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Pflughaupt P, Sahakyan AB. Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule. Nucleic Acids Res 2023; 51:7409-7423. [PMID: 37293966 PMCID: PMC10415130 DOI: 10.1093/nar/gkad477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Chargaff's second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.
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Affiliation(s)
- Patrick Pflughaupt
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Aleksandr B Sahakyan
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
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2
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Moeckel C, Zaravinos A, Georgakopoulos-Soares I. Strand Asymmetries Across Genomic Processes. Comput Struct Biotechnol J 2023; 21:2036-2047. [PMID: 36968020 PMCID: PMC10030826 DOI: 10.1016/j.csbj.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Across biological systems, a number of genomic processes, including transcription, replication, DNA repair, and transcription factor binding, display intrinsic directionalities. These directionalities are reflected in the asymmetric distribution of nucleotides, motifs, genes, transposon integration sites, and other functional elements across the two complementary strands. Strand asymmetries, including GC skews and mutational biases, have shaped the nucleotide composition of diverse organisms. The investigation of strand asymmetries often serves as a method to understand underlying biological mechanisms, including protein binding preferences, transcription factor interactions, retrotransposition, DNA damage and repair preferences, transcription-replication collisions, and mutagenesis mechanisms. Research into this subject also enables the identification of functional genomic sites, such as replication origins and transcription start sites. Improvements in our ability to detect and quantify DNA strand asymmetries will provide insights into diverse functionalities of the genome, the contribution of different mutational mechanisms in germline and somatic mutagenesis, and our knowledge of genome instability and evolution, which all have significant clinical implications in human disease, including cancer. In this review, we describe key developments that have been made across the field of genomic strand asymmetries, as well as the discovery of associated mechanisms.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
- Corresponding author at: Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus.
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Corresponding author.
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3
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Rue CR, Selwyn JD, Cockett PM, Gillis B, Gurski L, Jose P, Kutil BL, Magnuson SF, Ángela López de Mesa L, Overath RD, Smee DL, Bird CE. Genetic diversity across the mitochondrial genome of eastern oysters ( Crassostrea virginica) in the northern Gulf of Mexico. PeerJ 2021; 9:e12205. [PMID: 34692250 PMCID: PMC8485835 DOI: 10.7717/peerj.12205] [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] [Received: 06/07/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with pooled restriction-site-associated DNA sequencing (ezRAD), (2) evaluate the validity of the mitochondrial genome assemblies including comparison with Sanger sequencing data, and (3) evaluate genetic differentiation both between the Delaware and Texas genomes, as well as among three bays in Texas. The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. In the comparison between the Delaware and Texas genome, 27 of 38 coding regions exhibited variability between the two populations, which were differentiated by 273 mutations, versus 1-13 mutations among the Texas samples. Using the full PAGs, there was no additional evidence for population structure among the three Texas bays. While population genetics is rapidly moving towards larger high-density datasets, studies of mitochondrial DNA (and genomes) can be particularly useful for comparing historic data prior to the modern era of genomics. As such, being able to reliably compile mitochondrial genomes from genomic data can improve the ability to compare results across studies.
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Affiliation(s)
- Chani R Rue
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Jason D Selwyn
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Patricia M Cockett
- Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Bryan Gillis
- Conrad Blucher Institute, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Lauren Gurski
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Philip Jose
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Brandi L Kutil
- Department of Undergraduate Studies, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Sharon F Magnuson
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Luz Ángela López de Mesa
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - R Deborah Overath
- Department of Mathematics and Sciences, Texas Southmost College, Brownsville, TX, United States of America
| | - Delbert Lee Smee
- Dauphin Island Sea Lab, Dauphin Island, AL, United States of America.,Marine Sciences, University of South Alabama, Mobile, AL, United States of America
| | - Christopher E Bird
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America.,Hawai'i Institute of Marine Biology, University of Hawaii at Mānoa, Kāne'ohe, Hawai'i, United States of America
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Fariselli P, Taccioli C, Pagani L, Maritan A. DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule. Brief Bioinform 2021; 22:2172-2181. [PMID: 32266404 PMCID: PMC7986665 DOI: 10.1093/bib/bbaa041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/27/2020] [Accepted: 03/05/2020] [Indexed: 01/13/2023] Open
Abstract
Most living organisms rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered as the main target of evolution. However, here we show that symmetries and patterns in the dsDNA sequence can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. The randomness justifies the human codon biases and context-dependent mutation patterns in human populations. Thus, the DNA 'exceptional symmetries,' emerged from the randomness, have to be taken into account when looking for the DNA encoded information. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the selective biological processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.
