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Ramaswamy, R.

Publications and source records attributed to Ramaswamy, R..

11 recordsLinked to original sources

Microbiome histidine competition mediates dietary control of systemic imidazole propionate

The gut microbiome produces numerous metabolites that influence mammalian health. While microbiome composition and diet influence metabolite concentrations, how these factors interact remains incompletely defined. Here we find production of imidazole propionate (ImP), a microbial metabolite associated with cardiometabolic and neurodegenerative diseases, is determined by the balance of competing metabolic pathways that catabolize histidine to ImP or short-chain fatty acids (SCFAs). We show glutamate serves as a preferred substrate that selectively inhibits histidine conversion to SCFAs, redirecting flux to increased ImP production across mouse- and human-derived microbial communities. We find dietary monosodium glutamate (MSG) acting via this mechanism boosts ImP production in the mouse gut, transiently impairing glucose tolerance and increasing systemic ImP. These findings show that predictable interactions between dietary substrate and microbial competition control systemic ImP levels, providing a mechanistic framework for understanding microbiome metabolite production more broadly.

microbiology↗

Distinct trajectories of urbanization shape the human gut microbiome across South Asia

Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Although urbanization is consistently associated with increased abundance of disease-linked taxa, microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat- and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase non-persistence. Microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography and underscoring the need for community-specific investigations of health impacts.

microbiology↗

Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway

Steroid hormone metabolism by the gut microbiome affects host physiology, but the underlying microbial pathways remain incompletely understood. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducensT strain HCS.1 that reduces cortisol and related steroid hormones to 3{beta},5{beta}-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-{Delta}1-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-- a frontline Crohns disease therapy. OsrB is a 3-oxo-{Delta}4-steroid reductase that converts steroid hormones to 5{beta}-dihydrosteroid intermediates, which OsrC subsequently reduces to 3{beta},5{beta}-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in Crohns disease patient metagenomes. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.

microbiology↗

RNA binding protein Musashi1 interacts with the viral genomic RNA and restricts SARS-CoV-2 infection by repressing translation

Musashi RNA binding proteins are important post-transcriptional regulators of stem cell homeostasis and are known to be involved in viral infections. However, their role in SARS-CoV-2 infection remains largely unknown. Using computational studies, in vivo RNA immunoprecipitation and biochemical assays, here, we establish that Musashi1 (Msi1) interacts with viral genomic RNA through direct binding to the SARS-CoV-2 3UTR. Importantly, binding of Msi1 to the viral 3UTR results in translational repression mediated by inhibition of Poly (A) binding protein (PABP). Conversely, Msi1 knockout promotes robust viral replication and increased viral protein expression. Using 2D cell cultures, stem cells and 3D organoids, we show that depletion of Msi1 in intestinal cells augments infection. This finding explains why the human intestine serves as a reservoir for the SARS-CoV-2 virus, wherein differentiated enterocytes, which have negligible levels of Msi1, are highly affected. Contrarily, stem cells which are enriched for Msi1 expression, are known to be less permissive to SARS-CoV-2 infection despite expressing the entry receptors. Our findings show how translation repression of SARS-CoV-2 by stem cell RNA binding proteins such as Msi1 could help evasion of infection.

cell biology↗

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.

microbiology↗

Cold-induced loss of interaction with HSC70 triggers inflammasome activity of familial cold autoinflammatory syndrome-causing mutants of NLRP3

NLRP3 is a cytoplasmic receptor protein, which initiates caspase-1 mediated inflammatory immune response upon detection of invading pathogen or a wide array of internal distress signals. Several gain-of function mutations of NLRP3 cause hereditary disorder of cold-induced hyper-inflammation known as familial cold autoinflammatory syndrome-1 (FCAS1). Although, caspase-1 activation and downstream interleukin-1{beta} / interleukin-18 maturation are common effectors in pathophysiology of this disorder, molecular mechanisms of how exposure to subnormal temperature triggers mutant NLRP3-inflammsome activity is not understood. Here, we show that endogenous NLRP3 is in complex with HSC70 (HSPA8), and this interaction is reduced upon exposure to cold. FCAS-causing NLRP3-L353P and NLRP3-R260W mutants show enhanced interaction with HSC70. Upon exposure to subnormal temperature, NLRP3-L353P and NLRP3-R260W show enhanced inflammasome formation, increased caspase-1 activation and reduced interaction with HSC70. Knockdown of HSC70 results in increased inflammasome formation by L353P and R260W mutants of NLRP3. Our results suggest that interaction with HSC70 suppresses inflammasome formation by FCAS-causing NLRP3 mutants at physiological temperature, and loss of this inhibitory association at subnormal temperature causes aggravated inflammasome formation and caspase-1 activation leading to interleukin-1{beta} maturation. These results provide evidence for HSC70 being a cold-sensor and a temperature-dependent regulator of inflammatory signaling by FCAS-causing NLRP3 mutants.

