Biology subjects

Salje, J.

Publications and source records attributed to Salje, J..

16 recordsLinked to original sources

bioRxiv2026

Complete loss of lipoprotein biosynthesis machinery in an obligate intracellular bacterium

Orientia tsutsugamushi is a cytoplasm-dwelling, obligate intracellular, diderm bacterium with an unusual cell envelope. It lacks lipopolysaccharide and possesses only a minimal peptidoglycan-like cell wall. Here, we report that O. tsutsugamushi also lacks the two acyltransferase components of the lipoprotein biosynthesis pathway (Lgt, Lnt) and the entire lipoprotein transport machinery (Lol system). O. tsutsugamushi encodes several proteins that are conserved as lipoproteins among other organisms, including Pal and components of the beta-barrel assembly machine (BAM) complex, but these lack the canonical lipobox motif, consistent with the absence of lipidation pathways. Instead, we find that O. tsutsugamushi Pal compensates for the lack of lipidation by incorporating two predicted amphipathic helices, a feature not observed in Pal homologues from other organisms. These findings suggest that O. tsutsugamushi has compensated for a lack of lipoprotein assembly machinery through alternative mechanisms. We speculate on the possible evolutionary advantage of this highly unusual loss of the lipoprotein biosynthesis machinery in the context of an already minimal cell envelope.

microbiology↗

bioRxiv2026

Gentamicin Treatment in a Murine Infection Model Suggests Extracellular Orientia tsutsugamushi Contributes to Systemic Dissemination

Orientia tsutsugamushi, an obligate intracellular bacterial pathogen, infects multiple cell types and disseminates via the blood and lymphatic system to affect various organs in human and other mammalian hosts. This bacterium replicates exclusively within living cells; however, it also exists transiently in a metabolically inactive extracellular form. While infected leukocytes are known contributors to the systemic spread of the bacterium, the role of the inactive extracellular form in dissemination has been unclear. In this study, we demonstrate that extracellular bacteria are present in the cell-free plasma fraction of infected human and murine blood. Furthermore, treatment with gentamicin, a membrane-impermeable antibiotic, significantly reduces systemic bacterial growth in a murine infection model. These findings suggest a potential role for the extracellular form of the bacterium in the spread of infection and raise the possibility of exploring the use of gentamicin to augment conventional antibiotic therapy during scrub typhus infection.

microbiology↗

bioRxiv2026

Symmetric Inheritance of the Cytoplasmic Bacterium Orientia tsutsugamushi During Mitosis

For long-term stable residence within host cells, endosymbionts must evolve mechanisms to ensure their segregation into both daughter cells during cell division, and to coordinate their division with the host cell cycle. This regulation was also a prerequisite for the evolution of mitochondria, enabling their transition from free-living bacteria to an organelle. Here, we examine Orientia tsutsugamushi and Rickettsia rhipicephali, two obligate intracellular Rickettsiales that replicate directly in the host cytoplasm, during host mitosis. Using cell cycle synchronisation and immunofluorescence microscopy, we demonstrate that O. tsutsugamushi frequently localise near the spindle poles during mitosis, and are distributed between daughter cells in a manner dependent on its surface protein ScaC, that drives dynein-dependent motility of the bacterium along microtubules. In contrast, R. rhipicephali, which does not interact with microtubules, largely inhibits host mitosis and is randomly distributed in the few cells that divide. Overall, our findings reveal distinct strategies for mitotic adaptation among these two Rickettsiales and suggest that associations with the hosts cytoskeletal elements may be critical for near-equal distribution into daughter cells.

cell biology↗

bioRxiv2026

A genome-wide RNAi screen identifies host cell cycle regulation as a determinant of Orientia tsutsugamushi infection

