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Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that “mitochondrial translation factors” mTRAN1 and mTRAN2 are land plant–specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)–like RNA binding proteins of the mitoribosomal “small” subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5′ regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.

Protein assemblies are some of the most complex molecular machines in nature. They facilitate many cellular functions, from DNA replication to molecular motion, energy production, and even the production of other proteins. In a series of 3 papers, we analyzed the structure, developed structure prediction tools, and design tools, for different protein assemblies. Many of the studies were centered around viral protein capsids. Viral capsids are protein coats found inside viruses that contain and protect the viral genome. In one paper, we studied the interfaces of these capids and their energy landscapes. We found that they differ from regular homomers in terms of the amino acid composition and size, but not in the quality of interactions. This contradicts existing experimental and theoretical studies that suggest that the interactions are weak. We hypothesise that the occlusion by our models of electrostatic and entropic contributions might be at play. In another paper, we developed methods to predict large cubic symmetrical protein assemblies, such as viral capsids, from sequence. This method is based upon AlphaFold, a new AI tool that has revolutionized protein structure prediction. We found that we can predict up to 50% of the structures of these assemblies. The method can quickly elucidate the structure of many relevant proteins for humans, and for understanding structures relevant to disease, such as the structures of viral capsids. In the final paper, we developed tools to design capsid-like proteins called cages – structures that can be used for drug delivery and vaccine design. A fundamental problem in designing cage structures is achieving different architectures and low porosity, goals that are important for vaccine design and the delivery of small drug molecules. By explicitly modelling the shapes of the subunits in the cage and matching the shapes with proteins from structural databases, we find that we can create structures with many different sizes, shap

Plant mitochondria produce the majority of adenosine triphosphate (ATP) – the cellular energy currency for metabolic reactions needed for plant growth, development, and maintenance. Despite a relatively thorough understanding of basic mitochondrial functions, many mitochondrial proteins and processes remain poorly understood. The aims of this thesis are to i) review and compare the mitochondrial unfolded protein response (UPRmt) and related signalling across eukaryotic kingdoms, to ii) describe an efficient isolation method of Arabidopsis mitochondria using continuous Percoll density gradients, and to iii) characterize two Arabidopsis thaliana genes, mTRAN1 and mTRAN2. Paper I summarizes the current knowledge of UPRmt across eukaryotic kingdoms, and describes a meta-analysis of UPRmt regulators and target genes. UPRmt is a mitochondria-to-nucleus “retrograde” response that regulates nuclear gene expression during mitochondrial dysfunction to maintain mitochondrial homeostasis. Although UPRmt has been extensively studied in animals, relatively little is known about the plant UPRmt and only few regulators have recently been identified. In yeast, very few unfolded protein responses that seem to be related to UPRmt have been described. Here, the UPRmt in animals, yeast and plants are compared. Our study indicates that each kingdom has evolved their own specific regulators, which however induce very similar groups of target genes. Our meta-analysis identifies homologs of known UPRmt regulators and responsive genes across eukaryotic kingdoms.Paper II describes a strategy for efficient purification of Arabidopsis mitochondria using continuous Percoll density gradients. By using this method, the purity of isolated mitochondria is greatly improved. Obtained mitochondria can be either used for assays requiring highly intact and functional mitochondria, e.g. import assay or respiration measurement, or be stored for later use, e.g. BN-PAGE or western blot.Paper III describes th

Chromatin organization controls transcription by modulating 3D-interactions between enhancers and promoters in the nucleus. Alterations in epigenetic states and 3D-chromatin organization result in gene expression changes contributing to cancer. Here, we map the promoter-enhancer interactome and regulatory landscape of glioblastoma, the most aggressive primary brain tumour. Our data reveals profound rewiring of promoter-enhancer interactions, chromatin accessibility and redistribution of histone marks in glioblastoma. This leads to loss of long-range regulatory interactions and overall activation of promoters, which orchestrate changes in the expression of genes associated to glutamatergic synapses, axon guidance, axonogenesis and chromatin remodelling. SMAD3 and PITX1 emerge as major transcription factors controlling genes related to synapse organization and axon guidance. Inhibition of SMAD3 and neuronal activity stimulation cooperate to promote proliferation of glioblastoma cells in co-culture with glutamatergic neurons, and in mice bearing patient-derived xenografts. Our findings provide mechanistic insight into the regulatory networks that mediate neurogliomal synaptic communication.

Folding of newly synthesized proteins poses challenges for a functional proteome. Dedicated protein quality control (PQC) systems either promote the folding of nascent polypeptides at ribosomes or, if this fails, ensure their degradation. Although well studied for cytosolic protein biogenesis, it is not understood how these processes work for mitochondrially encoded proteins, key subunits of the oxidative phosphorylation (OXPHOS) system. Here, we identify dedicated hubs in proximity to mitoribosomal tunnel exits coordinating mitochondrial protein biogenesis and quality control. Conserved prohibitin (PHB)/m-AAA protease supercomplexes and the availability of assembly chaperones determine the fate of newly synthesized proteins by molecular triaging. The localization of these competing activities in the vicinity of the mitoribosomal tunnel exit allows for a prompt decision on whether newly synthesized proteins are fed into OXPHOS assembly or are degraded.

