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Additional file 5 Complementation of DXR-deficient E. Coli cells with putative DXR-II sequences from Chloroflexus auranticus J-10-fl. The putative DXR-II sequences were PCR-amplified from genomic DNA and cloned into pJET1.2. The corresponding constructs and positive and negative controls (C-, empty vector; C+, DXR-II () from B. Melitensis biovar abortus 2308) were used to transform EcAB4-10 cells []. Ability of the cloned gene to rescue growth of this DXR-deficient mutant strain was ascertained by monitoring growth on plates either supplemented (+) or not (−) with 1 mM MVA as indicated.

1), 2), and 3). Additional file 6 Table S1. List of amino acid sites detected as related to functional divergence of DXR-II vs DLO1 and DXR-II vs DLO2. List of sequences used as queries in BLAST searches for enzymes of the MEP, MVA and CP pathway, and the corresponding bacterial strain. Distribution of enzymes of the MEP, MVA and the CP pathways across 128 whole sequenced bacterial strains. GC content of DXR-II genes and corresponding genomes.

May 18, 2009 - Institute of Plant Breeding, Genetics & Genomics. Buchanan et al. Biochemistry & Molecular Biology of Plants. American Society of.

3:1 relative dinucleotide frequencies at DXR-II genes and their corresponding genomes and statistical tests of co-variation. RSCU values at DXR-II genes and their corresponding genomes and statistical tests of independence. CAI values for DXR-II genes and the average for all genes in the corresponding genomes.

Results Searches through 1498 bacterial complete proteomes detected 130 sequences with similarity to DXR-II. Phylogenetic analysis identified three well-resolved clades: the DXR-II family (clustering 53 sequences including eleven experimentally verified as functional enzymes able to produce MEP), and two previously uncharacterized NAD(P)-dependent oxidoreductase families (designated DLO1 and DLO2 for DXR-II-like oxidoreductases 1 and 2). Our analyses identified amino acid changes critical for the acquisition of DXR-II biochemical function through type-I functional divergence, two of them mapping onto key residues for DXR-II activity.

DXR-II showed a markedly discontinuous distribution, which was verified at several levels: taxonomic (being predominantly found in Alphaproteobacteria and Firmicutes), metabolic (being mostly found in bacteria with complete functional MEP pathways with or without DXR-I), and phenotypic (as no biological/phenotypic property was found to be preferentially distributed among DXR-II-containing strains, apart from pathogenicity in animals). By performing a thorough comparative sequence analysis of GC content, 3:1 dinucleotide frequencies, codon usage and codon adaptation indexes (CAI) between DXR-II sequences and their corresponding genomes, we examined the role of horizontal gene transfer (HGT), as opposed to an scenario of massive gene loss, in the evolutionary origin and diversification of the DXR-II subfamily in bacteria. Conclusions Our analyses support a single origin of the DXR-II family through functional divergence, in which constitutes an exceptional model of acquisition and maintenance of redundant gene functions between non-homologous genes as a result of convergent evolution. Subsequently, although old episodic events of HGT could not be excluded, the results supported a prevalent role of gene loss in explaining the distribution of DXR-II in specific pathogenic eubacteria. Pioneer virtual dj free download. Our results highlight the importance of the functional characterization of evolutionary shortcuts in isoprenoid biosynthesis for screening specific antibacterial drugs and for regulating the production of isoprenoids of human interest. Background Isoprenoids constitute the largest family of natural compounds both at a structural and functional level [-]. They are found in all the three domains of life (bacteria, archaea, and eukaryotes).

Despite their diversity in structures and functions, all isoprenoids derive from the common five-carbon precursors isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). IPP can be synthesized through two independent metabolic pathways, the mevalonate (MVA) pathway, or the more recently elucidated methylerythritol 4-phosphate (MEP) pathway [] (Figure ). In most eubacteria, isoprenoids are synthesized through the MEP pathway, while a few species use the MVA pathway, both pathways, or none, the latter obtaining their isoprenoids from host cells [-]. Previous analysis suggested that eukaryotes have inherited MEP and MVA pathways genes from eubacteria and archaebacteria, respectively, as reflected by their phylogenetic distribution []. In plants, plastidial IPP and DMAPP are synthesized through the MEP pathway, whereas cytosolic and mitochondrial isoprenoids are synthesized through the MVA pathway [,].