Iron and Stress

Iron is a metal that is essential for all living things as it is heavily involved in cell redox reactions and the electron transport chain (a major part of aerobic respiration). However it is strongly reactive with oxygen - outside of living organisms this leads to rust, inside it can lead to the production of dangerous reactive oxygen species - and therefore needs to be controlled and contained within the cell. In order to provide this control, all living organisms (apart from yeast, weirdly enough) use a protein called ferritin. Multiple subunits of ferritin proteins (usually 24, although occasionally only 12) form an outer shell, with a central cavity that can contain around 2000-400 individual ferric ions (iron ions) keeping them safely out of harms way.

Diagram shows the shell created by ferritin (iron, or ferrous, ions help inside). Image from wikimedia commons.

In plants, the ferritin proteins are found in non-chlorophyll containing plastids, and occasionally in mitochondria (although no one is quite sure why). Many plants contain a number of different genes coding for ferritin proteins which, due to a high similarity in sequence identity and functional redundancy (i.e. most of them do similar things) makes individual ferritins difficult to study. The small weed Arabidopsis thaliana is a good model organism in this case as it contains only four ferritins, imaginatively names AtFer1-4.

These four ferritins are expressed differently at different stages of the cell lifecycle, and in responses to different materials. The diagram below shows which genes are upregulated in response to the oxidative compound H2O2, free iron (Fe) and the plant hormone abscisic acid (ABA):

Upstream of the AtFer1 gene is a 15 base pair sequence named IDRS (iron-dependent regulatory sequence) which is used to repress the gene under iron deficient conditions. This is thought to be upregulated by a phosphatase (which would remove phosphate from a DNA binding protein bound to the IDRS) which in turn is upregulated by the plant hormone NO (nitric oxide). The kinetics of AtFer3 are very similar to AtFer1 and it is therefore thought to be regulated by a similar system. AtFer2 may be activated in a different manner, and it shows very different kinetics to the other three genes. It does contain an IDRS sequence upstream of the gene, but it is not certain whether this is functional.

Despite containing a large source of iron, ferritins are likely to function more to prevent the damage caused by reactive oxygen species (caused by reactions of free iron) rather than as an iron store. Mutant plants containing no ferritin do not have an immediately obvious phenotype (outward appearance) although if extra iron is added they have to produce a large number of energetically wasteful detoxifying enzymes, in order to combat the dangers of oxidative stress. Ferritins therefore seem to have evolved not as an iron storage system, but as a buffering mechanism, to allow increases in iron within a plant to have a beneficial, rather than damaging, effect.

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Briat JF, Ravet K, Arnaud N, Duc C, Boucherez J, Touraine B, Cellier F, & Gaymard F (2010). New insights into ferritin synthesis and function highlight a link between iron homeostasis and oxidative stress in plants. Annals of botany, 105 (5), 811-22 PMID: 19482877

The Predictive Power of Evolution

This post is not a breakdown of a paper, but purely an opinion piece based on my own views. I'd love to hear any different opinions people have, feel free to leave them in the comments box.

Definitions of scientific theory can vary slightly (usually depending on the theory the person currently making the definition has in mind) but they tend to boil down to a few basic elements. Explaining observational data, creating a model, falsifiability and predictive power are some of the most usual phrases used. The idea of the predictive power of a theory is an important one, both because it's a good way to make a distinction between a theory and an observation and because it imparts some kind of real-world use to the science.

One of the criticisms of the Theory of Evolution is that at first glance it appears not to contain any appreciative predictive power. You can trace the evolutionary lineage of a horse, or a whale (or a staphylococcus bacteria if you are so inclined) but you can't make any predictions about what they're going to turn into next. What strange creatures will be walking the earth in five thousand years time is occasionally brought up on random TV shows but there's hardly a way to test the accuracy, and it's not exactly science.

However this criticism seems to be conflating 'prediction' with 'predicting the future'. Very few scientific theories can predict the future. Mendelian theory can predict the likelihood of future outcomes, and I'm lead to believe that Newtonian physics can predict planet orbitals to a certain extent (provided you nudge mercury sideways occasionally) but generally the predictive power of a theory can be used to provide explanations for observations without needing to try and head into the future at all.