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Affiliation(s)
- Piero Fariselli
- Department of Medical Sciences of the University of Turin, Italy
| | | | - Luca Pagani
- Department of Biology of the University of Padova, Italy
| | - Amos Maritan
- Department of Physics of the University of Padova, Italy
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Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature. J Mol Evol 2020; 89:165-171. [PMID: 33216148 DOI: 10.1007/s00239-020-09974-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Over twenty years ago Galtier and Lobry published a manuscript entitled "Relationships between Genomic G + C Content, RNA Secondary Structure, and Optimal Growth Temperature" in the Journal of Molecular Evolution that showcased the lack of a relationship between genomic G + C content and optimal growth temperature (OGT) in a set of about 200 prokaryotes. Galtier and Lobry also assessed the relationship between RNA secondary structures (rRNA stems, tRNAs) and OGT, and in this case a clear relationship emerged. Increasing structured RNA G + C content (particularly in regions that are double-stranded) correlates with increased OGT. Both of these fundamental relationships have withstood test of many additional sequences and spawned a variety of different applications that include prediction of OGT from rRNA sequence and computational ncRNA identification approaches. In this work, I present the motivation behind Galtier and Lobry's original paper and the larger questions addressed by the work, how these questions have evolved over the last two decades, and the impact of Galtier and Lobry's manuscript in fields beyond these questions.
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Afreixo V, Rodrigues JMOS, Bastos CAC, Tavares AHMP, Silva RM. Exceptional Symmetry by Genomic Word : A Statistical Analysis. Interdiscip Sci 2016; 9:14-23. [PMID: 27866321 DOI: 10.1007/s12539-016-0200-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 01/12/2023]
Abstract
Single-strand DNA symmetry is pointed as a universal law observed in the genomes from all living organisms. It is a somewhat broadly defined concept, which has been refined into some more specific measurable effects. Here we discuss the exceptional symmetry effect. Exceptional symmetry is the symmetry effect beyond that expected in independence contexts, and it can be measured for each word, for each equivalent composition group, or globally, combining the effects of all possible words of a given length. Global exceptional symmetry was found in several species, but there are genomic words with no exceptional symmetry effect, whereas others show a very high exceptional symmetry effect. In this work, we discuss a measure to evaluate the exceptional symmetry effect by symmetric word pair, and compare it with others. We present a detailed study of the exceptional symmetry by symmetric pairs and take the CG content into account. We also introduce and discuss the exceptional symmetry profile for the DNA of each organism, and we perform a multiple comparison for 31 genomes: 7 viruses; 5 archaea; 5 bacteria; 14 eukaryotes.
