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Off we go to Mexico!

November 27, 2011

Two weeks ago, I was on my way to Mexico at the invitation of the UNAM Centro de Ciencias Genómicas – the Genomic Sciences Centre of the National Autonomous University of Mexico.  It is located in Cuernavaca, a pleasant city an hour’s drive south of the capital, Mexico City. The CCG was celebrating its 30th anniversary with a conference that featured both invited and in-house speakers.  The programme is available on the CCG website, but I am also attaching a copy (CCG 30th Anniversary Symposium).  Thirty years ago, there was no such thing as “genomic sciences”, of course, and no CCG.  At that time, the centre was known as the Centre for Nitrogen Fixation Research (CIFN).  The founders, Rafael Palacios and Jaime Mora, developed this into a world-class institution with a special emphasis on rhizobium research.  Rhizobium etli was described there and became their focal organism.  It is a symbiont of the common bean, Phaseolus vulgaris, which is the most important legume in Mexican cuisine.

In its thirty years, the Centre has produced hundreds of publications in international journals, and made many significant contributions to our understanding of rhizobia and their symbiosis.  In 2003 they initiated an important innovation: an undergraduate degree programme in genomic sciences.  This very successful specialist course, one of rather few in the world, has attracted excellent students and is training the next generation of genomic researchers.  In 2004, the Centre became the CCG and broadened its remit, so research now includes the genomics of humans and human pathogens, among other things, although rhizobia remain an important strand.  Since this is a rhizobium blog, I have picked out some of the rhizobium papers that the CCG has published during 2011.

First is a paper I have already mentioned in this blog, a review of host specificity in which the authors propose the term “symbiovar”.  See my post of 26 October for more about this.

Rogel, M.A., Ormeño-Orrillo, E., and Martinez Romero, E. (2011) Symbiovars in rhizobia reflect bacterial adaptation to legumes. Systematic and Applied Microbiology 34: 96-104. DOI:  10.1016/j.syapm.2010.11.015

Next is a real genomics study, an analysis of genomic diversity in Rhizobium etli based on two complete and six draft genome sequences, all obtained at CCG.  The authors estimated recombination between strains, which was detectable but relatively low.  They also noted that CFN42, the type strain of the species, was the most distant of the genomes they examined.  In other words, in this case, the type is not very “typical”.  I was told, though, that this may be a reflection of the particular strains that were chosen for analysis, and there are in fact many other R. etli isolates that are more like CFN42.  From my point of view, it was interesting that the distance of some of these R. etli sequences from “our” R. leguminosarum 3841 was not much greater than some distances within R. etli.  Whether these sister species are truly separate or form parts of a continuum of genetic diversity remains an open question until we have more thorough sampling of the genomic space.

Acosta, J., Eguiarte, L., Santamaria, R., Bustos, P., Vinuesa, P., Martinez-Romero, E. et al. (2011) Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination. BMC Evolutionary Biology 11: 305. DOI:  10.1186/1471-2148-11-305

Plasmids have always been a favourite topic in Cuernavaca, and a couple of interesting papers continue this theme.  The first sheds new light on the functioning of repABC plasmids, which make up the majority of plasmids in the alphaproteobacteria.  RepA and RepB are actually partitioning proteins that ensure that each daughter cell receives a copy of the plasmid at cell division.  It is the RepC protein that controls replication, and this paper shows that, in the R. etli plasmid p42d, the repC gene is all that is necessary, because the origin of replication is located within the gene itself.  This is probably also true of other repABC plasmids.  The second paper describes a plasmid in a strain of Sinorhizobium fredii (GR64) isolated from a Phaseolus vulgaris bean nodule in Spain.  Parts of this plasmid resemble a section of the chromosome of Sinorhizobium sp. NGR234, while other parts look like regions of the plasmids p42a and p42d of R. etli CFN42.  The authors describe this as a chimeric plasmid, and propose a plausible story of its origin by recombination between S. fredii and R. etli parents.  This interesting example certainly illustrates gene transfer and recombination between these two genera, but I would make two points.  Firstly, NGR234 and CFN42 are certainly not the actual parents, or even closely related to them, because the sequences, while undoubtedly homologous, are substantially diverged, often by 20% or more, indicating many millions of years since a common ancestor.  Secondly, it is not trivial to reconstruct the ancestral sequences and the subsequent recombination events.  It is tempting to explain a new finding (GR64) in terms of data obtained earlier (CFN42 and NGR234), but if we had sequenced GR64 first, would we describe p42a and p42d as chimeric plasmids containing parts of an S. fredii plasmid?  Can we really say that mobile genes “belong” to the strain in which we first find them?

