Publications

pyrroloquinoline quinone ethanol dehydrogenase in methylobacterium extorquens am1 extends lanthanide-dependent metabolism to multicarbon substrates.	lanthanides are utilized by microbial methanol dehydrogenases, and it has been proposed that lanthanides may be important for other type i alcohol dehydrogenases. a triple mutant strain (mxaf xoxf1 xoxf2; named mdh-3), deficient in the three known methanol dehydrogenases of the model methylotroph methylobacterium extorquens am1, is able to grow poorly with methanol if exogenous lanthanides are added to the growth medium. when the gene encoding a putative quinoprotein ethanol dehydrogenase, exaf, ...	2016	27573017
(1)h, (13)c, and (15)n resonance assignments and secondary structure information for methylobacterium extorquens pqqd and the complex of pqqd with pqqa.	the ribosomally synthesized and post-translationally modified peptide (ripp), pyrroloquinoline quinone (pqq), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. ripps represent a rapidly expanding and diverse class of natural products-many of which have therapeutic potential-and the biosynthetic pathways for these are gaining attention. five gene products from the pqq operon (pqqa, pqqb, pqqc, pqqd, and pqqe) are essential for pqq biosynthesis. the subs ...	2016	27638737
mxay regulates the lanthanide-mediated methanol dehydrogenase switch in methylomicrobium buryatense.	many methylotrophs, microorganisms that consume carbon compounds lacking carbon-carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. the mxafi methanol dehydrogenase (mdh) contains calcium in its active site, while the xoxf enzyme contains a lanthanide in its active site. the genes encoding the mdh enzymes are differentially regulated by the presence of lanthanides. in this study, we found that the histidine kinase mxay controls the lanthani ...	2016	27651996
the opportunity for high-performance biomaterials from methane.	polyhydroxyalkanoate (pha) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. further, they are the only commodity polymer that can be synthesised intracellularly, ensuring stereoregularity and high molecular weight. however, despite offering enormous pot ...	2016	27681905
experimental horizontal gene transfer of methylamine dehydrogenase mimics prevalent exchange in nature and overcomes the methylamine growth constraints posed by the sub-optimal n-methylglutamate pathway.	methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic proteobacteria: methylamine dehydrogenase and the n-methylglutamate pathway. recent work suggests the n-methylglutamate (nmg) pathway may be more common in na ...	2015	27682079
interactions of methylotrophs with plants and other heterotrophic bacteria.	methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and co₂, the two most important greenhouse gases. this review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. methanol-utilizing methylotrophs ...	2015	27682083
parallel and divergent evolutionary solutions for the optimization of an engineered central metabolism in methylobacterium extorquens am1.	bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. here, we highlight experimental evolution as an effective means for optimizing an engineered methylobacterium extorquens am1. replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered methylobacterium, but growth rapidly recovered after s ...	2015	27682084
c₁-pathways in methyloversatilis universalis fam5: genome wide gene expression and mutagenesis studies.	methyloversatilis universalis fam5 utilizes single carbon compounds such as methanol or methylamine as a sole source of carbon and energy. expression profiling reveals distinct sets of genes altered during growth on methylamine vs methanol. as expected, all genes for the n-methylglutamate pathway were induced during growth on methylamine. among other functions responding to the aminated source of c₁-carbon, are a heme-containing amine dehydrogenase (qhp), a distant homologue of formaldehyde acti ...	2015	27682085
identification of unanticipated and novel n-acyl l-homoserine lactones (ahls) using a sensitive non-targeted lc-ms/ms method.	n-acyl l-homoserine lactones (ahls) constitute a predominant class of quorum-sensing signaling molecules used by gram-negative bacteria. here, we report a sensitive and non-targeted hplc-ms/ms method based on parallel reaction monitoring (prm) to identify and quantitate known, unanticipated, and novel ahls in microbial samples. using a hybrid quadrupole-high resolution mass analyzer, this method integrates ms scans and all-ion fragmentation ms/ms scans to allow simultaneous detection of ahl pare ...	2016	27706219
