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Slager J, Aprianto R, Veening JW. Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. Nucleic Acids Res 2019; 46:9971-9989. [PMID: 30107613 PMCID: PMC6212727 DOI: 10.1093/nar/gky725] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/30/2018] [Indexed: 12/27/2022] Open
Abstract
A precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportunistic human pathogens and how they cause disease. Using single-molecule real-time (PacBio) sequencing we unambiguously determined the genome sequence of Streptococcus pneumoniae strain D39 and revealed several inversions previously undetected by short-read sequencing. Significantly, a chromosomal inversion results in antigenic variation of PhtD, an important surface-exposed virulence factor. We generated a new genome annotation using automated tools, followed by manual curation, reflecting the current knowledge in the field. By combining sequence-driven terminator prediction, deep paired-end transcriptome sequencing and enrichment of primary transcripts by Cappable-Seq, we mapped 1015 transcriptional start sites and 748 termination sites. We show that the pneumococcal transcriptional landscape is complex and includes many secondary, antisense and internal promoters. Using this new genomic map, we identified several new small RNAs (sRNAs), RNA switches (including sixteen previously misidentified as sRNAs), and antisense RNAs. In total, we annotated 89 new protein-encoding genes, 34 sRNAs and 165 pseudogenes, bringing the S. pneumoniae D39 repertoire to 2146 genetic elements. We report operon structures and observed that 9% of operons are leaderless. The genome data are accessible in an online resource called PneumoBrowse (https://veeninglab.com/pneumobrowse) providing one of the most complete inventories of a bacterial genome to date. PneumoBrowse will accelerate pneumococcal research and the development of new prevention and treatment strategies.
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Affiliation(s)
- Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Rieza Aprianto
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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Szymanska-Michalak A, Wawrzyniak D, Framski G, Stawinski J, Barciszewski J, Kraszewski A. New antiglioma zwitterionic pronucleotides with an FdUMP framework. Eur J Med Chem 2017; 144:682-691. [PMID: 29289891 DOI: 10.1016/j.ejmech.2017.12.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
We have designed and synthesized new 5-fluoro-2'-deoxyuridine 5'-phosphate pronucleotides which can function as potential agents against the glioblastoma multiforme tumor. Their anti-malignant potency has been tested against T98G, U-118 MG, U-87 MG gliomas, HeLa, and Caco-2 cancer cell lines, using MRC-5 healthy cells as a reference. Five of the sixteen compounds (4c, 4f-i) exhibited significant anticancer potency and high selectivity indices (SI 12-66). It is likely that these zwitterionic pronucleotides may function in a similar manner to zwitterionic phospholipids, by inducing cell membrane charge disorder, making the cell permeable to bioactive agents. The most promising therapeutic pronucleotides 4c, 4f-h, have high intestinal-blood uptake potency (Caco-2 cell line), and may be considered as potential, orally administrated, anticancer drugs.
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Affiliation(s)
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Grzegorz Framski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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McGuigan C, Nicholls SR, O'Connor TJ, Kinchington D. Synthesis of Some Novel Dialkyl Phosphate Derivatives of 3′-Modified Nucleosides as Potential Anti-AIDS Drugs. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029000100105] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reaction of thymidine with diethyl, dipropyl, and dibutyl phosphorochloridates yields novel 5′-(dialkyl phosphates), characterized by spectroscopic and analytical data. These are readily mesylated at the 3′-position. Similar reaction of 3′- O-acetyl and 3′- O-ethyl thymidine with dialkyl phosphorochloridates gives an analogous series of compounds. Lastly, reaction of the anti-AIDS drug AZT with these phosphorylating agents gives the corresponding 3′-azido products. It was hoped that these might act as membrane-soluble pro-drugs of the bio-active free nucleotides of AZT and that the alternative 3′-substituents might also confer similar activity. In fact, none of the compounds studied displayed any anti-HIV activity in vitro. This is attributed to the metabolic stability of the trialkyl phosphate moiety.
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Affiliation(s)
- C. McGuigan
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - S. R. Nicholls
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - T. J. O'Connor
- Division of Virology, Department of Medical, Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
| | - D. Kinchington
- Division of Virology, Department of Medical, Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
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Pompon A, Lefebvre I, Imbach JL, Kahn S, Farquhar D. Decomposition Pathways of the Mono- and Bis(Pivaloyloxymethyl) Esters of Azidothymidine 5′-Monophosphate in Cell Extract and in Tissue Culture Medium: An Application of the ‘on-line ISRP-Cleaning’ HPLC Technique. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500205] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bis(pivaloyloxymethyl) azidothymidine 5′-monophosphate (piv2-AZTMP) was designed as a cell membrane-permeable precursor of AZTMP. We have reported previously that when incubated with CEM cells deficient in thymidine kinase, piv2-AZTMP gives rise to intracellular AZTMP and the corresponding diphosphate (AZTDP) and triphosphate (AZTTP). Under similar conditions, no intracellular nucleotides were formed with AZT. However, the mechanism by which piv2-AZTMP is converted to AZTMP has not been established. To address this question, we have used the recently developed ‘on-line ISRP-cleaning’ HPLC technique to investigate the stability and metabolic fate of piv2-AZTMP (1) in RPMI 1640 medium, (2) in RPMI containing 10% heat-inactivated fetal calf serum, and (3) in CEM cell extracts. Similar studies were conducted starting with mono(pivaloyloxymethyl) azidothymidine 5′-monophosphate (piv2 AZTMP). From the kinetics of these reactions, it appears that piv2-AZTMP is slowly hydrolyzed to piv1-AZTMP in RPMI and that the metabolic sequence in cell extract and in tissue culture medium is clearly: piv2-AZTMP→ piv1AZTMP→ AZTMP→ AZT. The rate constants are quite different in these three media. Although it is evident that the first step in the metabolism of piv2-AZTMP is catalysed by carboxylate esterase, the enzyme(s) responsible for the second step, piv1-AZTMP→ AZTMP, is less apparent, as carboxylate esterases and/or phosphodiesterases can be taken in account. However, analysis of the kinetic data strongly suggests that carboxylate esterase does not play a significant role and that this second step is mediated by phosphodiesterases. Collectively, these studies demonstrate that piv2-AZTMP is an effective prodrug of AZTMP. They also establish that prv1-AZTMP is an intermediate in this process, and define the sequence of the overall metabolic reaction. With this increased understanding of the metabolism of piv2-AZTMP, it should be possible rationally to design analogues with optimal structural and pharmacological properties for use in vivo.
