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Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous <b><i>Desulfonema limicola</i></b> and <b><i>Desulfonema magnum</i></b>

2021; Volume: 31; Issue: 1 Linguagem: Inglês

10.1159/000513383

2673-1673

Vanessa Schnaars, Lars Wöhlbrand, Sabine Scheve, Christina Hinrichs, Richard Reinhardt, Ralf Rabus,

Protist diversity and phylogeny

The genus <i>Desulfonema</i> belongs to the deltaproteobacterial family <i>Desulfobacteraceae</i> and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of <i>Dn. limicola</i> 5ac10^T (6.91 Mbp; 6,207 CDS) and <i>Dn. magnum</i> 4be13^T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other <i>Desulfobacteraceae</i> members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of <i>Dn. limicola</i> and <i>Dn. magnum</i> have the following general characteristics: 98 <i>versus</i> 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 <i>versus</i> 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The <i>Dn. magnum</i> typifying capacity for aromatic compound degradation (e.g., <i>p</i>-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in <i>Dn. limicola</i>). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69–96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both <i>Desulfonema</i> strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of <i>Dn. limicola</i> and <i>Dn. magnum</i> to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.