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Affiliation(s)
- Vera Afreixo
- iBiMED-Institute of Biomedicine, IEETA-Institute of Electronic Engineering and Informatics of Aveiro, CIDMA- Center for Research and Development in Mathematics and Applications, Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
| | - João M O S Rodrigues
- IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Carlos A C Bastos
- IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Ana H M P Tavares
- iBiMED-Institute of Biomedicine, Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Raquel M Silva
- iBiMED-Institute of Biomedicine, IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Medical Sciences, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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9
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Afreixo V, Rodrigues JMOS, Bastos CAC, Silva RM. The exceptional genomic word symmetry along DNA sequences. BMC Bioinformatics 2016; 17:59. [PMID: 26842742 PMCID: PMC4738807 DOI: 10.1186/s12859-016-0905-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/19/2016] [Indexed: 01/05/2023] Open
Abstract
Background The second Chargaff’s parity rule and its extensions are recognized as universal phenomena in DNA sequences. However, parity of the frequencies of reverse complementary oligonucleotides could be a mere consequence of the single nucleotide parity rule, if nucleotide independence is assumed. Exceptional symmetry (symmetry beyond that expected under an independent nucleotide assumption) was proposed previously as a meaningful measure of the extension of the second parity rule to oligonucleotides. The global exceptional symmetry was detected in long and short genomes. Results To explore the exceptional genomic word symmetry along the genome sequences, we propose a sliding window method to extract the values of exceptional symmetry (for all words or by word groups). We compare the exceptional symmetry effect size distribution in all human chromosomes against control scenarios (positive and negative controls), testing the differences and performing a residual analysis. We explore local exceptional symmetry in equivalent composition word groups, and find that the behaviour of the local exceptional symmetry depends on the word group. Conclusions We conclude that the exceptional symmetry is a local phenomenon in genome sequences, with distinct characteristics along the sequence of each chromosome. The local exceptional symmetry along the genomic sequences shows outlying segments, and those segments have high biological annotation density.
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Affiliation(s)
- Vera Afreixo
- Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. .,Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal, Campus Universitário de Santiago, Aveiro, Portugal. .,IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
| | - João M O S Rodrigues
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. .,IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
| | - Carlos A C Bastos
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. .,IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
| | - Raquel M Silva
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal, Campus Universitário de Santiago, Aveiro, Portugal. .,IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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Afreixo V, Rodrigues JMOS, Bastos CAC. Analysis of single-strand exceptional word symmetry in the human genome: new measures. Biostatistics 2014; 16:209-21. [PMID: 25190514 DOI: 10.1093/biostatistics/kxu041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Some previous studies suggest the extension of Chargaff's second rule (the phenomenon of symmetry in a single DNA strand) to long DNA words. However, in random sequences generated under an independent symbol model where complementary nucleotides have equal occurrence probabilities, we expect the phenomenon of symmetry to hold for any word length. In this work, we develop new statistical methods to measure the exceptional symmetry. Exceptional symmetry is a refinement of Chargaff's second parity rule that highlights the words whose frequency of occurrence is similar to that of its reversed complement but dissimilar to the frequencies of occurrence of other words which contain the same number of nucleotides A or T. We analyze words of lengths up to 12 in the complete human genome and in each chromosome separately. We assess exceptional symmetry globally, by word group, and by word. We conclude that the global symmetry present in the human genome is clearly exceptional and significant. The chromosomes present distinct exceptional symmetry profiles. There are several exceptional word groups and exceptional words with a strong exceptional symmetry.
