Gabriela Guerrero

Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.

BackgroundComparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes.ResultsWe analyzed the genomic sequences of four fast growing Rhizobiales (Sinorhizobium meliloti, Agrobacterium tumefaciens, Mesorhizobium loti and Brucella melitensis). We made a comprehensive gene classification to define chromosomal orthologs, genes with homologs in other replicons such as plasmids, and those which were species-specific. About two thousand genes were predicted to be orthologs in each chromosome and about 80% of these were syntenic. A striking gene colinearity was found in pairs of organisms and a large fraction of the microsyntenic regions and operons were similar. Syntenic products showed higher identity levels than non-syntenic ones, suggesting a resistance to sequence variation due to functional constraints; also, an unusually high fraction of syntenic products contained membranal segments. Syntenic genes encode a high proportion of essential cell functions, presented a high level of functional relationships and a very low horizontal gene transfer rate. The sequence variability of the proteins can be considered the species signature in response to specific niche adaptation. Comparatively, an analysis with genomes of Enterobacteriales showed a different gene organization but gave similar results in the synteny conservation, essential role of syntenic genes and higher functional linkage among the genes of the microsyntenic regions.ConclusionSyntenic bacterial genes represent a commonly evolved group. They not only reveal the core chromosomal segments present in the last common ancestor and determine the metabolic characteristics shared by these microorganisms, but also show resistance to sequence variation and rearrangement, possibly due to their essential character. In Rhizobiales and Enterobacteriales, syntenic genes encode a high proportion of essential cell functions and presented a high level of functional relationships.

Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis

ABSTRACT Rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. Endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. We isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. Nine isolates were obtained, covering most known bean symbiont species, which belong to the Rhizobium and Sinorhizobium groups. The strains showed several large plasmids, except for a Sinorhizobium americanum isolate. Two strains, one Rhizobium phaseoli and one S. americanum strain, were thoroughly characterized. Optimal symbiotic performance was observed for both of these strains. The S. americanum strain showed biotin prototrophy when subcultured, as well as high pyruvate dehydrogenase (PDH) activity, both of which are key factors in maintaining optimal growth. The R. phaseoli strain was a biotin auxotroph, did not grow when subcultured, accumulated a large amount of poly-β-hydroxybutyrate, and exhibited low PDH activity. The physiology and genomes of these strains showed features that may have resulted from their lifestyle inside the seeds: stress sensitivity, a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, a homocitrate synthase (usually present only in free-living diazotrophs), a hydrogenase uptake cluster, and the presence of prophages. We propose that colonization by rhizobia and their presence in Phaseolus seeds may be part of a persistence mechanism that helps to retain and disperse rhizobial strains.

Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins

BackgroundChromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements.ResultsWe analyzed 7080 genes (five groups of 1416 orthologs each) from Rhizobiales species (S. meliloti, R. etli, and M. loti, plant symbionts; A. tumefaciens, a plant pathogen; and B. melitensis, an animal pathogen). We evaluated their phylogenetic relationships and observed three main topologies. The first, with closer association of R. etli to A. tumefaciens; the second with R. etli closer to S. meliloti; and the third with A. tumefaciens and S. meliloti as the closest pair. This was not unusual, given the close relatedness of these three species. We calculated the synonymous (dS) and nonsynonymous (dN) substitution rates of these orthologs, and found that informational and metabolic functions showed relatively low dN rates; in contrast, genes from hypothetical functions and cellular processes showed high dN rates. An alternative measure of sequence variability, percentage of changes by species, was used to evaluate the most specific proportion of amino acid residues from alignments. When dN was compared with that measure a high correlation was obtained, revealing that much of evolutive information was extracted with the percentage of changes by species at the amino acid level. By analyzing the sequence variability of orthologs with a set of five properties (polarity, electrostatic charge, formation of secondary structures, molecular volume, and amino acid composition), we found that physico-chemical characteristics of proteins correlated with specific functional roles, and association of species did not follow their typical phylogeny, probably reflecting more adaptation to their life styles and niche preferences. In addition, orthologs with low dN rates had residues with more positive values of polarity, volume and electrostatic charge.ConclusionsThese findings revealed that even when orthologs perform the same function in each genomic background, their sequences reveal important evolutionary tendencies and differences related to adaptation.This article was reviewed by: Dr. Purificación López-García, Prof. Jeffrey Townsend (nominated by Dr. J. Peter Gogarten), and Ms. Olga Kamneva.

Rhizobium etli bacteroids engineered for Vitreoscilla hemoglobin expression alleviate oxidative stress in common bean nodules that reprogramme global gene expression

The common bean (Phaseolus vulgaris L.)–Rhizobium etli symbiosis and crop productivity are highly affected by adverse environmental conditions that cause oxidative stress. Based on the improved symbiosis of common bean inoculated with engineered R. etli expressing the Vitreoscilla hemoglobin (VHb) (Ramírez et al., Mol Plant Microbe Interact 12:1008–1015, 1999), in this work we analyzed the effect of this strain in plants exposed to the herbicide paraquat (PQ) which generates oxidative stress. PQ-treated plants inoculated with the engineered (VHb) R. etli strain showed higher nitrogenase activity and ureide content than plants inoculated with the wild type strain. We performed microarray transcriptomic analysis to identify PQ-responsive genes in nodules elicited by engineered vs wild type strains. An evident reprogramming of the transcriptional profile was observed in PQ-treated nodules, and the global changes in gene expression were different between nodules elicited with each strain. The most relevant difference was the increased number of up-regulated PQ-responsive genes in wild type strain nodules as compared to VHb-expressing nodules. The majority of these genes were classified into biological processes/functional categories related to defense, response to abiotic stress or signaling, as revealed by Gene Ontology and MapMan analysis. Taken together our analysis suggests that the expression of VHb in R. etli bacteroids contributes to buffering the damage caused by increased reactive oxygen species, and this is reflected in nodule cells that showed decreased sensitivity to oxidative stress and response of stress-related genes. Biotechnological applications of VHb-expressing rhizobia inoculants could be further explored.

Cambios en la frontera Chcichimeca en la región centr-norte de la Nueva España durante el siglo XVI

Resumen. El limite que separo a los grupas indigenas cazadores y recolectores de la uina a M a del norte, con los pueblos sedentarios del centro y sur de Meaco, fue la linea formada por el cauce de los rios Lerma y Panuco. Los conquistadoras espanoles, en su afan de avanzar hacia el norte, se expandieron sobre estas temtonos tan peligrosos y deshabbdos, debido principalmente al descubrimiento de las grandes vetas mheras. onmero sn Zacateoas v lomo en Goanaiuato v San Luis Potosi: no obstante a lo atractivo de la reaion. tuvieron sue modificar ~. ,~ , .. . . su estratege expansonisla por medio de una polika de ocupaci0n teiiiorial a IfavBs oe a fundacmn de orferenies Ipos oe dseniamlentos. como fueran las villas. niisiones. presiaios centros mineros y pueblos de ind,os. ademas de nteiesarse m i s en la scg~ idao y defmsii Clm trajo como consecuencia qdo la linea fronteriza can los chich mecas Ibera denp~azindose cada ver iii6s al none. modificando0 en una frontera movil y comba t i .