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Nucleic Acids Research Dec 2020Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture...
Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.
Topics: Amino Acid Sequence; Catalytic Domain; Cryptochromes; DNA Damage; DNA Repair; DNA, Single-Stranded; Deoxyribodipyrimidine Photo-Lyase; Methylobacterium; Pyrimidine Dimers; Rhodobacteraceae; Ultraviolet Rays
PubMed: 33270891
DOI: 10.1093/nar/gkaa1147 -
Biomolecular NMR Assignments Oct 2016The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not...
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 substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD. PqqA is unstructured in solution, and only binds to PqqE when in complex with PqqD. PqqD is a member of a growing family of RiPP chaperone proteins (or domains in most cases) that present their associated peptide substrates to the initial RiPP biosynthesis enzymes. An X-ray crystal structure exists for dimeric Xanthomonas campestris PqqD (PDB ID: 3G2B), but PqqD is now known to act as a monomer under physiological conditions. In this study, the PqqD truncation from naturally fused Methylobacterium extorquens (Mex) PqqCD was overexpressed in Escherichia coli and MexPqqA was chemically synthesized. Solution NMR (1)H-,(15)N-HSQC chemical shift studies have identified the PqqD residues involved in binding PqqA, and (1)H, (13)C, and (15)N peak assignments for PqqD alone and for PqqD bound to PqqA are reported herein.
Topics: Amino Acid Sequence; Bacterial Proteins; Methylobacterium extorquens; Nuclear Magnetic Resonance, Biomolecular; PQQ Cofactor; Protein Structure, Secondary
PubMed: 27638737
DOI: 10.1007/s12104-016-9705-8 -
International Journal of Environmental... Jan 2021is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa....
is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa. In hyperaccumulators, metal detoxification has also been linked or attributed to the activities of endophytes, and, in this regard, metal detoxification can be considered a form of endophytic behavior. Therefore, we report herein on the identification of proteins that confer heavy metal resistance, the in vitro characterization of heavy metal resistance, and the production of plant growth-promoting (PGP) volatiles by MAMP 4754. Multigenome comparative analyses of MAMP 4754 against eight other endophytic strains led to the identification of zinc, copper, and nickel resistance proteins in the genome of this endophyte. The maximum tolerance concentration (MTC) of this strain towards these metals was also investigated. The metal-exposed cells were analyzed by transmission electron microscopy (TEM). The ethyl acetate and chloroform extracts (1:1 /) of heavy metal untreated MAMP 4754 were also screened for the production of PGP compounds by Gas Chromatography-Mass Spectroscopy (GC/MS). The MTC was recorded at 15 mM, 4 mM, and 12 mM for zinc, copper, and nickel, respectively. The TEM analysis showed the accumulation of metals in the intracellular environment of MAMP 4754, while the GC/MS analysis revealed several plant growth-promoting compounds, including alcohols, phthalate esters, alkenes, ketones, sulfide derivatives, phenols, and thiazoles. Our findings suggest that the genetic makeup of MAMP 4754 encodes heavy metal resistant proteins that indicate hyperaccumulator-specific endophytic behavior and the potential for application in bioremediation. The production of plant growth-promoting volatiles in pure culture by MAMP 4754 is a characteristic feature for plant growth-promoting bacteria.
Topics: Combretum; Genomics; Metals, Heavy; Methylobacterium; Soil Pollutants; South Africa
PubMed: 33498657
DOI: 10.3390/ijerph18030997 -
Frontiers in Microbiology 2015Rhizobiales (Alphaproteobacteria) are well-known beneficial partners in plant-microbe interactions. Less is known about the occurrence and function of Rhizobiales in the...
Rhizobiales (Alphaproteobacteria) are well-known beneficial partners in plant-microbe interactions. Less is known about the occurrence and function of Rhizobiales in the lichen symbiosis, although it has previously been shown that Alphaproteobacteria are the dominating group in growing lichen thalli. We have analyzed the taxonomic structure and assigned functions to Rhizobiales within a metagenomic dataset of the lung lichen Lobaria pulmonaria L. One third (32.2%) of the overall bacteria belong to the Rhizobiales, in particular to the families Methylobacteriaceae, Bradyrhizobiaceae, and Rhizobiaceae. About 20% of our metagenomic assignments could not be placed in any of the Rhizobiales lineages, which indicates a yet undescribed bacterial diversity. SEED-based functional analysis focused on Rhizobiales and revealed functions supporting the symbiosis, including auxin and vitamin production, nitrogen fixation and stress protection. We also have used a specifically developed probe to localize Rhizobiales by confocal laser scanning microscopy after fluorescence in situ hybridization (FISH-CLSM). Bacteria preferentially colonized fungal surfaces, but there is clear evidence that members of the Rhizobiales are able to intrude at varying depths into the interhyphal gelatinous matrix of the upper lichen cortical layer and that at least occasionally some bacteria also are capable to colonize the interior of the fungal hyphae. Interestingly, the gradual development of an endosymbiotic bacterial life was found for lichen- as well as for fungal- and plant-associated bacteria. The new tools to study Rhizobiales, FISH microscopy and comparative metagenomics, suggest a similar beneficial role for lichens than for plants and will help to better understand the Rhizobiales-host interaction and their biotechnological potential.
PubMed: 25713563
DOI: 10.3389/fmicb.2015.00053 -
PLoS Biology May 2021Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in...
Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.
Topics: Bacteria; Formaldehyde; Methylobacterium; Methylobacterium extorquens; Stress, Physiological
PubMed: 34038406
DOI: 10.1371/journal.pbio.3001208 -
PloS One 2023A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis...
A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.
