Caracterización de un Consorcio Microbiano Metanogénico de una Mina de Carbón en la Cuenca de Bogotá / Characterization of a Methanogenic Microbial Consortium from a Coal Mine in Bogotá Basin

RESUMEN En el trabajo se estudió un consorcio microbiano metanogénico de una mina de carbón de la cuenca de Bogotá en Colombia. Se establecieron cultivos de enriquecimiento de carbón ex situ para el crecimiento y la producción de gas de novo. El gas biogénico producido por los cultivos se analizó mediante cromatografía de gases con detectores de ionización de llama y conductividad térmica. Los cultivos se utilizaron para aislar estirpes microbianas y para generar bibliotecas del gene 16S rARN empleando de cebadores de bacteria y de arquea. El análisis de cromatografía de gases mostró producción de metano a 37 oC, pero no a 60 oC, donde el CO2 fue el componente principal del gas biogénico. El análisis de la secuencia del gen 16S rARN de estirpes microbianos y de las bibliotecas de clones, estableció que el consorcio microbiano metanogénico estuvo formado por especies de bacterias de los géneros Bacillus y Gracilibacter más la arquea del género Methanothermobacter. El consorcio microbiano metanogénico identificado es potencialmente responsable de la generación de gas biogénico en la mina de carbón La Ciscuda. Los resultados sugirieron que los metanógenos de este consorcio producían metano por vía hidrogenotrófica o de reducción de CO2.

ABSTRACT The work studied the methanogenic microbial consortium in a coal mine from the Bogotá basin in Colombia. Ex situ coal-enrichment cultures were established for in vitro growth and de novo gas production. Biogenic gas produced by cultures was analyzed by gas chromatography using thermal conductivity and flame ionization detectors. Cultures were used to isolate microbial specimens and to generate 16S rRNA gene libraries employing bacterial and archaeal primer sets. The gas chromatographic analysis showed methane production at 37 oC, but not at 60 oC, where CO2 was the major component of the biogenic gas. 16S rRNA gene sequence analysis of microbial isolates and clone libraries established that the methanogenic microbial consortium was formed by bacteria species from Bacillus and Gracilibacter genera plus archaea from the Methanothermobacter genus. This meth-anogenic microbial consortium was potentially responsible for biogenic gas generation in La Ciscuda coal mine. The results suggested that these methanogens produced methane by hydrogenotrophic or CO2 reduction pathways.

Recombination of chl-fus gene (Plastid Origin) downstream of hop: a locus of chromosomal instability.

BACKGROUND: The co-chaperone Hop [heat shock protein (HSP) organizing protein] has been shown to act as an adaptor for protein folding and maturation, in concert with Hsp70 and Hsp90. The hop gene is of eukaryotic origin. Likewise, the chloroplast elongation factor G (cEF-G) catalyzes the translocation step in chloroplast protein synthesis. The chl-fus gene, which encodes the cEF-G protein, is of plastid origin. Both proteins, Hop and cEF-G, derived from domain duplications. It was demonstrated that the nuclear chl-fus gene locates in opposite orientation to a hop gene in Glycine max. We explored 53 available plant genomes from Chlorophyta to higher plants, to determine whether the chl-fus gene was transferred directly downstream of the primordial hop in the proto-eukaryote host cell. Since both genes came from exon/module duplication events, we wanted to explore the involvement of introns in the early origin and the ensuing evolutionary changes in gene structure. RESULTS: We reconstructed the evolutionary history of the two convergent plant genes, on the basis of their gene structure, microsynteny and microcolinearity, from 53 plant nuclear genomes. Despite a high degree (72%) of microcolinearity among vascular plants, our results demonstrate that their adjacency was a product of chromosomal rearrangements. Based on predicted exon--intron structures, we inferred the molecular events giving rise to the current form of genes. Therefore, we propose a simple model of exon/module shuffling by intronic recombinations in which phase-0 introns were essential for domain duplication, and a phase-1 intron for transit peptide recruiting. Finally, we demonstrate a natural susceptibility of the intergenic region to recombine or delete, seriously threatening the integrity of the chl-fus gene for the future. CONCLUSIONS: Our results are consistent with the interpretation that the chl-fus gene was transferred from the chloroplast to a chromosome different from that of hop, in the primitive photosynthetic eukaryote, and much later before the appearance of angiosperms, it was recombined downstream of hop. Exon/module shuffling mediated by symmetric intron phases (i.e., phase-0 introns) was essential for gene evolution. The intergenic region is prone to recombine, risking the integrity of both genes.

Caracterización de actinobacterias raras, degradadoras de lignocelulosa: demostración de actividad lacasa en dos aislados de Tsukamurella sp y Cellulosimicrobium sp / Characterization of lignocellulose-degrading rare actinobacteria: demostration of laccase activity in two isolates of Tsukamurella sp and Cellulosimicrobium sp

