Joy of joys my most recent paper has just been published in Nucleic Acids Research!
I'll give a little bit of background to the paper. I actually alluded to it last year when we were in the early stages of writing up.
It started with these papers by Gaur et al and Yassin et al, which claim that an insertion in mitochondrial initiation factor mIF2 evolved to compensate for a total lack of IF1 in mitochondria, which is universal in bacteria. This idea is really cute, and in fact they found that bovine mIF2 compensates for a lack of IF2+IF1 in E. coli. In addition, cryo-EM structures suggest the insertion occupies an overlapping site of the ribosome as IF1 does. However, I made an alignment of mIF2 from a broad distribution of eukaryotes and found there's a significant flaw with this hypothesis: mIF1 is absent in all eukaryotes, but the conserved insertion is only present in vertebrates. So somehow most eukaryotes through most of their evolutionary history have managed just fine without IF1 or the mIF2 insertion. This is a really nice example of how you really should do the comparative genomics of you want to make such sweeping claims as X evolved to replace Y. Here's the pic I made for my older blog post:
My partner in life and crime, Vasili and I were thinking of writing up a teeny tiny paper about this, but then I started checking out more mitochondrial initiation factors...
Most eukaryotes carry have an orthologue of mitochondrial mIF3, but a homologue had never been found in Saccharomyces cerevisiae. Considering how important IF3 is for bacterial translation, and also how human mIF3 is associated with Parkinson's disease, it was a real bummer that this wasn't present in the yeast mitochondrial system. Well, actually, people just weren't looking hard enough. mIF3 is a small protein with a very biased amino acid content, so if just searching with BlastP, you only pick up a few of the most closely related sequences. I tried the more sensitive PSI-Blast and found an S. cerevisiae homolog called Aim23p. Aim23p was known to be a mitochondrial protein, but its function had not been predicted. Phylogenetic analysis confirmed Aim23p is the orthologue of mIF3. Cool! So our teeny tiny paper suddenly got more substantial.
But the really cool stuff happened when we got our friends and collaborators from the lab of Piotr Kamenski in Moscow on board. Piotr's group showed that a knock-out of Aim23p can be complemented by Schizosaccharomyces pombe mIF3, strongly suggesting that Aim23 is the functional equivalent of mIF3 as well as the evolutionary orthologue.
I'm really happy about the results of this paper. It's a great feeling to predict something in silico that gets verified in vivo. Our next collaborative project with Piotr's group is a longer shot, but also bloody exciting, so fingers crossed!
Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae.
Atkinson GC, Kuzmenko A, Kamenski P, Vysokikh MY, Lakunina V, Tankov S, Smirnova E, Soosaar A, Tenson T, Hauryliuk V.
It started with these papers by Gaur et al and Yassin et al, which claim that an insertion in mitochondrial initiation factor mIF2 evolved to compensate for a total lack of IF1 in mitochondria, which is universal in bacteria. This idea is really cute, and in fact they found that bovine mIF2 compensates for a lack of IF2+IF1 in E. coli. In addition, cryo-EM structures suggest the insertion occupies an overlapping site of the ribosome as IF1 does. However, I made an alignment of mIF2 from a broad distribution of eukaryotes and found there's a significant flaw with this hypothesis: mIF1 is absent in all eukaryotes, but the conserved insertion is only present in vertebrates. So somehow most eukaryotes through most of their evolutionary history have managed just fine without IF1 or the mIF2 insertion. This is a really nice example of how you really should do the comparative genomics of you want to make such sweeping claims as X evolved to replace Y. Here's the pic I made for my older blog post:
 |
| Just replace "protein 1" with IF2 and "protein 2" with IF1. Simple! The point is, if you only look at humans and bacteria, you may jump to a conclusion that isn't supported when you sample broadly across taxa. |
My partner in life and crime, Vasili and I were thinking of writing up a teeny tiny paper about this, but then I started checking out more mitochondrial initiation factors...
Most eukaryotes carry have an orthologue of mitochondrial mIF3, but a homologue had never been found in Saccharomyces cerevisiae. Considering how important IF3 is for bacterial translation, and also how human mIF3 is associated with Parkinson's disease, it was a real bummer that this wasn't present in the yeast mitochondrial system. Well, actually, people just weren't looking hard enough. mIF3 is a small protein with a very biased amino acid content, so if just searching with BlastP, you only pick up a few of the most closely related sequences. I tried the more sensitive PSI-Blast and found an S. cerevisiae homolog called Aim23p. Aim23p was known to be a mitochondrial protein, but its function had not been predicted. Phylogenetic analysis confirmed Aim23p is the orthologue of mIF3. Cool! So our teeny tiny paper suddenly got more substantial.
 |
| The two domains of mIF3. The yellow sites are those that are strongly conserved between mIF3 and Aim23p. They are mainly internal, probably important for stabilising the structure. The outer faces are more variable, possibly reflecting lineage-specific evolution of inter-molecular interactions. |
But the really cool stuff happened when we got our friends and collaborators from the lab of Piotr Kamenski in Moscow on board. Piotr's group showed that a knock-out of Aim23p can be complemented by Schizosaccharomyces pombe mIF3, strongly suggesting that Aim23 is the functional equivalent of mIF3 as well as the evolutionary orthologue.
I'm really happy about the results of this paper. It's a great feeling to predict something in silico that gets verified in vivo. Our next collaborative project with Piotr's group is a longer shot, but also bloody exciting, so fingers crossed!
Atkinson, G., Kuzmenko, A., Kamenski, P., Vysokikh, M., Lakunina, V., Tankov, S., Smirnova, E., Soosaar, A., Tenson, T., & Hauryliuk, V. (2012). Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae Nucleic Acids Research DOI: 10.1093/nar/gks272
Although not (at all) main topic of your paper, what caught my eye is a strange position of ciona intestinalis in your phylogenetic tree of IF2s. There were recently some controversy concerning taxonomic position of Tunicates. Was its sequence somehow anomalous (indels or else)?
ReplyDeleteHi anonymous,
ReplyDeleteThanks for your comment. I wouldn't make any inferences about such deep organismal relationships with a single gene tree. As you can see in the tree, there is good support for the Ciona sequence being with animals, but no statistical support for its placement within animals. I tend to find that Ciona sequences are quite divergent, so it never really surprises me when they end up in unusual places in trees.
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ReplyDeleteVery nice article and useful . thank you for sharing something useful . very happy to read all the articles here . two thumbs up!
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