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Ishikawa K, Soejima S, Nishimura T, Saitoh S. Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability. J Cell Biol 2025; 224:e202404085. [PMID: 39378339 PMCID: PMC11465072 DOI: 10.1083/jcb.202404085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 09/06/2024] [Accepted: 09/22/2024] [Indexed: 10/10/2024] Open
Abstract
The fission yeast, Schizosaccharomyces pombe, is an excellent eukaryote model organism for studying essential biological processes. Its genome contains ∼1,200 genes essential for cell viability, most of which are evolutionarily conserved. To study these essential genes, resources enabling conditional perturbation of target genes are required. Here, we constructed comprehensive arrayed libraries of plasmids and strains to knock down essential genes in S. pombe using dCas9-mediated CRISPRi. These libraries cover ∼98% of all essential genes in fission yeast. We estimate that in ∼60% of these strains, transcription of a target gene was repressed so efficiently that cell proliferation was significantly inhibited. To demonstrate the usefulness of these libraries, we performed metabolic analyses with knockdown strains and revealed flexible interaction among metabolic pathways. Libraries established in this study enable comprehensive functional analyses of essential genes in S. pombe and will facilitate the understanding of essential biological processes in eukaryotes.
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Affiliation(s)
- Ken Ishikawa
- Department of Cell Biology, Institute of Life Science, Kurume University, Kurume, Japan
| | - Saeko Soejima
- Department of Cell Biology, Institute of Life Science, Kurume University, Kurume, Japan
| | - Takashi Nishimura
- Laboratory of Metabolic Regulation and Genetics, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Shigeaki Saitoh
- Department of Cell Biology, Institute of Life Science, Kurume University, Kurume, Japan
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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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Kroth PG, Schroers Y, Kilian O. The peculiar distribution of class I and class II aldolases in diatoms and in red algae. Curr Genet 2005; 48:389-400. [PMID: 16273368 DOI: 10.1007/s00294-005-0033-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 09/23/2005] [Accepted: 09/27/2005] [Indexed: 10/25/2022]
Abstract
Diatom plastids probably evolved by secondary endocytobiosis from a red alga that was up by a eukaryotic host cell. Apparently, this process increased the complexity of the intracellular distribution of metabolic enzymes. We identified genes encoding fructose-bisphosphate aldolases (FBA) in two centric (Odontella sinensis, Thalassiosira pseudonana) and one pennate (Phaeodactylum tricornutum) diatoms and found that four different aldolases are present in both groups: two plastid targeted class II enzymes (FBAC1 and FBAC2), one cytosolic class II (FBA3) and one cytosolic class I (FBA4) enzyme. The pennate Phaeodactylum possesses an additional plastidic class I enzyme (FBAC5). We verified the classification of the different aldolases in the diatoms by enzymatic characterization of isolated plastids and whole cell extracts. Interestingly, our results imply that in plastids of centric and pennate diatoms mainly either class I or class II aldolases are active. We also identified genes for both class I and class II aldolases in red algal EST databases, thus presenting a fascinating example of the reutilization and recompartmentalization of different aldolase isoenzymes during secondary endocytobiosis but as well demonstrating the limited use of metabolic enzymes as markers for the interpretation of phylogenetic histories in algae.
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Affiliation(s)
- Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, Postfach M611, Konstanz, Germany.
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Nakahara K, Yamamoto H, Miyake C, Yokota A. Purification and characterization of class-I and class-II fructose-1,6-bisphosphate aldolases from the cyanobacterium Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2003; 44:326-33. [PMID: 12668779 DOI: 10.1093/pcp/pcg044] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The whole genome sequence database for Synechocystis sp. PCC 6803 has revealed the presence of genes encoding class-I (CI) and class-II (CII) fructose-1,6-bisphosphate aldolases (FBAs) in this organism. Two types of FBA from Synechocystis sp. PCC 6803 were separated by chromatography on phenyl-Sepharose. The activity of the enzyme in the major peak was inhibited by the presence of 25 mM EDTA; however, the activity in the minor peak was not. Therefore, the FBA in the former fractions was designated as CII-FBA, and in the latter designated as CI-FBA. CI-FBA was functionally redundant in Synechocystis sp. PCC 6803, while no disruptant for the gene encoding CII-FBA was obtained under photoautotrophic conditions. The kinetic parameters of CI- and CII-FBAs purified from Synechocystis sp. PCC 6803 in the cleavage reaction of FBP were generally similar, except in their reactivity for SBP. The SBP/FBP activity ratio of the CII-FBA was two times higher than that of the CI-FBA.
