Lectures by Kathleen FitzpatrickSimon Fraser University

Copyright © 2012 Pearson Education Inc. Mark F. Sanders John L. Bowman

G E N E T I CA N I N T E G R A T E D A P P R O A C H

A N A LY S I S Chapter 19Cytoplasmic Inheritance

and the Evolution of Organelle Genomes

P. 641-653, 662-670.

Covering sections 19.1, 19.2 & 19.5

IS THERE OTHER GENETIC MATERIAL IN OUR CELLS THAT WE DEPEND ON TO LIVE?

So far we have been talking about our chromosomal genetic material….

Cross section of Chlamydomamas showing three cellular compartments each with their own genetic material: nucleus (blue), mitochondria (red), and chloroplast (green)

Cross section of Chlamydomamas showing three cellular compartments each with their own genetic material: nucleus (blue), mitochondria (red), and chloroplast (green)

19.1 Cytoplasmic Inheritance Transmits Genes Carried on Organelle Chromosomes

• Cytoplasmic inheritance refers to transmission of genes on mitochondrial and chloroplast chromosomes, as opposed to nuclear chromosomes

• In many eukaryotic species, mitochondria and chloroplasts in fertilized eggs are uniparental, usually maternal, in origin

• In some species, cytoplasmic organelles are contributed to the zygote by both parents, i.e., biparental in origin

The Study of Cytoplasmic Inheritance Differs from the Study of Nuclear Inheritance

• Individual cells may contain multiple organelles

• Each mitochondria or chloroplast may contain multiple copies of its chromosome

• The sizes, numbers, and identity of genes in organelles differs among species

• Trait controlled by cytoplasmic inheritance can also be influenced by nuclear genes

The Discovery of Cytoplasmic Inheritance

• Baur and Correns independently discovered non-Mendelian inheritance pattern in plants in 1908

• Correns studied leaf-color inheritance in the four o’clock plant

• He found that when flowers were self-fertilized, the seeds produced gave rise to plants with leaves of the same color as the branch (green leaves, white leaves, or variegated leaves) upon which the flower was found stephgreenspace.blogspot.com

Results of Correns’ Studies

• Correns made reciprocal crosses between flowers on branches with differently colored leaves

• The results of the tests showed that progeny invariably exhibited the same phenotype as the female parent in the cross

• This suggested that transmission of leaf color occurs by maternal inheritance, through genes transmitted in the ovule only

Explanation for Maternal Inheritance

• In the 1950s, Chiba and colleagues suggested that mitochondria and chloroplasts had their own genomes

• This was based on observation of Feulgen-stained material in the organelles; Feulgen specifically stains DNA

Homoplasmy and Heteroplasmy

• The number of copies of the organelle genome per organelle can vary from one to many

• A cell or organism in which all copies of an organelle gene are the same is called homoplasmic, or said to exhibit homoplasmy

• A cell or organism in which not all copies of an organelle gene are the same is called heteroplasmic, or said to exhibit heteroplasmy

Homoplasmy and Heteroplasmy Explain Maternal Inheritance of Leaf-Color Phenotypes

• In Correns’ work, ovules from variegated plants can produce progeny with green, white, or variegated leaves

• Ovules derived from variegated branches may be heteroplasmic; with chloroplasts that can and some that cannot produce chlorophyll

• During meiosis and mitosis, the chloroplasts are segregated randomly into daughter cells, so that variegated, white, or green progeny could be produced

Genome Replication in Organelles

• Organelle DNA is packaged into protein-DNA complexes in an area called the nucleoid

• Each nucleoid contains multiple copies of the organelle genome

• Replication of the organelle genomes is not tightly coupled to the cell cycle

Factors Affecting Genome Replication in Organelles

• Organelle transmission genetics depends on three factors:

1. The growth, division, and segregation of the organelles themselves

2. The division and segregation of nucleoids in the organelle

3. The replication of the individual organelle genomes

Variable Segregation of Organelle Genomes

• The variation in numbers of organelles and their genomes can influence the phenotypic effects of mutant alleles of organelle genes

• Heteroplasmic cells can produce heteroplasmic and homoplasmic descendants

• If a mutation arises in a chloroplast genome, chloroplasts can arise in which all copies of the genome harbor the mutation; homoplasmic descendants can occur by chance

Replicative Segregation

• Random segregation of organelles during replication is called replicative segregation

• It can lead to genetically mosaic organisms with some mutant cells and some wild-type cells

• Homoplastic cells can arise by chance

Heteroplasmic Individuals & Disease

• In heteroplasmic individuals, penetrance and expressivity depend on the ratio of mutant to wild-type alleles, which can vary among cells and tissues

• The number of chloroplast or mitochondrial genomes present in germ cells influences the ratio of mutant to wild-type organelles in the gametes

Mitochondrial Fusion and Fission

• Mitochondria have been observed to undergo frequent fusion and fission

• This creates the potential for individual mitochondria to have genomes of mixed origin

• It also allows for the genomes of mitochondria within a cell to become homogenized

• In contrast, chloroplasts do not usually undergo fusion

http://www.sciencemag.org

Mother-Child Identity of Mitochondrial DNA

• Mothers and all of their children share identical mitochondrial DNA

• Mitochondrial DNA is used to find matches between mothers and offspring, or grandmothers and grandchildren

• This was most dramatically used in Argentina, to reunite kidnapped children with their grandparents

• 1970s: Argentinean dictatorship kidnapped and murdered political dissidents. Pregnant women were allowed to give birth before execution.

