GENETICS OF ORGANELLES III. GENE 330

THE ORIGIN AND EVOLUTION OF MITOCHONDRIA AND CHLOROPLASTS Life on earth originated more than 3 billion years ago. The first cellular organisms were prokaryotic; they lacked true nuclei and cytoplasmic organelles and were heterotrophic. Eukaryotic organisms evolved 1 to 1.5 billions years ago. The first known eukaryotes were filamentous green algae, with nuclei and elaborate intracellular organization, including subcellular organelles. In the 1970 Lynn Margulis forcefully argued that both mitochondria and chloroplasts were once free-living organisms that became incorporated into primitive eukaryotic cells.

Eukaryotic Organelles as Endosymbiots Symbiosis is a condition in which two or more organisms live together in close association for their mutual benefit. Endosymbiosis is a special case in which one of the symbiotic partners lives inside the other. Evidence from biochemical, genetic, and molecular studies suggests that mitochondria and chloroplasts originated as a bacterial endosymbiots. Mitochondria and chloroplasts are both about the size of some bacteria, and both contain circular DNA molecules much like bacterial chromosomes. Both mitochondria and chloroplasts contain their own distinctive ribosomes, and both utilize a distinctive RNA polymerase DNA sequencing studies have demonstrated that some genes in the mitochondrial and chloroplast DNA are similar to bacterial genes. All these facts strongly suggest that mitochondria and chloroplasts originated when bacteria were incorporated into primitive eukaryotic cells, probably more than a billion years ago.

Eukaryotic Organelles as Endosymbiots Since the formation of these relationships, each of the symbiotic partners has undergone significant changes, and considerable genetic shuffling has taken place among the mitochondrial, chloroplast, and nuclear DNAs. For example, in most plant species the small subunit of ribulose 1,5-biphosphate carboxylase is encoded by a nuclear gene, but in some species of algae, it is encoded by a chloroplast gene. It has been estimated that between 400 and 2200 of the projected 25 000 genes in the nuclear genome of the plant Arabidopsis thaliana are derived from bacteria, presumably through transfers from the endosymbionts that eventually became the mitochondria and chloroplasts in this species. Because of this gene shuffling, neither mitochondria nor chloroplasts are able to sustain themselves without materials specified by the nucleus. Even major components of the genetic systems of the mitochondria and chloroplasts are derived from nuclear gene products. These include the DNA and RNA polymerases, some tRNAs, and many, if not all, of the ribosomal proteins.

The Evolution of Mitochondria and Chloroplasts Variation among the DNAs of mitochondria and chloroplasts indicates that genomes of these organelles have undergone significant changes. First there is variation in gene content. In plants the repertoire of mitochondrial genes has been augmented by the acquisition of a large number of unassigned reading frames, noncoding sequences, and introns. Plant mtDNA molecules are more like the ancestral condition. Second, there is structural variation, or variation in the order of genes within the DNA. For example, human and Drosophila mtDNAs contain the same set of genes, but these genes are arranged differently in their respective mtDNAs. Third, there is variation in the nucleotide sequences of particulars genes. For example, when we compare the genes for cytochrome b in human and Drosophila mtDNAs, we find many nucleotide differences. This kind of variation indicates that the sequences of these genes have evolved since they diverged from a common ancestor.

The Evolution of Mitochondria and Chloroplasts Geneticists have put considerable effort into studying the rate of mitochondrial gene evolution and comparing it with the rate of nuclear gene evolution. The surprising finding is that in some groups of organisms such as vertebrate animals mitochondrial genes evolve faster, perhaps 5 to 10 times faster, than nuclear genes. The reason for this rapid evolution are not clear. Perhaps mitochondrial gene products are more flexible and are therefore able to tolerate more amino acid changes than are nuclear gene products, or perhaps the mutation rate is simply greater in the mitochondria than it is in the nucleus (due, possibly, to less efficient DNA repair systems in the mitochondria). Mitochondria and chloroplasts are almost always transmitted through the female. There is some evidence for paternal transmission – but it seems to be infrequent. Thus, the genomes of these organelles evolve mainly by an asexual process.

