The FEBS Journal

S15/uS19 is one of the fifteen universally conserved ribosomal proteins of the small ribosomal subunit. While prokaryotic uS19 is located away from the mRNA decoding site, cross-linking studies identified eukaryotic uS19 C-terminal tail as contacting the A site on the 80S ribosome. Here, we study the effects of uS19 mutations isolated as translation accuracy mutations in the filamentous fungus Podospora anserina. All mutations alter residues of uS19 C-terminal tail, and cluster to the eukaryote-specific decapeptide 138-PGIGATHSSR-147. All mutations modify fungal development and cytosolic translation, albeit differently. Two mutations (P138S and S145F) increase fungus longevity and display mild effects on translation, while others (G139D and G139C) decrease longevity, have stronger effects on translation and confer hypersensitivity to paromomycin. By mimicking P. anserina mutations in the yeast Saccharomyces cerevisiae RPS15 gene, we further show that P138S and S145F induce hyperaccurate recognition of the three stop codons, whereas G139D and G139C impair UAG and UAA codon recognition. Noteworthy, in P. anserina, uS19 genetically interacts with the eRF1 and eRF3 release factors. All together, our data indicate that uS19 C-terminal tail contributes in vivo to eukaryotic translation termination, and identify key amino acids of uS19 that potentially modulate eRF1-eRF3 interaction in the pre-termination complex. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/940346v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1739f4eorg.highwire.dtl.DTLVardef@1dffb40org.highwire.dtl.DTLVardef@1e86856org.highwire.dtl.DTLVardef@11a0c02_HPS_FORMAT_FIGEXP M_FIG C_FIG Abbreviated SummaryS15/uS19 is a conserved small ribosomal protein that in eukaryotes harbors a flexible C-terminal extension proposed to interact with the A site mRNA codon during translation. Here, we describe how C-terminal variants variously affect Podospora anserina development and longevity and impact fungal ribosome and polysome formation. We reveal that stop codon recognition is significantly altered by the presence of those C-terminal variants, which either expand or on the contrary restrict termination ambiguity.

Legionella pneumophila, the causative agent of a life-threatening pneumonia, intracellularly replicates in a specialized compartment in lung macrophages, the Legionella-containing vacuole (LCV). Secreted proteins of the pathogen govern important steps in the intracellular life cycle including bacterial egress. Among these is the type II secreted PlaA which, together with PlaC and PlaD, belongs to the GDSL phospholipase family found in L. pneumophila. PlaA shows lysophospholipase A (LPLA) activity which increases after secretion and subsequent processing by the zinc metalloproteinase ProA at residue E266/L267 located within a disulfide loop. Activity of PlaA contributes to the destabilization of the LCV in the absence of the type IVB-secreted effector SdhA. We here present the 3D structure of PlaA which shows a typical /{beta} hydrolase fold and reveals that the uncleaved disulfide loop forms a lid structure covering the catalytic triad S30/D278/H282. This leads to reduction of both substrate access and membrane interaction before activation; however, the catalytic and membrane interaction site gets more accessible when the disulfide loop is processed. After structural modelling, a similar activation process is suggested for the GDSL hydrolase PlaC, but not for PlaD. Furthermore, the size of the PlaA substrate binding site indicated preference towards phospholipids comprising ~16 carbon fatty acid residues which was verified by lipid hydrolysis, suggesting a molecular ruler mechanism. Indeed, mutational analysis changed the substrate profile with respect to fatty acid chain length. In conclusion, our analysis revealed the structural basis for the regulated activation and substrate preference of PlaA.

Withdrawal noticeThe authors have withdrawn their manuscript. The lipidomic data presented in the manuscript were based on an excel summary sheet provided by VIT, whose group (AP and KM) conducted the analysis using an Orbitrap mass spectrometer. However, after submitting to BioRxiv, the VIT group could not recover the RAW (primary source) files from the lipidomic platform because these files were deleted due to the maintenance protocol used for the Orbitrap mass spectrometer. It was agreed to reconduct the lipidomic analysis. As the Orbitrap mass spectrometer was out of service at that time, the lipidomic analysis was conducted with the help of a QToF mass spectrometer. Important differences were noted for the relative abundance and species of many lipids across the strains compared to the previously reported data hence casting some doubt on their interpretation. Therefore, until further analysis can be carried out the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

