Biology subjects

Jakob, U.

Publications and source records attributed to Jakob, U..

12 recordsLinked to original sources

bioRxiv2026

Polyamines control inorganic polyphosphate levels during bacterial nitrogen starvation

Inorganic polyphosphate (polyP) is a ubiquitous, multifunctional biomolecule that supports stress survival in bacteria. During nitrogen (N) starvation, Escherichia coli rapidly accumulates polyP, which drives the formation of RNA protein granules that sustain long term survival. What triggers this upregulation has remained unknown. Here we show that polyamines, a group of highly conserved, amino acid-derived polycations, regulate polyP accumulation during N starvation. We found that deleting all nine polyamine biosynthesis genes elevates polyP during exponential growth and by more than 5fold under N starvation, with shorter chains preferentially accumulating. To dissect which polyamine matters, we further deleted the three catabolic enzymes that consume polyamines as a nitrogen source, which enabled complementation assays. Supplying any one of the three physiological polyamines, putrescine, spermidine, or cadaverine, restored wild type polyP levels during N starvation. We found that the absence of polyamines did not affect the steady state levels of either the polyP synthesizing kinase PPK or the exopolyphosphatase PPX, pointing instead to posttranslational control of enzyme activity or to as yet unidentified polyamine dependent regulators. These findings establish a direct metabolic link between two universal, functionally intertwined biomolecules and suggest that the polyamine decline upon N starvation contributes to the observed polyP accumulation.

microbiology↗

bioRxiv2026

The filopodial scaffold polyphosphate dictates cell adhesion-versus-invasion decisions

Inorganic polyphosphate (polyP) is an ancient polymer conserved across all life, serving cell type and location specific functions in every major compartment. Yet its role at the plasma membrane, where it accumulates to peak levels in many primary cells, is largely unknown. Here we identify polyP as a stabilizing component of filopodia, actin based membrane protrusions that govern cell adhesion, contact inhibition, and chemotaxis. Elevating cellular polyP increases filopodial stability and enhances cell adhesion, whereas reducing polyP accelerates filopodial disassembly and promotes cell migration. Mechanistically, we find that polyP acts as a structural filopodial scaffold, recruiting and organizing IRSp53, a membrane curvature inducing protein. We show that metastatic fibroblasts and breast cancer organoids carry markedly reduced and intracellularly reorganized polyP levels relative to their non transformed counterparts. Restoring endogenous polyP via lipid nanoparticle delivery suppresses their invasive phenotypes and reverses prometastatic gene expression signatures, implicating polyP as a primordial tumor suppressor.

cell biology↗

bioRxiv2026

Microprotein Regulates G-quadruplex Driven RNA Aggregation

Repeat expansions of the hexanucleotide GGGGCC in C9orf72 form aberrant phase transitions that have been linked to Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. RNA structures such as G-quadruplexes and hairpins play important roles in these processes. Here, we show that the human microprotein ZNF706 acts as a modulator of G-quadruplex formation and RNA phase behavior. ZNF706 antagonizes pathological gel-solid transitions by melting hexanucleotide repeat G-quadruplex structures converting gel-like aggregates into more dynamic condensates. Loss of ZNF706 enhances the cellular production clearance of hexanucleotide repeat-mediated dipeptide repeat proteins, while overexpression suppresses their production and promotes clearance. Mechanistically, ZNF706 influences hexanucleotide repeat condensate fluidity and viscoelasticity. We find ZNF706 acts as an RNA chaperone that remodels repeat RNA structures and solubilizes RNA aggregates. This activity represents one mechanism whereby cells can regulate G-quadruplex driven phase transitions linked to neurodegenerative diseases.

cell biology↗

bioRxiv2025

Paralogs with distinct phase behaviors broaden the in vivo stress response range of condensates

Paralogs are widespread, but their physiological roles are often masked by redundancy. H-NS, a nucleoid-associated protein in Gram-negative bacteria, typically coexists with paralogs such as StpA, whose functions have remained obscured due to the lack of strong phenotypes. We demonstrate here that the interaction between H-NS and StpA fine-tunes the physico-chemical properties of heterochromatin-forming condensates. H-NS forms dynamic condensates, while StpA assembles into stable insoluble fibrils. Yet together, the two proteins form heterotypic condensates, whose fluidity and stability are tunable by their relative stoichiometry. By increasing the levels of StpA over H-NS, bacteria increase heterochromatin-associated condensate stability, thus preserving gene repression and optimizing bacterial growth under stress conditions. Structural differences at these proteins dimerization sites help explain their distinct phase behaviors. Our findings reveal a novel paradigm in which paralogs that are positioned at the opposite ends of the phase spectrum can fine-tune condensates to promote survival in fluctuating environments.

biochemistry↗

bioRxiv2025

HP-Bodies - Ancestral Condensates that Regulate RNA Turnover and Protein Translation in Bacteria