Aim: A functional proteome is essential for life and maintained by protein quality control (PQC) systems in the cytosol and organelles. Protein aggregation is an indicator of a decline of PQC linked to aging and disease. Mitochondrial PQC is critical to maintain mitochondrial function and thus cellular fitness. How mitochondria handle aggregated proteins is not well understood. Here we tested how the metabolic status impacts on formation and clearance of aggregates within yeast mitochondria and assessed which proteins are particularly sensitive to denaturation. Methods: Confocal microscopy, electron microscopy, immunoblotting and genetics were applied to assess mitochondrial aggregate handling in response to heat shock and ethanol using the mitochondrial disaggregase Hsp78 as a marker for protein aggregates. Results: We show that aggregates formed upon heat or ethanol stress with different dynamics depending on the metabolic state. While fermenting cells displayed numerous small aggregates that coalesced into one large foci that was resistant to clearance, respiring cells showed less aggregates and cleared these aggregates more efficiently. Acute inhibition of mitochondrial translation had no effect, while preventing protein import into mitochondria by inhibition of cytosolic translation prevented aggregate formation. Conclusion: Collectively, our data show that the metabolic state of the cells impacts the dynamics of aggregate formation and clearance, and that mainly newly imported and not yet assembled proteins are prone to form aggregates. Because mitochondrial functionality is crucial for cellular metabolism, these results highlight the importance of efficient protein biogenesis to maintain the mitochondrial proteome operational during metabolic adaptations and cellular stress.

The nuclear pore complex (NPC) has long been assumed to be the sole route across the nuclear envelope, and under normal homeostatic conditions it is indeed the main mechanism of nucleo-cytoplasmic transport. However, it has also been known that e.g. herpesviruses cross the nuclear envelope utilizing a pathway entitled nuclear egress or envelopment/de-envelopment. Despite this, a thread of observations suggests that mechanisms similar to viral egress may be transiently used also in healthy cells. It has since been proposed that mechanisms like nuclear envelope budding (NEB) can facilitate the transport of RNA granules, aggregated proteins, inner nuclear membrane proteins, and mis-assembled NPCs. Herein, we will summarize the known roles of NEB as a physiological and intrinsic cellular feature and highlight the many unanswered questions surrounding these intriguing nuclear events.

While proteins populating their native conformations constitute the functional entities of cells, protein aggregates are traditionally associated with cellular dysfunction, stress and disease. During recent years, it has become clear that large aggregate-like protein condensates formed via liquid-liquid phase separation age into more solid aggregate-like particles that harbor misfolded proteins and are decorated by protein quality control factors. The constituent proteins of the condensates/aggregates are disentangled by protein disaggregation systems mainly based on Hsp70 and AAA ATPase Hsp100 chaperones prior to their handover to refolding and degradation systems. Here, we discuss the functional roles that condensate formation/aggregation and disaggregation play in protein quality control to maintain proteostasis and why it matters for understanding health and disease.

Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.

The NAM, ATAF1/2, and CUC2 (NAC) domain transcription factor VND-INTERACTING2 (VNI2) negatively regulates xylem vessel formation by interacting with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel formation. Here, we screened interacting proteins with VNI2 using yeast two-hybrid assay and isolated two NAC domain transcription factors, Arabidopsis thaliana ACTIVATION FACTOR 2 (ATAF2) and NAC DOMAIN CONTAINING PROTEIN 102 (ANAC102). A transient gene expression assay showed that ATAF2 upregulates the expression of genes involved in leaf senescence, and VNI2 effectively inhibits the transcriptional activation activity of ATAF2. vni2 mutants accelerate leaf senescence, whereas ataf2 mutants delay leaf senescence. In addition, the accelerated leaf senescence phenotype of the vni2 mutant is recovered by simultaneous mutation of ATAF2. Our findings strongly suggest that VNI2 interacts with and inhibits ATAF2, resulting in negatively regulating leaf senescence.

WaaG is a glycosyltransferase (GT) involved in the synthesis of the bacterial cell wall, and in Escherichia coli it catalyzes the transfer of a glucose moiety from the donor substrate UDP-glucose onto the nascent lipopolysaccharide (LPS) molecule which when completed constitutes the major component of the bacterium's outermost defenses. Similar to other GTs of the GT-B fold, having two Rossman-like domains connected by a short linker, WaaG is believed to undergo complex inter-domain motions as part of its function to accommodate the nascent LPS and UDP-glucose in the catalytic site located in the cleft between the two domains. As the nascent LPS is bulky and membrane-bound, WaaG is a peripheral membrane protein, adding to the complexity of studying the enzyme in a biologically relevant environment. Using specific 5-fluoro-Trp labelling of native and inserted tryptophans and 19F NMR we herein studied the dynamic interactions of WaaG with lipids using bicelles, and with the donor substrate. Line-shape changes when bicelles are added to WaaG show that the dynamic behavior is altered when binding to the model membrane, while a chemical shift change indicates an altered environment around a tryptophan located in the C-terminal domain of WaaG upon interaction with UDP-glucose or UDP. A lipid-bound paramagnetic probe was used to confirm that the membrane interaction is mediated by a loop region located in the N-terminal domain. Furthermore, the hydrolysis of the donor substrate by WaaG was quantified by 31P NMR.

The obligate intracellular bacterium Chlamydia trachomatis inserts a family of inclusion membrane (Inc) proteins into the membrane of its vacuole (the inclusion). The Inc CpoS is a critical suppressor of host cellular immune surveillance, but the underlying mechanism remained elusive. By complementing a cpoS mutant with various natural orthologs and variants of CpoS, we linked distinct molecular interactions of CpoS to distinct functions. Unexpectedly, we found CpoS to be essential for the formation of inclusion membrane microdomains that control the spatial organization of multiple Incs involved in signaling and modulation of the host cellular cytoskeleton. While the function of CpoS in microdomains was uncoupled from its role in the suppression of host cellular defenses, we found the ability of CpoS to interact with Rab GTPases to be required not only for the manipulation of membrane trafficking, such as to mediate transport of ceramide-derived lipids (sphingolipids) to the inclusion, but also for the inhibition of Stimulator of interferon genes (STING)-dependent type I interferon responses. Indeed, depletion of Rab35 phenocopied the exacerbated interferon responses observed during infection with CpoS-deficient mutants. Overall, our findings highlight the role of Inc-Inc interactions in shaping the inclusion microenvironment and the modulation of membrane trafficking as a pathogenic immune evasion strategy. IMPORTANCE: Chlamydia trachomatis is a prevalent bacterial pathogen that causes blinding ocular scarring and urogenital infections that can lead to infertility and pregnancy complications. Because Chlamydia can only grow within its host cell, boosting the intrinsic defenses of human cells may represent a novel strategy to fight pathogen replication and survival. Hence, CpoS, a Chlamydia protein known to block host cellular defenses, or processes regulated by CpoS, could provide new opportunities for therapeutic intervention. By revealing CpoS as a multifunction

