Biology subjects

Swarup, S.

Publications and source records attributed to Swarup, S..

13 recordsLinked to original sources

bioRxiv2026

Components of an ESCRT-independent nuclear envelope assembly pathway

In many cells, the nuclear envelope (NE) must be reassembled after mitosis and holes in the nuclear membrane must be "sealed." During NE assembly, the NE-specific adaptor, Cmp7, recruits/activates ESCRT-III proteins to mediate NE sealing. However, recent evidence suggests the presence of additional mechanisms. In a screen using the fission yeast, S. japonicus, we recently implicated the ESCRT adaptor, Alx1, and a conserved, but little studied protein, Vid27, in Cmp7-independent NE assembly. Here, we provide direct evidence that Alx1 functions in a Cmp7- and ESCRT-independent NE assembly pathway via positive regulation of Vid27. Consistent with a role in membrane remodeling, Vid27 localizes to sites of postmitotic NE sealing and is essential in S. japonicus. Alx1 and Vid27 interact and mutations disrupting the predicted interaction interface abolish Alx1s enhancement of Vid27 function at the NE. These findings define components of a new Cmp7- and ESCRT-independent NE assembly pathway, advancing our understanding of mechanisms that maintain the integrity of the nucleus.

cell biology↗

bioRxiv2025

Live-Exudation Assisted Phytobiome Cultromics System (LEAP-CS): A High-Throughput Cultromics System for Studying Plant-Microbiome Interactions through Non-Contact Metabolic Exchange.

This study introduces an innovative methodology for co-cultivating plants and microbes, employing a membrane-based structure to facilitate their physical separation. The Live-Exudation Assisted Phytobiome Cultromics System (LEAP-CS) has the capability to investigate the complex interaction of plant and soil microbiome under in vitro conditions, offering potential benefits. Subsequent validation and testing can be performed through pot, greenhouse, and field trials. The system can efficiently function as a high-throughput screening tool for assessing plant-microbiome interactions and their associated metabolic signatures. Our phytobiome culturing technique harnesses root exudation from live plants, capitalizing on the membranes selective separation to prevent direct physical interaction between plant and microbiome components. Consequently, the interaction is solely through chemical-mediated signalling. By employing this method, we can intricately dissect complex plant-microbiome interactions while faithfully maintaining and emulating the contact independent inherent associations prevalent within these phytobiomes. In conclusion, this user-friendly and reproducible in-vitro model holds immense potential for shedding light on the intricate community and metabolic exchange dynamics of plant-microbiome interactions, thus significantly advancing our understanding in this area.

plant biology↗

bioRxiv2025

A cell-free bacterial signal orchestrates trans-kingdom fitness tradeoff to enhance sulfur deficiency tolerance in plants

Plant-associated microorganisms interact with each other and host plants via intricate chemical signals, offering multiple benefits, including plant nutrition. We report such a mechanism through which the rhizosphere microbiome improves plant growth under sulfur (S) deficiency. Disruption of plant S homeostasis resulted in a coordinated shift in composition and S-metabolism of the rhizosphere microbiome. Using this insight, we developed an 18-membered synthetic rhizosphere bacterial community (SynCom) that rescued growth of Arabidopsis and a leafy Brassicaceae vegetable under S-deficiency. This beneficial trait is taxonomically widespread among SynCom members, with bacterial pairs predominantly providing synergistic benefits to host plants. Notably, stronger competitive interactions among SynCom members conferred greater fitness benefits to the host, suggesting a trans-kingdom fitness tradeoff. Finally, guided chemical screening, deletion knockout mutant, and targeted metabolomics identified and validated microbially released glutathione (GSH) as the necessary bioactive signal that orchestrates plant-microbe (trans-kingdom) fitness tradeoff and improves plant growth under sulfur limitation. HighlightsO_LIAlteration in plant sulfur (S) homeostasis leads to coordinated shifts in the composition and S-metabolism of the rhizosphere microbiome. C_LIO_LITaxonomically divergent bacterial members within the rhizosphere microbiome improve plant growth under S-deficiency. C_LIO_LIStronger competitive interactions within rhizosphere bacterial members provide greater fitness benefit to the host plant under S-deficiency, suggesting a trans-kingdom fitness tradeoff. C_LIO_LIMicrobially released glutathione (GSH) is a necessary bioactive signal that improves plant growth under sulfur limitation and orchestrates plant-microbe (trans-kingdom) fitness tradeoff. C_LI

microbiology↗

bioRxiv2024

Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2

Lysosomal storage diseases (LSDs) comprise [~]50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multi-omic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lyso-phosphatidylcholine species and multi-lamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS- complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.

cell biology↗

bioRxiv2023

High methane flux in a tropical peatland post-fire is linked to homogenous selection of diverse methanogenic archaea

