Nitric Oxide Ameliorates the Effects of Hypoxia in Mice by Regulating Oxygen Transport by Hemoglobin.

Xiaoying Zhou, Wenting Su, Quanwei Bao, Yu Cui, Xiaoxu Li, Yidong Yang, Chengzhong Yang, Chengyuan Wang, Li Jiao, Dewei Chen, and Jian Huang. Nitric oxide ameliorates the effects of hypoxia in mice by regulating oxygen transport by hemoglobin. High Alt Med Biol. 00:00-00, 2024.-Hypoxia is a common pathological and physiological phenomenon in ischemia, cancer, and strenuous exercise. Nitric oxide (NO) acts as an endothelium-derived relaxing factor in hypoxic vasodilation and serves as an allosteric regulator of hemoglobin (Hb). However, the ultimate effects of NO on the hematological system in vivo remain unknown, especially in extreme environmental hypoxia. Whether NO regulation of the structure of Hb improves oxygen transport remains unclear. Hence, we examined whether NO altered the oxygen affinity of Hb (Hb-O2 affinity) to protect extremely hypoxic mice. Mice were exposed to severe hypoxia with various concentrations of NO, and the survival time, exercise capacity, and other physical indexes were recorded. The survival time was prolonged in the 5 ppm NO (6.09 ± 1.29 minutes) and 10 ppm NO (6.39 ± 1.58 minutes) groups compared with the 0 ppm group (4.98 ± 1.23 minutes). Hypoxia of the brain was relieved, and the exercise exhaustion time was prolonged when mice inhaled 20 ppm NO (24.70 ± 6.87 minutes vs. 20.23 ± 6.51 minutes). In addition, the differences in arterial oxygen saturation (SO2%) (49.64 ± 7.29% vs. 42.90 ± 4.30%) and arteriovenous SO2% difference (25.14 ± 8.95% vs. 18.10 ± 6.90%) obviously increased. In ex vivo experiments, the oxygen equilibrium curve (OEC) left shifted as P50 decreased from 43.77 ± 2.49 mmHg (0 ppm NO) to 40.97 ± 1.40 mmHg (100 ppm NO) and 38.36 ± 2.78 mmHg (200 ppm NO). Furthermore, the Bohr effect of Hb was enhanced by the introduction of 200 ppm NO (-0.72 ± 0.062 vs.-0.65 ± 0.051), possibly allowing Hb to more easily offload oxygen in tissue at lower pH. The crystal structure reveals a greater distance between Asp94ß-His146ß in nitrosyl -Hb(NO-Hb), NO-HbßCSO93, and S-NitrosoHb(SNO-Hb) compared to tense Hb(T-Hb, 3.7 Å, 4.3 Å, and 5.8 Å respectively, versus 3.5 Å for T-Hb). Moreover, hydrogen bonds were less likely to form, representing a key limitation of relaxed Hb (R-Hb). Upon NO interaction with Hb, hydrogen bonds and salt bridges were less favored, facilitating relaxation. We speculated that NO ameliorated the effects of hypoxia in mice by promoting erythrocyte oxygen loading in the lung and offloading in tissues.

A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program.

Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report that Rof is a conserved antiterminator and determine the cryogenic electron microscopy structure of Rho-Rof antitermination complex. Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rof's N-terminal α-helix undergoes conformational changes upon binding with Rho, and is key in facilitating Rof-Rho interactions. Rof binds to Rho's primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo analyses in Salmonella Typhimurium show that Rof is required for virulence gene expression and host cell invasion, unveiling a physiological function of Rof and transcription termination in bacterial pathogenesis.

Visualized Tracking and Multidimensional Assessing of Mitochondria-Associated Pyroptosis in Cancer Cells by a Small-Molecule Fluorescent Probe.