Mitochondrial Codes Codon Universal code Mitochondrial codes Differences between the universal genetic code and mitochondrial codes _____________________________________________________________ Codon Universal code Mitochondrial codes Mammals Invertebrates Yeasts Plants ______________________________________________________ UGA Stop Trp Trp Trp Stop AUA Ile Met Met Met Ile CUA Leu Leu Leu Thr Leu AGA/AGG Arg Stop Ser Arg Arg

KEY POINTS Mitochondria and chloroplasts seem to have originated as bacteria that were incorporated into eukaryotic cells about a billion years ago. As the endosymbiotic bacteria evolved into organelles, many of their genes were lost; other genes were transferred into the host cell’s genome or into the genome of another endosymbiotic bacterium. Organellar DNA, especially mtDNA, has been very useful in studying the evolution of different groups of organisms.

Mitochondrial Diseases A large, complex, and heterogeneous group of diseases is caused by mutations or deletions in human mtDNA. The clinical spectrum and age of onset of mitochondrial diseases vary widely. Organs with high-energy requirements are particularly vulnerable: brain, heart, skeletal muscle, eye, ear, liver, pancreas, and kidney. The mutation rate of mtDNA is ten times higher than that of nuclear DNA. Mutations accumulate because effective DNA repair and protective histones are lacking. At birth most mtDNA molecules are identical (homoplasmy); later they differ as a result of mutations accumulated in different mitochondria (heteroplasmy).

Mitochondrial Diseases Mutations and deletions in mtDNA in man Both deletions and point mutations are causes of mitochondrial genetic disorders. Some are characteristic and recur in different, unrelated patients. Maternal inheritance of a mitochondrial disease Hereditary mitochondrial diseases are transmitted only through the maternal line, since spermatozoa contain hardly any mitochondria. Thus, the disease will not be transmitted from an affected man to his children. Heteroplasmy for mitochondrial mutations Many mutations and deletions in mitochondria are acquired during an individual’s lifetime. Their proportion may be different in different tissues (heteroplasmy) and influenced by age. This contributes to the variability of mitochondrial diseases.

Mitochondrial Diseases More than 95% of polypeptides of the respiratory chain are encoded by genes that reside in nucleus, so one would expect that numerous mitochondrial disorders would be traced to nuclear mutations. The most serious disorders usually stem from mutations (or deletions) that affect genes encoding mitochondrial tRNAs, which are required for the synthesis of all 13 polypeptides produced in human mitochondria. The inheritance of mitochondrial disorders contrasts in several ways with the Mendelian inheritance of nuclear genes. The mitochondria present in the cells of a human embryo are derived from mitochondria that were present in the egg at the time of conception –mitochondrial disorders are inherited maternally.

Mitochondrial Diseases Mitochondrial mutations are particularly likely to accumulate in cells that remain in the body for long periods of time, such as those of nerve and muscle tissue. Parkinson’s disease (PD) might be a consequence of degenerative changes in mitochondrial function. This possibility originally came to light in the early 1980s when a number of young drug addicts reported to hospitals with the sudden onset of severe muscular tremors that are characteristic of advanced PD. It was discovered, that these individuals had intravenously injected themselves with a synthetic heroin that was contaminated with a compound called MPTP. MPTP caused a damage to complex I of the mitochondrial respiratory chain, leading to the death of nerve cells in the same region of the brain that is affected in patients with PD. More recently - pesticides (particularly rotenone) act as inhibitors complex I (an environmental risk factor for development of PD?).