Many proteins undergo a post-translational lipid attachment, which increases their hydrophobicity, thus strengthening their membrane association properties or aiding in protein interactions. Geranylgeranyltransferase-I (GGTase-I) is an enzyme involved in a three-step post-translational modification (PTM) pathway that attaches a 20-carbon lipid group called geranylgeranyl at the carboxy-terminal cysteine of proteins ending in a canonical CaaL motif (C - cysteine, a - aliphatic, L - often leucine, but can be phenylalanine, isoleucine, methionine, or valine). Genetic approaches involving two distinct reporters were employed in this study to assess S. cerevisiae GGTase-I specificity, for which limited data exists, towards all 8000 CXXX combinations. Orthogonal biochemical analyses and structure-based alignments were also performed to better understand the features required for optimal target interaction. These approaches indicate that yeast GGTase-I best modifies the Cxa[L/F/I/M/V] sequence that resembles but is not an exact match for the canonical CaaL motif. We also observed that minor modification of non-canonical sequences is possible. A consistent feature associated with well-modified sequences was the presence of a non-polar a2 residue and a hydrophobic terminal residue, which are features recognized by mammalian GGTase-I. These results thus support that mammalian and yeast GGTase-I exhibit considerable shared specificity. Article SummaryThis work investigates yeast GGTase-I specificity through genetics, high throughput sequencing, and two distinct reporter systems. This approach allows for comprehensive evaluation of all CXXX sequence space, which has not been possible with earlier approaches. We identified CXXX sequences supporting geranylgeranylation that differ from the historically defined CaaL sequence often cited in the literature as the GGTase-I target motif, and our results indicate that the last two amino acids of the target motif largely dictate GGTase-I specificity.

Cyclic-di-nucleotide based secondary messengers regulate various physiological processes including the stress responses in bacteria. In the past decade, cyclic diadenosine monophosphate (c-di-AMP) has emerged as a crucial second messenger, implicated in fatty acid metabolism, antibiotic resistance, biofilm formation, virulence, DNA repair, ion homeostasis, sporulation etc. The level of c-di-AMP is maintained in the cell by the action of two opposing enzymes, namely diadenylate cyclase (DAC) and phosphodiesterase (PDE). In mycobacteria, this molecule is essential for its regulatory role in bacterial physiology and host-pathogen interactions. However, such modulation of c-di-AMP remains to be explored in Mycobacterium smegmatis. Here, we systematically characterised the c-di-AMP synthase (MsDisA) and a hydrolase (MsPDE) from M. smegmatis at different pH and osmolytic conditions in vitro. Our biochemical assays show that the MsDisA activity is enhanced during the alkaline stress and c-di-AMP is readily produced without any intermediates. At pH 9.4, the MsDisA promoter activity in vivo increases significantly, strengthening this observation. However, under physiological conditions, the activity of MsDisA was moderate with the formation of intermediates. To get further insights into the structural characteristics, we determined the cryo-EM structure of the MsDisA, revealing some interesting features. Biochemical analysis of individual domains shows that the N-terminal minimal region alone can form a functional octamer. Altogether, our results reveal the biochemical and structural regulation of mycobacterial c-di-AMP in response to various environmental stress.

The practice of designating two or more authors as equal contributors (EC) on a scientific publication is increasingly common as a form of sharing credit. However, EC authors are often unclearly attributed on CVs or citation engines, and it is unclear how research teams determine author order within an EC listing. In response to studies showing that male authors were more likely to be placed first in an EC listing, the American Society of Microbiology (ASM) required that authors explain the reasons for author order beginning in 2020. In this study we analyze data from over 2500 ASM publications to see how this policy affected gender bias and how research teams are making decisions on author order. Data on publications from 2018-2021 show that gender bias was largely nonsignificant both before and after authors were asked by ASM to provide an EC statement. The most likely reasons for EC order included alphabetical order, seniority, and chance, although there were differences for publications from different geographic regions. However, many research teams used unique methods in order selection, highlighting the importance of EC statements to provide clarity for readers, funding agencies, and tenure committees.

