Biology subjects

Bartosik, D.

Publications and source records attributed to Bartosik, D..

7 recordsLinked to original sources

bioRxiv2026

A novel membrane-spanning one-component system controls β-glucan utilization in marine Bacteroidota

One of the most prevalent and bioavailable glycans in marine systems is the {beta}-glucan laminarin. Members of the phylum Bacteroidota are particularly well adapted to degrade this and other polysaccharides. Here, we describe a membrane-spanning one-component system that regulates laminarin utilization in marine Bacteroidota. We analyzed this {beta}-glucan utilization regulator (BguR) type in the marine model bacterium Formosa agariphila KMM3901T. Deletion of the regulator gene abolishes growth on laminarin, whereas the wild type exhibits more than 80-fold induction of the associated genomic gene cluster, indicating the regulators role as a transcriptional activator for laminarin utilization. Structural predictions show that its periplasmic sensor domain resembles those of hybrid two-component systems (HTCSs), although the absence of phosphorylation domains and distinct architecture indicate a completely different, ATP-independent mode-of-action. Comparative genomics show that this regulator is widespread among Bacteroidota, exhibiting lineage-specific distribution patterns similar to hallmark features such as tandem SusCD-like pairs. BguR is frequently found in close proximity to {beta}-glucan-targeting PULs in the genome, implying a defined substrate preference that extends beyond laminarin. These findings suggest a previously unrecognized regulatory mechanism for glycan sensing in marine bacteria, shedding light on an important facet of the marine carbon cycle. IMPORTANCEAlthough recent research has provided detailed insights into the enzymatic breakdown of algal glycans by marine bacteria, the regulatory mechanisms that govern specific carbohydrate utilization strategies remain largely unexplored. This study reveals a novel regulatory mechanism for {beta}-glucan use by marine Bacteroidota. We identified a membrane-embedded one-component regulator that directly links sensing and utilization of laminarin, a major algal polysaccharide in the oceans. Unlike traditional two-component systems, the new regulator operates without phosphorelays. The regulator and its associated laminarin PULs are widely conserved across diverse marine bacteria and even linked to other {beta}-glucan types, indicating a shared regulatory strategy for carbon acquisition from structurally related substrates. These findings advance our understanding of how key ocean microbes coordinate polysaccharide breakdown.

microbiology↗

bioRxiv2025

pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences

MotivationThe increasing number of fully sequenced bacterial plasmids being annotated and cataloged has prompted the development of computational tools for comparing and classifying them. Existing approaches typically compare full-length DNA sequences (e.g., Mash, BLASTn) or translated open reading frames (ORFs) (e.g., BLASTp, DIAMOND), with plasmid-level scores obtained by aggregating ORF-to-ORF similarities; however, they are either restricted to closely related plasmids or become computationally demanding in large-scale analyses. ResultsWe describe pLAST (plasmid Language Analysis and Search Tool), a plasmid-search tool built using word2vec representations capturing both ORF-to-ORF similarity and gene neighborhood conservation. Benchmarks indicate that pLAST outperforms both DNA- and ORF-based methods in identifying functionally similar plasmids and, compared to the widely used Mash, it achieves 37%, 30%, and 13% improvements in detecting shared mating-pair formation (MPF) system, relaxase, and oriT types, respectively. This performance scales to datasets comprising thousands of sequences, as exemplified by clustering analyses of [~]56,000 plasmids, which reveal expected functional groups. Beyond global similarity, pLAST also returns per-ORF plasmid-plasmid alignments, enabling detection of shared functional modules. Availability and implementationpLAST is freely accessible as a web server at https://plast.lbs.cent.uw.edu.pl/ and available as a Python module along with a precomputed database at https://github.com/labstructbioinf/pLAST for customized analysis.

bioinformatics↗

bioRxiv2025

Replication coordination marks the domestication of large extrachromosomal replicons in bacteria