Mother-Child Identity of Mitochondrial DNA

• Grandmothers of the Plaza de Mayo demanded return of their adopted grandchildren

• Comparisons of mitochondrial DNA revealed exact matches between individual abuelas and specific children of the murdered women, allowing many abuelas to be reunited with their grandchildren, whose mothers had ‘disappeared’.

Mitochondrial DNA Sequences and Species Evolution

• Mitochondrial DNA sequences are used as a tool for deciphering genealogical history and evolutionary relationships of mammalian species

• Mitochondria are strictly maternally inherited in mammals, with no recombination of alleles

• Once a mitochondrial mutation occurs in the germ cell of a female, the mutation is transmitted to all of her offspring; maternal lineages can be traced back in time and can allow identification of a common ancestor

Mitochondrial Eve

• Analyses of mitochondrial DNA variation in human populations has helped distinguish between two models of human evolution and migration. Looking for a Most Recent Common Ancestor.

• These results are very controversial.

• The results only consider mitochondrial DNA!

• Also looking at Y-MRCA (Most Recent Common Ancestor, Male (Y))

• Also looking at 6 Neanderthal genomes

• The multiregional (MRE) model suggests that modern humans emerged gradually and simultaneously from Homo erectus on different continents

• The recent African origin (RAO) model proposes that modern humans evolved from a small African population that migrated out of Africa, displacing other species

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• The MRE model suggests that modern humans arose about 2 million years ago, and predicts uniform genetic diversity among most world populations

• The RAO model suggests an earlier origin (120,000 to 200,000 years ago), and predicts that more genetic diversity should be observed in the oldest populations, in Africa

mtDNA Analysis Supports the RAO Model

• mtDNA analysis shows that African populations are most diverse and that diversity elsewhere is based on a subset of African alleles

• Researchers determined an average rate of base changes in mitochondrial DNA by comparing human and chimpanzee sequences

• Then they calculated the minimum divergence time of humans, and obtained an estimate of 200,000 years

LIKE PHYLO!

Mitochondrial Mutations and Human Genetic Disease

• Mitochondrial mutations can result in human genetic diseases

• The phenotypes of such diseases are often highly pleiotropic, because of the dependence of cells on mitochondrial function

• Leber’s hereditary optic neuropathy (LHON) causes blindness in late adolescence/early adulthood; there are a variety of pleiotropic defects, including heart abnormalities

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Penetrance of LHON Is Not Complete

• In mitochondrial disorders such as LHON, while all affected children have an affected mother, the converse is not true

• There are three possible reasons for incomplete penetrance of the disorder: the effects of heteroplasmy, the influence of nuclear genes, and the effect of environmental factors

• In human pedigrees, heteroplasmic mothers may produce heteroplasmic or homoplasmic (both types) offspring

Mitochondrial Transmission in Mammals

• Human oocytes typically have a few large mitochondria (10) that are later divided into smaller mitochondria, representing up to 2000 mitochondrial genomes

• This relatively small number of original mitochondria allows for the possibility of producing homoplasmic offspring that are wild type

Replicative Segregation in Somatic Cells• Heteroplasmic individuals

undergo replicative segregation in somatic cells, which may lead to variable wild-type : mutant mitochondrial ratios in different cells and tissues

• Disease symptoms will develop only if the tissues that are vulnerable to the disorder contain a high proportion of mutant mitochondria

• This will affect the expressivity of the disease

Mating Type and Chloroplast Segregation in Chlamydomonas

• Chlamydomonas reinhardii is a single-celled, haploid green alga with a single large chloroplast containing 50 to 100 genomes, divided among 5 to 15 nucleoids

• Chlamydomonas cells of different mating type, mt or mt, produce diploid cells that then undergo meiosis to produce haploid progeny

• Both mating types contribute to the cytoplasmic content of the zygote, but in 95% of matings, the chloroplast genome is contributed by the mt parent

A Chloroplast Mutant in Chlamydomonas

• The first mutation in a chloroplast gene in Chlamydomonas was discovered by Ruth Sager in 1954, and confers streptomycin resistance (strR)

• During mating, the two cells of opposite mating type fuse, and the chloroplasts from each parent fuse to form a single chloroplast

• The mt cell’s chloroplast is usually eliminated; and its genome is likely degraded at some point during mating

Elimination of One Chloroplast

from the Zygote

• Reciprocal crosses between resistance and sensitive strains of each mating type confirmed that the chloroplast genotype is predominantly contributed by the mt parent

• The mechanism for the uniparental transmission is unknown

• Chlamydomonas cells will rarely show biparental inheritance (5% of matings will be biparental)

• In this case, the presence of two types of genomes in the same organelle allows recombination between them