Recently, we described that glyceraldehyde-3-phosphate dehydrogenase from Leishmania major (LmGAPDH) was present in extracellular vesicles and it inhibited host TNF- expression during infection via post-transcriptional repression. The LmGAPDH binding with the AU-rich elements in 3-untranslated region of TNF- mRNA (TNF- ARE) is sufficient for limiting this cytokine production, but the TNF- ARE binding residues in LmGAPDH are still unexplored. RNA electrophoretic mobility shift assay (REMSA) and catalytic activity measurement revealed that the inhibition by TNF- ARE was competitive with respect to cofactor NAD+ in LmGAPDH. To identify the TNF- ARE binding residues of the LmGAPDH, we exploited a systematic mutational analysis of its NAD+ binding domain. Catalytic activity measurement indicates that both R13 and N336 amino acids in the NAD+ binding site are absolutely required for activity whereas other mutants including I14A, R16A, D39A and T112A showed higher Km (lower affinity) value for NAD+ binding and lower catalytic activity. REMSA studies revealed that the replacement of Arg-13 with Ala/Lys or Asn-336 with Ala resulted in complete loss of binding with the TNF- ARE. I14A, R16A, D39A and T112A residues at or near NAD+ binding site showed lower binding with the TNF- ARE compared to the wild-type protein. The protein induced fluorescence enhancement (PIFE) studies and in vitro protein translation assay further confirmed the REMSA results. Based on our findings, the NAD+ binding residues in LmGAPDH are important for TNF ARE binding.

Hyaluronic acid (HA) is a biologically versatile polysaccharide synthesized by vertebrates and several microbial pathogens. To date, Cryptococcus neoformans CPS1p is the only reported hyaluronic acid synthase (HAS) in fungi, which is functionally related to bacterial HASs. Considering the phylogenetic and biochemical connection between chitin synthases (CHSs), essential for fungal cell wall synthesis, and HASs, it is reasonable to hypothesize the latter might be more common in fungi than expected. In this work, a comprehensive in silico survey of putative HASs in the Fungal Tree of Life was carried out. 68 putative HASs, mainly in Basidiomycota, were found, although other AI-inferred HASs were found among Ascomycota. Global fold and arrangement of essential amino acids were shared by all kingdoms HASs; however, fungal HASs showed additional exclusive conserved sequence signatures. Moreover, fungal HASs bore an only 3-helices transmembranal pore and their gating loop, which regulates the entrance of substrates to the catalytic site, was directly connected to an also exclusive intrinsically disordered (IDR) C-terminus. Phylogenetically, fungal HASs were found in a clade different to that of bacterial, animal and viral HASs, and all HASs shared the same ancestor with class VI CHSs. The atypical features of fungal HASs could influence the size and biological role of the HA they synthesize and also highlight potential regulatory differences among HASs at the gating loop configuration level. ImportanceDespite the report of CPS1p, the hyaluronic acid synthase (HAS) of Cryptococcus neoformans, the diversity, structural features and biochemical assets of fungal HASs remain unknown. Here, 68 putative fungal HASs were identified, mainly among Basidiomycota. Although their fold is similar to that of already characterized HASs, their transmembranal pore, integrated by only 3 helices, and their atypical gating loop configuration, suggest they could be also differently regulated, influencing size and function of HA they synthesize.

External stress can disrupt protein homeostasis in organisms, necessitating the involvement of heat shock proteins (Hsps) to restore equilibrium and ensure survival. Unlike other organisms, the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius lacks Hsp100, Hsp90, and Hsp70, possessing only two small heat shock proteins (Hsp14 and Hsp20) and one group II chaperonin, Hsp60. This raises questions about how protein substrates are protected and transferred to Hsp60 for refolding without other chaperones. Our study focused on ATP-dependent Hsp60 in S. acidocaldarius, revealing its formation of oligomeric structures in the presence of ATP. While ATP hydrolysis is not essential for oligomer formation and lid closure, it is crucial for Hsp60s chaperone activity, effectively folding stress-denatured substrate proteins by stabilizing their folded conformations. The mechanism involves hydrophobic recognition of unfolded substrates, encapsulating and releasing them in a more folded state. Negatively charged inner surface of the ring seems to be responsible for driving the folding of the substrate. Importantly, Hsp14 was found to transfer substrate proteins to Hsp60{beta}, orchestrating their refolding into an active state. Beyond protein folding, Hsp60{beta} protects the membrane under stress, contributing to maintaining membrane rigidity. Hsp60 exhibits nested cooperativity in ATPase activity, adapting to ATP concentration changes and interestingly Hsp60{beta} and Hsp60{beta} complex shows a mosaic behaviour during ATP hydrolysis belonging to both group I and group II chaperonin respectively. In conclusion, our study provides insights into the intricate mechanisms employed by Hsp60 in S. acidocaldarius to maintain protein homeostasis. It offers a comprehensive understanding of Hsp60s role in the heat shock response pathway, shedding light on fundamental cellular processes in extremophilic archaea.