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Affiliation(s)
- Vera Afreixo
- Department of Mathematics, University of Aveiro, 3810-193 Aveiro, PortugalCIDMA, University of Aveiro, 3810-193 Aveiro, PortugalIEETA, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João M O S Rodrigues
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, PortugalIEETA, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlos A C Bastos
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, PortugalIEETA, University of Aveiro, 3810-193 Aveiro, Portugal
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Afreixo V, Bastos CA, Garcia SP, Rodrigues JM, Pinho AJ, Ferreira PJ. The breakdown of the word symmetry in the human genome. J Theor Biol 2013; 335:153-9. [DOI: 10.1016/j.jtbi.2013.06.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 01/13/2023]
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12
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Da Silva M, Upton C. Using purine skews to predict genes in AT-rich poxviruses. BMC Genomics 2005; 6:22. [PMID: 15720717 PMCID: PMC552303 DOI: 10.1186/1471-2164-6-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Accepted: 02/18/2005] [Indexed: 11/13/2022] Open
Abstract
Background Clusters or runs of purines on the mRNA synonymous strand have been found in many different organisms including orthopoxviruses. The purine bias that is exhibited by these clusters can be observed using a purine skew and in the case of poxviruses, these skews can be used to help determine the coding strand of a particular segment of the genome. Combined with previous findings that minor ORFs have lower than average aspartate and glutamate composition and higher than average serine composition, purine content can be used to predict the likelihood of a poxvirus ORF being a "real gene". Results Using purine skews and a "quality" measure designed to incorporate previous findings about minor ORFs, we have found that in our training case (vaccinia virus strain Copenhagen), 59 of 65 minor (small and unlikely to be a real genes) ORFs were correctly classified as being minor. Of the 201 major (large and likely to be real genes) vaccinia ORFs, 192 were correctly classified as being major. Performing a similar analysis with the entomopoxvirus amsacta moorei (AMEV), it was found that 4 major ORFs were incorrectly classified as minor and 9 minor ORFs were incorrectly classified as major. The purine abundance observed for major ORFs in vaccinia virus was found to stem primarily from the first codon position with both the second and third codon positions containing roughly equal amounts of purines and pyrimidines. Conclusion Purine skews and a "quality" measure can be used to predict functional ORFs and purine skews in particular can be used to determine which of two overlapping ORFs is most likely to be the real gene if neither of the two ORFs has orthologs in other poxviruses.
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Affiliation(s)
- Melissa Da Silva
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
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Abstract
The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.
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Affiliation(s)
- Eduardo P C Rocha
- Atelier de Bioinformatique, Université Pierre et Marie Curie, 12, Rue Cuvier, 75005 Paris, and Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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Chargaff E. Initiation of enzymic synthesis of deoxyribonucleic acid by ribonucleic acid primers. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 16:1-24. [PMID: 766078 DOI: 10.1016/s0079-6603(08)60754-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Evidence of the presence of messenger ribonucleic acid (mRNA) in dormant spores of Bacillus subtilis has been obtained. The bulk RNA from spores was isolated and labeled in vitro with tritiated dimethyl sulfate. The spore RNA hybridized to 2.4 to 3.2% of the B. subtilis genome. The RNA hybridized to both the complementary heavy and light fractions of deoxyribonucleic acid (DNA). Bulk RNA from log-phase cells competed with virtually all the spore RNA for the heavy DNA fraction and with part of the spore RNA for the light DNA fraction. Bulk RNA from stage IV cells in sporulation also competed with all of the spore RNA for the heavy DNA fraction and with essentially all the spore RNA for the light DNA fraction. These results indicate that dormant spores contain mRNA species present in both log-phase cells and stage IV cells of sporulation. The RNA polymerase in the developing forespore must be able to recognize promotor sites for both log-phase and sporulation genes.
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Wang HF, Sternglanz R. Thymine-labelled deoxyoligonucleotide involved in DNA chain growth in Bacillus subtilis. Nature 1974; 248:147-50. [PMID: 4362087 DOI: 10.1038/248147a0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Notani NK, Setlow JK. Mechanism of bacterial transformation and transfection. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1974; 14:39-100. [PMID: 4152450 DOI: 10.1016/s0079-6603(08)60205-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Rudner R, Remeza V. Chromatographically fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid: biological properties. J Bacteriol 1973; 113:739-53. [PMID: 4347925 PMCID: PMC285289 DOI: 10.1128/jb.113.2.739-753.1973] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Biological, physical, and chromatographic properties of methylated albuminkieselguhr (MAK)-fractionated complementary strands, designated as light (L) and heavy (H), of Bacillus subtilis deoxyribonucleic acid (DNA) are presented. The pattern of transforming activity along the MAK elution profile of alkilidenatured DNA shows that the residually active molecules selectively fractionated ahead of the L strand fraction, whereas the most active self-annealed molecules fractionated preferentially at the trailing end of the H strand fraction. The restoration rate of transforming activity in the late-eluting H molecules was rapid and independent of concentration during the annealing reaction. The data suggest that the self-annealing activity in the H strand is due in part to the formation of intrastrand secondary structures. Hydroxyapatite chromatography of self-annealed L and H strands yielded a major fraction (I) of highly purified strand preparations devoid of transforming activity and hypochromicity, and a minor "nativelike" fraction (II). Sedimentation velocity measurements show that, in addition to the mutual complementary nature of the L and H fractions, they differ in molecular size and possibly configuration.
