NonMendelian Inheritance Mitochondria Chloroplasts Examples of nonMendelian inheritance

Non-Mendelian Inheritance ü Mitochondria ü Chloroplasts ü Examples of non-Mendelian inheritance ü Human mt. DNA defects Other forms of non-Mendelian Inheritance: ü Infectious cytoplasmic inheritance ü Maternal effect ü Genomic (parental) imprinting

Extranuclear Genomes: Mitochondria (animals and plants) Chloroplasts (plants) 1. Mitochondria and chloroplasts occur outside the nucleus, in the cytoplasm of the cell. 2. Contain genomes (mt. DNA/cp. DNA) and genes, i. e. , extrachromosomal genes, cytoplasmic genes, organelle genes, or extranuclear genes. 3. Inheritance is non-Mendelian (e. g. , cytoplasm typically is inherited from the mother).

Origin of mitochondria and chloroplasts: Both mitochondria and chloroplasts are believed to be derived from: Endosymbiotic bacteria = free-living prokaryotes that invaded ancestral eukaryotic cells and established a mutually beneficial relationship. 1. Mitochondria - derived from a photosynthetic purple bacterium that entered a eukaryotic cell >billion years ago. 2. Chloroplasts - derived from a photosynthetic cyanobacterium.

Organization of the mt. DNA genome: • mt. DNAs occur in all aerobic eukaryotic cells and generate energy for cell function by oxidative phosphorylation (OXPHOS) producing ATP. • Most mt. DNA genomes are circular and supercoiled (linear mt. DNAs occur in some protozoa and some fungi). • In some species %GC is high, allowing easy separation of pure mt. DNA from nuclear DNA by gradient centrifugation. • mt. DNAs lack histone-like proteins (like bacteria). • Copy number is high, multiple genomes per mitochondria and many mitochondria per cell (makes mt. DNA easy to isolate and PCR). • Size of mt. DNA varies widely. • Humans and other vertebrates ~16 kb (all of the mt. DNA codes gene products) • • Yeast Plants (lots of non-coding mt. DNA) ~80 kb ~100 kb to 2 Mb

Replication of the mt. DNA genome: • Replication is semi-conservative (like nuclear DNA replication) and uses DNA polymerases specific to the mitochondria. • Occurs throughout the cell-cycle (not just S phase). • Control region (non-coding) forms a displacement loop (d-loop) that functions in mt. DNA replication. • Mitochondria (organelle) are not synthesized de novo, but grow and divide like other cells (e. g. , mitosis).

Fig. 23. 3, mt. DNA replication

Contents of the mt. DNA genome: • mt. DNA contains genes for: • • • t. RNAs r. RNAs cytochrome oxidase, NADH-dehydrogenase, & ATPase subunits. mt. DNA genes occur on both strands. Functions of all human mt. DNA ORFs are assigned. Mitochondria’s genetic information also occurs in the nuclear DNA: • • DNA polymerase, replication factors RNA polymerase, transcription factors ribosomal proteins, translation factors, aa-t. RNA synthetase Additional cytochrome oxidase, NADH, ATPase subunits. • Most required mitochondrial (and chloroplast) proteins are coded by nuclear genes in the nuclear genome. • Copies of the true mt. DNA genes can be transposed to the nucleus (a distinct set of genes from above): numt. DNA = nuclear mt. DNA

Fig. 23. 4, Physical map of the human mt. DNA

Transcription of the mt. DNA genome: • m. RNAs from the mt. DNA are synthesized and translated in the mitochondria. • Gene products encoded by nuclear genes are transported from the cytoplasm to the mitochondria. • Mammalian and other vertebrate mt. DNAs are transcribed as a single large RNA molecule (polycistronic) and cleaved to produce m. RNAs, t. RNAs, and r. RNAs before they are processed. • Most mt. DNA genes are separated by t. RNAs that signal transcription termination. • In plants and yeast (mt. DNA is much larger): • • • t. RNAs do not separate genes Gaps between genes are large Transcription is signaled by non-t. RNA sequences Introns occur (do not occur in animal mt. DNA) Some lack a complete stop codon (3’ end is U or UA; poly (A) tail completes the stop codon) Transcription is monocistronic

Translation of the mt. DNA genome: • Mitochondria m. RNAs do not have a 5’ cap (yeast and plant mt m. RNAs have a leader). • Specialized mt. DNA-specific initiation factors (IFs), elongation factors (EFs), and release factors (RFs) are used for translation. • AUG is the start codon (binds with f. Met-t. RNA like bacteria). • Only plants use the “universal” genetic code. Codes for mammals, birds, and other organisms differ slightly. • Extended wobble also occurs in t. RNA-m. RNA base-pairing (22 t. RNAs are sufficient rather than 32 t. RNA needed for standard wobble).

