14 June 2006

Reshuffling regulons

When discussing mobile elements in DNA, we usually talk about jumping genes, meaning open reading frames, or even better - fully functional proteins whose encoding genes can either transfer themselves from one place to the other inside its genome or copy itself, thereby creating apparently redundant amount of genetic material.

However, one recent paper that caught my eye is describing a slightly different picture: it is not the gene that is jumping, it is the promoter:

The genome of Tolypothrix sp. PCC 7601 carries two copies of a novel insertion sequence, ISTosp1. One of the two copies is located upstream of the gene encoding glutamyl-tRNA synthetase, an enzyme playing a key role in protein and pigment synthesis. The tnpA gene of the IS element and gltX were co-transcribed and their expression was transiently upregulated upon retrieval of the ammonium source irrespective of whether nitrate or no nitrogen source were available. The second copy is also transcribed and shows a similar regulatory pattern. Structural elements of the promoter (-10 and -35 sequences) directing the expression of the tnpA-gltX operon have been localized within the IS. Regulatory sequences involving the NtcA transcription factor in the control of tnpA-gltX expression were found both within and in sequences upstream of the insertion element. The expression of gltX in a closely related cyanobacterium, Nostoc sp. PCC 7120, which lacks the insertion upstream of gltX, decreased upon ammonium retrieval, a regulatory pattern that markedly differs from that observed in Tolypothrix sp. PCC 7601. ISTosp1 constitutes a good example of how cells can make use of a transposable element to evolve an original regulatory mechanism.

It is quite an interesting concept. Just imagine a nitrogen response element being able to jump from place to place in cyanobacterial genome and regulate a different sets of genes every time, in response to a nitrogen stress. One can only assume that the number of different regulatory possibilities would be huge and that different variants produced by the regulon shifting would have different fitness levels at different nutrient stress conditions. For example, a variant whose nitrogen response element has inserted itself before the genes for photosynthetic complexes would be able to decrease the level of photosynthetic activity in response to the lack of nitrogen, in addition to its previous abilities to regulate the photosynthesis in response to light conditions. Such variant would have much greater fitness than the non-shuffled "wildtype". This removes a whole dimension of randomality from the shoulders of the evolution of microorganisms...

SAR11 - update

OK, so here is the long promised SAR11 update. Actually it is quite a nice story.

While looking for material about the way bacteria adapt to oligotrophic environment, i stumbled upon mention of a convention that took place in Berlin in 1979. The name of convention was Dahlem Konferenzen and the topic was "Strategies of Microbial Life in Extreme Environments". It was impossible to find proceedings from the conference since they were definitely not to be found online or in any other digital format. I went to consult the professor responsible for the course i was taking and he had the proceedings on his shelf! Go figure.

Anyways, in one of the sessions of the conference called "Life under conditions of low nutrient concentrations", the participants tried to list a number of general traits that would be typical of an microorganism in oligotrophic conditions. So i thought it would be cool to take the predictions from 1979 and see whether they are confirmed in the case of SAR11. So here is what i came up with:

1979 Dahlem Konferenzen Prediction



A high surface-to-volume ratio

SAR11 is one of the smallest known prokaryotes. Its’ bean shaped cell is about 0.5 µm long and 0.2 µm wide


Preferential usage of metabolic energy for nutrient uptake

SAR11 has an average of 62% more genes encoding membranal transporters than any other bacteria with a sequenced genome. From 50% of total transporters and almost all of the nutrient uptake related transporters are ABC transporters, meaning that they are using ATP in order to bring in the nutrients from the outside.


Possession of high-affinity, low-specificity transport systems

ABC transporters are considered to generally be a high affinity enzymes with a very high turnover number. Additionally, genome sequence analysis of SAR11 shows that it posseses both high affinity transporters (Ammonia, Urea, Simple amino acids, Spermidine (co-factor), Putrescine (growth factor) transporters) as well as low specificity transporters (Sugars, Branched amino acids, Dicarboxylic acids, Tricarboxylic acids, Osmolytes (glycine, betaine, proline, mannitol, etc.)


Establishment of accumulation reserves following nutrient uptake

SAR11 was found to accumulate several types of metabolites after the uptake, such as amino acids and DMSP


Biosynthetic rates regulated in accordance with the nutrient uptake rate

Genome sequence analysis of SAR11 shows a large number of different regulatory proteins:

  • PhoR/PhoB/PhoC homologues (phosphate limitation response regulators)
  • NtrY/NtrX homologues (nitrogen limitation response regulators)
  • Fur (iron limitation response regulator)
  • envZ/OmpR homologues (osmotic stress regulator)
  • RegB/RegA homologues (redox stress regulator)


Cool, no ?

There are some other things that make this microorganism such a success in oligotropich oceans:

  • the number of active genes in the genome is brought to the minimum - 1354 ORFs
  • the amount of the non-coding DNA was reduced to the astonishing 3 basepairs in average! That is the most reduced known genome in the world!
  • the G:C to A:T ratio was reduced to a point of 29.7% G:C content, which means about 30% less nitrogen atoms per DNA molecule needed.
  • some of its preferred metabolites serve also as osmolites, which adaptes SAR11 to oligotrophic saline environments
  • they seem to have dual energy production system: its genome shows both genes for aerobic respiration and light-driven proteorhodopsin. It is assumed that the proteorhodopsin gives SAR11 advantage over other organisms in the conditions of organic electron donor scarcity

I am generally fascinated by the mechanisms used by microorganisms to adopt to extreme conditions, especially the minimized metabolic pathways and greatly reduced genomic content. SAR11 seems to be a champion of both strategies and can present an important evolutionary example of mechanisms of adaptation driven by extreme environmental conditions

BTW the if anyone wants to search for the Dahlem Konferenzen article, here is the citation:

Hirsch, P, Bernhard, M, Cohen, SS, Ensign, JC, Jannasch, HW, Koch, AL, Marshall, KC Poindexter, JS, Rittenberg, SC, Smith, DC, Veldkamp, H (1979); "Life under conditions of low nutrient concentrations." In: Strategies of Microbial Life in Extreme Environments, Dahlem Konferenzen, Berlin, pp 357-372