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Affiliation(s)
- A. Pompon
- Laboratoire de Chimie Bio-Organique, U.R.A. CNRS no. 488, case 008, Université Montpellier II, Place E. Bataillon, 34095 Montpellier cédex 5, France
| | - I. Lefebvre
- Laboratoire de Chimie Bio-Organique, U.R.A. CNRS no. 488, case 008, Université Montpellier II, Place E. Bataillon, 34095 Montpellier cédex 5, France
| | - J.-L. Imbach
- Laboratoire de Chimie Bio-Organique, U.R.A. CNRS no. 488, case 008, Université Montpellier II, Place E. Bataillon, 34095 Montpellier cédex 5, France
| | - S. Kahn
- Department of Medical Oncology, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - D. Farquhar
- Department of Medical Oncology, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
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Périgaud C, Girardet JL, Lefebvre I, Xie MY, Aubertin AM, Kirn A, Gosselin G, Imbach JL, Sommadossi JP. Comparison of Cytotoxicity of Mononucleoside Phosphotriester Derivatives Bearing Biolabile Phosphate Protecting Groups in Normal Human Bone Marrow Progenitor Cells. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029600700607] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The effects of three mononucleoside phosphotriester derivatives of 3′-azido-2′,3′-dideoxythymidine (AZT) which incorporate biolabile phosphate protecting groups, namely S-acetyl-2-thioethyl (MeSATE), S-(2-hydroxyethylsulfidyl)-2-thioethyl (DTE), and pivaloyloxymethyl (POM) were studied and compared to their nucleoside parent in human myeloid colony-forming cells. Moreover, the relative antiviral potency of these three pronucleotides were determined in primary human peripheral blood mononuclear cells infected with human immunodeficiency virus type 1. The results indicate that the SATE and DTE pro-moieties, as well as their degradation products, do not induce additional toxicity. The bis(MeSATE) phosphotriester derivative of AZT emerged as the most selective inhibitor with an in-vitro therapeutic index of the same order of magnitude as observed for AZT. This study has been extended to the corresponding bis(MeSATE) and bis(DTE) phosphotriester derivatives of 2′,3′-dideoxyuridine (ddU).
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Affiliation(s)
- C. Périgaud
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Counter 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - J.-L. Girardet
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Counter 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - I. Lefebvre
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Counter 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - M.-Y. Xie
- Department of Pharmacology, Centre for AIDS Research, Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - A.-M. Aubertin
- Institut de Virologie de la Faculté de Médecine de Strasbourg, Unité INSERM 74, 3 rue Koeberlé, 67000 Strasbourg, France
| | - A. Kirn
- Institut de Virologie de la Faculté de Médecine de Strasbourg, Unité INSERM 74, 3 rue Koeberlé, 67000 Strasbourg, France
| | - G. Gosselin
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Counter 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - J.-L. Imbach
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Counter 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - J.-P. Sommadossi
- Department of Pharmacology, Centre for AIDS Research, Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Jones BCNM, McGuigan C, O'Connor TJ, Jeffries DJ, Kinchington D. Synthesis and anti-HIV Activity of Some Novel Phosphorodiamidate Derivatives of 3′-azido-3′-deoxythymidine (AZT). ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029100200106] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The reaction of 3′-azido-3′-deoxythymidine (AZT) with phosphoryl chloride followed by amino acid methyl esters gave novel diamidate derivatives of AZT 5′-monophosphate (AZTMP). It was hoped that the 5′-phosphorodiamidates might act as membrane-soluble prodrugs of the bio-active free nucleotides of AZT. Five different amino acids were employed, covering a range of structures and polarities. The reaction was also conducted with propylamine, and with diethylamine. The derivatives were tested for their inhibitory effect on human immunodeficiency virus type 1 (HIV-1) proliferation in a human lymphoblastoid cell line. The amino acid derivatives were potent inhibitors of viral proliferation, small changes in structure leading to marked changes in activity.
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Affiliation(s)
- B. C. N. M. Jones
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - C. McGuigan
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - T. J. O'Connor
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
| | - D. J. Jeffries
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
| | - D. Kinchington
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
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7
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McGuigan C, O'Connor TJ, Nicholls SR, Nickson C, Kinchington D. Synthesis and anti-HIV Activity of Some Novel Substituted Dialkyl Phosphate Derivatives of AZT and ddCyd. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029000100603] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reaction of thymidine, AZT (Fig. 1, compound 1) and ddCyd (Fig. 1, compound 2) with bis(2,2,2-trichloroethyl) phosphorochloridate gave novel 5′-bis(2,2,2-trichloroethyl) phosphates, characterized by spectroscopic and analytical data. Analogous reactions with bis(2,2,2-trifluoroethyl) phosphorochloridate gave the corresponding AZT and ddCyd derivatives. In both of the ddCyd reactions, by-products were isolated and characterized as O5′, W4-diphosphorylated materials. It was hoped that the 5′-phosphate triesters might act as membrane-soluble pro-drugs of the bio-active free nucleotides of AZT or ddCyd. In fact, all of the 5′-phosphate derivatives of AZT and ddCyd displayed anti-HIV activity in vitro. Surprisingly, the thymidine compound also displayed very slight anti-HIV activity. The striking activity of the AZT and ddCyd derivatives is attributed to the metabolic instability of the substituted trialkyl phosphate moiety.
