Journal: International journal of systematic and evolutionary microbiology

Article Title: Whole genome-based taxonomy of Shewanella and Parashewanella .

doi: 10.1099/ijsem.0.005438

Figure Lengend Snippet: Fig. 1. Cumulative number of Shewanella, Parashewanella and Psychrobium species over time. Data based on LPSN as of 22 December 2021 with the amendments described in the text.

Article Snippet: 1 Whole genome- based taxonomy of Shewanella and Parashewanella Author affiliations: 1Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; 2Department of Bioinformatics and Databases, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany.

Techniques:

Journal: Nature

Article Title: Structural basis of Gabija anti-phage defence and viral immune evasion

doi: 10.1038/s41586-023-06855-2

Figure Lengend Snippet: a , Schematic model of GajAB–Gad1 co-complex formation and domain organization of phage Phi3T Gad1. b , Cryo-EM density map of Bc GajAB in complex with Phi3T Gad1, shown in three different orientations. The map is coloured by the model, with Gad1 monomers depicted in two shades of green. c , d , Side view of the complete Gad1 octameric complex ( c ) and top-down view of the Gad1 tetrameric interface ( d ), with boxes highlighting views that are magnified in e – h . e , f , Magnified views of major Gad1–GajA interface contacts including a Gad1 positively charged loop ( e ) and hydrophobic interactions with GajA α2 D ( f ). g , h , Magnified views of major Gad1–Gad1 oligomerization interactions including disulfide bonds in the C-terminal shoulder domain ( g ) and fist–fist domain contacts modelled by rigid-body placement of an AlphaFold2 fist-domain structure prediction into the cryo-EM map ( h ). i , Two distinct conformations of Gad1 observed in the GajAB–Gad1 co-complex structure. Differences in the rotation of the Gad1 arm domain are highlighted on the right. j , Analysis of the effect of Gad1 mutations in the GajA–Gad1 and Gad1–Gad1 multimerization interfaces on the ability of Gad1 to enable evasion of Gabija defence. Data represent PFU ml −1 of phage SPβ infecting cells expressing Bc Gabija and Shewanella sp. phage 1/4 Gad1, or negative control (NC) cells expressing empty vector for either plasmid. Shewanella sp. phage 1/4 Gad1 residues are numbered according to the Phi3T Gad1 structure. Shewanella sp. phage 1/4 Gad1 N-terminal and C-terminal truncations (N-term and C-term, respectively) are M1–L152 and V153–E348, respectively. Data are the average of three biological replicates, with individual data points shown.

Article Snippet: Because Gad1 was toxic in B. subtilis cells containing Gabija, Shewanella sp. phage 1/4 Gad1 was used and synthesized by GenScript.

Techniques: Cryo-EM Sample Prep, Expressing, Negative Control, Plasmid Preparation

Journal: Nature

Article Title: Structural basis of Gabija anti-phage defence and viral immune evasion

doi: 10.1038/s41586-023-06855-2

Figure Lengend Snippet: a , Structure-guided alignment of Gad1 proteins from indicated phage or prophage genomes coloured according to amino acid conservation. The Bacillus phage Phi3T Gad1 secondary structure is displayed according to the two different conformations observed in the GajAB–Gad1 co-complex structure. Oligomerization interface residues are annotated according to the key below. b , c , Magnified views of Gad1–GajA interface contacts including hydrophobic interactions in AlphaFold2 arm domain structure of Gad1 and the Toprim domain of GajA ( b ) and Gad1 shoulder domain residue Q244 interaction with GajA dimerization domain residue E277 ( c ). d , Magnified view of Gad1–Gad1 oligomerization interactions between shoulder domains of Gad1 protomers. e , SDS–PAGE analysis of the ability of Shewanella phage 1/4 Gad1 mutant proteins to interact with the GajAB complex. Shewanella phage 1/4 Gad1 mutant proteins were co-expressed with SUMO2-tagged GajAB (GajA-tagged) and co-purified by Ni-NTA pull-down. Shewanella sp . phage 1/4 Gad1 residues are numbered according to the Phi3T Gad1 structure. To measure high stringency of GajAB–Gad1 interactions, complexes were washed with a 1 M NaCl buffer prior to elution and co-purification. Notably, the Gad1 mutant C282E is no longer able to interact with GajAB in vitro under these stringent conditions, but retains the ability to disrupt Gabija defence in vivo, suggesting that lower-affinity interactions still occur. f , SDS–PAGE analysis of the ability of Shewanella phage 1/4 Gad1 fist–fist interface mutant proteins to interact with the GajAB complex. Shewanella phage 1/4 Gad1 mutant proteins were co-expressed with SUMO2-tagged GajAB (GajA-tagged), co-purified by Ni-NTA pull-down, and treated with SENP2 to cleave the SUMO2 tag prior to SDS–PAGE gel loading. Shewanella sp . phage 1/4 Gad1 residues are numbered according to the Phi3T Gad1 structure. g , Agarose gel analysis of the ability of GajAB–Gad1 mutant complexes to cleave target 56-bp dsDNA after a 1 min or 20 min incubation. h , Superposition of the GajAB crystal structure and GajAB from the GajAB–Gad1 cryo-EM structure demonstrates no significant conformational change after Gad1 binding. Data in e – g are representative of 3 independent experiments.

