Biology subjects

Malitsky, S.

Publications and source records attributed to Malitsky, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Intracellular carbon storage enables starvation survival in marine bacteria

Heterotrophic marine bacteria frequently experience fluctuations in carbon availability driven by phytoplankton dynamics. As a result, bacteria undergo repeated cycles of rapid growth during brief resource pulses followed by prolonged starvation. Yet the mechanisms that support bacterial survival during nutrient limitation remain poorly understood. Here, we investigate starvation survival in the algal-associated bacterium Phaeobacter inhibens. We show that cells remain viable for extended periods under carbon depletion while undergoing physiological and morphological changes. Using electron microscopy, metabolomics, and genetic approaches, we identify intracellular polyhydroxybutyrate (PHB) granules as a key factor supporting survival during starvation. PHB accumulates during growth and is progressively consumed under carbon limitation. Deletion of the PHB synthase gene (phaC) eliminates granule formation and reduces long-term viability. Comparative analyses show that the genetic capacity for PHB biosynthesis is widespread among members of the Roseobacter group, suggesting a conserved strategy among algal-associated bacteria. However, species lacking PHB also survive starvation, indicating that additional mechanisms contribute to persistence under nutrient limitation. Together, our results identify intracellular carbon storage as a central mechanism linking bacterial physiology to survival in fluctuating marine environments, and highlight the diversity of strategies shaping microbial community dynamics and carbon cycling in the ocean.

microbiology↗

bioRxiv2026

Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases

Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts.

microbiology↗

bioRxiv2025

A multiplexed approach for genetic screening of human cells by electron microscopy uncovers a critical effector of mitochondrial cristae shape

Mitochondria form complex and diverse membrane-architectures essential for their multiple functions. Whereas critical proteins sculpting mitochondrial membranes have been identified, the molecular basis for many key features remains enigmatic. Exploration of membrane ultrastructure, in general, is limited by the tradeoff between resolution and throughput: electron microscopy (EM) is essential to resolve their ultrastructure but lacks scalability for systematic functional discovery. To overcome this limitation, we developed a high-resolution screening pipeline for EM of multiplexed human cell pools, hMultiCLEM (human Multiplexed Correlative Light and EM). To showcase the power of hMultiCLEM we performed a genetic screen exploring mitochondrial ultrastructure. hMultiCLEM confirmed proposed cristae modulators and uncovered additional ones illuminating the protein networks driving cristae organization. Validation of candidates highlighted an intermembrane space (IMS) protein linked to Menieres disease, which we named MISHA (Mitochondrial-IMS membrane-SHApe-impacting protein). More broadly, hMultiCLEM transforms the EM field, enabling genetic/chemical screening in basic and medical research.

cell biology↗

bioRxiv2025

Bacteria sense virus-induced genome degradation via methylated mononucleotides

Phages often degrade the genome of their bacterial host to individual nucleotides and use these nucleotides to build their own genome. In this study, we describe a bacterial defense system that directly senses phage-mediated host genome degradation. This system, called Metis, aborts phage infection once it detects the accumulation of the modified mono-nucleotide N-methyl-deoxyadenosine monophosphate (mdAMP). As methylation of deoxy adenosines occurs only in the context of the DNA polymer, intracellular accumulation of mdAMP serves as a definitive signal that the host genome has been degraded to its individual constituents. In type I Metis, sensing of mdAMP activates an NAD+ diphosphatase, leading to rapid NAD depletion and cessation of the infection process; while the effector in type II Metis is a transmembrane-spanning protein whose toxicity is triggered in response to the modified mono-nucleotide. We further show that Metis defense depends on endogenous DNA methylases, and that phages can escape Metis via mutations that inactivate phage-mediated host genome degradation. Our results demonstrate how molecular byproducts released during virus-induced cell exploitation can be used as specific danger signals that trigger host immunity.

microbiology↗

bioRxiv2025

Algal Betaine Triggers Bacterial Hydrogen Peroxide Production that Promotes Algal Demise

Hydrogen peroxide (H2O2) plays various roles in the ocean, acting as a signaling molecule at low concentrations and causing oxidative stress when accumulated. While many marine microbes produce H2O2, its role in microbial interactions remains unclear. Here, we used transcriptomics, genetics, and metabolomics to study H2O2 dynamics in the interaction between Emiliania huxleyi algae and Phaeobacter inhibens bacteria. We found that H2O2 levels rise during algal death and that bacterial H2O2 production triggers this demise. Manipulating H2O2 levels shifted the outcome of the interaction. We also uncovered a link between H2O2 and betaine metabolism: aging algae release betaine, which promotes bacterial H2O2 production and, in turn, accelerates algal death. Genes involved in H2O2 and betaine metabolism were upregulated in environmental samples from an algal bloom. Together, our findings identify H2O2 and betaine as key molecules that modulate algal-bacterial interactions, potentially impacting microbial dynamics in marine ecosystems.

