Significant dispersed recurrent DNA sequences in the Escherichia coli genome: Several new groups

B. Edwin Blaisdell, Kenneth E. Rudd, A. Matin, Samuel Karlin

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

New computer and statistical methods were used to determine significant direct and inverted repeats in the Escherichia coli contig sequence collection of aggregate 1.6 × 106 base-pairs. Eight groups of mostly new structural repeat identities were uncovered. Apart from the high statistical significance of these repeat sequences, there are suggestive relationships of the group matches in terms of neighboring genes, of genomic distributions, of their texts, and of their potentials for secondary structure. Four of these groups are relatively numerous, 11 to 26 members, one is in coding sequences and three are in non-coding. The coding group consists of the ATP-activated transmembrane component of a typical high-affinity protein-binding transport system. One of the non-coding groups consists of a special rho-independent transcription termination signal closely following an operon. The gene neighbors of this group often appear to be involved in some way in processing RNA or DNA. A second non-coding group has, for one or both neighboring genes, a component of a system responding to stress or starvation for some nutrient.

Original languageEnglish
Pages (from-to)833-848
Number of pages16
JournalJournal of Molecular Biology
Volume229
Issue number4
StatePublished - Dec 1 1993
Externally publishedYes

Fingerprint

Genome
Escherichia coli
Gene Components
Nucleic Acid Repetitive Sequences
Protein Transport
Operon
Starvation
Protein Binding
Base Pairing
Genes
Adenosine Triphosphate
RNA
Food
DNA

Keywords

  • Escherichia coli, protein binding transport
  • rho-independent transcription terminators
  • Statistically significantly long common words
  • Systems inducible by nutrient starvation

ASJC Scopus subject areas

  • Virology

Cite this

Blaisdell, B. E., Rudd, K. E., Matin, A., & Karlin, S. (1993). Significant dispersed recurrent DNA sequences in the Escherichia coli genome: Several new groups. Journal of Molecular Biology, 229(4), 833-848.

Significant dispersed recurrent DNA sequences in the Escherichia coli genome : Several new groups. / Blaisdell, B. Edwin; Rudd, Kenneth E.; Matin, A.; Karlin, Samuel.

In: Journal of Molecular Biology, Vol. 229, No. 4, 01.12.1993, p. 833-848.

Research output: Contribution to journalArticle

Blaisdell, BE, Rudd, KE, Matin, A & Karlin, S 1993, 'Significant dispersed recurrent DNA sequences in the Escherichia coli genome: Several new groups', Journal of Molecular Biology, vol. 229, no. 4, pp. 833-848.
Blaisdell, B. Edwin ; Rudd, Kenneth E. ; Matin, A. ; Karlin, Samuel. / Significant dispersed recurrent DNA sequences in the Escherichia coli genome : Several new groups. In: Journal of Molecular Biology. 1993 ; Vol. 229, No. 4. pp. 833-848.
@article{8206445bb0db4f9297c58840e2655d36,
title = "Significant dispersed recurrent DNA sequences in the Escherichia coli genome: Several new groups",
abstract = "New computer and statistical methods were used to determine significant direct and inverted repeats in the Escherichia coli contig sequence collection of aggregate 1.6 × 106 base-pairs. Eight groups of mostly new structural repeat identities were uncovered. Apart from the high statistical significance of these repeat sequences, there are suggestive relationships of the group matches in terms of neighboring genes, of genomic distributions, of their texts, and of their potentials for secondary structure. Four of these groups are relatively numerous, 11 to 26 members, one is in coding sequences and three are in non-coding. The coding group consists of the ATP-activated transmembrane component of a typical high-affinity protein-binding transport system. One of the non-coding groups consists of a special rho-independent transcription termination signal closely following an operon. The gene neighbors of this group often appear to be involved in some way in processing RNA or DNA. A second non-coding group has, for one or both neighboring genes, a component of a system responding to stress or starvation for some nutrient.",
keywords = "Escherichia coli, protein binding transport, rho-independent transcription terminators, Statistically significantly long common words, Systems inducible by nutrient starvation",
author = "Blaisdell, {B. Edwin} and Rudd, {Kenneth E.} and A. Matin and Samuel Karlin",
year = "1993",
month = "12",
day = "1",
language = "English",
volume = "229",
pages = "833--848",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "4",

}

TY - JOUR

T1 - Significant dispersed recurrent DNA sequences in the Escherichia coli genome

T2 - Several new groups

AU - Blaisdell, B. Edwin

AU - Rudd, Kenneth E.

AU - Matin, A.

AU - Karlin, Samuel

PY - 1993/12/1

Y1 - 1993/12/1

N2 - New computer and statistical methods were used to determine significant direct and inverted repeats in the Escherichia coli contig sequence collection of aggregate 1.6 × 106 base-pairs. Eight groups of mostly new structural repeat identities were uncovered. Apart from the high statistical significance of these repeat sequences, there are suggestive relationships of the group matches in terms of neighboring genes, of genomic distributions, of their texts, and of their potentials for secondary structure. Four of these groups are relatively numerous, 11 to 26 members, one is in coding sequences and three are in non-coding. The coding group consists of the ATP-activated transmembrane component of a typical high-affinity protein-binding transport system. One of the non-coding groups consists of a special rho-independent transcription termination signal closely following an operon. The gene neighbors of this group often appear to be involved in some way in processing RNA or DNA. A second non-coding group has, for one or both neighboring genes, a component of a system responding to stress or starvation for some nutrient.

AB - New computer and statistical methods were used to determine significant direct and inverted repeats in the Escherichia coli contig sequence collection of aggregate 1.6 × 106 base-pairs. Eight groups of mostly new structural repeat identities were uncovered. Apart from the high statistical significance of these repeat sequences, there are suggestive relationships of the group matches in terms of neighboring genes, of genomic distributions, of their texts, and of their potentials for secondary structure. Four of these groups are relatively numerous, 11 to 26 members, one is in coding sequences and three are in non-coding. The coding group consists of the ATP-activated transmembrane component of a typical high-affinity protein-binding transport system. One of the non-coding groups consists of a special rho-independent transcription termination signal closely following an operon. The gene neighbors of this group often appear to be involved in some way in processing RNA or DNA. A second non-coding group has, for one or both neighboring genes, a component of a system responding to stress or starvation for some nutrient.

KW - Escherichia coli, protein binding transport

KW - rho-independent transcription terminators

KW - Statistically significantly long common words

KW - Systems inducible by nutrient starvation

UR - http://www.scopus.com/inward/record.url?scp=0027466453&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0027466453&partnerID=8YFLogxK

M3 - Article

C2 - 8445651

AN - SCOPUS:0027466453

VL - 229

SP - 833

EP - 848

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 4

ER -