Pyridoxal-phosphate binding proteins (PLPBP) are involved in the homeostasis of B6 vitamers and amino/keto acids, share a high degree of sequence conservation and are represented in all three domains of life. Despite the obligate presence of the catalyst cofactor PLP, attempts to show enzymatic activity have been unsuccessful. Instead, evidence of RNA binding activity has been provided for several members of the family. Here we use PipY, one of the few PLBPB members studied so far, as a model system to address the phenotypic impact in the cyanobacterium Synechococcus elongatus of mutations K26A, P63L and R210Q, which respectively prevent PLP binding or are equivalent to those conferring B6-dependent epilepsy in humans with a recessive inheritance pattern. We found that while mutation K26A at the PLP-binding residue abrogated all phenotypes associated to PipY overexpression and toxicity, P63L and R210Q behaved as dominant gain-of-function mutations that inhibited bacterial growth. We provide in vivo evidence of PipY performing PLP-independent functions, in which mutant variant PipYK26A but not PipYP63L or PipYR210Q would be defective. A model integrating our observations with previous data from other organims and PLPBP variants is discussed.

Redox - enzyme maturation proteins (REMP) ensure co-factor loading and folding of proteins targeted to the twin-arginine translocation (Tat) pathway. The details of the interaction of a REMP with the corresponding signal sequence of its substrate are not well understood. Here, we demonstrate the features of the signal sequence for the Tat substrate DmsA (ssDmsA) responsible for complex formation with its REMP, DmsD, and with the Tat membrane complex TatB & TatC (TatBC). A heterologously expressed ssDmsA/DmsD complex forms two stochiometric populations corresponding to monomeric and dimeric forms of the complex. The monomeric complex has a higher affinity for the TatBC complex than the dimeric, which imply higher level regulation process to ensure the maturation of protein before translocation. Results from various binding studies yielded the shortest signal peptide required for ssDmsA/DmsA interaction and the region responsible for the TatBC interaction. Further experiments like alanine scanning in this peptide highlight the possible residues that are essential for this complex formation.

GroEL/Hsp60 chaperonins are key proteins that control cell metabolism, stress adaptation and survival. They usually form a tetradecameric structure that assists, coupled to ATP hydrolysis, 10% of all cellular protein folding. Using recombinant E. coli, human mitochondrial and M. tuberculosis chaperonins, we found that these proteins have thioesterase, esterase and even, for some of them, auto-acyltransferase activities. The smaller oligomers of Hsp60 and M. tuberculosis GroEL1 were more prone to use the long acyl carbon chain substrate palmitoyl-CoA compared to tetradecameric E. coli GroEL and Hsp60. Enzymatic competition and replacement of M. tuberculosis GroEL1 residues allow identifying Asp86 and Thr89 in the ATP-binding pocket and an additional Ser393 influencing the thioesterase activity. Additionally, M. tuberculosis GroEL1 might enhance palmitoylation of the PpsE protein, which plays a role in the phthiocerol dimycocerosate (PDIM) biosynthesis. This could explain at least partly the involvement of GroEL1 in PDIM biosynthesis and antibiotic resistance.

Cellular responses leading to development, proliferation, and differentiation rely on RAF/MEK/ERK signaling that integrates and amplifies signals from various stimuli to cellular downstream responses. The clinical significance of C-RAF activation has been reported in many types of tumor cell proliferation and developmental disorders, which requires the discovery of potential C-RAF protein regulators. Here, we identify a novel and specific protein interaction between C-RAF, among the RAF kinase paralogs, and SIRT4 among the mitochondrial sirtuin family members SIRT3, SIRT4, and SIRT5. Structurally, C-RAF binds to SIRT4 through the N-terminal cysteine-rich domain (CRD; a.a. 136-187), and on the other side, SIRT4 requires predominantly the C-terminus (a.a. 255-314) for full interaction with C-RAF. Interestingly, SIRT4 interacts specifically with C-RAF in a pre-signaling inactive (serine 259 phosphorylated) state. Consistent with this finding, ectopic expression of SIRT4 in HEK293 cells results in upregulation of pS259-C-RAF levels and concomitant reduction of MAPK signaling as evidenced by strongly decreased phospho-ERK signals. Thus, our findings propose another extra-mitochondrial role of SIRT4 and suggest that SIRT4 functions as a cytosolic tumor suppressor of C-RAF-MAPK signaling, besides its known metabolic tumor suppressor role towards glutamate dehydrogenase and glutamine levels in mitochondria.