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Affiliation(s)
- Ken Nakahara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0101 Japan
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da Fonseca CA, Jesuino RS, Felipe MS, Cunha DA, Brito WA, Soares CM. Two-dimensional electrophoresis and characterization of antigens from Paracoccidioides brasiliensis. Microbes Infect 2001; 3:535-42. [PMID: 11418327 DOI: 10.1016/s1286-4579(01)01409-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Paracoccidioides brasiliensis is a fungal pathogen of humans. To identify antigens from P. brasiliensis we fractionated a crude preparation of proteins from the fungus and detected the IgG reactive proteins by immunoblot assays of yeast cellular extracts with sera of patients with paracoccidioidomycosis (PCM). We identified and characterized six new antigens by amino acid sequencing and homology search analyses with other proteins deposited in a database. The newly characterized antigens were highly homologous to catalase, fructose-1,6-biphosphate aldolase (aldolase), glyceraldehyde-3-phosphate dehydrogenase, malate dehydrogenase and triosephosphate isomerase from several sources. The characterized antigens presented preferential synthesis in yeast cells, the host fungus phase.
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Affiliation(s)
- C A da Fonseca
- Laboratório de Biologia Molecular, ICBII, UFG, Universidade Federal de Goiás, 74001-970, Go, Goiânia, Brazil
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Flores CL, Rodríguez C, Petit T, Gancedo C. Carbohydrate and energy-yielding metabolism in non-conventional yeasts. FEMS Microbiol Rev 2000; 24:507-29. [PMID: 10978549 DOI: 10.1111/j.1574-6976.2000.tb00553.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sugars are excellent carbon sources for all yeasts. Since a vast amount of information is available on the components of the pathways of sugar utilization in Saccharomyces cerevisiae it has been tacitly assumed that other yeasts use sugars in the same way. However, although the pathways of sugar utilization follow the same theme in all yeasts, important biochemical and genetic variations on it exist. Basically, in most non-conventional yeasts, in contrast to S. cerevisiae, respiration in the presence of oxygen is prominent for the use of sugars. This review provides comparative information on the different steps of the fundamental pathways of sugar utilization in non-conventional yeasts: glycolysis, fermentation, tricarboxylic acid cycle, pentose phosphate pathway and respiration. We consider also gluconeogenesis and, briefly, catabolite repression. We have centered our attention in the genera Kluyveromyces, Candida, Pichia, Yarrowia and Schizosaccharomyces, although occasional reference to other genera is made. The review shows that basic knowledge is missing on many components of these pathways and also that studies on regulation of critical steps are scarce. Information on these points would be important to generate genetically engineered yeast strains for certain industrial uses.
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Affiliation(s)
- C L Flores
- Instituto de Investigaciones Biomédicas Alberto Sols C.S.I.C.-UAM, Unidad de Bioquímica y Genética de Levaduras, 28029, Madrid, Spain
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D'Souza SE, Altekar W. A Class II fructose-1,6-bisphosphate aldolase from a halophilic archaebacterium Haloferax mediterranei. J GEN APPL MICROBIOL 1998; 44:235-241. [PMID: 12501417 DOI: 10.2323/jgam.44.235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fructose-1,6-bisphosphate (FBP) aldolase (EC 4.1.2.13) was purified 97-fold from a halophilic archaebacterium Haloferax mediterranei, with a specific activity of 2.8. The enzyme was characterized as a Class II aldolase on the basis of its inhibition by EDTA and other metal chelators. The enzyme had a specific requirement for divalent metal Fe(2+) for activity. Sulfhydryl compounds enhanced aldolase activity.
