genomic species are ecological species as revealed by comparative genomics in agrobacterium tumefaciens.the definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remains largely unknown. we used the agrobacterium tumefaciens species complex, and particularly the genomic species presently called genomovar g8, which includes the sequenced strain c58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciati ...201121795751
analysis of hydroxycinnamic acid degradation in agrobacterium fabrum reveals a coenzyme a-dependent, beta-oxidative deacetylation pathway.the soil- and rhizosphere-inhabiting bacterium agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme a (feruloyl-coa), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl-coa, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl-coa, vanillic acid, and protocatechuic acid. the genes atu1416, atu14 ...201424657856
the identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic living organisms, the conversion of urate into allantoin requires three consecutive enzymes. the pathway was lost in hominid, predisposing humans to hyperuricemia and gout. among other species, the genomic distribution of the two last enzymes of the pathway is wider than that of urate oxidase (uox), suggesting the presence of unknown genes encoding uox. here we combine gene network analysis with association rule learning to identify the missing urate oxidase. in contrast with the known solubl ...201526349049
coordinated regulation of species-specific hydroxycinnamic acid degradation and siderophore biosynthesis pathways in agrobacterium fabrum.the rhizosphere-inhabiting species agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (hcas), especially ferulic acid and p-coumaric acid, via the novel a. fabrum hca degradation pathway. gene expression profiles of a. fabrum strain c58 were investigated in the presence of hcas, using a c58 whole-genome oligoarray. both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the c58 g ...201627060117
single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the agrobacterium/rhizobium supercluster characterized by the presence of a linear chromid.linear chromosomes are atypical in bacteria and likely a secondary trait derived from ancestral circular molecules. within the rhizobiaceae family, whose genome contains at least two chromosomes, a particularity of agrobacterium fabrum (formerly a. tumefaciens) secondary chromosome (chromid) is to be linear and hairpin-ended thanks to the tela protelomerase. linear topology and tela distributions within this bacterial family was screened by pulse field gel electrophoresis and pcr. in a. rubi, a. ...201424440816
the abundance of endofungal bacterium rhizobium radiobacter (syn. agrobacterium tumefaciens) increases in its fungal host piriformospora indica during the tripartite sebacinalean symbiosis with higher plants.rhizobium radiobacter (syn. agrobacterium tumefaciens, syn. "agrobacterium fabrum") is an endofungal bacterium of the fungal mutualist piriformospora (syn. serendipita) indica (basidiomycota), which together form a tripartite sebacinalean symbiosis with a broad range of plants. r. radiobacter strain f4 (rrf4), isolated from p. indica dsm 11827, induces growth promotion and systemic resistance in cereal crops, including barley and wheat, suggesting that r. radiobacter contributes to a successful ...201728450855
a novel aerobic degradation pathway for thiobencarb is initiated by the tmoab two-component flavin mononucleotide-dependent monooxygenase system in acidovorax sp. strain t1.thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. however, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. in this study, a novel thiobencarb degradation pathway was proposed in acidovorax sp. strain t1. thiobencarb was oxidized and cleaved at the c-s bond, generating diethylcarbamothioic s-acid and 4-chlorobenzaldehyde (4cda). 4cda w ...201728939603
small rna deep-sequencing analyses reveal a new regulator of virulence in agrobacterium fabrum c58.novel ways of regulating ti plasmid functions were investigated by studying small rnas (srnas) that are known to act as posttranscriptional regulators in plant pathogenic bacteria. srna-seq analyses of agrobacterium fabrum c58 allowed us to identify 1,108 small transcripts expressed in several growth conditions that could be srnas. a quarter of them were confirmed by bioinformatics or by biological experiments. antisense rnas represent 24% of the candidates and they are over-represented on the p ...201526024442
key amino acids in the bacterial (6-4) photolyase phrb from agrobacterium fabrum.photolyases can repair pyrimidine dimers on the dna that are formed during uv irradiation. phrb from agrobacterium fabrum represents a new group of prokaryotic (6-4) photolyases which contain an iron-sulfur cluster and a dmrl chromophore. we performed site-directed mutagenesis in order to assess the role of particular amino acid residues in photorepair and photoreduction, during which the fad chromophore converts from the oxidized to the enzymatically active, reduced form. our study showed that ...201526489006