Cervantes-Rivera, R., Pedraza-Lopez, F., Perez-Segura, G., and Cevallos, M. (2011) The replication origin of a repABC plasmid. BMC Microbiology 11: 158. DOI:  10.1186/1471-2180-11-158

Cervantes, L., Bustos, P., Girard, L., Santamaria, R., Davila, G., Vinuesa, P. et al. (2011) The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain. BMC Microbiology 11: 149. DOI:  10.1186/1471-2180-11-149

Still on the plasmid theme, here are two more papers.  Both of these document genes on the two largest plasmids of R. etli CFN42, p42f and p42e, that are core genes of primary metabolism and carried on the chromosome in most other bacteria.  Hence, they provide specific support for the idea of a “chromid”, which was put forward by my student Peter Harrison in his PhD studies (Harrison, P.W., Lower, R.P.J., Kim, N.K.D., and Young, J.P.W. (2010) Introducing the bacterial chromid: not a chromosome, not a plasmid. Trends in Microbiology 18: 141-148. DOI:  10.1016/j.tim.2009.12.010).  Chromids are plasmids that have become chromosome-like by the acquisition of core genes, and Peter included p42f and p42e in his list of chromids.  Furthermore, related chromids are usually found throughout a genus, and both these papers point out that the equivalent replicons in other Rhizobium genomes also have these genes.

Landeta, C., Dávalos, A., Cevallos, M.Á., Geiger, O., Brom, S., and Romero, D. (2011) Plasmids with a Chromosome-Like Role in Rhizobia. Journal of Bacteriology 193: 1317-1326. DOI:  10.1128/jb.01184-10

Villasenor, T., Brom, S., Davalos, A., Lozano, L., Romero, D., and los Santos, A. (2011) Housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in Rhizobium etli and Rhizobium leguminosarum. BMC Microbiology 11: 66. DOI:  10.1186/1471-2180-11-66

Moving from plasmids to metabolism, here is a bunch of papers about gene regulation and enzyme function.

Vences-Guzmán, M.Á., Guan, Z., Ormeño-Orrillo, E., González-Silva, N., López-Lara, I.M., Martínez-Romero, E. et al. (2011) Hydroxylated ornithine lipids increase stress tolerance in Rhizobium tropici CIAT899. Molecular Microbiology 79: 1496-1514. DOI:  10.1111/j.1365-2958.2011.07535.x

Dunn, M. (2011) Anaplerotic Function of Phosphoenolpyruvate Carboxylase in Bradyrhizobium japonicum USDA110. Current Microbiology 62: 1782-1788. DOI:  10.1007/s00284-011-9928-y

Gómez-Hernández, N., Reyes-González, A., Sánchez, C., Mora, Y., Delgado, M.J., and Girard, L. (2011) Regulation and Symbiotic Role of nirK and norC Expression in Rhizobium etli. Molecular Plant-Microbe Interactions 24: 233-245. DOI:  10.1094/mpmi-07-10-0173

Díaz, R., Vargas-Lagunas, C., Villalobos, M.A., Peralta, H., Mora, Y., Encarnación, S. et al. (2011) argC Orthologs from Rhizobiales Show Diverse Profiles of Transcriptional Efficiency and Functionality in Sinorhizobium meliloti. Journal of Bacteriology 193: 460-472. DOI:  10.1128/jb.01010-10

Finally, here is a systems biology paper that constructs a model of the metabolism of R. etli CFN42 when it is fixing nitrogen inside a bean nodule.  Data from gene expression microarrays and proteomics are used to guide the model.

Resendis-Antonio, O., Hernandez, M., Salazar, E., Contreras, S., Batallar, G., Mora, Y., and Encarnacion, S. (2011) Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling. BMC Systems Biology 5: 120. DOI:  10.1186/1752-0509-5-120

These recent papers give a flavour of the rhizobium studies at CCG.  During the conference, we heard more about this work and the directions that it is now taking.  The CCG has never been very large, but it has a strong “family” atmosphere and has proved very stable.  Indeed, about twenty of the original staff who were there thirty years ago when the CIFN opened are still working in the CCG today.  It is clear that we can expect the output of significant research achievements to continue unabated into the future.  Thank you, CCG!

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From → Genomics, Papers

3 Comments
  1. Claudia Silva permalink

    I want to add a commentary on the comment about the interpretation of the data of the chimeric plasmid of GR64. The point raised about the assignment of recombinant DNA regions of strains to “parent strains” is very important. I think that in many studies the recombination evidences based on the strains available are taken “too literally”. For example, the output of some programs used to detect recombination within a sample (such as RDP3) is a list of recombinant strains and their respective “parental strains”. As in the case of GR64, these parental strains are probably not the actual parents, they may represent the lineages related of the original parental strains that actually were engaged in recombination.
    It was a pleasure to have Peter in Mexico,
    Thanks,
    Claudia Silva

  2. Thanks, Claudia! You reinforce my first point, which is that when we postulate natural recombination events, we rarely have available the exact parents. Instead, we may have “cousins” of those parents that have a similar gene arrangement. My second point is also important: it is often not clear which is “parent” and which is “recombinant”. For example, if we found sequences ABCDEF and ABCJKL, where ABC are homologs but the other genes are unrelated, we can justifiably postulate a recombination breakpoint after gene C. If we already have a sequence GHIJKL, we can be tempted to describe ABCJLK as a recombinant between the parents ABCDEF and GHIJKL, as the authors do for GR64. If, on the other hand, we had not found GHIJKL but MNODEF, then we might think that ABCDEF was the recombinant, and its parents were ABCJKL and MNODEF. These few sequences alone do not provide enough information for us to reconstruct history. This requires many more sequences and/or other information such as historical distributions (e.g. records of the spread of bean cultivation).

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