Sunday, April 13, 2008

Bacillus coahuilensis : the genomical TexMex

After a long publication struggle, two articles from two close friends have finally been published: the description of novel species Bacillus coahuilensis by my former bacteriology teacher and former owner while doing my Social Service and actually the one to blame for my adscription to the lab I work in now, René Cerritos (a.k.a. Dr. Chapultepec) in the IJSEM Journal. The other is the publication of the complete genome sequence of the very same strain in PNAS by my former schoolmate, my former Represenant in the Universitary Council and beermate Luis Alcaraz (a.k.a. The Dude). Both are the product of a weird collaboration between the CINVESTAV and LANGEBIO in Iruapuato, the Texan universities of Rice and Houston and the institutes Biotechnology and Ecology in UNAM, where I'm at.

In short:

Cuatrociénegas Valley is in a 750 m basin above sea level in North Mexico, deep in the Chihuahuan Desert and formerly a coastal region during the Jurassic. It is characterized by the presence of many oligotrophic ponds in the middle of the desert supporting large bacterial communities, appearingly from a marine origin (as shown by Souza and Desnues), that have been studied by my labgroup leaded by Valeria Souza and Luis Eguiarte (the very same place where I'm conducting my Theses). Cerritos isolated many bacilli strains from one of the widest and shallowest pond (Churince's Laguna Grande) and found many moderately halophilic species (that tolerate slightly salty envirnoments). A novel aerobic strain (m44) belonged to a group of aquatic, moderatedly halophilic species (B .marisflavi, B. aquimaris, B. vietnamensis) , and could not grow on most sugar-contaning media (uncommon for the bacilli). The team in CINVESTAV sequenced the genome (leaded by Gaby Olmedo and Luis Herrera-Estrella) and Alcaraz anotated it. He also conducted most of the sequence analises, with some help of Siefert from Rice University, Putonti from the UofH and me, during our stay in Houston a year ago. The genome turned out to be the smallest genome within bacilli with 3.35 Mbp with many mobile elements.

The most important feature of B. coahuilensis is that this is the second mexican microbial genome sequenced to date (the two bacteria genomes sequenced in Mexico are Rhizobium etli by the CCG and this), but whose sequence has been analized in the light of ecology and evolution (remember Dobzhansky's maxima?), that is, the adaptations of a formerly marine lineage to an oligotrophic lentic environment.

That is, the sequence pointed towards an adaptation to growth within low-phosphorus environment: namely the presence of sulfoquinovose synthase (sdq1) that synthesises sulfolipids to replace membrane phospholipids (which constitute around 30% of the total phosphorus), never reported before outside chloroplasts and unicellular cyanobacteria. The CINVESTAV team looked into the membrane and corroborated its sulfolipid composition.

The genome also codes for a sensory bacteriorrhodopsin gene, reminiscent of its marine origin where they are very abundant (see work by Venter and Rusch). The expression analyses proved it to be constitutive and not -light dependent, suggesting it to be an adaptation to shallow-water irradiance exposure.

Analysing the enconded transmembrane importers is a good way to analyse what the organism is uptaking for the environment, that is, it's "feeding-habits". The family of Iron-Siderophore importers is overrerpresented in B. coahuilensis, a feature shared with other aquatic bacilli, suggesting that marine bacilli actively scavenge for iron. It also show a preference for the uptake of single aminoacids and not large polypeptides, with absolute requirement of 8 aa and partial of another 5, a feature shared by the aquatic, small-genome organism Minibacterium massiliensis.

This, taken together with the fact that it has the lowest number of genes involved in nitrogen cycle, together with the experimental evidence of being incapable of utilizing a wide variety of sugars, suggests that this organism is totally dependent of the rest of the community to live on, and has evolved from a primitive bacterial component of that community with specific adaptations for a novel environment.

I'm very proud of the product of this collaboration and expect to continue this way. And also very happy because from the moment of this publication on, The Dude is able to obtain its PhD!!!