Transcription Mapping of the Escherichia Coli Chromosome by Electron Microscopy

Overview

Journal J Bacteriol

Publisher American Society for Microbiology

Specialty Microbiology

Date 1989 Aug 1

PMID 2666391

Citations 47

Authors

S L French

O L MILLER Jr

Affiliations

Soon will be listed here.

Abstract

The distinctive double Christmas tree morphology of rRNA operons as visualized by electron microscopy makes them easy to recognize in chromatin spreads from Escherichia coli. On the basis of the pattern of nascent transcripts on nearby transcription units and the relative distances of the operons from one another and the replication origin, we are now able to specifically identify five of the seven rRNA operons in E. coli. The use of rRNA operons as markers of both position and distance has resulted in the morphological mapping of a significant portion of the E. coli chromosome; over 600 kilobase pairs in the 84- to 90-min and 72-min regions can now be recognized. Since individual rRNA operons could be identified, direct comparisons could be made of their transcriptional activities. As judged by the densities of RNA polymerases along the operons, rrnA, rrnB, rrnC, rrnD, and rrnE were all transcribed at similar levels, with one RNA polymerase every 85 base pairs. The ability to recognize individual operons and specific regions of the chromosome allows direct comparisons of various genetic parameters.

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References

Bell A, Buckel S, Groarke J, Hope J, Kingsley D, Hermodson M . The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12. J Biol Chem. 1986; 261(17):7652-8. View

Hope J, Bell A, Hermodson M, Groarke J . Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase. J Biol Chem. 1986; 261(17):7663-8. View

Osheim Y, MILLER Jr O, Beyer A . Two Drosophila chorion genes terminate transcription in discrete regions near their poly(A) sites. EMBO J. 1986; 5(13):3591-6. PMC: 1167398. DOI: 10.1002/j.1460-2075.1986.tb04687.x. View

Zuber M, Patterson T, Court D . Analysis of nutR, a site required for transcription antitermination in phage lambda. Proc Natl Acad Sci U S A. 1987; 84(13):4514-8. PMC: 305120. DOI: 10.1073/pnas.84.13.4514. View

Kohara Y, Akiyama K, Isono K . The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987; 50(3):495-508. DOI: 10.1016/0092-8674(87)90503-4. View

Delius H, Westphal H, Axelrod N . Length measurements of RNA synthesized in vitro by Escherichia coli RNA polymerase. J Mol Biol. 1973; 74(4):677-87. DOI: 10.1016/0022-2836(73)90056-9. View

Hamkalo B, MILLER Jr O . Electronmicroscopy of genetic activity. Annu Rev Biochem. 1973; 42:379-96. DOI: 10.1146/annurev.bi.42.070173.002115. View

Laird C, Wilkinson L, Foe V, Chooi W . Analysis of chromatin-associated fiber arrays. Chromosoma. 1976; 58(2):169-90. DOI: 10.1007/BF00701357. View

Neidhardt F, Bloch P, Pedersen S, Reeh S . Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli. J Bacteriol. 1977; 129(1):378-87. PMC: 234936. DOI: 10.1128/jb.129.1.378-387.1977. View

10.

Lindahl S, Yamamoto M, Nomura M . Mapping of a cluster of genes for components of the transcriptional and translational machineries of Escherichia coli. J Mol Biol. 1977; 109(1):23-47. DOI: 10.1016/s0022-2836(77)80044-2. View

11.

McKnight S, Sullivan N, MILLER Jr O . Visualization of the silk fibroin transcription unit and nascent silk fibroin molecules on polyribosomes of Bombyx mori. Prog Nucleic Acid Res Mol Biol. 1976; 19:313-8. DOI: 10.1016/s0079-6603(08)60928-9. View

12.

Zyskind J, Deen L, Smith D . Temporal sequence of events during the initiation process in Escherichia coli deoxyribonucleic acid replication: roles of the dnaA and dnaC gene products and ribonucleic acid polymerase. J Bacteriol. 1977; 129(3):1466-75. PMC: 235124. DOI: 10.1128/jb.129.3.1466-1475.1977. View

13.

Kiss A, Sain B, VENETIANER P . The number of rRNA genes in Escherichia coli. FEBS Lett. 1977; 79(1):77-9. DOI: 10.1016/0014-5793(77)80354-2. View

14.

Morgan E, Ikemura T, Nomura M . Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli. Proc Natl Acad Sci U S A. 1977; 74(7):2710-4. PMC: 431257. DOI: 10.1073/pnas.74.7.2710. View

15.

Cozzarelli N . The mechanism of action of inhibitors of DNA synthesis. Annu Rev Biochem. 1977; 46:641-68. DOI: 10.1146/annurev.bi.46.070177.003233. View

16.

Lindahl L, Post L, Zengel J, Gilbert S, Strycharz W, Nomura M . Mapping of ribosomal protein genes by in vitro protein synthesis using DNA fragments of lambdafus3 transducing phage DNA as templates. J Biol Chem. 1977; 252(20):7365-83. View

17.

Varshavsky A, Nedospasov S, Bakayev V, Bakayeva T, Georgiev G . Histone-like proteins in the purified Escherichia coli deoxyribonucleoprotein. Nucleic Acids Res. 1977; 4(8):2725-45. PMC: 342604. DOI: 10.1093/nar/4.8.2725. View

18.

Hofmann S, MILLER Jr O . Visualization of ribosomal ribonucleic acid synthesis in a ribonuclease III-Deficient strain of Escherichia coli. J Bacteriol. 1977; 132(2):718-22. PMC: 221915. DOI: 10.1128/jb.132.2.718-722.1977. View

19.

McKnight S, MILLER Jr O . Electron microscopic analysis of chromatin replication in the cellular blastoderm Drosophila melanogaster embryo. Cell. 1977; 12(3):795-804. DOI: 10.1016/0092-8674(77)90278-1. View

20.

Nomura M, Morgan E . Genetics of bacterial ribosomes. Annu Rev Genet. 1977; 11:297-347. DOI: 10.1146/annurev.ge.11.120177.001501. View