Alexey D. Nikulin

The central role of YB-1 in messenger ribonucleoprotein particle (mRNP) metabolism and stress-granule biology highlights the importance of defining the determinants of its self-assembly. YB-1 fibrillogenesis has been attributed primarily to the cold shock domain (CSD). Here, we show that the YB-1 fragment spanning residues 1–129 (AP–CSD) form amyloid fibrils under near-physiological ionic strength (0.12–0.15 M KCl). Fibrillization proceeds without a pronounced exponential growth phase and increases approximately linearly over 45–50 h. Far-UV circular dichroism (CD) and attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) indicate no substantial change in overall secondary-structure content during aggregation. In parallel, ¹H nuclear magnetic resonance (NMR) spectroscopy reveals the depletion of soluble species, and oriented fiber X-ray diffraction displays the hallmark cross-β reflections at approximately 4.7 Å and 10 Å. The prolonged formation time implies an activation barrier that is unlikely to require global refolding. Instead, it may reflect early association events such as dimerization or other local rearrangements required for primary nucleation, followed by consolidation into stable intermolecular contacts. Aggregation that preserves a largely native-like fold while establishing cross-β order may reduce recognition by cellular quality-control systems that preferentially target globally unfolded or strongly destabilized states. This provides a plausible framework for how YB-1 derived assemblies could persist under stress and during age-associated proteostasis decline.

RNA chaperones play a crucial role in the biogenesis and function of various RNAs in bacteria. They facilitate the interaction of small regulatory trans-encoded sRNAs with mRNAs, thereby significantly altering the pattern of gene expression in cells. This allows bacteria to respond quickly to changing environmental conditions, such as stress or adaptation to host organisms. Despite the identification of a large number of sRNAs in mycobacteria, none of the most common RNA chaperones have been found in their genomes. We determined the crystal structure of the cold shock protein CspB from Mycobacterium tuberculosis. It forms a dimer due to its elongated C-terminal region, which is a hairpin composed of two α-helices. It was also demonstrated that CspB from M. tuberculosis exhibits high affinity for MTS0997 sRNA and MTS1338 sRNA from the same organism, which is consistent with classical RNA chaperons such as Hfq and ProQ. Based on the putative RNA chaperone activity of bacterial proteins with cold-shock domains, we propose that CspB from M. tuberculosis may be involved in the regulation of mycobacterial pathogenesis through interaction with sRNAs.

RNA chaperones play a crucial role in the biogenesis and function of various RNAs in bacteria. They facilitate the interaction of small regulatory trans-encoded sRNAs with mRNAs, thereby significantly altering the pattern of gene expression in cells. This allows bacteria responses quickly to changing environmental conditions, such as stress or adaptation to host organisms. Despite the identification of a large number of sRNAs in mycobacteria, none of the most common RNA chaperones has been found in their genomes. We characterized the cold shock protein CspB from Mycobacterium tuberculosis as a potential RNA chaperone. It forms a dimer due to its elongated C-terminal region, which is a hairpin composed of two α-helices. We demonstrated that CspB from M. tuberculosis exhibits high affinity for the two studied sRNAs from the same organism and, unlike the single-domain CspA, could be considered as a potential RNA chaperone in mycobacteria. Thus, it may be involved in the regulation of bacterial pathogenesis via interactions with sRNAs.

The structure of the Hfq protein from the bacterium Chromobacterium haemolyticum, which forms crystals in two different spatial groups, has been determined. In both cases, the protein has a specific quaternary hexamer-ring structure. The obtained structure showed a previously undescribed interaction between the C-terminal unstructured part of Hfq and the amino acid residues of the proximal RNA-binding site of the protein. This contact may contribute to the regulation of the binding of RNA molecules to the Hfq protein.

The structure of the Hfq protein from the bacterium Chromobacterium haemolyticum, which forms crystals in two different spatial groups, has been determined. In both cases, the protein has a specific quaternary hexamer-ring structure. The obtained structure showed a previously undescribed interaction between the C-terminal unstructured part of Hfq and the amino acid residues of the proximal RNA-binding site of the protein. This contact may contribute to the regulation of the binding of RNA molecules to the Hfq protein.

A giant multidomain protein of striated and smooth vertebrate muscles, titin, consists of tandems of immunoglobulin (Ig)- and fibronectin type III (FnIII)-like domains representing β-sandwiches, as well as of disordered segments. Chicken smooth muscles express several titin isoforms of ~500–1500 kDa. Using various structural-analysis methods, we investigated in vitro nonspecific amyloid aggregation of the high-molecular-weight isoform of chicken smooth-muscle titin (SMT_HMW, ~1500 kDa). As confirmed by X-ray diffraction analysis, under near-physiological conditions, the protein formed amorphous amyloid aggregates with a quaternary cross-β structure within a relatively short time (~60 min). As shown by circular dichroism and Fourier-transform infrared spectroscopy, the quaternary cross-β structure—unlike other amyloidogenic proteins—formed without changes in the SMT_HMW secondary structure. SMT_HMW aggregates partially disaggregated upon increasing the ionic strength above the physiological level. Based on the data obtained, it is not the complete protein but its particular domains/segments that are likely involved in the formation of intermolecular interactions during SMT_HMW amyloid aggregation. The discovered properties of titin position this protein as an object of interest for studying amyloid aggregation in vitro and expanding our views of the fundamentals of amyloidogenesis.

Interleukin-17 (IL-17) is a cytokine produced by the Th17 cells. It is involved in chronic inflammation in patients with autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, and psoriasis. The antibodies targeting IL-17 and/or IL-17R are therapy tools for these diseases. Netakimab is an IL-17A-specific antibody containing a Lama glama V_HH derivative domain and a VL variable domain. We have determined the crystal structure of the IL-17A-specific V_HH domain in complex with IL-17A at 2.85 Å resolution. Certain amino acid residues of the three complementary-determining regions of the V_HH domain form a network of solvent-inaccessible hydrogen bonds with two epitope regions of IL-17A. The β-turn of IL-17A, which forms the so-called epitope-1, appears to be the main region of IL-17A interaction with the antibody. Contacts formed by the IL-17A mobile C-terminal region residues (epitope-2) further stabilize the antibody–antigen complex.

ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to a uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in strongly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and in a reduced amount of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins. Consequently, the physiological roles of proteins predicted as homologs seem to be far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate, activation of both was not so prominent. During the growth with glucose, maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests, thus suggesting the involvement of UxuR in the regulation of bacterial motility and biofilm formation.

ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to the uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in significantly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and inhibition of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins.This suggests that the roles of proteins predicted as homologs are far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate activation of both was not so prominent. During growth on glucose, the maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests thus suggesting involvement of UxuR in the regulation of bacterial motility and biofilm formation.