A report on Escherichia coli and Base pair

Depiction of the adenine–thymine Watson–Crick base pair
Model of successive binary fission in E. coli
Redistribution of fluxes between the three primary glucose catabolic pathways: EMPP (red), EDP (blue), and OPPP (orange) via the knockout of pfkA and overexpression of EDP genes (edd and eda).
A colony of E. coli growing
E. coli on sheep blood agar.
E. coli growing on basic cultivation media.
Scanning electron micrograph of an E. coli colony.
An image of E. coli using early electron microscopy.
Escherichia coli bacterium, 2021, Illustration by David S. Goodsell, RCSB Protein Data Bank This painting shows a cross-section through an Escherichia coli cell. The characteristic two-membrane cell wall of gram-negative bacteria is shown in green, with many lipopolysaccharide chains extending from the surface and a network of cross-linked peptidoglycan strands between the membranes. The genome of the cell forms a loosely-defined "nucleoid", shown here in yellow, and interacts with many DNA-binding proteins, shown in tan and orange. Large soluble molecules, such as ribosomes (colored in reddish purple), mostly occupy the space around the nucleoid.
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.

In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed and inserted it into cells of the common bacterium E. coli that successfully replicated the unnatural base pairs through multiple generations.

- Base pair

It is a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes.

- Escherichia coli

4 related topics with Alpha

Overall

DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.

DNA replication

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Biological process of producing two identical replicas of DNA from one original DNA molecule.

Biological process of producing two identical replicas of DNA from one original DNA molecule.

DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.
DNA polymerases adds nucleotides to the 3′ end of a strand of DNA. If a mismatch is accidentally incorporated, the polymerase is inhibited from further extension. Proofreading removes the mismatched nucleotide and extension continues.
Overview of the steps in DNA replication
Steps in DNA synthesis
Role of initiators for initiation of DNA replication.
Formation of pre-replication complex.
Scheme of the replication fork.
a: template, b: leading strand, c: lagging strand, d: replication fork, e: primer, f: Okazaki fragments
Many enzymes are involved in the DNA replication fork.
The assembled human DNA clamp, a trimer of the protein PCNA.
E. coli Replisome. Notably, the DNA on lagging strand forms a loop. The exact structure of replisome is not well understood.
The cell cycle of eukaryotic cells.
Dam methylates adenine of GATC sites after replication.
Replication fork restarts by homologous recombination following replication stress
Epigenetic consequences of nucleosome reassembly defects at stalled replication forks

Nucleobases are matched between strands through hydrogen bonds to form base pairs.

In E. coli the primary initiator protein is DnaA; in yeast, this is the origin recognition complex.

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).

Protein

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Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).
John Kendrew with model of myoglobin in progress
Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.
Resonance structures of the peptide bond that links individual amino acids to form a protein polymer
A ribosome produces a protein using mRNA as template
The DNA sequence of a gene encodes the amino acid sequence of a protein
The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: All-atom representation colored by atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).
Molecular surface of several proteins showing their comparative sizes. From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme).
The enzyme hexokinase is shown as a conventional ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.
Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen
Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white)
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units

It has been estimated that average-sized bacteria contain about 2 million proteins per cell (e.g. E. coli and Staphylococcus aureus).

The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes.

Figure 1. During meiosis, homologous recombination can produce new combinations of genes as shown here between similar but not identical copies of human chromosome 1.

Homologous recombination

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Type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids .

Type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids .

