Publications

love the one you're with: replicate viral adaptations converge on the same phenotypic change.	parallelism is important because it reveals how inherently stochastic adaptation is. even as we come to better understand evolutionary forces, stochasticity limits how well we can predict evolutionary outcomes. here we sought to quantify parallelism and some of its underlying causes by adapting a bacteriophage (id11) with nine different first-step mutations, each with eight-fold replication, for 100 passages. this was followed by whole-genome sequencing five isolates from each endpoint. a large ...	2016	27547540
difference in c3-c4 metabolism underlies tradeoff between growth rate and biomass yield in methylobacterium extorquens am1.	two variants of methylobacterium extorquens am1 demonstrated a trade-off between growth rate and biomass yield. in addition, growth rate and biomass yield were also affected by supplementation of growth medium with different amounts of cobalt. the metabolism changes relating to these growth phenomena as well as the trade-off were investigated in this study. (13)c metabolic flux analysis was used to generate a detailed central carbon metabolic flux map with both absolute and normalized flux value ...	2016	27435978
metabolic footprint of epiphytic bacteria on arabidopsis thaliana leaves.	the phyllosphere, which is defined as the parts of terrestrial plants above the ground, is a large habitat for different microorganisms that show a high extent of adaption to their environment. a number of hypotheses were generated by culture-independent functional genomics studies to explain the competitiveness of specialized bacteria in the phyllosphere. in contrast, in situ data at the metabolome level as a function of bacterial colonization are lacking. here, we aimed to obtain new insights ...	2016	26305156
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
systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization.	plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. to gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upo ...	2016	27457762
selection maintains apparently degenerate metabolic pathways due to tradeoffs in using methylamine for carbon versus nitrogen.	microorganisms often encode multiple non-orthologous metabolic modules that catalyze the same reaction. however, little experimental evidence actually demonstrates a selective basis for metabolic degeneracy. many methylotrophs-microorganisms that grow on reduced single-carbon compounds-like methylobacterium extorquens am1 encode two routes for methylamine oxidation: the periplasmic methylamine dehydrogenase (madh) and the cytoplasmic n-methylglutamate (nmg) pathway. in methylobacterium extorquen ...	2016	27212407
calorespirometric feeding control enhances bioproduction from toxic feedstocks-demonstration for biopolymer production out of methanol.	the sustainable production of fuels and industrial bulk chemicals by microorganisms in biotechnological processes is promising but still facing various challenges. in particular, toxic substrates require an efficient process control strategy. methanol, as an example, has the potential to become a major future feedstock due to its availability from fossil and renewable resources. however, besides being toxic, methanol is highly volatile. to optimize its dosage during microbial cultivations, an in ...	2016	27043974
[functionality of the xoxf gene in methylobacterium dichloromethanicum dm4].	activation of expression of the xoxfgene encoding pqq-dependent methanol/ethanol dehydrogenase (metdi2492) in dichloromethane- (dcm) -grown methylobacterium dichloromethanicum dm4 was first demonstrated. the sequence of the only xoxf homolog found in the genome of strain dm4 exhibited 50% identity to that of the protein (mxaf) of the large subunit of methanol dehydrogenase (mdh). a knockout mutant with the inactivate xoxf gene (δxoxf) was found to be unable to grow on methanol due to the absence ...	2016	26964359
the one-carbon carrier methylofuran from methylobacterium extorquens am1 contains a large number of α- and γ-linked glutamic acid residues.	methylobacterium extorquens am1 uses dedicated cofactors for one-carbon unit conversion. based on the sequence identities of enzymes and activity determinations, a methanofuran analog was proposed to be involved in formaldehyde oxidation in alphaproteobacteria. here, we report the structure of the cofactor, which we termed methylofuran. using an in vitro enzyme assay and lc-ms, methylofuran was identified in cell extracts and further purified. from the exact mass and ms-ms fragmentation pattern, ...	2016	26895963
non-targeted determination of (13)c-labeling in the methylobacterium extorquens am1 metabolome using the two-dimensional mass cluster method and principal component analysis.	a novel analytical workflow is presented for the analysis of time-dependent (13)c-labeling of the metabolites in the methylotrophic bacterium methylobacterium extorquens am1 using gas chromatography time-of-flight mass spectrometry (gc-tofms). using (13)c-methanol as the substrate in a time course experiment, the method provides an accurate determination of the number of carbons converted to the stable isotope. the method also extracts a quantitative isotopic dilution time course profile for (13 ...	2016	26787164
associations between ectomycorrhizal fungi and bacterial needle endophytes in pinus radiata: implications for biotic selection of microbial communities.	studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. as such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. interactions between co ...	2016	27065966
bioconversion of methanol to value-added mevalonate by engineered methylobacterium extorquens am1 containing an optimized mevalonate pathway.	methylotrophic biosynthesis using methanol as a feedstock is a promising and attractive method to solve the over-dependence of the bioindustry on sugar feedstocks derived from grains that are used for food. in this study, we introduced and engineered the mevalonate pathway into methylobacterium extorquens am1 to achieve high mevalonate production from methanol, which could be a platform for terpenoid synthesis. we first constructed a natural operon (mve) harboring the mvas and mvae genes from en ...	2016	26521242
(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
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
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
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
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
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