Love your LOV domains

A remarkable new paper in Science (subscription required for full text) shows that several Bacteria express a flavin-containing light-activated protein kinase. Amazingly, in Brucella abortus, the photoreceptor is apparently required for full virulence. An accompanying commentary speculates that when the pathogen is expelled from its host, virulence genes are up-regulated by light in order to prepare it for re-infection of a new host.

Swartz, T.E., Tseng, T-S., Frederickson, M.A., Paris, G., Comerci, D., Rajashekara, G., Kim, J-G., Mudgett, M.B., Splitter, G.A., Ugalde, R.A., Goldbaum, F.A., Briggs, W.R. and Bogomolni, R.A. (2007) Blue-light-activated histidine kinases: two-component sensors in Bacteria. Science 317: 1090-1093

More musing on reviewing

I found this interesting post from FemaleScienceProfessor, who has (as a journal Editor) conducted some informal research into the time taken to review papers, in reviewers sorted into groups by seniority.  In general, early career and retired scientists are the fastest reviewers, with some outliers.  Individual reviewers tend to be consistent in the time taken to review:

I thought there would be more variation because the time frame might be affected by how busy someone is, as well as factors related to the manuscript length and quality: some manuscripts are easy to review and some require a huge amount of time. But no.. time-to-review seems to be a personality trait more than anything else.

From my own experience as an Editor soliciting reviews I would entirely agree with this.  And, as a reviewer, I almost always return reviews before the deadline, irrespective of how busy I am or how difficult the paper.

Why are regulatory genes often close to their targets on the chromosome?

This question is addressed in an interesting new paper just published online in PNAS. The authors draw a distinction between two types of regulator: ‘global’ (or pleiotropic) regulators control the expression of many genes; ‘local’ regulators have few (in this case defined as less than 4) targets. The authors show that, in bacterial genomes, local regulatory genes are frequently genetically linked to one of their target transcription units. They make the argument that this arrangement shortens the time required for a newly synthesized transcription factor to find its binding site on the DNA. The optimal arrangement (which statistically is over-represented) is where the regulatory gene is upstream of its target gene or operon, and transcribed in the same direction. In this case the ‘travel distance’ for the newly synthesised regulator (from the 3’ end of its mRNA to its binding site in the promoter of the downstream gene) is shortest. Where genes are convergently transcribed the travel distance is longer, and this arrangement is less common. Global regulators have many targets, most of which have to be distantly located on the chromosome. For transcription factors of this type, the proposal is that the search time is shortened by expressing the regulator at a higher concentration. Experimental data show that global regulators are typically made at much higher concentrations than local regulators, and the ideas in this paper may provide part of the explanation. I am interested in a system where a regulatory gene is divergently transcribed from its target, in many genomes. In this case, the regulatory gene is subject to negative auto-regulation, and the target gene is activated. Interestingly, in different genomes the gene that is the target for regulation may be different, but the gene arrangement is conserved, and I’ve often wondered why. The regulator is made at very low abundance, but it is constitutively bound to DNA (which is unusual for bacterial regulatory proteins). The paper suggests that having a regulator bound to DNA all the time is a strategy used in eukaryotes, where gene co-localization doesn’t work to shorten the search time because the regulatory protein is synthesised outside of the nucleus. Anyway, it’s unfortunate from my point of view that, because of the extra complications introduced by auto-regulation, they don’t discuss regulatory genes and their targets that are divergently transcribed.

Kolesov, G., Wunderlich, Z., Laikova, O.N., Gelfand, M.S. and Mirny, L.A. (2007) How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci USA 104: 13948-13953

More on reviewing

I received this message yesterday: “you are due to retire from the [editorial] board but, in view of your very active support of the Journal, we would like you to stay on as a member of the new board“. Which illustrates the (perhaps obvious) point made in my last post: editors like reviewers who do a decent job. Of course I have somewhat mixed feelings about this: it’s flattering to be asked and to be involved, and interesting to be reviewing manuscripts. But to review a paper properly is a lot of work, sometimes spread over several days.

Peer reviewing

I have reviewed a lot of papers this year. From Bala I found a link to Twelve Tips for Reviewers. These are extremely helpful, for novice and experienced reviewers alike. I would add one thing: if you are a conscientious reviewer expect to be rewarded with lots of manuscripts

Bridges

Listening to NPR in the car I caught a snatch of what sounded like an interesting piece about bridge design. The website has a famous video of the collapse of the Tacoma Narrows Bridge in 1940, video I remember watching in a physics class at school. Two bridges I would really like to see are the Millau Viaduct and the Pontcysyllte Aqueduct (is that a bridge?). The latter is a marvel of 19th century engineering, which we don’t get to see a lot of here in Texas. Speaking of which, my birthplace Stockport is home to another, the railway viaduct built in 1830, which may or may not be the largest (and longest) brick structure in Europe.