Biology subjects

Kulik, A.

Publications and source records attributed to Kulik, A..

10 recordsLinked to original sources

bioRxiv2026

Conserved cis and trans communication domains mediate module interaction in glycopeptide antibiotic NRPS assembly lines

Non-ribosomal peptide synthetases (NRPSs) assemble structurally complex and clinically important natural products, yet the mechanisms coordinating communication between multiple enzymes remain incompletely understood. Here, we dissected the NRPS system underlying biosynthesis of the glycopeptide antibiotic (GPA) balhimycin in Amycolatopsis balhimycina to elucidate principles of inter-enzyme communication. Genetic perturbation of short terminal structural elements markedly reduced balhimycin production, demonstrating their critical role in biosynthesis. AlphaFold3 predictions identified these elements as trans-COM domains mediating specific NRPS interactions, primarily through hydrophobic contacts. Quantitative binding studies using microscale thermophoresis confirmed the importance of the trans-COM domains for multiprotein interaction, extending current models of NRPS communication. Comparative structural analysis further uncovered a conserved class of cis-COM domains within condensation domains across GPA NRPS assembly lines. Together, our findings establish a unified model in which trans- and cis-interfaces cooperatively maintain assembly line fidelity, redefining NRPS architecture and enabling rational engineering strategies.

microbiology↗

bioRxiv2026

PP2A-dependent internalisation of GABAB receptors in somatostatin interneurons regulates function and plasticity.

Cortical circuits rely on a precise balance of inhibitory and excitatory neurotransmission to encode information reliably and prevent pathology. Metabotropic GABAB receptors (GABABRs) are key regulators of inhibitory signalling in mammalian neurons. In GABAergic interneurons (INs), GABABR activation reduces inhibition overall, leading to disinhibitory mechanisms. In the hippocampus, somatostatin-expressing (SST) INs form a major subtype that provides feedback inhibition to the distal dendrites of principal cells (PCs) and other INs. Plasticity of SST INs is well established as a mechanism controlling hippocampal circuit function through both inhibitory and disinhibitory pathways and depends on metabotropic glutamate receptors (mGluRs) and GABABRs. However, whether activation of GABABRs induces metaplastic changes in SST INs, and how this influences circuit function and behaviour, remains unclear. Here, we combined quantitative SDS-digested freeze-fracture replica immunoelectron microscopy, ex vivo electrophysiology, in vivo behavioural testing, and pharmacological manipulation of GABABRs. We show that receptor activation directly regulates SST IN plasticity via protein phosphatase 2A (PP2A)-dependent internalisation. GABABR activation not only controls its own surface expression but also regulates membrane levels of mGluR1 and high-voltage-activated Cav1.2 (L-type) Ca2+ channels. This GABABR-dependent metaplasticity shifts circuit plasticity toward greater enhancement of long-range inputs to the CA1 region and disrupts contextual memory formation. These findings demonstrate that receptor-mediated surface dynamics in SST INs are critical for maintaining physiological neurotransmission and proper hippocampal microcircuit function.

neuroscience↗

bioRxiv2026

Conversion of CO2 into valuable products: Engineering the PirC-PGAM switch in cyanobacteria to direct carbon flux into desired products

