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Purhonen J, Hofer A, Kallijärvi J. Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription. Nucleic Acids Res 2024; 52:e6. [PMID: 38008466 PMCID: PMC10783517 DOI: 10.1093/nar/gkad1091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/28/2023] Open
Abstract
Enzymatic methods to quantify deoxyribonucleoside triphosphates have existed for decades. In contrast, no general enzymatic method to quantify ribonucleoside triphosphates (rNTPs), which drive almost all cellular processes and serve as precursors of RNA, exists to date. ATP can be measured with an enzymatic luminometric method employing firefly luciferase, but the quantification of other ribonucleoside mono-, di-, and triphosphates is still a challenge for a non-specialized laboratory and practically impossible without chromatography equipment. To allow feasible quantification of ribonucleoside phosphates in any laboratory with typical molecular biology and biochemistry tools, we developed a robust microplate assay based on real-time detection of the Broccoli RNA aptamer during in vitro transcription. The assay employs the bacteriophage T7 and SP6 RNA polymerases, two oligonucleotide templates encoding the 49-nucleotide Broccoli aptamer, and a high-affinity fluorogenic aptamer-binding dye to quantify each of the four canonical rNTPs. The inclusion of nucleoside mono- and diphosphate kinases in the assay reactions enabled the quantification of the mono- and diphosphate counterparts. The assay is inherently specific and tolerates concentrated tissue and cell extracts. In summary, we describe the first chromatography-free method to quantify ATP, ADP, AMP, GTP, GDP, GMP, UTP, UDP, UMP, CTP, CDP and CMP in biological samples.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki 00290, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Helsinki 00290, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
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2
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Rosell-Garcia T, Rivas-Muñoz S, Kin K, Romero-Albillo V, Alcaraz S, Fernandez-Tornero C, Rodriguez-Pascual F. Multimerization of HIF enhances transcription of target genes containing the hypoxia ancillary sequence. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194963. [PMID: 37499936 DOI: 10.1016/j.bbagrm.2023.194963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
Transcriptional activity of the hypoxia inducible factor (HIF) relies on the formation of a heterodimer composed of an oxygen-regulated α-subunit and a stably expressed β-subunit. Heterodimeric HIF activates expression by binding to RCGTG motifs within promoters of hypoxia-activated genes. Some hypoxia targets also possess an adjacent HIF ancillary sequence (HAS) reported to increase transcription but whose function remains obscure. Here, we investigate the contribution of the HAS element to the hypoxia response and its mechanism of action, using the HAS-containing prolyl 4-hydroxylase subunit α1 (P4HA1) as a gene model in NIH/3T3 mouse embryonic fibroblasts and HEK293 human embryonic kidney cells. Our HIF overexpression experiments demonstrate that the HAS motif is essential for full induction by hypoxia and that the presence of the tandem HAS/HIF, as opposed to HIF-only sequences, provides HIF proteins with the capacity to form complexes of stoichiometry beyond the classical heterodimer, likely tetramers, to cooperatively potentiate hypoxia-induced transcription. We also provide evidence of the crucial role played by the Fα helix of the PAS-B domain of the HIF1β subunit to support the interaction between heterodimers. Functional analysis showed that human genes containing the HAS/HIF motifs are better responders to hypoxia, and their promoters are enriched for specific transcription factor binding sites. Gene ontology enrichment revealed a predominance of HAS/HIF in genes primarily related to tissue formation and development. Our findings add an extra level of regulation of the hypoxia/HIF signaling through multimerization of HIF proteins on regulatory elements containing the HAS/HIF motifs.
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Affiliation(s)
- Tamara Rosell-Garcia
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas (C.S.I.C.)-Universidad Autónoma de Madrid (U.A.M.), Madrid, Spain
| | - Sergio Rivas-Muñoz
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas (C.S.I.C.)-Universidad Autónoma de Madrid (U.A.M.), Madrid, Spain
| | - Koryu Kin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Verónica Romero-Albillo
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas (C.S.I.C.)-Universidad Autónoma de Madrid (U.A.M.), Madrid, Spain
| | - Silvia Alcaraz
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas (C.S.I.C.)-Universidad Autónoma de Madrid (U.A.M.), Madrid, Spain
| | | | - Fernando Rodriguez-Pascual
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas (C.S.I.C.)-Universidad Autónoma de Madrid (U.A.M.), Madrid, Spain.