THE ENDOSYMBIOSIS THEORYSection 19.5

19.5 The Endosymbiosis Theory Explains Mitochondrial and Chloroplast Evolution

• Endosymbiosis is a mutually beneficial relationship in which one organism inhabits the body of another

• Evidence indicates that mitochondria and chloroplasts are descendants of free-living bacteria that took part in ancient infections of eukaryotic cells

learn.genetics.utah.edu

Evidence for the Endosymbiosis Theory

• The double-membrane system in chloroplasts and mitochondria is derived from a similar membrane system found in bacteria

• The organelles are similar in size to bacteria

• Organelle DNA is packaged similarly to that of bacteria, and differently than nuclear DNA

More Evidence for the Endosymbiosis Theory

• The transcriptional and translational machinery of the organelles closely resembles that of bacteria

• The protein-coding sequences of organelle genes are more like those of bacteria than they are like either nuclear genes of eukaryotes or the sequences of archaea

Evolution of Mitochondria

• Evidence indicates that mitochondria are monophyletic, all descended from a single ancestor

• A single endosymbiotic event gave rise to mitochondria after a global rise in atmospheric oxygen that began 2 billion years ago.

• The closest living relatives of mitochondria are free-living -proteobacteria

• Extant -proteobacteria have larger genomes than mitochondria, indicating gene loss.

Evolution of Chloroplasts

• Chloroplasts are also monophyletic, descended from a single endosymbiotic event at least 1.2 billion years ago

• The closest relatives of chloroplasts are free-living cyanobacteria

• Existing cyanobacteria have much larger genomes than chloroplasts, thus large-scale gene loss took place during the evolution of chloroplasts

Mitochondria and chloroplasts are monophyletic -All descended from a single common ancestor

Land plants and algaeLand plants and algae

Animals & FungiAnimals & Fungi

• Many of the genes “lost” from chloroplast and mitochondrial genomes have been relocated to the nuclear genome

• Nuclear genomes of eukaryotes show evidence of both ancient and recent DNA transfer between organellar and nuclear genomes (more recently transferred sequences will be more similar between nuclear and organelle genomes)

Approaches to Detecting Organellar DNA Transfer

• Comparison between Arabidopsis nuclear genome and that of three cyanobacteria species shows that about 4300 nuclear genes have a cyanobacterial origin!

• The importance of the enormous amount of genetic information in the evolution of eukaryotes is difficult to overestimate!

• Comparisons between several eukaryotic nuclear genomes and -protobacteria detected at least 630 nuclear genes derived from the endosymbiont that gave rise to mitochondria

Recent Transfers of Organelle Sequences to Nuclear Genomes

• Recent transfers of mitochondrial and chloroplast genes are included in all nuclear genomes

• NUMTS are nuclear mitochondrial sequences; these are genes in the nucleus derived from mitochondrial genomes

• NUPTS are nuclear plastid sequences, genes in the nucleus derived from plastid genomes

http://scienceblogs.com/digitalbio/2006/08/04/digital-biology-friday-hey-who/

Conclusions Based on Observation of NUMTS and NUPTS

• Given the level of sequence similarity between NUMTS and NUPTS and their respective organelle sequences, the transfers to the nucleus seem to be relatively recent

• Entire organelle genomes were likely transferred to the nuclear genome multiple times in evolutionary history

• The process is ongoing; DNA continues to move between the organelles and the nucleus and the rate of transfer is surprisingly high

Arabidopsis Chromosomes 1, 4, and 10 of Rice

NUPTs NUMTs NUPTs NUMTs

Total number 301 572 677 566

Genic regions 79 166 177 138

Intergenic regions

222 406 500 428

Total number of tight clusters

47 (151) 60 (288) 101 (467) 80 (367)

Homogenous clusters

37 49 68 47

Heterogeneous clusters

10 33Mol Biol Evol (2004) 21 (10)

Encoding of Organellar Proteins

• Organelles contain many more proteins than they encode in their genomes; most organelle proteins are encoded in nuclei

• The nuclear-encoded proteins are translated in the cytoplasm and then transported into the organelles

• Organellar proteins are targeted to their final locations by signal sequences, 15-25 amino acids long at their amino ends; different sequences target the protein to different locations within the organelle

http://dblab.rutgers.edu/paulinella/background.php

Encoding of Organellar Proteins, continued

• Contrary to expectation, not all of the nuclear genes originally derived from an organelle are now targeted to that organelle

• For example, in Arabidopsis, less than half of the genes originally from the cyanobacterial endosymbiont are targeted to the chloroplast

• Conversely, a number of proteins now targeted to the chloroplast did not originate in the cyanobacterial endosymbiont

IF MITOCHONDRIA HAVE THEIR OWN DNA, DO WE NECESSARILY NEED TO GET THEM FROM OUR MOTHER OR FATHER?

Three Parent Babies!

• Nuclear DNA from the egg of woman carrying mitochondrial defects is transferred into the enucleated cytoplasm of a donor egg that harbors nonmutated mtDNA

• The egg is then fertilized in vitro by male sperm and then implanted in the uterus of the mother with the mitochondrial disorder

• The resulting embryo will contain genetic information from three parents

https://www.youtube.com/watch?v=jQxsW_H5qr4

Questions?