Chi site
Encyclopedia
A Chi site or Chi sequence is a short stretch of DNA
in the genome
of a bacterium near which homologous recombination
is unusually likely to occur. Chi sites serve as stimulators of DNA double-strand break repair
in bacteria, which can arise from radiation
or chemical treatments, or result from replication fork
breakage during DNA replication
. The sequence
of the Chi site is unique to each group of closely related organisms; in E. coli
and other enteric bacteria, such as Salmonella, the sequence is 5'-GCTGGTGG-3'. The existence of Chi sites was originally discovered in the genome of bacteriophage lambda, a virus
that infects E. coli, but is now known to occur about 1000 times in the E. coli genome.
The Chi sequence serves as a signal to the RecBCD
helicase-exonuclease
that triggers a major change in the activities of this enzyme. Upon encountering the Chi sequence as it unwinds DNA, RecBCD cuts the DNA a few nucleotides to the 3’ side of Chi; depending on the reaction conditions, this cut is either a simple nick on one strand or the change of nuclease activity from cutting the 3’-ended strand to cutting the 5’ended strand. In either case the resulting 3’ single-stranded DNA (ssDNA) is bound by multiple molecules of RecA
protein that facilitate "strand invasion," in which one strand of a homologous double-stranded DNA is displaced by the RecA-associated ssDNA. Strand invasion forms a joint DNA molecule called a D-loop. Resolution of the D-loop is thought to occur by replication primed by the 3’ end generated at Chi (in the D-loop). Alternatively, the D-loop may be converted into a Holliday junction
by cutting of the D-loop and a second exchange of DNA strands; the Holliday junction can be converted into linear duplex DNA by cutting of the Holliday junction and ligation of the resultant nicks. Either type of resolution can generate recombinant DNA molecules if the two interacting DNAs are genetically different, as well as repair the initially broken DNA.
Chi sites are sometimes referred to as "recombination hot spots". The name "Chi" is an abbreviation of crossover hotspot instigator. The term is sometimes written as "χ site", using the Greek letter chi
.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
in the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
of a bacterium near which homologous recombination
Homologous recombination
Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks...
is unusually likely to occur. Chi sites serve as stimulators of DNA double-strand break repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
in bacteria, which can arise from radiation
Radiation
In physics, radiation is a process in which energetic particles or energetic waves travel through a medium or space. There are two distinct types of radiation; ionizing and non-ionizing...
or chemical treatments, or result from replication fork
Replication fork
The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching "prongs", each one made up of a single strand of DNA...
breakage during DNA replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
. The sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
of the Chi site is unique to each group of closely related organisms; in E. coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
and other enteric bacteria, such as Salmonella, the sequence is 5'-GCTGGTGG-3'. The existence of Chi sites was originally discovered in the genome of bacteriophage lambda, a virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
that infects E. coli, but is now known to occur about 1000 times in the E. coli genome.
The Chi sequence serves as a signal to the RecBCD
RecBCD
RecBCD, also known as Exonuclease V, is an enzyme of the E. coli bacterium that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host of other factors...
helicase-exonuclease
Exonuclease
Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs. Its close relative is the endonuclease, which cleaves phosphodiester bonds in the middle ...
that triggers a major change in the activities of this enzyme. Upon encountering the Chi sequence as it unwinds DNA, RecBCD cuts the DNA a few nucleotides to the 3’ side of Chi; depending on the reaction conditions, this cut is either a simple nick on one strand or the change of nuclease activity from cutting the 3’-ended strand to cutting the 5’ended strand. In either case the resulting 3’ single-stranded DNA (ssDNA) is bound by multiple molecules of RecA
RecA
RecA is a 38 kilodalton Escherichia coli protein essential for the repair and maintenance of DNA. RecA has a structural and functional homolog in every species in which it has been seriously sought and serves as an archetype for this class of homologous DNA repair proteins...
protein that facilitate "strand invasion," in which one strand of a homologous double-stranded DNA is displaced by the RecA-associated ssDNA. Strand invasion forms a joint DNA molecule called a D-loop. Resolution of the D-loop is thought to occur by replication primed by the 3’ end generated at Chi (in the D-loop). Alternatively, the D-loop may be converted into a Holliday junction
Holliday junction
A Holliday junction is a mobile junction between four strands of DNA. The structure is named after Robin Holliday, who proposed it in 1964 to account for a particular type of exchange of genetic information he observed in yeast known as homologous recombination...
by cutting of the D-loop and a second exchange of DNA strands; the Holliday junction can be converted into linear duplex DNA by cutting of the Holliday junction and ligation of the resultant nicks. Either type of resolution can generate recombinant DNA molecules if the two interacting DNAs are genetically different, as well as repair the initially broken DNA.
Chi sites are sometimes referred to as "recombination hot spots". The name "Chi" is an abbreviation of crossover hotspot instigator. The term is sometimes written as "χ site", using the Greek letter chi
Chi (letter)
Chi is the 22nd letter of the Greek alphabet, pronounced as in English.-Greek:-Ancient Greek:Its value in Ancient Greek was an aspirated velar stop .-Koine Greek:...
.
External links
- Homologous Recombination Interactive Animation, online artwork from Trun N and Trempy J, Fundamental Bacterial Genetics.