mtDNA and Human Diseases Recent research has demonstrated that several human diseases are caused by mitochondrial defects, and in some cases, these defects are due to mutations in the mtDNA. One such disease is Leber’s hereditary optic neuropathy (LHON), a condition characterized by the sudden onset of blindness in adults. This disease is associated with the death of the optic nerve (at a physiological level), and with mutation in any of several mitochondrial genes (at a molecular level). Each mutation changes an amino acid in one of the mitochondrial proteins – reducing the efficiency of oxidative phosphorylation. The reduction is great enough to destroy the function of the optic nerve and cause total blindness. It is not known why this effect is limited to the optic nerve. LHON is inherited strictly through the maternal line. Another disorder caused by a mutation in the mtDNA is a Pearson marrow-pancreas syndrome, characterized by a loss of bone-marrow cells during childhood, is frequently fatal. It is caused by a fairly large deletions in the mtDNA. People with this syndrome almost never have affected parents. Thus, the causative deletion probably occurs spontaneously during development in the child or during oogenesis in the mother. Individuals with Pearson syndrome actually have a mixture of deleted and normal mtDNA – an example of mitochondrial heteroplasmy. Homoplasmic individuals have never been observed.

mtDNA to Study Human Evolution Some of the most insightful studies of human evolution have involved the analysis of mtDNA. There are two reasons why mtDNA is useful: (1) much of it evolves faster than nuclear DNA, and (2) it is transmitted through the female. There is relatively little variation in the mtDNA from different human populations and the greatest variation is found in the mtDNA from population in Africa. Given the rate at which mtDNA is know to evolve, these discoveries suggested that modern human beings originated rather recently, probably within the last 200,000 years, and probably in Africa. The mtDNA in all modern groups of humans is descended from an mtDNA molecule that existed in a single woman who lived in Africa about 200,000 years ago – “Mitochondrial Eve”.

mtDNA to Study Human Evolution However, researchers did not claim that one woman alone gave rise to all modern human beings. The mass of human nuclear DNA, which is inherited equally from males and females, and which varies among the members of a breeding population, cannot be traced to e single individual. Migrants from this original African population presumably founded the early human populations of Europe and Asia, and of others continents. This evolutionary scenario has been called the “Out of Africa” hypothesis. Another hypothesis proposes that humans evolved simultaneously in many regions of the world from groups that were long established in those regions.

mtDNA to Study Human Evolution The Neanderthals have always been an enigmatic group for study of human evolution. Fossils remains indicate that they were quite different from modern humans: thicker bones, greater musculature, and different body proportions clearly set them apart. The questions are: - were the Neanderthals ancestral to modern human, - did they interbreed with the populations that ultimately produced modern humans, or - were they a separate and distinct species altogether? In 1997 was published the sequence of 379 bp of mtDNA extracted from a fossilized Neanderthal arm bone (fossil's age between 30,000 and 100,000 years) and amplified by PCR.

mtDNA to Study Human Evolution Biochemical analysis of this amplified material showed that Neanderthal mtDNA differs from modern human mtDNA in 28 of the 379 nucleotides that were analyzed. The mtDNA isolated from the different modern human typically shows only 8 nucleotide substitutions in this region. Thus, Neanderthal mtDNA is significantly unlike that of modern humans. Computer analysis of the DNA sequences suggested that the human and Neanderthal mtDNA lineages began to evolve separately between 550,000 and 690,000 years ago, and the modern human mtDNAs originated between 120,000 and 150,000 years ago. Thus, Neanderthals were almost certainly not ancestral to modern humans, they evolved separately, and became extinct.

Human Genetics Sidelight – Nucleotide differences within a 379-bp noncoding region of the mtDNA of a Neanderthal fossil and that of a modern human being. The sequenced region lies between the genes for the phenylalanine (Phe) and proline (Pro) tRNAs. For each nucleotide difference (highlighted), the upper nucleotide is found in modern human mtDNA and the lower one is found in the Neanderthal mtDNA. Human Genetics Sidelight – Nucleotide differences within a 379-bp noncoding region of the mtDNA of a Neanderthal fossil and that of a modern human being.

Question 9.19 The following pedigree shows the occurrence and severity of cardiomyopathy in a family. The following pedigree shows the occurrence and severity of cardiomyopathy in a family. © 2003 John Wiley and Sons Publishers