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Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production. mSystems 2022; 7:e0019922. [PMID: 36094082 PMCID: PMC9600765 DOI: 10.1128/msystems.00199-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Streptomyces rimosus is an industrial streptomycete, best known as a producer of oxytetracycline, one of the most widely used antibiotics. Despite the significant contribution of Streptomyces species to the pharmaceutical industry, most omics analyses have only been conducted on the model organism Streptomyces coelicolor. In recent years, protein phosphorylation on serine, threonine, and tyrosine (Ser, Thr, and Tyr, respectively) has been shown to play a crucial role in the regulation of numerous cellular processes, including metabolic changes leading to antibiotic production and morphological changes. In this study, we performed a comprehensive quantitative (phospho)proteomic analysis during the growth of S. rimosus under conditions of oxytetracycline production and pellet fragmentation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis combined with phosphopeptide enrichment detected a total of 3,725 proteins, corresponding to 45.6% of the proteome and 417 phosphorylation sites from 230 phosphoproteins. Significant changes in abundance during three distinct growth phases were determined for 494 proteins and 98 phosphorylation sites. Functional analysis revealed changes in phosphorylation events of proteins involved in important cellular processes, including regulatory mechanisms, primary and secondary metabolism, cell division, and stress response. About 80% of the phosphoproteins detected during submerged growth of S. rimosus have not yet been reported in streptomycetes, and 55 phosphoproteins were not reported in any prokaryote studied so far. This enabled the creation of a unique resource that provides novel insights into the dynamics of (phospho)proteins and reveals many potential regulatory events during antibiotic production in liquid culture of an industrially important bacterium. IMPORTANCE Streptomyces rimosus is best known as a primary source of oxytetracycline (OTC). The significant global market value of OTC highlights the need for a better understanding of the regulatory mechanisms that lead to production of this antibiotic. Our study provides, for the first time, a detailed insight into the dynamics of (phospho)proteomic profiles during growth and antibiotic production in liquid culture of S. rimosus. Significant changes in protein synthesis and phosphorylation have been revealed for a number of important cellular proteins during the growth stages that coincide with OTC production and morphological changes of this industrially important bacterium. Most of these proteins have not been detected in previous studies. Therefore, our results significantly expand the insight into phosphorylation events associated with important cellular processes and antibiotic production; they also greatly increase the phosphoproteome of streptomycetes and contribute with newly discovered phosphoproteins to the database of prokaryotic phosphoproteomes. This can consequently lead to the design of novel research directions in elucidation of the complex regulatory network in Streptomyces.
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Shanbhag P, Bhave S, Vartak A, Kulkarni-Almeida A, Mahajan G, Villanueva I, Davies J. Screening of Microbial Extracts for Anticancer Compounds Using Streptomyces Kinase Inhibitor Assay. Nat Prod Commun 2015. [DOI: 10.1177/1934578x1501000738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Eukaryotic kinases are known to play an important role in signal transduction pathways by phosphorylating their respective substrates. Abnormal phosphorylations by these kinases have resulted in diseases. Hence inhibitors of kinases are of considerable pharmaceutical interest for a wide variety of disease targets, especially cancers. A number of reports have been published which indicate that eukaryotic-like kinases may complement two-component kinase systems in several bacteria. In Streptomyces sp. such kinases have been found to have a role in formation of aerial hyphae, spores, pigmentation & even in antibiotic production in some strains. Eukaryotic kinase inhibitors are seen to inhibit formation of aerial mycelia in Streptomyces without inhibiting vegetative mycelia. This property has been used to design an assay to screen for eukaryotic kinase inhibitors. The assay involves testing of compounds against Streptomyces 85E ATCC 55824 using agar well diffusion method. Inhibitors of kinases give rise to “bald” colonies where aerial mycelia and sporulation inhibition is seen. The assay has been standardized using known eukaryotic protein kinase inhibiting anticancer agents like AG-490, AG-1295, AG-1478, Flavopiridol and Imatinib as positive controls, at a concentration ranging from 10 μg/well to 100 μg/well. Anti-infective compounds which are not reported to inhibit eukaryotic protein kinases were used as negative controls. A number of microbial cultures have been screened for novel eukaryotic protein kinase inhibitors. Further these microbial extracts were tested in various cancer cell lines like Panc1, HCT116, Calu1, ACHN and H460 at a concentration of 10 μg/mL/ well. The anticancer data was seen correlating well with the Streptomyces kinase assay thus validating the assay.
