Biology subjects

Sipari, N.

Publications and source records attributed to Sipari, N..

10 recordsLinked to original sources

bioRxiv2026

Queuosine modification mediates cold-active growth in Shewanella glacialimarina

Efficient protein synthesis in cold-active bacteria requires precise coordination within the translation machinery to overcome the kinetic challenges imposed by growth at near-freezing temperatures (< 5 {degrees}C). Post-transcriptional modifications (PTMs) on transfer RNA (tRNA)--particularly those located at the wobble position 34--are central to this coordination as they regulate decoding speed and fidelity. Here, we show that queuosine (Q) modification in the cold-active marine bacterium Shewanella glacialimarina TZS-4T is dynamically regulated in response to bacterial growth and environmental conditions. Importantly, we demonstrate that Q levels are modulated in a tRNA isoacceptor-specific manner during cold-active growth, while Q-deficiency produces a cold-sensitive phenotype that underscores the functional importance of Q modification. Proteomic analysis of the Q-deficient {Delta}tgt mutant revealed that tRNAHis Q-hypomodification activates the histidine biosynthesis pathway, whereas the concomitant phosphate-starvation-like response reflects a general consequence of global disruption of Q-modified tRNAs. Consequently, we propose a model where Q modification maintains efficient codon decoding and protein quality control at near-freezing temperatures, whereas loss of Q destabilizes codon decoding and ultimately compromises protein homeostasis.

microbiology↗

bioRxiv2026

Queuosine promotes wecB-dependent phage resistance and biofilm formation in marine bacterium Shewanella glacialimarina

Transfer RNA (tRNA) modifications critically fine-tune translational accuracy and efficiency, influencing bacterial adaptation to environmental challenges. Among these, the queuosine (Q) modification has recently emerged as a regulator of biofilm formation, yet its role during phage infection remains unknown. Here, we investigate how Q modification links host translational control to phage infection. We show that phage infection activates the Q biosynthetic pathway, leading to elevated Q levels and enhanced translation of NAT-biased genes. This shift drives two interconnected outcomes, namely increased biofilm formation and enhanced mutagenesis mediated by translesion synthesis polymerases. We further identify conserved, slippage-prone regions within surface-related genes that act as hotspots for adaptive variation. Together, our findings uncover a novel mechanistic link between tRNA modification and phage-driven bacterial diversification. AUTHOR SUMMARYTo survive changing environmental conditions, bacteria constantly adjust their metabolic processes, including how they translate their genetic information into proteins. One such adjustment mechanism involves carefully balancing the level of chemical modification on transfer RNA (tRNA), the key adapter molecule that carries amino acids but also regulates protein synthesis. In this study, we explore how a cold-active bacterium relies on queuosine, a wobble position tRNA modification, to mediate host cell responses to bacteriophage infection. We observe that as viral infection progresses, the bacterial host cells increase the level of queuosine modification present on tRNAs. This alters the efficiency by which specific proteins are produced, favoring those that are involved in biofilm synthesis and thereby form protective communities that help bacteria survive stress. At the same time, queuosine also promotes error-prone DNA replication processes that lead to an overall increase in bacterial mutation rates. Taken together, our results reveal how a small molecular change in tRNA can reshape bacterial responses to viral infection, ultimately driving genetic diversity and survival.

microbiology↗

bioRxiv2025

Photosynthetic adjustments maintain lettuce growth under dynamically changing lighting in controlled indoor farming setups

Studies have uncovered delicate mechanisms that enable plant acclimation to fluctuating light. Translating the knowledge to controlled environment agriculture could advance the development of cost-effective dynamic lighting strategies, but the effects of varying light intensities on vegetable crops remain poorly understood. Here we recorded chlorophyll fluorescence, photosynthetic activity, metabolic responses, and growth of lettuce (Lactuca sativa L.) cv. Katusa under dynamic lighting. The light intensity was varied at different times of the photoperiod with uniform daily light integral. Three setups, including a plant phenotyping facility, a small-scale vertical farm testbed and a larger-scale vertical farm were utilized to address the physiological responses and scalability of lighting strategies. We found that dynamic lighting supported lettuce cv. Katusa growth in all three indoor cultivation setups, even under artificial "split-night" regimes where the photoperiod was interrupted by two periods of darkness. The lettuce plants displayed delicate adjustments in photosynthetic light reactions and carbon metabolism, the latter of which followed the cumulative daily light integral under different lighting regimes. However, the overall metabolic composition of lettuce leaves did not respond to the changing light intensities. Our findings support the conclusion that dynamic lighting enables cost-effective lighting via optimization of electricity use in indoor cultivation. HighlightPhotosynthetic adjustments maintain lettuce (Lactuca sativa L.) cv. Katusa growth under dynamic lighting. This enables cost-effective cultivation via optimization of electricity use in controlled environment agriculture.