Orientia tsutsugamushi (Ot) is an obligate intracellular bacterium that causes scrub typhus, a potentially life-threatening disease. To systematically identify host factors regulating early stages of infection, we performed a microscopy-based genome-wide siRNA screen in HeLa cells. This approach identified 2,989 genes grouped into 55 functional networks that modulate bacterial entry and intracellular translocation. In addition to confirming previously described pathways, including endocytosis and microtubule-dependent trafficking, the screen revealed an association between Ot infection and host cell cycle regulation. We found that Ot preferentially infects and/or replicates in host cells in the S and G2 phases, where intracellular bacterial accumulation is increased relative to G1. Early infection was associated with a shift in host cell cycle distribution, consistent with a delay in progression through S and G2 phases. Longitudinal analysis further showed that these cell cycle states support enhanced bacterial expansion. In parallel, infected cells exhibited reduced proliferation compared to uninfected cells, suggesting that Ot infection alters host cell division dynamics. Together, these findings support a model in which host cell cycle state influences susceptibility to Ot infection and intracellular growth. This work provides a systems-level map of host pathways involved in early infection and identifies cell cycle regulation as an important component of host-pathogen interactions in scrub typhus. Author SummaryScrub typhus is a potentially life-threatening disease caused by the bacterium Orientia tsutsugamushi, which can only survive and replicate inside human cells. Although some host factors involved in infection have been identified, many remain unknown. In this study, we used a large-scale screening approach to systematically identify human genes that influence the bacteriums ability to enter and move within host cells. Our analysis uncovered multiple pathways required for infection, including a role for the host cell cycle. We found that O. tsutsugamushi preferentially accumulates in cells during specific stages of the cell cycle, particularly when cells are preparing to divide. At the same time, infection slows host cell division, suggesting that the bacterium alters the cellular environment to support its own growth. These findings provide new insight into how O. tsutsugamushi interacts with human cells and identify potential host processes that could be targeted to limit infection.

cell biology↗

bioRxiv2025

Morphological and molecular characterisation of Orientia tsutsugamushi grown in tick cells

Orientia tsutsugamushi (Ot), the causative agent of scrub typhus, is an obligate intracellular bacterium naturally maintained in Leptotrombidium mites, yet its interactions within arthropod hosts remain poorly understood. Here, we developed two tick cell lines, Ixodes scapularis ISE6 and Rhipicephalus microplus BME/CTVM23, as arthropod models to investigate the intracellular lifecycle of Ot strains TA686 and Karp. Both strains efficiently infected and replicated within tick cells, with ISE6 supporting more robust growth. Electron microscopy images revealed that Ot maintains its characteristic cytoplasmic, non-vacuolar location in tick cells and exits infected cells by budding off the surface in a membrane-encased structure. Time-course immunofluorescence imaging demonstrated progressive intracellular replication and dynamic expression of Ot outer membrane autotransporters ScaA and ScaC, with ScaC enriched early in infection and ScaA at later stages. Metabolic labelling using a clickable methionine analog L-homopropargylglycine showed that high ScaA abundance correlated with reduced translational activity, suggesting a link between ScaA abundance and late-stage or extracellular-like developmental states. The subcellular location of Ot in tick cells differs from the characteristic dynein-driven perinuclear clustering observed in mammalian cells, and was not sensitive to disruption of microtubules, indicating a distinct mode of distribution. Together, these findings identify tick cell lines as tractable and biologically relevant arthropod models for studying Ot and dissecting host-microbe interactions.

microbiology↗

bioRxiv2025

Developmental Progression and Single-Cell Heterogeneity of Orientia tsutsugamushi during Intracellular Infection

Orientia tsutsugamushi, the causative agent of human scrub typhus disease, is an obligate intracellular bacterium transmitted by mites. It replicates exclusively within eukaryotic cells, inhabiting a range of host cell types in mammals and mites. Previously, we demonstrated that its extracellular, non-replicative form is developmentally distinct from the intracellular replicative form. In this study, we investigated spatial and temporal heterogeneity within the intracellular bacterial population. By quantifying bacterial DNA replication, protein synthesis, cell division, and subcellular localization, we defined four distinct intracellular growth stages: pre-active, lag, log, and maturation. Using microscopy-based single-cell analysis of selected transcripts and proteins, we further revealed transcriptional and translational heterogeneity within microcolonies. These findings highlight the complex, asynchronous nature of intracellular O. tsutsugamushi growth and underscore the importance of single-cell analysis in understanding its pathobiology. ImportanceScrub typhus is a serious, sometimes life-threatening disease caused by the bacterium Orientia tsutsugamushi, which is spread by the bites of tiny mites and is common in many rural parts of Asia. This bacterium can only survive and grow inside living cells, where hundreds of individual bacteria may infect a single host cell. Until now, it was unclear whether all the bacteria inside a cell behaved the same way or if they existed in different stages of growth. In this study, we show that O. tsutsugamushi goes through several distinct stages while growing inside host cells and that not all bacteria are at the same stage at the same time. Even within a single infected cell, some bacteria are actively dividing, while others are preparing to leave the cell. Understanding these stages provides a new framework for exploring how the bacterium develops, spreads, and causes disease -- insights that could help guide future research and improve ways to control or treat scrub typhus.