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Affiliation(s)
- C. McGuigan
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | - T. J. O'Connor
- Department of Virology, Medical College of St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - S. R. Nicholls
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | - C. Nickson
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | - D. Kinchington
- Department of Virology, Medical College of St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
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8
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McGuigan C, Devine KG, O'Connor TJ, Galpin SA, Jeffries DJ, Kinchington D. Synthesis and Evaluation of Some Novel Phosphoramidate Derivatives of 3′-Azido-3′-Deoxythymidine (AZT) as Anti-HIV Compounds. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029000100205] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A series of monophosphate triester derivatives of 3′-azido-3′-deoxythymidine (AZT), designed as membrane-soluble pro-drugs of the nucleotide (AZTMP), have been tested for activity against the human immunodeficiency virus (HIV-1). It has been found that when carboxyl-protected, amino-linked amino acids, and alkyl chains, are asymmetrically substituted on the 5′-phosphate a significant antiviral effect is observed. Moreover, the activity of the compounds is profoundly dependent on the structure of the phosphate moiety, and in particular on the nature of the amino acid.
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Affiliation(s)
| | | | - T. J. O'Connor
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
| | - S. A. Galpin
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
| | - D. J. Jeffries
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
| | - D. Kinchington
- Division of Virology, Department of Medical Microbiology, St Mary's Hospital Medical School, Norfolk Place, Paddington, London W2 1PG, UK
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Iglesias LE, Lewkowicz ES, Medici R, Bianchi P, Iribarren AM. Biocatalytic approaches applied to the synthesis of nucleoside prodrugs. Biotechnol Adv 2015; 33:412-34. [PMID: 25795057 DOI: 10.1016/j.biotechadv.2015.03.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Nucleosides are valuable bioactive molecules, which display antiviral and antitumour activities. Diverse types of prodrugs are designed to enhance their therapeutic efficacy, however this strategy faces the troublesome selectivity issues of nucleoside chemistry. In this context, the aim of this review is to give an overview of the opportunities provided by biocatalytic procedures in the preparation of nucleoside prodrugs. The potential of biocatalysis in this research area will be presented through examples covering the different types of nucleoside prodrugs: nucleoside analogues as prodrugs, nucleoside lipophilic prodrugs and nucleoside hydrophilic prodrugs.
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Affiliation(s)
- Luis E Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Rosario Medici
- Biocatalysis Group, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Paola Bianchi
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina; Laboratorio de Química de Ácidos Nucleicos, INGEBI-CONICET, Vuelta de Obligado 2490, 1428 Ciudad Autónoma de Buenos Aires, Argentina.
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Gemcitabine-based therapy for pancreatic cancer using the squalenoyl nucleoside monophosphate nanoassemblies. Int J Pharm 2014; 482:38-46. [PMID: 25448549 DOI: 10.1016/j.ijpharm.2014.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 12/23/2022]
Abstract
Gemcitabine is currently the most effective agent against advanced pancreatic cancer. However, the major therapeutic hurdles using gemcitabine include rapid inactivation by blood deaminases and fast development of cell chemoresistance, induced by down-regulation of deoxycytidine kinase or nucleoside transporters. To overcome the above drawbacks we designed recently a novel nanomedicine strategy based on squalenoyl prodrug of 5'-monophosphate gemcitabine (SQdFdC-MP). This amphiphilic conjugate self-organized in water into unilamellar vesicles with a mean diameter of 100 nm. In this study the antitumor efficacy of SQdFdC-MP nanoassemblies (NAs) on chemoresistant and chemosensitive pancreatic adenocarcinoma models have been investigated. Cell viability assays showed that SQdFdC-MP NAs displayed higher antiproliferative and cytotoxic effects, particularly in chemoresistant pancreatic tumor cells. In in vivo studies, SQdFdC-MP NAs decreased significantly the growth (∼70%) of human MiaPaCa2 xenografts, also preventing tumor cell invasion, whereas native dFdC did not display any anticancer activity when tumor growth inhibition was only 35% with SQdFdC NAs. These results correlated with a reduction of Ki-67 antigen and the induction of apoptosis mediated by caspase-3 activation in tumor cells. These findings demonstrated the feasibility of utilizing SQdFdC-MP NAs to make tumor cells more sensitive to gemcitabine and thus providing an efficient new therapeutic alternative for pancreatic adenocarcinoma.
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Ivanov MA, Aleksandrova LA. [Bicyclic furano[2,3-D] derivatives of pyrimidine nucleosides--synthesis and antiviral properties]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:26-45. [PMID: 23844505 DOI: 10.1134/s1068162013010044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The methods of synthesis of furano- and pyrrolo[2,3-dlpyrimidine nucleosides as well as structure activity relationship of obtained compounds towards viruses of varicella zoster, hepatitis C, bovine viral diarrhea and some others are reviewed.
