Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK)

Chiu, A.; Liu, L.; Seibold, S.; Battaile, K.; Craig, J.; Harmon, E.; Subramanian, S.; Chakafana, G.; Early, J.; Cron, L.; Staker, B.; Myler, P. J.; Lovell, S. J.; Van Voorhis, W.; Asojo, O.

doi:10.64898/2026.03.28.715000

bioRxiv · 10.64898/2026.03.28.715000

Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK)

Chiu, A.·Liu, L.·Seibold, S.·Battaile, K.·Craig, J.·Harmon, E.·Subramanian, S.·Chakafana, G.·Early, J.·Cron, L.·Staker, B.·Myler, P. J.·Lovell, S. J.·Van Voorhis, W.·Asojo, O.

View original source ↗Export metadata ↓

Abstract

Trichomonas vaginalis causes trichomoniasis, the most common non-viral sexually transmitted disease in humans. T. vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK) is a putative target for rational, structure-based drug discovery, given its absence in mammals and its importance for parasite survival. TvPPi-PFK is a cytosolic enzyme that catalyzes the phosphorylation of fructose-6-phosphate using pyrophosphate (PPi) as the phosphoryl donor. This reversible reaction, catalyzed by TvPPi-PFK, is the first committed step in glycolysis. Its reverse reaction is vital for gluconeogenesis in T. vaginalis. The purification, crystallization, structure determination, and crystal structures of TvPPi-PFK are reported. TvPPi-PFK is the first reported eukaryotic PPi-PFK structure. TvPPi-PFK retains the overall PPi-PFK topology observed in bacterial PPi-PFK including conserved motifs essential for pyrophosphate binding and PPi-PFK catalytic activity. In addition to the catalytic PPi-PFK binding sites, TvPPi-PFK has two additional ligand binding sites. The first binds AMP usurped during protein production and helps stabilize the TvPPi-PFK tetramer. A second ligand binding site was observed in proximity to the AMP-binding site and accommodates sugar phosphates soaked into preformed crystals. This sugar phosphates binding site is distinct from the TvPPi-PFK active site that binds fructose-6-phosphate. Future mutagenesis and activity studies are planned to determine the relevance of both sites. SynopsisThe production, crystallization, and crystal structures of a pyrophosphate-dependent phosphofructokinase from Trichomonas vaginalis (TvPPi-PFK) are reported. TvPPi-PFK has a prototypical PPi-PFK active site as well as unexpected AMP and sugar-phosphate binding sites at the dimer interface.

Explore related subjects

biochemistry Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Chiu, A., Liu, L., Seibold, S., Battaile, K., Craig, J., Harmon, E., Subramanian, S., Chakafana, G., Early, J., Cron, L., Staker, B., Myler, P. J., Lovell, S. J., Van Voorhis, W., Asojo, O.. 2026-03-28. Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK). https://doi.org/10.64898/2026.03.28.715000

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Aging Remodels the Female Skeletal Muscle Proteome Toward Matrix, Chromatin and Lysosomal Programs that Track Loss of Physical Function

Loss of skeletal muscle strength and mobility is among the most consequential features of human aging, yet the molecular programs that accompany this decline in women remain poorly understood. Here, we performed deep comprehensive data-independent acquisition (DIA) proteomic profiling of vastus lateralis biopsies from 10 younger (24-30 years) and 10 older (70-84 years) healthy women enrolled through the NIH Common Fund Cellular Senescence Network (SenNet), with matched measurements of grip strength and gait speed. Of 2,391 quantified protein groups, 163 were significantly altered with age, and partial least squares-discriminant analysis completely separated the age groups (cross-validated AUC = 1.00). Older muscle showed increased extracellular matrix and vascular remodeling proteins (TIMP3, COL8A1, ELN, FBN1), nuclear, chromatin and RNA-binding proteins (HMGB1, HMGB2, histone H1.0, MATR3, NCL), and lysosomal and senescence-associated secretory phenotype (SASP)-associated proteins (CTSZ, CTSD, PSAP), together with reduced glycolytic and energetic proteins (GAPDH, ENO3, PHKA1, CYCS). Age effects were robust to adjust for body mass index (BMI). Integrating differential abundance, multivariate importance and participant-level consistency, we defined a 24-protein skeletal muscle aging signature whose score separated all younger from all elderly women. Combining grip strength and gait speed into a combined function score, we found that 23 of the 24 signature proteins correlated with physical function (FDR < 0.05), and the signature score correlated strongly with function (r = -0.79). The senescence-associated alarmins HMGB1 and HMGB2 emerged as lead proteins: HMGB1 showed the strongest association with function (r = -0.86), and both remained associated after adjustment for age group. Together, these data define a senotype proteomic program in aging female skeletal muscle and a molecular signature of muscle function that, after validation, may serve as a readout for interventions that aim to preserve physical performance in elderly women.

