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J. Harry Caufield

The wonders of combustion. Photo by Stewart Butterfield.
Happy new year to you, reader!

The keyword at this time of year is usually resolutions*, so I'll share one with you: I will read more papers from my field. It's usually not to difficult for me to skim a paper or two each day, at least, but they frequently aren't directly relevant to what I'm doing. There's just so much interesting material out there! Keeping a wide scope when reading research papers certainly aids with perspective but it provides less material to implement immediately.

Luckily, fresh research has never been easier to find. I'll find at least one directly-relevant paper each week and briefly discuss it on this blog. "Directly-relevant" could include computational microbiology, evolution, bacteriophage biology, or even just novel methods and software.

Today's material is a short report by Marc del Grande and Gabriel Moreno-Hagelsieb in BMC Research Notes. It's relevant because it deals with a concept I've explored lately: gene conservation across numerous bacterial species. A group led by Moreno-Hagelsieb already developed a tool for generating a set of non-redundant genomes**, but here they use it to generate a set of prokaryote*** genomes to analyze co-conservation of their transcription factors (TFs). Why transcription factors? Bacterial genomes contain many transcription factors - even more if we count predicted ones - but it isn't clear if they're broadly conserved in pathways or if they usually show up through rapid evolutionary processes like horizontal gene transfer.**** The set of genomes in this paper doesn't include genomes smaller than 2.5 Mb, presumably to avoid the bias of minimal genomes, but it would have been nice to see them.

As with similar studies, this one was limited by the available data. It's difficult to make predictions about TF interactor conservation when we're not sure what these TFs interact with in the first place. In the end, the authors had to predict the existence of TFs across 857 genomes, then examine the TFs and their interactors in their chosen models of E. coli and B. subtilis. Their conclusion: compared to other protein-coding genes, those coding for TFs have fewer conserved potential interactions across Bacteria. The emphasis is mine as these are predicted interactions based on conservation. That's fine unless the TF has some other reason for its conservation. It's an interesting comparison so I'm curious to see how TF interactions look across bacterial protein interactomes (spoiler alert: available data sources are still a limiting factor).  

Del Grande, M. & Moreno-Hagelsieb, G. The loose evolutionary relationships between transcription factors and other gene products across prokaryotes. BMC Res. Notes 7, 928 (2014).

*I'm also resolving to use more images in my blog posts.

**Their report promised a web interface but that doesn't seem to have happened.

***The term "prokaryote" is archaic, isn't it? This paper is really only talking about Bacteria.

****These two models aren't mutually exclusive.