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Jesse Woodson


I am an ex-microbiologist now working with the flowering plant Arabidopsis as a postdoc at the Salk Institute and have recently been interested in this very question.

So far, there has been no single satisfactory explanation to why mitochondria and chloroplasts contain their own genomes, but since hundreds of different proteins encoded in the nucleus are required to maintain a genetic system in an organelle encoding between 3-200 proteins, it seems reasonable to conclude that complete transfer of the organelle genome is either impossible, or that there is a selective advantage to it. The “it has not been long enough” hypothesis seems unlikely to me as organelle to nucleus DNA transfer is a constant process that occurs at a very high frequency and there is conservation among exactly which organelle genes are left in the mitochondria and chloroplasts. This suggests that the organelle genome we see today has probably been relatively constant for a very long time.

So maybe moving certain genes is impossible. The genes found in organelles usually includes those for the genetic system (ribosome subunits, rRNA genes, tRNA genes, and a bacteria-like polymerase in chloroplasts) and those encoding the proteins for photosynthesis and the electron transport chain in chloroplasts and mitochondria respectively. Many of these are integral membrane proteins that are very hydrophobic and it is possible that they cannot be efficiently imported from the cytoplasm into the organelles or that their presence in the cytoplasm may be toxic. This is contradicted by experiments that have successfully imported chloroplast-encoded photosynthetic proteins by inserting their genes in the nucleus and encoding a fused chloroplast-targeting peptide. Also, this hypothesis does not explain why only certain proteins are encoded in organelles as the most hydrophobic of the photosynthesis proteins, the chlorophyll-binding proteins, are encoded in the nucleus. Lastly, the large subunit or RUBISCO is always encoded in the chloroplast and it is completely soluble.

One of the other posts mentioned the CORR (co-location by redox regulation) hypothesis, which suggests that encoding photosynthetic or respiratory proteins on site allows for rapid regulation. Moreover, the organelle does not have to send a signal to the nucleus for more protein. This would not only be slower, but the nucleus would have no way of knowing which organelle made the request if there are several mitochondria or chloroplasts. While this hypothesis may sound more likely than the previous one, there is not much evidence supporting it. There are only two cases I know of where the redox state of an organelle regulates gene expression. In one case, the redox state of land plant chloroplasts, which fluctuates due to light quality/quantity regulates the transcription of the chloroplast-encoded light harvesting centers to increase photosynthetic efficiency. In the second example, nuclear-encoded post-transcriptional regulators in green algae respond to the redox state of the organelle and bind to or release mRNA transcripts. There are no examples or this type of regulation in mitochondria. In the end, both of these hypotheses may help explain why organelle genomes are retained as they are not mutually exclusive.

If you look through the literature three are still other hypothesis that people have put forward, but many are falling out of favor as we sequence more organelle genomes. For instance, one early hypothesis suggested that the alternate genetic code in mitochondria and the rare codon usage in chloroplasts made it more difficult to move genes to the nucleus. This, however, cannot explain why only certain genes have been retained and now we know that these alternative genetic systems evolved secondarily to the organelle. Thus, this may actually be a clever mechanism to ensure genes are NOT lost the nucleus.

One last thought. Some mitochondria that do not perform respiration have lost their genomes. All chloroplasts, however, have genomes. Even those that do not do photosynthesis. Because heme biosynthesis occurs in chloroplasts (in organisms that have chloroplasts, otherwise it occurs in the mitochondria) and requires the chloroplast tRNA-GLU as the starting precursor (which is always encoded in the chloroplast for unknown reasons), it has recently been hypothesized that chloroplasts must retain genomes in order to synthesize heme for the rest of the cell.

Thank you for reading this. I hope it has piqued your interest in eukaryotic biology.

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