Figure 1. During meiosis, homologous recombination can produce new combinations of genes as shown here between similar but not identical copies of human chromosome 1.
Figure 2. An early illustration of crossing over from Thomas Hunt Morgan
Figure 3. Homologous recombination repairs DNA before the cell enters mitosis (M phase). It occurs only during and shortly after DNA replication, during the S and G2 phases of the cell cycle.
Figure 4. Double-strand break repair models that act via homologous recombination
Figure 5. The DSBR and SDSA pathways follow the same initial steps, but diverge thereafter. The DSBR pathway most often results in chromosomal crossover (bottom left), while SDSA always ends with non-crossover products (bottom right).
Figure 6. Recombination via the SSA pathway occurs between two repeat elements (purple) on the same DNA duplex, and results in deletions of genetic material. (Click to view animated diagram in Firefox, Chrome, Safari, or Opera web browsers.)
Figure 7. Crystal structure of a RecA protein filament bound to DNA. A 3' overhang is visible to the right of center.
Figure 8A. Molecular model for the RecBCD pathway of recombination. This model is based on reactions of DNA and RecBCD with ATP in excess over Mg2+ ions. Step 1: RecBCD binds to a double-stranded DNA end. Step 2: RecBCD unwinds DNA.  RecD is a fast helicase on the 5’-ended strand, and RecB is a slower helicase on the 3'-ended strand (that with an arrowhead) [ref 46 in current Wiki version].  This produces two single-stranded (ss) DNA tails and one ss loop.  The loop and tails enlarge as RecBCD moves along the DNA.  Step 3:  The two tails anneal to produce a second ss DNA loop, and both loops move and grow.  Step 4:  Upon reaching the Chi hotspot sequence (5' GCTGGTGG 3'; red dot) RecBCD nicks the 3’-ended strand.  Further unwinding produces a long 3'-ended ss tail with Chi near its end.  Step 5:  RecBCD loads RecA protein onto the Chi tail.  At some undetermined point, the RecBCD subunits disassemble.  Step 6:  The RecA-ssDNA complex invades an intact homologous duplex DNA to produce a D-loop, which can be resolved into intact, recombinant DNA in two ways.  Step 7:  The D-loop is cut and anneals with the gap in the first DNA to produce a Holliday junction.  Resolution of the Holliday junction (cutting, swapping of strands, and ligation) at the open arrowheads by some combination of RuvABC and RecG produces two recombinants of reciprocal type.  Step 8:  The 3' end of the Chi tail primes DNA synthesis, from which a replication fork can be generated.  Resolution of the fork at the open arrowheads produces one recombinant (non-reciprocal) DNA, one parental-type DNA, and one DNA fragment.
Figure 8B. Beginning of the RecBCD pathway. This model is based on reactions of DNA and RecBCD with Mg2+ ions in excess over ATP. Step 1: RecBCD binds to a DNA double strand break.  Step 2: RecBCD initiates unwinding of the DNA duplex through ATP-dependent helicase activity.  Step 3: RecBCD continues its unwinding and moves down the DNA duplex, cleaving the 3' strand much more frequently than the 5' strand. Step 4: RecBCD encounters a Chi sequence and stops digesting the 3' strand; cleavage of the 5' strand is significantly increased. Step 5: RecBCD loads RecA onto the 3' strand. Step 6: RecBCD unbinds from the DNA duplex, leaving a RecA nucleoprotein filament on the 3' tail.
Schematic representation of the s2m RNA secondary structure, with tertiary structural interactions indicated as long range contacts.
Figure 9. Joining of single-ended double strand breaks could lead to rearrangements
Figure 10. Protein domains in homologous recombination-related proteins are conserved across the three main groups of life: archaea, bacteria and eukaryotes.
Figure 11. As a developing embryo, this chimeric mouse had the agouti coat color gene introduced into its DNA via gene targeting. Its offspring are homozygous for the agouti gene.

This work established E. coli as a model organism in genetics, and helped Lederberg win the 1958 Nobel Prize in Physiology or Medicine.

These sites are non-randomly located on the chromosomes; usually in intergenic promoter regions and preferentially in GC-rich domains These double-strand break sites often occur at recombination hotspots, regions in chromosomes that are about 1,000–2,000 base pairs in length and have high rates of recombination.

Illustration of a bacterium showing chromosomal DNA and plasmids (Not to scale)

Plasmid

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Small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.

Small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.

Illustration of a bacterium showing chromosomal DNA and plasmids (Not to scale)
There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas episomes, the lower example, can integrate into the host chromosome.
Overview of bacterial conjugation
Electron micrograph of a DNA fiber bundle, presumably of a single bacterial chromosome loop
Electron micrograph of a bacterial DNA plasmid (chromosome fragment)
A schematic representation of the pBR322 plasmid, one of the first plasmids to be used widely as a cloning vector. Shown on the plasmid diagram are the genes encoded (amp and tet for ampicillin and tetracycline resistance respectively), its origin of replication (ori), and various restriction sites (indicated in blue).

Plasmids vary in size from 1 to over 400 kbp, and the number of identical plasmids in a single cell can range anywhere from one to thousands under some circumstances.

Some plasmids or microbial hosts include an addiction system or postsegregational killing system (PSK), such as the hok/sok (host killing/suppressor of killing) system of plasmid R1 in Escherichia coli.