The chloroplast lumen contains at least 80 proteins whose function and regulation are not yet fully understood. Isolating the chloroplast lumen enables the characterization of the lumenal proteins. The lumen can be isolated in several ways through thylakoid disruption using a Yeda press or sonication, or through thylakoid solubilization using a detergent. Here, we present a simple procedure to isolate thylakoid lumen by sonication using leaves of the plant Arabidopsis thaliana. The step-by-step procedure is as follows: thylakoids are isolated from chloroplasts, loosely associated thylakoid surface proteins from the stroma are removed, and the lumen fraction is collected in the supernatant following sonication and centrifugation. Compared to other procedures, this method is easy to implement and saves time, plant material, and cost. Lumenal proteins are obtained in high quantity and purity; however, some stromal membrane-associated proteins are released to the lumen fraction, so this method could be further adapted if needed by decreasing sonication power and/or time.

Listeria monocytogenes is a facultative Gram-positive bacterium that causes listeriosis, a severe foodborne disease. We previously discovered that ring-fused 2-pyridone compounds can decrease virulence factor expression in Listeria by binding and inactivating the PrfA virulence activator. In this study, we tested PS900, a highly substituted 2-pyridone that was recently discovered to be bactericidal to other Gram-positive pathogenic bacteria, such as Staphylococcus aureus and Enterococcus faecalis. We show that PS900 can interact with PrfA and reduce the expression of virulence factors. Unlike previous ring-fused 2-pyridones shown to inactivate PrfA, PS900 had an additional antibacterial activity and was found to potentiate sensitivity toward cholic acid. Two PS900-tolerant mutants able to grow in the presence of PS900 carried mutations in the brtA gene, encoding the BrtA repressor. In wild-type (WT) bacteria, cholic acid binds and inactivates BrtA, thereby alleviating the expression of the multidrug transporter MdrT. Interestingly, we found that PS900 also binds to BrtA and that this interaction causes BrtA to dissociate from its binding site in front of the mdrT gene. In addition, we observed that PS900 potentiated the effect of different osmolytes. We suggest that the increased potency of cholic acid and osmolytes to kill bacteria in the presence of PS900 is due to the ability of the latter to inhibit general efflux, through a yet-unknown mechanism. Our data indicate that thiazolino 2-pyridones constitute an attractive scaffold when designing new types of antibacterial agents. IMPORTANCE: Bacteria resistant to one or several antibiotics are a very large problem, threatening not only treatment of infections but also surgery and cancer treatments. Thus, new types of antibacterial drugs are desperately needed. In this work, we show that a new generation of substituted ring-fused 2-pyridones not only inhibit Listeria monocytogenes virulence gene expression, presumably

Virulence factors enable pathogenic bacteria to infect host cells, establish infection, and contribute to disease progressions. In Gram-positive pathogens such as Staphylococcus aureus (Sa) and Enterococcus faecalis (Ef), the pleiotropic transcription factor CodY plays a key role in integrating metabolism and virulence factor expression. However, to date, the structural mechanisms of CodY activation and DNA recognition are not understood. Here, we report the crystal structures of CodY from Sa and Ef in their ligand-free form and their ligand-bound form complexed with DNA. Binding of the ligands - branched chain amino acids and GTP - induces conformational changes in the form of helical shifts that propagate to the homodimer interface and reorient the linker helices and DNA binding domains. DNA binding is mediated by a non-canonical recognition mechanism dictated by DNA shape readout. Furthermore, two CodY dimers bind to two overlapping binding sites in a highly cooperative manner facilitated by cross-dimer interactions and minor groove deformation. Our structural and biochemical data explain how CodY can bind a wide range of substrates, a hallmark of many pleiotropic transcription factors. These data contribute to a better understanding of the mechanisms underlying virulence activation in important human pathogens., CodY

Geobacter species are common in iron-rich environments and can contribute to formation of methylmercury (MeHg), a neurotoxic compound with high bioaccumulation potential formed as a result of bacterial and archaeal physiological activity. Geobacter sulfurreducens can utilize various electron acceptors for growth including iron hydroxides or fumarate. However, it remains poorly understood how the growth on these compounds affects physiological properties of bacterial cells in biofilms, including the capacity to produce MeHg. The purpose of this study was to determine changes in the biochemical composition of G. sulfurreducens during biofilm cultivation in media containing iron hydroxide or fumarate, and to quantify mercury (Hg) methylation capacity of the formed biofilms. Biofilms were characterized by Fourier-transform infrared spectroscopy in the attenuated total reflection mode (ATR-FTIR), Resonance Raman spectroscopy and confocal laser scanning microscopy. MeHg formation was quantified by mass spectrometry after incubation of biofilms with 100 nM Hg. The results of ATR-FTIR experiments showed that in presence of fumarate, G. sulfurreducens biofilm formation was accompanied by variation in content of the energy-reserve polymer glycogen over time, which could be cancelled by the addition of supplementary nutrients (yeast extract). In contrast, biofilms cultivated on Fe(III) hydroxide did not accumulate glycogen. The ATR-FTIR results further suggested that Fe(III) hydroxide surfaces bind cells via phosphate and carboxylate groups of bacteria that form complexes with iron. Furthermore, biofilms grown on Fe(III) hydroxide had higher fraction of oxidized cytochromes and produced two to three times less biomass compared to conditions with fumarate. Normalized to biofilm volume, the content of MeHg was similar in assays with biofilms grown on Fe(III) hydroxide and on fumarate (with yeast extract and without). These results suggest that G. sulfurreducens biofilms produce

