Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana)dokdonensis DSW-6 and identification of a novel class of rhodopsins
Rhodopsin-containing marine microbes such as those in the Flavobacteria
play a pivotal role in the biogeochemical cycle of the oceans. Flavobacteria
are believed to be major carriers of microbial rhodopsins called
proteorhodopsins (PRs). Rhodopsins show wide taxonomic distribution through
horizontal gene transfer between domains and phyla but despite the great
diversity, these proteins share structural features. The structure and function
of archaeal bacteriorhodopsins (BRs) with the retinal chromophore have been
studied most recently. BRs move protons across the membrane out of
the cell using light energy to generate an electrochemical proton gradient,
which in turn can be used for ATP production. PRs
have been shown to share high sequence similarity with BRs, Recently a related
study on PR-containing marine flavobacterium showed light driven proton
transport activity that was sufficient for ATP generation.
Deciphering the genome information of Flavobacteria and
uncovering the diversity and ecological impact of Rhodopsins is important in
understanding and preserving global ecosystems. In
this study, Kwon et al analyzed the genome sequence of the flavobacterium, Nonlabens
dokdonensis (DSW-6). This
organism was chosen because it provides a glimpse to the survival strategy of a
photoheterotroph in the oligotrophic ocean.
In addition to a typical PR
found during genetic analysis, Kwon et al also found a new type of rhodopsin
with a unique motif formation, dubbed the NQ Rhodopsin. Homologs of the
NQ rhodopsin gene were found to be conserved throughout the bacteria domain and
even found in some diatoms in the eukaryote domain. They all contain the
characteristic NQ motif and form a phylogenetically distinct group, according to
the authors. To better understand the characteristics
of the NQ Rhodopsin, its gene expression in DSW-6 was monitored under various
light levels, nutrient levels, and NaCl levels. The NQ Rhodopsin gene in DSW-6 was
induced at high NaCl concentrations, as well as in the presence of light and
the absence of nutrients suggesting its involvement in sodium metabolism. This
study has demonstrated the diversity of these NQ Rhodopsins in nature using
metagenomic analysis and highlights there importance in understanding the
diversity of these Rhodopsin proteins.
We have come a long way since the first study by Beja et al in 2001! But
this investigation highlights that we still have much to learn.
So in summary Kwon et al have proposed the existence of a
new type of rhodopsin with a function that is unique among proton pumps and is
related to salinity...apparently. This
proposal was based on the expression of the NQ rhodopsin gene in DSW-6 because
they correlate with illumination, nutrient levels, and, most importantly, the
NaCl concentration. Also these Rhodopsins are widely distributed in geographic
environments exposed to high salinity, according to the genomic and metagenomic
datasets used by Kwon et al.
So what is my opinion? Get ready for the most used phrase
in literature…More research is needed. This study speculates a lot of uses of
the NQ Rhodopsin from its structure (see discussion) and where it is found but
none of this is directly tested. The only evidence I can see for its
involvement in Sodium metabolism is its expression in higher NaCl
concentrations. This provides the basis for some many more questions such as "why
does it increase?"
Hi James,
ReplyDeletedo you think perhaps a further study would be nice looking specifically at the function of the NQ Rhodopsin in intertidal rock pools and its effect on the related species living there? Perhaps in an area where condensation is prevalent with in these rock pools so to see a greater change in salinity over a shorter time, perhaps creating a more stressful environment?
Thats a good idea and a very interesting oportunity for a insitu investigation J. Why don't you do it for your masters?!
ReplyDeleteI think there are many more steps before we get to that stage however. To me it seems like the authors got a bit carried away speculating its functions like fact. We first need to estbalish if it is actuelly involved in sodium metabolism as its increase in expression could have been due to a variety of factors.
Hope that helps
Jimbob
Yes you are probably right Little James, laboratory testing to prove its function is clearly the first step, then should it prove successful perhaps field science, take it to the intertidal pools where costs wouldn't be to much of an issue and can be observed easier!Nice paper though! And no sir not for my Masters :)
ReplyDeleteAlright Jimbo,
ReplyDeleteFantastic blogg! I was wondering; the paper says NQ is from a heterotrophic bacteria found in oligotrophic waters, is this ocean wide or from specific locations, say those with relatively high NaCl concentrations?
Sean
Nice blog James, I was wondering, if this bacteria comes from oligotrophic oceaqnic enviroment do you thin t is likley to encounter a change in enviromental salinity undernatural conditions?
ReplyDeleteSorry James, I'm notsure where the link to sodium metabolism is, can you explain this a bit please. Given its expresssion under chnanging salinity do yo think that the NQ Rhodopsin could be a stress response protein?
Thanks Matt
Hi all, I decided I couldn’t miss out on some rhodopsin discussion!
ReplyDeleteI too was intrigued by the link with NaCl so had a little look over the paper. In the introduction there really isn’t any explanation as to why they would investigate expression under different NaCl conditions however, they provide quite thorough rational in the discussion. So firstly they point out that when they did the phylogenetic search they found some of the organisms that have this novel NQ Rhodopsin live in hypersaline environments. Specifically in their metagenomic search they found NQ sequences were most abundant in a hypersaline microbial mat with the salinity of 9%, which fits nicely into their result that NQ Rhodopsin genes were expressed highest in 10% salinity. From here they go onto to speculate about the significance of this finding, obviously sodium and chloride are the two most abundant dissolved ions in seawater and they discuss the possibility of using sodium as a substrate for the pump. They hypothesise that NQ Rhodopsin could be generating sodium motive force to make ATP rather than the proton motive force, which is a pretty spectacular idea and they’ve made some neat links to other literature to expand this theory! Of course they could instead just be involved in osmoregulation and nothing to do with sodium motive forces.
Matt, with regards to your comment re NQ Rhodopsin as stress proteins, I think it’s fairly likely that the NQ Rhodopsin kicks in when times are bad to keep thing ticking over (see the hybrid car post that Anna and I wrote).
Overall I think it’s pretty cool they’ve found a new type of Rhodopsin, and they’ve made some huge and rather speculative suggestions for function. Of course, now all they need to do is all the work on functionality which has been done with the other rhodopsins to understand the significance of this protein in marine ecosystems.
Thanks for your posts, apologies for not replying at shorted notice.
ReplyDeleteSo Sean, just to be clear, as Vickie posted, the authors found the NQ Rhodopsin in a range of organisms that can live in hypersaline environments- it is not made very clear whether it was ocean wide. I suspect it was as from specific locations as the data from these organisms came from datalogs.
Matt and Vickie- i disagree with Vickie about this salinity stress. As i said in my blog he only evidence I can see for its involvement in Sodium metabolism is its expression in higher NaCl concentrations. This gives huge potential for future studies that could prove Vickie's theory but there just is not enough evidence from this study to suggest this. As me and Vickie have both said There is a huge amount of speculation that goes on here about all these neat theories that the NQ rhodopsin could do but there just is not enough evidence...yet
Thanks James and Vickie, that does help shed light on this.
ReplyDeleteNot 100% on the topic BUT Brian Cox is talking about the conserved evolution of Rhodopsin molecules on his programme "The Wonders of Life"... it’s pretty cool and I highly recommend it.
ReplyDelete:)