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Affiliation(s)
- Prashant Shanbhag
- Piramal Enterprises Limited, 1-Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai-400063, Maharashtra State, India
| | - Sarita Bhave
- Piramal Enterprises Limited, 1-Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai-400063, Maharashtra State, India
| | - Ashwini Vartak
- Piramal Enterprises Limited, 1-Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai-400063, Maharashtra State, India
| | - Asha Kulkarni-Almeida
- Piramal Enterprises Limited, 1-Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai-400063, Maharashtra State, India
| | - Girish Mahajan
- Piramal Enterprises Limited, 1-Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai-400063, Maharashtra State, India
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Julian Davies
- Department of Microbiology and Immunology, Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver BC V6T 1Z3, Canada
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Paradzik T, Ivic N, Filic Z, Manjasetty BA, Herron P, Luic M, Vujaklija D. Structure-function relationships of two paralogous single-stranded DNA-binding proteins from Streptomyces coelicolor: implication of SsbB in chromosome segregation during sporulation. Nucleic Acids Res 2013; 41:3659-72. [PMID: 23393191 PMCID: PMC3616714 DOI: 10.1093/nar/gkt050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The linear chromosome of Streptomyces coelicolor contains two paralogous ssb genes, ssbA and ssbB. Following mutational analysis, we concluded that ssbA is essential, whereas ssbB plays a key role in chromosome segregation during sporulation. In the ssbB mutant, ∼30% of spores lacked DNA. The two ssb genes were expressed differently; in minimal medium, gene expression was prolonged for both genes and significantly upregulated for ssbB. The ssbA gene is transcribed as part of a polycistronic mRNA from two initiation sites, 163 bp and 75 bp upstream of the rpsF translational start codon. The ssbB gene is transcribed as a monocistronic mRNA, from an unusual promoter region, 73 bp upstream of the AUG codon. Distinctive DNA-binding affinities of single-stranded DNA-binding proteins monitored by tryptophan fluorescent quenching and electrophoretic mobility shift were observed. The crystal structure of SsbB at 1.7 Å resolution revealed a common OB-fold, lack of the clamp-like structure conserved in SsbA and previously unpublished S-S bridges between the A/B and C/D subunits. This is the first report of the determination of paralogous single-stranded DNA-binding protein structures from the same organism. Phylogenetic analysis revealed frequent duplication of ssb genes in Actinobacteria, whereas their strong retention suggests that they are involved in important cellular functions.
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Affiliation(s)
- Tina Paradzik
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Nives Ivic
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Zelimira Filic
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Babu A. Manjasetty
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Paul Herron
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Marija Luic
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Dusica Vujaklija
- 1Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 2Division of Physical Chemistry, Rudjer Boskovic Institute, Zagreb 10002, Croatia, 3European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, Grenoble CEDEX 9, 3265, France and 4Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK,*To whom correspondence should be addressed. Tel: +385 1 4571 258; Fax: +385 1 4561 177;
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Mijakovic I, Macek B. Impact of phosphoproteomics on studies of bacterial physiology. FEMS Microbiol Rev 2012; 36:877-92. [DOI: 10.1111/j.1574-6976.2011.00314.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 10/21/2011] [Accepted: 10/22/2011] [Indexed: 11/27/2022] Open
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A novel tyrosine-phosphorylated protein inhibiting the growth of Streptomyces cells. Biochem Biophys Res Commun 2009; 385:534-8. [PMID: 19470379 DOI: 10.1016/j.bbrc.2009.05.091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 05/20/2009] [Indexed: 11/21/2022]
Abstract
Very few of the tyrosine-phosphorylated proteins in Streptomyces have been identified. Here, we identify a tyrosine-phosphorylated protein from Streptomyces coelicolor A3(2), designated as SCO5717. The protein possesses Walker motifs and a tyrosine cluster at the C-terminus. When sco5717 harboring its own promoter was introduced into the S. coelicolor cell, the growth was inhibited. An sco5717-disrupted mutant formed aerial mycelium earlier than the wild-type strain, suggesting that SCO5717 controls the cell growth of S. coelicolor. Although the recombinant SCO5717 showed an ATPase activity, it lacked self-phosphorylation ability, suggesting that SCO5717 is a novel tyrosine-phosphorylated protein, which is distinguishable from bacterial protein tyrosine kinases known so far.
