Biology subjects

Rucks, E. A.

Publications and source records attributed to Rucks, E. A..

5 recordsLinked to original sources

bioRxiv2024

Effect of tryptophan starvation on inclusion membrane composition and chlamydial-host interactions

Chlamydia is an obligate intracellular bacterial pathogen that develops within a membrane-bound vacuole called an inclusion. Throughout its developmental cycle, Chlamydia modifies the inclusion membrane (IM) with type III secreted (T3S) membrane proteins, known as inclusion membrane proteins (Incs). Via the IM, Chlamydia manipulates the host cell to acquire lipids and nutrients necessary for its growth. One key nutrient is tryptophan (Trp). As a Trp auxotroph, Chlamydia is very sensitive to Trp starvation and, in response to low Trp levels induced by the immune response, enters a viable but nonreplicating state called persistence. To maintain viability during persistence, Chlamydia must necessarily maintain both the integrity of the IM and its ability to modify host cell responses, but how Trp starvation affects IM composition and subsequent interactions with the host cell remains poorly understood. We hypothesize that, under Trp starvation conditions, Inc expression/stability or T3S function during persistence alters IM composition but that key host-Chlamydia interactions will be preserved. To examine host-Chlamydia interactions during persistence, we examined sphingomyelin, cholesterol, and transferrin trafficking to the inclusion, as well as localization of host proteins that bind to specific Incs. We identified IM composition changes during persistence by monitoring endogenous Inc abundance at the IM. Chlamydial T3S is generally functional during persistence. Specific changes in Inc composition in the IM can be linked to Trp content of a specific Inc or effector-specific defects in chlamydial T3S. Overall, our findings reveal that critical host-Chlamydia interactions are maintained during persistence mediated by Trp starvation.

microbiology↗

bioRxiv2023

Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence

Upon nutrient starvation, Chlamydia trachomatis serovar L2 (CTL) shifts from its normal growth to a non-replicating form, termed persistence. It is unclear if persistence is an adaptive response or lack of it. To understand that transcriptomics data were collected for nutrient-sufficient and nutrient-starved CTL. Applying machine learning approaches on transcriptomics data revealed a global transcriptomic rewiring of CTL under stress conditions without having any global stress regulator. This indicated that CTLs stress response is due to lack of an adaptive response mechanism. To investigate the impact of this on CTL metabolism, we reconstructed a genome-scale metabolic model of CTL (iCTL278) and contextualized it with the collected transcriptomics data. Using the metabolic bottleneck analysis on contextualized iCTL278, we observed phosphoglycerate mutase (pgm) regulates the entry of CTL to the persistence. Later, pgm was found to have the highest thermodynamics driving force and lowest enzymatic cost. Furthermore, CRISPRi-driven knockdown of pgm and tryptophan starvation experiments revealed the importance of this gene in inducing persistence. Hence, this work, for the first time, introduced thermodynamics and enzyme-cost as tools to gain deeper understanding on CTL persistence.

systems biology↗

bioRxiv2023

FLI1 localization to the chlamydial inclusion involves multiple mechanisms

Following entry into a host cell, the obligate intracellular pathogen, Chlamydia trachomatis, establishes an intracellular niche within a membrane derived vacuole called the chlamydial inclusion. The resulting inclusion membrane is modified by the pathogen and is a hybrid host-chlamydial structure. From within this intracellular niche, C. trachomatis must orchestrate numerous host-pathogen interactions to surreptitiously acquire nutrients from its host and to limit detection by the host innate immune system. C. trachomatis mediates many of these interactions with the host, in part, by using a family of type III secreted membrane proteins, termed inclusion membrane proteins (Incs). Incs are embedded within the inclusion membrane, and some function to recruit host proteins to the inclusion. Two such recruited host proteins are leucine rich repeat Flightless-1 interacting protein 1 (LRRF1/LRRFIP1) and its binding partner Flightless 1 (FLI1/FLII). LRRF1 interacts with Inc protein Ct226. However, interactions of FLI1 with candidate Incs or with LRRF1 during infection have not been defined. We hypothesized that FLI1 recruitment to the inclusion would be dependent on LRRF1 localization. To test this hypothesis, we used siRNA targeting lrrf1 or fli1, revealing that FLI1 can localize to the inclusion independently of LRRF1. Therefore, to further characterize FLI1 localization, we developed and characterized a series of CRISPRi knockdown and complementation strains in C. trachomatis serovar L2 that target ct226 and co-transcribed candidate Incs, ct225 and ct224, to understand the mechanisms of FLI1 and LRRF1 localization to the inclusion. Our results indicate that FLI1 is recruited to the inclusion by multiple mechanisms. IMPORTANCEChlamydia trachomatis is a leading cause of both preventable infectious blindness and bacterial sexually transmitted infections worldwide. Since C. trachomatis must grow and replicate within human host cells, it has evolved several ways of manipulating the host to establish a successful infection. As such, it is important to describe the interactions between host proteins and chlamydial proteins to understand which strategies C. trachomatis uses to shape its intracellular environment. This study looks in detail at such interactions of two host proteins, FLI1 and LRRF1, during chlamydial infection. Importantly, the series of knockdown and complement strains developed in this study suggest these proteins have both independent and overlapping mechanisms for localization, which ultimately will dictate how these proteins function during chlamydial infection.

