Biology subjects

Kamenik, Z.

Publications and source records attributed to Kamenik, Z..

7 recordsLinked to original sources

bioRxiv2026

The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures

Bile acids and related steroidal metabolites are among the most studied biomolecules, yet recent work has revealed far greater structural diversity than previously recognized, much of it shaped by the microbiome. We previously introduced a repository-scale bile acid MS/MS library built from queries targeting C24 bile acid fragmentation, limited to Orbitrap Q Exactive datasets within GNPS/MassIVE. Here we announce a major expansion of this library: a bile acid and steroidal MS/MS spectral library assembled across three major metabolomics repositories, now capturing C23, C24 (including alkamine), C26 (C-C bonded aceto derivatives), and C27 bile acids, as well as C28 bile alcohols. The expanded libraries comprise 640,141 unique MS/MS spectra, of which 120,293 (18.8%) match 2,529 reference spectra, leaving most of this steroidal chemical space structurally unassigned. Linked to harmonized pan-repository metadata, the library provides a starting point for classifying MS/MS spectra as likely bile acids or related steroids, with two example analyses illustrated here. This resource allows researchers to flag candidate bile acid and steroidal signatures in their own data for further characterization.

bioinformatics↗

bioRxiv2025

CluSeek: Bioinformatics Tool to Identify and Analyze Gene Clusters

Gene clusters are key structural and functional units that encode diverse phenotypes in genomes, from metabolism to pathogenesis. As genome sequencing expands, tools for systematic exploration of this growing data are increasingly needed. We present CluSeek, an open-source, Python-based platform for discovering, visualizing, and analyzing gene clusters across all GenBank data. Unlike existing tools, CluSeek does not rely on predefined cluster types or reference libraries but enables mining of any gene neighborhoods containing colocalized homologs of user-specified genes. It features an intuitive graphical interface suitable for non-bioinformaticians and is freely available at https://cluseek.com. We demonstrate the versatility of Cluseek in two distinct case studies: (i) mining of specialized metabolites, where CluSeek uncovered over 16 new classes containing the bioactivity-enhancing 4-alkyl-L-proline moiety, previously known in only three Golden Era antibiotic classes; and (ii) analysis of type III secretion systems present in Bordetella species, revealing previously unrecognized taxonomic distribution, and genetic variants, including gene multiplications and novel components with potential functional significance. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/676505v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1767e2eorg.highwire.dtl.DTLVardef@5603e3org.highwire.dtl.DTLVardef@1193475org.highwire.dtl.DTLVardef@1c32e83_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

ABCF Protein-Mediated Resistance Shapes Bacterial Responses to antibiotics Based on THEIR Type and Concentration

ABCF ATPases are increasingly recognized as translation factors that rescue stalled ribosomes, whether they encounter challenging mRNA templates or antibiotic-induced stalling. The latter defines ARE ABCF proteins, known for their role in antibiotic resistance. However, in this study, we reveal a broader role of ARE ABCFs in antibiotic-responsive regulation. Using genetic, OMICs, and biochemical approaches we showed that ARE ABCF proteins TiaA and Are5sc in Streptomyces coelicolor use their resistance functions to modulate specialized metabolism and proteosynthesis in response to lincosamide, streptogramin A, and pleuromutilin (LSAP) antibiotics. Although under LSAP exposure, either Are5sc or TiaA is essential for activating the biosynthesis of the redox-active antimicrobial actinorhodin, these proteins exhibit distinct functions at the proteome level, defined by their resistance profiles and temporally regulated expression. Are5sc facilitates early adaptive responses by modulating the WblC regulon across a broad range of LSAP concentrations, while TiaA is induced later, specifically at higher concentrations, where it suppresses antibiotic stress responses, particularly against pleuromutilins. TiaA function thus reflects the ecological context of LSAP antibiotics as pleuromutilins are produced by fungi, whereas lincosamides/streptogramins originate from actinomycetes. Our findings demonstrate that ARE ABCF proteins, through their resistance function, act as global regulators of translation, mirroring the roles of non-ARE ABCF proteins like EttA. This highlights their broader ecological and physiological significance, extending beyond their established role in antibiotic resistance. IMPORTANCEBacteria adapt to diverse stimuli mainly through transcriptional changes that regulate adaptive protein factors. Here, we show that responses to protein synthesis-inhibiting antibiotics are fine-tuned by antibiotic resistance ABCF proteins at the translational level, enabling bacteria to differentiate between antibiotic classes and concentrations for a tailored response. Additionally, we have demonstrated that these proteins can specialize in conferring high-level resistance to specific antibiotics. Given their prevalence in pathogenic bacteria, ARE ABCF proteins may play a crucial role in resistance development, particularly against new antibiotics targeting the ribosomal catalytic center, presenting a significant challenge for antimicrobial therapy.