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Mijakovic I, Petranovic D, Macek B, Cepo T, Mann M, Davies J, Jensen PR, Vujaklija D. Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine. Nucleic Acids Res 2006; 34:1588-96. [PMID: 16549871 PMCID: PMC1405823 DOI: 10.1093/nar/gkj514] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) are required for repair, recombination and replication in all organisms. Eukaryotic SSBs are regulated by phosphorylation on serine and threonine residues. To our knowledge, phosphorylation of SSBs in bacteria has not been reported. A systematic search for phosphotyrosine-containing proteins in Streptomyces griseus by immunoaffinity chromatography identified bacterial SSBs as a novel target of bacterial tyrosine kinases. Since genes encoding protein-tyrosine kinases (PTKs) have not been recognized in streptomycetes, and SSBs from Streptomyces coelicolor (ScSSB) and Bacillus subtilis (BsSSB) share 38.7% identity, we used a B.subtilis protein-tyrosine kinase YwqD to phosphorylate two cognate SSBs (BsSSB and YwpH) in vitro. We demonstrate that in vivo phosphorylation of B.subtilis SSB occurs on tyrosine residue 82, and this reaction is affected antagonistically by kinase YwqD and phosphatase YwqE. Phosphorylation of B.subtilis SSB increased binding almost 200-fold to single-stranded DNA in vitro. Tyrosine phosphorylation of B.subtilis, S.coelicolor and Escherichia coli SSBs occured while they were expressed in E.coli, indicating that tyrosine phosphorylation of SSBs is a conserved process of post-translational modification in taxonomically distant bacteria.
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Affiliation(s)
| | | | - Boris Macek
- Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern DenmarkDK-5230 Odense M, Denmark
| | - Tina Cepo
- Department of Molecular Biology, Rudjer Boskovic Institute10002 Zagreb, Croatia
| | - Matthias Mann
- Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern DenmarkDK-5230 Odense M, Denmark
| | - Julian Davies
- Department of Microbiology and Immunology, University of British ColumbiaVancouver, British Columbia, V6T 1Z3, Canada
| | | | - Dusica Vujaklija
- Department of Molecular Biology, Rudjer Boskovic Institute10002 Zagreb, Croatia
- To whom correspondence should be addresed. Tel: +385 14 57 12 58; Fax: +385 14 56 91 77;
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Komatsu M, Kuwahara Y, Hiroishi A, Hosono K, Beppu T, Ueda K. Cloning of the conserved regulatory operon by its aerial mycelium-inducing activity in an amfR mutant of Streptomyces griseus. Gene 2003; 306:79-89. [PMID: 12657469 DOI: 10.1016/s0378-1119(03)00405-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report cloning and characterization of a 2.8 kb DNA fragment that suppressed the aerial mycelium-deficient phenotype of an amfR mutant of Streptomyces griseus when it was introduced on a high-copy-number plasmid. Nucleotide sequencing revealed that the cloned DNA fragment contained a part of a regulatory operon homologous to one of the conserved operons identified in the genome of Streptomyces coelicolor A3(2). The operon appeared to consist of 5 CDSs (rarA-E; restoration of aerial mycelium formation in an amfR mutant): rarA encoded a membrane protein with weak similarity to the histidine kinase of the two-component regulatory system; rarB and rarC products did not show marked similarity to other proteins with known function; rarD encoded a G-protein carrying two GTP-binding consensus sequences conserved in the eukaryotic Ras-like proteins; rarE product showed end-to-end homology to cytochrome P450. The 2.8 kb fragment contained a 5'-end incomplete rarA and complete rarB-D in the downstream from the promoter region of mel operon of the vector plasmid. Subcloning showed that the region containing rarA only is sufficient for the aerial mycelium-inducing activity. The truncation of rarA at its 5' terminus was essential for the restoration activity, which implied that the mutated rarA product causes unusual signaling that directs the onset of morphogenesis without amfR function. Inactivation of both rarA in Streptomyces griseus and cvnD9, a rarD ortholog in S. coelicolor resulted in precocious and glucose-resistant formation of aerial mycelium and secondary metabolites, which suggested that the operon negatively regulates the onset of differentiation. S1 nuclease protection analysis showed that the transcriptional activity of the promoter preceding rarA is developmentally regulated in an amfR- and glucose-dependent manner.