Las características fisicoquímicas de la lignina y su compactación con la celulosa han dificultado la explotación biotecnológica de enormes cantidades de biomasa vegetal. Las lacasas constituyen una subfamilia de oxidasas multicobre que intervienen en la despolimerización de la lignina. Si bien han sido ampliamente caracterizadas en los hongos, los estudios de la diversidad y las funcionalidades de las lacasas en los procariotas se han centrado especialmente en isoformas enzimáticas de Streptomyces sp. En este trabajo se aislaron 20 cepas de actinobacterias del suelo. La actividad lacasa de 17 de ellas fue evidenciada en ensayos cualitativos con guayacol y dos cepas seleccionadas fueron caracterizadas en detalle. Las pruebas morfológicas y el análisis de las secuencias del gen 16S rRNA apuntan a que estos dos aislados pertenecen a los géneros Tsukamurella y Cellulosimicrobium. En cultivo sumergido con agitación, AC01 (Tsukamurella sp.) expresó una máxima actividad de oxidación de ABTS (2,2’-azino-bis-(3-etilbenzotiazolin-6-sulfonato) de 108 U/L. Por otra parte, AC18 (Cellulosimicrobium sp.) que había exhibido una actividad oxidativa de guayacol superior a las 16 cepas restantes y demostró ser resistente a niveles tóxicos de cobre, logró un valor máximo de oxidación del ABTS de 0,56 U/L. Estos resultados sugieren que en el aislado AC18 operaría un fenómeno de especificidad de sustrato o de inductor, regulador de la expresión y de la actividad lacasa cuantificable. La caracterización genómica y funcional de las lacasas de nuevas actinobacterias lignocelulósicas ampliará la gama de centros redox con aplicaciones biotecnológicas específicas, además de facilitar el establecimiento de sus relaciones evolutivas con las eucariotas.

The physicochemical characteristics of lignin and its compaction with cellulose have restricted the biotechnological exploitation of enormous amounts of plant biomass. Laccases are a subfamily of multicopper oxidases involved in lignin depolymerization. Although they have been extensively characterized in fungi, studies of the diversity and functions of laccases in prokaryotes are mainly on enzyme isoforms of Streptomyces sp. In this work we isolated 20 strains of soil actinomycetes. The laccase activity of 17 of them was evidenced in qualitative assays with guaiacol, and two selected strains were characterized in detail. The morphological evidence and the analysis of the 16S rRNA gene sequences suggest that these two isolates belong to the genera Tsukamurella and Cellulosimicrobium. In submerged cultures with shaking, AC01 (Tsukamurella sp.) exhibited a maximal oxidation activity of ABTS (2,2 '-azino-bis-(3-ethylbenzthiazoline-6-sulfonate) of 108 U/L. On the other hand, AC18 (Cellulosimicrobium sp.) that exhibited a higher oxidative activity of guaiacol than the other 16 isolated strains and showed resistance to toxic levels of copper, reached a maximum ABTS oxidation rate of 0.56 U/L. These results suggest that in AC18 operates a mechanism of substrate or inducer specificity, regulating the measurable laccase activity and laccase gene expression. Genomic and functional characterization of laccases of new ligninolytic actinomycetes may help to extend the range of redox centers with specific biotechnological applications, as well as establishing their evolutionary relationships with eukaryotes.

Gene pools in wild Lima bean (Phaseolus lunatus L.) from the Americas: evidences for an Andean origin and past migrations.

The aims of this research were to assess the genetic structure of wild Phaseolus lunatus L. in the Americas and the hypothesis of a relatively recent Andean origin of the species. For this purpose, nuclear and non-coding chloroplast DNA markers were analyzed in a collection of 59 wild Lima bean accessions and six allied species. Twenty-three chloroplast and 28 nuclear DNA haplotypes were identified and shown to be geographically structured. Three highly divergent wild Lima bean gene pools, AI, MI, and MII, with mostly non-overlapping geographic ranges, are proposed. The results support an Andean origin of wild Lima beans during Pleistocene times and an early divergence of the three gene pools at an age that is posterior to completion of the Isthmus of Panama and major Andean orogeny. Gene pools would have evolved and reached their current geographic distribution mainly in isolation and therefore are of high priority for conservation and breeding programs.

ITS-RFLP- and RAPD-based genetic variability of Trypanosoma cruzi I, human and vector strains in Santander, Colombia.

Chagas disease is a severe public health problem in Latin-American countries. In Colombia, the predominance of Trypanosoma cruzi I has been described in the literature, with a broad heterogeneity between strains. However, most of the studies carried out centered on isoenzyme analysis, with a smaller number that focus on other molecular methods. In this report, we discuss the results of a molecular analysis of T. cruzi I strains, isolated from the domestic cycle, from the department of Santander, one of the territorial divisions where the prevalence of infection is highest. Internal transcribed spacer-restriction fragment length polymorphism and random amplification of polymorphic DNA were used to characterize 16 strains from human and vector (Triatominae) hosts. The data reveal a clustering based on the biological origin. Human and vector strains grouped separately; however, three vector strains clustered together with human strains. These results indicate that genetic differences exist in the strains that infect both hosts. We conclude that T. cruzi I populations in the domestic cycle of transmission of Chagas disease in Santander are heterogeneous and are composed of different clones. The epidemiological and biological implications are discussed.

Sequence analyses reveal that a TPR-DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR-DP domains and prokaryotic GerD proteins.

The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR-DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR-DP domains.

Tandem duplications of a degenerated GTP-binding domain at the origin of GTPase receptors Toc159 and thylakoidal SRP.

The evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown. Therefore, sequences of GTPase proteins constituting the Arabidopsis thaliana translocon at the outer membrane of chloroplast (atToc) complexes were analyzed by means of HCA. In particular, atToc159 and related proteins (atToc132, atToc120, and atToc90) do not have proven homologues of prokaryotic or eukaryotic ancestry. We established that the three domains commonly referred to as A, G, and M originate from the GTPase G domain, tandemly repeated, and probably evolving toward an unstructured conformation in the case of the A domain. It resulted from this study a putative common ancestor for these proteins and a new domain definition, in particular the splitting of A into three domains (A1, A2, and A3), has been proposed. The family of Toc159, previously containing A. thaliana and Pisum sativum, has been extended to Medicago truncatula and Populus trichocarpa and it has been revised for Oryza sativa. They have also been compared to GTPase subunits involved in the cpSRP system. A distant homology has been revealed among Toc and cpSRP GTP-hydrolyzing proteins of A. thaliana, and repetitions of a GTPase domain were also found in cpSRP protein receptors, by means of HCA analysis.