The building blocks for RNA and DNA are made in the cytosol, meaning mitochondria depend on the import and salvage of ribonucleoside triphosphates (rNTPs) and deoxyribonucleoside triphosphates (dNTPs) for the synthesis of their own genetic material. While extensive research has focused on mitochondrial dNTP homeostasis due to its defects being associated with various mitochondrial DNA (mtDNA) depletion and deletion syndromes, the investigation of mitochondrial rNTP homeostasis has received relatively little attention. In this issue of the EMBO Journal, Grotehans et al provide compelling evidence of a major role for NME6, a mitochondrial nucleoside diphosphate kinase, in the conversion of pyrimidine ribonucleoside diphosphates into the corresponding triphosphates. These data also suggest a significant physiological role for NME6, as its absence results in the depletion of mitochondrial transcripts and destabilization of the electron transport chain (Grotehans et al, 2023).

Assessing the levels of oxidative stress markers and antioxidant enzymes in the brain is crucial in evaluating its antioxidant capacity and understanding the influence of various dietary patterns on brain well-being. This study aimed to investigate the antioxidant status and oxidative damage in the brain of bat species with different feeding habits to gain insights into their protective mechanisms against oxidative stress and their interspecific variation. The levels of oxidative damage markers and the activities of antioxidants were measured in the brain of four bat species with different feeding habits, namely insectivorous, frugivorous, nectarivorous, and hematophagous. Insectivorous bats showed higher levels of SOD and fumarase compared to the other groups, while hematophagous bats showed lower levels of these enzymes. On the other hand, the activities of glutathione peroxidase and glutathione S-transferase were higher in hematophagous bats and lower in insectivorous bats. The carbonyl groups and malondialdehyde levels were lower in frugivores, while they were similar in the other feeding guilds. Nitrite and nitrate levels were higher in the hematophagous group and relatively lower in all other groups. The GSSG/GSH ratio was higher in the hematophagous group and lower in frugivores. Overall, our results indicate that the levels of oxidative stress markers and the activities of antioxidant enzymes in the brain vary significantly among bat species with different feeding habitats. The findings suggest that the antioxidant status of the brain is influenced by diet and feeding habits.

Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and a neutralizing antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins), we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralization by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralizing mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralization, while in multidomain antitoxins the neutralization is mediated by other domains, such as PAD1, Phd-C, and ZFD. We hypothesize that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 NetFlax TA systems and used domain annotations and metabolic labeling assays to predict their potential mechanisms of toxicity (such as membrane disruption, and inhibition of cell division or protein synthesis) as well as biological functions (such as antiphage defense). We have validated the antiphage activity of a RosmerTA system encoded by Gordonia phage Kita, and used fluorescence microscopy to confirm its predicted membrane-depolarizing activity. The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/.

In thylakoid membranes, photosystem II (PSII) monomers from the stromal lamellae contain the subunits PsbS and Psb27 (PSIIm-S/27), while PSII monomers (PSIIm) from granal regions lack these subunits. Here, we have isolated and characterized these 2 types of PSII complexes in tobacco (Nicotiana tabacum). PSIIm-S/27 showed enhanced fluorescence, the near absence of oxygen evolution, and limited and slow electron transfer from QA to QB compared to the near-normal activities in the granal PSIIm. However, when bicarbonate was added to PSIIm-S/27, water splitting and QA to QB electron transfer rates were comparable to those in granal PSIIm. The findings suggest that the binding of PsbS and/or Psb27 inhibits forward electron transfer and lowers the binding affinity for bicarbonate. This can be rationalized in terms of the recently discovered photoprotection role played by bicarbonate binding via the redox tuning of the QA/QA•- couple, which controls the charge recombination route, and this limits chlorophyll triplet-mediated 1O2 formation. These findings suggest that PSIIm-S/27 is an intermediate in the assembly of PSII in which PsbS and/or Psb27 restrict PSII activity while in transit using a bicarbonate-mediated switch and protective mechanism.

Epigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure that ultimately benefits the repression is largely unclear. Polycomb group proteins comprise a family of evolutionarily conserved epigenetic repressors. They act as multi-subunit complexes one of which tri-methylates histone H3 at Lysine 27 (H3K27). Here we describe a novel Monte Carlo–Molecular Dynamics simulation framework, which we employed to discover that stochastic interaction of Polycomb Repressive Complex 1 (PRC1) with tri-methylated H3K27 is sufficient to fold the methylated chromatin. Unexpectedly, such chromatin folding leads to spatial clustering of the DNA elements bound by PRC1. Our results provide further insight into mechanisms of epigenetic repression and the process of chromatin folding in response to histone methylation.