Article Snippet: Because Gad1 was toxic in B. subtilis cells containing Gabija, Shewanella sp. phage 1/4 Gad1 was used and synthesized by GenScript.

Techniques: Residue, SDS Page, Mutagenesis, Purification, Copurification, In Vitro, In Vivo, Agarose Gel Electrophoresis, Incubation, Cryo-EM Sample Prep, Binding Assay

Journal: Nature

Article Title: Structural basis of Gabija anti-phage defence and viral immune evasion

doi: 10.1038/s41586-023-06855-2

Figure Lengend Snippet: a , Cartoon representation of the GajAB–Gad1 co-complex structure with modelled DNA (orange), based on structural homology with E. coli MutS (PDB ID 3K0S ) . b , Top, isolated GajA protomer with modelled DNA (orange) bound to the Toprim domain. Bottom, the same GajA promoter with Gad1, showing substantial steric clashes between Gad1 and the path of the DNA. c , d , Biochemical analysis of GajAB 56-bp target DNA binding ( c ) and target cleavage ( d ) shows that Gad1 potently inhibits the activity of GajAB. Data are representative of three independent experiments. e , Model of Gabija anti-phage defence and mechanism of Gad1 immune evasion.

Article Snippet: Because Gad1 was toxic in B. subtilis cells containing Gabija, Shewanella sp. phage 1/4 Gad1 was used and synthesized by GenScript.

Techniques: Isolation, Binding Assay, Activity Assay

Journal: Frontiers in Microbiology

Article Title: Global occurrence of the bacteria with capability for extracellular reduction of iodate

doi: 10.3389/fmicb.2022.1070601

Figure Lengend Snippet: Genetic organization of identified mtrCAB and dmsEFAB gene clusters. The relative positions of genes identified within the complete genomes are shown. The identified genes are labeled with arrows. The arrow sizes indicate the relative lengths of identified genes. The arrow orientation indicates the presumed direction of gene transcription. The numbers above the identified genes are part of their locus tags. Group I: S. japonica KCTC 22435, S. livingstonensis LMG 19866, S. putrefaciens CN32 (CN32), S. woodyi ATCC 51908, Shewanella sp. ARC9_LZ, Shewanella sp. SUN WT4 and Shewanella sp. WPAGA9; Group II: S. fidelis ATCC-BAA-318, S. marisflavi EP1, S. piezotolerans WP3, S. schlegeliana JCM 11561, S. xiamenensis NUITM-VS1, Shewanella sp. 8A , Shewanella sp. ISTPL2, Shewanella sp. LZH-2, Shewanella sp. MBTL60-112-B1, Shewanella sp. MBTL60-112-B2 and Shewanella sp. MR-4 (MR-4); Group III: Ferrimonas sp. SCSIO 43195, S. frigidimarina NCIMB 400 (Sfri), Shewanella sp. Actino-trap-3 and Shewanella sp. KX20019; Group IV: Ferrimonas balerica DSM 9799 (Fbal) and S. oneidensis MR-1; Group V: F. lipolytica S7 (S7) and S. psychromarinicola M2; Group VI: S. eurypsychrophilus YLB-08 (YLB-08); and Group VII: S. sediminis HAW-EB3 and Shewanella sp. YLB-09 (YLB-09). OM c -Cyt: the outer membrane c -type cytochrome. See text for details.

Article Snippet: Group III bacteria included Ferrimonas sp. SCSIO 43195, S. frigidimarina NCIMB 400, Shewanella sp. Actino-trap-3 and Shewanella sp. KX20019, among which an additional gene for the outer membrane multiheme c -Cyt associated with the mtrCAB gene cluster of S. frigidimarina NCIMB 400, Shewanella sp. Actino-trap-3 and Shewanella sp. KX20019 (Group III, ; ).

Techniques: Labeling, Membrane