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Affiliation(s)
- Mamoru Komatsu
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
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8
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Elizarov SM, Danilenko VN. Multiple phosphorylation of membrane-associated calcium-dependent protein serine/threonine kinase in Streptomyces fradiae. FEMS Microbiol Lett 2001; 202:135-8. [PMID: 11506921 DOI: 10.1111/j.1574-6968.2001.tb10793.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In Streptomyces fradiae, calcium ions induce alterations in intensity and specificity of the secondary metabolism and stimulate aerial mycelium formation and sporulation. Using in vitro labeling, we demonstrate that in S. fradiae in the late exponential growth phosphorylation of 65-kDa membrane-associated protein is also influenced by Ca(2+) added exogenously. Calcium ions at physiological concentration stimulate intensive Ca(2+)-dependent phosphorylation of 65-kDa protein at multiple sites on serine, threonine, and tyrosine residues. Assay of protein kinases in situ demonstrated in the fraction of membrane-associated proteins the presence of two autophosphorylating protein serine/threonine kinases with molecular masses of 127 kDa and 65 kDa. Autophosphorylation of both proteins is also Ca(2+)-dependent.
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Affiliation(s)
- S M Elizarov
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
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9
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Neu JM, Wright GD. Inhibition of sporulation, glycopeptide antibiotic production and resistance in Streptomyces toyocaensis NRRL 15009 by protein kinase inhibitors. FEMS Microbiol Lett 2001; 199:15-20. [PMID: 11356561 DOI: 10.1111/j.1574-6968.2001.tb10644.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Production of the glycopeptide antibiotic A47934 by Streptomyces toyocaensis NRRL 15009 begins in the late exponential phase in liquid culture and peaks in the early stationary phase. The pattern of cellular phosphoprotein production changes upon onset of A48934 production with the appearance of several novel phosphoproteins only when an antibiotic is being produced. Phosphoamino acid analysis revealed that S. toyocaensis NRRL 15009 produces proteins phosphorylated on His, Ser, Thr and Tyr, with most being membrane-associated. Addition of the isoflavones genistein or quercetin abolishes A47934 production in liquid culture and sporulation on solid medium. Furthermore, genistein slows the onset of inducible glycopeptide antibiotic resistance in S. toyocaensis NRRL 15009. These results support the participation of protein kinase pathways in A47934 biosynthesis and resistance and cell differentiation in S. toyocaensis NRRL 15009.
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Affiliation(s)
- J M Neu
- Antimicrobial Research Centre, Department of Biochemistry, McMaster University, 1200 Main Street West, L8N 3Z5, Hamilton, ON, Canada
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11
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Umeyama T, Naruoka A, Horinouchi S. Genetic and biochemical characterization of a protein phosphatase with dual substrate specificity in Streptomyces coelicolor A3(2). Gene 2000; 258:55-62. [PMID: 11111042 DOI: 10.1016/s0378-1119(00)00450-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A gene encoding a protein phosphatase (SppA) with a phosphoesterase motif, which was predicted by the genome project of the Gram-positive bacterium Streptomyces coelicolor A3(2), was cloned by PCR in pET32a(+) and expressed in Escherichia coli. SppA fused to thioredoxin (TRX-SppA) showed distinct heat-stable phosphatase activity toward p-nitrophenyl phosphate with optimal pH 8.0 and optimal temperature 55 degrees C. Mn2+ greatly enhanced enzyme activity, as is found with other protein Ser/Thr phosphatases. TRX-SppA was not inhibited by sodium orthovanadate or okadaic acid, both of which are known to be specific inhibitors of protein phosphatases. TRX-SppA showed phosphatase activity toward not only phosphoThr (pThr) and pTyr but also oligopeptides containing pSer, pThr, and pTyr, indicating that SppA is a protein phosphatase with dual substrate specificity. Disruption of the chromosomal sppA gene resulted in severe impairment of vegetative growth. All of these observations show that SppA, a protein phosphatase with dual specificity, plays an important, but not essential, role in vegetative growth of S. coelicolor A3(2). The presence of a single copy of sppA in all the 13 Streptomyces species examined, as determined by Southern hybridization, suggests a common role of SppA in general in Streptomyces species.