BackgroundIn response to rising CO2 emissions driving global warming, there is an urgent need for a transition toward a sustainable bioeconomy. Photo-biotechnological processes based on oxygenic photosynthesis hold high potential for achieving CO2 neutrality and in this regard, cyanobacteria have emerged as promising biocatalysts. Rational metabolic engineering of cyanobacteria depends on a thorough understanding of native regulatory mechanisms governing primary metabolism, which can limit metabolic flux through specific pathways and, consequently, the formation of target products. Recent insights have identified a key regulatory node at the 2,3-bisphosphogylcerate-independent phosphoglycerate mutase (PGAM) reaction, where the metabolic flux from newly fixed carbon is redirected from the Calvin-Benson-Bassham (CBB) cycle towards lower glycolysis. This metabolic valve is controlled by the small inhibitor protein PirC, whose binding to PGAM is determined by the central signal transduction protein PII. ResultsIn this study, we exploit the PirC-PGAM interaction as a novel target for regulatory metabolic engineering in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). Chassis strains with engineered control of PGAM, defined as PGAM-ON or PGAM-OFF states, were generated using two complementary approaches: tuning pgam gene expression and modulating PirC abundance to regulate PGAM activity. The effectiveness of this regulatory engineering strategy was demonstrated by redirecting carbon flux toward two representative, naturally occurring products: sucrose, produced via gluconeogenesis fueled by the Calvin-Benson-Bassham (CBB) cycle, and succinate, an intermediate of the tricarboxylic acid (TCA) cycle. Narrowing the PGAM valve resulted in a threefold increase in sucrose accumulation. In contrast, opening the PGAM valve by relieving PGAM inhibition through pirC deletion or separate pgam overexpression resulted in up to an 18-fold increase in succinate excretion. Furthermore, similar genetic configurations were applied to enhance production of a heterologous compound, isoprene, derived from pyruvate. ConclusionsThis study establishes the PGAM valve as a tunable control point for the rational re-direction of carbon flux in Synechocystis and highlights small regulatory proteins as powerful targets for metabolic engineering. Together, these findings provide proof of concept for an advanced level of molecular engineering in cyanobacteria and to fully harness their biocatalytic potential in future photosynthesis-driven biotechnological applications.

bioengineering↗

bioRxiv2025

SnRK2.4 and SnRK2.10 redundantly control developmental leaf senescence by sustaining ABA production and signaling

Plants constantly and precisely control their growth by inducing distinct developmental programs to survive and produce high-quality offspring in the changing environment. The fine-tuning of the development according to endogenous and environmental signals requires exact intercellular signaling and a balanced response. Kinases of the Sucrose non-fermenting-1-Related protein Kinases type 2 (SnRK2s) family primarily take part in the response and adaptation to environmental stress factors. Notably, here we show that two ABA-non-activated SnRK2s, SnRK2.4 and SnRK2.10, are also activated in non-stress conditions in developmentally senescing leaves of Arabidopsis thaliana. Phenotypic, biochemical, and molecular analyses performed on single snrk2.4 or snrk2.10, and double snrk2.4/2.10 kinase mutants showed that SnRK2.4 and SnRK2.10, acting redundantly, promote developmental leaf senescence. Further, SnRK2.4 and SnRK2.10 enhance ABA accumulation in senescing leaves by inducing NCED2, one of key ABA biosynthesis-related genes. The two kinases induce developmental leaf senescence by modulating the expression of multiple ABA-responsive, osmotic stress, and senescence-related genes, such as the senescence master regulators ORE1, ORS1, WRKY33, WRKY75, and ANAC087. Furthermore, we show that SnRK2.4 and SnRK2.10 act upstream of MAPK signaling by enhancing the expression and activity of MAPKKK18, a senescence-inducing kinase. These results document a new regulatory function of SnRK2.4 and SnRK2.10: they are activated in Arabidopsis leaves in response to endogenous signals and redundantly induce developmental leaf senescence by stimulating ABA production and sustaining major ABA-dependent and -independent signaling pathways.

plant biology↗

bioRxiv2024

Parvalbumin expression identifies subicular principal cells with high projection specificity

The calcium-binding protein parvalbumin is an established marker for a subset of cortical inhibitory interneurons with similar biophysical features and connectivity. However, parvalbumin is also expressed in a small population of excitatory cells in layer 5 of the neocortex with specific sub-cortical projection targets. Parvalbumin may thus also in principal cells identify particular subclasses with distinct connectivity and function. Here we investigated whether parvalbumin is expressed in excitatory neurons of the hippocampal formation and if so, whether it delineated neurons with specific features. We report parvalbumin-expressing glutamatergic cells in the distal subiculum, which -based on location, connectivity and gene expression - separated into two subclasses: neurons in deep layers, which specifically project to the antero-ventral thalamus and neurons in superficial layers, which project to the mamillary bodies. Contrary to most adjacent pyramidal cells parvalbumin-positive neurons were non-bursting and displayed straight apical dendrites devoid of oblique dendrites. Functionally, the projections diverged from classical driver/modulator subdivisions. Parvalbumin expression thus marks two sub-types of subicular projection neurons with high target specificity and unique functional features.

neuroscience↗

bioRxiv2023

GlnA3Mt is able to glutamylate spermine but it is not essential for the detoxification of spermine in Mycobacterium tuberculosis