immunology↗

Toxoplasma surface coat protein TgSRS57 (TgSAG3) regulates complement deposition, Factor H recruitment, and promotes parasite persistence

The surface coat of Toxoplasma gondii possesses a lectin-like activity that activates host complement. Serum resistance relies on specific recruitment of host regulators Factor H (FH) and C4BP to the parasite surface to inactivate bound C3 and evade the complement system. TgSRS57 (TgSAG3) was previously reported to possess a lectin-like activity specific for sulfated proteoglycans (SPGs) that facilitated host cell attachment and parasite invasion. To investigate whether TgSRS57 actively recruits Factor H to the parasite surface to regulate the complement cascade, we generated Type I RH and Type II CZ1 knockout strains. {Delta}srs57 parasites showed a reduction in both C3 deposition and FH recruitment indicating that TgSRS57 is a C3 acceptor and regulates complement activation. However, {Delta}srs57 parasites showed no attachment defect, possessed normal extracellular survival and intracellular replication kinetics, and were more virulent than WT strains in low dose murine infections, contrary to previous findings. To better understand the genetic and cellular data, we determined the 1.59[A] resolution TgSRS57 crystal structure. Notably, TgSRS57 did not possess a dimer dependent basic surface groove as originally modeled, nor did it bind heparin. However, approximately 10 distinct parasite proteins were identified that interact specifically with SPGs. Infection studies showed that Type II {Delta}srs57 parasites achieved higher parasite burdens and elevated inflammatory responses compared to WT parasites. Infection of C3 deficient mice established that TgSRS57-dependent protection was C3-dependent and that T. gondii actively parasitizes the complement system. Our results suggest that the interaction between TgSRS57 and C3 plays a critical role in disease tolerance by controlling both parasite proliferation and persistence in vivo. AUTHOR SUMMARYThe Toxoplasma gondii surface coat is dominated by a superfamily of developmentally expressed, antigenically distinct adhesins collectively called the SRS proteins, which are structurally analogous to the Plasmodium 6-CYS surface proteins. These proteins are thought to possess lectin-like activities, facilitate parasite attachment and entry into host cells, and regulate innate effectors of the host immune response. Disease tolerance in hosts is critically dependent on the induction of sufficient immunity to limit parasite replication and promote host survival without inducing bystander immune damage. In this study we employed a combination of genetic, cellular and structural biology approaches to establish that the surface antigen TgSRS57 regulates complement C3 deposition on parasite surfaces by specifically recruiting host Factor H to actively resist serum killing and limit the formation of the C5b-9 membrane attack complex. Further, that the presence of C3 was host protective, as C3-deficient mice failed to control parasite replication. The ability of the parasites to inactivate C3 was also necessary to resist serum killing and promote chronic infection. Because complement exists as a potent inflammatory mediator, the active regulation of complement by Toxoplasma ensures that the parasite is not lysed by C3 but also limits the induction of lethal immunopathology, thereby promoting an immune balance, disease tolerance, and the long-term persistence of transmissible parasites.

microbiology↗

Parasitic nematode fatty acid- and retinol-binding proteins compromise host immunity by interfering with host lipid signaling pathways

Parasitic nematodes cause significant morbidity and mortality globally. Excretory/secretory products (ESPs) such as fatty acid- and retinol- binding proteins (FARs) are hypothesized to suppress host immunity during infection, yet little is known about their interactions with host tissues. Leveraging the insect parasitic nematode, Steinernema carpocapsae, we provide the first in vivo study that shows FARs modulate animal immunity, causing an increase in susceptibility to bacterial infection. Next we determined that FARs dampen various aspects of the fly immune response including the phenoloxidase cascade and antimicrobial peptide (AMP) production. Finally, we found that FARs deplete lipid signaling precursors in vivo as well as bind to these fatty acids in vitro, suggesting that FARs elicit their immunomodulatory effects by altering the availability of lipid signaling molecules necessary for a functional immune response. Collectively, these data reveal a complex role for FARs in immunosuppression and provide detailed mechanistic insight into parasitism in phylum Nematoda. SignificanceA central aspect of parasitic nematode success is their ability to modify host biology, including evasion and/or subversion of host immunity. Modulation of host biology and the pathology caused by parasitic nematodes is largely effected through the release of proteins and small molecules. There are hundreds of proteins released by nematodes during an infection and few have been studied in detail. Fatty acid- and retinol-binding proteins (FARs) are a unique protein family released during infection. We report that nematode FARs from S. carpocapsae, C. elegans and A. ceylanicum dampen fly immunity decreasing resistance to infection. Mechanistically, this is achieved through modulation of the phenoloxidase cascade and antimicrobial peptide production. Furthermore, FARs alter the availability of lipid immune signaling precursors in vivo and show binding specificity in vitro. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/436866v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@48f582org.highwire.dtl.DTLVardef@1ee4292org.highwire.dtl.DTLVardef@1548248org.highwire.dtl.DTLVardef@13574d6_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