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Affiliation(s)
- T Umeyama
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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12
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Abstract
Reversible phosphorylation of serine, threonine and tyrosine residues by the interplay of protein kinases and phosphatases plays a key role in regulating many different cellular processes in eukaryotic organisms. A diversity of control mechanisms exists to influence the activity of these enzymes and choreograph the correct concert of protein modifications to achieve distinct biological responses. Such enzymes and their adaptor molecules were long thought to be specific to eukaryotic cellular processes. However, there is increasing evidence that many prokaryotes achieve regulation of key components of cellular function through similar mechanisms.
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Affiliation(s)
- C J Bakal
- Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
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Umeyama T, Lee PC, Ueda K, Horinouchi S. An AfsK/AfsR system involved in the response of aerial mycelium formation to glucose in Streptomyces griseus. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 9):2281-2292. [PMID: 10517581 DOI: 10.1099/00221287-145-9-2281] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Streptomyces coelicolor A3(2), a protein serine/threonine kinase (AfsK) and its target protein (AfsR) control secondary metabolism. AfsK and AfsR homologues (AfsK-g and AfsR-g) from Streptomyces griseus showed high end-to-end similarity in amino acid sequence with the respective S. coelicolor A3(2) proteins, as determined by cloning and nucleotide sequencing. AfsK-g and a fusion protein between AfsK-g and thioredoxin (TRX-AfsK-g) produced in high yield as inclusion bodies in Escherichia coli were solubilized with urea, purified by column chromatography and then refolded to an active form by dialysis to gradually remove the urea. AfsR-g was also fused to glutathione S-transferase (GST-AfsR-g); the fusion product in the soluble fraction in E. coli was purified. Incubation of AfsK-g or TRX-AfsK-g in the presence of [gamma-32P]ATP yielded autophosphorylated products containing phosphoserine and phosphothreonine residues. In addition, TRX-AfsK-g phosphorylated serine and threonine residues of GST-AfsR-g in the presence of [gamma-32P]ATP. Disruption of chromosomal afsK-g had no effect on A-factor or streptomycin production, irrespective of the culture conditions. The afsK-g disruptants did not form aerial mycelium or spores on media containing glucose at concentrations higher than 1%, but did form spores on mannitol- and glycerol-containing media; this suggests that afsK-g is essential for morphogenesis in the presence of glucose. Introduction of afsK-g restored aerial mycelium formation in the disruptants. The phenotype of afsR-g disruptants was similar to that of afsK-g disruptants; introduction of afsR-g restored the defect in aerial mycelium formation on glucose-containing medium. Thus the AfsK/AfsR system in S. griseus is conditionally needed for morphological differentiation, whereas in S. coelicolor A3(2) it is conditionally involved in secondary metabolism.
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Affiliation(s)
- Takashi Umeyama
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan1
| | - Ping-Chin Lee
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan1
| | - Kenji Ueda
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan1
| | - Sueharu Horinouchi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan1
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Jagtap P, Ray MK. Studies on the cytoplasmic protein tyrosine kinase activity of the Antarctic psychrotrophic bacterium Pseudomonas syringae. FEMS Microbiol Lett 1999; 173:379-88. [PMID: 10227168 DOI: 10.1111/j.1574-6968.1999.tb13529.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Antarctic psychrotrophic bacterium Pseudomonas syringae contains a 66-kDa cytoplasmic protein which was found to by phosphorylated on a tyrosine residue [Ray, M.K. et al. (1994) FEMS Microbiol. Lett. 122, pp. 49-54]. To investigate the nature of the cytoplasmic protein tyrosine kinase and its role in the bacterial physiology, we carried out some biochemical studies of the enzyme in vitro in the presence of exogenous peptide substrates and expression studies in vivo at low and high temperature during various phases of growth. The results suggest that the protein tyrosine kinase associated with the cytoplasmic fraction of the bacterium has certain similarities and dissimilarities with the known eukaryotic tyrosine kinases. The protein tyrosine kinase could phosphorylate exogenous substrate corresponding to the N-terminal peptide of p34cdc2 kinase but could not do so on poly(Glu:Tyr). The enzyme could not be inhibited by genistein, staurosporine and dimethyl aminopurine, but could be inhibited by piceatannol which is a known competitive inhibitor of the peptide binding site of mammalian protein tyrosine kinases. The enzyme activity in the cytoplasm is uniquely inhibited by sodium orthovanadate (IC50 = 20 microM) which is a known protein tyrosine phosphatase inhibitor. The expression studies show that the enzyme is produced more at a higher temperature (22 degrees C) of growth than at lower temperature (4 degrees C) and during the stationary phase of growth of P. syringae.