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Rudner R, Remeza V. Chromatographically fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid: transformation of hybrids. J Bacteriol 1973; 113:754-62. [PMID: 4347926 PMCID: PMC285290 DOI: 10.1128/jb.113.2.754-762.1973] [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: 01/10/2023] Open
Abstract
The annealing properties as measured by the restoration of transforming activity and hypochromicity of methylated albumin-kieselguhr (MAK)-fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA) are presented. Temperature-absorbance measurements performed on annealed mixtures of various L and H strand fractions indicated the existence of a complementarity gradient between the two MAK peaks. The markers purA16, leu-8, metB(5), thr-5, and the linked marker hisB(2)-try-2 exhibited different bimodal distributions on MAK columns. The transforming efficiency of heteroduplex mixtures, prepared by cross-annealing resolved complementary strands of wild-type and recipient DNA, was compared. The transforming efficiency of the wild-type L and H strands was equal in one preparation and unequal in a second preparation. It was found that in the second strand preparation the heteroduplex DNA containing the H strand from wild type was more efficient for all of the markers tested. The variations in transforming efficiencies of the complementary strands in heteroduplex molecules reported here and by others are due in part to strands of unequal length and probably to the self-annealing property of the H strands. At present, no conclusion could be made regarding the existence of strand selection bias during integration of donor DNA in competent B. subtilis cells.
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Sobell HM. Symmetry in protein-nucleic acid interaction and its genetic implications. ADVANCES IN GENETICS 1973; 17:411-90. [PMID: 4130596 DOI: 10.1016/s0065-2660(08)60175-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Rudner R, Ledoux M, Mazelis A. Distribution of pyrimidine oligonucleotides in strands L and H of Bacillus subtilis DNA. Proc Natl Acad Sci U S A 1972; 69:2745-9. [PMID: 4341707 PMCID: PMC427031 DOI: 10.1073/pnas.69.9.2745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The distribution of pyrimidine oligodeoxynucleotide clusters in L and H strands of Bacillus subtilis DNA separated by methylated albumin-Kieselguhr has been determined. Preparations of native and single-stranded DNA were degraded with diphenylamine in formic acid, and the released isostichs with the general formula of Py(n)P(n+1) were separated on DEAE-cellulose by chain length. Eleven isostichs were obtained for strands L and H in unequal proportions. Each isostich fraction was subfractionated by base composition on DEAE-cellulose at pH 3.0. 61 Pyrimidine oligonucleotide clusters were separated from the H strand and only 46 from the L strand. The findings show a higher degree of asymmetry between the strands in the distribution of cytosine-rich clusters as compared with thymine-rich clusters. The longest cytosine oligodeoxynucleotide present in both strands is of chain length 5. There is an unusually high distribution of thymine oligodeoxynucleotides of length 5-11. Up to chain length 6, the distribution of thymine oligodeoxynucleotides between the strands is about equal; from chain length 7 to 11 they occur predominantly in the H strand.
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25
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Hussey C, Pero J, Shorenstein RG, Losick R. In vitro synthesis of ribosomal RNA by Bacillus subtilis RNA polymerase. Proc Natl Acad Sci U S A 1972; 69:407-11. [PMID: 4621834 PMCID: PMC426468 DOI: 10.1073/pnas.69.2.407] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Two kinds of hybridization competition experiments show that Bacillus subtilis RNA polymerase synthesizes ribosomal RNA (rRNA) in vitro with B. subtilis DNA as a template. First, RNA synthesized in vitro competes with the hybridization of [(32)P]rRNA synthesized in vivo to the heavy strand of B. subtilis DNA. Second, unlabeled rRNA synthesized in vivo competes with the hybridization of [(3)H]RNA synthesized in vitro to denatured DNA or heavy-strand DNA, but not to light-strand DNA. The ability of RNA polymerase holoenzyme to synthesize rRNA in vitro is not lost after extensive purification. RNA polymerase core enzyme, however, which is missing the sigma factor, synthesizes little rRNA in vitro.RNA polymerase purified from wild-type sporulating cells synthesizes little rRNA in vitro, while the in vitro synthesis of rRNA by RNA polymerase from stationary phase cells of the sporulation-defective mutant rfr 10 is apparently unimpaired.