molecular biology↗

A stochastic model of homeostasis: the roles of noise and nuclear positioning in deciding cell fate

We study a population based cellular model starting from a single stem cell which stochastically divides to give rise to either daughter stem cells or differentiated daughter cells. There are three main components in the model: nucleus position, gene-regulatory network, and stochastic segregation of transcription factors in daughter cells. We study the proportion of self-renewal and differentiated cell lines as a function of the nucleus position, which in turn decides the plane of cleavage. Both nuclear position and noise play an important role in determining the stem cell genealogies and these results can be compared with a Markov model that ignores nucleus position. We have observed long and short genealogies from model simulation which compares well with experimental results from neuroblast and B-cell division. Symmetric cellular divisions were observed when the nucleus is apical, while asymmetric division occurs when the nucleus is towards the base. The number of clones decreases as a function of time in this model, although the average clone size increases.

developmental biology↗

The crystal structure and localization of Trypanosoma brucei invariant surface glycoproteins suggest a more permissive VSG coat in the tsetse-transmitted metacyclic stage

Trypanosoma brucei spp. develop into mammalian-infectious metacyclic trypomastigotes inside the tsetse salivary glands. Besides acquiring a variant surface glycoprotein (VSG) coat, nothing is known about expression of invariant surface antigens by the metacyclic stage. Proteomic analysis of saliva from T. brucei-infected flies revealed a novel family of hypothetical GPI-anchored surface proteins herein named Metacyclic Invariant Surface Proteins (MISP). MISP are encoded by five homolog genes and share ~80% protein identity. The crystal structure of MISP N-terminus at 1.82 [A] resolution revealed a triple helical bundle that shares key features with other trypanosome surface proteins. However, molecular modelling combined with live fluorescent microscopy suggest that MISP N-termini are extended above the metacyclic VSG coat, exposing immunogenic epitopes. Collectively, we suggest that the metacyclic cell surface architecture appears more permissive than bloodstream forms in terms of expression of invariant GPI-anchored glycoproteins, which could be exploited for the development of novel vaccines against African trypanosomiases.

microbiology↗

Modeling long lifespans in eusocial insect populations

Along with division of labour, and life-history complexities, a characteristic of eusocial insect societies is the greatly extended lifespan for queens. The colony structure reduces the extrinsic mortality of the queen, and according to classical evolutionary theories of ageing, this greatly increases the lifespan. We explore the relationship between the evolution of longevity and the evolution of eusociality by introducing age-structure into a previously proposed evolutionary model and also define an associated agent-based model. A set of three population structures are defined: (i) solitary with all reproductive individuals, (ii) monogynous eusocial with a single queen, and (iii) polygynous eusocial, with multiple queens.\n\nIn order to compare the relative fitnesses we compete all possible pairs of these strategies as well as all three together, analysing the effects of parameters such as the probability of progeny migration, group benefits, and extrinsic mortality on the evolution of long lifespans. Simulations suggest that long lifespans appear to evolve only in eusocial populations, and further, that long lifespans enlarge the region of parameter space where eusociality evolves. When all three population strategies compete, the agent-based simulations indicate that solitary strategies are largely confined to shorter lifespans. For long lifespan strategies the solitary behaviour results only for extreme (very low or very high) migration probability. For median and small values of migration probability, the polygynous eusocial and monogynous eusocial strategies give advantage to the population respectively. For a given migration probability, with an increase in lifespan, the dominant strategy changes from solitary to polygynous to monogynous eusociality. The evolution of a long lifespan is thus closely linked to the evolution of eusociality, and our results are in accord with the observation that the breeding female in monogynous eusocial species has a longer lifespan than those in solitary or polygynous eusocial species.

evolutionary biology↗