@misc{FriedrichHollensteinerScherfetal., author = {Friedrich, Ines and Hollensteiner, Jacqueline and Scherf, Janna and Weyergraf, Judith and Klassen, Anna and Poehlein, Anja and Hertel, Robert and Daniel, Rolf}, title = {Complete Genome Sequence of Stenotrophomonas indicatrix DAIF1}, series = {Microbiology Resource Announcements}, volume = {10}, journal = {Microbiology Resource Announcements}, number = {6}, issn = {2576-098X}, doi = {10.1128/MRA.01484-20}, pages = {1 -- 3}, abstract = {We present the complete genome of Stenotrophomonas indicatrix DAIF1, which was isolated from an oligotrophic pond in a water protection area. Whole-genome alignments indicated that strain DAIF1 belongs to the species Stenotrophomonas indicatrix. The whole genome (4,639,375 bp) harbors 4,108 protein-encoding genes, including 3,029 genes with assigned functions.}, language = {en} } @misc{HollensteinerFriedrichHollsteinetal., author = {Hollensteiner, Jacqueline and Friedrich, Ines and Hollstein, Lucas and Lamping, Jan-Philipp and Wolf, Kalina and Liesegang, Heiko and Poehlein, Anja and Hertel, Robert and Daniel, Rolf}, title = {Complete Genome Sequence of Kinneretia sp. Strain DAIF2, Isolated from a Freshwater Pond}, series = {Microbiology Resource Announcements}, volume = {10}, journal = {Microbiology Resource Announcements}, number = {8}, issn = {2576-098X}, doi = {10.1128/MRA.00003-21}, pages = {1 -- 3}, abstract = {Kinneretia sp. strain DAIF2 was isolated from a eutrophic freshwater pond. The genome consists of a single chromosome (6,010,585 bp) with a GC content of 69.3\%. The whole-genome-based phylogeny of DAIF2 revealed a closest relation to the genus Kinneretia.}, language = {en} } @misc{FriedrichHollensteinerSchneideretal., author = {Friedrich, Ines and Hollensteiner, Jacqueline and Schneider, Dominik and Poehlein, Anja and Hertel, Robert and Daniel, Rolf}, title = {First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and their Comparative Genome Analysis}, series = {Genome Biology and Evolution}, volume = {12}, journal = {Genome Biology and Evolution}, number = {10}, issn = {1759-6653}, doi = {10.1093/gbe/evaa148}, pages = {1782 -- 1788}, abstract = {We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in G{\"o}ttingen. The strains were phylogenetically classified by ANI analysis and showed a species assignment to Janthinobacterium lividum with 97.72\% (EIF1) and 97.66\% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species Janthinobacterium lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98\%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63\% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21\%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a non-ribosomal peptide synthetase cluster (NRPS) with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites.}, language = {en} } @misc{RichtsHertelPototetal., author = {Richts, Bj{\"o}rn and Hertel, Robert and Potot, S{\´e}bastien and Poehlein, Anja and Daniel, Rolf and Schyns, Ghislain and Pr{\´a}gai, Zolt{\´a}n and Commichau, Fabian M.}, title = {Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1}, series = {Microbiology Resource Announcements}, volume = {9}, journal = {Microbiology Resource Announcements}, number = {32}, issn = {2576-098X}, doi = {10.1128/MRA.00825-20}, pages = {3}, abstract = {Here, we present the complete genome sequence of the Bacillus subtilis strain SP1. This strain is a descendant of the laboratory strain 168. The strain is suit- able for biotechnological applications because the prototrophy for tryptophan has been restored. Due to laboratory cultivation, the strain has acquired 24 additional sequence variations.}, language = {en} } @misc{HertelSchoeneMittelstaedtetal., author = {Hertel, Robert and Sch{\"o}ne, Kerstin and Mittelst{\"a}dt, Carolin and Meißner, Janek and Zschoche, Nick and Collignon, Madeline and Kohler, Christian and Friedrich, Ines and Schneider, Dominik and Hoppert, Michael and Kuhn, Ramona and Schwedt, Inge and Scholz, Patricia and Poehlein, Anja and Martienssen, Marion and Ischebeck, Till and Daniel, Rolf and Commichau, Fabian M.