**3. Why Dunaliella**

Given the title of this book, the author intends to clarify the importance and role of adaptation and flexibility of transcription regulation of all proteins encoding proteins in organelles genomes, especially chloroplasts, by focusing on popular microalgae *D. salina*.

*D. salina* is considered for high ability in production and accumulation of massive amounts of β-carotene. Because of its spatial properties, various fields of scientists and researchers like *D. salins*. From 1870 decades of investigation about mechanisms and strategies for optimization of production, extraction and application started and followed now. But it is not only about orange pigment and other subjects, such as genetics, proteins, bioactive compounds, and phytoremediation properties, also attractive [7–13]. Among all *Dunaliella* spices, *D. salina* is a typic organism for the magic and strong power of survival in harsh environments.

*D. salina* lives in saline rivers, saline lakes exposed to intense light and dryness, and out-of-mind places on earth. Azúa-Bustos and his collage in 2010 reported a novel subaerial *Dunaliella* species growing on cave spiderwebs in the Atacama Desert, which was very surprising. In ancient Atacameño culture and the original language of the Atacameños "Kunza," there is no word equivalent to "rain," and the growth and survival of a photosynthetic organism in such conditions are very wonderful.

Easiness of cultivation, diversity of known strains (such as CCAP19/18, CCAP 19/20, and CCAP 19/30) and geographical isolates, lack of disturbing rigid cell wall for DNA extraction, being unicellular and having only one cup shape chloroplast (that means only a plastid genome that facilitates the develop homoplasmic lines of plastid transformants versus multicellular species) and relativity with *C. reinhardtii* and *Volvox carteri,* has made *D. salina* marvelous algae for organelle genome research and plastome engineering [14].

Such a large area and habitation in a diverse environment in terms of physical and chemical conditions can only indicate and confirm the fact that "*D. salina* has the solution to deal with any environmental fluctuations." *D. salina* can easily and quickly understand the changes in its living environment and select and implement the best response leading to survival.

Environmental changes can include light intensity, temperature, acidity (pH), the amount and concentration of nutrients, the amount of water, salinity, heavy metals, and even the presence of other organisms for which they may appear as pathogens or pests.

Understanding such a variety of physicochemical and biological factors requires highly sensitive and efficient sensors and receivers that can transmit environmental messages to the cell control room scilicet NUCLEUS.

In the next step, the nucleus genome modulates the biosynthesis of some metabolites and overproduces some other metabolites, including glycerol and beta-carotene, by regulating the transcription of specific genes, especially those involved in specific metabolic pathways.

The presence of some protein-coding genes in organelle genomes inevitably regulates their transcription and coordination with the transcription process of nuclear genes. Therefore, the nucleus sends representatives, including transcription factors, to the organelles to control transcription. Each TF is affected by one or more environmental factors. It carries the message to genes that have the corresponding transcription elements and the TF binding site above the initial codon.

One or more TF may be located in the regulatory and promoter region of a gene or gene clusters (some organelles genes, especially in chloroplasts, are operated under the control of a promoter), the result of which can accelerate gene recognition by RNA polymerase and start transcription, or vice versa, prevent the establishment of RNA polymerase in its area and do not allow transcription.

#### **3.1** *Dunaliella* **organellar genome**

The *D. salina* mitochondrial and plastid genomes are 28.3 and 269 kb, respectively, and assemble as circular molecules The mitochondrial genome (mtDNA) of *D. salina* is average, 51.5 kb; the size of the *D. salina* plastid genome (ptDNA) is more pronounced than its mitochondrial counterpart, being the largest ptDNA sequenced thus far, complete mitochondrial DNA named mtDNA and plastid DNA as ptDNA. A pair of inverted repeats (14.4 kb), in the *D. salina* ptDNA, divide into a large (127.3 kb) and a small single-copy region (112.9 kb), named the LSC and SSC regions.

The GC content of the *D. salina* mitochondria DNAs is 34.4% and plastid 32.1%, which regarding other Archaeplastida organelle genomes is common.

*D. salina* organelles in the members of the *Chlamydomonadales* are poor in GC or rich in AT, which is important because the *Chlamydomonadales* contain species with GC-rich mitochondrial genomes. The different regions of the *D. salina* mitochondrial and plastid genomes have relatively constant GC content. As:


It is better to know the GC content for the different codon-site positions of the mtDNA and ptDNA protein-coding regions, is approximately.


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

The *D. salina* organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, this amount of noncoding DNA led to placing them among the most inflated organelle DNAs sampled from the Chlorophyta. The *D. salina* plastid genome, about 269 kb, is the largest complete plastid DNA sequence currently deposited in GenBank. *D. salina* organelle genomes have uniquely high intron densities. For mitochondria DNA ~1.5 and plastid DNA ~0.4 introns per gene [14].

#### **3.2 Transfer of genetic material between the** *Dunaliella* **chloroplast and nucleus**

The CoRR theory seems to explain well the presence of independent genomes of organelles comes from the Endosymbiotic theory. But the grade of independence of organelle genomes has changed over time.

In this way, several genes have been transferred to the nucleus genome, and some have been intelligently conserved in the organelle's genome. But the same genes located in the organelle's genome can be controlled and regulated by the nucleus genome.

Numerous regulatory regions and sites can be identified above the origin codon organelle's genome. Cis-regulatory elements are known to be controllable by organspecific transcription factors. These transcription factors originate from the nuclear genome and enter the organelle to regulate the transcription of the organelle's genome.