Pyroptosis is closely related to the development and treatment of various cancers; thus, comprehensive studies of the correlations between pyroptosis and its inductive or inhibitive factors can provide new ideas for the intervention and diagnosis of tumors. The dysfunction of mitochondria may induce pyroptosis in cancer cells, which can be reflected by the fluctuations of the microenvironmental parameters in mitochondria as well as the changes of mitochondrial DNA level and morphology, etc. To precisely track and assess the mitochondria-associated pyroptosis process, simultaneous visualization of changes in multiphysiological parameters in mitochondria is highly desirable. In this work, we reported a nonreaction-based, multifunctional small-molecule fluorescent probe Mito-DK with the capability of crosstalk-free response to polarity and mtDNA as well as mitochondrial morphology. Accurate assessment of mitochondria-associated pyroptosis induced by palmitic acid/H2O2 was achieved through monitoring changes in mitochondrial multiple parameters with the help of Mito-DK. In particular, the pyroptosis-inducing ability of an antibiotic doxorubicin and the pyroptosis-inhibiting capacity of an anticancer agent puerarin were evaluated by Mito-DK. These results provide new perspectives for visualizing mitochondria-associated pyroptosis and offer new approaches for screening pyroptosis-related anticancer agents.

How digital finance impacts listed companies' green innovation in China: a product market perspective.

We empirically test whether and how digital finance impact green innovation utilizing data from Chinese listed companies and the Digital Inclusive Finance Index at the city level over the period from 2011 to 2020. The results show the following: (a) digital finance has a positive impact on green innovation, (b) improving consumer demand and strengthening market competition are two important influence channels, (c) customer concentration and corporate social responsibility are two important moderating variables that affect the aforementioned product market mechanisms, and (d) the positive impact of digital finance is more prominent within state-owned enterprises, companies with high financial risks, economically underdeveloped regions, and low-polluting industries. This research provides insights for China and similar economies on how to leverage the significant role of digital finance in achieving their net-zero-carbon targets.

Post-annealing effect of low temperature atomic layer deposited Al2O3on the top gate IGZO TFT.

Electronical properties of top gate amorphous InGaZnO4thin film transistors (TFTs) could be controlled by post-annealing treatment, which has a great impact on the Al2O3insulator. To investigate the effect of post-annealing on Al2O3, Al/Al2O3/p-Si MOS capacitoras with Al2O3films treated under various post-deposition annealing (PDA) temperature were employed to analysis the change of electrical properties, surface morphology, and chemical components by electrical voltage scanning, atomic force microscope (AFM), and x-ray photoelectron spectroscopy (XPS) technologies. After PDA treatment, the top gate TFTs had a mobility about 7 cm2V-1s-1and the minimum subthreshold swing (SS) about 0.11 V/dec, and the threshold voltage (Vth) shifted from positive direction to negative direction as the post-annealing temperature increased. Electrical properties of MOS capacitors revealed the existence of positive fixed charges and the variation of trap state density with increasing PDA temperature, and further explained the change of negative bias stress (NBS) stability in TFT. AFM results clarified the increased leakage current, degraded SS, and NBS stability in MOS capacitors and TFTs, respectively. XPS results not only illuminated the origin of fixed charges and the trap density variation with PDA temperatures of Al2O3films, but also showed the O and H diffusion from Al2O3into IGZO during post-annealing process, which led to the deviation ofVth, the change of current density, and the negativeVthshift after positive bias stress in TFTs.

Functionalized [2.2]Paracyclophanedienes as Monomers for Poly(p-phenylenevinylene)s.

Poly(p-phenylenevinylene)s (PPVs) featuring complex side-chains, to date, have only been synthesized by nonliving polymerization methods which have no control over PPV molecular weights, dispersities, or end groups. [2.2]Paracyclophane-1,9-diene (pCpd) has gained attention as a monomer for its ability to be ring-opened to PPV in a living fashion. pCpd, an organic cyclic scaffold with planar chirality, has seen minimal structural diversity due to the harsh reaction conditions required to afford the highly strained compound. Herein, we introduce a general method to overcome this by targeting the synthesis of a monohydroxy-pCpd via mono-demethylation of a dialkoxy-pCpd. The monohydroxy-pCpd can then be functionalized easily, which we demonstrate using three distinct side-chains with four moieties commonly incorporated in conjugated polymers: an alkyl bromide, an oligo(ethylene glycol) chain, an enantiomerically pure side-chain, and a Boc-protected amine. These monofunctionalized-pCpds were investigated as monomers in the ring-opening metathesis polymerization (ROMP) to afford functionalized PPVs in a living manner. The functional-group-containing PPVs are synthesized with full control over their end groups, repeat units, and dispersities. The feasibility of post-polymerization modifications to incorporate any desired moiety to PPV fabricated by this method was demonstrated using an azide-alkyne click reaction. All synthesized PPVs were soluble in organic solvents and display the same fluorescent emission, indicating their conjugated backbones are unaltered.

