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Open Access Research article

PhaP phasins play a principal role in poly-β-hydroxybutyrate accumulation in free-living Bradyrhizobium japonicum

Ken-ichi Yoshida*, Yuki Takemoto, Takayuki Sotsuka, Kosei Tanaka and Shinji Takenaka

BMC Microbiology 2013, 13:290  doi:10.1186/1471-2180-13-290

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On the synthesis of polyhydroxyalkanoate and the consistency of gene names

Anibal Lodeiro   (2014-01-02 17:26)  Universidad Nacional de La Plata email

The authors performed an interesting work on the phasins of Bradyrhizobium japonicum (now renamed as B. diazoefficiens) USDA 110, and addressed the study of genes for polyhydroxyalkanoate (PHA) biosynthesis. However, in this part of their work they overlooked our article published in May, 2013 [1] where we performed a thoughtful characterization of the five PHA synthase (phaC) genes of USDA 110, and we described their functions in free-living and symbiotic bacterial states.

Thus, although Fig. 1 and Fig. 4A of the Yoshida et al. paper reproduce our results about these five genes, confusion might arise because Yoshida et al. gave different names to these genes than those previously assigned by us. For instance, the two more important PHA synthase genes, encoded in the ORFs bll4360 and bll6073, which we named previously as phaC1 and phaC2, appear in the Yoshida et al. paper as phbC3 and phbC5 respectively. On the one hand, we disagree with the use of the abbreviation “phb” because it seems to mean “polyhydroxybutyrate” (PHB) and in the absence of proof that the PHA produced by B. diazoefficiens USDA 110 is actually PHB, we favor the use of the more general abbreviation “pha”, as in the well-studied model in Ralstonia eutropha. On the other hand, we stand for a consistent use of gene names unless renaming them is justified to better illustrate their function (for instance, “phaR” for “phasin regulator”, instead of “aniA” for “anaerobically induced gene A”).

Moreover, we found no evidence of a “negative correlation between the rate of nitrogen fixation and PHB accumulation” that the authors, based on older literature, stated in the Introduction section. As discussed in our article [1], the hydrogenase activity of USDA 110 might explain at least in part this lack of negative correlation.

The authors compared growth and PHA production in YEM, TY and PSY media and concluded that PHA synthesis requires “conditions in which carbon sources are in excess relative to nitrogen sources”. Although YEM medium certainly has higher C/N ratio than TY or PSY media, extracting straightforward conclusions about bacterial metabolism from comparisons in three completely different complex media is, to our view, too risky and reductionist. Indeed, by using a unique minimal medium (Götz) where only the amount of N-source was varied, and where the extent of N-limitation was evaluated by growth and glutamine-synthetase activity measurements, we observed that PHA synthesis was actually prevented under C-excess and N-limitation [2, 3]. To stimulate PHA synthesis, growth had to be limited by a nutrient other than N, even when the C/N ratio of the culture medium was high (similar to YEM), thus indicating that the mere C/N ratio of the culture medium is not a faithful indicator of the direction of cell internal C-fluxes towards reserve or extracellular polymers.

 

References.

1. Quelas JI et al. (2013) J. Bacteriol. 195:3145-3155.

2. López-García SL et al. (2001) J. Bacteriol. 183: 7241-7252.

3. Quelas JI et al. (2006) Arch. Microbiol. 186:119-128.

Competing interests

I have no competing interests.

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