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3
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Maximizing transcription of nucleic acids with efficient T7 promoters. Commun Biol 2020; 3:439. [PMID: 32796901 PMCID: PMC7429497 DOI: 10.1038/s42003-020-01167-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/21/2020] [Indexed: 11/08/2022] Open
Abstract
In vitro transcription using T7 bacteriophage polymerase is widely used in molecular biology. Here, we use 5'RACE-Seq to screen a randomized initially transcribed region of the T7 promoter for cross-talk with transcriptional activity. We reveal that sequences from position +4 to +8 downstream of the transcription start site affect T7 promoter activity over a 5-fold range, and identify promoter variants with significantly enhanced transcriptional output that increase the yield of in vitro transcription reactions across a wide range of template concentrations. We furthermore introduce CEL-Seq+ , which uses an optimized T7 promoter to amplify cDNA for single-cell RNA-Sequencing. CEL-Seq+ facilitates scRNA-Seq library preparation, and substantially increases library complexity and the number of expressed genes detected per cell, highlighting a particular value of optimized T7 promoters in bioanalytical applications.
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4
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Schaerli Y, Jiménez A, Duarte JM, Mihajlovic L, Renggli J, Isalan M, Sharpe J, Wagner A. Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution. Mol Syst Biol 2018; 14:e8102. [PMID: 30201776 PMCID: PMC6129954 DOI: 10.15252/msb.20178102] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/22/2022] Open
Abstract
Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such biases are still poorly understood. Gene regulatory networks have been proposed as one cause of constrained phenotypic variation. However, most pertinent evidence is theoretical rather than experimental. Here, we study evolutionary biases in two synthetic gene regulatory circuits expressed in Escherichia coli that produce a gene expression stripe-a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. Consequently, seemingly equivalent networks can indeed be distinct in how they constrain the outcome of further evolution.
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Affiliation(s)
- Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Alba Jiménez
- Systems Biology Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
| | - José M Duarte
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Ljiljana Mihajlovic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | | | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - James Sharpe
- Systems Biology Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
- EMBL Barcelona European Molecular Biology Laboratory, Barcelona, Spain
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
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5
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Paksa A, Bandemer J, Hoeckendorf B, Razin N, Tarbashevich K, Minina S, Meyen D, Biundo A, Leidel SA, Peyrieras N, Gov NS, Keller PJ, Raz E. Repulsive cues combined with physical barriers and cell-cell adhesion determine progenitor cell positioning during organogenesis. Nat Commun 2016; 7:11288. [PMID: 27088892 PMCID: PMC4837475 DOI: 10.1038/ncomms11288] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/09/2016] [Indexed: 01/15/2023] Open
Abstract
The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step during organogenesis. Using primordial germ cells that participate in gonad formation, we present the developmental mechanisms maintaining a motile progenitor cell population at the site where the organ develops. Employing high-resolution live-cell microscopy, we find that repulsive cues coupled with physical barriers confine the cells to the correct bilateral positions. This analysis revealed that cell polarity changes on interaction with the physical barrier and that the establishment of compact clusters involves increased cell–cell interaction time. Using particle-based simulations, we demonstrate the role of reflecting barriers, from which cells turn away on contact, and the importance of proper cell–cell adhesion level for maintaining the tight cell clusters and their correct positioning at the target region. The combination of these developmental and cellular mechanisms prevents organ fusion, controls organ positioning and is thus critical for its proper function. The precise positioning of organ progenitor cells is essential for organ development and function. Here the authors use live imaging and mathematical modelling to show that the confinement of a motile progenitor cell population results from coupled physical barriers and cell-cell interactions.