plant biology↗

bioRxiv2023

Enzymatic assay for UDP-GlcNAc and its application in the parallel assessment of substrate availability and protein O-GlcNAcylation

O-linked N-acetylglucosaminylation (O-GlcNAcylation) is a ubiquitous and dynamic yet still relatively poorly understood non-canonical glycosylation of intracellular proteins. Several vital branches of metabolism converge at the hexosamine biosynthetic pathway (HBP) to produce the substrate for protein O-GlcNAcylation the uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). Availability of this metabolite is considered a key regulator of O-GlcNAcylation. Yet UDP-GlcNAc concentrations are rarely reported in studies exploring the HBP and O-GlcNAcylation, most likely because the methods to measure it restrict to specialized chromatographic procedures. To overcome this limitation, we introduce here an enzymatic method to quantify cellular and tissue UDP-GlcNAc. The method is based on O-GlcNAcylation of a substrate peptide by recombinant O-linked N-acetylglucosamine transferase (OGT) and detection of the modification with a specific antibody. The assay can be performed in dot blot or microplate formats. The key to successful assay was the removal of strong inhibition of OGT by the reaction side product, uridine diphosphate (UDP). We applied the assay to provide the first systematic report of UDP-GlcNAc concentrations in mouse tissues and cultured cells. Furthermore, we show how changes in UDP-GlcNAc levels correlate with O-GlcNAcylation and the expression of OGT and O-GlcNAcase (OGA).

biochemistry↗

bioRxiv2023

Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria

Accumulating evidence suggests mitochondria as key modulators of normal and premature aging, yet whether primary deficiency of oxidative phosphorylation (OXPHOS) can cause progeroid disease remains unclear. Here, we show that mice with severe isolated respiratory complex III (CIII) deficiency display nuclear DNA damage, cell cycle arrest, aberrant mitoses, cellular senescence, and laminopathy-like nuclei in the affected organs such as liver and kidney, and a systemic phenotype strikingly resembling juvenile-onset laminopathic and DNA repair-deficient progeroid syndromes. Mechanistically, CIII deficiency triggered presymptomatic cancer-like c-MYC upregulation followed by excessive anabolic metabolism and illicit cell proliferation against lack of energy and biosynthetic precursors. CIII-independent coenzyme Q oxidation dampened mitochondrial integrated stress response and the c-MYC induction, suppressed the illicit proliferation, and prevented juvenile lethality despite that canonical OXPHOS-linked functions remained uncorrected. Inhibition of c-MYC by expression of a dominant-negative Omomyc protein relieved the DNA damage in CIII-deficient hepatocytes in vivo. Our results unequivocally connect primary OXPHOS deficiency to genomic instability and progeroid disease and suggest that targeting c-MYC and aberrant cell proliferation may provide novel therapeutic strategies in mitochondrial diseases.

pathology↗

bioRxiv2021

Convergent evolution of mevalonate pathway in Inonotus obliquus and Betula pendula.

Inonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses revealed a lineage-specific whole genome duplication event and an expansion of Cytochrome P450 superfamily. Fungal biosynthetic clusters were enriched for tandemly duplicated genes, suggesting that biosynthetic pathway evolution has proceeded through small-scale duplications. Metabolomic fingerprinting confirmed a highly complex terpene biosynthesis chemistry when compared against related fungal species lacking the genome duplication event.