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Affiliation(s)
- P Jagtap
- Centre for Cellular and Molecular Biology, Hyderabad, India
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15
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Daigle DM, McKay GA, Thompson PR, Wright GD. Aminoglycoside antibiotic phosphotransferases are also serine protein kinases. CHEMISTRY & BIOLOGY 1999; 6:11-8. [PMID: 9889150 DOI: 10.1016/s1074-5521(99)80016-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Bacterial resistance to aminoglycoside antibiotics occurs primarily through the expression of modifying enzymes that covalently alter the drugs by O-phosphorylation, O-adenylation or N-acetylation. Aminoglycoside phosphotransferases (APHs) catalyze the ATP-dependent phosphorylation of these antibiotics. Two particular enzymes in this class, APH(3')-IIIa and AAC(6')-APH(2"), are produced in gram-positive cocci and have been shown to phosphorylate aminoglycosides on their 3' and 2" hydroxyl groups, respectively. The three-dimensional structure of APH (3')-IIIa is strikingly similar to those of eukaryotic protein kinases (EPKs), and the observation, reported previously, that APH(3')-IIIa and AAC(6')-APH(2") are effectively inhibited by EPK inhibitors suggested the possibility that these aminoglycoside kinases might phosphorylate EPK substrates. RESULTS Our data demonstrate unequivocally that APHs can phosphorylate several EPK substrates and that this phosphorylation occurs exclusively on serine residues. Phosphorylation of Ser/Thr protein kinase substrates by APHs was considerably slower than phosphorylation of aminoglycosides under identical assay conditions, which is consistent with the primary biological roles of the enzymes. CONCLUSIONS These results demonstrate a functional relationship between aminoglycoside and protein kinases, expanding on our previous observations of similarities in protein structure, enzyme mechanism and sensitivity to inhibitors, and suggest an evolutionary link between APHs and EPKs.
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Affiliation(s)
- D M Daigle
- Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
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16
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Pope MK, Green B, Westpheling J. The bldB gene encodes a small protein required for morphogenesis, antibiotic production, and catabolite control in Streptomyces coelicolor. J Bacteriol 1998; 180:1556-62. [PMID: 9515926 PMCID: PMC107057 DOI: 10.1128/jb.180.6.1556-1562.1998] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mutants blocked at the earliest stage of morphological development in Streptomyces species are called bld mutants. These mutants are pleiotropically defective in the initiation of development, the ability to produce antibiotics, the ability to regulate carbon utilization, and the ability to send and/or respond to extracellular signals. Here we report the identification and partial characterization of a 99-amino-acid open reading frame (ORF99) that is capable of restoring morphogenesis, antibiotic production, and catabolite control to all of the bldB mutants. Of the existing bld mutants, bldB is of special interest because the phenotype of this mutant is the most pleiotropic. DNA sequence analysis of ORF99 from each of the existing bldB mutants identified base changes either within the coding region of the predicted protein or in the regulatory region of the gene. Primer extension analysis identified an apparent transcription start site. A promoter fusion to the xylE reporter gene showed that expression of bldB is apparently temporally regulated and that the bldB gene product is involved in the regulation of its own expression.