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26
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Karkas JD, Stavrianopoulos JG, Chargaff E. Action of DNA polymerase I of Escherichia coli with DNA-RNA hybrids as templates. Proc Natl Acad Sci U S A 1972; 69:398-402. [PMID: 4621833 PMCID: PMC426466 DOI: 10.1073/pnas.69.2.398] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Experiments indicating the ability of the ribo strand of a DNA-RNA template to guide polydeoxynucleotide synthesis by highly purified DNA polymerase I of E. coli (EC 2.7.7.7) are presented. With poly(rA).poly(dT) as template, poly(dT) is formed with a high efficiency, but almost no poly(dA). The specific activity of the enzyme, when tested with this template under suitable conditions, is eight times greater than that found for the poly(dA-dT) template. Single-stranded DNA fractions, with no template activity for DNA polymerase, are converted to efficient templates after their transcription by RNA polymerase. A concerted polymerization reaction, in which the action of DNA polymerase is dependent on that of RNA polymerase, can also be demonstrated with synthetic polydeoxynucleotides and single-stranded fractions of denatured DNA as templates.
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27
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Harris WJ, Barr GC. Structural features of DNA in competent Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1971; 113:316-30. [PMID: 5004185 DOI: 10.1007/bf00272332] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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28
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Margulies L, Remeza V, Rudner R. Asymmetric template function of microbial deoxyribonucleic acids: transcription of messenger ribonucleic acid. J Bacteriol 1971; 107:610-7. [PMID: 4328752 PMCID: PMC246978 DOI: 10.1128/jb.107.3.610-617.1971] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In Bacillus subtilis and Escherichia coli, pulse-labeled ribonucleic acid (RNA) synthesized during step-down growth hybridized preferentially with the heavy (H) strand of methylated albumin-Kieselguhr-fractionated deoxyribonucleic acid (DNA). At high RNA inputs, the ratio of RNA hybridized with the H strand to that hybridized with the light (L) strand was 8.7 for B. subtilis and 2.0 for E. coli. At high DNA inputs, the H/L hybridization ratio increased by a factor of two. This change in the hybridization ratio was attributable to the fraction of the pulse-labeled RNA which is in stable RNA components. The hybridization peak of pulse-labeled RNA was specifically located in the late-eluting region of the absorbance profile of the H strand. This region was considered to represent the most actively transcribing H strand templates.
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29
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Geider K, Hoffmann-Berling H. DNA synthesis in nucleotide permeable Escherichia coli cells. Chain elongation in specific regions of the bacterial chromosome. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 21:374-84. [PMID: 4936449 DOI: 10.1111/j.1432-1033.1971.tb01479.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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Udvardy A, Venetianer P. Isolation of the ribosomal RNA genes of Salmonella typhimurium. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 20:513-7. [PMID: 4932299 DOI: 10.1111/j.1432-1033.1971.tb01421.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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31
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Yamakawa T, Doi RH. Preferential transcription of Bacillus subtilis light deoxyribonucleic acid strands during sporulation. J Bacteriol 1971; 106:305-10. [PMID: 4324802 PMCID: PMC285097 DOI: 10.1128/jb.106.2.305-310.1971] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Messenger ribonucleic acid (RNA) from log and sporulation stages of growth were transcribed mainly from the heavy strand of the complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA). During sporulation a slight transcription shift from heavy to light DNA strands was observed. RNA-DNA hybrid competition experiments revealed that this shift was due to sporulation-specific transcription from light-DNA strands.