microbiology↗

bioRxiv2025

High levels of antisense transcription from numerous genes in the obligate intracellular bacterium Orientia tsutsugamushi.

Orientia tsutsugamushi (Ot) is a cytoplasmic, Gram-negative, obligate intracellular bacterium that causes the human disease scrub typhus. It has a highly repetitive genome whereby approximately 50% is composed of multiple copies of a proliferated integrative and conjugative element, the Rickettsial amplified Genetic Element (RAGE). Previous RNA sequencing analysis revealed a high level of antisense transcription in Ot, particularly from RAGE-encoded genes, with 18% of all genes having a sense:antisense ratio <1 and 5% with a ratio <0.1. In our current study, we have confirmed the earlier RNA sequencing findings via PCR-based methods and established that this antisense transcription is a consistent feature across eight distinct Ot strains. Furthermore, we have utilized PCR to monitor differences in sense and antisense expression between intracellular and extracellular bacteria. Our findings lend weight to the hypothesis that antisense transcription in Ot is a regulated mechanism, possibly playing a crucial role in the pathogens lifecycle during infection.

microbiology↗

bioRxiv2025

Comparative Dual RNA-Seq Analysis of Eight Orientia tsutsugamushi Strains in Endothelial Cells Reveals Regulatory Patterns in Bacterial and Host Pathways During Infection

Orientia tsutsugamushi is an obligate intracellular bacterium that causes the mite-borne human disease scrub typhus. The species is characterised by having many strains that differ in their ability to cause disease in murine infection models and in human patients. The genomes of a diverse set of Orientia tsutsugamushi strains have recently been analysed in detail, revealing broadly similar gene content with genomes differing primarily in synteny and in the composition of a large arsenal of predicted secreted effector proteins. Given the similarity in gene content, here we asked whether the observed differences in virulence were driven by genome-wide differences in gene expression of bacterial genes, and differences in the ensuing response of infected host cells. To explore this, we carried out a dual RNA sequencing analysis of eight diverse strains of Orientia tsutsugamushi grown in cultured human endothelial cells. An overall analysis found no clear patterns in the bacterial or host gene expression patterns that correlate with the ability to cause disease. We found that all strains induce a strong type 1 interferon response in endothelial cells, but that within that broad response each strain has a unique fingerprint of induced genes likely leading to different disease outcomes when combined with a complex immune system in vivo. We compared expression levels of orthologous genes between different strains and identified some bacterial pathways with constant expression levels whilst others were more variable, leading to the identification of specific pathways under tight transcriptional control during cellular infection. Together our data show that inter-strain differences in virulence are not defined by expression levels of any one set of bacterial or host genes and also reveal insights into transcriptional regulation of different pathways in Orientia tsutsugamushi.

microbiology↗

bioRxiv2025

Comparative virulence analysis of seven diverse strains of Orientia tsutsugamushi reveals a multifaceted and complex interplay of virulence factors responsible for disease.