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12
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Alexandrova LA. 4′-C-nucleoside derivatives: Synthesis and antiviral properties. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:723-44. [DOI: 10.1134/s1068162011060021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Spanova M, Daum G. Squalene - biochemistry, molecular biology, process biotechnology, and applications. EUR J LIPID SCI TECH 2011. [DOI: 10.1002/ejlt.201100203] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Caron J, Reddy LH, Lepêtre-Mouelhi S, Wack S, Clayette P, Rogez-Kreuz C, Yousfi R, Couvreur P, Desmaële D. Squalenoyl nucleoside monophosphate nanoassemblies: new prodrug strategy for the delivery of nucleotide analogues. Bioorg Med Chem Lett 2010; 20:2761-4. [PMID: 20363623 DOI: 10.1016/j.bmcl.2010.03.070] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 03/16/2010] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
Abstract
4-(N)-1,1',2-trisnor-squalenoyldideoxycytidine monophosphate (SQddC-MP) and 4-(N)-1,1',2-trisnor-squalenoylgemcitabine monophosphate (SQdFdC-MP) were synthesized using phosphoramidite chemistry. These amphiphilic molecules self-assembled to about hundred nanometers size nanoassemblies in aqueous medium. Nanoassemblies of SQddC-MP displayed significant anti-HIV activity whereas SQdFdC-MP nanoassemblies displayed promising anticancer activity on leukemia cells. These results suggested that squalene conjugate of negatively charged nucleotide analogues efficiently penetrated within cells. Thus, we propose a new prodrug strategy for improved delivery of nucleoside analogues to ameliorate their biological efficacy.
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Affiliation(s)
- Joachim Caron
- Université Paris-Sud, Faculté de Pharmacie, UMR CNRS 8076, 5 rue J.-B. Clément, 92296 Châtenay-Malabry, France
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Jyssum S, Jyssum K. Utilization of thymine, thymidine and TMP by neisseria meningitidis. 1. Growth response and uptake of labelled material. ACTA PATHOLOGICA ET MICROBIOLOGICA SCANDINAVICA. SECTION B: MICROBIOLOGY AND IMMUNOLOGY 2009; 78:683-91. [PMID: 4994086 DOI: 10.1111/j.1699-0463.1970.tb04358.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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Kakehi M, Usuda Y, Tabira Y, Sugimoto S. Complete deficiency of 5'-nucleotidase activity in Escherichia coli leads to loss of growth on purine nucleotides but not of their excretion. J Mol Microbiol Biotechnol 2007; 13:96-104. [PMID: 17693717 DOI: 10.1159/000103601] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli has many periplasmic phosphatase activities. To test whether it can take up and excrete purine nucleotides, we attempted to completely disrupt periplasmic 5'-nucleotidase activity. A 5'-nucleotidase activity was induced in ushA knockout mutant cells, which lack major 5'-nucleotidase activity, when they were grown with purine nucleotides as the sole carbon source. Using DNA macroarrays to compare global gene expression in wild-type and ushA knockout mutant cells cultured with IMP or GMP as the sole carbon source, we identified two genes that were induced in the ushA knockout mutant cells and encoded signal sequence needed for secretion. One of the genes, aphA, encoded a 5'-nucleotidase activity and was induced by IMP or inosine. An ushA aphA double knockout mutant was shown to be unable to grow on purine nucleotides as the sole carbon source. To investigate the excretion of purine nucleotides, we constructed an ushAaphA double knockout mutant of an inosine-producing strain and found that it accumulated IMP in the medium. In addition, when the guaBA operon was introduced into the ushAaphA double knockout IMP producer, GMP was released into the medium. These observations imply the existence of efflux activity for purine nucleotides in E. coli.
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Affiliation(s)
- Masahiro Kakehi
- Fermentation and Biotechnology Laboratories, Ajinomoto Co., Kawasaki, Japan
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Dietz GW. The hexose phosphate transport system of Escherichia coli. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 44:237-59. [PMID: 775939 DOI: 10.1002/9780470122891.ch7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Palchevskiy V, Finkel SE. Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient. J Bacteriol 2006; 188:3902-10. [PMID: 16707682 PMCID: PMC1482900 DOI: 10.1128/jb.01974-05] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 03/01/2006] [Indexed: 11/20/2022] Open
Abstract
Natural genetic competence is the ability of cells to take up extracellular DNA and is an important mechanism for horizontal gene transfer. Another potential benefit of natural competence is that exogenous DNA can serve as a nutrient source for starving bacteria because the ability to "eat" DNA is necessary for competitive survival in environments containing limited nutrients. We show here that eight Escherichia coli genes, identified as homologs of com genes in Haemophilus influenzae and Neisseria gonorrhoeae, are necessary for the use of extracellular DNA as the sole source of carbon and energy. These genes also confer a competitive advantage to E. coli during long-term stationary-phase incubation. We also show that homologs of these genes are found throughout the proteobacteria, suggesting that the use of DNA as a nutrient may be a widespread phenomenon.