The MYC associated factor X (MAX) is the heterodimeric partner of the MYC paralogs (MYC, MYCN and MYCL). When deregulated, high level of the MYC paralogs contribute to all aspects of tumorigenesis and tumor growth. MAX can also heterodimerize with the MXD proteins, MNT and MGA. Heterodimerization and sequence specific DNA binding to the E-Box sequences at gene promoters is controlled by their heterodimerization with the MAX b-HLH-LZ. As a heterodimer with MAX, MYC proteins activate genes involved in cell metabolism, growth and proliferation whereas MXD proteins, MNT and MGA repress them. MAX can also bind to the E-Bos sequence as a homodimer. Being devoid of a transactivation domain it can act as an antagonist of the MYC/MAX heterodimers. Variants of MAX have been reported to be linked to cancer. These variants are either not expressed, inactivated or lead to missense mutations. This has led to the notion that MAX may have a tumor suppressor role. Here, we characterize three of those variants with missense mutations in the basic region, i.e. E32K, R35P and R35C. We analyzed their heterodimerization with the b-HLH-LZ of MYC and their DNA binding properties as homo-and heterodimers. The R35C variant b-HLH-LZ was found to have a markedly increased affinity for the b-HLH-LZ of MYC. We also observed that all three b-HLH-LZ variants have a lower affinity as homodimers for the E-Box than the WT. This was shown to lead to a preferential binding of all the heterodimeric b-LHLH-LZ to the E-Box. This effect is exacerbated in the case of the R35C variant. We argue that this preferential binding of MYC as heterodimers with these variants to E-Box sequences could contribute to tumorigenesis. Hence, our results suggest that, mechanistically, the MAX homodimer bound to the E-Box could act as a tumor suppressor. MATERIALS AND METHODSO_ST_ABSMolecular modelingC_ST_ABSThe open source version 1.7.6.0 of Pymol was used for modeling and molecular rendering [1]. The crystal structure of the MAX homodimer bound to the E-Box (1HLO [2]) was used as a template for the generation of the models. The variants were generated using the mutagenesis function in the wizard. The conformation of the K32 side chain was manually set in order to avoid introducing steric clashes with DNA. Protein expression and purificationThe cDNA, coding for the MAX b-HLH-LZ (Max* hereafter, residues 22-103, UniProt entry P61244-1) to which are added the GSGC residues in c-terminal, inserted in the pET3a vector was already available in the laboratory [3] and was used as a template to generate the plasmids with inserts coding for each of the mutants (E32K, R35C and R35P) through quick-change PCR with Q5 DNA polymerase and DpnI from New England Biolabs. The primers used were purchased from IDT DNA, their sequences are listed in Table S1. Sequence for each construct was confirmed by Sanger sequencing at the Plateforme de sequencage SANGER - Centre de recherche du CHU de Quebec - Universite Laval. The primary structure for the basic region of each construct is given in Fig. 2A. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/715400v1_fig2.gif" ALT="Figure 2"> View larger version (41K): org.highwire.dtl.DTLVardef@1b05d5eorg.highwire.dtl.DTLVardef@1c1d692org.highwire.dtl.DTLVardef@ee469dorg.highwire.dtl.DTLVardef@15e0ba4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Structure schematics, specific and non-specific interactions dictating specificity and stability of binding of the basic region of MAX to the canonical (CACGTG) E-Box. A. Primary structure for the basic region of MAX and each of the variants. Positions making the most important contacts with the E-box are indicated by black arrows. Positions for the variants studied here are colored according to the Zappo colour scheme, following their physico-chemical properties: red for negative, blue for positive, magenta for proline and yellow for cysteine. B. The side chain (carboxylate) of E32 receives H-Bonds from the CA nucleobases in the leading strand (white carbon atoms). R35 and R36 make a salt bridges with phosphate groups while and the guanidino moiety of R36 makes a specific H-Bond with the nucleobase of the G in the strand of the reverse complement (cyan carbon atoms). C. The R35C mutation removes one non-specific salt-bridge at the interface of the complex. D. The aliphatic portion of the K side chain in the E32K variant is unable to accept the H-Bonds from the CA nucleobases and leads to the stabilisation of the complex and the helical structure of the basic region. E. In addition to removing a salt-bride, the Pro residue in the R35P kinks the path of the basic region, prevents the establishment of the specific H-Bonds mandatory for recognition of the E-Box and leads to unfolding of the helical state. C_FIG The MYC b-HLH-LZ (Myc*), the Max*WT b-HLH-LZ and its variants were expressed and purified as previously described [3,4] After lyophilisation, the b-HLH-LZs were kept at -20{degrees}C and solubilised in Myc buffer (50 mM NaCl, 50 mM NaH2PO4 pH 5.5) for Myc* or PBS for Max* at a final concentration of 1 mM before use. Circular dichroismAll circular dichroism (CD) measurements were performed on a Jasco J-810 spectropolarimeter equipped with a Peltier-type thermostat. The instrument was routinely calibrated using an aqueous solution of d-10-(+)-camphorsulfonic acid at 290.5 nm. Samples were prepared as follows: Max* (either WT or a variant) was diluted in 100 {micro}l 2X CD buffer (40 mM KCl, 11.4 mM K2HPO4, 28.6 mM KH2PO4, pH 6.8) and the volume adjusted to 106 {micro}l with PBS. 10 {micro}l TCEP 16 mM were added, and the volume further adjusted to 192 {micro}l with ddH2O before samples were incubated overnight at room temperature. After reduction, Myc* was added and the volume adjusted to 198 {micro}l with Myc buffer (Na2HPO4 0.95 mM, NaH2PO4 49.05 mM, 50 mM NaCl, pH 5.5). The DNA complexes were prepared as follows. After a 10 minutes incubation of the protein samples at room temperature, 0, 1 or 2 {micro}l of 2 mM of specific or non-specific DNA duplexes in 10 mM Tris pH 8.0 were added and the volume adjusted to 200 {micro}l with 10 mM Tris pH 8.0. The strands of the specific probe were: 5-ATT ACC CAC GTG TCC T*AC-3 and 5-GTA GGA CAC GTG GGT* AAT-3 (with the E-box sequence underlined) and the non-specific probe: 5-ATT ACC TCC GGA TCC T*AC-3 and 5-GTA GGA TCC GGA GGT* AAT-3 (Integrated DNA Technologies). Samples were further incubated for 10 minutes at room temperature and transferred to a 1 mm path length quartz cuvette. All spectra were recorded from 250 to 195 nm at 0.1 nm intervals by accumulating 10 spectra at 25 {degrees}C. Thermal denaturations were recorded at 222 nm from 5 to 95 {degrees}C at a heating rate of 1 {degrees}C/min. CD signal for spectra and thermal denaturations was corrected by substracting the signal from corresponding spectra or thermal denaturation either for buffer alone or the appropriate DNA duplex. CD signal was then converted to mean residue ellipticity using the following formula [5]: [{theta}] = {delta} {middle dot} MRW/(10{middle dot}c l) where [{theta}] is the mean residue ellipticity in deg {middle dot} cm2 dmol-1, {delta} is the CD signal in millidegrees, MRW is the mean residue weight, c is the concentration in mg/ml and l is the pathlength in mm. For the heterodimers, the concentration used was the sum of Max* and Myc* and the MRW was determined using a weighted average.

