Biology subjects

Purhonen, J.

Publications and source records attributed to Purhonen, J..

10 recordsLinked to original sources

bioRxiv2026

DEADMON: A protocol for long-term monitoring of deadwood-associated species

Dead wood has a vital role in maintaining biodiversity and ecosystem processes in boreal forests. A large proportion of deadwood-dependent species are threatened by habitat loss and degradation resulting from intensive forest management practices. In Finland, approximately 25% of all forest-dwelling species, around 5,000 species, are dependent on deadwood, of which 596 are red-listed. Currently, there is no large-scale, long-term monitoring programme for saproxylic species in Finland, and the tools required to implement such monitoring remain underdeveloped. Here, we develop, test and report a DNA-based monitoring method for dead wood associated organisms including fungi, lichens, bryophytes, and insects. Three study sites were selected for the research, one from each boreal vegetation zone. From each study site, 16 study logs were selected and permanently marked for long-term monitoring. Our results show that the method is applicable to all studied species groups. However, especially fungi and lichens show considerable difference between species detected morphologically and those detected using DNA-based methods. We conclude that two partly contrasting strategies emerge for implementing long-term monitoring of deadwood -associated boreal species. The first strategy emphasizes as comprehensive geographical sampling of habitat types and tree species as possible. The second approach focuses on long-term monitoring of individual deadwood units across their full decomposition trajectory. We recommend that solutions for unifying the currently fragmented monitoring research on deadwood-associated organisms would be sought together with potential coordinating institutions.

ecology↗

bioRxiv2026

ISG15-USP18 signaling restrains viperin-dependent metabolic antiviral restriction

Type I interferon (IFN-I) responses are tightly regulated to balance antiviral defense with cellular homeostasis. In humans, interferon-stimulated gene 15 (ISG15) functions as a critical negative regulator of IFN-I signaling by stabilizing the IFN negative regulator USP18, yet the functional consequences of ISG15 deficiency remain elusive. Here, we show that the loss of ISG15 exaggerates the JAK-STAT activation and, downstream, amplifies multiple ISGs including the nucleotide-modifying enzyme RSAD2 (viperin). Our quantitative proteomics, genetic reconstitution, and signaling analyses establish that defective USP18 stabilization skews the IFN response towards viperin expression. This amplified ISG network promotes viperin-catalyzed accumulation of the antiviral nucleotide analog ddhCTP, resulting in enhanced inhibition of viral RNA synthesis and the replication of Crimean-Congo hemorrhagic fever virus and SARS-CoV-2. Together, these findings demonstrate an ISG15-USP18-viperin axis that can be targeted to boost the metabolic antiviral restriction.

microbiology↗

bioRxiv2025

Hepatic gene replacement restores energy metabolism and doubles the survival in mouse model of GRACILE syndrome, a neonatal mitochondrial disease

Preclinical gene therapy studies of mitochondrial diseases remain limited due to their multisystemic manifestations and the scarcity of physiologically relevant animal models. Mutations in BCS1L, a nuclear gene encoding an assembly factor for mitochondrial complex III (CIII), are the most common cause of pediatric CIII deficiency. The most severe phenotype, GRACILE syndrome, is caused by a homozygous Finnish founder mutation (c.A232G, p.S78G). The corresponding Bcs1lp.S78G knock-in mouse model effectively recapitulates the human disease, with juvenile-onset hepatopathy, tubulopathy, growth restriction, segmental progeria, and short survival. Here, we performed recombinant adeno-associated virus (rAAV)-mediated gene replacement in this model, which features a postnatal presymptomatic window until weaning. A single intraperitoneal injection of rAAV encoding wild-type Bcs1l restored CIII assembly and activity in the liver, preventing hepatopathy. Hepatocyte-specific correction was sufficient to ameliorate hypoglycemia, improve growth, normalize systemic metabolism, and extend survival by nearly two-fold, despite persistent CIII deficiency in other tissues. Remarkably, liver-directed rescue also prevented skeletal muscle transcriptomic changes, particularly those linked to altered energy substrate utilization. These results underscore the central role of the liver in systemic energy homeostasis and growth regulation in multiorgan mitochondrial diseases and demonstrate the therapeutic potential of hepatocyte-directed gene replacement in phenotypes with prominent hepatopathy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/677965v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@b1cf50org.highwire.dtl.DTLVardef@1a1c2e2org.highwire.dtl.DTLVardef@101bdb6org.highwire.dtl.DTLVardef@14e11e3_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

physiology↗

bioRxiv2025

Evolutionarily conserved temperature dependency leads to loss of protein O-GlcNAc in mammalian hypothermia

