One of the particular features of Planctomycetes, and some other PVCs, is that they have lost the otherwise ubiquitous FtsZ gene. FtsZ is the main building block of the constriction ring that all other bacterial cells use to divide by fission. It is so important that it is one of the few proteins that are found in all bacteria, with very few exceptions. One of them, of course, are some of the PVCs, and in particular almost all Planctomycetes. And we know they have lost it, because the dcw cluster is still present but showing different degrees of erosion in actual PVCs, demonstrating that it was present in the Last PVC Ancestor, and most likely functional (see fig. 2 in the Pilhofer 2008 publication). So the very important question of "how do Planctomycetes divide, and in particular achieve the last steps of cytokinesis?".
This is the question that Jogler et a., 2102 Jbact address in their latest publication. Initial Phylogenetic analysis (Fig. 1)
The authors then go on to define the (non-anammox) planctomycetal core genome, by identifying those genes that have homologues in all selected genomes and discarding the ones that are also found in 'classical' bacteria such as E. coli and B. subtilis. They identified 114 clusters of exclusively planctomycetal proteins. No doubt that some of them should be related to the particular mode of division of those organisms. By example, one such cluster contain 39 membrane-coat like proteins that are structurally related to eukaryotic ones and likely to be involved in the membrane organisation in Planctomycetes (see Santarella-Mellwig et al., 2010 PLoS Biology,). Interestingly, a new FtsZ-like protein was recently described and found in a few Planctomycetes. However, Jogler et al. failed to detect homoloues in all other sequenced planctomycetes despite the use of a very similar strategy. Thus this FtsZ-like family might not be involved in division, at least not in all Planctomycetes.
They then provide an interesting analysis of the proteins found in this core planctomycetal genome and their domain composition.
One of the most interesting result is the finding that Planctomycetes are very poor in DNA-binding one-component systems (classical receptor-operator single proteins in bacteria, direct link between signal and output), but very rich in Ser/Thr protein kinases, which are common among eukaryotes and usually rare in bacteria. Again another striking relationship between those bacteria and eukaryotes.
They also found more two-components systems that are orphan genes, pointing toward a more complex regulation in planctomycetes.
But even more interesting, is their finding related to ECFs. ECFs are extracytoplasmic function sigma factors. In contrast to other bacteria, all planctomycetes are particularly rich in ECFs. Most planctomycetes ECFs can NOT be classified in the previously defined classes, which is probably just a reflexion of the bias towards model bacteria. G. obscuriglobus in particular is the second most ECF-rich bacteria, with the deltaproteobacterium Plesiocystis pacifica. They also identified a new class of ECFs that is specific to G. obscuriglobus. This class also contain more than half of the ECFs in the G. obscuriglobus genomes pointing to a recent evolution of those genes. Importantly, these are also the first membrane-anchored ECFs in bacteria. Given the conspicuous endomembrane organisation in this organism, it make sense that those proteins will play an important role in its regulation.
In conclusion, very interesting paper, even if not resolving the mystery of PVC division. On the other side, I would have found it interesting to do the same analysis on all PVC members. No doubt though that PVCs remains fascinating organisms, as this article beautifully illustrates.
provided a phylogenetic criterion to leave anammox bacteria out of our analysisThis is already important since it clearly splits the Planctomycetes in two group, the anammox on one side and all other non-anammox planctomycetes on the other. Anammox have been claimed to be early branching Planctomycetes and have particular biochemical reactions, endomembrane organization and dividing mode (most likely). Thus, it make sense to separate them from the other planctomycetes. This first analysis clearly puts them apart from the others.
The authors then go on to define the (non-anammox) planctomycetal core genome, by identifying those genes that have homologues in all selected genomes and discarding the ones that are also found in 'classical' bacteria such as E. coli and B. subtilis. They identified 114 clusters of exclusively planctomycetal proteins. No doubt that some of them should be related to the particular mode of division of those organisms. By example, one such cluster contain 39 membrane-coat like proteins that are structurally related to eukaryotic ones and likely to be involved in the membrane organisation in Planctomycetes (see Santarella-Mellwig et al., 2010 PLoS Biology,). Interestingly, a new FtsZ-like protein was recently described and found in a few Planctomycetes. However, Jogler et al. failed to detect homoloues in all other sequenced planctomycetes despite the use of a very similar strategy. Thus this FtsZ-like family might not be involved in division, at least not in all Planctomycetes.
They then provide an interesting analysis of the proteins found in this core planctomycetal genome and their domain composition.
One of the most interesting result is the finding that Planctomycetes are very poor in DNA-binding one-component systems (classical receptor-operator single proteins in bacteria, direct link between signal and output), but very rich in Ser/Thr protein kinases, which are common among eukaryotes and usually rare in bacteria. Again another striking relationship between those bacteria and eukaryotes.
They also found more two-components systems that are orphan genes, pointing toward a more complex regulation in planctomycetes.
But even more interesting, is their finding related to ECFs. ECFs are extracytoplasmic function sigma factors. In contrast to other bacteria, all planctomycetes are particularly rich in ECFs. Most planctomycetes ECFs can NOT be classified in the previously defined classes, which is probably just a reflexion of the bias towards model bacteria. G. obscuriglobus in particular is the second most ECF-rich bacteria, with the deltaproteobacterium Plesiocystis pacifica. They also identified a new class of ECFs that is specific to G. obscuriglobus. This class also contain more than half of the ECFs in the G. obscuriglobus genomes pointing to a recent evolution of those genes. Importantly, these are also the first membrane-anchored ECFs in bacteria. Given the conspicuous endomembrane organisation in this organism, it make sense that those proteins will play an important role in its regulation.
In conclusion, very interesting paper, even if not resolving the mystery of PVC division. On the other side, I would have found it interesting to do the same analysis on all PVC members. No doubt though that PVCs remains fascinating organisms, as this article beautifully illustrates.
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