microbiology↗

bioRxiv2020

Beyond self-resistance: ABCF ATPase LmrC is a signal-transducing component of an antibiotic-driven signaling cascade hastening the onset of lincomycin biosynthesis

In natural environments, antibiotics are an important instrument of inter-species competition. At subinhibitory concentrations, they act as cues or signals inducing antibiotic production: however, our knowledge of well-documented antibiotic-based sensing systems is limited. Here, for the soil actinobacterium Streptomyces lincolnensis we describe a fundamentally new ribosome-mediated signaling cascade that accelerates the onset of lincomycin production in response to an external ribosome-targeting antibiotic to synchronize the antibiotic production within the population. The entire cascade is encoded within the lincomycin biosynthetic gene cluster (BGC) and besides the transcriptional regulator, LmbU it consists of three lincomycin resistance proteins: a lincomycin transporter, LmrA, a 23S rRNA methyltransferase, LmrB, both conferring a high resistance, and an ABCF ATPase LmrC that confers only moderate resistance but is indispensable for the antibiotic-induced signal transduction. Specifically, the antibiotic sensing occurs via a ribosome-mediated attenuation, which activates LmrC production in response to lincosamide, streptogramin A, or pleuromutilin antibiotics. Then, the ribosome-operating LmrC ATPase activity triggers the transcription of lmbU and consequently the expression of lincomycin BGC. Finally, the production of LmrC is downregulated by LmrA and LmrB which reduces the amount of the ribosome-bound antibiotic and thus fine-tune the cascade. We propose that analogous ABCF-mediated signaling systems are relatively common because many BGCs for ribosome-targeting antibiotics encode an ABCF-protein accompanied by additional resistance protein(s) and transcriptional regulators. Moreover, we revealed that three of eight co-produced ABCF proteins of S. lincolnensis are clindamycin-responsive thus the ABCF-mediated antibiotic signaling might be generally utilized tool of chemical communication. IMPORTANCEResistance proteins are perceived as mechanisms protecting bacteria from the inhibitory effect of their produced antibiotic or antibiotics from competitors. Here, we report that antibiotic resistance proteins regulate lincomycin biosynthesis in response to subinhibitory concentrations of antibiotics. Particularly, we show the dual character of ABCF ATPase LmrC which confers antibiotic resistance and simultaneously transduces a signal from ribosome-bound antibiotic to gene expression, where the 5 untranslated sequence upstream of its encoding gene functions as a primary antibiotic sensor. The ABCF-mediated antibiotic signaling can in principle function not only in the induction of antibiotic biosynthesis but in general in selective gene expression in response to any small molecules targeting the 50S ribosomal subunit, including clinically important antibiotics, to mediate intercellular antibiotic signaling and stress response induction. Moreover, the resistance-regulatory function of LmrC presented here for the first time unifies yet functionally inconsistent ABCF family involving the antibiotic resistance proteins and the translational regulators.

microbiology↗

bioRxiv2020

Ion Identity Molecular Networking in the GNPS Environment

Molecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.

bioinformatics↗

bioRxiv2019

Feature-based Molecular Networking in the GNPS Analysis Environment

Molecular networking has become a key method used to visualize and annotate the chemical space in non-targeted mass spectrometry-based experiments. However, distinguishing isomeric compounds and quantitative interpretation are currently limited. Therefore, we created Feature-based Molecular Networking (FBMN) as a new analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure. FBMN leverages feature detection and alignment tools to enhance quantitative analyses and isomer distinction, including from ion-mobility spectrometry experiments, in molecular networks.

bioinformatics↗

bioRxiv2019

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1

bioinformatics↗