One of the main characteristics, other than their pink coloured pigment derived from their carotenoids, of one third of the Roseobacter clade is the ability to utilise dissolved organic materials and harvest light energy (photoheterotrophic lifestyle). There is a growing awareness that horizontal gene transfer is a significant phenomenon as a dominant form of gene transfer, which may explain the sporadic distribution of photosynthetic gene clusters (PGCs) within the Roseobacter clade. Petersen et al. (2012) aimed to provide evidence for this mechanism of gene transfer using two cases of plasmid located PCGs from Roseobacter litoralis and Sulfitobacter guttiformis, both from the Rhodobacterales genus.
They sequenced the genes contained in each of S. guttiformis’ three plasmids. The largest (pSG118) and the smallest (pSG4) plasmids (118 and 4kb, respectively) were found to replicate using Rep-B type replicons while the medium sized plasmid (pSG53, 53kb) was found to replicate using a Rep-ABC type replicons. pSG4 did not possess the parAB partitioning module, usually found in alphaproteobacteria, which is usually missing in cryptic plasmids. It is not inferred whether pSG53 has this parAB partitioning module (which is a critical note to the paper) but pSG118 does.
Petersen et al. then compared the largest pSG118 plasmid to the genetic sequence of the photosynthetic plasmid of R. litoralis (data from previous study), as both of these plasmids contain the characteristic PGC of purple bacteria (~45kb). This comparison showed both of their replication modules to be located at the same position within the 45kb PGC as well as their different methods of replication; S. guttiformis uses Rep-B type replicons whereas R. litoralis uses DnaA type replicons. The phylogenetic analysis suggests an independent origin of their extra-chromosomal replicons, thus suggesting they are analogous and not as a result of vertical transfer (i.e. not originating from the same ancestor). It is suggested that the replicons are located at exactly the same place as this is an insertional hotspot or they are restricted at a molecular level to only a few sites that offer stable maintenance of photosynthesis, however they contradict themselves throughout the whole paper so this is not entirely clear.
Petersen et al. concluded that the replicons studied have “probably” been subjected to horizontal gene transfer at some point in their recent past. This suggests to us that they were not particularly confident in their results, however we can draw from it that it provides evidence for a “cheap” mechanism to which Rhodobacterales can gain access to the unique set of proteins that is the marine pan-genome.
We felt that this paper was extremely difficult to read, badly laid out and often contradictory. We think they should have focused on their actual results and presented these in a manner that clearly showed that they supported their hypothesis, rather than bringing in lots of alternative explanations, none of which were proven. Further research should look at the competition between a bacterium that possesses these PGCs on a plasmid with a mutant where they have been experimentally removed and determining whether there is an advantage to the extra-chromosomal PGCs, possibly comparing this with a bacterium possessing these in their nuclear genome.
Petersen, J., Brinkmann, H., Bunk, B., Michael, V., Pauker, O. & Pradella, S. (2012) Think pink: photosynthesis, plasmids and the Roseobacter clade. Environmental microbiology. 14, 2661-2672http://www.ncbi.nlm.nih.gov/pubmed/22732061
The full text is only available when logged on in university, if anyone is interested let me know (however we strongly discourage anyone from doing this!)
We also found this website: http://www.terradaily.com/reports/Think_Pink_Success_of_pink_bacteria_in_oceans_of_the_world_999.html
ReplyDeletewhich summarises what the group are looking to achieve in the long run and has an interview with the main author of the paper. It helped us a bit in our understanding...
Hi Carys and Robyn,
ReplyDeleteThis was a point I mentioned in the seminar, hopefully this is a simpler way of explaining it:
The entire paper relies on the successful classification of the bacteria since it looks into the ancestry of the replicons that allow them to function photoheterotrophically. The point that I mentioned was a point brought up in another module (Speciation and Diversity), in which the difficulty in classifying species, bacteria in particular, was highlighted.
“Bacterial 16S ribosomal RNA (rRNA) genes contain nine “hypervariable regions” (V1 – V9) that demonstrate considerable sequence diversity among different bacteria.” (Soumitesh et al, 2007). It is this section of the genome that is used to classify a bacteria as a particular species. However, this represents a small section of the genome relative to the rest of the genome, which varies frequently due to mutations and recombination of DNA etc.
Bacteria have been known to be reclassified, even as recent as 2006 when López-Cortés et al proposed the reclassification of Desulfovibrio vulgaris subspecies oxamicus as an indepenent species Desulfovibrio oxamicus. I wonder when these ‘species’ were last looked into in terms of classification, and whether they could in fact be from the same linage. This would result in false conclusions being drawn based on a mistake before Petersen, J et al even began their research.
This could be linked with the presently used identification technique only focusing on a small section of the genome, or indeed just the general high variation of the genome. As for an alternative to this identification, I have no idea how it could be done, and perhaps classification will be in constant reflux for bacteria, never giving a conclusive answer.
Chakravorty, S. Helb, D. Burday, M. Connell, N. and Alland, D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods. 69(2): 330–339. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562909/
López-Cortés, A. Fardeau, M. Fauque, G. Joulian, C and Ollivier, B (2006) Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov. IJSEM 56(7): 1495-
1499http://ijs.sgmjournals.org/content/56/7/1495.full
Hi Megan,
ReplyDeleteSorry this took me so long to reply - I only just noticed your comment!
I completely agree with you; if the authors had looked at the nuclear genome also I think it's completely possible that they may find it needs re-classifying. However, given how unclear etc. the entire paper was I am not shocked at all to find something else that they could have done better.
That said, I would probably be inclined to agree with anyone saying that bacteria can't really ever be classified successfully(probably a similar take to the ones that don't agree with the species concepts that have been discussed in Speciation and Diversity). I think it may be a little bit of a waste of time trying as they can so readily add and remove parts of their genome (relatively, anyway) that to have say an arbitrary 97% sequence similarity would mean that the two individuals probably need to have diverged much more recently than two eukaryotic individuals may have done.