Peptidylarginine deiminase 4 (PAD4) is a citrullinating enzyme that is gathering increasing attention due to its possible involvement in physiological processes as well as in the pathogenesis of diseases like rheumatoid arthritis or thrombosis. PAD4 is activated by calcium ions, but the details of this mechanism are elusive, because in the human body, Ca2+ concentrations are too low for full activity. Given that glycosaminoglycans (GAGs) are also implicated in the development and progression of rheumatoid arthritis, we investigated the activation of PAD4 by GAGs using heparin as a model. We employed activity assays, chromatography techniques, molecular interaction measurements (MST and SPR), FACS, and immunocytochemistry to demonstrate the activation of PAD4 by GAGs. Our data show that PAD4 binds heparin with high affinity and forms high molecular weight complexes with heparin, consistent with heparin-bound tetramer formation. Heparin activates PAD4 by increasing the enzymes Ca2+ affinity threefold. We also show that the effectiveness of activation with heparin depends on the length of GAG used and its negative charge. Direct measurement of heparin binding to PAD4 confirmed tight interaction with nanomolar affinity. Mutagenesis of regions likely responsible for heparin binding showed that dimerization of PAD4 is necessary for efficient activation, but the distinct binding site was not determined as interaction with heparin likely occurs over larger surface of PAD4. Furthermore, we show that other GAG family members, including heparan and chondroitin sulphates, are also able to activate PAD4. We also found that disturbed production of GAGs by CHO cells results in reduced PAD4 binding efficiency. Finally, heparin induces NETosis in hPMNs in concentration-dependent manner, as measured by the release of DNA and citrullination of histone H3. In summary, we identify the first natural coactivator of PAD4, which is present in all individuals, potentially explaining the regulation of PAD4 activity in physiological conditions, and providing new insight into the development of rheumatoid arthritis and other PAD4-related diseases.