Topics: Zea mays; Saccharum; Methylobacterium; RNA, Ribosomal, 16S; Edible Grain; Phylogeny
PubMed: 36749783
DOI: 10.1371/journal.pone.0281505 -
Internal Medicine (Tokyo, Japan) 2012A 48-year-old man was admitted with cloudy dialysate and diagnosed as peritoneal dialysis (PD)-related peritonitis caused by Roseomonas infection. This is the third case... (Review)
Review
A 48-year-old man was admitted with cloudy dialysate and diagnosed as peritoneal dialysis (PD)-related peritonitis caused by Roseomonas infection. This is the third case of PD-related peritonitis due to Roseomonas species and also the first case of peritonitis in automated peritoneal dialysis. Despite its low virulence and rare incidence in peritoneal dialysis, clinicians should be alert to the possibility of Roseomonas infection due to its high resistance to antibiotics. Literature on Roseomonas infection is also reviewed. The current guidelines for empirical peritonitis in PD patients do not adequately cover such infection. Refractory treatment in high risk cases should alert clinicians to upgrade antibiotics even for a vague manifestation.
Topics: Aged; Anti-Bacterial Agents; Ciprofloxacin; Female; Gentamicins; Gram-Negative Bacterial Infections; Humans; Male; Methylobacteriaceae; Middle Aged; Peritoneal Dialysis; Peritonitis; Risk Factors
PubMed: 22790133
DOI: 10.2169/internalmedicine.51.6737 -
Applied and Environmental Microbiology Mar 2017The genetic diversity of bacterial populations nodulating in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on...
The genetic diversity of bacterial populations nodulating in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on partial sequences of and grouped strains into seven clusters, five of which belong to the genus (28 isolates), one to (2 isolates), and one, remarkably, to (20 isolates). The largest cluster (17 isolates) grouped with the species, and the other five clusters were close to different recently defined species. Isolates close to were obtained from nodules of plants from four of the five sites sampled. We carried out an in-depth phylogenetic study with representatives of the seven clusters using sequences from housekeeping genes (, , , , and ) and obtained consistent results. A phylogeny based on the sequence of the symbiotic gene identified four groups, three formed by isolates and one by the and isolates. Symbiotic behaviors of the representative strains were tested, and some congruence between symbiovars and symbiotic performance was observed. These data indicate a remarkable diversity of root nodule symbionts in northern Tunisia, including strains from the , , and families, in contrast with those of the rhizobial populations nodulating lupines in the Old World, including from other Mediterranean areas, which are nodulated mostly by strains. is a legume broadly distributed in the Mediterranean region and plays an important role in soil fertility and vegetation coverage by fixing nitrogen and solubilizing phosphate in semiarid areas. Direct sowing to extend the distribution of this indigenous legume can contribute to the prevention of soil erosion in pre-Saharan lands of Tunisia. However, rhizobial populations associated with are poorly understood. In this context, the diversity of endosymbionts of this legume was investigated. Most species are nodulated by strains. This work showed that about half of the isolates from northern Tunisian soils were in fact symbionts, but the other half were found unexpectedly to be bacteria within the genera and These unusual endosymbionts may have a great ecological relevance. Inoculation with the appropriate selected symbiotic bacterial partners will increase survival with consequent advantages for the environment in semiarid areas of Tunisia.
Topics: Biodiversity; Bradyrhizobium; DNA Gyrase; DNA, Bacterial; Genes, Essential; Lupinus; Methylobacteriaceae; Phyllobacteriaceae; Phylogeny; Plant Root Nodulation; RNA, Ribosomal, 16S; Rec A Recombinases; Root Nodules, Plant; Soil Microbiology; Symbiosis; Tunisia
PubMed: 28062461
DOI: 10.1128/AEM.02820-16 -
Biochemistry Feb 2018The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond...
The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.
Topics: Bacterial Proteins; Crystallography, X-Ray; Electron Spin Resonance Spectroscopy; Endopeptidases; Iron-Sulfur Proteins; Methylobacterium extorquens; Models, Molecular; Protein Conformation; Temperature
PubMed: 29405700
DOI: 10.1021/acs.biochem.7b01097 -
Oxygen diffusion pathways in mutated forms of a LOV photoreceptor from : A molecular dynamics study.Biomolecular Concepts Mar 20224511 from is a photoreceptor of the light, oxygen voltage (LOV) family, binding flavin mononucleotide (FMN) as a chromophore. It exhibits the prototypical LOV...
4511 from is a photoreceptor of the light, oxygen voltage (LOV) family, binding flavin mononucleotide (FMN) as a chromophore. It exhibits the prototypical LOV photocycle, with the reversible formation of an FMN-Cys71 adduct via fast decay of the FMN triplet state. 4511 has high potential as a photosensitiser for singlet oxygen (SO) upon mutation of C71. 4511-C71S shows a triplet lifetime ( ) of several hundreds of microseconds, ensuring efficient energy transfer to dioxygen to form SO. In this work, we have explored the potential diffusion pathways for dioxygen within 4511 using molecular dynamics (MD) simulations. The structural model of wild-type (wt) 4511 showed a dimeric structure stabilised by a strong leucine zipper at the two C-terminal helical ends. We then introduced the C71S mutation and analysed transient and persistent oxygen channels. MD simulations indicate that the chromophore binding site is highly accessible to dioxygen. Mutations that might favour SO generation were designed based on their position with respect to FMN and the oxygen channels. In particular, the C71S-Y61T and C71S-Y61S variants showed an increased diffusion and persistence of oxygen molecules inside the binding cavity.
Topics: Flavin Mononucleotide; Methylobacterium; Molecular Dynamics Simulation; Oxygen
PubMed: 35334189
DOI: 10.1515/bmc-2022-0013