Bacterial genomes often include extrachromosomal replicons (ERs), ranging from small plasmids to nearly chromosome-sized elements, that foster genome plasticity and adaptation. Despite their prevalence, the mechanisms underlying ER domestication and their long-term adaptation within bacterial hosts remain largely unexplored. By analyzing over 40,000 complete bacterial genomes, we identified two main ER categories: small ERs with diverse GC content and large ERs ([≥]10% the size of the main chromosome) that closely match the GC content of the chromosome. Across multiple phyla, marker frequency analyses showed that large ERs maintain a 1:1 copy number with the chromosome. Another key finding of this study is that large ERs terminate replication in synchrony with the chromosome. Hi-C contact maps revealed consistent ori-ori interactions between chromosomes and ERs. In large ERs, inter-replichore and ter-ter interactions, along with the recruitment of key chromosomal segregation motifs, suggest the co-option of chromosome-associated replication and segregation machineries. Together, our findings indicate that as ERs become larger, they become increasingly reliant on chromosome-driven processes for stable inheritance, potentially explaining why they do not exceed the size of the chromosome.

microbiology↗

bioRxiv2024

Resource partitioning in organosulfonate utilization by free-living heterotrophic bacteria during a North Sea microalgal bloom

Blooming microalgae (phytoplankton) release diverse organic molecules that fuel the marine pools of dissolved and particulate organic matter. A highly specialized community of heterotrophic bacteria rapidly remineralizes substantial parts of this organic matter in the sun-lit upper ocean. In particular, microalgae produce large quantities of various organosulfur compounds that can serve as carbon and sulfur sources for bacteria. Here, we report on the analyses of a time series of previously generated 30 long-read metagenomes, 30 corresponding deeply sequenced short-read metatranscriptomes and 15 metaproteomes from 0.2-3 {micro}m size fractions that we sampled in 2020 during a biphasic phytoplankton bloom in the German Bight (Southern North Sea). We analyzed the assembled contigs as well as 70 bacterial metagenome-assembled genomes that recruited the highest transcript numbers with respect to the utilization of methyl sulfur compounds (dimethylsulfoniopropionate (DMSP), dimethyl sulfide (DMS), dimethyl sulfone (DMSO2)), C3-sulfonates (2,3-dihydroxypropane-1-sulfonate (DHPS), 3-sulfolactate, 3-sulfopyruvate) and 2-aminoethanesulfonic acid (taurine). We observed a pronounced resource partitioning among bacterial clades that utilize distinct organosulfur compounds, which may explain successions of these clades during the studied bloom. Alphaproteobacteria were the most active and degraded a variety of organosulfonates via various metabolic routes. However, we also found previously underreported roles of members of the Bacteroidota and Gammaproteobacteria as efficient degraders of DMSP, DMS, and DMSO2. One striking observation was a strong preference for DMSP cleavage in Bacteroidota as opposed to DMSP demethylation in Alphaproteobacteria and indications for a particular proficiency for taurine utilization in Ilumatobacter_A and Acidimicrobiia. ImportanceSulfur-containing low-molecular-weight algal metabolites play an important role in overall marine carbon and sulfur fluxes. This study highlights that such compounds may play a crucial role in governing the succession of distinct bacterioplankton clades in response to phytoplankton blooms in coastal shelf areas of the temperate zone, such as the German Bight of the North Sea. While Alphaproteobacteria are the most versatile and competitive degraders of dissolved organosulfur compounds during such blooms, this study repositions clades previously thought to play only a more limited role in dissolved organosulfur metabolism in situ, such as Gammaproteobacteria, Bacteroidota, and Acidimicrobiia, as crucial contributors to the remineralization of organosulfur compounds in the upper ocean. This study also highlights the high level of interconnectedness of bacterial carbon and sulfur cycling during phytoplankton blooms.