Uncovering what drives select biomolecules to form phase-separated condensates in vivo and identifying their physiological significance are topics of fundamental importance. Here we show that nitrogen-starved Escherichia coli produce long-chain polyphosphates, which scaffold the RNA chaperone Hfq into phase-separating high molecular weight complexes together with components of the RNA translation and processing machinery. The presence of polyphosphate within these condensates, which we termed HP-bodies, controls Hfq function by selectively stabilizing polyadenylated RNAs involved in transcription and protein translation, and promoting interactions with translation- and RNA-metabolism-associated proteins involved in de novo protein synthesis. Lack of polyphosphate prevents HP-body formation, which increases cell death and significantly hinders recovery from N-starvation. In functional analogy, we demonstrate that polyP contributes specifically to the formation of Processing (P)-bodies in human cell lines, revealing that a single, highly conserved and ancestral polyanion serves as the universal scaffold for functional phase-separated condensate formation across the tree of life.

microbiology↗

bioRxiv2024

A dynamic redox switch turns TRC40 into a chaperone protecting human cells against ATP-depleting, oxidative stress

Oxidative stress represents a major challenge for cellular proteostasis. The accumulation of reactive oxygen species, such as hydrogen peroxide, impairs the fidelity of protein biosynthesis and causes non-specific oxidative protein modifications and aggregation. This situation is further aggravated by the oxidative stress-mediated drop in cellular ATP levels, which reduces the activity of ATP-dependent chaperones and proteases. We now demonstrate that to cope with oxidative unfolding stress, human cells rely on the moonlighting function of TRC40, which turns from an ATP-dependent targeting factor into an ATP-independent chaperone upon oxidation. Controlled by a highly conserved redox switch, oxidized TRC40 forms chaperone-active tetramers and high-molecular complexes which prevent the aggregation of unfolding proteins. Acute oxidative stress leads to the reversible formation of distinct TRC40 foci, associated with the canonical chaperones Hsp70 and Hsp110, suggesting a role of these stress-induced structures in recovering and sorting aberrant proteins. Consistently, we discovered that TRC40 is essential upon ATP-depleting, oxidative stress conditions to counteract the accumulation of mis- and unfolded proteins, which are rapidly cleared in an TRC40-dependent manner. Our data reveal that TRC40 is an integral part of protein quality control and support its role as a triaging factor in cellular proteostasis.

cell biology↗

bioRxiv2024

Amyloid Accelerator Polyphosphate Implicated as the Mystery Density in α-Synuclein Fibrils

Aberrant aggregation of -Synuclein is the pathological hallmark of a set of neurodegenerative diseases termed synucleinopathies. Recent advances in cryo-electron microscopy have led to the structural determination of the first synucleinopathy-derived -Synuclein fibrils, which contain a non-proteinaceous, "mystery density" at the core of the protofilaments, hypothesized to be highly negatively charged. Guided by previous studies that demonstrated that polyphosphate (polyP), a universally conserved polyanion, significantly accelerates -Synuclein fibril formation, we conducted blind docking and molecular dynamics simulation experiments to model the polyP binding site in -Synuclein fibrils. Here we demonstrate that our models uniformly place polyP into the lysine-rich pocket, which coordinates the mystery density in patient-derived fibrils. Subsequent in vitro studies and experiments in cells revealed that substitution of the two critical lysine residues K43 and K45 leads to a loss of all previously reported effects of polyP binding on -Synuclein, including stimulation of fibril formation, change in filament conformation and stability as well as alleviation of cytotoxicity. In summary, our study demonstrates that polyP fits the unknown electron density present in in vivo -Synuclein fibrils and suggests that polyP exerts its functions by neutralizing charge repulsion between neighboring lysine residues.

biophysics↗

bioRxiv2020

Polyphosphate Functions In Vivo as Iron Chelator and Fenton Inhibitor

Maintaining cellular iron homeostasis is critical for organismal survival. Whereas iron depletion negatively affects the many metabolic pathways that depend on the activity of iron-containing enzymes, any excess of iron can cause the rapid formation of highly toxic reactive oxygen species (ROS) through Fenton chemistry. Although several cellular iron chelators have been identified, little is known about if and how organisms can prevent the Fenton reaction. By studying the effects of cisplatin, a commonly used anticancer drug and effective antimicrobial, we discovered that cisplatin elicits severe iron stress and oxidative DNA damage in bacteria. We found that both of these effects are successfully prevented by polyphosphate (polyP), an abundant polymer consisting solely of covalently linked inorganic phosphates. Subsequent in vitro and in vivo studies revealed that polyP provides a crucial iron reservoir under non-stress conditions, and effectively complexes free iron and blocks ROS formation during iron stress. These results demonstrate that polyP, a universally conserved biomolecule, plays a hitherto unrecognized role as an iron chelator and an inhibitor of the Fenton reaction.