evolutionary biology↗

bioRxiv2020

Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS

Post-transcriptional RNA modifications play an important role in cellular metabolism with homeostatic disturbances manifesting as a wide repertoire of phenotypes, reduced stress tolerance and translational perturbation, developmental defects, and diseases, such as type II diabetes, leukemia and carcinomas. Hence, there has been an intense effort to develop various methods for investigating RNA modifications and their roles in various organisms, including sequencing-based approaches and, more frequently, liquid chromatography mass spectrometry (LC-MS)-based methods. Although LC-MS offers numerous advantages, such as being highly sensitive and quantitative over a broad detection range, some stationary phase chemistries struggle to resolve positional isomers. Furthermore, the demand for detailed analyses of complex biological samples often necessitates long separation times, hampering sample-to-sample turnover and making multisample analyses time consuming. To overcome this limitation, we have developed an ultra-performance LC-MS (UPLC-MS) method that uses an octadecyl carbon chain (C18)-bonded silica matrix for the efficient separation of 50 modified ribonucleosides, including positional isomers, in a single 9 min sample-to-sample run. To validate the performance and versatility of our method, we analyzed tRNA modification patterns of representative microorganisms from each kingdom of life, namely Archaea (Methanosarcina acetivorans), Bacteria (Pseudomonas syringae) and Eukarya (Saccharomyces cerevisiae). Additionally, our method is flexible and readily applicable for detection and relative quantification using stable isotope labelling and targeted approaches like multiple reaction monitoring (MRM). In conclusion, this method represents a fast and robust tool for broad-range exploration and quantification of ribonucleosides, facilitating future homeostasis studies of RNA modification in complex biological samples.

molecular biology↗

bioRxiv2020

Genetic screen to saturate guard cell signaling network reveals a role of GDP-L-fucose metabolism in stomatal closure

Guard cells regulate plant gas exchange by controlling the aperture of stomatal pores. The process of stomatal closure involves a multi-input signaling network that governs the activity of ion channels, which in turn regulate guard cell turgor pressure and volume. Here we describe a forward genetic screen to identify novel components involved in stomatal movements. Through an ozone-sensitivity approach combined with whole-rosette gas exchange analysis, 130 mutants of established stomatal regulators and 76 novel mutants impaired in stomatal closure were identified. One of the novel mutants was mapped to MURUS1 (MUR1), the first enzyme in de novo GDP-L-fucose biosynthesis. Defects in synthesis or import of GDP-L-Fuc into the Golgi apparatus resulted in impaired stomatal closure to multiple stimuli. Stomatal phenotypes observed in mur1 were independent from the canonical guard cell signaling and instead could be related to altered mechanical properties of guard cell walls. Impaired fucosylation of xyloglucan, N-linked glycans and arabinogalactan proteins did not explain the aberrant function of mur1 stomata, however our data suggest that the stomatal phenotypes observed in mur1 can at least partially be attributed to defective dimerization of rhamnogalactouronan-II. In addition to providing the genetic framework for future studies on guard cell signaling, our work emphasizes the impact of fucose metabolism on stomatal movement.

plant biology↗

bioRxiv2020

Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor

A caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge is how to make an integrated use of omics profiles of cancer cell lines for reliable discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics profiling studies across 12 research laboratories for 2018 cell lines. To account for relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. Extension of the approach identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient cells on RNA helicases. HighlightsO_LIA comprehensive meta-analysis of 53 multi-modal omics profiles of >2000 cancer cell lines from 12 research laboratories C_LIO_LIAn unexpected lack of consistency between TMT-labelled and non-labelled global proteomic profiles C_LIO_LIA non-parametric approach to integrate omics profiles from multiple laboratories and to identify robust molecular patterns in individual cell lines C_LIO_LIThe multi-modal data integration reveals novel drivers and potential therapeutic targets, including ECHDC1 in breast cancers and DDX27 in PTEN mutant cancers. C_LI

cancer biology↗

bioRxiv2018

RCD1 Coordinates Chloroplastic and Mitochondrial Electron Transfer through Interaction with ANAC Transcription Factors

Signaling from chloroplasts and mitochondria, both dependent on reactive oxygen species (ROS), merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). ROS produced in the chloroplasts affect the abundance, thiol redox state and oligomerization of RCD1. RCD1 directly interacts in vivo with ANAC013 and ANAC017 transcription factors, which are the mediators of the ROS-related mitochondrial complex III retrograde signa and suppresses activity of ANAC013 and ANAC017. Inactivation of RCD1 leads to increased expression of ANAC013 and ANAC017-regulated genes belonging to the mitochondrial dysfunction stimulon (MDS), including genes for mitochondrial alternative oxidases (AOXs). Accumulating AOXs and other MDS gene products alter electron transfer pathways in the chloroplasts, leading to diminished production of chloroplastic ROS and increased protection of photosynthetic apparatus from ROS damage. RCD1-dependent regulation affects chloroplastic and mitochondrial retrograde signaling including chloroplast signaling by 3-phosphoadenosine 5-phosphate (PAP). Sensitivity of RCD1 to organellar ROS provides feedback control of nuclear gene expression.

plant biology↗