{beta}-mannans are plant structural and storage polysaccharides prevalent in the human diet. Their degradation in the gastrointestinal tract is mediated by the human gut microbiota (HGM) through expression of a plethora of carbohydrate-active enzymes (CAZymes), although our understanding of the details of mannan breakdown is lacking. In this study, a prominent HGM member, Bacteroides cellulosilyticus, was found to be exceptionally efficient at utilising {beta}-mannans, mediated by the expression of a single polysaccharide utilisation locus (PUL). Amongst the predicted surface CAZymes encoded in the PUL, we identified a family 26 glycoside hydrolase of an unusual molecular architecture. BcWH2_GH26 contains a putative carbohydrate-binding module (CBM) directly intercalated into its catalytic domain, unlike classical CBMs which are located at the N- or C-termini of the catalytic domain. Phylogenetic and functional analyses of this internal CBM, and a homologue from another mannan user Bacteroides uniformis, revealed a narrow specificity for {beta}-mannan and support their classification as a novel CBM family. To investigate the evolutionary basis for the unusual enzyme architecture, the effect of the CBM on the catalytic activity of the enzyme was assessed. No significant differences in the kinetic parameters were found between the full-length and CBM deletion constructs against both soluble and insoluble mannans. The potential role of the internal CBM in enzyme function is discussed in the context of the likely localisation of the BcWH2_GH26 in the outer membrane utilisome encoded by the Bc mannan PUL.

Unfolded protein response is a dynamic signalling pathway, which is involved in the maintenance of proteostasis and cellular homeostasis. IRE1, a transmembrane signalling protein represents the start point of a highly conserved UPR signalling cascade. IRE1 is endowed with kinase and endoribonuclease activities. The activation of the kinase domain of IRE1 by trans-autophosphorylation leads to the activation of its RNAse domain. RNAse domain performs atypical splicing of Xbp1 mRNA and degradation of mRNAs by an effector function known as Regulated IRE1 Dependent Decay (RIDD). The regulation of the distinctive nature of the IRE1 ribonuclease function is potentially mediated by a dynamic protein structure UPRosome that is an assembly of a huge number of proteins on IRE1. Here, we reported that Bid is a novel recruit to UPRosome, which directly interacts with the cytoplasmic domain of IRE1. Bid controls the auto-phosphorylation of IRE1 in a negative manner where Bid overexpression conditions displayed reduced phosphorylation levels of IRE1 and Bid knockdown cells showed slightly enhanced IRE1 phosphorylation. This effect was reciprocated with JNK, a downstream target of IRE1. Our Insilico analysis revealed that Bid binding to IRE1 dimer averts its structural flexibility and thereby preventing its trans-autophosphorylation activity. We found that the effect of Bid is specific to the IRE1 branch of UPR signalling and competitive in nature. The highlighting observation of the study was that Bid stimulated a differential activity of the IRE1 RNAse domain towards Xbp1 splicing and RIDD. These results together establish that Bid is a part of the UPRosome and modulates IRE1 in a way to differentially regulate its RNAse outputs.

