Biology subjects

Derman, A. I.

Publications and source records attributed to Derman, A. I..

4 recordsLinked to original sources

bioRxiv2026

The ferredoxin/flavodoxin-NADP+ oxidoreductase YumC is essential for isoprenoid and peptidoglycan biosynthesis in Bacillus subtilis

Redox reactions mediated by ferredoxin/flavodoxin-NADP+ oxidoreductases (FNRs) and their associated electron-carrier proteins, ferredoxins and flavodoxins, are essential in biology. Although the biochemical activities of these redox proteins are conserved, their precise physiological roles can differ among organisms and cannot be easily inferred. Here we have defined an essential role for Bacillus subtilis YumC, a member of a distinct group of bacterial FNRs that resemble thioredoxin reductase. We have used targeted protein degradation, cytological profiling, metabolomics, and genetic complementation to show that YumC catalyzes the transfer of electrons from NADPH, through ferredoxin (Fer) or through the flavodoxin YkuP, to the isoprenoid biosynthesis pathway, and specifically to the redox enzyme IspG. When YumC was degraded, isoprenoid biosynthesis was compromised, and the level of undecaprenyl phosphate, the isoprenoid lipid carrier for peptidoglycan building block translocation, was diminished. Degradation of YumC or of Fer in a {Delta}ykuP strain led to defective peptidoglycan biosynthesis, activation of the {sigma}M-dependent cell-wall stress response, and lethality. The introduction into B. subtilis of an alternative pathway for isoprenoid biosynthesis that does not require input from electron-carrier proteins could complement the degradation of Fer in a {Delta}ykuP strain, but not the degradation of YumC. This finding indicates that YumC is required for other essential processes that do not necessarily involve Fer and YkuP. This work provides an explanation for why YumC is essential, reveals how reducing power is delivered to isoprenoid biosynthesis in B. subtilis, and illustrates how the varied roles of redox systems among bacteria depend upon metabolic context.

microbiology↗

bioRxiv2024

Catabolism of germinant amino acids is required to prevent premature spore germination in Bacillus subtilis

Spores of Bacillus subtilis germinate in response to specific germinant molecules that are recognized by receptors in the spore envelope. Germinants signal to the dormant spore that the environment can support vegetative growth, so many germinants, such as alanine and valine, are also essential metabolites. As such, they are also required to build the spore. Here we show that these germinants cause premature germination if they are still present at the latter stages of spore formation and beyond, but that B. subtilis metabolism is configured to prevent this: alanine and valine are catabolized and cleared from wild-type cultures even when alternative carbon and nitrogen sources are present. Alanine and valine accumulate in the spent media of mutants that are unable to catabolize these amino acids, and premature germination is pervasive. Premature germination does not occur if the germinant receptor that responds to alanine and valine is eliminated, or if wild-type strains that are able to catabolize and clear alanine and valine are also present in coculture. Our findings demonstrate that spore-forming bacteria must fine-tune the concentration of any metabolite that can also function as a germinant to a level that is high enough to allow for spore development to proceed, but not so high as to promote premature germination. These results indicate that germinant selection and metabolism are tightly linked, and suggest that germinant receptors evolve in tandem with the catabolic priorities of the spore-forming bacterium.

microbiology↗

bioRxiv2020

Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals

The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcares most potent antibiotics are becoming obsolete. Approximately two-thirds of the worlds antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, in order to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 101 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.

microbiology↗

bioRxiv2017

Polymer dynamics of Alp7A reveals two ‘critical’ concentrations that govern dynamically unstable actin-like proteins

ABSTRACTDynamically unstable polymers capture and move cellular cargos in both bacteria and eukaryotes, but the regulation of their assembly remains poorly understood. Here we describe polymerization of Alp7A, a bacterial Actin-Like Protein (ALP) that segregates the low copy-number plasmid pLS20 in Bacillus subtilis. Purified Alp7A forms dynamically unstable polymers with two critical points: an intrinsic critical concentration (0.6 M), observed when ATP hydrolysis is blocked, and a dynamic critical concentration (10.3 M), observed when ATP hydrolysis occurs. From biochemical and kinetic analysis, the intrinsic critical concentration reflects a balance between filament elongation and shortening, while the dynamic critical concentration reflects a balance between filament nucleation and catastrophic disassembly. Although Alp7A does not form stable polymers at physiological concentrations, rapid nucleation by an accessory factor, Alp7R, decreases the dynamic critical concentration into the physiological range. Intrinsic and dynamic critical concentrations are fundamental parameters that can be used to describe the behavior of all dynamically unstable polymers.

biochemistry↗