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MESH Headings
- Amino Acid Sequence
- Anti-Bacterial Agents/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Carbon/metabolism
- Catechol 2,3-Dioxygenase
- Cloning, Molecular
- Codon, Initiator
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- Dioxygenases
- Gene Expression Regulation, Bacterial
- Genes, Reporter
- Molecular Sequence Data
- Open Reading Frames
- Oxygenases/genetics
- Plasmids
- Polymerase Chain Reaction
- Promoter Regions, Genetic
- RNA, Bacterial/analysis
- RNA, Bacterial/isolation & purification
- Recombinant Fusion Proteins
- Restriction Mapping
- Sequence Analysis, DNA
- Signal Transduction/genetics
- Streptomyces/genetics
- Streptomyces/growth & development
- Streptomyces/metabolism
- Transcription, Genetic
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Affiliation(s)
- M K Pope
- Genetics Department, University of Georgia, Athens 30302, USA
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17
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Ramponi G, Stefani M. Structure and function of the low Mr phosphotyrosine protein phosphatases. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1341:137-56. [PMID: 9357953 DOI: 10.1016/s0167-4838(97)00087-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phosphotyrosine protein phosphatases (PTPases) catalyse the hydrolysis of phosphotyrosine residues in proteins and are hence implicated in the complex mechanism of the control of cell proliferation and differentiation. The low Mr PTPases are a group of soluble PTPases displaying a reduced molecular mass; in addition, a group of low molecular mass dual specificity (ds)PTPases which hydrolyse phosphotyrosine and phosphoserine/threonine residues in proteins are known. The enzymes belonging to the two groups are unrelated to each other and to other PTPase classes except for the presence of a CXXXXXRS/T sequence motif containing some of the catalytic residues (active site signature) and for the common catalytic mechanism, clearly indicating convergent evolution. The low Mr PTPases have a long evolutionary history since microbial (prokaryotic and eukaryotic) counterparts of both tyrosine-specific and dsPTPases have been described. Despite the relevant number of data reported on the structural and catalytic features of a number of low Mr PTPases, only limited information is presently available on the substrate specificity and the true biological roles of these enzymes, in prokaryotic, yeast and eukaryotic cells.
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Affiliation(s)
- G Ramponi
- Department of Biochemical Sciences, University of Florence, Italy
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18
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Piepersberg W. Molecular Biology, Biochemistry and Fermentation of Aminoglycoside Antibiotics. DRUGS AND THE PHARMACEUTICAL SCIENCES 1997. [DOI: 10.1201/b14856-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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19
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AV-GAY YOSSEF, DAVIES JULIAN. Components of Eukaryotic-like Protein Signaling Pathways inMycobacterium tuberculosis. ACTA ACUST UNITED AC 1997. [DOI: 10.1089/omi.1.1997.2.63] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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20
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Umeyama T, Tanabe Y, Aigle BD, Horinouchi S. Expression of the Streptomyces coelicolor A3(2) ptpA gene encoding a phosphotyrosine protein phosphatase leads to overproduction of secondary metabolites in S. lividans. FEMS Microbiol Lett 1996; 144:177-84. [PMID: 8900062 DOI: 10.1111/j.1574-6968.1996.tb08527.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A DNA fragment that caused pigment production in Streptomyces lividans was isolated from a gene library of PstI-digested chromosomal fragments of S. coelicolor A3(2). Subcloning and nucleotide sequencing proved the identity of the cloned gene to ptpA encoding a low-molecular-mass phosphotyrosine protein phosphatase. The S. lividans transformant containing ptpA on pIJ41 with a copy number of 3 4 per genome produced large amounts of undecylprodigiosin and A-factor, in addition to the pigmented antibiotic actinorhodin, whereas the transformant containing ptpA on an SCP2* derivative with a copy number of 1-2 did not. The PtpA protein produced as a fusion to the maltose binding protein in Escherichia coli showed phosphatase activity toward o-phosphotyrosine, but not toward o-phosphoserine or a-threonine. Introduction of a mutant ptpA gene encoding an inactive protein with serine instead of the 9th cysteine caused no pigmentation. Disruption of the chromosomal ptpA gene of S. coelicolor A3(2), however, appeared to cause no detectable effect on the production of the pigmented antibiotics or A-factor and the ptpA disruptants developed aerial mycelium and spores normally.
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Affiliation(s)
- T Umeyama
- Department of Biotechnology, University of Tokyo, Japan
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21
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Kennelly PJ, Potts M. Fancy meeting you here! A fresh look at "prokaryotic" protein phosphorylation. J Bacteriol 1996; 178:4759-64. [PMID: 8759835 PMCID: PMC178254 DOI: 10.1128/jb.178.16.4759-4764.1996] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bacteria play host to a wide range of protein phosphorylation-dephosphorylation systems (Fig. 1). As little as five years ago the known systems were thought to be late-emerging and absolutely prokaryote specific. Today we know that most protein kinases and protein phosphatases are descended from a set of common, and possibly quite ancient, prototypes. Prokaryote- and eukaryote-specific protein kinases and protein phosphatases are rare and represent exceptions, not the rule as previously thought. Commonality suggests that a dynamic and versatile regulatory mechanism was first adapted to the modulation of protein function as early if not earlier than more "basic" mechanisms such as allosterism, etc. The existence of common molecular themes confirms that the microbial world offers a unique, largely untapped library and a powerful set of tools for the understanding of a regulatory mechanism which is crucial to all organisms, tools whose diversity and experimental malleability will provide new avenues for exploring and understanding key modes of cellular regulation.