Tropical peatlands in South-East Asia are some of the most carbon dense ecosystems in the world. Recurrent wildfires in repurposed peatlands release massive amounts of carbon and other greenhouse gases, strongly alter peat geochemistry and physicochemical conditions. However, little is known about the impact of fire on peat microbiome composition, microbial guilds contributing to greenhouse gas emissions, and their predictability based on environmental conditions. Here, we address this gap by studying peat microbiomes from fire-affected and intact areas of a tropical peatland in Brunei using high-throughput sequencing and ecological process modelling at the community and clade levels. We show that fire disrupts depth-stratification of peat microbiomes with the strongest effects observed at 1m below the surface. The enrichment of specific taxa and methanogenic archaea at such depths suggests an adaptation to low-energy conditions post-fire. Finally, fire shifts archaeal community composition and clades containing abundant methanogens in a homogeneous manner that can be predicted from environmental conditions and functional traits. Together, our findings provide a biological basis for earlier work which reported elevated methane flux 2-3 years post-fire and show that such changes follow predictable trajectories with important implications for post-fire microbiome forecasting and ecosystem recovery efforts.

ecology↗

bioRxiv2022

Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3-YIPF4 as membrane receptors for Golgiphagy

During nutrient stress, macroautophagy is employed to degrade cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodeling the proteome. While the machinery responsible for initiation of macroautophagy is well characterized, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms is limited. Here, we use orthogonal proteomic strategies to provide a global molecular inventory of autophagic cargo during nutrient stress in mammalian cell lines. Through prioritization of autophagic cargo, we identify a heterodimeric pair of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF4 is mobilized into ATG8-positive vesicles that traffic to lysosomes as measured via Golgiphagy flux reporters in a process that requires the VPS34 and ULK1-FIP200 arms of the autophagy system. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of Golgi membrane proteins during nutrient stress. By merging absolute protein abundance with autophagic turnover, we create a global protein census describing how autophagic degradation maps onto protein abundance and subcellular localization. Our results, available via an interactive web tool, reveal that autophagic turnover prioritizes membrane-bound organelles (principally Golgi and ER) for proteome remodeling during nutrient stress. One-Sentence SummaryDuring nutrient stress, macroautophagy uses organelle-phagy receptors to prioritize recycling of Golgi and ER membrane proteins.

cell biology↗

bioRxiv2022

Early Endosome Capture Proteomics and its Application to Amyloid Precursor Protein Intramembrane Processing by β and γ-Secretases

Degradation and recycling of plasma membrane-localized proteins occurs via the endolysosomal system, wherein endosomes bud into the cytosol from the plasma membrane and subsequently mature into degradative lysosomal compartments. The endolysosomal system also participates in intracellular membrane protein trafficking, signaling, and protein degradation via autophagy. Our understanding of the endolysosomal system has been significantly advanced through the development of methods for selective capture of lysosomes (termed Lyso-IP), but methods for analogous isolation of early intermediates in the endolysosomal system are lacking. Here, we develop an approach for rapid isolation of early/sorting endosomes through affinity capture of the early endosome-associated protein EEA1 (Endo-IP) and provide proteomic and lipidomic snapshots of early endosomes in action. In addition to resident endosomal components, we identify numerous recycling, regulatory and membrane fusion complexes as well as candidate cargo, providing a proteomic landscape of early/sorting endosomes that we distinguished from lysosomes via comparative proteomics. The approach allows capture of internalized transferrin within minutes of its addition to cells, indicating the utility of the approach for dynamic analysis of early/sorting endosomes. Among the endocytic cargo identified by Endo-IP was the amyloid precursor protein (APP) genetically linked with Alzheimers disease. Processing of APP to amyloidogenic A{beta} peptides by {beta}- and {gamma}-Secretases can occur within the endolysosomal system among other compartments, but methods for spatial quantification of A{beta} products in individual organelles are lacking. We combined Endo- and Lyso-IP with targeted proteomics to provide a spatial digital snapshot of A{beta} products. This analysis revealed that products of A{beta} processing by {beta}- and {gamma}-Secretases, and alterations in the specificity of cleavage by small molecule {gamma}-Secretase modulators, can be quantified in both early/sorting endosomes and lysosomes. We anticipate that the Endo-IP approach will facilitate systematic interrogation of the many processes that are coordinated on early endosomes.

cell biology↗

bioRxiv2021

Progranulin deficiency results in reduced bis(monoacylglycero)phosphate (BMP) levels and gangliosidosis