O-N-acetylglucosaminylation (O-GlcNAcylation) is a conserved, non-canonical glycosylation of intracellular proteins suggested to regulate a wide spectrum of fundamental cell processes and stress responses. O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) add and remove, respectively, O-GlcNAc on protein serines and threonines. O-GlcNAcylation is thought to be primarily regulated by the availability of its substrate, UDP-GlcNAc, produced by the hexosamine biosynthetic pathway (HBP). We observed a body-wide loss of O-GlcNAcylated proteins in Bcs1l mutant mice, a model of mitochondrial complex III deficiency. UDP-GlcNAc precursors glutamine, UTP and acetyl-CoA were decreased in the mutant liver but, surprisingly, UDP-GlcNAc was not consistently decreased in the organs that showed low O-GlcNAc. Neither N-acetylglucosamine supplementation nor overexpression of the HBP rate-limiting enzyme GFPT1 restored the protein O-GlcNAc levels. The Bcs1l mutant mice become hypothermic and, interestingly, earlier evidence suggest that O-GlcNAcylation depends on ambient temperature in Drosophila embryos. We found that temperature determined O-GlcNAc abundance also in adult flies of tropical and boreal Drosophila species, in the poikilothermic vertebrate zebrafish, and in cultured mammalian cells. In cultured cells, the OGT-OGA protein ratio coincided with temperature and O-GlcNAc level, providing a regulatory mechanism. Pharmacological OGA inhibition decoupled the O-GlcNAc temperature dependency in cultured cells, as did an OGA null allele in Drosophila. In Bcs1l mutant mice, O-GlcNAc levels strongly correlated with body temperature. Increasing the mouse body temperature through transgenic expression of the heat-generating mitochondrial alternative oxidase (AOX) or housing at 35{degrees}C prevented the loss of O-GlcNAc. Pharmacological restoration of O-GlcNAc in the Bcs1l mutant mice produced minimal effects, suggesting that the bulk of O-GlcNAc is dispensable in mild hypothermia. Our findings imply an evolutionarily ancient role of protein O-GlcNAcylation in temperature adaptation and, instead of protein function-specific roles, argue for a global role of O-GlcNAc in temperature control of proteostasis.

physiology↗

bioRxiv2024

Restoration of mitochondrial complex III function in hepatocytes highlights the liver as a key thermogenic organ independent of brown adipocyte activation

Liver is the key hub of systemic energy metabolism and growth regulation, yet its roles in mitochondrial disease pathophysiology remain relatively understudied. Bcs1lp.S78G knock-in mice, carrying a patient mutation causing respiratory complex III (CIII)-deficiency, present juvenile-onset liver and kidney disease, growth restriction, lipodystrophy, and early death. We restored CIII function in the hepatocytes of these mice using recombinant adeno-associated viral vectors (rAAVs) expressing wild-type Bcs1l. A single intraperitoneal injection of rAAVs into presymptomatic juvenile mice prevented liver disease, improved hypoglycemia and growth, normalized hepatic fuel utilization, and doubled the survival. The mutant mice showed hypothermia and brown adipose tissue (BAT) inflammation, and lacked BAT activation basally and upon acute cold challenge. Disrupted foot pad innervation suggested sensory neuropathy and impaired thermosensation as a contributor to the BAT inactivity. Surprisingly, the rAAV-treated mice maintained near-normal body temperature without significant effect on BAT. Increasing cellular respiration via transgenic alternative oxidase (AOX) was sufficient to prevent the hypothermia. The CIII-deficient mice did not reach euthermia until at an ambient temperature of 35{degrees}C, housing at which relieved metabolic stress and ameliorated hepatocyte senescence. We conclude that mitochondrial respiration in hepatocytes is essential for euthermia in mice. Our findings highlight the crucial role of the liver in thermoregulation, hypothermia as a consequence of mitochondrial dysfunction, and the therapeutic potential of rAAV-based gene delivery in a preclinical model of a multiorgan mitochondrial disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=150 HEIGHT=200 SRC="FIGDIR/small/612616v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1cc59ecorg.highwire.dtl.DTLVardef@1239b01org.highwire.dtl.DTLVardef@95697eorg.highwire.dtl.DTLVardef@140fa94_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