Orientia tsutsugamushi is an obligate intracellular bacterium found in Leptotrombidium mites that causes the human disease scrub typhus. A distinguishing feature of O. tsutsugamushi is its extensive strain diversity, yet differences in virulence between strains are not well defined nor well understood. We sought to determine the bacterial drivers of pathogenicity by comparing murine infections using seven strains combined with epidemiological human data to rank each strain in terms of relative virulence. Murine cytokine expression data revealed that the two most virulent strains, Ikeda and Kato, induced higher levels of IL-6, IL-10, IFN-{gamma} and MCP-1 than other strains, consistent with increased levels of these cytokines in severe human scrub typhus patients. We sought to identify the mechanistic basis of the observed differential virulence between strains by comparing their genomes, in vitro growth properties and cytokine/chemokine induction in host cells. We found that there was no single gene or gene group that correlated with virulence, and no clear pattern of in vitro growth rate that predicted disease. However, microscopy-based analysis of the intracellular infection cycle revealed that the only fully avirulent strain in our study, TA686, differed from all the virulent strains in its subcellular localisation and expression of its surface protein ScaC. We conclude that drivers of pathogenicity in Orientia tsutsugamushi are distributed throughout the genome, likely in the large and varying arsenal of effector proteins encoded by different strains, and that these interact in complex ways to induce differing immune responses and thus differing disease outcomes in mammalian hosts. Author SummaryScrub typhus is a vector-borne human disease caused by the bacterium Orientia tsutsugmushi and spread by mites. There are numerous different strains of this bacterium with some causing more severe disease in humans than others, and some that do not cause any illness at all. The factors driving these differences are not yet understood, and gaining insight into them could aid in vaccine development and help predict the severity of disease caused by new isolates. To better determine the mechanistic basis of pathogenicity in scrub typhus, we carried out experiments in which we compared seven diverse strains for virulence in animals. We measured their ability to cause disease in mice, so that we could reliably classify them as virulent or avirulent in this model. We then analysed various genomic and biological aspects to identify disease markers in both mice and humans. We report here that there is no single factor that predicts whether a strain will be pathogenic or not, but that disease in scrub typhus is a complex process resulting from the activity of multiple bacterial genes working together to drive different immune responses in the host, resulting in either clearance of the bacteria from the host, or escalating disease. Future work exploring the relationship of bacterial effector proteins will help to disentangle this complex relationship in mechanistic detail.

microbiology↗

bioRxiv2024

A comparison of super-resolution microscopy techniques for imaging tightly packed microcolonies of an obligate intracellular bacterium

Conventional optical microscopy imaging of obligate intracellular bacteria is hampered by the small size of bacterial cells, tight clustering exhibited by some bacterial species and challenges relating to labelling such as background from host cells, a lack of validated reagents, and a lack of tools for genetic manipulation. In this study we imaged intracellular bacteria from the species Orientia tsutsugamushi (Ot) using five different fluorescence microscopy techniques: standard confocal, Airyscan confocal, instant Structured Illumination Microscopy (iSIM), three-dimensional Structured Illumination Microscopy (3D-SIM) and Stimulated Emission Depletion Microscopy (STED). We compared the ability of each to resolve bacterial cells in intracellular clumps in the lateral (xy) axis, using full width half maximum (FWHM) measurements of a labelled outer membrane protein (ScaA) and the ability to detect small, outer membrane vesicles external to the cells. We next compared the ability of each technique to sufficiently resolve bacteria in the axial (z) direction and found 3D-STED to be the most successful method for this. We then combined this approach with a custom 3D cell segmentation and analysis pipeline using the open-source, deep learning software, Cellpose to segment the cells and subsequently the commercial software Imaris to analyze their 3D shape and size. Using this combination, we demonstrated differences in bacterial shape, but not their size, when grown in different mammalian cell lines. Overall, we compare the advantages and disadvantages of different super-resolution microscopy techniques for imaging this cytoplasmic obligate intracellular bacterium based on the specific research question being addressed.

microbiology↗

bioRxiv2024

The intracellular bacterium Orientia tsutsugamushi hijacks the adaptor protein BICD2 for dynein-based motility

The intracellular bacterium Orientia tsutsugamushi relies on the microtubule cytoskeleton and the motor protein dynein to traffic to the perinuclear region within infected cells. However, it remains unclear how the bacterium is coupled to the dynein machinery and how transport is regulated. Here, we discover that O. tsutsugamushi uses its autotransporter protein ScaC to recruit the dynein adaptor BICD2 to the bacterial surface. We show that ScaC is sufficient to engage dynein-based motility in the absence of other bacterial proteins and that BICD2 is required for efficient movement of O. tsutsugamushi during infection. Using TIRF single-molecule assays, we demonstrate that ScaC induces BICD2 to adopt an open conformation which activates the assembly of dynein-dynactin complexes. Our results reveal a novel role for BICD2 during bacterial infection and provide mechanistic insights into the life cycle of an important human pathogen.

microbiology↗

bioRxiv2023

Orientia tsutsugamushi: analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium.

