**2. Endosymbiotic theory and the origin of the organelle genome**

Endosymbiosis proposes that the origin of today's eukaryotic organelles evolved through a symbiosis process between two primitive free-living cells. One prokaryote cell was swallowed by the precursor of modern eukaryotes. According to Martin et al. [1], the primary nucleus probably consists of pressing a piece of the cytoplasmic membrane around chromosomes. The nucleated primary cell, which moved like an amoeba by creating false feet, then swallowed the primary prokaryotic cells during phagocytosis, and, for some unknown reason, a number of the ingested prokaryotes survived inside the amoebic cell and became the basis for the symbiosis of abovementioned cells [1].

According to endosymbiont theory, ingested early prokaryotes retained their specific traits while surviving. They benefited their nucleated host from the advantages of their specific metabolic abilities. It is believed that a bacterium capable of oxidative metabolism is the ancestor of primary mitochondria and a photosynthetic bacterium is the ancestor of primary chloroplast [2].

They eventually lost their cell wall and much of their DNA because they were useless inside the host cell. Thus, both mitochondria and chloroplasts have their DNA, but both also depend on nuclear genes for some functions [2]. Some organellar protein genes (as whole or partial) are present in the nucleus.

Three issues mentioned by Mereschkowsky [3] about plastid insertion into eucaryotic cells are as follows:


The following provides further evidence for the Endosymbiotic Theory:


*DOI: http://dx.doi.org/10.5772/intechopen.105125 Transcription Flexibility of* Dunaliella *Chloroplast Genome*

• Mitochondria and chloroplasts have their organellar ribosomes (the 30S and 50S subunits), not 40S and 60S [1].

The possibility of the presence of some genes outside the nucleus – which were originally known as extra-chromosomal genes –was first proposed in the 1950s to justify the unusual inherited pattern of some genes in the fungus *Neurospora crassa*, the yeast *Saccharomyces cerevisiae*, and the photosynthetic alga *Chlamydomonas reinhardtii*.

Simultaneous biochemical and electron microscopy studies have increased the possibility of the presence of DNA in mitochondria and chloroplasts. As a result, in the early 1960s, different sets of data were put together and the existence of chloroplasts and mitochondria genomes was accepted independently of the eukaryotic nucleus genome.

The theory of endosymbiotic is corroborated by observations in which the processes of gene expression in organelles are similar to those processes in bacteria. In addition, when the nucleotide sequences were compared, the genes of the organelles were very similar to their counterparts in the bacteria rather than to the genes in the eukaryotic nucleus.

The theory of endosymbiotic was confirmed by the discovery of organisms that show more primitive stages of endosymbiosis than mitochondria and chloroplasts. For example, the early stages of endosymbiosis have been observed in the singlecalled *Cyanophora paradox*, whose photosynthetic structures are different from those of chloroplasts and consist of a community of ingested cyanobacteria. In a similar vein, Rickettsia, which lives inside eukaryotic cells, is likely to be an advanced type of bacteria that makes up mitochondria.

According to the theory of endosymbiotic, after the primary cyanobacteria eaten by the primary eukaryotic cell are not digested for unknown reasons, the newcomer's behavior must be controlled by the host and transform from a selfsufficient organism to a semi-self-sufficient employee. They exchanged genetic material and somehow divided tasks. Regarding the information required for the biosynthesis of the important photosynthetic enzyme Rubisco, this division of tasks has been done in such a way that the genes related to the large subunit remain in the genome of the old cyanobacterium and the new organ that had been the feature of oxygen photosynthesis. However, small subunit genes that were responsible for regulating enzyme function and activity were transferred to the host cell nucleus. It seems that the original genome thus wanted and was able to control and initiate the function and status and activity of the enzyme within the primary chloroplast. Another group of genes in the chloroplast organelle genome is related to the proteins and nucleic acids of the organellar ribosomes.