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32
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Paribok VP, Tomilin NV. Recognition of pyrimidine dimers in DNA by the incision enzyme from Micrococcus lysodeikticus. NATURE: NEW BIOLOGY 1971; 230:210-1. [PMID: 5280170 DOI: 10.1038/newbio230210a0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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33
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Strauss N. Transformation of Bacillus subtilis using hybrid DNA molecules constructed by annealing resolved complementary strands. Genetics 1970; 66:583-93. [PMID: 4997170 PMCID: PMC1212516 DOI: 10.1093/genetics/66.4.583] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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34
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Okazaki R, Sugimoto K, Okazaki T, Imae Y, Sugino A. DNA chain growth: in vivo and in vitro synthesis in a DNA polymerase-negative mutant of E. coli. Nature 1970; 228:223-6. [PMID: 4320306 DOI: 10.1038/228223a0] [Citation(s) in RCA: 96] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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35
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Margulies L, Remeza V, Rudner R. Asymmetric template function of microbial deoxyribonucleic acids: transcription of ribosomal and soluble ribonucleic acids. J Bacteriol 1970; 103:560-8. [PMID: 4319834 PMCID: PMC248127 DOI: 10.1128/jb.103.3.560-568.1970] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In Bacillus subtilis and Escherichia coli, 16 and 23S ribosomal ribonucleic acid (rRNA) hybridize exclusively with the heavy (H) strand of methylated albuminkieselguhr (MAK)-fractionated complementary deoxyribonucleic acid (DNA) strands. All the soluble RNA (4S RNA) in B. subtilis and 66 to 75% of the 4S RNA in E. coli also hybridize with the H strand. Interspecific hybridization shows that E. coli 23S rRNA also binds selectively to the DNA H strand of Salmonella typhimurium. The hybridization peak for all three cellular RNA components is specifically located in the late-eluting region of the absorbance profile of the DNA H strand. The early-eluting region of the light (L) strand preferentially inhibits the hybridization between the peak region of the H strand and 23S rRNA. These regions are considered to represent the transcribing sequences and their complements for 23S rRNA in the separated H and L strands of DNA, respectively.
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36
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Cassuto E, Chargaff E. Translational complementarity of RNA transcripts of native and denatured B. subtilis DNA. Proc Natl Acad Sci U S A 1970; 66:863-8. [PMID: 4987628 PMCID: PMC283130 DOI: 10.1073/pnas.66.3.863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Previous evidence has suggested that the L and H fractions into which denatured DNA of B. subtilis can be separated by chromatography are complementary to each other with regard to base compositon, nucleotide sequence, and template properties, and that they may be regarded as families of fragments of the respective DNA strands. The present study tests the proposition that these fractions should also exhibit features of translational complementarity with respect to the DNA-dependent or the RNA-dependent incorporation of amino acids into ribosomes. This has been shown to be the case with the use of two pairs of amino acids: (1) lysine and phenylalanine; (2) proline and glycine.
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Cassuto E, Stein M, Chargaff E. Complementarity of RNA produced by enzymic transcription of native and denatured B. subtilis DNA. Proc Natl Acad Sci U S A 1970; 66:197-203. [PMID: 4991519 PMCID: PMC286107 DOI: 10.1073/pnas.66.1.197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
This paper describes the preparation and some of the properties of the RNA specimens synthesized with the aid of the RNA polymerase of E. coli by transcription of the following DNA templates: (a) undenatured B. subtilis DNA (yielding N-RNA); (b) separated strand fractions L and H isolated by chromatography of the denatured DNA on methylated albumin (yielding L-RNA and H-RNA, respectively). The study of the hybridization behavior of the various RNA products showed that N-RNA, though able to form hybrids with either strand, hybridized with H-DNA to twice as great an extent as with L-DNA. The transcripts of the separated L and H fractions exhibited complete specificity with respect to complexing: L-RNA hybridized only with L-DNA, H-RNA only with H-DNA.
