Essential Genes in Light Harvesting.

Perhaps think about photosynthesis as you look at an evergreen tree if you’re reading this in December (maybe even your Christmas tree), or new budding growth in springtime, depending on where you are in the world.

Last week, I mentioned how some new research suggests that light harvesting complexes used by some bacteria and plants use a quantum mechanical mechanism to transfer the light-stimulated elections in the antennae complex or molecules to the reaction center efficiently. The jury is still open as to whether this confers a fitness advantage (as far as we know, all photosynthesis uses this mechanism, so at least in modern times, there’s no differences for nature to select; nature requires variation for selection to occur), It is perfectly possible nature tried many different kinds of complexes with less efficient transfer mechanisms before hitting upon the few different complexes that exist today.

Or dismissed as simply “Plants convert light into sugar”. It is that, but so much more.

Photosynthesis’s importance can’t be understated, and yet it is often thought of as a boring topic when it’s taught in many schools. Or dismissed as simply “Plants convert light into sugar”. It is that, but so much more.

Photosynthesis word cloud. Image by Kheng Guan Toh. Via Shutterstock.
Photosynthesis word cloud. Image by Kheng Guan Toh. Via Shutterstock.

It is far from boring. For one, seeing the image of photosynthesis as portrayed on the page of a textbook belies just how dynamic a process it is. First, light is constantly streaming in during the day and the plant does have to adjust to constantly changing conditions. Some plants adjust leaf angles, move chloroplasts within cells, and likely alter light harvesting complexes to take advantage of as much radiation as possible. And it all happens fast. Julius Sachs got hints that the rate of oxygen evolution could vary by observing the rate of bubble production in aquatic plants. And there is a lot of evidence that chloroplasts and the nucleus of the cell (where most of the genes are) coordinate with one another too. There’s a lot going on (also, plant cells have many chloroplasts to coordinate)*.

Some plants adjust leaf angles, move chloroplasts within cells, and likely alter light harvesting complexes to take advantage of as much radiation as possible. And it all happens fast

In the light reactions, electrons go on what amounts to a roller coaster ride through protein complexes in the inner membrane of chloroplasts (probably thousands of reaction centers/chloroplast, all in various states at any given time). Photosystem II (PSII), as it’s known, is probably the most important step to life evolving as we know it. It’s responsible for oxygenating Earth’s atmosphere over the course of 1,000,000,000 (one billion) years from ~3.4 to 2.5 billion years ago. Where does the oxygen come from? Part of photosystem II is the tearing apart of water molecules into 4 hydrogen ions, 4 electrons, and one molecule of O2, oxygen, that we breathe. The water tearing mechanism has at its core a cluster of manganese metal ions, that are able, with the input of light energy exciting (displacing) electrons, to break the bonds of hydrogen and oxygen*. It’s quite violent, and as noted above, happens quickly.

In the process of all the electrons flying around, water breaking, and more, the core proteins of PSII are damaged and have to be replaced. Maintaining photosynthesis is no small task for the photosynthesizing organism.

Electrons zoom through various protein complexes and along with the splitting of water molecules, hydrogen ions (H+) get pumped into the lumen (the “inside”) of the inner chloroplast membrane system to create a concentration gradient while electrons wend their way through the membrane creating reducing power for the dark reactions. A big protein complex called ATP synthase pumps hydrogen in the opposite direction generates energy molecules for the cell in the form of ATP. There are also some molecules that get oxidized by the hydrogen that can then be used in a reduction to get CO2 from the air to make carbon-based molecules that comprise most of plant life (and life period- plants/photosynthesizers are the base of most food chains)*.

When viewed as a dynamic process, it’s anything but boring. But just how much of this system is essential?

When viewed as a dynamic process, it’s anything but boring. But just how much of this system is essential?

A paper published in the Proceedings of the National Academy of Sciences in October by Rubin et al** attempts to answer that question.