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Affiliation(s)
- Vyacheslav Palchevskiy
- Molecular and Computational Biology Program, Department of Biological Sciences, MCB 201B, University of Southern California, Los Angeles, CA 90089-2910, USA
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19
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Weiss E. Adenosine Triphosphate and Other Requirements for the Utilization of Glucose by Agents of the Psittacosis-Trachoma Group. J Bacteriol 2006; 90:243-53. [PMID: 16562025 PMCID: PMC315620 DOI: 10.1128/jb.90.1.243-253.1965] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Weiss, Emilio (Naval Medical Research Institute, Bethesda, Md.). Adenosine triphosphate and other requirements for the utilization of glucose by agents of the psittacosis-trachoma group. J. Bacteriol. 90:243-253. 1965.-The agent of meningopneumonitis cultivated in the allantoic cavity of chick embryos and purified by differential centrifugations was employed for most of the studies of the requirements for glucose utilization. The evolution of C(14)O(2) from glucose-1-C(14) was used as the criterion of metabolic activity in most experiments. The rate of glucose utilization increased somewhat during the first hour of incubation at 34.4 C and became approximately constant during the second hour. Changes in glucose concentration from 1 to 5 mm did not appreciably affect metabolic activity. More vigorous CO(2) production was obtained when the ratio of K(+)-Na(+) was >1 and, under certain conditions, when the concentration of inorganic phosphate was relatively high (0.05 m). Glucose utilization was entirely dependent on added adenosine triphosphate (ATP) and Mg(++). The effect of ATP was greatly reduced when the microorganisms were partially disrupted with sonic energy. Adenosine diphosphate (ADP) could be substituted for ATP, but the activity was reduced to less than 20%. ATP was not required when glucose-6-phosphate was substituted for glucose. With ADP and glucose, glucose-6-phosphate was an effective competitor of glucose utilization. Nicotinamide adenine dinucleotide phosphate (NADP) enhanced CO(2) production from carbon 1, but not from other carbons, with glucose and, especially, glucose-6-phosphate as substrates. ATP and NADP produced the above-described effects only when their concentrations were comparable to those of the substrates. These concentrations always exceeded the amount of CO(2) produced (0.05 to 0.5 mumole/mg of agent protein). The concentration of NADP could be reduced when oxidized glutathione was added. Diphosphothiamine had no effect on CO(2) production. Qualitatively similar results were obtained with the agent of trachoma purified from yolk sac. These experiments furnish evidence that agents of the psittacosistrachoma group, despite their enzymatic capabilities, require an exogenous source of energy.
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Affiliation(s)
- E Weiss
- Department of Microbiology, Naval Medical Research Institute, Bethesda, Maryland
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20
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Affiliation(s)
- David Kennell
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Shafiee M, Deferme S, Villard AL, Egron D, Gosselin G, Imbach JL, Lioux T, Pompon A, Varray S, Aubertin AM, Van Den Mooter G, Kinget R, Périgaud C, Augustijns P. New bis(SATE) prodrug of AZT 5'-monophosphate: in vitro anti-HIV activity, stability, and potential oral absorption. J Pharm Sci 2001; 90:448-63. [PMID: 11170035 DOI: 10.1002/1520-6017(200104)90:4<448::aid-jps1003>3.0.co;2-h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The in vitro anti-HIV activity, stability, and potential for oral absorption of a phosphotriester derivative of AZT (zidovudine; 3'-azido-2',3'-deoxythymidine) bearing a new esterase-labile S-acyl-2-thioethyl (SATE) group as transient phosphate protection are reported. The biolabile protection is characterized by the presence of a hydroxyl function in the acyl chain. In accordance with previously reported data in the bis(SATE) prodrug series, the present results demonstrate that the studied bis(hydroxytBuSATE)phosphotriester exerts its biological effects via intracellular delivery of the 5'-monophosphate of AZT. The hydroxyl function confers a high resistance against esterase hydrolysis, and the studied prodrug is able to cross the Caco-2 cell monolayers in intact form, suggesting that its further development as a possible anti-HIV pronucleotide candidate is warranted.
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Affiliation(s)
- M Shafiee
- Laboratorium voor Farmacotechnologie en Biofarmacie, O & N, Gasthuisberg, K.U. Leuven, B-3000 Leuven, Belgium
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22
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HAMPTON A, HAMPTON EG, EIDINOFF ML. Nucleotides. III. Synthesis and effects with cells in culture of 131-I-labeled 5-iodo-2'-deoxyuridine-5'-phosphate. Biochem Pharmacol 1998; 11:155-9. [PMID: 13904241 DOI: 10.1016/0006-2952(62)90102-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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KANDASWAMY TS, HENDERSON JF. Intracellular differentiation of purine ribonucleotides derived from endogenous and exogenous sources. ACTA ACUST UNITED AC 1998; 61:86-93. [PMID: 14453547 DOI: 10.1016/0926-6550(62)90034-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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HUBERT-HABART M, COHEN SS. The toxicity of 9-beta-D-arabinofuranosyladenine to purine-requiring Escherichia coli. ACTA ACUST UNITED AC 1998; 59:468-71. [PMID: 14449647 DOI: 10.1016/0006-3002(62)90198-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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MALEY F. Nucleotide interconversions. VII. The effect of halogenated and N-methyl derivatives of deoxycytidylic acid on deoxycytidylate deaminase and thymidylate synthetase. ACTA ACUST UNITED AC 1998; 61:135-8. [PMID: 14468886 DOI: 10.1016/0926-6550(62)90040-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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McGuigan C, Tsang HW, Sutton PW, De Clercq E, Balzarini J. Synthesis and anti-HIV activity of some novel chain-extended phosphoramidate derivatives of d4T (stavudine): esterase hydrolysis as a rapid predictive test for antiviral potency. Antivir Chem Chemother 1998; 9:109-15. [PMID: 9875382 DOI: 10.1177/095632029800900202] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Novel chain-extended nucleoside phosphoramidates of the anti-human immunodeficiency virus (HIV) drug d4T (stavudine) have been prepared as possible membrane-permeable prodrugs of the bio-active free 5'-monophosphates. Phosphorochloridate chemistry gave the target compounds in moderate to high yields, and all materials were fully characterized by spectroscopic and analytical methods. The compounds are related to the previously reported phenyl methoxyalaninyl derivative of d4T, which was shown to be a potent and selective inhibitor of HIV. In this study the amino acid nitrogen and ester moieties were separated by methylene spacers of between two and six carbon atoms. In vitro evaluation of these compounds indicated an almost complete lack of anti-HIV activity, the compounds being several orders of magnitude less potent than the corresponding alpha-amino acid derivatives. The reasons for the virtual lack of anti-HIV activity appear to involve poor enzyme-mediated hydrolysis.
