b6ims1 rhodospirillum centenum  (ATCC)

Journal: BMC Microbiology

Article Title: The photosensor protein Ppr of Rhodocista centenaria is linked to the chemotaxis signalling pathway

doi: 10.1186/1471-2180-10-281

Figure Lengend Snippet: Domain structure of the Ppr photosensor protein of R. centenaria . The Ppr protein consists of a photoactive yellow protein domain (Pyp; residues 1-135) which carries the blue light absorbing chromophore p -hydroxycinnamic acid, a central bacteriophytochrome bilin binding domain (residues 136-601) with the red light absorbing biliverdin chromophore, and a histidine kinase domain (Pph; residues 602-884). The truncated Pph protein consists of the histidine kinase domain (residues 602-884). In the mutant Pph H670A the putative autophosphorylated histidine residue (H670) is replaced by an alanine.

Article Snippet: R. centenaria (ATCC 43720) was obtained from the culture collection. (For anaerobic photosynthetic growth R. centenaria was cultured in screw cap bottles filled to the top with PYVS medium [ ] and illuminated by an 80 W tungsten bulb (Concentra, Osram, Germany) at 42°C.

Techniques: Binding Assay, Mutagenesis

Journal: BMC Microbiology

Article Title: The photosensor protein Ppr of Rhodocista centenaria is linked to the chemotaxis signalling pathway

doi: 10.1186/1471-2180-10-281

Figure Lengend Snippet: Interaction between Pph and the chemotactic protein Rc-CheW. (A) The binding of the histidine kinase domain Pph and CheW was analyzed in pull-down assays. R. centenaria 6his-Rc-CheW was expressed in E. coli C41 cells and purified. The Pph protein was translated in vitro in the presence of [ 35 S]-methionine (lane 1 and 4). Rc-CheW was added (50 μg) to the reaction and incubated at 37°C. The sample was applied to a Cu-Sepharose column and after washing the bound complexes were eluted (lanes 3 and 6). The fractions were analysed by phosphorimaging. The in vitro translating protein extracts are shown in lanes 1 and 4, the final wash steps in lanes 2 and 5 and the elution fractions in lanes 3 and 6, respectively. The co-elution rate was calculated and is indicated. The positions of molecular weight markers are indicated. (B) The binding of the Pph protein and Rc-CheW was analysed in the presence of ATP. The Pph protein was translated and Rc-CheW was added as described in (A). ATP or apyrase was added to each reaction as indicated and the samples were analysed as described in (A). The co-elution rate was calculated and is indicated in % as bound Pph protein.

Article Snippet: R. centenaria (ATCC 43720) was obtained from the culture collection. (For anaerobic photosynthetic growth R. centenaria was cultured in screw cap bottles filled to the top with PYVS medium [ ] and illuminated by an 80 W tungsten bulb (Concentra, Osram, Germany) at 42°C.

Techniques: Binding Assay, Purification, In Vitro, Incubation, Co-Elution Assay, Molecular Weight

Journal: BMC Microbiology

Article Title: The photosensor protein Ppr of Rhodocista centenaria is linked to the chemotaxis signalling pathway

doi: 10.1186/1471-2180-10-281

Figure Lengend Snippet: Oligomeric state of the histidine kinase Pph. (A) Alignment of the dimerization domains of the Pph protein from R. centenaria and EnvZ from E. coli . The identity was 27% whereas the similarity was calculated with about 57%. The alignment was performed with the Clustal X software. (B) Purified Pph was analysed by gel filtration on a Sephadex G-200 column. Aliquots of the elution fractions (39-48) were separated by SDS-PAGE and blotted on a nitrocellulose membrane. The Pph protein was detected with a conjugate raised against the C-terminal StrepTag II. The position of the Pph protein is indicated. The following proteins werde used as molecular weight markers: β-amylase (200 kDa), alcohol dehydrogenase (150 kDa), albumin (66 kDa), carboanhydrase (29 kDa) and cytochrome c (12 kDa) were used.

Article Snippet: R. centenaria (ATCC 43720) was obtained from the culture collection. (For anaerobic photosynthetic growth R. centenaria was cultured in screw cap bottles filled to the top with PYVS medium [ ] and illuminated by an 80 W tungsten bulb (Concentra, Osram, Germany) at 42°C.

Techniques: Software, Purification, Filtration, SDS Page, Molecular Weight

Journal: BMC Microbiology

Article Title: The photosensor protein Ppr of Rhodocista centenaria is linked to the chemotaxis signalling pathway

doi: 10.1186/1471-2180-10-281

Figure Lengend Snippet: Protein complexes containing Pph isolated from R. centenaria . The Pph protein C-terminally fused to a strep-tag was expressed in R. centenaria and bound to a streptactin-Sepharose column. The elution fractions were analyzed by SDS-PAGE, silver staining (A) and Western blot with antibodies to strep-tag II (B) or to Rc-CheW (C), respectively. The crude protein extract (lanes 1 and 4), the last washing step (lanes 2 and 5) as well as the elution step (lanes 3 and 6) are shown. The positions of molecular weight markers are indicated.

Article Snippet: R. centenaria (ATCC 43720) was obtained from the culture collection. (For anaerobic photosynthetic growth R. centenaria was cultured in screw cap bottles filled to the top with PYVS medium [ ] and illuminated by an 80 W tungsten bulb (Concentra, Osram, Germany) at 42°C.