microbiology↗

bioRxiv2022

Localized Cardiolipin Synthesis is Required for the Assembly of MreB During the Polarized Cell Division of Chlamydia trachomatis

Pathogenic Chlamydia species are coccoid bacteria that use the rod-shape determining protein MreB to direct septal peptidoglycan synthesis during their polarized cell division process. How the site of polarized budding is determined in this bacterium, where contextual features like membrane curvature are seemingly identical, is unclear. We hypothesized that the accumulation of the phospholipid, cardiolipin (CL), in specific regions of the cell membrane induces localized membrane changes that trigger the recruitment of MreB to the site where the bud will arise. To test this, we ectopically expressed cardiolipin synthase (Cls) and observed a polar distribution for this enzyme in Chlamydia trachomatis. In early division intermediates, Cls was restricted to the bud site where MreB is localized and peptidoglycan synthesis is initiated. The localization profile of Cls throughout division mimicked the distribution of lipids that stain with NAO, a dye that labels CL. Treatment of Chlamydia with 3,6-dinonylneamine (diNN), an antibiotic targeting CL-containing membrane domains, resulted in redistribution of Cls and NAO-staining phospholipids. In addition, MreB localization was altered by diNN treatment, suggesting an upstream regulatory role for CL-containing membranes in directing the assembly of MreB. This hypothesis is consistent with the observation that the clustered localization of Cls is not dependent upon MreB function or peptidoglycan synthesis. Furthermore, expression of a CL-binding protein at the inner membrane of C. trachomatis dramatically inhibited bacterial growth supporting the importance of CL in the division process. Our findings implicate a critical role for localized CL synthesis in driving MreB assembly at the bud site during the polarized cell division of Chlamydia.

microbiology↗

bioRxiv2019

Proximity Labeling to Map Host-Pathogen Interactions at the Membrane of a Bacteria Containing Vacuole in Chlamydia trachomatis Infected Human Cells

As an obligate intracellular pathogenic bacterium, C. trachomatis develops within a membrane-bound vacuole, termed the inclusion. The inclusion membrane is modified by chlamydial inclusion membrane proteins (Incs), which act as the mediators of host-pathogen interactions. An in vivo understanding of Inc-Inc and Inc-eukaryotic protein interactions and how these contribute to overall host-chlamydial interactions at this unique membrane is lacking. Previous bacterial two-hybrid studies established that certain Incs have the propensity to bind other Incs while others have limited Inc-Inc interactions. We hypothesize some Incs organize the inclusion membrane whereas other Incs bind eukaryotic proteins to promote chlamydial-host interactions. To test this hypothesis, we used the ascorbate peroxidase proximity labeling system (APEX2), which labels proximal proteins with biotin in vivo, and chose to analyze Inc proteins with varying Inc-binding propensities. We inducibly expressed these Incs fused to APEX2 in Chlamydia trachomatis L2, verified their localization and labeling activities by transmission electron microscopy, and used affinity purification-mass spectrometry to identify biotinylated proteins. To analyze our mass spectrometry results for statistical significance, we used Significance Analysis of INTeractome (SAINT), which demonstrated that our Inc-APEX2 constructs labeled Inc proteins as well as known and previously unreported eukaryotic proteins that localize to the inclusion. Our results broadly support two types of Inc interactions: Inc-Inc versus Inc-host. One eukaryotic protein, LRRFIP1 (LRRF1) was found in all of our Inc-APEX2 datasets, which is consistent with previously published AP-MS datasets. For the first time, we demonstrate by confocal and super-resolution microscopy that endogenous LRRF1 localizes to the chlamydial inclusion. We also used bacterial two-hybrid studies and pulldown assays to determine if LRRF1 was identified as a true interacting protein or was proximal to our Inc-APEX2 constructs. Combined, our data highlight the utility of APEX2 to capture the complex in vivo protein-protein interactions at the chlamydial inclusion.\n\nAuthor summaryMany intracellular bacteria, including the obligate intracellular pathogen Chlamydia trachomatis, grow within a membrane-bound \"bacteria containing vacuole\" (BCV) that, in most cases, prevents association with the lysosome. Secreted cytosolic effectors modulate host activity, but an understanding of the host-pathogen interactions that occur at the BCV membrane is limited by the difficulty in purifying membrane fractions from infected host cells. Here, we used the ascorbate peroxidase proximity labeling system (APEX2), which labels proximal proteins with biotin in vivo, to study the interactions that occur at the chlamydial vacuolar, or inclusion, membrane. The inclusion membrane is modified by chlamydial type III secreted inclusion membrane proteins (Incs), which act as the mediators of host-pathogen interactions. Our results broadly support two types of Inc interactions: Inc-Inc versus Inc-host. Our data highlight the utility of APEX2 to capture the complex protein-protein interactions at a membrane site in vivo in the context of infection.

microbiology↗