microbiology↗

bioRxiv2025

A pipeline for screening condition-specific enzymes uncovers a function for the alcohol dehydrogenase Bdh2

Cells possess intricate metabolic networks comprised of hundreds of enzymes. Despite extensive research, many of these enzymes remain uncharacterized. Identifying such enzymes is crucial for advancing our understanding of metabolism. However, multiple enzymes are not expressed in standard conditions, making them challenging to study. To overcome this challenge, we created a pipeline for characterizing the expression of condition-specific enzymes in yeast. We assembled a collection of 110 yeast strains, each containing an uncharacterized putative enzyme fused to a fluorophore under the regulation of their own promotor. By subjecting them to 43 diverse growth or stress environments, we identified the biologically relevant conditions for the expression of 19 proteins. We focused on one such putative alcohol dehydrogenase, Bdh2, and functionally characterized it. More broadly, our discovery pipeline lays the foundation for uncovering new condition-specific enzymes. This has implications in cell biology and biotechnology and should expand our understanding of metabolism.

cell biology↗

bioRxiv2024

TIR signaling activates caspase-like immunity in bacteria

Proteases of the caspase family, as well as Toll/Interleukin-1 Receptor (TIR)-domain proteins, have central roles in innate immunity and regulated cell death in humans. In this study we describe a bacterial immune system comprising both a caspase-like protease and a TIR-domain protein. We found that the TIR protein, once it recognizes phage invasion, produces the previously unknown immune signaling molecule ADP-cyclo[N7:1'']-ribose (N7-cADPR). This molecule specifically activates the bacterial caspase-like protease which then indiscriminately degrades cellular proteins to halt phage replication. The TIR-caspase defense system, which we denote as type IV Thoeris, is abundant in bacteria and efficiently protects against phage propagation. Our study highlights the diversity of TIR-produced immune signaling molecules and demonstrates that cell death regulated by proteases of the caspase family is an ancient mechanism of innate immunity.

microbiology↗

bioRxiv2024

The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites

Contact-sites are specialized zones of proximity between two organelles, essential for organelle communication and coordination. The formation of contacts between the Endoplasmic Reticulum (ER), and other organelles, relies on a unique membrane environment enriched in sterols. However, how these sterol-rich domains are formed and maintained had not been understood. We found that the yeast membrane protein Yet3, the homolog of human BAP31, is localized to multiple ER contact sites. We show that Yet3 interacts with all the enzymes of the post-squalene ergosterol biosynthesis pathway and recruits them to create sterol-rich domains. Increasing sterol levels at ER contacts causes its depletion from the plasma membrane leading to a compensatory reaction and altered cell metabolism. Our data shows that Yet3 provides on-demand sterols at contacts thus shaping organellar structure and function. A molecular understanding of this proteins functions gives new insights into the role of BAP31 in development and pathology.

cell biology↗

bioRxiv2024

Phages reconstitute NAD+ to counter bacterial immunity

Bacteria defend against phage infection via a variety of antiphage defense systems. Many defense systems were recently shown to deplete cellular nicotinamide adenine dinucleotide (NAD+) in response to infection, by breaking NAD+ to ADP-ribose (ADPR) and nicotinamide. It was demonstrated that NAD+ depletion during infection deprives the phage from this essential molecule and impedes phage replication. Here we show that a substantial fraction of phages possess enzymatic pathways allowing reconstitution of NAD+ from its degradation products in infected cells. We describe NAD+ reconstitution pathway 1 (NARP1), a two-step pathway in which one enzyme phosphorylates ADPR to generate ADPR-pyrophosphate (ADPR-PP), and the second enzyme conjugates ADPR- PP and nicotinamide to generate NAD+. Phages encoding the NARP1 pathway can overcome a diverse set of defense systems, including Thoeris, DSR1, DSR2, SIR2-HerA, and SEFIR, all of which deplete NAD+ as part of their defensive mechanism. Phylogenetic analyses show that NARP1 is primarily encoded on phage genomes, suggesting a phage- specific function in countering bacterial defenses. A second pathway, NARP2, allows phages to overcome bacterial defenses by building NAD+ via metabolites different than ADPR-PP. Our findings report a unique immune evasion strategy where viruses rebuild molecules depleted by defense systems, thus overcoming host immunity.