CO2 emission prediction based on carbon verification data of 17 thermal power enterprises in Gansu Province.

The energy and power industry is an important field for CO2 emission reduction. The CO2 emitted by thermal power enterprises is a major cause of global climate change, and also a key challenge for China to achieve the goals of "carbon peaking and carbon neutrality." Therefore, it is essential to scientifically and accurately predict the CO2 emissions of key thermal power enterprises in the region. This will guide carbon reduction strategies and policy recommendations for leaders, and also provide a valuable reference for similar regions globally. This study utilizes the factor analysis method to extract the common factors influencing CO2 emissions based on the carbon verification data of 17 thermal power enterprises in Gansu Province. Additionally, the DISO (distance between indices of simulation and observation) index is employed to comprehensively evaluate three prediction models, namely multiple linear regression, support vector regression, and GA-BP neural network. Ultimately, this study provides a reasonable prediction of CO2 emissions for the aforementioned enterprises in Gansu Province. The results show that the three common factors obtained by factor analysis, namely energy consumption and output factor, energy quality factor, and energy efficiency factor, can effectively predict the CO2 emissions from thermal power enterprises. In the three prediction models, GA-BP neural network has the best overall performance with DISO value of 0.95, RMSE value of 11848.236, and MAE value of 7880.543. Over the period 2022-2030, CO2 emissions from 17 thermal power enterprises in Gansu Province are predicted to increase. Under the low-carbon, scenario baseline, and high-carbon scenarios, the CO2 emissions will reach 71.58 Mt, 79.25 Mt, and 87.97 Mt, respectively, by 2030.

Natural foods resources and dietary ingredients for the amelioration of Helicobacter pylori infection.

Helicobacter pylori (H. pylori) is a gastric-persistent pathogen that can cause peptic ulcer disease, gastric cancer, and mucosal-associated lymphoid tissue lymphoma. This pathogen is commonly treated with antibiotic-based triple or quadruple therapy. However, antibiotic therapy could result in the bacterial resistance, imbalance of gut microbiota, and damage to the liver and kidneys, etc. Therefore, there is an urgent need for alternative therapeutic strategies. Interestingly, natural food resources, like vegetables, fruits, spices, and edible herbs, have potent inhibitory effects on H. pylori. In this review, we systematically summarized these foods with supporting evidence from both animal and clinical studies. The results have indicated that natural foods may possess temporary inhibition effect on H. pylori rather than durable eradication, and may help to reduce H. pylori colonization, enhance the effect of antibiotics and modulate the host's immune response.

Structural basis of RfaH-mediated transcription-translation coupling.

The NusG paralog RfaH mediates bacterial transcription-translation coupling on genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here we report cryo-EM structures of transcription-translation complexes (TTCs) containing RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP, and with the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs, due to the more restricted flexibility of the RfaH interdomain linker. The results further show that the structural organization of RfaH-coupled TTCs in the "loading state," in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the "loaded state," in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling. One sentence summary: Cryo-EM reveals the structural basis of transcription-translation coupling by RfaH.

Structural basis of archaeal FttA-dependent transcription termination.

The ribonuclease FttA mediates factor-dependent transcription termination in archaea 1-3 . Here, we report the structure of a Thermococcus kodakarensis transcription pre-termination complex comprising FttA, Spt4, Spt5, and a transcription elongation complex (TEC). The structure shows that FttA interacts with the TEC in a manner that enables RNA to proceed directly from the TEC RNA-exit channel to the FttA catalytic center and that enables endonucleolytic cleavage of RNA by FttA, followed by 5'→3' exonucleolytic cleavage of RNA by FttA and concomitant 5'→3' translocation of FttA on RNA, to apply mechanical force to the TEC and trigger termination. The structure further reveals that Spt5 bridges FttA and the TEC, explaining how Spt5 stimulates FttA-dependent termination. The results reveal functional analogy between bacterial and archaeal factor-dependent termination, reveal functional homology between archaeal and eukaryotic factor-dependent termination, and reveal fundamental mechanistic similarities in factor-dependent termination in the three domains of life: bacterial, archaeal, and eukaryotic. One sentence summary: Cryo-EM reveals the structure of the archaeal FttA pre-termination complex.

