Lecture 13 Notes - Extra Chromosomal Inheritance PDF

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Dr Steve Bevan...

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Genetics Lecture 13: Extra Chromosomal Inheritance Bacterial Genetics – Mobile DNA  DNA does not always reside in chromosomes; genetic material can be extra-chromosomal – especially in bacteria  Mobile DNA – sequences which can be transferred between DNA molecules AND from one cell to another o Wide dissemination between population members very quickly o Allows between species sharing of DNA elements o Unique to bacterial genetic systems  Severe consequences – most antibiotic resistance genes located on mobile genetic elements, not as de novo mutation  Most common form of bacterial mobile DNA elements are plasmids o Small, (usually) circular DNA elements o Non-essential, NOT required for normal bacterial growth o Replicate independently of bacterial genome o Segregate independently, can be multiple copies per cell – high copy, 50/cell o Size range small (few kb) to large (few hundred kb)  Typical E. coli contains o 3 small plasmids – multiple copies of each o 1 large plasmid – single copy  Presence of particular plasmid is usually determined phenotypically, e.g. antibiotic resistance  Plasmid replication relies on host cell machinery, but initiation of replication controlled by the other  Plasmid contains genes that promote segregation into daughter cells – loss of a plasmid is rare Bacterial Genetics – F Plasmid  Many large plasmids code for genes that promote plasmid transfer between cells, e.g. F factor plasmid (f – fertility)  F+ used to denote cells carrying the F factor plasmid, F- denotes cells without o F factor plasmid contains genes that code for pili formation o Pili join in a process known as conjugation – cells effectively bridged via a hollow tube and the plasmid transfers from one cell to another o Most small plasmids are non-conjunctive and only copy through cell division  Replication process known as rolling circle replication  Plasmid is double-stranded o 1 strand is nicked and starts to unwind o As it unwinds DNA synthesis occurs o Results in 2 circular ds DNA molecules  Both donor and recipient cells are now F+ and act as donors o Transfer takes approx. 10 minutes o 10% E. coli in the wild are F+  Plasmids serve effectively as parasitic DNA, but can aid cell survival in certain environmental conditions Transposons  Not all DNA is static – transposons (transposable elements) are regions of DNA that can move around the genome o Also called jumping genes, after their ability to move around the genome  Their discovery in the 1940s led to a Nobel prose n 1983 for Barbara McClintok

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Noticed insertions, deletions and translocations in maize DNA leading to variable phenotypes including kernel colour Tip of chromosome 9 controls kernel colour Transposition of the ds transposon in the C (colour) gene on Chr. 9 results in colourless kernels Transposition out leads to colour formation – the late in development the fewer the coloured kernels Over 85% of the maize genome is made up of transposable elements Can be small 1-3kb – sometimes called insertion sequences or IS elements Contain a transposable gene and a gene that controls rate of transposition as a minimum Each end of the element contains an inverted repeat sequence as a recognition motif Larger transposable elements can contain other genes, e.g. genes for antibiotic resistance Generally, several kb long Nomenclature in bacteria is Tn followed by an italicised number, e.g. Tn5 Both IS elements and transposons can integrate into F plasmids as well as the bacterial genome All species contain transposable DNA, including humans – as much as 44% of the genome, only 0.05% is active

Transposon Classes  Class I – retrotransposons (also called copy and paste transposons) o Copy transcribed from DNA to RNA, RNA reverse transcribed to DNA, NDA copy inserted elseware into genome o Very similar to a specialised class of virus known as retroviruses, e.g. HIV o Commonest form of TE in humans accounting for 42% of the human genome  Class II – DNA transposons o No RNA synthesis, DNA simply excised between recognition motif sequences at each end o Inserted by transposase enzymes elseware in the genome o Rate form of TE in humans, accounting for 2% of the human genome  Both classes can also be o Autonomous – encodes all the enzymes necessary for replication o Non-autonomous – requires co-location with a second transposon with necessary transcription enzymes Transposons  Presence of either multiple copies of a transposon OR multiple recognition motifs, allows homologous recombination between DNA structures  In bacteria, this results in a composite plasmid called a cointegrate  If one plasmid is non-conjunctive, (F-) and the other conjunctive (F+) the cointegrate becomes conjunctive – a further method by which extra chromosomal DNA transfer between bacteria can occur Bacterial Genetics  Bacterial genomes are therefore not static structures, but rather a patchwork of diverse elements from multiple sources evolutionary advantage against negative external pressures  Allows rapid colonisation of new habitats  Can lead to rapid rise of antibiotic resistant strains  Independent isolates of E. coli show genome sizes vary by as much as 10%  All contain a common gene set of approx. 3,800 genes  Largest genome compared to smallest genome is enough to code for a further 1000 genes

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3,800 therefore probably the minimum core gene set required for E. coli to function Compare to humans who have a very regular genome, 3 million bases and 20,000 genes