ecology↗

bioRxiv2024

SusC/D-like proteins in Gammaproteobacteria that utilize fructans

Fructans are ubiquitous in terrestrial ecosystems, however, these glycans are unexplored in the marine environment. We have discovered that the Antarctic gammaproteobacterium Pseudoalteromonas distincta is highly adapted to the degradation of fructose-containing substrates. This is enabled by proteins encoded in several genomic regions, including a fructan polysaccharide utilization locus (PUL). In addition to a glycoside hydrolase from family 32 (GH32), the fructan PUL encodes two proteins that have been described as specific for Bacteroidota and were previously unknown for Gammaproteobacteria: a glycan-binding SusD-like protein and a SusC-like TonB-dependent transporter (TBDT), which work as a complex in glycan import. Proteome analyses and biochemistry results suggest that the SusC/D-like proteins of P. distincta shuttle small-sized inulin-type fructans directly into the cell, where they are degraded by a periplasmic exo-active GH32. A SusD-like protein could provide a competitive adavantage in the absence of extracelluar endo-active inulinases. Comparative genomics identified further SusC/D-like proteins in Gammaproteobacteria, most of which are co-encoded with GH32s, indicative of fructan PULs, and are frequently associated with the marine habitat. Our study thus shows the first known exception to the paradigm that only Bacteroidota use SusC/D-like proteins. It further suggests that fructans contribute to the marine glycan pool.

molecular biology↗

bioRxiv2023

Novel laminarin-binding CBMs in multimodular proteins of marine Bacteroidota feature prominently in phytoplankton blooms

The {beta}-(1,3)-glucan laminarin functions as storage polysaccharide in marine stramenophiles such as diatoms. Laminarin is abundant, water-soluble and structured simply, making it an attractive substrate for marine bacteria. As a consequence, many marine bacteria have developed competitive strategies to scavenge and decompose laminarin, which involves carbohydrate-binding modules (CBMs) as key players. We therefore functionally and structurally characterized two yet unassigned domains as laminarin-binding CBMs in multimodular proteins from our model bacterium Christiangramia forsetii KT0803T, hereby unveiling the novel laminarin-binding CBM families CBMxx and CBMyy (official CAZy numbering will be provided upon acceptance of the manuscript in a peer-reviewed journal). We discovered four CBMxx repeats in a surface glycan-binding protein (SGBP) and a single CBMyy combined with a glycoside hydrolase module from family 16 (GH16_3). Our analyses revealed that both modular proteins have an elongated shape, and that the GH16_3 displayed a higher flexibility than the SGBP. While motility of both polypeptide chains may facilitate recognition and/or degradation of laminarin, constraints in the SGBP may support docking of laminarin onto the bacterial surface. The exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea revealed that both laminarin-binding CBM families are widely distributed among marine Bacteroidota, illustrating the high adaptability of modularity in sugar-binding and -degrading proteins. High expression of CBMxx- and CBMyy-containing proteins during phytoplankton blooms further underpins their importance in marine laminarin usage.

biochemistry↗

bioRxiv2022

The unique structure and replication mode of the replication system of Klebsiella pneumoniae plasmid pIGMS31

Due to their relatively small size and the lack of housekeeping genes, bacterial plasmids are very convenient models for studying DNA replication. So, for a long time, they had been intensively studied in this regard. Unfortunately, only a limited number of model plasmid replication systems were analyzed in detail. In the era of high-throughput DNA sequencing, we are faced with an increasing gap in our knowledge of bacterial plasmid replication and a rapidly growing number of deposited new plasmid genome sequences. For this reason, we decided to investigate the replication system of the pIGMS31 plasmid, a representative of the newly described pHW126-like plasmids family. They are small replicons isolated from different clinical and environmental strains of Gamma proteobacteria. Whole shares unique replication modules with no significant similarities to known model plasmid replication systems. In this study, we identified and characterized the basic elements of the pIGMS31 replication module. Studies on regulatory mechanisms of replication initiation of this plasmid as well as on pIGMS31 replication mode were also performed. We revealed that the pIGMS31 replication module is composed of elements typical for both theta and rolling circle replicons. This mosaic structure is reflected in the unique course of replication of this plasmid, with both modes of replication. What is more, our results led us to conclude that pHW126-like plasmids, despite DNA sequence similarity, are a highly diverse group of replicons.

molecular biology↗