Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam - University of Amsterdam, Amsterdam, Netherlands
| | - Jingmei Yang
- West China College of Stomatology, Sichuan University, Chengdu, China.,Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam - University of Amsterdam, Amsterdam, Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam - University of Amsterdam, Amsterdam, Netherlands
| | - Jiyao Li
- West China College of Stomatology, Sichuan University, Chengdu, China
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam - University of Amsterdam, Amsterdam, Netherlands
| | - Cor van Loveren
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam - University of Amsterdam, Amsterdam, Netherlands
| | - Dong Mei Deng
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam - University of Amsterdam, Amsterdam, Netherlands.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
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49
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Cai Y, Li S, Jiao G, Sheng Z, Wu Y, Shao G, Xie L, Peng C, Xu J, Tang S, Wei X, Hu P. OsPK2 encodes a plastidic pyruvate kinase involved in rice endosperm starch synthesis, compound granule formation and grain filling. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1878-1891. [PMID: 29577566 PMCID: PMC6181219 DOI: 10.1111/pbi.12923] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/01/2018] [Accepted: 03/18/2018] [Indexed: 05/18/2023]
Abstract
Starch is the main form of energy storage in higher plants. Although several enzymes and regulators of starch biosynthesis have been defined, the complete molecular machinery remains largely unknown. Screening for irregularities in endosperm formation in rice represents valuable prospect for studying starch synthesis pathway. Here, we identified a novel rice white-core endosperm and defective grain filling mutant, ospk2, which displays significantly lower grain weight, decreased starch content and alteration of starch physicochemical properties when compared to wild-type grains. The normal starch compound granules were drastically reduced and more single granules filled the endosperm cells of ospk2. Meanwhile, the germination rate of ospk2 seeds after 1-year storage was observably reduced compared with wild-type. Map-based cloning of OsPK2 indicated that it encodes a pyruvate kinase (PK, ATP: pyruvate 2-O-phosphotransferase, EC 2.7.1.40), which catalyses an irreversible step of glycolysis. OsPK2 has a constitutive expression in rice and its protein localizes in chloroplasts. Enzyme assay showed that the protein product from expressed OsPK2 and the crude protein extracted from tissues of wild-type exhibits strong PK activity; however, the mutant presented reduced protein activity. OsPK2 (PKpα1) and three other putative rice plastidic isozymes, PKpα2, PKpβ1 and PKpβ2, can interact to form heteromer. Moreover, the mutation leads to multiple metabolic disorders. Altogether, these results denote new insights into the role of OsPK2 in plant seed development, especially in starch synthesis, compound granules formation and grain filling, which would be useful for genetic improvement of high yield and rice grain quality.
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Affiliation(s)
- Yicong Cai
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Sanfeng Li
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guiai Jiao
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhonghua Sheng
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yawen Wu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Gaoneng Shao
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lihong Xie
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Cheng Peng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Quality and Standard for Agro‐productsZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Junfeng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Quality and Standard for Agro‐productsZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Shaoqing Tang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xiangjin Wei
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Peisong Hu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
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50
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Monroe JD, Pope LE, Breault JS, Berndsen CE, Storm AR. Quaternary Structure, Salt Sensitivity, and Allosteric Regulation of β-AMYLASE2 From Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:1176. [PMID: 30154813 PMCID: PMC6102588 DOI: 10.3389/fpls.2018.01176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
The β-amylase family in Arabidopsis thaliana has nine members, four of which are both plastid-localized and, based on active-site sequence conservation, potentially capable of hydrolyzing starch to maltose. We recently reported that one of these enzymes, BAM2, is catalytically active in the presence of physiological levels of KCl, exhibits sigmoidal kinetics with a Hill coefficient of over 3, is tetrameric, has a putative secondary binding site (SBS) for starch, and is highly co-expressed with other starch metabolizing enzymes. Here we generated a tetrameric homology model of Arabidopsis BAM2 that is a dimer of dimers in which the putative SBSs of two subunits form a deep groove between the subunits. To validate this model and identify key residues, we generated a series of mutations and characterized the purified proteins. (1) Three point mutations in the putative subunit interfaces disrupted tetramerization; two that interfered with the formation of the starch-binding groove were largely inactive, whereas a third mutation prevented pairs of dimers from forming and was active. (2) The model revealed that a 30-residue N-terminal acidic region, not found in other BAMs, appears to form part of the putative starch-binding groove. A mutant lacking this acidic region was active and did not require KCl for activity. (3) A conserved tryptophan residue in the SBS is necessary for activation and may form π-bonds with sugars in starch. (4) Sequence alignments revealed a conserved serine residue next to one of the catalytic glutamic acid residues, that is a conserved glycine in all other active BAMs. The serine side chain points away from the active site and toward the putative starch-binding groove. Mutating the serine in BAM2 to a glycine resulted in an enzyme with a VMax similar to that of the wild type enzyme but with a 7.5-fold lower KM for soluble starch. Interestingly, the mutant no longer exhibited sigmoidal kinetics, suggesting that allosteric communication between the putative SBS and the active site was disrupted. These results confirm the unusual structure and function of this widespread enzyme, and suggest that our understanding of starch degradation in plants is incomplete.
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Affiliation(s)
- Jonathan D. Monroe
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Lauren E. Pope
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Jillian S. Breault
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Christopher E. Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA, United States
| | - Amanda R. Storm
- Department of Biology, Western Carolina University, Cullowhee, NC, United States
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