}, title = {Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution}, series = {Environmental Microbiology Reports}, volume = {14}, journal = {Environmental Microbiology Reports}, number = {1}, issn = {1758-2229}, doi = {10.1111/1758-2229.13022}, pages = {70 -- 84}, abstract = {Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia.}, language = {en} } @misc{RichtsLentesPoehleinetal., author = {Richts, Bj{\"o}rn and Lentes, Sabine and Poehlein, Anja and Daniel, Rolf and Commichau, Fabian M.}, title = {A Bacillus subtilis ΔpdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation}, series = {Environmental Microbiology Reports}, volume = {13}, journal = {Environmental Microbiology Reports}, number = {2}, issn = {1758-2229}, doi = {10.1111/1758-2229.12936}, pages = {218 -- 233}, abstract = {Pyridoxal-5'-phosphate (PLP), the biologically active form of vitamin B6, serves as a cofactor for many enzymes. The Gram-positive model bacterium Bacillus subtilis synthesizes PLP via the PdxST enzyme complex, consisting of the PdxT glutaminase and the PdxS PLP synthase subunits, respectively. PdxT converts glutamine to glutamate and ammonia of which the latter is channelled to PdxS. At high extracellular ammonium concentrations, the PdxS PLP synthase subunit does not depend on PdxT. Here, we assessed the potential of a B. subtilis ΔpdxT mutant to adapt to PLP limitation at the genome level. The majority of ΔpdxT suppressors had amplified a genomic region containing the pdxS gene. We also identified mutants having acquired as yet undescribed mutations in ammonium assimilation genes, indicating that the overproduction of PdxS and the NrgA ammonium transporter partially relieve vitamin B6 limitation in a ΔpdxT mutant when extracellular ammonium is scarce. Furthermore, we found that PdxS positively affects complex colony formation in B. subtilis. The catalytic mechanism of the PdxS PLP synthase subunit could be the reason for the limited evolution of the enzyme and why we could not identify a PdxS variant producing PLP independently of PdxT at low ammonium concentrations.}, language = {en} } @misc{KohmFloccariLutzetal., author = {Kohm, Katharina and Floccari, Valentina and Lutz, Veronika and Nordmann, Birthe and Mittelst{\"a}dt, Carolin and Poehlein, Anja and Dragos, Anna and Commichau, Fabian M. and Hertel, Robert}, title = {The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components}, series = {bioRxiv beta}, journal = {bioRxiv beta}, doi = {10.1101/2021.11.22.469490}, pages = {44}, abstract = {The Bacillus phage SPβ has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SPβ-like phages. We could also reveal the SPβ-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SPβ-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SPβ-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SPβ transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system.}, language = {en} } @misc{MichalikRederRichtsetal., author = {Michalik, Stephan and Reder, Alexander and Richts, Bj{\"o}rn and Faßhauer, Patrick and M{\"a}der, Ulrike and Pedreira, Tiago and Poehlein, Anja and Heel, Auke van and Tilburg, Amanda van and Altenbuchner, Josef and Klewing, Anika and Reuß, Daniel and Daniel, Rolf and Commichau, Fabian M. and Kuipers, Oscar and Hamoen, Leendert and V{\"o}lker, Uwe and St{\"u}lke, J{\"o}rg}, title = {The Bacillus subtilis Minimal Genome Compendium}, series = {ACS Synthetic Biology}, volume = {10}, journal = {ACS Synthetic Biology}, number = {10}, issn = {2161-5063}, doi = {10.1021/acssynbio.1c00339}, pages = {2767 -- 2771}, abstract = {To better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40\% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology.}, language = {en} }