Journal: Journal of Bacteriology

Article Title: Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens

doi: 10.1128/JB.00309-20

Figure Lengend Snippet: Seven DUF1127 proteins are predicted and produced in A. tumefaciens. (A) Characteristics of three SDPs and four LDPs. *, protein annotation was incorrect and adjusted at the N terminus (see Fig. S2B in the supplemental material). (B) Western blot analysis of chromosomally integrated C-terminal 3×FLAG fusions of all seven DUF1127 proteins at different growth phases in YEB medium at 30°C. A heat shock was applied for 20 min at 42°C and cold shock for 20 min at 17°C.

Article Snippet: The stacked bar chart shows the absolute frequency for the lengths of all DUF1127 proteins from InterPro.

Techniques: Produced, Western Blot

Journal: Journal of Bacteriology

Article Title: Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens

doi: 10.1128/JB.00309-20

Figure Lengend Snippet: DUF1127 proteins can be divided into clusters. (A) SDPs from A. tumefaciens show a high sequence similarity. Identical residues are marked with an asterisk, residues with highly similar properties are marked with a colon, and weakly conserved residues are marked with a period. Arginine residues are shaded in black. (B) The homology tree of all seven DUF1127 proteins from A. tumefaciens and YjiS from E. coli was calculated by Clustal Omega (109). (C) Subdivision of DUF1127 proteins. The stacked bar chart shows the absolute frequency for the lengths of all DUF1127 proteins from InterPro. A kernel density estimation (dashed line) was superimposed. DUF1127 proteins were divided into subclasses according to sequence similarity to either SDPs from A. tumefaciens or to YjiS from E. coli.

Article Snippet: The stacked bar chart shows the absolute frequency for the lengths of all DUF1127 proteins from InterPro.

Techniques: Sequencing

Journal: Journal of Bacteriology

Article Title: Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens

doi: 10.1128/JB.00309-20

Figure Lengend Snippet: Cooccurrence of DUF1127 proteins with LsrB and cuckoo sRNAs. The tree shows the phylogenetic relations of a selection of alpha- (α-proteo.) and gammaproteobacteria (γ-proteo.). For each strain, the numbers of SDPs, YjiS-like proteins, and LDPs are given. BLAST searches identified the proteins with the highest similarity to LsrB from A. tumefaciens (A9CI74, B5ZXG9, A0A068SS95, A0A081MRV5, C3MD12, W8I232, G7D4X2, Q2YRP4, Q3J274, Q9I1F9, A1JKA5, A0A0H2UWZ6, A0A0H3GNP2, P30864, and Q8ZRM6). Red and blue colors represent proteins with higher and lower sequence identity than 40%, respectively A genomic neighborhood to a trxB homolog is indicated by a check mark. Putative cuckoo sRNA sequences were extracted from each genome by searching for the pattern (CCTCCTCCC-N20–50)≥1-CCTCCTCCC. The numbers of sequences encoding two, three, or four CCUCCUCCC motifs are given.

Article Snippet: The stacked bar chart shows the absolute frequency for the lengths of all DUF1127 proteins from InterPro.

Techniques: Selection, Sequencing

Journal: Journal of Bacteriology

Article Title: Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens

doi: 10.1128/JB.00309-20

Figure Lengend Snippet: SDP and LDP genes are reciprocally regulated by the transcription factor LsrB. (A) Northern blot analyses of SDP- and LDP-encoding genes in the WT and lsrB mutant. Ethidium bromide (EtBr)-stained 16S or 23S rRNA served as a loading control. (B) Putative LsrB-binding sites marked in red match the TGC-N7-GCA motif, and orange sequences display the shorter TGC-N6-GCA motif. Previously described binding sites of the three DUF1127 genes from B. abortus (bab1_0914, bab2_0514, and bab2_0574) are underlined. The position relative to the transcriptional start site (+1) is indicated.

Article Snippet: The stacked bar chart shows the absolute frequency for the lengths of all DUF1127 proteins from InterPro.

Techniques: Northern Blot, Mutagenesis, Staining, Binding Assay

Journal: Scientific Reports

Article Title: Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems

doi: 10.1038/s41598-019-56058-x

Figure Lengend Snippet: Relative abundance of bacterial populations among all studied sites (AG – Aas, Grytelandsbekken; SB – Ski, Blåveisbekken; BJ – Bergen, Jordalsvatnet; OM – Oslo, Maridalsvannet; and TJ – Trondheim, Jonsvannet): ( a ) all bacterial phyla, ( b ) Proteobacteria class distribution. The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Article Snippet: The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Techniques: Generated

Journal: Scientific Reports

Article Title: Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems

doi: 10.1038/s41598-019-56058-x

Figure Lengend Snippet: Relative abundance of bacterial populations among all studied sites (AG – Aas, Grytelandsbekken; SB – Ski, Blåveisbekken; BJ – Bergen, Jordalsvatnet; OM – Oslo, Maridalsvannet; and TJ – Trondheim, Jonsvannet): ( a ) bacterial phyla other than Proteobacteria and Bacteroidetes ; ( b ) genera distribution of the other bacterial phyla. The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Article Snippet: The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Techniques: Generated

Journal: Scientific Reports

Article Title: Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems

doi: 10.1038/s41598-019-56058-x

Figure Lengend Snippet: Relative abundance of archaeal populations among all studied sites (AG – Aas, Grytelandsbekken; SB – Ski, Blåveisbekken; BJ – Bergen, Jordalsvatnet; OM – Oslo, Maridalsvannet; and TJ – Trondheim, Jonsvannet): ( a ) phylum and class level; ( b ) genus level. The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Article Snippet: The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Techniques: Generated

Journal: Scientific Reports

Article Title: Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems

doi: 10.1038/s41598-019-56058-x

Figure Lengend Snippet: Phylogenetic alpha diversity of all studied sites (AG – Aas, Grytelandsbekken; SB – Ski, Blåveisbekken; BJ – Bergen, Jordalsvatnet; OM – Oslo, Maridalsvannet; and TJ – Trondheim, Jonsvannet). The alpha rarefaction plot was generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Article Snippet: The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Techniques: Generated

Journal: Scientific Reports

Article Title: Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems

doi: 10.1038/s41598-019-56058-x

Figure Lengend Snippet: Beta diversity heat map with hierarchical clustering of the study sites (AG – Aas, Grytelandsbekken; SB – Ski, Blåveisbekken; BJ – Bergen, Jordalsvatnet; OM – Oslo, Maridalsvannet; and TJ – Trondheim, Jonsvannet). The hierarchical clustering heat map was generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Article Snippet: The stacked bar charts were generated using the tools in CLC Microbial Genomics Module version 2.5.1 (CLC Bio, QIAGEN Company, Aarhus, Denmark, https://www.qiagenbioinformatics.com/clc-microbial-genomics-module-latest-improvements ).

Techniques: Generated