Mycobacterium tuberculosis is well adapted to survive and persist in the infected host, escaping the host immune response. Since polyamines, which are synthesized by infected macrophages are able to inhibit the growth of M. tuberculosis, the pathogen needs strategies to cope with toxic spermine. The actinomycete Streptomyces coelicolor, closely related to M. tuberculosis makes use of a gamma-glutamylation pathway to functionally neutralize spermine. We therefore considered whether a similar pathway would be functional in M. tuberculosis. In the current study we demonstrated that M. tuberculosis growth was inhibited by the polyamine spermine. Using a glutamine synthetase-based in vitro enzymatic activity assay we determined that GlnA3Mt (Rv1878) is a gamma-glutamylspermine synthetase. In an in vitro phosphate release assay we showed that purified His-Strep-GlnA3Mt as well as native GlnA3Mt prefer spermine as a substrate to putrescine, cadaverine, spermidine or other monoamines and amino acids, suggesting that GlnA3Mt may play a specific role in the detoxification of the polyamine spermine. However, the deletion of the glnA3 gene in M. tuberculosis did not result in growth inhibition or enhanced sensitivity of M. tuberculosis in the presence of high spermine concentrations. Subsequent RNAsequencing of M. tuberculosis bacteria revealed that the gene cluster consisting of the efflux pump-encoding rv3065-rv3066-rv3067 genes is upregulated upon spermine treatment, suggesting its involvement in bacterial survival under elevated spermine concentrations. IMPORTANCEAntibiotics for the treatment of Mycobacterium tuberculosis infections attack classical bacterial targets, such as the cell envelope or the ribosome. Upon M. tuberculosis infection macrophages synthesize the polyamine spermine which - at elevated concentrations - is toxic for M. tuberculosis. Based on our investigations of spermine resistance in the closely related actinomycete Streptomyces coelicolor, we hypothesized that the glutamyl-sperminesynthetase GlnA3 may be responsible for resistance against toxic spermine. Here we show that the mycobacterial glutamyl-sperminesynthetase indeed can inactivate spermine by glutamylation. However, GlnA3 is probably not the only resistance mechanism since a glnA3 mutant of M. tuberculosis can survive under spermine stress. Gene expression studies suggest that an efflux pump may participate in resistance. The functional role of GlnA3Mt as well as of the spermine transporter in the pathogenicity of M. tuberculosis is of special interest for their validation as new targets of novel anti-tubercular drugs.

microbiology↗

bioRxiv2023

Lysosomal acid lipase-activity as a novel target to efficiently address triple-negative breast cancer high malignancy

Increased metabolism of neutral lipids, e.g. triglycerides and cholesterol esters, is a hallmark of malignant cancers such as triple-negative breast cancer (TNBC). Predominantly, cancer cells with a high epigenetic stem cell-associated signature increasingly utilize neutral lipids to maintain their high degree of tumor stemness, linking metabolic aberrations to epigenetically dysregulated differentiation processes. Lysosomal acid lipase (LIPA) is a central enzyme in the cellular utilization of exogenous and endogenous neutral lipids; however, the role of LIPA-activity in TNBC remains unexplored. We here show for the first time that pharmacological inhibition of LIPA, highly expressed in TNBC, reduces the expression markers of breast cancer stemness in cell culture models of TNBC. A role of LIPA in maintaining TNBC high cellular stemness was stressed by specific siRNA knock-down. Furthermore, inhibition of LIPA sensitized TNBC cells to therapy with Paclitaxel and Doxorubicin, two important chemotherapeutics in current TNBC treatment. When LIPA-activity was inhibited in a three-dinensional (3D) patient derived organoid model, we observed a significant reduction in TNBC cellular viability. Importantly, LIPA inhibition prevented tumor metastasis in a TNBC-zebrafish xenograft model in vivo. These findings introduce LIPA-activity as a novel pharmacological target in TNBC therapy to specifically address its high cancer malignancy with a potential for implementation of LIPA inhibitors into personalized treatment in the future.

