Evolution Basics: Endosymbiosis and the Origins of Mitochondria and Chloroplasts

Bookmark and Share

August 30, 2013 Tags: Genetics

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Evolution Basics: Endosymbiosis and the Origins of Mitochondria and Chloroplasts

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we examine the evidence that mitochondria and chloroplasts are the descendants of free-living bacteria that entered into mutualistic relationships with eukaryotic host cells.

In the last post in this series, we introduced the concept of mutualism: a symbiotic relationship where both species benefit the other. In the case of figs and fig wasps, the one species (fig trees) provides a home for the other (fig wasps) for a portion of its life cycle. Despite the closeness of this sort of mutualistic interaction, figs and wasps are, of course, recognizable as separate entities. Indeed, there is evidence that some wasp species have shifted to new host trees in the past, demonstrating their (partial) independence. Some mutualisms, however, are so old and so intertwined that the two entities are no longer considered separate. Mitochondria and chloroplasts – the organelles responsible for energy conversion in eukaryotes – are thought to be examples of this sort of ancient mutualism. Numerous lines of evidence support the hypothesis that these organelles are the descendants of endosymbiotic (literally, “living together, within”) bacteria.

Mitochondria and chloroplasts as endosymbionts?

Mitochondria, as you may recall from biology class in high school, are membrane-bound “organelles” responsible for energy conversion in all eukaryotes. Eukaryotes are defined as cells with a nucleus, another membrane-bound structure that houses DNA. Eukaryotes are one of the three “domains” of life, the other two being lineages that lack a nucleus (the so-called “prokaryotic” domains of bacteria and archaea). All animals, plants and fungi are eukaryotes, and all eukaryotes have mitochondria – with the exception of some lineages that have lost them.

Chloroplasts, on the other hand, are organelles capable of photosynthesis (using light energy to perform energy conversion). Whereas all eukaryotes have mitochondria, only some eukaryotes have chloroplasts (green algae and plants).

Both mitochondria and chloroplasts have features that were somewhat puzzling to biologists for a long time. Both organelles have their own genomes (a closed circle of DNA), and use protein translation machinery (ribosomes) that is distinct from cellular ribosomes. Both also divide through binary fission, and do not participate in exchange of membrane vesicles with other organelles. Closer examination of these (and other) features showed that in all cases these similarities grouped with bacteria rather than with eukaryotes: bacteria have circular DNA genomes; mitochondria and chloroplast ribosomes are more similar to bacterial ribosomes; and binary fission is a bacterial mode of replication. Gradually, the hypothesis that mitochondria and chloroplasts are the endosymbionic remnants of once free-living bacteria has become a theory in the scientific sense of the word. Recent whole-genome sequencing of mitochondria groups all mitochondrial lineages as more closely related to each other than any is to free-living bacteria (the closest living relatives being the SAR11 group of alphaproteobacteria), supporting the hypothesis that the endosymbiosis event that led to mitochondria happened once, very deep in evolutionary history (around 1.45 billion years ago or more, either prior to or shortly after the origin of eukaryotes). Similarly, chloroplast genomes group together as closest relatives when compared to existing cyanobacteria, their closest free-living relatives.

Late to the party

Until recently, all chloroplasts were thought to be the descendants of a single endosymbiosis event deep in evolutionary time (approximately 1 billion years ago). Work on the amoeba Paulinella chromatophora, however, has provided strong evidence for a second, independent endosymbiosis event producing a photosynthetic organelle. P. chromatophora is named for its two photosynthetic “chromatophores,” endosymbiotic, photosynthetic structures that bear an even more striking resemblance to free-living photosynthetic cyanobacteria than chloroplasts do. The DNA of P. chromatophora chromatophores does not group closely with chloroplasts, but rather with another free-living cyanobacteria lineage. Morphologically, P. chromatophora chromatophores retain some of the bacterial cell wall structure of their cyanobacterial ancestors that chloroplasts have lost. Additionally, the mechanism that shuttles proteins made from the host genome into the chromatophores is distinct from the mechanism used for host / chloroplast protein shuttling. Functionally, the amoeba is dependent on the chromatophores for photosynthesis, and the chromatophores cannot survive as free-living cyanobacteria. Sequence analysis indicates that several key chromatophore genes have been transferred to the host (nuclear) genome, a feature seen with mitochondria and chloroplasts as well. DNA sequence analysis to estimate the time of the chromatophore / cyanobacteria divergence (and thus the endosymbiosis event) places it in the range of 60 million years ago – a mere blink compared to the billion years since the ancestors of chloroplasts entered their host cell.  This second endosymbiosis event is thus another example of convergent evolution – broadly similar in that it produced an obligate, endosymbiotic, photosynthetic organelle, but divergent in the details: a distinct cyanobacteria was the ancestral free-living organism, and the details of the molecular integration of host and endosymbiont are different.

Going green

The ability to use solar energy for energy conversion within the cell is obviously a great advantage to photosynthetic organisms. Interestingly, some animal lineages have developed quasi-endosymbiotic relationships that allow them to photosynthesize using captured chloroplasts. For example, various species of sea slugs are able to retain chloroplasts from the algae they feed on, distribute them within their own tissues, and thereafter use them for photosynthesis, freeing them from the need to ingest additional food for months at a time.

The sea slug Elysia chlorotica employs chloroplasts obtained from the algae it feeds on to perform photosynthesis within its own tissues. (Source)

While not truly an endosymbiotic event (the chloroplasts were not free living to begin with, eventually die without reproducing, and thus must be replaced) it is tempting to speculate that perhaps a similar arrangement between an ancestral eukaryote and its cyanobacterial prey may have led to the original ancestor of modern-day chloroplasts. The formation of chromatophores in P. chromatophora may have started in similar fashion as well – hypotheses that may guide future research in this area.

The endosymbiosis events leading to mitochondria and chloroplasts were major landmarks in evolutionary history. In the next post in this series, we’ll examine another major event in evolution – the so-called Cambrian “explosion”. 

For further reading:

Martin, W. & Mentel, M. (2010) The Origin of Mitochondria. Nature Education 3(9): 58. http://www.nature.com/scitable/topicpage/the-origin-of-mitochondria-14232356

Thrush, J.C. et al., (2011). Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific Reports 1; 13doi:10.1038/srep00013. http://www.nature.com/srep/2011/110614/srep00013/full/srep00013.html

Archibald, J.M. (2006). Endosymbiosis: Double-Take on Plastid Origins. Current Biology 16: R690 – R692. http://www.sciencedirect.com/science/article/pii/S0960982206019804

Nakayama T. and Archibald, J.M. (2012).  Evolving a photosynthetic organelle. BMC Biology, 10:35. http://www.biomedcentral.com/1741-7007/10/35


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

< Previous post in series Next post in series >

View the archived discussion of this post

This article is now closed for new comments. The archived comments are shown below.

Page 1 of 1   1
Roger A. Sawtelle - #82541

August 30th 2013


Thank you for demonstrating the power of symbiosis in all its forms.

Thank you for highlighting the work of Lynn Margolis, one of the founders of modern ecology.

One would think that when science discovered the central role of symbiosis in ecology and evolution, it would pause to reconsider Darwinian natural selection which is based on conflict “fighting against” while symbiosis “working with” is the opposite of conflict.

Page 1 of 1   1