Molecular Biology Terms Starting With K
Molecular Biology Glossary: K
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Knockout Mouse
/ NOK-owt MOWS / · From knock out, to disable completely, and mouse, from Old English mus.
Knockout Mouse is a laboratory mouse in which one or more specific genes have been inactivated through targeted genetic engineering to study gene function and model human disease.
The classical method disrupts a target gene by introducing a selectable marker cassette via homologous recombination in mouse embryonic stem cells, which are then injected into blastocysts to generate chimeric founders that pass the disrupted allele to offspring. Mario Capecchi, Martin Evans, and Oliver Smithies developed this approach and shared the 2007 Nobel Prize in Physiology or Medicine for the work. CRISPR-Cas9 has since reduced the time needed to generate a knockout from more than a year to as few as three to six weeks by editing fertilized eggs directly.
The International Mouse Phenotyping Consortium has systematically knocked out more than 7,000 genes and phenotyped the resulting mice across dozens of biological parameters, revealing that roughly 30 percent of single-gene knockouts produce lethality before birth. Approximately 99 percent of mouse protein-coding genes have a human ortholog, making these models broadly applicable to understanding human genetic disease.
Some knockout mice lacking genes long assumed to be indispensable for survival develop with no obvious abnormality, a phenomenon attributed to genetic redundancy in which paralogous genes compensate for the missing one. The p53 tumor suppressor knockout mouse, generated in 1992 by Tyler Jacks and colleagues, was expected to die early but instead survived to adulthood before developing spontaneous tumors, revealing that p53 loss alone is insufficient to block normal development.
Knockout mice are the same as transgenic mice. Knockout mice carry inactivated endogenous genes, whereas transgenic mice carry foreign genes inserted into the genome, and the two approaches address fundamentally different experimental questions.
The leptin-deficient ob/ob mouse carries a nonsense mutation in the leptin gene on chromosome 6 and reaches body weights two to three times greater than wild-type littermates by eight weeks of age. These mice also develop hyperinsulinemia, hyperglycemia, and infertility, making them a standard model for studying the hormonal regulation of appetite and the pathophysiology of type 2 diabetes.
Kozak Sequence
/ KOH-zak SEE-kwens / · Named for Marilyn Kozak (1986)
Kozak Sequence is a short consensus sequence surrounding the AUG start codon in eukaryotic mRNA that modulates the efficiency with which scanning ribosomes initiate translation at that codon.
The optimal vertebrate Kozak context is gccRccAUGG, where R denotes a purine at position -3 and G at position +4 flanks the AUG start codon; these two positions contribute most strongly to initiation efficiency. Ribosomes assemble at the 5-prime cap and scan downstream until they encounter an AUG; those embedded in a strong Kozak context are recognized and used for initiation far more reliably than those in a weak context. Mutations at position -3 or +4 alone can reduce translation output by 10-fold or more, a magnitude comparable to removing a strong transcriptional enhancer.
Marilyn Kozak characterized this consensus through systematic mutagenesis experiments published between 1978 and 1987, establishing the scanning model of eukaryotic translation initiation. Weak Kozak contexts around upstream AUG codons in mRNA leaders allow ribosomes to bypass those codons and reach a downstream start site, a mechanism used by the ATF4 transcription factor mRNA to upregulate stress-response proteins under conditions of cellular stress.
Kozak sequence context matters even in gene therapy vectors. When researchers optimized the Kozak sequence surrounding the factor IX coding sequence in an adeno-associated virus vector, protein output in cultured cells increased approximately threefold without any change to the coding sequence itself, demonstrating that translational context can be as consequential as promoter strength for therapeutic protein production.
Translation Biology →Every AUG codon in an mRNA is used equally as a translation start site. Ribosome profiling experiments show that AUG codons in strong Kozak contexts initiate translation at rates up to 10 times higher than identical codons in weak contexts, and most ribosomes that encounter a weak upstream AUG simply continue scanning rather than initiating.
The mRNA encoding the proto-oncogene c-Myc in humans contains a relatively weak Kozak context around its primary AUG codon. Mutations that improve the -3 or +4 positions can increase initiation efficiency several-fold without changing mRNA abundance or the c-Myc amino acid sequence.
Ku Protein
/ KAY-YOO PROH-teen / · Named after the patient Ku, from whose cells the protein was first identified in autoimmune studies.
Ku Protein is a heterodimeric complex of Ku70 and Ku80 subunits that binds broken DNA ends and recruits the repair machinery that executes non-homologous end joining in eukaryotic cells.
Ku70 and Ku80 form a ring-shaped structure that threads onto double-strand break ends within seconds of break formation, binding with a dissociation constant in the low nanomolar range and protecting the ends from nucleolytic degradation. Once loaded, Ku recruits the DNA-dependent protein kinase catalytic subunit to form the active DNA-PK holoenzyme, which autophosphorylates and phosphorylates downstream factors including Artemis, XRCC4, and DNA ligase IV. Non-homologous end joining mediated by this pathway repairs the majority of double-strand breaks in mammalian cells and operates throughout the cell cycle, unlike homologous recombination, which is restricted to S and G2 phases.
Loss of Ku70 or Ku80 in mice causes severe combined immunodeficiency because VDJ recombination in developing lymphocytes depends on the same end-joining machinery. A single mammalian cell contains roughly one million Ku heterodimers, reflecting the frequency with which double-strand breaks must be managed across a lifetime of cell divisions.
Ku protein was first identified in 1981 as an autoantigen recognized by antibodies in the serum of a Japanese patient with the autoimmune disease scleroderma-polymyositis overlap syndrome. The patient's initials, Ku, gave the protein its name, and the autoimmune connection preceded by nearly a decade the discovery that Ku is a central component of DNA repair.
Ku protein directly ligates broken DNA ends. Ku positions and protects the ends but does not itself catalyze ligation; that chemistry is carried out by the DNA ligase IV and XRCC4 complex that Ku recruits to the break site.
In Chinese hamster ovary (Cricetulus griseus) cells exposed to X-rays delivering 2 gray of ionizing radiation, approximately 60 to 80 double-strand breaks form per cell, and Ku complexes accumulate at each break site within 30 seconds. Cells carrying mutations in Ku80 fail to rejoin these breaks efficiently and show radiation sensitivity roughly 10-fold greater than wild-type cells at the same dose.