Misfolding and aggregation of transthyretin (TTR) causeseveralamyloid diseases. Besides being an amyloidogenic protein, TTR hasan affinity for bicyclic small-molecule ligands in its thyroxine (T4)binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbenescaffold is also widely applied for amyloid fibril-specific ligandsused as fluorescence probes and as positron emission tomography tracersfor amyloid detection and diagnosis of amyloidosis. We have shownthat native tetrameric TTR binds to amyloid ligands based on the trans-stilbenescaffold providing a platform for the determination of high-resolutionstructures of these important molecules bound to protein. In thisstudy, we provide spectroscopic evidence of binding and X-ray crystallographicstructure data on tetrameric TTR complex with the fluorescent salicylicacid-based pyrene amyloid ligand (Py1SA), an analogue of the Congored analogue X-34. The ambiguous electron density from the X-ray diffraction,however, did not permit Py1SA placement with enough confidence likelydue to partial ligand occupancy. Instead, the preferred orientationof the Py1SA ligand in the binding pocket was determined by moleculardynamics and umbrella sampling approaches. We find a distinct preferencefor the binding modes with the salicylic acid group pointing intothe pocket and the pyrene moiety outward to the opening of the T4binding site. Our work provides insight into TTR binding mode preferencefor trans-stilbene salicylic acid derivatives as well as a frameworkfor determining structures of TTR-ligand complexes., Funding Agencies|German Research Foundation (DFG) [KO 5423/1-1]; Swedish e-Science Research Centre (SeRC); Swedish Research Council [2018-4343, 2019-04405]; Swedish Brain Foundation [ALZ2019-0004, ALZ2022-0004]; Gustaf V and Drottning Victorias Stiftelse

Seminal plasma contains many morphologically hetero-geneous extracellular vesicles (sEVs). These are sequentially released by cells of the testis, epididymis, and accessory sex glands and involved in male and fe-male reproductive processes. This study aimed to define in depth sEV subsets isolated by ultrafiltration and size exclusion chromatography, decode their proteomic profiles using liquid chromatography-tandem mass spectrometry, and quantify identified proteins using sequential window acquisition of all theoretical mass spectra. The sEV subsets were defined as large (L-EVs) or small (S-EVs) by their protein concentration, morphology, size distribution, and EV-specific protein markers and purity. Liquid chromatography-tandem mass spectrometry identified a total of 1034 proteins, 737 of them quantified by SWATH in S-EVs, L-EVs, and non-EVs-enriched samples (18-20 size exclusion chromatography-eluted fractions). The differential expression analysis revealed 197 differentially abundant proteins between both EV subsets, S-EVs and L-EVs, and 37 and 199 between S-EVs and L-EVs versus non-EVs-enriched samples, respectively. The gene ontology enrichment analysis of differentially abundant proteins suggested, based on the type of protein detected, that S-EVs could be mainly released through an apocrine blebbing pathway and be involved in modulating the im-mune environment of the female reproductive tract as well as during sperm-oocyte interaction. In contrast, L-EVs could be released by fusion of multivesicular bodies with the plasma membrane becoming involved in sperm physiological processes, such as capacitation and avoidance of oxidative stress. In conclusion, this study provides a procedure capable of isolating subsets of EVs from pig seminal plasma with a high degree of purity and shows differences in the proteomic profile between EV subsets, indicating different sources and biological functions for the sEVs., Funding Agencies|Spanish Ministry of Science and Innovation(MCIN/AEI) [PID2019- 105713GB-I00, RED2018-102411-T, 891382]; European Union [PROMETEO/2020/071]; Generalitat Valenciana [2019-00288]; FORMAS, Stockholm; Madrid, Spain; [PID2020-113493RB-I00]

The development of ligands for detecting protein aggregates is of great interest, as these aggregated proteinaceous species are the pathological hallmarks of several devastating diseases, including Alzheimers disease. In this regard, thiophene-based ligands have emerged as powerful tools for fluorescent assessment of these pathological entities. The intrinsic conformationally sensitive photophysical properties of poly- and oligothiophenes have allowed optical assignment of disease-associated protein aggregates in tissue sections, as well as real-time in vivo imaging of protein deposits. Herein, we recount the chemical evolution of different generations of thiophene-based ligands, and exemplify their use for the optical distinction of polymorphic protein aggregates. Furthermore, the chemical determinants for achieving a superior fluorescent thiophene-based ligand, as well as the next generation of thiophene-based ligands targeting distinct aggregated species are described. Finally, the directions for future research into the chemical design of thiophene-based ligands that can aid in resolving the scientific challenges around protein aggregation diseases are discussed., Funding Agencies|Swedish Research Council [2016-00748]; Swedish Brain Foundation; Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse; U.S. National Institutes of Health [U01NS110437]

Among the responders to microbial invasion, neutrophils represent the earliest and perhaps the most important immune cells that contribute to host defense with the primary role to kill invading microbes using a plethora of stored anti-microbial molecules. One such process is the production of reactive oxygen species (ROS) by the neutrophil enzyme complex NADPH-oxidase, which can be assembled and active either extracellularly or intracellularly in phagosomes (during phagocytosis) and/or granules (in the absence of phagocytosis). One soluble factor modulating the interplay between immune cells and microbes is galectin-3 (gal-3), a carbohydrate-binding protein that regulates a wide variety of neutrophil functions. Gal-3 has been shown to potentiate neutrophil interaction with bacteria, including Staphylococcus aureus, and is also a potent activator of the neutrophil respiratory burst, inducing large amounts of granule-localized ROS in primed cells. Herein, the role of gal-3 in regulating S. aureus phagocytosis and S. aureus-induced intracellular ROS was analyzed by imaging flow cytometry and luminol-based chemiluminescence, respectively. Although gal-3 did not interfere with S. aureus phagocytosis per se, it potently inhibited phagocytosis-induced intracellular ROS production. Using the gal-3 inhibitor GB0139 (TD139) and carbohydrate recognition domain of gal-3 (gal-3C), we found that the gal-3-induced inhibitory effect on ROS production was dependent on the carbohydrate recognition domain of the lectin. In summary, this is the first report of an inhibitory role of gal-3 in regulating phagocytosis-induced ROS production., Funding Agencies|Galecto Biotech AB [GB0139, TD139]