#### **2.1 Physical properties of the organelle genome**

Almost all eukaryotes have a mitochondrial genome and all photosynthetic eukaryotes have a chloroplast genome in addition to the mitochondrial ones. All organelle genomes were initially thought to be circular DNA molecules. Electron microscopy showed that in some organelles, DNA was present in both circular and linear shapes. But linear molecules were assumed to be simple fragments of circular genomes created by breaking circular genomes during sample preparation for electron microscopy.

The genomes of most mitochondria and chloroplasts are now believed to be circular, but it has recently been discovered that there are many different forms of genomes in different organisms. In many eukaryotes, circular genomes are present along with linear types in the organelles, and in chloroplasts, there are small circular fragments that make up the entire subset of the genome. A recent pattern culminates in seaweed Dinoflagellate, whose chloroplast genome is divided into many small rings, each carrying only one gene. We now find that the mitochondrial genomes of some microbial eukaryotes, such as Paramecium, Chlamydomonas, and the types of yeasts, are always linear.

The number of organelles genome copies is not well defined. Each mitochondrion of a human cell has approximately 10 identical molecules, reaching about 8000 copies per cell, but in *S. cerevisiae*, even if there are more than 100 genomic copies in each mitochondrion, the total number of genomes per cell is less (less than 6500) will be. Photosynthetic microorganisms, such as Chlamydomonas, have approximately 1000 chloroplast genomes per cell, which is about one-fifth of the number in the plant cell.

The size of the mitochondrial genome varies and does not depend on the complexity of the organism. Most multicellular organisms have small mitochondrial genomes with a compact genetic organization in which the genes are close together and slightly apart. Most lower eukaryotes, such as *S. cerevisiae* and flowering plants, have larger, less compact mitochondrial genomes, some of which have introns. The genome of chloroplasts is less varied in size and most of them have the same structure as the genome of rice chloroplast.

### **2.2 Genetic content of an organelle genome**

The genome of organelles is much smaller than the genome of the cell nucleus, so their gene content is expected to be very limited. In terms of genetic content, the mitochondrial genome shows more diversity. Their gene content varies from five genes in the malaria parasite Plasmodium falciparum to 92 genes in the *Reclinomonas americana* unicellular. All mitochondrial genomes have genes for noncoding rRNAs and some respiratory chain protein components that are linked to the main biochemical characteristics of mitochondria.

In genomes with higher gene content, there are genes for tRNA, ribosomal proteins, and proteins involved in the transcription, translation, and transfer of other proteins from the cell cytoplasm into the mitochondria. Most chloroplast genomes have a similar set of 200 genes or more than encode rRNA, tRNA, ribosomal proteins, and photosynthetic proteins.

An important principle of the endosymbiotic theory is the preservation of organelles genomes. Why have organelles preserved their DNA? John F. Allen's CoRR hypothesis (co-location for redox regulation) described the best answer to that question: It proposes that organelles have protected genomes to be independent in the expression of the respiratory and photosynthetic electron transport chains elements. This independence is essential to maintain **Redox Balance** in the bioenergetic membrane. Hence the CoRR hypothesis states that plastids and mitochondria have focused on genes encoded electron transport chain components, and organellar ribosome rRNA and proteins as organelle translation machine tools. The ribosome biogenesis and assembly process require that some proteins need to be co-expressed in the same compartment as their nascent rRNAs. The convergence observed in gene content in plastid and mitochondrial genomes is striking [4].

For the explanation of the redox balance phrase, can be said it refers to the smooth flow of electrons through the electron transport chain in mitochondria and chloroplasts. These two organelles have electron transport chains that generate proton gradients and produce ATP. Quinols and quinones are essential components in both electron transport chains [5].

If the flow of electrons through the inner mitochondrial membrane or the thylakoid as a bioenergetic membrane is disrupted, the steady-state quinol (reduced form of the quinones) concentration increases and the quinols can transfer electrons non-enzymatically to O2 and generate the superoxide radical (O2−), the start point of ROS dissemination. Electron flow disturbance occurs when, downstream components are in insufficient amounts, or upstream components are too active. Without retaining the genome, the electron transport chain and the redox state of the organelle will be abandoned, leading to the destruction of the organelle [6].