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Affiliation(s)
- Azadeh Paksa
- Institute for Cell Biology, ZMBE, Von-Esmarch-Street 56, 48149 Muenster, Germany
| | - Jan Bandemer
- Institute for Cell Biology, ZMBE, Von-Esmarch-Street 56, 48149 Muenster, Germany
| | | | - Nitzan Razin
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Sofia Minina
- Germ Cell Development, Max-Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37070 Göttingen, Germany
| | - Dana Meyen
- Institute for Cell Biology, ZMBE, Von-Esmarch-Street 56, 48149 Muenster, Germany
| | - Antonio Biundo
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany
| | - Nadine Peyrieras
- USR3695 BioEmergences, CNRS, Université Paris-Saclay, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Nir S Gov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Erez Raz
- Institute for Cell Biology, ZMBE, Von-Esmarch-Street 56, 48149 Muenster, Germany
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6
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Song MS, Choi SP, Lee J, Kwon YJ, Sim SJ. Real-time, sensitive, and specific detection of promoter-polymerase interactions in gene transcription using a nanoplasmonic sensor. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:1265-1269. [PMID: 23166096 DOI: 10.1002/adma.201203467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/15/2012] [Indexed: 06/01/2023]
Affiliation(s)
- Min Sun Song
- Department of Chemical Engineering, Sungkyunkwan University, Suwon 440-746, Korea
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7
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Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A 2012; 109:19498-503. [PMID: 23129659 PMCID: PMC3511131 DOI: 10.1073/pnas.1210678109] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cis-regulatory elements (CREs) control gene expression by recruiting transcription factors (TFs) and other DNA binding proteins. We aim to understand how individual nucleotides contribute to the function of CREs. Here we introduce CRE analysis by sequencing (CRE-seq), a high-throughput method for producing and testing large numbers of reporter genes in mammalian cells. We used CRE-seq to assay >1,000 single and double nucleotide mutations in a 52-bp CRE in the Rhodopsin promoter that drives strong and specific expression in mammalian photoreceptors. We find that this particular CRE is remarkably complex. The majority (86%) of single nucleotide substitutions in this sequence exert significant effects on regulatory activity. Although changes in the affinity of known TF binding sites explain some of these expression changes, we present evidence for complex phenomena, including binding site turnover and TF competition. Analysis of double mutants revealed complex, nucleotide-specific interactions between residues in different TF binding sites. We conclude that some mammalian CREs are finely tuned by evolution and function through complex, nonadditive interactions between bound TFs. CRE-seq will be an important tool to uncover the rules that govern these interactions.
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Affiliation(s)
- Jamie C. Kwasnieski
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| | - Ilaria Mogno
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| | - Connie A. Myers
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
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8
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High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol 2010; 27:1173-5. [PMID: 19915551 DOI: 10.1038/nbt.1589] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 10/26/2009] [Indexed: 11/08/2022]
Abstract
We present a method that harnesses massively parallel DNA synthesis and sequencing for the high-throughput functional analysis of regulatory sequences at single-nucleotide resolution. As a proof of concept, we quantitatively assayed the effects of all possible single-nucleotide mutations for three bacteriophage promoters and three mammalian core promoters in a single experiment per promoter. The method may also serve as a rapid screening tool for regulatory element engineering in synthetic biology.
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9
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Scholl D, Merril C. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J Bacteriol 2006; 187:8499-503. [PMID: 16321955 PMCID: PMC1317022 DOI: 10.1128/jb.187.24.8499-8503.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage K1F specifically infects Escherichia coli strains that produce the K1 polysaccharide capsule. Like several other K1 capsule-specific phages, K1F encodes an endo-neuraminidase (endosialidase) that is part of the tail structure which allows the phage to recognize and degrade the polysaccharide capsule. The complete nucleotide sequence of the K1F genome reveals that it is closely related to bacteriophage T7 in both genome organization and sequence similarity. The most striking difference between the two phages is that K1F encodes the endosialidase in the analogous position to the T7 tail fiber gene. This is in contrast with bacteriophage K1-5, another K1-specific phage, which encodes a very similar endosialidase which is part of a tail gene "module" at the end of the phage genome. It appears that diverse phages have acquired endosialidase genes by horizontal gene transfer and that these genes or gene products have adapted to different genome and virion architectures.