microbiology↗

bioRxiv2020

Mycobacterium tuberculosis Rv0991c is a redox-regulated molecular chaperone

The bacterial pathogen Mycobacterium (M.) tuberculosis is the leading cause of death by an infectious disease among humans. Here, we describe a previously uncharacterized M. tuberculosis protein, Rv0991c, as a molecular chaperone that is activated by oxidation. Rv0991c has homologues in most bacterial lineages and appears to function analogously to the well-characterized Escherichia coli redox-regulated chaperone Hsp33, despite a dissimilar protein sequence. Rv0991c is transcriptionally co-regulated with hsp60 and hsp70 chaperone genes in M. tuberculosis, suggesting that Rv0991c functions with these chaperones in maintaining protein quality control. Supporting this hypothesis, we found that, like oxidized Hsp33, oxidized Rv0991c prevents the aggregation of a model unfolded protein in vitro, and promotes its refolding by the M. tuberculosis Hsp70 chaperone system. Furthermore, Rv0991c interacts with DnaK and associates with many other M. tuberculosis proteins. Importantly, we found Rv0991c is required for the full virulence of M. tuberculosis in mice. We therefore propose that Rv0991c, which we named "Ruc" (redox-regulated protein with unstructured C-terminus), represents a founding member of a new chaperone family that protects M. tuberculosis and other species from proteotoxicity during oxidative stress. IMPORTANCEM. tuberculosis infections are responsible for more than one million human deaths per year. Developing effective strategies to combat this disease requires a greater understanding of M. tuberculosis biology. As in all cells, protein quality control is essential for the viability of M. tuberculosis, which likely faces proteome stress within a host. Here, we identify an M. tuberculosis protein, Ruc, that gains chaperone activity upon oxidation. Ruc represents a previously unrecognized family of redox-regulated chaperones found throughout the bacterial super-kingdom. In addition to elucidating the activity of this chaperone, we found that Ruc was required for full M. tuberculosis virulence in mice. This work contributes to a growing appreciation that oxidative stress may provide a particular strain on protein stability in cells, and may likewise play a role in M. tuberculosis pathogenesis.

microbiology↗

bioRxiv2019

Developmental Reactive Oxygen Species Target Histone Methylation to Individualize Stress resistance and Lifespan

A central aspect of aging research concerns the question as to when individuality in lifespan arises and what mechanism(s) promote and potentially manifest individual differences in longevity. We have now discovered that a transient increase in reactive oxygen species (ROS), which occurs naturally during early development in a subpopulation of synchronized Caenorhabditis elegans, sets processes into motion that increase stress resistance, improve redox homeostasis and ultimately prolong lifespan in those animals. We find that these effects are linked to the global ROS-mediated decrease in developmental histone H3K4me3 levels. Studies in HeLa cells confirmed that global H3K4me3 levels are ROS-sensitive, and that depletion of H3K4me3 levels increases stress resistance in mammalian cell cultures. In vitro studies identified the Set1-MML histone methyltransferase as the redox sensitive unit of the H3K4-trimethylating COMPASS complex. Our findings imply a novel link between early-life events, ROS-sensitive epigenetic marks, stress resistance and lifespan.

molecular biology↗

bioRxiv2019

Mechanistic Insights into the Protective Roles of Polyphosphate Against Amyloid Cytotoxicity

The universally abundant polyphosphate (polyP) accelerates fibril formation of disease-related amyloids and protects against amyloid cytotoxicity. To gain insights into the mechanism(s) by which polyP exerts these effects, we focused on -synuclein, a well-studied amyloid protein, which constitutes the major component of Lewy bodies found in Parkinsons Disease. Here we demonstrate that polyP is unable to accelerate the rate-limiting step of -synuclein fibril formation but effectively nucleates fibril assembly once -synuclein oligomers are formed. Binding of polyP to -synuclein either during fibril formation or upon fibril maturation substantially alters fibril morphology, and effectively reduces the ability of -synuclein fibrils to interact with cell membranes. The effect of polyP appears to be -synuclein fibril specific, and successfully prevents the uptake of fibrils into neuronal cells. These results suggest that altering the polyP levels in the extracellular space might be a potential therapeutic strategy to prevent the spreading of the disease.

cell biology↗

bioRxiv2019

Polyphosphate initiates tau aggregation through intra- and intermolecular scaffolding

The aggregation and deposition of tau is a hallmark of a class of neurodegenerative diseases called tauopathies. Despite intensive study, cellular and molecular factors that trigger tau aggregation are not well understood. Here we provide evidence for two mechanisms relevant to the initiation of tau aggregation in the presence of cytoplasmic polyphosphates (polyP): changes in the conformational ensemble of monomer tau and noncovalent cross-linking of multiple tau monomers. We identified conformational changes throughout full-length tau, most notably diminishment of long-range interactions between the termini coupled with compaction of the microtubule binding and proline rich regions. We found that while the proline rich and microtubule binding regions both contain polyP binding sites, the proline rich region is a requisite for compaction of the microtubule binding region upon binding. Additionally, both the magnitude of the conformational change and the aggregation of tau are dependent on the chain length of the polyP polymer. Longer polyP chains are more effective at intermolecular, noncovalent cross-linking of tau. These observations provide an understanding of the initial steps of tau aggregation through interaction with a physiologically relevant aggregation inducer.

biophysics↗