Transposons and Disease  Transposons, when the jump, may: o Insert itself into a functional gene and disrupt its function o Leave behind a recognition motif and disrupt DNA sequence or result in incorrect excision repair o Multiple repeats lead to incorrect pairing at mitosis/meiosis, e.g. Alu repeat accounts for 15-17% of human genome and exists as 300,000 to 2,000,000 copies of a 300bp sequence  Disease susceptible to transposons as a cause include: o Haemophilia (X-linked recessive condition, insertion of a repeat into the Factor VIII gene) o Some colorectal cancers (insertion of L1 into the APC gene) o Severe Combined Immunodeficiency (SCID) – disruption of T and B cell function, lack of immune system Eukaryotic extrachromosomal DNA – Organelles  Not all DNA is contained in the nucleus. Organelles are self-replicating cellular structures that contain extrachromosomal DNA, e.g. mitochondria in animals or chloroplasts in plants  Organelles tend to have specific functions, encode multiple genes and replicate in a form of binary fission o Replication is independent of the nucleus o Patters of replication can be very different to those of nuclear genes o Sometimes called extranuclear inheritance or cytoplasmic inheritance  Eukaryotic organelles probably evolved from internalised prokaryotic cells existing in symbiosis – endosymbiotic theory o Mitochondria thought to have evolved 1.8 billion years ago from aerobic bacteria o Common ancestor of all eukaryotes has mitochondria o Many genes transferred to nucleus over evolutionary time o Between 500 and 1000 nuclear encoded proteins contain mitochondrial entry motifs o Mitochondrial DNA often denoted as mtDNA  Chloroplasts thought to have evolved form cyanobacteria, also through an initial symbiotic relationship  Evidence for this mechanism o Mitochondrial and chloroplast genome are circular like bacterial genomes o Mitochondrial and chloroplast genomes are not associated with histone proteins o Many genes are closely located and transcribed as single units o Ribosomes in mitochondria and chloroplasts are similar to bacterial ribosomes  Chloroplast genome is small – 120-160kb  Mitochondrial genome is smaller, only 16.5kb in mammals coding for approx. 40 genes  Both perform a single specialised function (photosynthesis and cellular respiration respectively)  Genomes therefore likely to represent the minimal subset of genes that cannot be transferred to the nucleus Extranuclear Inheritance  Non-nuclear inheritance DOES NOT follow Mendelian inheritance o Extranuclear inheritance tends to be form one parent – uniparental inheritance o Determined by maternal and paternal contribution at time of fertilisation

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o Maternal inheritance from the mother, paternal inheritance from the father Size difference between egg and sperm accounts for maternal inheritance of mitochondrial in humans – egg contributes almost all the cytoplasm to the zygote Affected mother and normal father produce affected offspring, but an affected father and normal mother produce normal offspring – not the same as X or Y linked genes

Heteroplasmy  Mitochondria exist as multiple independent entities in the same cell, and these function as individual units  Genetic mutation in one mitochondria does not mean all mitochondria in the cell carry that same mutation  When two or more genetically distinct mitochondria are present in a cell this is known as heteroplasmy  A rare occurrence (mitochondrial genes perform a specific function, mutation tends towards lethality) o Where heteroplasmy does exist, it can be used to determine identity o Individual will vary by a percentage, not an absolute genotype Mitochondrial Disease  Mitochondrial disease as a result of mtDNA, mutation is possible, and usually indicated by its distinctive inheritance pattern, although phenotypic presentation can vary due to heteroplasmy  Most mtDNA mutations affect ATP synthesis and hence function of high energy demand cells such as muscle and nervous tissue – common phenotypes include blindness, deafness and stroke  Threshold effect – cut-off at which small number of mutant mitochondria have no phenotypic effect Ancestry through Mitochondrial DNA  Unlike nuclear DNA, mtDNA does not undergo genetic recombination – perfect transfer from parent to child o Maternal transfer, means maternal ancestors can be traces through mtDNA sequences o Non-lethal DNA mutation also shows maternal ancestry information o Allows degrees of relatedness to be determined between 2 individuals  Domestication of dogs from wolves estimated to begin 100,000 years ago by mtDNA sequences  2 independent periods of domestication plus multiple episodes of genetic admixture (dogwolf breeding)  Richard III; 1452-1484 o Died Battle of Bosworth Field of distinctive wounds o Had known skeletal deformation (scoliosis) o Existing relatives matched to skeleton via 18 generations mtDNA  Subsequence genome sequencing – first ancient person, with known historical identity to have genome sequences  Revealed maternal confirmation of identity, showed paternal variation o Not likely to be directly descended great-great grandson of Edward III o Depending on when, could invalidate entire Tudor dynasty Cytoplasmic Male Sterility in Plants

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Some plants do not produce functional pollen, but do have normal female organs – cytoplasmic male sterility (CMS) o Useful in agriculture, prevents self-pollination and allows the production of hybrids o Results from mutations in mtDNA that are toxic in pollen-producing tissues o Mutant protein present in all cells and reasons for toxicity not clear – unique my function in plants? CMS plants can only reproduce by crossing with a male fertile line but o Mitochondrial are maternally inherited, so all offspring are CMS and therefore sterile too o Presence of a dominant nuclear gene Rf (restorer of fertility) can correct CMS

Vegetative Segregation  Vegetative segregation – the sorting of heteroplasmic organelles in plant growth, e.g. leaf variation  Variegation – white areas due to lack of green chlorophyll o Completely white branches o Completely green branches o Variegated branches of green and white areas  9 possible crosses depending on whether white, green or variegated cutting provides the egg or pollen  Green female x white mate gives green plants  White female x green male gives white plants (lethal)  Variegated female x any male gives green, white or variegated  Female gamete determines offspring colour (maternal inheritance)  Green colour depends ion chloroplasts and pollen are too small to contain chloroplasts  Variegated plants must have heteroplasmic chloroplasts, random segregation during growth allows 3 phenotypes Maternal Inheritance and Maternal Effects  Maternal inheritance – hereditary determinants of a trait are extranuclear and genetic transmission is only through the maternal cytoplasm with no Mendelian segregation observed o Mitochondrial transfer  Maternal effects – nuclear genotype of the mother determines the phenotype of the progeny and will show Mendelian segregation o Substances resent in the egg that effect early development (protein products of nuclear genes) o Substances present in nurturing, e.g. components of breast milk...