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Affiliation(s)
- C McGuigan
- Welsh School of Pharmacy, University of Wales Cardiff, UK.
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27
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FURANO AV, GREEN JP. DIFFERENCES IN THE DISPOSITION OF ENDOGENOUS AND EXOGENOUS SUBSTANCES BY CELLS. Nature 1996; 199:380-1. [PMID: 14058575 DOI: 10.1038/199380a0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Nucleotides have shown interesting biological activities in a wide variety of antiviral, antiproliferative, immunomodulatory and other biological assays, and they present promising drug candidates. Because of their negative charge(s) nucleotides suffer from some disadvantages which can be successfully overcome by the utilization of nucleotide prodrugs. Nucleotide prodrugs were successfully used to increase oral absorption of nucleotides in vivo. By taking advantage of intracellular triggers (reducing potential, enzyme activity, pH), nucleotide prodrugs can be used in vitro for the intracellular delivery of the nucleotide resulting in enhanced potency and in some cases enhanced selectivity. Nucleotide prodrugs have also been utilized for tissue specific delivery of the nucleotides in vivo resulting in altered selectivity and reduced toxicity. For nucleotide prodrugs, their ultimate intended use is (in most cases) in vivo for the treatment of a disease. Thus, it is important to incorporate adequate assays and design criteria into any prodrug effort. In vivo systems are complicated because of metabolism, excretion and tissue distribution of the prodrug and the parent. Thus, results of in vitro assays have to be interpreted cautiously because they may be unsuitable predictors of the in vivo situation.
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Affiliation(s)
- R J Jones
- Gilead Sciences, Foster City, CA 94404, USA
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31
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Abstract
With the discovery of molecular chaperones and the development of heterologous gene expression techniques, protein folding in bacteria has come into focus as a potentially limiting factor in expression and as a topic of interest in its own right. Many proteins of importance in biotechnology contain disulphide bonds, which form in the Escherichia coli periplasm, but most work on protein folding in the periplasm of E. coli is very recent and is often speculative. This MicroReview gives a short overview of the possible fates of a periplasmic protein from the moment it is translocated, as well as of the E. coli proteins involved in this process. After an introduction to the specific physiological situation in the periplasm of E. coli, we discuss the proteins that might help other proteins to obtain their correctly folded conformation--disulphide isomerase, rotamase, parts of the translocation apparatus and putative periplasmic chaperones--and briefly cover the guided assembly of multi-subunit structures. Finally, our MicroReview turns to the fate of misfolded proteins: degradation by periplasmic proteases and aggregation phenomena.
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Affiliation(s)
- C Wülfing
- Biochemisches Institut, Universität Zurich, Switzerland
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32
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Rational design for cytosolic delivery of nucleoside monphosphates : “SATE” and “DTE” as enzyme-labile transient phosphate protecting groups. Bioorg Med Chem Lett 1993. [DOI: 10.1016/s0960-894x(01)80709-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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Le Bec C, Huynh-Dinh T. Synthesis of lipophilic phosphate triester derivatives of 5-fluorouridine and arabinocytidine as anticancer prodrugs. Tetrahedron Lett 1991. [DOI: 10.1016/0040-4039(91)80219-v] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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McGuigan C, Devine KG, O'Connor TJ, Kinchington D. Synthesis and anti-HIV activity of some haloalkyl phosphoramidate derivatives of 3'-azido-3'-deoxythymidine (AZT): potent activity of the trichloroethyl methoxyalaninyl compound. Antiviral Res 1991; 15:255-63. [PMID: 1888176 DOI: 10.1016/0166-3542(91)90071-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Phosphate triester derivatives of AZT have been prepared as membrane-soluble pro-drugs of the bio-active nucleotides, and have been evaluated against HIV-1 in vitro. In particular, the phosphorus centre carries a trichloro- or trifluoroethyl group and a carboxyl-protected, amino-linked amino acid. The compounds are prepared using phosphorochloridate chemistry, and are characterized by a range of techniques. They display potent anti-HIV activity and low host toxicity, but surprisingly this activity does not increase on the introduction of the haloalkyl moiety. The trichloroethyl methoxyalaninyl compound is exceptional: here the activity is enhanced 50-fold by the introduction of the trichloroethyl group.
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Affiliation(s)
- C McGuigan
- Department of Chemistry, University of Southampton, Highfield, U.K
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35
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Norton Hughes CA, Yotis WW. A study of the acid phosphatase of Treponema denticola. ZENTRALBLATT FUR BAKTERIOLOGIE : INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY 1990; 274:195-202. [PMID: 2085369 DOI: 10.1016/s0934-8840(11)80102-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This study describes some of the properties of the acid phosphatase of the potential periodontopathogen Treponema denticola. The highest enzyme activity was found in 87 h old cells. Two optimum pHs for enzyme activity were detected, one at pH 4.8 and another at pH 6.2. Divalent cations did not influence the acid phosphatase of T. denticola. The anion F- added in the form of NaF and at a level greater than 20 micrograms/ml F- diminished the activity of the acid phosphatase of intact cells of T. denticola. The addition of 10 micrograms/ml F- as SnF2 induced a statistically significant reduction of acid phosphatase activity. The apparent Km for the acid phosphatase was 7.3 mM with p-nitrophenyl phosphate as substrate. Fluoride appeared to be a noncompetitive inhibitor of the enzyme with an apparent Ki of 0.3 mM. Acid phosphatase may be released partially in osmotic shock fluids. Also, 7-diazonium-1, 3-naphthalene disulfonate, which is incapable of penetrating the bacterial permeability barrier and is known to inactivate enzymes found in the bacterial periplasmic place, suppressed the activity of the acid phosphatase in intact cells of T. denticola.