microbiology↗

bioRxiv2023

High-energy demand and nutrient exhaustion in MTCH2 knockout cells

Mitochondrial carrier homolog 2 (MTCH2) is a regulator of apoptosis, mitochondrial dynamics, and metabolism. Loss of MTCH2 results in mitochondrial fragmentation, an increase in whole-body energy utilization, and protection from diet-induced obesity. We now show using temporal metabolomics that MTCH2 deletion results in a high ATP demand, an oxidized environment, a high lipid/amino acid/carbohydrate metabolism, and in the decrease of many metabolites. Lipidomics analyses show a strategic adaptive decrease in membrane lipids and an increase in storage lipids in MTCH2 knockout cells. Importantly, all the metabolic changes in the MTCH2 knockout cells were rescued by MTCH2 re-expression. Interestingly, this imbalance in energy metabolism and reductive potential triggered by MTCH2-deletion inhibits adipocyte differentiation, an energy consuming reductive biosynthetic process. In summary, loss of MTCH2 results in an increase in energy demand that triggers a catabolic and oxidizing environment, which fails to fuel the anabolic processes during adipocyte differentiation.

cell biology↗

bioRxiv2023

The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure

An essential interaction between sunlight and eukaryotes involves the production of vitamin D through exposure to ultraviolet (UV) radiation. While extensively studied in vertebrates, the role of vitamin D in non-animal eukaryotes like microalgae remains unclear. To investigate the potential involvement of vitamin D in the response of microalgae to UV, we focus on Emiliania huxleyi, a microalga found in shallow ocean depths that are exposed to UV radiation. Our results show that E. huxleyi algae produce vitamin D2 and D3 in response to UV irradiation. We further demonstrate that E. huxleyi algae respond to external administration of vitamin D at the transcriptional level, regulating the expression of protective mechanisms that are also regulated in response to UV. Our data reveal that addition of vitamin D enhances the algal photosynthetic performance while reducing harmful reactive oxygen species buildup. This study contributes to understanding the function of vitamin D in E. huxleyi and sheds light on its role in non-animal eukaryotes, as well as its potential importance in marine ecosystems.

microbiology↗

bioRxiv2023

Bacterial lag phase shortening is triggered by methyl groups

The bacterial lag phase is a key period for resuming growth. Despite its significance, the lag phase remains underexplored, particularly in environmental bacteria. Here, we explore the lag phase of the model marine bacterium Phaeobacter inhibens when it transitions from starvation to growth with a microalgal partner. Utilizing transcriptomics and 13C-labeled metabolomics, our study reveals that methylated compounds, which are abundantly produced by microalgae, shorten the bacterial lag phase. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and demonstrate that methyl groups can be harvested from algal compounds and assimilated through the methionine cycle. Furthermore, we show that methylated compounds, characteristic of photosynthetic organisms, induce variable reductions in lag times among bacteria associated with algae and plants. These findings highlight the adjustability of the bacterial lag phase and emphasize the importance of studying bacteria in an environmental context. One-Sentence SummaryBacteria use algal compounds as a metabolic shortcut to transition from starvation to growth.

microbiology↗

bioRxiv2023

A conserved family of immune effectors cleaves cellular ATP upon viral infection

During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. In this study, we report a family of immune effectors in bacteria which, in response to phage infection, degrade cellular ATP and dATP by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems including CBASS, prokaryotic argonautes and NLR-like proteins, and we show that degradation of (d)ATP during infection halts phage propagation and aborts infection. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a new family of bacterial defense systems with a two-component phosphotransfer signaling architecture. The immune ATP nucleosidase domain is also encoded within a diverse set of eukaryotic proteins that have immune-like architectures, and we show biochemically that these eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.

microbiology↗

bioRxiv2023

Metabolic rewiring of the probiotic bacterium Lacticaseibacillus rhamnosus GG contributes to cell wall remodeling and antimicrobials production

Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the human intestinal tract and belongs to the family of lactic acid bacteria (LAB). This bacterium is a widely used probiotic and was suggested to provide numerous benefits for human health. However, as in most LAB strains, the molecular mechanisms that mediate the competitiveness of probiotics under different diets remain unknown. Fermentation is a fundamental process in LAB, allowing the oxidation of simple carbohydrates (e.g., glucose, mannose) for energy production under conditions of oxygen limitation, as in the human gut. Our results indicate that fermentation reshapes the metabolome, volatilome, and proteome architecture in LGG. Furthermore, fermentation alters cell envelope remodeling and peptidoglycan biosynthesis, which leads to altered cell wall thickness, aggregation properties, and cell wall composition. In addition, fermentable sugars induced secretion of known and novel metabolites and proteins targeting the enteric pathogens Enterococcus faecalis and Salmonella Enterica serovar Typhimurium. Overall, our results link the common metabolic regulation of cell wall remodeling, aggregation to host tissues, biofilm formation in probiotic strains, and connect the production of antimicrobial effectors with metabolome reprogramming. These findings provide novel insights into the role of nutrition in the establishment of LGG in the gastrointestinal tract.