the diversity of citrus endophytic bacteria and their interactions with xylella fastidiosa and host plants.	the bacterium xylella fastidiosa is the causal agent of citrus variegated chlorosis (cvc) and has been associated with important losses in commercial orchards of all sweet orange [citrus sinensis (l.)] cultivars. the development of this disease depends on the environmental conditions, including the endophytic microbial community associated with the host plant. previous studies have shown that x. fastidiosa interacts with the endophytic community in xylem vessels as well as in the insect vector, ...	2016	27727362
adaptation in bacillus cereus: from stress to disease.	bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. after ingestion, b. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic ph in the stomach and changing oxygen conditions in the human intestine. b. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and m ...	2016	27757102
evolutionary switches between two serine codon sets are driven by selection.	serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. the res ...	2016	27799560
a mutational hotspot and strong selection contribute to the order of mutations selected for during escherichia coli adaptation to the gut.	the relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. the large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. we followed the emergence of intra-species diversity in a commensal escherichia coli strain that previously acqui ...	2016	27812114
production of 2-hydroxyisobutyric acid from methanol by methylobacterium extorquens am1 expressing (r)-3-hydroxybutyryl coenzyme a-isomerizing enzymes.	the biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-hiba) via bacterial poly-3-hydroxybutyrate (phb) overflow metabolism requires suitable (r)-3-hydroxybutyryl coenzyme a (coa)-specific coenzyme b12-dependent mutases (rcm). here, we characterized a predicted mutase from bacillus massiliosenegalensis jc6 as a mesophilic rcm closely related to the thermophilic enzyme previously identified in kyrpidia tusciae dsm 2912 (m.-t. weichler et al., appl environ ...	2017	27836853
control of wilt and rot pathogens of tomato by antagonistic pink pigmented facultative methylotrophic delftia lacustris and bacillus spp.	the studies on the biocontrol potential of pink pigmented facultative methylotrophic (ppfm) bacteria other than the genus methylobacterium are scarce. in the present study, we report three facultative methylotrophic isolates; ppo-1, ppt-1, and ppb-1, respectively, identified as delftia lacustris, bacillus subtilis, and bacillus cereus by 16s rrna gene sequence analysis. hemolytic activity was tested to investigate the potential pathogenicity of isolates to plants and humans, the results indicate ...	2016	27872630
biosensor-assisted transcriptional regulator engineering for methylobacterium extorquens am1 to improve mevalonate synthesis by increasing the acetyl-coa supply.	acetyl-coa is not only an important intermediate metabolite for cells but also a significant precursor for production of industrially interesting metabolites. methylobacterium extorquens am1, a model strain of methylotrophic cell factories using methanol as carbon source, is of interest because it produces abundant coenzyme a compounds capable of directing to synthesis of different useful compounds from methanol. however, acetyl-coa is not always efficiently accumulated in m. extorquens am1, as ...	2017	27919791
regulation of root development in arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria.	in numerous experimental studies, seedlings of the model dicot arabidopsis thaliana have been raised on sterile mineral salt agar. however, under natural conditions, no plant has ever grown in an environment without bacteria. here, we document that germ-free (gnotobiotic) seedlings, raised on mineral salt agar without sucrose, develop very short root hairs. in the presence of a soil extract that contains naturally occurring microbes, root hair elongation is promoted; this effect can be mimicked ...	2017	28054231
structure of methylobacterium extorquens malyl-coa lyase: coa-substrate binding correlates with domain shift.	malyl-coa lyase (mcl) is an mg(2+)-dependent enzyme that catalyzes the reversible cleavage of (2s)-4-malyl-coa to yield acetyl-coa and glyoxylate. mcl enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. here, the 1.56 å resolution x-ray crystal structure of mcl from methylobacterium extorquens am1 with bound mg(2+) is presented. structural alignment with the closely related rhodobac ...	2017	28177317
hopanoid-free methylobacterium extorquens dm4 overproduces carotenoids and has widespread growth impairment.	hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxi ...	2017	28319163