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Affiliation(s)
- C A Norton Hughes
- Department of Microbiology, Loyola University Stritch School of Medicine, Maywood, IL 60153
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36
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Melamede RJ, Wallace SS. A possible secondary role for thymine-containing DNA precursors. BASIC LIFE SCIENCES 1985; 31:67-102. [PMID: 3888184 DOI: 10.1007/978-1-4613-2449-2_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Abstract
The respiration rate of Pi-deprived cells of Micrococcus lysodeikticus is markedly increased by Pi, and returns to the original level following Pi consumption. The stimulation of the respiration was found to be specific for Pi and arsenate. Although succinate and valinomycin enhanced the respiration of both Pi-grown and Pi-deprived cells, only the latter could be further stimulated by Pi. The effect of Pi on the respiration rate was found to be concentration dependent. The control of respiration by Pi is due to its rapid uptake and its subsequent polymerization to polyphosphate via ATP. Both of these processes are coupled to proton influx into the cell, and thus stimulate the proton efflux and the respiration rate.
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38
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Melamede RJ, Wallace SS. Incorporation of thymine-containing DNA precursors in wild-type and mutant T4-infected plasmolysed cells. MOLECULAR & GENERAL GENETICS : MGG 1983; 191:382-8. [PMID: 6355761 DOI: 10.1007/bf00425750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
T4-infected cells, plasmolysed 15 min after infection, incorporate low concentrations (less than 20 microM) of deoxythymidine (TdR) into DNA at a significantly greater rate than dTMP, dTTP or thymine. At higher concentrations (greater than 40 microM), dTMP incorporation rate is high, approaching that of TdR at 200 microM. TdR is selectively incorporated at all concentrations tested, and is not inhibited by the other thymine containing DNA precursors. Incorporation of low concentrations of TdR requires the T4-induced thymidine kinase (tk) and is not significantly affected by the presence or absence of T4-induced thymidylate synthetase (td). We show that, in T4-infected plasmolysed cells, exogenously added TdR is preferentially incorporated into short DNA fragments during short pulse times. To explain these and other data a model is proposed in which thymidine plays a modulatory role between leading and lagging strand precursor feeds.
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39
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DeVries JK, Wallace SS. Reversion of bacteriophage T4rII mutants by high levels of pyrimidine deoxyribonucleosides. MOLECULAR & GENERAL GENETICS : MGG 1982; 186:101-5. [PMID: 7050620 DOI: 10.1007/bf00422919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
High levels of pyrimidine deoxyribonucleosides, but not purine deoxyribonucleosides, increase the reversion rate of bacteriophage T4rII mutants to r+. This increased reversion rate is not observed when a thymidine kinase mutation is introduced into the bacteriophage, but the high reversion rate persists when the host, E. coli, harbors a thymidine kinase mutation.
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40
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Dassa E, Cahu M, Desjoyaux-Cherel B, Boquet PL. The acid phosphatase with optimum pH of 2.5 of Escherichia coli. Physiological and Biochemical study. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34481-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Hochman A, Bittan R, Carmeli C. Nucleotide exchange in membrane vesicles from the photosynthetic bacterium Rhodopseudomonas capsulata. Arch Biochem Biophys 1981; 211:413-8. [PMID: 7305378 DOI: 10.1016/0003-9861(81)90472-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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42
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Uerkvitz W, Beck C. Periplasmic phosphatases in Salmonella typhimurium LT2. A biochemical, physiological, and partial genetic analysis of three nucleoside monophosphate dephosphorylating enzymes. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)70147-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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43
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Stewart GJ, Fitzgerald JW. Metabolism of exogenous uridine 5'-triphosphate, adenosine 5'-triphosphate and pyrophosphate by alkylsulfatase-producing bacteria. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1981; 13:1019-26. [PMID: 6271608 DOI: 10.1016/0020-711x(81)90008-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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44
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Shearer G, Hubbard JC, Larsh HW. Non-specific incorporation of nucleic acid precursors in Blastomyces dermatitidis and Histoplasma capsulatum. Mycopathologia 1980; 72:111-9. [PMID: 7464897 DOI: 10.1007/bf00493820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Incorporation of thymidine, thymidine monophosphate (TMP), thymidine triphosphate (TTP), uridine and orotic acid into DNA, RNA and protein in Blastomyces dermatitidis and Histoplasma capsulatum was studied utilizing a specific acid hydrolysis technique developed for these fungi. Thymidine was incorporated to the greatest extent (approximately 0.5% of added label) followed by uridine, orotic acid, TMP and TTP. In Blastomyces, uridine and orotic acid labeled primarily RNA. TMP and TTP labeled RNA, DNA and protein at nearly the same level. In Histoplasma RNA was labeled poorly by any of these precursors. TMP and TTP labeled DNA predominately and protein to a slightly lower level. Deoxyadenosine or uridine media supplements of 250 micrograms/ml did not enhance incorporation. All precursors tested were found to be nonspecific in that RNA, DNA and protein were labeled. All data indicate that neither RNA nor DNA synthesis can be specifically measured in whole cells or acid precipitates by any of these precursors. Specific radiometric monitoring with these isotopes therefore requires the separation of these macromolecules.