Useful applications of mt. DNA: • Easy to isolate and PCR (high copy #). • Most mt. DNA is inherited maternally. Can be used to assess maternal population structure (to the exclusion of male-mediated gene flow) • Because it is “haploid” effective population size of mt. DNA is 1/4 that of a nuclear gene. • As a result, mt. DNA substitutions fix rapidly (due to genetic drift) and typically show higher levels of polymorphism and genetic differentiation between populations. Useful for: • • Maternity analysis Phylogenetic systematics Population genetics (and conservation genetics) Forensics (maternal ID)

Chloroplast genomes (cp. DNA): • Chloroplast organelles are the site of photosynthesis and occur only in green plants and photosynthetic protists, • Like mt. DNA, chloroplast genome is: • • • Circular, double-stranded Lacks structural proteins %GC content differs • Chloroplast genome is much larger than animal mt. DNA, ~80 -600 kb. • Chloroplast genomes occur in multiple copies and carry lots of noncoding DNA. • Complete chloroplast sequences have been determined for several organisms (tobacco 155, 844 bp; rice 134, 525 bp).

cp. DNA organization: • Nuclear genome encodes some chloroplast components, and cp. DNA codes the rest, including: • • 2 copies of each chloroplast r. RNA (16 S, 23 S, 4. 5 s, 5 S) t. RNAs (30 in tobacco and rice, 32 in liverwort) 100 highly conserved ORFs (~60 code for proteins required for transcription, translation, and photosynthesis). Genes are coded on both strands (like mt. DNA). cp. DNA translation- similar to prokaryotes: • Initiation uses f. Met-t. RNA. • Chloroplast specific IFs, EFs, and RFs. • Universal genetic code.

Fig. 23. 7 cp. DNA of rice

Rules of non-Mendelian inheritance for mt. DNA and cp. DNA: • Ratios typical of Mendelian segregation do not occur because meiotic segregation is not involved. • Reciprocal crosses usually show uniparental inheritance because zygotes typically receive cytoplasm only from the mother. • Genotype and phenotype of offspring is same as mother. • Paternal leakage occurs at low levels and usually is transient; mechanisms that degrade paternal mt. DNA/cp. DNA exist. • Heteroplasmy (mixture of mt. DNA/cp. DNA organelles with different DNA substitutions) results in rare cases.

http: //bmj-sti. highwire. org/content/77/3/158. full

Examples of non-Mendelian inheritance: • Variegated-shoot phenotypes in four o’clocks Mixed chloroplasts White/green Mutant chloroplast White non-photosynthetic Normal chloroplast Green photosynthetic Fig. 23. 8 b

Fig. 23. 9 Chloroplasts are inherited via the seed cytoplasm 3 types of eggs (female): Normal Mutant Mixed Assumption: Pollen (male) contributes no information

Examples of non-Mendelian inheritance: • Mutant [poky] Neurospora possess altered mt. DNA cytochrome complements that lead to slow growth. • [poky] phenotype is inherited with the cytoplasm. protoperitheca (sexual mating type) conidia (asexual mating type) Fig. 23. 10, Reciprocal crosses of poky and wild-type Neurospora.

Examples of maternally inherited human mt. DNA defects: • Leber’s hereditary optic neuropathy (LHON), OMIM-535000 • • • Kearns-Sayre Syndrome, OMIM-530000 • • • Mid-life adult blindness from optic nerve degeneration. Mutations in ND 1, ND 2, ND 4, ND 5, ND 6, cyt b, CO II, and ATPase 6 inhibit electron transport chain. Paralysis of eye muscles, accumulation of pigment and degeneration of the retina, and heart disease. Deletion of mt. DNA t. RNAs. Myoclonic epilepsy & ragged-red fiber disease (MERRF), OMIM 545000 • • Spasms and abnormal tissues, accumulation of lactic acid in the blood, and uncoordinated movement. Nucleotide substitution in the mt. DNA lysine t. RNA. Most individuals with mt. DNA disorders possess a mix of normal and mutant mt. DNA, therefore severity of diseases varies depending on the level of normal mt. DNA.

Exceptions to maternal inheritance: • Heteroplasmy, mice show paternal DNA present at 1/10, 000 the level of maternal DNA. • Occurs when mt. DNA from sperm leak into egg cytoplasm at the time of fertilization. • In these cases, maternal and paternal mt. DNA can recombine! • Paternal inheritance of chloroplasts commonly occurs in some plants (e. g. , gymnosperms). www. sciencemusings. com/

Maternal effect: Some maternal phenotypes are produced by the nuclear genome rather than the mt. DNA/cp. DNA genomes. • Proteins or m. RNA (maternal factors) deposited in the oocyte prior to fertilization; these are important for development. • Genes for maternal factors occur on nuclear chromosomes; no mt. DNA is involved (not epigenetic). • e. g. , shell coiling in the snail Limnaea peregra. • Determined by a pair of nuclear alleles; D produces dextral (right-handed) coiling, d produces sinistral (left-handed) coiling. • Shell coiling always is determined by the maternal genotype, not the alleles that the progeny carry or maternal phenotype. • If coiling were controlled by extranuclear gene (e. g. , mt. DNA), progeny would always have the same phenotype as mother. • Cause-female snail deposits products in the egg that regulate orientation of mitotic spindle and direction of cell cleavage.

Fig. 23. 17 dextral sinistral *****dextral *****

Maternal effect: • m. RNAs coded by maternal genes (not offspring) are essential for normal structural development and axis orientation. • Placement of bicoid m. RNA determines anterior end of developing Drosophila embryo. http: //scienceblogs. com/pharyngula/2006/06/maternal_effect_genes. php

Genomic (parental) imprinting: • Expression of genes (or alleles) is determined by whether the gene is inherited from the father or mother. • Results in expression of single allele (either from father or mother). • Mechanism is entirely different from maternal effect (e. g. , dextral/sinistral coiling of snail shells). • One allele frequently suppressed by methylation. • Prader-Willi syndrome, OMIM-176270 • Common in various cancers

Transovarial disease transmission - a type of maternal inheritance: • Infected cytoplasm infects the egg and is transmitted to offspring. • Many insect-vectored diseases show transovarial transmission. • Example - eggs and larvae of mosquitoes infected with West Nile Virus also are infected. http: //gsbs. utmb. edu/microbook/ch 056. htm