The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its [~]2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra) type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.

microbiology↗

bioRxiv2020

Developmental differentiation in a cytoplasm-dwelling obligate intracellular bacterium

Orientia tsutsugamushi (Ot) is an obligate intracellular bacterium in the family Rickettsiaceae that causes scrub typhus, a severe mite-borne human disease. Its mechanism of cell exit is unusual amongst Rickettsiaceae, as Ot buds off the surface of infected cells enveloped in plasma membrane. Here, we show that Ot bacteria that have budded out of host cells are in a distinct developmental stage compared with intracellular bacteria. We refer to these two stages as intracellular and extracellular bacteria (IB and EB, respectively). These two forms differ in physical properties: IB is elongated, and EB is round. Additionally, IB has higher levels of peptidoglycan and is physically robust compared with EB. The two bacterial forms differentially express proteins involved in bacterial physiology and host-pathogen interactions, specifically those involved in bacterial dormancy and stress response, secreted bacterial effectors, and outer membrane autotransporter proteins ScaA and ScaC. Whilst both populations are infectious, entry of IB Ot is sensitive to inhibitors of both clathrin-mediated endocytosis and macropinocytosis, whereas entry of EB Ot is only sensitive to a macropinocytosis inhibitor. Our identification and detailed characterization of two developmental forms of Ot significantly advances our understanding of the intracellular lifecycle of an important human pathogen. Author SummaryOrientia tsutsugamushi (Ot) is a bacterial pathogen that causes scrub typhus, a mite-transmitted human disease. This illness is traditionally known to be endemic in the Asia-Pacific, but recent reports of Orientia-like organisms from the Middle East, Africa, and Latin America suggest that it may be globally distributed. Scrub typhus is associated with high mortality if not treated promptly with appropriate antibiotics. Ot is a highly specialized bacterium that can only replicate within living cells, either within the mite vector or in mammalian or human hosts. Ot exits infected cells using a unique mechanism that involves budding off the surface of infected cells. We have discovered that this unusual aspect of its lifecycle involves the bacteria themselves differentiating into a distinct growth form. Different growth forms have not been described in other members of the family Rickettsiaceae, and no other family members have been shown to bud out of host cells in a manner similar to Ot. We find that the two forms of Ot, which we refer to as intracellular and extracellular bacteria (IB and EB respectively), differ in physical properties and protein expression and infect cells through different mechanisms. The identification of structurally and functionally distinct forms of Ot elucidates a vital aspect of this pathogens intracellular life cycle. The two forms are likely to have different antibiotic susceptibilities, therefore our findings may advance the development of novel interventions aimed at inhibiting Ot growth in scrub typhus patients.

microbiology↗

bioRxiv2019

Clickable methionine as a universal probe for labelling intracellular bacteria

Despite their clinical and biological importance, the cell biology of obligate intracellular bacteria is less well understood than that of many free-living model organisms. One reason for this is that they are mostly genetically intractable. As a consequence, it is not possible to engineer strains expressing fluorescent proteins and therefore fluorescence light microscopy - a key tool in host-pathogen cell biology studies - is difficult. Strain diversity limits the universality of antibody-based immunofluorescence approaches. Here, we have developed a universal labelling protocol for intracellular bacteria based on a clickable methionine analog. Whilst we have applied this to obligate intracellular bacteria, we expect it to be useful for labelling free living bacteria as well as other intracellular pathogens.

microbiology↗

bioRxiv2019

Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi

Emerging and neglected diseases pose challenges as their biology is frequently poorly understood, and genetic tools often do not exist to manipulate the responsible pathogen. Organism agnostic sequencing technologies offer a promising approach to understand the molecular processes underlying these diseases. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium and the causative agent of the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning, we investigated the transcriptional architecture of Ot, including operon structure and non-coding RNAs, and found evidence for wide-spread post-transcriptional antisense regulation. We compared the host response to two clinical isolates and identified distinct immune response networks that are up-regulated in response to each strain, leading to predictions of relative virulence which were confirmed in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.

microbiology↗

bioRxiv2018

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

BackgroundOrientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species.\n\nResultsWe report new high-quality genomes of Orientia tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia.\n\nConclusionsComplete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have large genomes with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.

genomics↗