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45
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Beacham IR. Periplasmic enzymes in gram-negative bacteria. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1979; 10:877-83. [PMID: 389690 DOI: 10.1016/0020-711x(79)90117-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Hochman A, Bittan R, Carmeli C. Nucleotide translocation across the cytoplasmic membrane in the photosynthetic bacterium Rhodopseudomonas capsulata. FEBS Lett 1978; 89:21-5. [PMID: 149026 DOI: 10.1016/0014-5793(78)80513-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Martin JF, Demain AL. Cleavage of adenosine 5'-monophosphate during uptake by Streptomyces griseus. J Bacteriol 1977; 132:590-5. [PMID: 410793 PMCID: PMC221900 DOI: 10.1128/jb.132.2.590-595.1977] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unlabeled adenine brought about a (delayed) decrease in radioactivity that had been taken up by phosphate-limited resting cells of Streptomyces griseus from [14C]adenine-labeled adenosine 5'-monophosphate (AMP). Inorganic phosphate, on the other hand, stimulated adenine uptake from AMP, presumably by activating an energy-dependent active transport mechanism. Unlabeled phosphate rapidly diluted the uptake of radioactivity from [32P]AMP. Adenine inhibited uptake of [32P]AMP but not that of [32P]orthophosphate; adenine is thought to act by inhibiting the cleavage of AMP. The uptake of 32P and 14C from double-labeled AMP showed marked differences; 32P was taken up much faster into both cells and nucleic acids. These data indicate that uptake of AMP components takes place after extracellular dephosphorylation of the nucleotide.
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48
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Kier LD, Weppelman R, Ames BN. Resolution and purification of three periplasmic phosphatases of Salmonella typhimurium. J Bacteriol 1977; 130:399-410. [PMID: 192712 PMCID: PMC235218 DOI: 10.1128/jb.130.1.399-410.1977] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A survey of Salmonella typhimurium enzymes possessing phosphatase or phosphodiesterase activity was made using several different growth conditions. These studies revealed the presence of three major enzymes, all of which were subsequently purified: a cyclic 2' ,3'-nucleotide phosphodiesterase (EC 3.1.4.d), an acid hexose phosphatase (EC 3.1.3.2), and a nonspecific acid phosphatase (EC 3.1.3.2). A fourth enzyme hydrolyzed bis-(p-nitrophenyl)phosphate but none of the other substrates tested. No evidence was found for the existence of an alkaline phosphatase (EC 3.1.3.1) or a specific 5'-nucleotidase (EC 3.1.3.5) in S. typhimurium LT2. All three phosphatases could be measured efficiently in intact cells, which suggested a periplasmic location; however, they were not readily released by osmotic shock procedures. The nonspecific acid phosphatase, which was purified to apparent homogeneity, yielded a single polypeptide band on both sodium dodecyl sulfate and acidic urea gel electrophoretic systems.
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Cohen L, Kaplan R. Accumulation of nucleotides by starved Escherichia coli cells as a probe for the involvement of ribonucleases in ribonucleic acid degradation. J Bacteriol 1977; 129:651-7. [PMID: 320188 PMCID: PMC234994 DOI: 10.1128/jb.129.2.651-657.1977] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The acid-soluble ribonucleic acid degradation products formed by Escherichia coli cells starved for a carbon source have been identified. They comprise oligonucleotides, nucleoside diphosphates, 5'- and 3'-nucleoside monophosphates, nucleosides, and free bases. The majority of these products are excreted phates, nucleosides, and free bases. The majority of these products are excreted into the medium, and only small and constant amounts are kept in the pool. During carbon starvation at elevated temperatures, mutants deficient in ribonuclease I do not form oligonucleotides and 3'-nucleoside monophosphates, and mutants that contain a modified form of polynucleotide phosphorylase do not accumulate nucleoside diphosphates. 5'-Nucleoside monophosphates do accumulate, however, in a mutant containing thermoabile ribonuclease II, under conditions where more than 95% of all enzyme activity had been destroyed. The data presented confirm the participation of ribonuclease I and polynucleotide phosphorylase in the final steps of ribonucleic acid degradation and indicate that an exonuclease forming 5'-nucleoside monophosphates is also involved.
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Kaplan R, Cohen L, Yagil E. Acid-soluble degradation products of ribonucleic acid in Escherichia coli and the role of nucleotidases in their catabolism. J Bacteriol 1975; 124:1159-64. [PMID: 1104575 PMCID: PMC236022 DOI: 10.1128/jb.124.3.1159-1164.1975] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The fate of the internally formed nucleotides resulting from the degradation of ribonucleic acid was studied. Prelabeled Escherichia coli cells were submitted to carbon starvation, and the acid-soluble products were separated by thin-layer chromatography. It was determined that free bases constitute some 75% of the end product, the balance consisting of nucleoside diphosphates, 5'-nucleoside monophosphates, 3'-nucleoside monophosphates, and nucleosides. The majority of degradation products, including phosphorylated derivatives, were excreted into the medium. The amount of products in the pool remained constant. The soluble products formed by E. coli mutants lacking either 5'-nucleotidase (Ush-) or 3'-nucleotidase (Cpd-) were compared with those produced by the parental strain with both enzymes. The results obtained indicated that 5'-nucleotidase is involved in the degradation of internally foromed nucleotides but that 3'-nucleotidase takes no part in the process.
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