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Colli W, Oishi M. Ribosomal RNA genes in bacteria: evidence for the nature of the physical linkage between 16S and 23S RNA genes in Bacillus subtilis. Proc Natl Acad Sci U S A 1969; 64:642-9. [PMID: 4982359 PMCID: PMC223392 DOI: 10.1073/pnas.64.2.642] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The nature of the arrangement of 16S and 23S ribosomal RNA genes on the Bacillus subtilis chromosome was studied by means of a Cs(2)SO(4) density gradient centrifugation technique after complexing DNA-(ribosomal) RNA hybrids with mercuric ions. It was observed that the same fragments of single-stranded DNA with an average molecular weight of 1.9 x 10(6) which hybridize with 23S RNA also hybridize with 16S RNA. This indicates that genes for both these species of ribosomal RNA are physically linked on such DNA fragments. Some evidence suggests that the two types of genes are interspersed with each other, perhaps in sets, each of which contains a 16S and a 23S ribosomal RNA gene.
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40
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Cheong LC, Chargaff E. Complementary fractions of denatured DNA of coliphage T3 as templates for transcription. Proc Natl Acad Sci U S A 1969; 64:241-6. [PMID: 5263007 PMCID: PMC286153 DOI: 10.1073/pnas.64.1.241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
This paper discusses the evidence that two fractions obtained by the chromatography of denatured DNA of phage T3 on columns of methylated albumin-kieselguhr represent the complementary strands. This evidence derives from a variety of temperature-absorbance measurements and from the base composition of the RNA products synthesized by RNA polymerase under the direction of the two single-stranded DNA templates.
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41
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Rudner R, Karkas JD, Chargaff E. Separation of microbial deoxyribonucleic acids into complementary strands. Proc Natl Acad Sci U S A 1969; 63:152-9. [PMID: 4980029 PMCID: PMC534015 DOI: 10.1073/pnas.63.1.152] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA preparations from seven bacterial species and from the E. coli phage T4 can, after denaturation with alkali, be separated chromatographically into two distinct components (L and H) through intermittent gradient elution from methylated albumin kieselguhr columns. The direct chemical analysis of the L and H fractions isolated from DNA specimens of the AT type shows them to exhibit a high degree of complementarity; but despite a bias in the distribution of purines and pyrimidines, either fraction contains equimolar quantities of 6-amino and of 6-keto nucleotides. In the L and H components derived from DNA of the equimolar and GC types, the distribution bias appears limited to guanine and cytosine. It is suggested that the L and H fractions represent the complementary DNA strands.
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42
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Oishi M. The transcribing strands of bacillus subtilis DNA for ribosomal and transfer RNA. Proc Natl Acad Sci U S A 1969; 62:256-62. [PMID: 4976948 PMCID: PMC285981 DOI: 10.1073/pnas.62.1.256] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
H(3)-labeled purified 16S and 23S ribosomal RNA's and transfer RNA's were found to hybridize exclusively with the H strand of the separated complementary strands of B. subtilis DNA. These results indicate that these RNA's are transcribed in vivo from a strand with a composition similar to that from which messenger RNA's are copied and presumably by the same mechanism.
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43
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Karkas JD, Rudner R, Chargaff E. Seapration of B. subtilis DNA into complementary strands. II. Template functions and composition as determined by transcription with RNA polymerase. Proc Natl Acad Sci U S A 1968; 60:915-20. [PMID: 4970113 PMCID: PMC225139 DOI: 10.1073/pnas.60.3.915] [Citation(s) in RCA: 50] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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44
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Rudner R, Karkas JD, Chargaff E. Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc Natl Acad Sci U S A 1968; 60:921-2. [PMID: 4970114 PMCID: PMC225140 DOI: 10.1073/pnas.60.3.921] [Citation(s) in RCA: 105] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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