Non- Mendelian Inheritance Mitochondria Chloroplasts Examples of non- Mendelian inheritance

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

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

3. 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. Mitochondria - derived from a photosynthetic purple bacterium that entered a eukaryotic cell >billion years ago. Chloroplasts - derived from a photosynthetic cyanobacterium.

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

5. Replication of the mtDNA 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 mtDNA replication. • Mitochondria (organelle) are not synthesized de novo, but grow and divide like other cells (e.g., mitosis).

6. Fig. 23.3, mtDNA replication

7. Contents of the mtDNA genome: • mtDNA contains genes for: • tRNAs • rRNAs • cytochrome oxidase, NADH-dehydrogenase, & ATPase subunits. • mtDNA genes occur on both strands. • Functions of all human mtDNA 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-tRNA 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 mtDNA genes can be transposed to the nucleus (a distinct set of genes from above): • numtDNA = nuclear mtDNA

8. Fig. 23.4, Physical map of the human mtDNA

9. Transcription of the mtDNA genome: • mRNAs from the mtDNA 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 mtDNAs are transcribed as a single large RNA molecule (polycistronic) and cleaved to produce mRNAs, tRNAs, and rRNAs before they are processed. • Most mtDNA genes are separated by tRNAs that signal transcription termination. • In plants and yeast (mtDNA is much larger): • tRNAs do not separate genes • Gaps between genes are large • Transcription is signaled by non-tRNA sequences • Introns occur (do not occur in animal mtDNA) • Some lack a complete stop codon (3’ end is U or UA; poly (A) tail completes the stop codon) • Transcription is monocistronic

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

11. Useful applications of mtDNA: • Easy to isolate and PCR (high copy #). • Most mtDNA 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 mtDNA is 1/4 that of a nuclear gene. • As a result, mtDNA 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)

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

15. cpDNA organization: • Nuclear genome encodes some chloroplast components, and cpDNA codes the rest, including: • 2 copies of each chloroplast rRNA (16S, 23S, 4.5s, 5S) • tRNAs (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 mtDNA). • cpDNA translation- similar to prokaryotes: • Initiation uses fMet-tRNA. • Chloroplast specific IFs, EFs, and RFs. • Universal genetic code.

16. Fig. 23.7 cpDNA of rice

17. Rules of non-Mendelian inheritance for mtDNA and cpDNA: • 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 mtDNA/cpDNA exist. • Heteroplasmy (mixture of mtDNA/cpDNA organelles with different DNA substitutions) results in rare cases.

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

19. 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. 23.8b

20. Fig. 23.9 Chloroplasts are inherited via the seed cytoplasm 3 types of eggs (female): Normal Mutant Mixed Assumption: Pollen (male) contributes no information

21. Examples of non-Mendelian inheritance: • Mutant [poky] Neurospora possess altered mtDNA 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.

22. Examples of maternally inherited human mtDNA defects: • Leber’s hereditary optic neuropathy (LHON), OMIM-535000 • Mid-life adult blindness from optic nerve degeneration. • Mutations in ND1, ND2, ND4, ND5, ND6, cyt b, CO I, CO II, and ATPase 6 inhibit electron transport chain. • Kearns-Sayre Syndrome, OMIM-530000 • Paralysis of eye muscles, accumulation of pigment and degeneration of the retina, and heart disease. • Deletion of mtDNA tRNAs. • 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 mtDNA lysine tRNA. • Most individuals with mtDNA disorders possess a mix of normal and mutant mtDNA, therefore severity of diseases varies depending on the level of normal mtDNA.

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

24. Maternal effect: • Some maternal phenotypes are produced by the nuclear genome rather than the mtDNA/cpDNA genomes. • Proteins or mRNA (maternal factors) deposited in the oocyte prior to fertilization; these are important for development. • Genes for maternal factors occur on nuclear chromosomes; no mtDNA is involved (not epigenetic). • e.g., shell coiling in the snail Limnaeaperegra. • 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., mtDNA), 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.

25. Fig. 23.17 dextralsinistral *****dextral ***** *****dextral *****

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

27. 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

29. 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/ch056.htm