Biology subjects

Boedeker, C.

Publications and source records attributed to Boedeker, C..

3 recordsLinked to original sources

bioRxiv2019

The novel shapeshifting bacterial phylum Saltatorellota

Our current understanding of a free-living bacterium - capable of withstanding a variety of environmental stresses-is represented by the image of a peptidoglycan-armored rigid casket. The making and breaking of peptidoglycan greatly determines cell shape. The cytoplasmic membrane follows this shape, pressed towards the cell wall by turgor pressure. Consequently, bacteria are morphologically static organisms, in contrast to eukaryotic cells that can facilitate shape changes. Here we report the discovery of the novel bacterial phylum Saltatorellota, that challenges this concept of a bacterial cell. Members of this phylum can change their shape, are capable of amoeba-like locomotion and trunk-formation through the creation of extensive pseudopodia-like structures. Two independent Saltatorellota cells can fuse, and they employ various forms of cell division from budding to canonical binary fission. Despite their polymorphisms, members of the Saltatorellota do possess a peptidoglycan cell wall. Their genomes encode flagella and type IV pili as well as a bacterial actin homolog, the saltatorellin. This protein is most similar to MamK, a dynamic filament-forming protein, that aligns and segregates magnetosome organelles via treadmilling. We found saltatorellin to form filaments in both, E. coli and Magnetospirillum gryphiswaldense, leading to the hypothesis that shapeshifting and pseudopodia formation might be driven by treadmilling of saltatorellin.

microbiology↗

bioRxiv2019

Dinoroseobacter shibae outer membrane vesicles are enriched for the chromosome dimer resolution site dif

Outer membrane vesicles (OMVs) of Gram-negative bacteria have key roles in pathogenesis. However, little is known about their biogenesis and cargo in marine bacteria. In Dinoroseobacter shibae, a marine member of the Rhodobacteraceae, OMVs were produced throughout exponential growth, and DNA could be detected by fluorescence microscopy inside appr. 65% of vesicles. Single cell analysis using time-lapse microscopy showed that individual cells secreted multiple OMVs, preferentially at the septum during cell division. OMVs were enriched for saturated fatty acids, thus their secretion likely increases the fluidity of the membrane of the releasing cell locally. DNA was isolated from the vesicle lumen and sequenced; it was up to 40fold enriched for the region around the terminus of replication (ter). Within this region, the peak of coverage of vesicle DNA was located at dif, a conserved 28 bp palindromic sequence required for binding of the site specific tyrosine recombinases XerCD which are activated by the divisome protein FtsK immediately prior to septum formation. Some of the most abundant proteins of the vesicle proteome were predicted to be required for direct interaction with peptidoglycan during cell division. Single cell analysis, electron microscopy, proteome and DNA cargo show that constitutive OMV secretion in D. shibae occurs mainly prior to septum formation. The footprint of the FtsK/XerCD molecular machinery which resolves chromosome dimers suggests a novel highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of this type of vesicles.

microbiology↗

bioRxiv2017

The Plastid Genome In Cladophorales Green Algae Is Encoded By Hairpin Plasmids

Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin plasmids. Short and long read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1-7 kb DNA contigs with an exceptionally high GC-content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin plasmids. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in the plastid genome architecture.

genomics↗