Sugar is a vital sustenance for most forms of life. For a cell to take up sugar, specialized transport proteins embedded into the membrane bilayer known as sugar porters, are required. Dysfunction of sugar porters is associated with some metabolic diseases, and their expression is upregulated in many cancers as they typically require more sugar than normal cells. Furthermore, sugar porters also play a role in the vitality of the malaria parasite. The mechanism of sugar transport is known as a rocker-switch alternating access mechanism. Simplistically, sugar binds between two similar domains on the outside of a sugar transporter and the domains then move around the sugar, so the sugar is exposed to the inside. During this domain movement, protein mass will block the sugar binding site from both outside and inside, forming the occluded state which is essential to ensure no substrate leakage during transport. Despite this relatively simple model of transport, little is known about how different sugar porters display diverse substrate specificity, affinity, and turnover. In the four papers making up this thesis, we structurally characterize missing pieces of the sugar transport cycle, identify how these states are connected with simulations, and assess factors contributing to sugar transport by functional assays. With simulations, we show how sugar catalyzes conformational change by interacting with the occluded state. We demonstrate our functional proteoliposome-based transport assay, which allows us to measure the effect of protein mutations, inhibitors, and lipid influences in sugar recognition and turnover. Characterization of the malaria parasite hexose transporter PfHT1 has allowed us to understand antimalarial inhibitor specificity against this protein which could have implications in combating the disease, as well as pharmacological control of sugar porters in general.

The communication between plants and bacteria involves a complex chemical signaling network that mediates responses to various biotic and abiotic stresses, as well as establishing symbiotic relationships between different organisms. The first part of the thesis focuses on a mechanism for symbiotic communication between plants and bacteria and more specifically on how C-glycosylated aromatic polyketide compounds produced by plants can be used as a mechanism for plants to communicate with beneficial bacteria. In their glycosylated form, these compounds are substrates for symbiotic bacteria, which in return deglycosylate them and release the sugar-free part, the active aglycone. The aglycone can then mediate several functions beneficial to the plant, for example facilitating nitrogen fixation or acting as an antibacterial agent against plant pathogens. Results from studies covered in the thesis show that the soil bacteria Deinococcus aerius, Streptomyces canus and Microbacterium testaceum produce enzymes that can cleave the carbon-carbon bond between the sugar and the aglycone in C-glycosyl compounds. Deglycosylation first requires oxidation of the sugar by an oxidoreductase, after which the carbon-carbon bond can be cleaved by a C-glycosyl deglycosidase (CGD). Biochemical and structural characterization as well as results from phylogenetic analyzes of the amino-acid sequences of CGD enzymes provided new knowledge about these relatively unexplored enzymatic processes, as well as increased insight into how C-glycosylated aromatic polyketides participate in the interaction between plant and bacteria. The second part of the thesis explores pathogenic interactions between plants and bacteria. The virulence of pathogenic bacteria is dependent on lipoproteins that are attached to the bacteria's outer membrane and that have a decisive role for the bacteria's survival and pathogenicity. The localization of lipoproteins takes place through a process abbreviated Lol. The Lol sys, Kommunikationen mellan växter och bakterier omfattar ett komplext kemiskt signaleringsnätverk som förmedlar svar på olika biotiska och abiotiska påfrestningar, samt etablerar symbiotiska relationer mellan olika organismer. Den första delen av avhandlingen fokuserar på en mekanism för symbiotisk kommunikation mellan växter och bakterier och mer specifikt på hur C-glykosylerade aromatiska polyketidföreningar producerade av växter kan utnyttjas som en mekanism för växter att kommunicrea med goda bakterier. I sin glykosylerade form utgör dessa föreningar substrat for symbiotiska bakterier som i gengäld deglykosylerar dem och frigör den sockerfria delen, det aktiva aglykonet. Aglykonet kan sedan förmedla ett flertal för växten fördelaktiga funktioner, till exempel underlättande av kvävefixering eller fungera som ett antibakteriellt medel mot växtpatogener. I avhandlingen visas att jordbakterierna Deinococcus aerius, Streptomyces canus och Microbacterium testaceum producerar enzymer som ansvarar för klyning av kol-kol-bindingen mellan sockret och aglykonet i C-glykosylföreningar. Deglykosylering kräver först oxidation av sockret med hjälp av ett oxidoreduktas, varefter kol-kol-bindningen kan klyvas av ett C-glykosyldeglykosidas (CGD). Biokemisk och strukturell karakterisering samt resultat från fylogenetiska analyser av CGD-enzymers aminosyra-sekvenser ger ny kunskap om dessa relativt outforskade enzymatiska processer, samt ökad insikt om hur C-glykosylerade aromatiska polyketider deltar i samspelet mellan växt och bakterie. Den andra delen av avhandlingen utforskar patogena interaktioner mellan växter och bakterier. Patogena bakteriers virulens är beroende av lipoproteiner som är fästa i bakteriens yttermembran och som har en avgörande roll för bakteriens överlevnad och patogenicitet. Lokaliseringen av lipoproteier sker genom en process som förkortas Lol. Lol-systemet hos den problematiska växtpatogenen Xanthomonas campestris studerades för att bättre förstå de underligg, QC 2023-11-10

