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Related Concept Videos

Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
Stringent Response in E. coli01:23

Stringent Response in E. coli

Bacterial growth is closely tied to nutrient availability, with cells proliferating exponentially under favorable conditions and entering a stationary phase when resources become scarce. This transition is mediated by a regulatory mechanism known as the stringent response, which allows bacteria to adapt to nutrient deprivation by modulating gene expression and metabolic activity.During nutrient scarcity, intracellular amino acid levels decline. It results in the accumulation of uncharged tRNAs...
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
Bacterial Gastroenteritis01:18

Bacterial Gastroenteritis

Bacterial gastroenteritis, characterized by diarrhea, abdominal cramps, and vomiting, is often caused by ingestion of contaminated food or water and is frequently associated with pathogenic Escherichia coli strains. These microbes exploit two principal mechanisms to inflict disease.Shiga toxin–producing E. coli, also referred to as STEC—notably O157:H7—release Shiga toxins that target ribosomes, blocking protein synthesis. The B subunit of the toxin binds the host glycolipid receptor...

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Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

EcoGene: a genome sequence database for Escherichia coli K-12.

K E Rudd1

  • 1Department of Biochemistry, University of Miami School of Medicine, Miami, FL 33101-6129, USA. rudd@molbio.med.miami.edu

Nucleic Acids Research
|December 11, 1999
PubMed
Summary

The EcoGene database offers updated Escherichia coli K-12 gene and protein sequences, improving genome annotation accuracy. This resource aids researchers in computational and functional analyses of bacterial genomes.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • The EcoGene database compiles gene and protein sequences from the Escherichia coli K-12 genome.
  • It serves as a source for re-annotated sequences integrated into SWISS-PROT and Colibri databases.
  • EcoGene data is utilized for genetic and physical map compilations.

Purpose of the Study:

  • To present the EcoGene12 release, detailing significant updates and improvements over existing genome annotations.
  • To provide a comprehensive and accurate set of gene and protein sequences for Escherichia coli K-12.
  • To facilitate genome-scale computational and functional analyses through an accessible database.

Main Methods:

  • Re-annotation of gene and protein sequences based on the Escherichia coli K-12 genome.
  • Correction of gene start sites, frame-shifts, and interrupted protein sequences.
  • Integration of literature survey data for N-terminal amino acid verification.
  • Cross-referencing with extensive literature citations.

Main Results:

  • The EcoGene12 release contains 4293 genes, with substantial revisions including 706 gene start site adjustments.
  • 61 frame-shifts and 14 interrupted protein sequences were corrected or reconstructed.
  • 92 predicted partially deleted gene fragments were identified.
  • 717 proteins had their N-terminal amino acids verified by sequencing, with 12,446 cross-references to 6,835 literature citations.

Conclusions:

  • EcoGene12 provides a significantly refined annotation of the Escherichia coli K-12 genome, enhancing data accuracy.
  • The database facilitates advanced research through improved sequence data and extensive cross-referencing.
  • Accessible via a dedicated website, EcoGene supports diverse genome-scale research and analysis.