A recently evolved BAHD acetyltransferase, responsible for bitter soyasaponin A production, is indispensable for soybean seed germination.

Soyasaponins are major small molecules that accumulate in soybean (Glycine max) seeds. Among them, type-A soyasaponins, fully acetylated at the terminal sugar of their C22 sugar chain, are responsible for the bitter taste of soybean-derived foods. However, the molecular basis for the acetylation of type-A soyasaponins remains unclear. Here, we identify and characterize GmSSAcT1, encoding a BADH-type soyasaponin acetyltransferase that catalyzes three or four consecutive acetylations on type-A soyasaponins in vitro and in planta. Phylogenetic analysis and biochemical assays suggest that GmSSAcT1 likely evolved from acyltransferases present in leguminous plants involved in isoflavonoid acylation. Loss-of-function mutants of GmSSAcT1 exhibited impaired seed germination, which attribute to the excessive accumulation of null-acetylated type-A soyasaponins. We conclude that GmSSAcT1 not only functions as a detoxification gene for high accumulation of type-A soyasaponins in soybean seeds but is also a promising target for breeding new soybean varieties with lower bitter soyasaponin content.

Fluorination of naphthalimide-cyanostilbene derivatives to achieve dual-state emission luminogens with strong fluorescence in highly polar environments for bioimaging.

Organic luminogens (OLs) that emit strong fluorescence in both solution and the aggregated state, referred to as dual-state emission luminogens (DSEgens), are highly desirable because of their capability to achieve multiple functions within onefold materials. The fluorescence of OLs, including DSEgens, with intramolecular charge transfer characteristics, often decreases in solution as the solvent polarity increases, namely the positive solvatokinetic effect, resulting in inferior environmental stability. In this work, fluorination to naphthalimide (NI)-cyanostilbene (CS) derivatives was adopted to construct novel DSEgens (NICSF-X, X = B, P, M, and T, respectively). Steady-state and transient spectroscopies were utilized to study their photophysical properties, evidencing their DSE properties with fluorescence quantum yields (φ) ∼0.2-0.4 in solution and ∼0.5-0.9 as solids. In particular, strong fluorescence emission in highly polar solvents i.e., φ up to ∼0.4-0.5 in ethanol, was sustained for NICSF-Xs, possibly assisted by hydrogen bonding (H-bonding) formation. Theoretical calculations and single-crystal structure analysis rationalized the intense photoluminescence (PL) emission of NICSF-Xs in the solid state. In addition, NICSF-Xs showed two-photon absorption (2PA) behaviors in dual states and were successfully applied for HepG2 cell imaging with one-photon and 2PA excitation, with lipid droplet targeting. Our study suggests that functionalization of molecules by fluorination to introduce H-bonding is a promising strategy to enhance the environmental stability of fluorescence in solution and realize strong PL emission in highly polar solvents, which could be favorable for bioimaging.

Structural and functional characterization of a mycobacterial methylenetetrahydrofolate reductase utilizing NADH as the exclusive cofactor.

5,10-Methylenetetraydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. MSMEG_6649, a non-canonical MTHFR from Mycobacterium smegmatis, was previously reported as a monomeric protein lacking the flavin coenzyme. However, the structural basis for its unique flavin-independent catalytic mechanism remains poorly understood. Here, we determined the crystal structures of apo MTHFR MSMEG_6649 and its complex with NADH from M. smegmatis. Structural analysis revealed that the groove formed by the loops 4 and 5 of non-canonical MSMEG_6649 interacting with FAD was significantly larger than that of canonical MTHFR. Meanwhile, the NADH-binding site in MSMEG_6649 is highly similar to the FAD binding site in canonical MTHFR, suggesting that NADH plays the same role (immediate hydride donor for methylenetetraydrofolate) as FAD in the catalytic reaction. Using biochemical analysis, molecular modeling, and site-directed mutagenesis, the critical residues participating in the binding of NADH and the substrate 5,10-methylenetetrahydrofolate as well as the product 5-methyltetrahydrofolate were identified and validated. Taken together, this work not only provides a good starting point for understanding the potential catalytic mechanism for MSMEG_6649, but also identifies an exploitable target for the development of anti-mycobacterial drugs.

