Biology subjects

Kjellin, J.

Publications and source records attributed to Kjellin, J..

7 recordsLinked to original sources

bioRxiv2026

OmrA sRNA Inhibits Translation of Phosphoenolpyruvate Carboxylase to Impair TCA-Cycle Flux

Small RNAs (sRNAs) rarely cause strong growth phenotypes upon overexpression, complicating efforts to link regulatory interactions to physiological outcomes. Here, we report that high levels of the Escherichia coli sRNA OmrA, but not its sibling OmrB, severely inhibit growth in glucose minimal medium. Genetic, biochemical, and physiological analyses indicate that OmrA-dependent toxicity results from reduced flux through the tricarboxylic acid (TCA) cycle. A UV-based suppressor screen identified mutations in the gene encoding Hfq, the RNA-chaperone that aids sRNA-mRNA interactions. Secondly, three independent mutations clustered in the ribosome-binding site of ppc, encoding phosphoenolpyruvate carboxylase, a key anaplerotic enzyme. OmrA directly inhibits Ppc translation via Hfq-dependent base-pairing in the ppc 5' UTR, including the mutated nucleotides obtained in the genetic screen. OmrA is significantly more effective than OmrB in ppc repression in vivo and in vitro, consistent with sequence divergence in their central regions. Supplementation with glutamate, glutamine, or downstream TCA cycle metabolites fully restores growth, linking reduced Ppc levels to metabolic limitation. These results identify ppc as a physiologically relevant OmrA target and suggest how RNA toxicity can uncover central metabolic nodes used by sRNAs to modulate bacterial physiology.

microbiology↗

bioRxiv2026

upSPLAT: Early-Barcoded Library Preparation for Cost-Effective Population-Scale Genomics

Advances in high-throughput sequencing have substantially reduced sequencing costs, yet library preparation remains a major financial and logistical bottleneck, particularly for high-throughput applications or low-quality DNA inputs. Here, we introduce upscaled Splinted Ligation Adapter Tagging (upSPLAT), a library preparation strategy that combines early sample barcoding with single-stranded splinted ligation to enable highly multiplexed pooled sequencing at substancially reduced cost. upSPLAT supports flexible high-plex pooling and reduces per-sample library preparation costs by approximately 10-fold compared to conventional workflows. By leveraging single-strand ligation, upSPLAT is compatible with a wide range of DNA inputs, including degraded, damaged or denatured double stranded DNA, bisulfite or enzymatically converted DNA, and viral single-stranded DNA. We present two complementary workflows and evaluate their performance across multiple species and DNA qualities, demonstrating robust demultiplexing, uniform sample representation, and low barcode cross-assignment. Together, upSPLAT provides a scalable, cost-effective solution for sequencing-based studies requiring large sample numbers while preserving individual-level information.

genomics↗

bioRxiv2026

Roles of bacterial growth competition systems in colonization of the murine gut

The gut microbiome is essential for human health. Although the gut microbiota is largely stable at the species level in healthy individuals, strain-level variation remains less understood. Many bacterial strains encode toxin delivery systems that may shape competition within the gut. Here, we investigate how contact-dependent growth inhibition (CDI) and colicins influence intestinal colonization by a competitive murine Escherichia coli isolate, R12. We show that R12 can colonize an intact mouse gut microbiota by displacing resident Enterobacteriaceae, but success depends on multiple interacting factors. CDI systems and colicins provide a competitive advantage against resident E. coli, particularly during early colonization, while metabolic flexibility and access to alternative carbon sources support long-term persistence. Colonization outcomes vary between hosts and are shaped by resident microbiota composition, strain-level competition, and the initial invader-to-resident ratio. Overall, successful gut invasion is determined by the combined effects of bacterial antagonistic systems, metabolic capacity, and ecological context.

microbiology↗

bioRxiv2024

A delivered DNase toxin creates population heterogeneity through transient intoxication of siblings.

Population heterogeneity is important for multicellular behavior and division of labor. Bacterial toxin delivery has been implicated in generating population heterogeneity, but the molecular mechanisms behind this are not well understood. Here we investigate how CdiA toxins generate heterogeneity in isogenic populations. Using a DNase toxin as proxy, we find that E. coli populations able to deliver the toxin show a heterogeneous expression of the SOS-response gene sulA. Heterogeneity results from excessive delivery of toxin into some cells, which become intoxicated due to insufficient immunity. Intoxication is transiently reversible, and intoxicated cells can be rescued by de novo synthesis of cognate immunity protein. Expression of sulA is regulated by both DNA damage and redox status. Interestingly, kin-delivery changes redox status, whereas intoxicated non-kin cells induce the SOS DNA damage response. The former results in changed expression of metabolic genes whereas the latter induces prophage excision, which may promote horizontal gene transfer. In conclusion, we identify a molecular mechanism by which heterogeneity is generated through toxin delivery among kin, and the consequences of said heterogeneity. Significance statementBacteria communicate through secretion of chemical signaling molecules to perform multicellular behavior. Recent advances suggest that contact-mediated toxin delivery allow bacteria to participate also in direct cell-cell communication. How such toxin-mediated communication would work mechanistically is however unclear. Here we elucidate a molecular mechanism of a toxin-mediated communication, where kin-cells transiently intoxicate each other, resulting in physiological changes. These changes depend on the toxic activity, i.e. other toxins with different activities are likely to give rise to other responses. Thus, the arsenal of toxins that a bacterium harbors could affect their ability to communicate. Understanding the molecular mechanism of how toxins could mediate polyphenism is important for our understanding of what this signaling is used for.

microbiology↗

bioRxiv2024

Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis

Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni-to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.

genomics↗

bioRxiv2023

Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum, and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, greatly expanding the total number of protists harbouring miRNAs. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. Our results show that miRNAs are rapidly lost and gained in Amoebozoa, and that miRNAs were not required for transition from uni- to multicellular life.

evolutionary biology↗

bioRxiv2020

Abundantly expressed class of non-coding RNAs conserved through the multicellular evolution of dictyostelid social amoebae

BackgroundAggregative multicellularity has evolved multiple times in diverse groups of eukaryotes. One of the most well-studied examples is the development of dictyostelid social amoebae, e.g. Dictyostelium discoideum. However, it is still poorly understood why multicellularity emerged in these amoebae while the great majority of other members of Amoebozoa are unicellular. Previously a novel type of non-coding RNA, Class I RNAs, was identified in D. discoideum and demonstrated to be important for normal multicellular development. In this study we investigated Class I RNA evolution and its connection to multicellular development. ResultsNew Class I RNA genes were identified by constructing a co-variance model combined with a scoring system based on conserved up-stream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis validated that our search approach can identify expressed Class I RNA genes with high accuracy and sensitivity. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share several highly conserved structure and sequence motifs. Class I RNA genes appear to be unique to dictyostelid social amoebae since they could not be identified in searches in outgroup genomes, including the closest known relatives to Dictyostelia. ConclusionOur results show that Class I RNA is an ancient abundant class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Taken together, our current knowledge of Class I RNAs suggests that they may have been involved in evolution of multicellularity in Dictyostelia.

evolutionary biology↗