Techniques: Isolation, Strep-tag, SDS Page, Silver Staining, Western Blot, Molecular Weight

Journal: Genome Biology and Evolution

Article Title: Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists

doi: 10.1093/gbe/evt008

Figure Lengend Snippet: Gene order comparison of jakobid mtDNA and α-proteobacteria. Conservation of ribosomal gene organization in the mitochondrial genome of jakobids, compared with the generally contiguous L11, L10, Beta, streptomycin (Str), S10, spectinomycin (Spc), and Alpha operons of α-proteobacteria. Species abbreviations and GenBank Accession nos. are: Azos. spec., Azospirillum sp., NC_013854; Magn. magn., Magnetospirillum magneticum , NC_007626; Midi. mito ., Candidatus Midichloria mitochondrii , NC_015722; Orie. tsut ., Orientia tsutsugamushi str. Ideda, NC_010793; Rhod. cent ., Rhodospirillum centenum , NC_011420; Rhod. rubr ., Rhodospirillum rubrum ATCC 11170, NC_007643; Rick. prow ., Rickettsia prowazekii str. Madrid, NC_000963; Tist. mobi ., Tistrella mobilis KA081020-065, NC_017966; and Wolb -Droso., Wolbachia endosymbiont of Drosophila melanogaster , NC_002978.

Article Snippet: Ideda, NC_010793; Novosphingobium aromaticivorans , NC_007794; Rhodospirillum centenum , NC_011420; Rhodospirillum rubrum ATCC 11170, NC_007643; Rickettsia prowazekii str.

Techniques:

Journal: Genome Biology and Evolution

Article Title: Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists

doi: 10.1093/gbe/evt008

Figure Lengend Snippet: Phylogeny based on mtDNA-encoded proteins. The tree was constructed based on concatenated mtDNA-encoded protein sequences from jakobids, slowly evolving representatives of other, major eukaryotic groups, 16 α-proteobacteria (a total of 52 species and 5,791 aligned amino acid positions), and Magnetococcus as a close, non α-proteobacterial outgroup species. Reclinomas -94 represents all four, very similar Reclinomonas species studied here. The tree shown was inferred with PhyloBayes, the CAT + Gamma model, and six discrete categories , based on 19 mtDNA-encoded, concatenated proteins. Numbers indicate jackknife support values; branches without numbers have 100% support values. Short, basal branches with less than 60% support were collapsed. Posterior probability values (PhyloBayes analysis with four independent chains) other than 1.0 are indicated in brackets, following the corresponding jackknife value. Maximum likelihood inference predicts a similar tree (not shown), except for a strong (100% bootstrap value) regrouping of the fast-evolving Amoebozoa with haptophytes, which is probably an LBA artifact. Full taxon names and corresponding GenBank accession numbers for bacterial sequences: Agrobacterium radiobacter , NC_011985, NC_011983; Alphaproteobacterium BAL199, NZ_ABHC01000000; Azospirillum brasilense , NC_016617; Bradyrhizobium japonicum , NC_004463; Ehrlichia canis , NC_007354; Magnetococcus sp., NC_008576; Micavibrio aeruginosavorus , NC_016026; Magnetospirillum magnetotacticum , NZ_AAAP00000000; Mezorhizobium loti , NC_002682, NC_002679, NC_002678; Midichloria mitochondrii , NC_015722; Neorickettsia sennetsu , NC_007798; Orientia tsutsugamushi str. Ideda, NC_010793; Novosphingobium aromaticivorans , NC_007794; Rhodospirillum centenum , NC_011420; Rhodospirillum rubrum ATCC 11170, NC_007643; Rickettsia prowazekii str. Madrid, NC_000963; Tistrella mobilis , NC_017966; and Wolbachia endosymbiont of Drosophila melanogaster , NC_002978. Full taxon names and corresponding GenBank accession numbers for mitochondrial sequences: Acanthamoeba castellanii , NC_001637; Andalucia godoyi , this report, Bigelowiella natans , HQ840955; Capsaspora owczarzaki , (unpublished, available upon request); Chaetosphaeridium globosum , NC_004118; Chondrus crispus , NC_001677; Chattonella marina , NC_013837; Cyanidioschyzon merolae , NC_000887; Cyanophora paradoxa , NC_017836; Desmarestia viridis , NC_007684; Emiliania huxleyi , NC_005332; Geodia neptuni , NC_006990; Glaucocystis nostochinearum , NC015117; Hartmannella vermiformis , NC_013986; Hemiselmis andersenii , NC_010637; Histiona aroides , this report; Jakoba bahamiensis , this report; J. libera , this report; Malawimonas californiana (unpublished, available upon request); Marchantia polymorpha , NC_001660; Mesostigma viride , NC_008240; Nephroselmis olivacea , NC_008239; Malawimonas jakobiformis , NC_002553; Monosiga brevicollis , NC_004309; Pavlova lutheri , HQ908424; Phytophthora infestans , NC_002387; Porphyra purpurea , NC_002007; Prototheca wickerhamii , NC_001613; Reclinomonas americana , NC_001823; Rhodomonas salina , NC_002572; Seculamonas ecuadoriensis , this report; and Thalassiosira pseudonana , NC_007405.

Article Snippet: Ideda, NC_010793; Novosphingobium aromaticivorans , NC_007794; Rhodospirillum centenum , NC_011420; Rhodospirillum rubrum ATCC 11170, NC_007643; Rickettsia prowazekii str.

Techniques: Construct