Size- and Chirality-Dependent Structural and Mechanical Properties of Single-Walled Phenine Nanotubes.

Phenine nanotubes (PNTs) have recently been synthesized as a promising new one-dimensional material for high-performance electronics. The periodically distributed vacancy defects in PNTs result in novel semiconducting properties, but may also compromise their mechanical properties. However, the role of these defects in modifying the structural and mechanical properties is not yet well understood. To address this, we conducted systematic molecular dynamics simulations investigating the structural evolution and mechanical responses of PNTs under various conditions. Our results demonstrated that the twisting of linear carbon chains in both armchair and zigzag PNTs led to interesting structural transitions, which were sensitive to chiralities and diameters. Additionally, when subjected to tensile and compressive loading, PNTs' cross-sectional geometry and untwisting of linear carbon chains resulted in distinct mechanical properties compared to carbon nanotubes. Our findings provide comprehensive insights into the fundamental properties of these new structures while uncovering a new mechanism for modifying the mechanical properties of one-dimensional nanostructures through the twisting-untwisting of linear carbon chains.

Competition between Hydration Shell and Ordered Water Chain Induces Thickness-Dependent Desalination Performance in Carbon Nanotube Membrane.

Exploring new reverse osmosis (RO) membranes that break the permeability-selectivity trade-off rule is the ultimate goal in seawater desalination. Both nanoporous monolayer graphene (NPG) and carbon nanotube (CNT) channels have been proposed to be promising candidates for this purpose. From the perspective of membrane thickness, both NPG and CNT can be classified into the same category, as NPG is equivalent to the thinnest CNT. While NPG has the advantage of a high water flux rate and CNT is excellent at salt rejection performance, a transition is expected in practical devices when the channel thickness increases from NPG to infinite-sized CNTs. By employing molecular dynamics (MD) simulations, we find that as the thickness of CNT increases, the water flux diminishes but the ion rejection rate increases. These transitions lead to optimal desalination performance around the cross-over size. Further molecular analysis reveals that this thickness effect originates from the formation of two hydration shells and their competition with the ordered water chain structure. With the increase in CNT thickness, the competition-dominated ion path through CNT is further narrowed. Once above this cross-over size, the highly confined ion path remains unchanged. Thus, the number of reduced water molecules also tends to stabilize, which explains the saturation of the salt rejection rate with the increasing CNT thickness. Our results offer insights into the molecular mechanisms of the thickness-dependent desalination performance in a one-dimensional nanochannel, which can provide useful guidance for the future design and optimization of new desalination membranes.

Orthogonal Supramolecular Assemblies Using Side-Chain Functionalized Helical Poly(isocyanide)s.

Mimicking the structure of proteins using synthetic polymers requires building blocks with structural similarity and the use of various noncovalent and dynamic covalent interactions. We report the synthesis of helical poly(isocyanide)s bearing diaminopyridine and pyridine side-chains and the multistep functionalization of the polymers' side-chains using hydrogen bonding and metal coordination. The orthogonality of the hydrogen bonding and metal coordination was proved by varying the sequence of the multistep assembly. The two side-chain functionalizations are reversible through the use of competitive solvents and/or competing ligands. Throughout the assembly and disassembly, the helical conformation of the polymer backbone is sustained as proved by circular dichroism spectroscopy. These results open the possibility to incorporate helical domains into complex polymer architectures and create a helical scaffold for smart materials.

Whey Protein Isolate-Mesona chinensis Polysaccharide Conjugate: Characterization and Its Applications in O/W Emulsions.