Homozygous mutations of granulin precursor (GRN) lead to neuronal ceroid lipofuscinosis1, a severe neurodevelopmental disease, in humans and neuroinflammation in mice2. Haploinsufficiency of GRN almost invariably causes frontotemporal dementia (FTD)3,4. The GRN locus produces progranulin (PGRN), a lysosomal precursor protein that is cleaved to granulin peptides5,6. Despite intensive investigation, the function of granulins and the reason why their absence causes neurodegeneration remain unclear. Here, we investigated PGRN function in lipid degradation, a major function of lysosomes. We show that PGRN-knockout human cells, PGRN-deficient murine brain, and frontal lobes of human brains from patients with GRN mutation-related FTD have increased levels of gangliosides, highly abundant sialic acid-containing glycosphingolipids (GSL) that are degraded in lysosomes. Probing how PGRN deficiency causes these changes, we found normal levels and activities of enzymes that catabolize gangliosides. However, levels of bis(monoacylglycero)phosphate (BMP), a lysosomal lipid required for ganglioside catabolism7, were markedly reduced in PGRN-deficient cells and patient brain tissues. These data indicate that granulins are required to maintain BMP levels, which regulate ganglioside catabolism, and that PGRN deficiency in lysosomes leads to gangliosidosis. This aberrant accumulation of gangliosides may contribute to neuroinflammation and neurodegeneration susceptibility.

cell biology↗

bioRxiv2021

Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy

Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding Galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their inter-relationships, remain poorly understood, including the role and identity of cargo receptors required for completion of lysophagy. Here, we employ quantitative organelle capture and proximity biotinylation proteomics of autophagy adaptors, cargo receptors, and Galectins in response to acute lysosomal damage, thereby revealing the landscape of lysosomal proteome remodeling during lysophagy. Among proteins dynamically recruited to damaged lysosomes were ubiquitin-binding autophagic cargo receptors. Using newly developed lysophagic flux reporters including Lyso-Keima, we demonstrate that TAX1BP1, together with its associated kinase TBK1, are both necessary and sufficient to promote lysophagic flux in both Hela cells and induced neurons (iNeurons). While the related receptor OPTN can drive damage-dependent lysophagy when overexpressed, cells lacking either OPTN or CALCOCO2 still maintain significant lysophagic flux in HeLa cells. Mechanistically, TAX1BP1-driven lysophagy requires its N-terminal SKICH domain, which binds both TBK1 and the autophagy regulatory factor RB1CC1, and requires upstream ubiquitylation events for efficient recruitment and lysophagic flux. These results identify TAX1BP1 as a central component in the lysophagy pathway and provide a proteomic resource for future studies of the lysophagy process.

cell biology↗

bioRxiv2020

Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem

Freshwater ecosystems of tropical urban canals systems (TrUCS), are highly dynamic and experience constant pressures from interspersed effects of land-use and rain. The dynamic nature of TrUCS ecosystems presents a unique opportunity to unravel the signature interactions between the macro-organisms (top-down), sedimentary microbial communities (SedMICs), their functioning and the geochemical environment (bottom-up). A systems level understanding of the molecular and mechanistic basis of the highly dynamic behaviour that leads to specific ecosystem outcomes, is currently lacking. Therefore, a research framework to identify the direct link between top-down and bottom-up ecological effects on SedMICs in a highly dynamic urban canal sedimentary system is needed. Here, we present a framework of integrated multi-dimensional data across system-level biotic and abiotic ecological descriptors, such as environmental variables and active SedMICs. We followed the ecosystem shifts after a natural disturbance (rain) in two different anthropogenic disturbance (land-use) regimes. Shifts in profiles of metabolically active community were conserved across different land-use types, indicating resilience to perturbation is an intrinsic property of the TrUCs ecosystem. Three distinct phases, which were dominated sequentially by autotrophy, anoxic-heterotrophy and oxic-heterotrophy, were identified within these shifts. The first two phases were influenced by the bottom-up effects of specific metal-ion combinations of nitrates and sulfates with magnesium, aluminum and iron, and the third phase was triggered by top-down influences of bioturbation. This generalized systems-level approach, which provides an ecosystem-centric understanding of TrUCS and integrates them in sustainable management practices, can also be extended to other freshwater ecosystems.