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Affiliation(s)
- Dean Scholl
- National Institutes of Mental Health, National Institutes of Health, Building 49, Room B1B20, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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10
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Chen Z, Schneider TD. Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases. Nucleic Acids Res 2005; 33:6172-87. [PMID: 16260472 PMCID: PMC1275584 DOI: 10.1093/nar/gki915] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, φA1122, T3, φYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used to scan the corresponding genomes, a significant gap in the individual information distribution was observed between functional promoter sites and other sequences, suggesting that the models can be used to identify new T7-like promoters. When a combined 76-site model was used to scan the eight phages, 108 of the total 109 promoters were found, while none were found for other T7-like phages, φKMV, P60, VpV262, SIO1, PaP3, Xp10, P-SSP7 and Ppu40, indicating that these phages do not belong to the T7 group. We propose that the T7-like transcription system, which consists of a phage-specific RNA polymerase and a set of conserved T7-like promoters, is a hallmark feature of the T7 group and can be used to classify T7-like phages. Phylogenetic trees of the T7-like promoter models and their corresponding RNA polymerases are similar, suggesting that the eight phages of the T7 group can be classified into five subgroups. However the SP6-like polymerases have apparently diverged from other polymerases more than their promoters have diverged from other promoters.
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Affiliation(s)
| | - Thomas D. Schneider
- To whom correspondence should be addressed. Tel: +1 301 846 5581; Fax: +1 301 846 5598;
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11
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Dittmer WU, Kempter S, Rädler JO, Simmel FC. Using gene regulation to program DNA-based molecular devices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2005; 1:709-12. [PMID: 17193511 DOI: 10.1002/smll.200500074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Wendy U Dittmer
- Department of Physics and Center for Nanoscience, University of Munich, Geschwister Scholl Platz 1, 80539 Munich, Germany
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12
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Dobbins AT, George M, Basham DA, Ford ME, Houtz JM, Pedulla ML, Lawrence JG, Hatfull GF, Hendrix RW. Complete genomic sequence of the virulent Salmonella bacteriophage SP6. J Bacteriol 2004; 186:1933-44. [PMID: 15028677 PMCID: PMC374404 DOI: 10.1128/jb.186.7.1933-1944.2004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete genome sequence of enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is approximately 5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.
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Affiliation(s)
- Aleisha T Dobbins
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Washington, DC 20059, USA
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13
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Scholl D, Kieleczawa J, Kemp P, Rush J, Richardson CC, Merril C, Adhya S, Molineux IJ. Genomic Analysis of Bacteriophages SP6 and K1-5, an Estranged Subgroup of the T7 Supergroup. J Mol Biol 2004; 335:1151-71. [PMID: 14729334 DOI: 10.1016/j.jmb.2003.11.035] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have determined the genome sequences of two closely related lytic bacteriophages, SP6 and K1-5, which infect Salmonella typhimurium LT2 and Escherichia coli serotypes K1 and K5, respectively. The genome organization of these phages is almost identical with the notable exception of the tail fiber genes that confer the different host specificities. The two phages have diverged extensively at the nucleotide level but they are still more closely related to each other than either is to any other phage currently characterized. The SP6 and K1-5 genomes contain, respectively, 43,769 bp and 44,385 bp, with 174 bp and 234 bp direct terminal repeats. About half of the 105 putative open reading frames in the two genomes combined show no significant similarity to database proteins with a known or predicted function that is obviously beneficial for growth of a bacteriophage. The overall genome organization of SP6 and K1-5 is comparable to that of the T7 group of phages, although the specific order of genes coding for DNA metabolism functions has not been conserved. Low levels of nucleotide similarity between genomes in the T7 and SP6 groups suggest that they diverged a long time ago but, on the basis of this conservation of genome organization, they are expected to have retained similar developmental strategies.
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Affiliation(s)
- D Scholl
- Section of Biochemical Genetics, The National Institute of Mental Health, NIH, 9000 Rockville Pike, Bethesda, MD 20895, USA.
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14
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Affiliation(s)
- Inkyung Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejon 305-701, Republic of Korea
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