microbiology↗

bioRxiv2022

Novel lipid biomarkers for algal resistance to viral infection in the ocean

Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to discover lipid biomarkers for the resistance of the bloom-forming alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). We identified novel glycosphingolipids (GSLs) that characterize resistant E. huxleyi strains by applying an untargeted lipidomics approach. Further, we detected these lipid biomarkers in E. huxleyi isolates that were recently collected from E. huxleyi blooms and used them to detect resistant cells in the demise phase of an open ocean E. huxleyi bloom. Lastly, we show that the GSL composition of E. huxleyi cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and co-evolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.

microbiology↗

bioRxiv2022

Kynurenic acid, a key L-tryptophan-derived metabolite, protects the heart from an ischemic damage

BackgroundRenal injury induces major changes in plasma and cardiac metabolites. We sought to identify a key metabolite that may affect cardiac mitochondria following an acute kidney injury (AKI) that may be harnessed to protect the heart following an acute ischemic event. Methods and ResultsMetabolomics profiling of cardiac lysates and plasma samples derived from rats that underwent AKI 1 or 7 days earlier by 5/6 nephrectomy versus sham-operated controls was performed. We detected only 26 differential metabolites in both heart and plasma samples at the two selected time points, relative to sham. Out of which, kynurenic acid (kynurenate, KYNA) seemed most relevant. Interestingly, KYNA given at 10 mM concentration significantly rescued the viability of H9C2 cardiac myoblast cells grown under anoxic conditions and largely improved their mitochondrial structure and function as determined by flow cytometry and cell staining with MitoTracker dyes. Moreover, KYNA diluted in the drinking water of animals induced with an acute myocardial infarction, highly enhanced their cardiac recovery according to echocardiography and histopathology. Conclusion and translational aspectKYNA may represent a key metabolite absorbed by the heart following AKI. This metabolite can enhance cardiac cell viability following an ischemic event in a mechanism that is mediated, at least in part, by the protection of the cardiac mitochondria. A short-term administration of KYNA may be highly beneficial in the treatment of the acute phase of kidney disease in order to attenuate progression to CRS and in ischemic cardiac conditions to reduce ischemic myocardial damage. HighlightsO_LIThe levels of the L-Tryptophan-derived metabolite, Kynurenic acid (KYNA), are significantly elevated in the heart and the plasma of animals induced with an acute kidney disease. C_LIO_LIKYNA rescues the viability of cardiac cells from an ischemic damage both in vitro and in vivo. C_LIO_LIKYNA can protect the structure & function of cardiac mitochondria in H9C2 cardiomyoblast cells upon exposure to anoxia. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=140 HEIGHT=200 SRC="FIGDIR/small/492275v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f2a49aorg.highwire.dtl.DTLVardef@14a501org.highwire.dtl.DTLVardef@15d016aorg.highwire.dtl.DTLVardef@10800e7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways

Lissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the activity of the molecular motor cytoplasmic dynein. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it regulates the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the expression of extracellular matrix (ECM) and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post- transcriptional regulation underlying development and mechanosensitive processes.

cell biology↗

bioRxiv2022

Accelerated cognitive decline in obese mouse model of Alzheimer's disease is linked to sialic acid-driven immune deregulation

Systemic immunity supports healthy brain homeostasis. Accordingly, conditions causing systemic immune deregulation may accelerate onset of neurodegeneration in predisposed individuals. Here we show that, in the 5xFAD mouse model of Alzheimers disease (AD), high-fat diet-induced obesity accelerated cognitive decline, which was associated with immune deviations comprising increased splenic frequencies of exhausted CD4+ T effector memory cells and CD4+FOXP3+ regulatory T cells (Tregs). Non-targeted plasma metabolomics identified N-acetylneuraminic acid (NANA), the predominant sialic acid, as the major obesity-induced metabolite in 5xFAD mice, the levels of which directly correlated with Tregs abundance and inversely correlated with cognitive performance. Visceral adipose tissue macrophages were identified by sNuc-Seq as one potential source of NANA. Exposure to NANA led to immune deregulation in middle-aged wild-type mice, and ex vivo in human T cells. Our study identified diet-induced immune deregulation, potentially via sialic acid, as a previously unrecognized link between obesity and AD.

neuroscience↗