Chi Site
   HOME

TheInfoList



OR:

A Chi site or Chi sequence is a short stretch of
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
in the
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
of a
bacterium Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the ...
near which
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in Cell (biology), cellular organi ...
is more likely to occur than on average across the genome. Chi sites serve as stimulators of DNA double-strand break repair in bacteria, which can arise from
radiation In physics, radiation is the emission or transmission of energy in the form of waves or particles through space or a material medium. This includes: * ''electromagnetic radiation'' consisting of photons, such as radio waves, microwaves, infr ...
or chemical treatments, or result from
replication fork In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms, acting as the most essential part of biological inheritanc ...
breakage during
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all life, living organisms, acting as the most essential part of heredity, biolog ...
. The
sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is cal ...
of the Chi site is unique to each group of closely related organisms; in '' E. coli'' and other enteric bacteria, such as Salmonella, the core sequence is 5'-GCTGGTGG- 3' plus important nucleotides about 4 to 7 nucleotides to the 3' side of the core sequence. The existence of Chi sites was originally discovered in the genome of bacteriophage lambda, a
virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...
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 Exodeoxyribonuclease V (EC 3.1.11.5, RecBCD, Exonuclease V, ''Escherichia coli'' exonuclease V, ''E. coli'' exonuclease V, gene recBC endoenzyme, RecBC deoxyribonuclease, gene recBC DNase, gene recBCD enzymes) is an enzyme of ''E. coli'' that ini ...
helicase-
nuclease In biochemistry, a nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds that link nucleotides together to form nucleic acids. Nucleases variously affect single and ...
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, within the important sequences noted above; depending on the reaction conditions, this cut is either a simple nick on the 3'-ended 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 is a 38 kilodalton protein essential for the repair and maintenance of DNA in bacteria. Structural and functional homologs to RecA have been found in all kingdoms of life. RecA serves as an archetype for this class of homologous DNA repair p ...
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 In molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. An R-loop is similar to a D-loop, but in that cas ...
. 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 A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the j ...
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 In reference to ''E. coli'' phage lambda, the term is sometimes written as "χ site", using the Greek letter chi; for ''E. coli'' and other bacteria the term "Chi" is proper.


References

*Amundsen SK, Sharp JW, Smith GR (2016) RecBCD Enzyme "Chi Recognition" Mutants Recognize Chi Recombination Hotspots in the Right DNA Context. Genetics 204(1):139-52. *Taylor AF, Amundsen SK, Smith GR (2016) Unexpected DNA context-dependence identifies a new determinant of Chi recombination hotspots. Nucleic Acids Res. 44(17):8216-28. *Smith GR. (2012). How RecBCD Enzyme and Chi Promote DNA Break Repair and Recombination: a Molecular Biologist's View. ''Microbiol Mol Biol Rev.'' 76(2): 217-28. *Dillingham MS, Kowalczykowski SC. (2008). RecBCD enzyme and the repair of double-stranded DNA breaks. ''Microbiol Mol Biol Rev.'' 72(4): 642-671. *Amundsen SK, Taylor AF, Reddy M, Smith GR. (2007). Intersubunit signaling in RecBCD enzyme, a complex protein machine regulated by Chi hot spots. ''Genes Dev'' 21(24): 3296-3307. *Stahl FW. (2005). Chi: A little sequence controls a big enzyme. ''Genetics'' 170(2): 487–493. {{PMID, 15980270


External links


Homologous Recombination Interactive Animation
online artwork from Trun N and Trempy J, ''Fundamental Bacterial Genetics''. Biochemistry Genetics