Bacteria prephenate dehydrogenase (PDH) participates in the metabolic pathway for tyrosine biosynthesis. PDHs within the Bacilaceae phylum contain an ACT domain which enables them to be allosterically regulated by tyrosine. The mechanism via which the ACT domain introduces allostery onto PDH enzymes remains elusive. Furthermore, the evolutionary and biological advantages of ACT domain mediated regulation of metabolic pathways are highly debated. Building on our previous study, in which we solved the crystal structure of a Bacillus antraces ACT-containing PDH and proposed a model for its allosteric regulation by tyrosine, we now present further structural, and functional analyses in support of this model. In this study, we generated truncated PDH protein constructs lacking the ACT domain, determined their crystal structure and evaluated the role of tyrosine in modulating their enzymatic activity. We determined that the truncated PDH remains catalytically active, however, it is no longer allosterically regulated by tyrosine. Comparative structural analysis between the truncated PDH and PDHs naturally lacking the ACT domain that are known to be competitively inhibited by tyrosine revealed only minor changes in a loop region in the prephenate binding site. Attempts to introduce amino acids identified from the competitively inhibited PDH into the truncated construct did not restore tyrosine sensitivity, even at high concentration. This indicates that additional main chain amino acids away from the substrate binding site also contribute competitive inhibition by tyrosine. Analysis of a highly represented phylogenetic tree revealed that ACT containing PDHs are predominantly distributed amongst Firmicute and Actinomycetota. Representative organisms from both groups colonize nutrient limited and extreme environments. This distribution suggests that acquisition of the ACT domain may confer an evolutionary advantage by enabling organisms to efficiently partition chorismate, the end product of the shikimate pathway, for the biosynthesis of tyrosine and other essential aromatic compounds.

In fungi, salicylate catabolism was believed to proceed only through the catechol branch of the 3-oxoadipate pathway, as shown e.g. in Aspergillus nidulans. However, the observation of a transient accumulation of gentisate upon cultivation of Aspergillus terreus in salicylate media questions this concept. To address this we have run a comparative analysis of the transcriptome of these two species after growth in salicylate using acetate as a control condition. The results revealed the high complexity of the salicylate metabolism in A. terreus with the concomitant positive regulation of several pathways for the catabolism of aromatic compounds. This included the unexpected joint action of two pathways: the nicotinate and the 3-hydroxyanthranilate, possibly crucial for the catabolism of aromatics in this fungus. New genes participating in the nicotinate metabolism are here proposed, whereas the 3-hydroxyanthranilate catabolic pathway in fungi is described for the first time. The transcriptome analysis showed also for the two species an intimate relationship between salicylate catabolism and secondary metabolism. This study emphasizes that the central pathways for the catabolism of aromatic hydrocarbons in fungi hold many mysteries yet to be discovered. IMPORTANCEAspergilli are versatile cell factories used in industry for production of organic acids, enzymes and pharmaceutical drugs. To date, organic acids bio-based production relies on food substrates. These processes are currently being challenged to switch to renewable non-food raw materials; a reality that should inspire the use of lignin derived aromatic monomers. In this context, Aspergilli emerge at the forefront of future bio-based approaches due to their industrial relevance and recognized prolific catabolism of aromatic compounds. Notwithstanding considerable advances in the field, there are still important knowledge gaps in the central catabolism of aromatic hydrocarbons in fungi. Here, we disclosed a novel central pathway, defying previous established ideas on the central metabolism of the aromatic amino acid tryptophan in Ascomycota. We also observed that the catabolism of the aromatic salicylate greatly activated the secondary metabolism, furthering the significance of using lignin derived aromatic hydrocarbons as a distinctive biomass source.

Structural motion and conformational flexibility are often linked to biological functions of proteins. Whether the endothelial protein C receptor (EPCR), like other molecules, is vulnerable to folding transitions or might adopt alternative conformations remains unknown. The current understanding points to a rigid molecular structure suitable for binding of its ligands, like the anticoagulant protein C, or the CIDR1 domains of Plasmodium falciparum. In this study, we have identified a novel conformation of EPCR, captured by X-ray diffraction analyses, whereby Tyr154 shows a dramatically altered structural arrangement, likely incompatible with protein C binding. Biolayer interferometry analysis confirms previous results supporting a critical role for this position in protein C binding. Importantly, the conformational change has no apparent effect in the bound lipid. We conclude these findings reveal a site of conformational vulnerability in EPCR and inform a highly malleable region that could modulate EPCR functions.