Using a cyanobacteria (something akin to what oxygenated the Earth billions of years ago) called Synechococcus elongatus as a system, they created a population of them that had insertions in nearly every part of the genome. These insertions presumably disrupt any function of sequences they land in. They then mapped every insertion site in their population and asked the following question: Where is there a low density of insertions in the genome? They reasoned that a low density of insertions suggested that that site in the genome was essential under laboratory conditions for Synechococcus elongatus survival (see Figure below). They conclude that most energy harvesting genes, including those for photosynthesis are essential.

Figure 1 from Rubin et al 2015, PNAS**
Figure 1 from Rubin et al 2015, PNAS**. This figure shows the insertion density of their population as well as an example of what they call an essential gene.

They also made calls of regions where there were some insertions, but not too many as an indicator of genes that would be beneficial to the bacteria. Comparing their list of genes to those of other sequenced cyanobacterial species, they found a large amount of them were conserved– reinforcing the idea that these genes are important for not just synecchococcus, but all cyanobacteria (and possibly any organism). In the paper, an example of an essential gene they note is a subunit of RNA polymerase (see figure), an enzyme that any organism requires to function properly and would be expected to show up as essential. Included in the essential list

One limitation of their screen is that they are not likely to find essential genes that have backup copies, or redundancy, which does happen in biological systems. That limitation aside, they did identify 718 essential genes and 157 beneficial ones. They also found something interesting: that Synechococcus elongatus really relies on its photosynthetic lifestyle because a few genes essential to other life involved in the Krebs cycle that helps split sugar molecules are not essential. Part of the cycle is there, but Synechococcus elongatus sapparently has workarounds to generate all of the essential carbon molecules it needs (amino acids, nucleotides, lipids).

Another fascinating aspect of this study was that they looked for non-coding RNAs. These are sequences of DNA in the genome that do make RNA but don’t code for proteins. These have been a hot area of study lately. They found 10 non-coding RNAs that they could confirm were likely to be non-coding RNAs that many have distinct functions that remain to be seen. They also found a tRNA, or transfer RNA, that was essential. Transfer RNAs have a really important job in the cells. They get charged with aspecfic amino acid, leucine in this case, to carry. The tRNAleu has a specific 3 base-pair code that lets it only be incorporated where a leucine should in a growing protein chain. This is translation, the 2nd part of the central dogma of biology. What’s really interesting is that there are 5 other tRNAleu genes in the Synechococcus elongatus genome, but because of the prevalence of the specific codon recognized by the essential tRNAleu (that sequence is UAA in this case) in the genome. This specific tRNA is essential, the other codons that code for leucine just aren’t as common.

Overall, the Rubin et. al. 2015 paper provides a sense of just what a minimal set of genes needed to be a photosynthetic organism might look like, at least under controlled and largely good, conditions of the laboratory. Other scientists can now take these data and start seeing how good the predictions of essentiality or boon to survival is and start to test differing conditions, as some genes may prove essential only in a dynamically changing environment.

Plants take light and carbon from the sun and air, respectively, and convert it into everything ecosystems use to survive and thrive.

In a future post, I’ll cover the synthesis part of photosynthesis, namely the part that doesn’t require light: the fixing (incorporation of) carbon dioxide into sugar molecules that then go on to get converted into the thousands of difference chemical compounds plants create, the physical world of plants we experience. That’s the other essential part of photosynthesis to create the environments we animals exist in. Plants take light and carbon from the sun and air, respectively, and convert it into everything ecosystems use to survive and thrive.

References:

*Zhang, R., Roose, J. and Williams, M.E. (November 30, 2015). Light-Dependent Reactions of Photosynthesis.  Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/10.1105/tpc.115.tt0515.

**Rubin B.E., Wetmore K.M., Price M.N., Diamond S., Shultzaberger R.K., Lowea L.C., Curtin G., Arkin A.P., Deutschbauer A., and Golden S.S.The essential gene set of a photosynthetic organism. PNAS112:E6634. doi: 10.1073/pnas.1519220112


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