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

Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription

Enzymatic methods to quantify deoxyribonucleoside triphosphates have existed for decades. In contrast, no general enzymatic method to quantify ribonucleoside triphosphates (rNTPs), which drive almost all cellular processes and serve as precursors of RNA, exists to date. ATP can be measured with an enzymatic luminometric method employing the firefly luciferase, but the quantification of the other ribonucleoside mono-, di-, and triphosphates is still a challenge for a non-specialized laboratory and practically impossible without chromatography equipment. To allow feasible quantification of ribonucleoside phosphates in any laboratory with typical molecular biology and biochemistry tools, we developed a robust microplate assay based on real-time detection of the Broccoli aptamer during in vitro transcription. The assay employs the bacteriophage T7 and SP6 RNA polymerases, two oligonucleotide templates encoding the 49-nucleotide Broccoli aptamer, and a high-affinity fluorogenic aptamer-binding dye to quantify each of the four canonical rNTPs. The inclusion of nucleoside mono- and diphosphate kinases in the assay reactions enabled the quantification of the mono- and diphosphate counterparts. The assay is inherently specific and tolerates concentrated tissue and cell extracts. In summary, we describe the first chromatography-free method to quantify ATP, ADP, AMP, GTP, GDP, GMP, UTP, UDP, UMP, CTP, CDP, and CMP in biological samples.

molecular biology↗

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↗

bioRxiv2022

Growth form matters: crustose lichens are sensitive to forest management on dead wood

Lichens have a vital role in forest ecosystems and they are a threatened group in boreal forests. However, the conservation ecology of the total lichen community has very rarely been studied. Here we studied lichen species and communities, including macrolichens (= foliose and fruticose growth forms) and rarely studied crustose lichens, on decaying wood in boreal spruce-dominated forests in Finland. We also studied obligate lignicoles that grow only on dead wood and are mostly crustose in growth form. Species richness and community composition were examined on decaying logs and natural or cut stumps of Picea abies at different decay stages (2-5) in 14 stands, half of which were natural or seminatural and half recently managed. We used thorough search to yield a species list as close to complete as possible. Our study questions were: 1) Are species richness and lichen communities different in natural and managed forests, and if so, are there differences between macrolichens, crustose lichens and obligate lignicoles in how they respond to forest management? 2) How does the decay stage and dead wood type affect the lichens, i.e. are there differences between stumps and logs? We found a total of 127 lichen species. Most (75%) of the recorded lichen species were crustose. With a generalized linear model we found that crustose lichens and obligate lignicoles had a higher species richness in natural than managed forests, but macrolichen richness was not significantly affected by forest management. Utilizing non-metric multidimensional scaling we discovered that site level community composition of macrolichens, crustose lichens and obligate lignicoles was also significantly different between natural and managed forests. We found that on dead wood unit level the decay stage had a significant effect on species richness and community composition, so that the species richness of all studied groups declined during the decay process. The dead wood type (stump vs. log) had a significant effect on species richness of macrolichens and obligate lignicoles, as well as on the communities of crustose lichens.

ecology↗

bioRxiv2019

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye, and inhibitor-resistant high-fidelity DNA polymerase

Deoxyribonucleotide triphosphates (dNTPs) are vital for the biosynthesis and repair of DNA. Their cellular concentration peaks during the S phase of the cell cycle. In non-proliferating cells dNTP concentrations are low, making their reliable quantification from tissue samples of heterogeneous cellular composition challenging. Partly because of this, the current knowledge related to regulation of and disturbances in cellular dNTP concentrations derive from cell culture experiments with little corroboration at the tissue or organismal level. Here, we fill the methodological gap by presenting a simple non-radioactive microplate assay for the quantification of dNTPs with a minimum requirement of 10 to 30 mg of biopsy material. In contrast to published assays, this assay is based on long (~200 nucleotides) synthetic single-stranded DNA templates, an inhibitor-resistant high-fidelity DNA polymerase, and the double-stranded-DNA-binding EvaGreen dye. The assay quantifies reliably as little as 100 fmol of each of the four dNTPs. Importantly, the assay allowed measurement of minute dNTP concentrations in mouse liver, heart, and skeletal muscle.

molecular biology↗