To use an example from my current revision: chloroplast gene movement. Chloroplasts are little organelles in plants that carry out photosynthesis and contain the green-coloured pigment that makes plants look mostly green. They are thought to have arisen (and there is by now lots of substantive evidence for this) when a free-living cell engulfed a little photosynthesising bacteria (image below taken from George Washington University page explaining eukaryote evolution):

As the little photosynthesising bacteria contained its own DNA the new chloroplast containing cell now has two genomes, the one in the nucleus and the one in the newly-made chloroplast (ignoring mitochondria for the minute to make things simpler). However when you look at modern plants and compare the chloroplast genome to any bacteria genome you can see that the chloroplast genome is massively reduced. Most of the genes have been lost. Further research will identify several of these chloroplast genes inside the nucleus. The genes have migrated out of the chloroplast, and into the nucleus, where they are being expressed by the nucleus.

There's plenty of reasons why the genes would want to be in the nucleus. It provides centralised control, it keeps the DNA safe from all the reactive oxygen species in the chloroplast, and it means that the chloroplast genes can experience sexual selection. However not all of the genes have left. Some have remained inside the chloroplast, and the question is, why? If the nucleus is such a good place to be, why do some genes get left behind?

In answering this (in fact in answering many question here, including why the genes left as well as why some remain) the theory of evolution can be used to provide a predictive framework in which to suggest an answer. These predictions can then be tested with the data to see which ones fit. In the case of why genes remain in the chloroplast, for example, our theory tells us that if there is a reason (they might just have remained through chance if it was one event that transferred the genes, or they might still be moving) it will be to give the cell an evolutionary advantage. These are genes, and there is a lot of selective pressure on what happens to genes, especially in bacteria, which have a limited supply. The genes that stay behind must provide a selective advantage, there must be a reason why these genes help the chloroplast, and the cell to survive, better than they would if the genes moved to the nucleus.

Once in the nucleus, the genes are used to make the corresponding protein, and this protein is then transported back into the chloroplast. In view of this, one of the first suggestions made was that the genes left behind coded for big bulky proteins that were hard to transport through the chloroplast membrane. Chloroplasts that lost these genes would loose valuable proteins, leaving them at a disadvantage. It's a nice prediction, but unfortunately it got shot down after a close examination of the genes that had actually moved revealed that some of them did code for quite big bulky proteins. And artificially moving some of the bigger and bulkier protein-coding genes into the nucleus showed they could get back into the chloroplasts quite happily, although not quite as efficiently.

Another prediction made (which is looking far more likely) is that the genes left behind very specifically control the redox potential (the balance of positive and negative ions) inside the chloroplast. Due to the photosynthesis the chloroplast is carrying out, the redox potential can change quite dramatically (and regularly) and it needs to be sorted out quickly if it does, as it has the potential to cause a lot of problems within the chloroplast. Having the genes that need to respond to redox change in the nucleus means that a) it takes a lot longer for the signal to get to the nucleus and get the proteins made and b) once the proteins are made they will be sent to all the chloroplasts, despite the face that different chloroplasts will be in different redox states. So far the evidence supports this prediction.

Without the theory of evolution behind this, there's almost no reason to look for a reason. Why the genes moved, and why some stayed behind can be answered by 'they just did'. The framework of an answer that requires an increase in the 'fitness' of the resulting organism helps to give suggestions, and predictions, that can be looked into with further study and gives a focus for directed research.

Extended Hiatus

I had hoped that my little holiday-hiatus wouldn't last much longer than two weeks. However due to a certain volcano going off, I am now stranded in the land of Dial-Up Internet and not quite sure when I'll be getting back. The time I do spend on the internet is spent contacting my partner, trying to download papers and trying desperately to get in touch with my supervisor who has an electronic copy of my (as yet unchecked) dissertation I would really like her to take a look at.

I have a horrible feeling she's stuck in an airport in Canada...

So while the forces of plate-techtonics conspire against my Finals I don't have all that much time for blogging. I'll return as soon as I can, with lots of science stuff (most of it about plants probably, as I'll still be revising) but until the ash clears there won't be anything.

It's really irritating, as I want to get into proper paper-trail revision, which I can't do without an internet source. And the deadline for my dissertation is the Wednesday after next, so I really need to be back by then.

Also I have a library book with me that just went overdue...

(On an unrelated note something happened on the 11th - my page views took a spike. Thank you to whoever-it-was that caused that! Much appreciated, expecially as I'm not able to write much at the moment).