cancer biology↗

bioRxiv2020

GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals

The connection from medial habenula (MHb) to interpeduncular nucleus is critical for aversion- and addiction-related behaviors. This pathway is unique in selective expression of R-type voltage-gated Ca2+ channels (Cav2.3) in its terminals, and robust potentiation of release via presynaptic GABAB receptors (GBRs). To understand the mechanism underlying this peculiar GBR effect, we examined the presynaptic localization and function of Cav2.3, GBR, and its auxiliary subunits, K+-channel tetramerization domain-containing (KCTD) proteins. We found selective co-expression of KCTD12b and Cav2.3 at the presynaptic active zone. GBR-mediated potentiation remained intact in KCTD12b KO mice but lasted significantly shorter. This impairment was associated with increased release and an insertion of KCTD8 into the active zone. In heterologous cells, we found direct binding of KCTD8 and KCTD12b to Cav2.3, and potentiation of Cav2.3 currents by KCTD8. The unexpected interaction of Cav2.3 with KCTDs therefore provides a means to scale synaptic strength independent of GBR activation.

neuroscience↗

bioRxiv2020

Mechanism of BceAB-type transporter: Resistance by lipid II flipping

Treatment of bacterial infections are the great challenge of our era due to the evolved resistance mechanisms against antibiotics. The Achilles heel of bacteria is the cell wall especially during the needs of its synthesis and cell division. Here lipid II is an essential cell wall precursor component synthesized in the cytosol and flipped into the outer leaflet of the membrane prior to its incorporation into the cell wall. Compounds targeting the cell wall or its biosynthesis precursors have been around for decades and have been used as antibiotics against bacterial infections like meningitis, pneumonia and endocarditis. Antimicrobial peptides (AMPs) have proven to be a promising weapon against multiresistant bacteria. However, the Bacitracin efflux (BceAB)-type ATP binding cassette transporters expressed in the membrane of human pathogenic bacteria have been shown to confer resistance to these alternative antibiotics, thereby hampering their medical development. In Streptococcus agalactiae COH1 the BceAB-type transporter NsrFP (SaNsrFP) confers high-level resistance against the antimicrobial peptide nisin, a member of the lantibiotic subfamily. We showed that SaNsrFP provides a novel resistance mechanism by flipping lipid II back into the cytosol, thereby preventing the binding of nisin as well as other lipid II targeting compounds. This is intriguing since a relatively simple reaction mediates resistance to human pathogenic bacteria to lipid II targeting antibiotics, regardless of their structure. Significance StatementThe ABC-transporter NsrFP from Streptococcus agalactiae (SaNsrFP) belongs to the BceAB-type transporters. Several BceAB-type transporters are known to confer resistance against multiple antimicrobial peptides. In this study a new resistance mechanism was identified, which is based on the reduction of the number of cell wall precursor lipid II molecules on the cell surface mediated by SaNsrFP. SaNsrFP flips lipid II, which are considered to be the target for many antibiotics, back into the cytoplasm. With this newly gained knowledge about the resistance mechanism of BceAB-type transporters, novel strategies can be established to overcome or bypass this resistance in human pathogenic bacteria.

microbiology↗

bioRxiv2019

Biochemical, Biophysical, and Functional Analyses of Two Isoforms of the SnRK2 Inhibitor AtSCS

SNF1-related protein kinases 2 (SnRK2s) are key signaling elements that regulate abscisic acid (ABA)-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) is an inhibitor of SnRK2 activity. In Arabidopsis thaliana, the use of alternative transcription start sites located within AtSCS gene results in two in-frame transcripts and subsequently two proteins, which differ only by the sequence position of the N-terminus. We described the longer AtSCS-A earlier, and now we describe the shorter AtSCS-B and compare both isoforms. The two forms differ significantly in their expression profiles in plant organs and in response to environmental stresses, in calcium binding properties, and conformational dynamics in the presence and absence of Ca2+. The results show that only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but differ with respect to calcium dependence, as AtSCS-A requires calcium for inhibition, while AtSCS-B does not. Analysis of Arabidopsis plants stably expressing 35S::AtSCS-A-c-myc or 35S::AtSCS-B-c-myc in the scs-1 knockout mutant revealed that in planta both forms are negative regulators of the SnRK2 activity induced in response to ABA and regulate plant defense against water deficit. Moreover, the data present biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.\n\nOne sentence SummaryTwo isoforms of SnRK2-interacting calcium sensor are expressed in Arabidopsis; they differ in calcium binding properties, but both of them inhibit SnRK2s and subsequently fine tune ABA signaling.

plant biology↗