biochemistry↗

bioRxiv2026

SUMOylation Regulates IRF2BP2 Nuclear Localization and Stability

Interferon Regulatory Factor-2 Binding Protein 2 (IRF2BP2) is a transcriptional cofactor implicated in diverse biological processes. Although it functions primarily as a repressor, it can also activate gene expression. However, the mechanisms governing IRF2BP2 regulation remain poorly understood. Here, we demonstrate that IRF2BP2 interacts with UBE2I, the SUMO E2 ligase, and undergoes multi-SUMOylation, which enhances its nuclear localization. We further show that IRF2BP2 nuclear import is importin-{beta}-dependent and requires the functional nuclear localization signal (NLS). IRF2BP2 preferentially accumulates in transcriptionally active euchromatin in both resting and S-phase cells, consistent with its role in transcriptional control. We further reveal that SUMOylation contributes to IRF2BP2 stability. Moreover, IRF2BP2 is also ubiquitinated, predominantly through K6-linked ubiquitin chains, a non-proteolytic modification that aligns with our observation that IRF2BP2 is not degraded by the proteasome. Together, these findings identify SUMOylation and non-proteolytic ubiquitination as key mechanisms regulating IRF2BP2, highlighting a novel SUMO1-NLS-importin-{beta}-dependent pathway that governs its localization.

biochemistry↗

bioRxiv2026

S-adenosylmethionine supply controls DNA methylation turnover in synovial sarcoma

Background: Methionine is the nutrient source of the metabolite S-adenosylmethionine (SAM) used to methylate chromatin for regulation of gene expression. Disruptions to this metabolic supply, including nutritional deficiency of certain B vitamins, alter chromatin methylation and have been implicated in tumor growth. Objective: To define how cellular SAM supply controls DNA methylation dynamics and the disruption of oncogenic gene expression in synovial sarcoma. Methods: Cell line models of synovial sarcoma were treated with the DNA methyltransferase inhibitor azacitidine or the small-molecule MAT2A inhibitor AG-270, which blocks SAM synthesis from methionine. Intracellular SAM concentrations were quantified by liquid chromatography-mass spectrometry. Global DNA methylation rates were measured by stable isotope tracing with [2H3-methyl]-methionine. Genomic sites of altered DNA methylation were identified by EM-seq and the associated transcriptional changes measured by RNA-seq. Results: Inhibition of SAM synthesis reduced intracellular SAM concentration from 94 uM to 5.6 uM (p value < 0.0001) at 24 hours. This was associated with a 19% decrease (p value < 0.0001) in the global 5-methyldeoxycytosine turnover rate, while total DNA methylation levels were maintained. In contrast to the global DNA hypomethylation induced by azacitidine, SAM depletion resulted in a redistribution of DNA methylation with loss at 252 and gain at 206 genomic sites, and the transcriptional response to SAM depletion was not associated with changes in promoter methylation at the altered genes. Both azacitidine and SAM depletion activated mesenchymal genes, while suppressing cell cycle progression. Conclusions: Metabolic supply of SAM is a major regulator of DNA methylation turnover providing a mechanism by which nutritional or genetic disruptions to SAM metabolism can alter chromatin methylation and gene expression.

biochemistry↗