Editing Symbiogenesis (section)

=== Plastomes and mitogenomes ===

[[File:Map of the human mitochondrial genome.svg|thumb|upright=1.5|The [[Human mitochondrial genetics|human mitochondrial genome]] has retained genes encoding 2 [[rRNA]]s (blue), 22 [[tRNA]]s (white), and 13 redox [[protein]]s (yellow, orange, red).]]

Some endosymbiont genes remain in the organelles. Plastids and mitochondria retain genes encoding rRNAs, tRNAs, proteins involved in redox reactions, and proteins required for transcription, translation, and replication. There are many hypotheses to explain why organelles retain a small portion of their genome; however no one hypothesis will apply to all organisms, and the topic is still quite controversial. The hydrophobicity hypothesis states that highly [[hydrophobic]] (water hating) proteins (such as the membrane bound proteins involved in [[redox]] reactions) are not easily transported through the cytosol and therefore these proteins must be encoded in their respective organelles. The code disparity hypothesis states that the limit on transfer is due to differing genetic codes and RNA editing between the organelle and the nucleus. The redox control hypothesis states that genes encoding redox reaction proteins are retained in order to effectively couple the need for repair and the synthesis of these proteins. For example, if one of the [[photosystem]]s is lost from the plastid, the intermediate electron carriers may lose or gain too many electrons, signalling the need for repair of a photosystem. The time delay involved in signalling the nucleus and transporting a cytosolic protein to the organelle results in the production of damaging [[reactive oxygen species]]. The final hypothesis states that the assembly of membrane proteins, particularly those involved in redox reactions, requires coordinated synthesis and assembly of subunits; however, translation and protein transport coordination is more difficult to control in the cytoplasm.<ref name="Timmis2004"/><ref name="LilaKoumandou2004"/><ref name="Barbrook2006"/><ref>{{Cite journal |last1=Giannakis |first1=Konstantinos |last2=Arrowsmith |first2=Samuel J. |last3=Richards |first3=Luke |last4=Gasparini |first4=Sara |last5=Chustecki |first5=Joanna M. |last6=Røyrvik |first6=Ellen C. |last7=Johnston |first7=Iain G. |display-authors=3 |date=16 September 2022 |title=Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention |journal=Cell Systems |volume=13 |issue=11 |pages=874–884.e5 |doi=10.1016/j.cels.2022.08.007 |pmid=36115336|s2cid=252337501 |doi-access=free |hdl=11250/3045694 |hdl-access=free }}</ref>