ecology↗

bioRxiv2020

Crosskingdom growth benefits of fungus-derived phytohormones in Choy Sum

Soil-borne beneficial microbes establish symbioses with plant hosts, and play key roles during growth and development therein. In this study, fungal strains FLP7 and B9 were isolated from the rhizosphere microbiome associated with Choy Sum (Brassica rapa var. parachinen-sis) and barley (Hordeum vulgare), respectively. Sequence analyses of the internal transcribed spacer and 18S ribosomal RNA genes combined with colony and conidial morphology identified FLP7 and B9 to be isolates of Penicillium citrinum. Plant-fungus interaction assays revealed that B9, but not FLP7, showed significant growth promotion effect in Choy Sum cultivated in normal soil, whereas FLP7 enhanced Choy Sum growth under phosphate-limiting condition. In comparison to the mock control, B9-inoculated plants showed a 34% increase in growth in aerial parts, and an 85% upsurge in the fresh weight of roots when cultivated in sterilized soil. The dry biomass of inoculated Choy Sum increased by 39% and 74% for the shoots and roots, respectively. Root colonization assays showed that P. citrinum associates directly with the root surface but does not enter/invade the roots of inoculated Choy Sum plants. Preliminary results also indicated that P. citrinum can promote growth in Choy Sum via volatile metabolites too. Interestingly, we detected relatively higher amounts of indole acetic acid and cytokinins in axenic P. citrinum culture filtrate through liquid-chromatography mass-spectrometry analyses. This could plausibly explain the overall growth promotion in Choy Sum. Furthermore, the phenotypic growth defects associated with the Arabidopsis ga1 mutant could be chemically complemented by the exogenous application of P. citrinum culture filtrate, which also showed accumulation of fungus-derived active gibberellins. Our study underscores the importance of trans-kingdom beneficial effects of such mycobiome-derived phytohormone-like metabolites in host plant growth.

microbiology↗

bioRxiv2019

Host developmental stage is associated with shifts in the exosphere microbiome of urban-farmed Asian green leafy vegetables

Green leafy vegetables (GLVs) comprise a significant part of urban South-East Asian (SEA) diets and are intensively farmed in SEA cities, including Singapore. Urban farming practices and urban-adapted vegetable cultivars likely select for specific above- and below-ground microbial communities - microbiomes - that assemble in close proximity to the plant tissues - the exosphere. A healthy exosphere microbiome is important for plant growth and safe human consumption. Using 16S rDNA gene amplicon sequencing compositional analyses, we show here that the exosphere microbiome of two commonly-consumed GLVs - Choy Sum (Brassica oleracea Alboglabra Group) and Gai Lan (Brassica chinensis var. parachinensis) - dominated by Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Actinobacteria. Shifts in exosphere microbiome composition were strongly associated with plant developmental stage. Finally, microbial taxa consistently detected in the exosphere comprise a small subset, which are predicted to harbour plant-beneficial traits.\n\nSignificanceAmong plant crops, GLVs form an integral part of the Asian diet, especially so in Southeast Asia. Some of these GLVs have short life-cycles ({bsim}30-45 days), which makes them suitable for urban farms in terms of cost advantage as short cycle crops are preferred in urban farms. From a food-security perspective, GLVs forms an important target food group and efforts are being made to increase its productivity to meet the increasing food demands. Current farming practices often place lot of importance on chemical fertilizers and nutrient inputs to improve the fertility of non-arable urban lands to increase the crop productivity. Furthermore, farms in urban settings are also associated with anthropogenic inputs and eutrophic conditions. These together, contribute to negative environmental externalities questioning the sustainability and eco-sustenance of urban farming. Microbial based management systems can not only resolve these challenging issues, but can also enhance plant growth, nutrient use efficiency and disease tolerance. However, their use as microbial adjuncts to agricultural practices is currently limited in urban environments, which could possibly be due to the restricted knowledge-base on these urban phytobiomes.

systems biology↗

bioRxiv2017

Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism

Enterococci are important human commensals and significant opportunistic pathogens associated with endocarditis, urinary tract infections, wound and surgical site infections, and medical device associated infections. These infections often become chronic upon the formation of biofilm. The biofilm matrix establishes properties that distinguish this state from free-living bacterial cells and increase tolerance to antimicrobial interventions. The metabolic versatility of the Enterococci is reflected in the diversity and complexity of environments and communities in which they thrive. Understanding metabolic factors governing colonization and persistence in different host niches can reveal factors influencing the transition from commensal to opportunistic pathogen. Here, we report a new form of iron-dependent metabolism for Enterococcus faecalis where, in the absence of heme, respiration components can be utilised for extracellular electron transfer (EET). Iron augments E. faecalis biofilm growth and generates alterations in biofilm matrix, cell spatial distribution, and biofilm matrix properties. We identify the genes involved in iron-augmented biofilm growth and show that it occurs by promoting EET to iron within biofilm.\n\nSignificanceBacterial metabolic versatility is often key in dictating the outcome of host-pathogen interactions, yet determinants of metabolic shifts are difficult to resolve. The bacterial biofilm matrix provides the structural and functional support that distinguishes this state from free-living bacterial cells. Here, we show that the biofilm matrix provides access to resources necessary for metabolism and growth which are otherwise inaccessible in the planktonic state. Our data shows that in the absence of heme, components of Enterococcus faecalis respiration (l-lactate dehydrogenase and acetaldehyde dehydrogenase) may function as initiators of EET through the cytoplasmic membrane quinone pool and utilize matrix-associated iron to carry out EET. The presence of iron resources within the biofilm matrix leads to enhanced biofilm growth.

microbiology↗