Sensation provides a pivotal ability, allowing animals to survive in complex environments. The cues sensed by animals are represented by external stimuli and internal signals. However, the mechanisms mediating sensations in molecular and cellular level are still not well-studied. In this thesis, by using free-living nematodes C. elegans with relatively simple nerve system, we are trying to get better understandings of molecular mechanisms by which animals sense and interpret external cues and internal signals. G protein-coupled receptors (GPCRs), as one of the major families of transmembrane proteins, participate in a variety of physiological responses to both external stimuli and internal cues. Previous studies have shown that GPCR signals are broadly involved in many processes in C. elegans, such as olfactory sensing, nociceptive responses, social behavior, pathogen responses, and mating. However, the complexity and diversity of GPCRs pose significant challenges to systematic dissection of their function as well as identification of receptor-ligand pairs which play crucial roles for animals´ sensory behaviors. Interestingly, the genome of C. elegans encodes one of the largest GPCR repertoires among any sequenced organisms, indicating a dramatical expansion and high degree of gene redundancy. To comprehensively dissect GPCR signaling in C. elegans and gain more insights into their roles in sensations, we developed an approach by employing CRISPR/Cas9-based gene editing to mutate closely related GPCRs and neuropeptide genes (internal signals) in a single strain on a genome-wide scale, resulting in disrupting nearly all the GPCR and neuropeptide genes (more than 1800 genes in total) and eliminating high degree of gene redundancy as well. Then using these two genetic libraries, we successfully identified neuropeptide (FLP -1) and cognate receptors (DMSR-4, DMSR-7 and DMSR-8) required for hypoxia-evoked locomotory responses, obtained a set of novel regulators of the pa

Engineering naturally occurring proteins enables us to customize affinity domains according to our specific needs, tailoring them to become an important tool in a wide array of applications limited merely by our creativity. One of nature’s ways to regulate protein activity is by creating a functional change through alteration of a protein’s tertiary structure upon interaction with metal ions. Inspired by this elegant solution, this thesis has focused on engineering calcium-regulated affinity proteins using two different strategies and protein scaffolds. The first strategy revolved around designing and selecting a calcium- binding motif that can render the inherent target affinity of a naturally occurring protein domain to be turned on or off depending on whether calcium is present or not. The subject of this part of the thesis was one of the immunoglobulin-binding domains derived from Streptococcal Protein G. A library of various loops with prerequisites for attracting calcium was inserted between the IgG-binding surfaces of the domain prior to performing cell display selections aimed for rendering the inherent target interaction dependent on the presence of calcium. Successful selections resulted in a calcium-dependent version of the IgG-binding protein and its structure could be solved using NMR. A deeper investigation of the incorporated structural calcium-dependency could explain the underlying mechanisms giving rise to the functional on-and-off switch in target affinity and show how it derived from the evolutionary selection pressures applied. The second strategy included the creation of a combinatorial library based on a calcium-dependent protein scaffold, derived from Staphylococcal Protein A, for development of small calcium-regulated affinity – CaRA –imolecules with novel target specificities. Mimicking the multifaceted usefulness of naturally occurring metalloproteins, this second part of the thesis aimed at performing phage display selection campaigns tow, När biologi kombineras med ingenjörers strukturerade tankesätt kan naturligt förekommande proteiner förvandlas till användbara verktyg, skräddarsydda för en mängd olika applikationer som endast verkar begränsas av vår fantasi. Naturligt förekommande proteiner har oftast en dedikerad funktion, en uppgift att utföra, och aktivitetsgraden kan styras genom förändringar i proteinets struktur via interaktion med andra småmolekyler, såsom exempelvis metalljoner. Inspirerad av naturens eleganta lösningar utforskar denna avhandling olika tillvägagångssätt för att konstruera metallreglerade proteiner vars interaktion med ett målprotein kan slås på eller stängas av genom tillgång till kalcium. Den första strategin kretsar kring att förädla ett existerande protein som redan kan känna igen och interagera med antikroppar till att endast kunna upprätthålla den förmågan i närvaro av kalcium. Tack vare banbrytande molekylärbiologiska tekniker som möjliggjort att vi idag kan klippa och klistra i arvsmassa (DNA) så finns möjligheten att infoga och kombinera gener som uttrycker olika proteinfunktioner. I detta fall kombinerades ett protein som molekylärt kan känna igen och har affinitet för vissa antikroppar med diverse strukturella motiv som kan binda kalcium. För att lyckas utveckla ett kalciumbindande motiv som kan påverka den existerande affiniteten till antikroppar byggdes ett bibliotek med olika motiv med olika förutsättningar för att attrahera kalciumjoner och detta infogades mellan de antikroppsbindande ytorna på proteinet, i hopp om att strukturen och funktionen hos proteinet skulle kunna regleras genom inbindningen av kalcium. Biblioteket genomsöktes efter varianter som uppvisade den eftersökta förmågan, kalciumberoende interaktion med antikroppar, och viiiihittade flera varianter som uppfyllde detta. Genom att undersöka proteinstrukturen på en av dessa nya kalciumberoende antikroppsbindande varianter så kunde vi förkla, QC 2023-10-26

Photoprotection mechanisms in plants play a crucial role in maintaining photosystem integrity and preventing photooxidative damage. In this study, we aimed to identify new molecular players involved in the qH process, a sustained photoprotective mechanism. We performed a forward genetic screen to select mutants with altered phenotype related to non-photochemical quenching (NPQ) and photosynthetic parameters. The mutants were classified into three main classes based on their NPQ phenotype, further subcategorized by photosynthetic parameters and chlorophyll content. Whole genome sequencing and mapping-by-sequencing approaches were employed to identify putative causative genes for the observed phenotypes. Potential causative mutations were retrieved by direct allelic comparison, gene ontology analysis, or mapping-by-sequencing. Sanger sequencing was utilized to validate the identified mutations and immunoblot analysis to confirm the protein accumulation disruptions in the mutants. We found in the genetic screen multiple putative genes altering qH. We investigated the role in qH of two of them, low photosystem II accumulation 1 (LPA1) and photosynthesis affected mutant 68 (PAM68). Mutants lacking LPA1 or PAM68 exhibit lower NPQ compared to the parental line soq1 npq4. We show that photosystem II (PSII) integrity is important for qH to occur. We also used a reverse genetic screen to decrypt the involvement of the different PSII antennae in qH. We demonstrated that qH can occur in the trimeric antennae, independent of a specific major antenna. Surprisingly, mutants with decreased or without major antennae accumulation still exhibited active qH to a high level. We found that qH can occur in the minor antennae in these mutants. However, qH is decreased in the soq1 lhcb6 mutant. Our findings provide novel insights into the molecular players and mechanism underlying photoprotective qH.