spectroscopic investigation on the primary photoreaction of bathy phytochrome agp2-pr of agrobacterium fabrum: isomerization in a ph-dependent h-bond network.bathy phytochrome agp2 from agrobacterium fabrum exhibits an unusually low pka =7.6 in the pr state in contrast to a pka >11 in the pfr state, indicating a ph-dependent charge distribution and h-bond network in the pr chromophore binding pocket around neutral ph. here, we report on ultrafast uv/vis absorption spectroscopy of the primary pr photoisomerization of agp2 at ph 6 and ph 9 and upon h2 o/d2 o buffer exchange. the triexponential pr kinetics slows down at increased ph and pronounced ph-de ...201627075723
bacteriophytochromes control conjugation in agrobacterium fabrum.bacterial conjugation, the transfer of single stranded plasmid dna from donor to recipient cell, is mediated through the type iv secretion system. we performed conjugation assays using a transmissible artificial plasmid as reporter. with this assay, conjugation in agrobacterium fabrum was modulated by the phytochromes agp1 and agp2, photoreceptors that are most sensitive in the red region of visible light. in conjugation studies with wild-type donor cells carrying a pbin-gusint plasmid as report ...201627261700
the crystal structures of the n-terminal photosensory core module of agrobacterium phytochrome agp1 as parallel and anti-parallel dimers.agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium agrobacterium fabrum that acts as a light-regulated histidine kinase. crystal structures of the photosensory core modules (pcms) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (pr) and the far-red light-absorbing state (pfr). these changes include secondary structure rearrangemen ...201627466363
crystal structures of bacterial (6-4) photolyase mutants with impaired dna repair activity.phrb from agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) uv dna photoproducts. the protein harbors three cofactors: the enzymatically active fad chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (dmrl) and a cubane-type fe-s cluster. tyr424 of phrb is part of the dna-binding site and could provide an electron link to the fe-s cluster. the phrby424f mutant showed reduced binding of lesion dna and loss of dna repair. the mutant phrbi51w is characterize ...201727992645
divalent cations increase dna repair activities of bacterial (6-4) photolyases.the (6-4) photolyases of the fes-bcp group can be considered as the most ancient type among the large family of cryptochrome and photolyase flavoproteins. in contrast to other photolyases, they contain an fe-s cluster of unknown function, a dmrl chromophore, an interdomain loop, which could interact with dna, and a long c-terminal extension. we compared dna repair and photoreduction of two members of the fes-bcp family, agrobacterium fabrum phrb and rhodobacter sphaeroides rscryb, with a eukaryo ...201727992646
intersubunit distances in full-length, dimeric, bacterial phytochrome agp1, as measured by pulsed electron-electron double resonance (peldor) between different spin label positions, remain unchanged upon photoconversion.bacterial phytochromes are dimeric light-regulated histidine kinases that convert red light into signaling events. light absorption by the n-terminal photosensory core module (pcm) causes the proteins to switch between two spectrally distinct forms, pr and pfr, thus resulting in a conformational change that modulates the c-terminal histidine kinase region. to provide further insights into structural details of photoactivation, we investigated the full-length agp1 bacteriophytochrome from the soi ...201728289094
phytochromes from agrobacterium fabrum.agrobacterium fabrum is a widely used model bacterium for gene transfer from pro- to eukaryote, for genetics and metabolism. the phytochrome system of agrobacterium, encompassing the two phytochromes agp1 and agp2, has provided deep insight into phytochrome action in a bacterial organism. this review summarizes recent results on phytochrome evolution, phytochrome regulation of conjugation and plant infection and biochemical studies including the crystal structure of agp1-pcm, the photosensory co ...201728500698
structural and vibrational characterization of the chromophore binding site of bacterial phytochrome agp1.agp1 is a prototypical bacterial phytochrome from agrobacterium fabrum harboring a biliverdin cofactor which reversibly photoconverts between a red-light-absorbing (pr) and a far-red-light-absorbing (pfr) states. the reaction mechanism involves the isomerization of the bilin-chromophore followed by large structural changes of the protein matrix that are coupled to protonation dynamics at the chromophore binding site. histidines his250 and his280 participate in this process. although the three-di ...201728500721
the stringent response induced by phosphate limitation promotes purine salvage in agrobacterium fabrum.agrobacterium fabrum induces tumor growth in susceptible plant species. the upregulation of virulence genes that occurs when the bacterium senses plant-derived compounds is enhanced by acidic ph and limiting inorganic phosphate. nutrient starvation may also trigger the stringent response, and purine salvage is among the pathways expected to be favored under such conditions. we show here that phosphate limitation induces the stringent response, as evidenced by production of (p)ppgpp, and that the ...201729027458
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