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Affiliation(s)
- Sandra E. D'Souza
- Radiation Biology and Biochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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Reizer J, Ramseier TM, Reizer A, Charbit A, Saier MH. Novel phosphotransferase genes revealed by bacterial genome sequencing: a gene cluster encoding a putative N-acetylgalactosamine metabolic pathway in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 2):231-250. [PMID: 8932697 DOI: 10.1099/13500872-142-2-231] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have analysed a gene cluster in the 67 center dot 4-76 center dot 0 min region of the Escherichia coli chromosome, revealed by recent systematic genome sequencing. The genes within this cluster include: (1) five genes encoding homologues of the E. coli mannose permease of the phosphotransferase system (IIB, IIB', IIC, IIC' and IID); (2) genes encoding a putative N-acetylgalactosamine 6-phosphate metabolic pathway including (a) a deacetylase, (b) an isomerizing deaminase, (c) a putative carbohydrate kinase, and (d) an aldolase; and (3) a transcriptional regulatory protein homologous to members of the DeoR family. Evidence is presented suggesting that the aldolase-encoding gene within this cluster is the previously designated kba gene that encodes tagatose-1,6-bisphosphate aldolase. These proteins and a novel IIAMan-like protein encoded in the 2 center dot 4-4 center dot 1 min region are characterized with respect to their sequence similarities and phylogenetic relationships with other homologous proteins. A pathway for the metabolism of N-acetylgalactosamine biochemically similar to that for the metabolism of N-acetylglucosamine is proposed.
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Affiliation(s)
- Jonathan Reizer
- Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Tom M Ramseier
- Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Aiala Reizer
- Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Alain Charbit
- Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H Saier
- Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
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van den Bergh ER, Baker SC, Raggers RJ, Terpstra P, Woudstra EC, Dijkhuizen L, Meijer WG. Primary structure and phylogeny of the Calvin cycle enzymes transketolase and fructosebisphosphate aldolase of Xanthobacter flavus. J Bacteriol 1996; 178:888-93. [PMID: 8550527 PMCID: PMC177739 DOI: 10.1128/jb.178.3.888-893.1996] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Xanthobacter flavus, a gram-negative facultatively autotrophic bacterium, employs the Calvin cycle for the fixation of carbon dioxide. Cells grown under autotrophic growth conditions possess an Fe(2+)-dependent fructosebisphosphate (FBP) aldolase (class II) in addition to a class I FBP aldolase. By nucleotide sequencing and heterologous expression in Escherichia coli, genes encoding transketolase (EC 2.2.1.1.; CbbT) and class II FBP aldolase (EC 4.1.2.13; CbbA) were identified. A partial open reading frame encoding a protein similar to pentose-5-phosphate 3-epimerase was identified downstream from cbbA. A phylogenetic tree of transketolase proteins displays a conventional branching order. However, the class II FBP aldolase protein from X. flavus is only distantly related to that of E. coli. The autotrophic FBP aldolase proteins from X. flavus, Alcaligenes eutrophus, and Rhodobacter sphaeroides form a tight cluster, with the proteins from gram-positive bacteria as the closest relatives.
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Affiliation(s)
- E R van den Bergh
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, NN Haren, The Netherlands
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Qamar S, Marsh K, Berry A. Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli. Protein Sci 1996; 5:154-61. [PMID: 8771208 PMCID: PMC2143241 DOI: 10.1002/pro.5560050119] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Treatment of the Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with the arginine-specific alpha-dicarbonyl reagents, butanedione or phenylglyoxal, results in inactivation of the enzyme. The enzyme is protected from inactivation by the substrate, fructose 1,6-bisphosphate, or by inorganic phosphate. Modification with [7-14C] phenylglyoxal in the absence of substrate demonstrates that enzyme activity is abolished by the incorporation of approximately 2 moles of reagent per mole of enzyme. Sequence alignment of the eight known Class II FBP-aldolases shows that only one arginine residue is conserved in all the known sequences. This residue, Arg-331, was mutated to either alanine or glutamic acid. The mutant enzymes were much less susceptible to inactivation by phenylglyoxal. Measurement of the steady-state kinetic parameters revealed that mutation of Arg-331 dramatically increased the K(m) for fructose 1,6-bisphosphate. Comparatively small differences in the inhibitor constant Ki for dihydroxyacetone phosphate or its analogue, 2-phosphoglycolate, were found between the wild-type and mutant enzymes. In contrast, the mutation caused large changes in the kinetic parameters when glyceraldehyde 3-phosphate was used as an inhibitor. Kinetic analysis of the oxidation of the carbanionic aldolase-substrate intermediate of the reaction by hexacyanoferrate (III) revealed that the K(m) for dihydroxyacetone phosphate was again unaffected, whereas that for fructose 1,6-bisphosphate was dramatically increased. Taken together, these results show that Arg-331 is critically involved in the binding of fructose bisphosphate by the enzyme and demonstrate that it interacts with the C-6 phosphate group of the substrate.
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Affiliation(s)
- S Qamar
- Department of Biochemistry, University of Cambridge, United Kingdom
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