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Affiliation(s)
- P J Kennelly
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308, USA.
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22
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Abstract
Tyrosine phosphorylation is an extremely rare event in prokaryotes, occurring almost exclusively in multicellular eukaryotes. We have identified, for the first time, by the use of antiphosphotyrosine monoclonal antibody and Western blot (immunoblot) analysis, two tyrosine-phosphorylated membrane proteins in the multicellular prokaryote Myxococcus xanthus. The pattern of tyrosine phosphorylation was shown to change during development, indicating a possible role for this regulatory modification during two stages of development, i.e., aggregation and sporulation. Furthermore, the altered pattern of tyrosine phosphorylation observed in a variety of signaling mutants was shown to differ from that observed in the wild type, suggesting further the possible involvement of tyrosine phosphorylation during the development program.
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Affiliation(s)
- S C Frasch
- Department of Microbiology, University of Minnesota, Minneapolis, 55455, USA
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23
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Li Y, Strohl WR. Cloning, purification, and properties of a phosphotyrosine protein phosphatase from Streptomyces coelicolor A3(2). J Bacteriol 1996; 178:136-42. [PMID: 8550407 PMCID: PMC177630 DOI: 10.1128/jb.178.1.136-142.1996] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe the isolation and characterization of a gene (ptpA) from Streptomyces coelicolor A3(2) that codes for a protein with a deduced M(r) of 17,690 containing significant amino acid sequence identity with mammalian and prokaryotic small, acidic phosphotyrosine protein phosphatases (PTPases). After expression of S. coelicolor ptpA in Escherichia coli with a pT7-7-based vector system, PtpA was purified to homogeneity as a fusion protein containing five extra amino acids. The purified fusion enzyme catalyzed the removal of phosphate from p-nitrophenylphosphate (PNPP), phosphotyrosine (PY), and a commercial phosphopeptide containing a single phosphotyrosine residue but did not cleave phosphoserine or phosphothreonine. The pH optima for PNPP and PY hydrolysis by PtpA were 6.0 and 6.5, respectively. The Km values for hydrolysis of PNPP and PY by PtpA were 0.75 mM (pH 6.0, 37 degrees C) and 2.7 mM (pH 6.5, 37 degrees C), respectively. Hydrolysis of PNPP by S. coelicolor PtpA were 0.75 mM (pH 6.0, 37 degrees C) and 2.7 mM (pH 6.5, 37 degrees C), respectively. Hydrolysis of PNPP by S. coelicolor PtpA was competitively inhibited by dephostatin with a Ki of 1.64 microM; the known PTPase inhibitors phenylarsine oxide, sodium vanadate, and iodoacetate also inhibited enzyme activity. Apparent homologs of ptpA were detected in other streptomycetes by Southern hybridization; the biological functions of PtpA and its putative homologs in streptomycetes are not yet known.
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Affiliation(s)
- Y Li
- Department of Microbiology, Ohio State University, Columbus 43210-1292, USA
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Huang HJ, Lin SH, Yang BC, Cheng CM, Yang CC, Kuo TT. Rapid inhibition of protein histidine phosphorylation by UV-irradiation in Xanthomonas oryzae pv. oryzae. FEMS Microbiol Lett 1995; 134:189-94. [PMID: 8586267 DOI: 10.1111/j.1574-6968.1995.tb07936.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Exposure of Xanthomonas oryzae pv. oryzae cells to 254 nm UV radiation resulted in an alteration of protein phosphorylation. Labelling of the phosphohistidine-containing proteins with molecular masses of 81 and 32 kDa, named p81 and p32, was rapidly reduced following UV irradiation in the early exponential cells, but the decrease was not detected in mid-exponential cells. Mitomycin C, a DNA replication inhibitor, and rifampicin, a drug generally used to inhibit RNA synthesis and DNA replication, were also found to reduce the histidyl phosphorylation. However, this alteration of protein phosphorylation was not hindered by chloramphenicol treatment. A possible role for these histidyl phosphoproteins in sensing UV light is proposed.
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Affiliation(s)
- H J Huang
- Institute of Botany, Academia Sinica, Taipei, Taiwan
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