Sugar is a vital sustenance for most forms of life. For a cell to take up sugar, specialized transport proteins embedded into the membrane bilayer known as sugar porters, are required. Dysfunction of sugar porters is associated with some metabolic diseases, and their expression is upregulated in many cancers as they typically require more sugar than normal cells. Furthermore, sugar porters also play a role in the vitality of the malaria parasite. The mechanism of sugar transport is known as a rocker-switch alternating access mechanism. Simplistically, sugar binds between two similar domains on the outside of a sugar transporter and the domains then move around the sugar, so the sugar is exposed to the inside. During this domain movement, protein mass will block the sugar binding site from both outside and inside, forming the occluded state which is essential to ensure no substrate leakage during transport. Despite this relatively simple model of transport, little is known about how different sugar porters display diverse substrate specificity, affinity, and turnover. In the four papers making up this thesis, we structurally characterize missing pieces of the sugar transport cycle, identify how these states are connected with simulations, and assess factors contributing to sugar transport by functional assays. With simulations, we show how sugar catalyzes conformational change by interacting with the occluded state. We demonstrate our functional proteoliposome-based transport assay, which allows us to measure the effect of protein mutations, inhibitors, and lipid influences in sugar recognition and turnover. Characterization of the malaria parasite hexose transporter PfHT1 has allowed us to understand antimalarial inhibitor specificity against this protein which could have implications in combating the disease, as well as pharmacological control of sugar porters in general.

This thesis investigates responses to external cues in oral bacteria on a molecular level. Paper I maps Ser/Thr/Tyr phosphorylated proteins in relation to the general proteome in an oral commensal streptococcus (Streptococcus gordonii DL1). The identified phosphoproteins were involved in various bacterial processes, several associated to dysbiosis and development of biofilm-induced disease. Comparison against phosphoproteomes of other bacteria showed many similarities. This is of interest for the identification of shared phosphorylation profiles. Paper II studies differences between the S. gordonii DL1 general proteomes in planktonic and biofilm growth phases, and the regulatory effects of salivary mucin MUC5B on protein expression in the biofilm cells. Regulations in protein expression between the different growth conditions provides insights in bacterial mechanisms for adaptation to the biofilm lifestyle. Paper III examines the regulatory roles of salivary MUC5B on biofilm attachment and metabolic output in two clinical isolates of oral commensals, S. gordonii CW and Actinomyces naeslundii CW. S. gordonii facilitated adhesion of A. naeslundii to MUC5B during early attachment. Both bacteria were also able to utilize MUC5B as a sole nutrient source during early biofilm formation, individually and synergistically in a dual species biofilm. The specific responses elicited by MUC5B in paper II-III seem to promote commensal colonization while down-regulating dysbiosis-related biofilm activities. Microbiological studies are often focused on dysbiosis and development of disease. However, mechanisms that promote eubiosis are equally important to understand how health can be maintained. Findings associated with responses to external cues in oral bacteria may contribute to future development of novel preventative strategies and identification of predictive biomarkers for oral health., Avhandlingen undersöker orala bakteriers svar till utifrån kommande signaler på en molekylärbiologisk nivå. I delarbete I kartläggs proteiner med serin/treonin/ tyrosin fosforylering i relation till det generella proteomet hos en oral streptokock (Streptococcus gordonii DL1). De identifierade fosfoproteinerna kunde kopplas till olika bakteriella processer, varav flera av intresse ur kariessynpunkt. Jämförelse mot andra bakteriers fosfoproteom visade många likheter, vilket är av intresse för identifiering av delade fosforyleringsprofiler. I delarbete II undersöks skillnader i det generella proteomet hos S. gordonii DL1 mellan tillväxtfaserna planktonisk och biofilm, samt reglerande effekter av salivmucinet MUC5B på biofilmscellerna proteinuttryck. Skillnaderna i proteinuttryck mellan tillväxtfaser ger ledtrådar om bakteriernas mekanismer för anpassning till biofilmstillväxt. Delarbete III studeras salivmucinet MUC5Bs reglerande roll på vidhäftning och metabolism i biofilmer med kliniska isolat av S. gordonii CW samt Actinomyces naeslundii CW. S. gordonii ökade vidhäftningen av A. naeslundii till MUC5B. Båda arterna kunde också använda MUC5B som enda näringskälla under tidig biofilmsbildning, både enskilt och tillsammans. Responserna som MUC5B framkallade i biofilmerna (paper II och III) verkar främja kolonisering av kommensaler och samtidigt nedreglera kariesrelaterade aktiviteter. Mikrobiologiska studier fokuserar ofta på dysbiosis och sjukdomsutveckling, men mekanismer som bibehåller eubiosis är minst lika viktiga för att förstå hur oral hälsa kan främjas. Resultat kopplade till orala bakteriers svar på utifrån kommande signaler kan bidra till framtida utveckling av nya strategier för prevention och identifiering av prediktiva biomarkörer för oral hälsa., Foresight

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