Mesona chinensis polysaccharide (MCP), a common thickener, stabilizer and gelling agent in food and pharmaceuticals, also has antioxidant, immunomodulatory and hypoglycemic properties. Whey protein isolate (WPI)-MCP conjugate was prepared and used as a stabilizer for O/W emulsion in this study. FT-IR and surface hydrophobicity results showed there could exist interactions between -COO- in MCP and -NH3+ in WPI, and hydrogen bonding may be involved in the covalent binding process. The red-shifted peaks in the FT-IR spectra suggested the formation of WPI-MCP conjugate, and MCP may be bound to the hydrophobic area of WPI with decreasing surface hydrophobicity. According to chemical bond measurement, hydrophobic interaction, hydrogen bond and disulfide bond played the main role in the formation process of WPI-MCP conjugate. According to morphological analysis, the O/W emulsion formed by WPI-MCP had a larger size than the emulsion formed by WPI. The conjugation of MCP with WPI improved the apparent viscosity and gel structure of emulsions, which was concentration-dependent. The oxidative stability of the WPI-MCP emulsion was higher than that of the WPI emulsion. However, the protection effect of WPI-MCP emulsion on ß-carotene still needs to be further improved.

Heteromerization of short-chain trans-prenyltransferase controls precursor allocation within a plastidial terpenoid network.

Terpenes are the largest and most diverse class of plant specialized metabolites. Sesterterpenes (C25), which are derived from the plastid methylerythritol phosphate pathway, were recently characterized in plants. In Arabidopsis thaliana, four genes encoding geranylfarnesyl diphosphate synthase (GFPPS) (AtGFPPS1 to 4) are responsible for the production of GFPP, which is the common precursor for sesterterpene biosynthesis. However, the interplay between sesterterpenes and other known terpenes remain elusive. Here, we first provide genetic evidence to demonstrate that GFPPSs are responsible for sesterterpene production in Arabidopsis. Blockage of the sesterterpene pathway at the GFPPS step increased the production of geranylgeranyl diphosphate (GGPP)-derived terpenes. Interestingly, co-expression of sesterTPSs in GFPPS-OE (overexpression) plants rescued the phenotypic changes of GFPPS-OE plants by restoring the endogenous GGPP. We further demonstrated that, in addition to precursor (DMAPP/IPP) competition by GFPPS and GGPP synthase (GGPPS) in plastids, GFPPS directly decreased the activity of GGPPS through protein-protein interaction, ultimately leading to GGPP deficiency in planta. Our study provides a new regulatory mechanism of the plastidial terpenoid network in plant cells.

Conjugating Coumarin with Tetraphenylethylene to Achieve Dual-State Emission for Reversible Mechanofluorochromism and Live Cell Imaging.

Dual-state emission luminogens (DSEgens) are receiving research interest in the construction of multifunctional materials due to their inherent advantage of high emission efficiency in both the molecularly dispersed solution state and the solid state. However, it remains challenging in synthesizing DSEgens via a delicate manipulation of the molecular structures. This work presents an example of bright DSEgen synthesis by tuning the molecular electronic structures and conformations. Three coumarin-tetraphenylethylene (TPE) molecules with a donor-acceptor electronic structure and highly twisting conformations have been synthesized. While compound resulting from direct conjugation of coumarin with a TPE unit shows aggregation-induced emission, compound with an N,N-diaminoethyl modification on the 7-position of coumarin and compound with a further phenyl linker between coumarin and TPE units feature strong dual-state emission. Benefiting from their strong solid emission and twisting conformations, these fluorophores display reversible mechanofluorochromism. Finally, applications for rewritable information storage in the solid state and live-cell imaging in the solution state were demonstrated.

Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria.

Gene transcription in bacteria is carried out by the multisubunit RNA polymerase (RNAP), which is composed of a catalytic core enzyme and a promoter-recognizing σ factor. The core enzyme comprises two α subunits, one ß subunit, one ß' subunit, and one ω subunit. The ω subunit plays critical roles in the assembly of the core enzyme and other cellular functions, including the regulation of bacterial growth, the stress response, and biofilm formation. However, the identity of an ω subunit for the obligate intracellular bacterium Chlamydia has not previously been determined. Here, we report the identification of the hypothetical protein CTL0286 as the probable chlamydial ω subunit based on sequence, synteny, and AlphaFold and AlphaFold-Multimer three-dimensional-structure predictions. Our findings indicate that CTL0286 functions as the missing ω subunit of chlamydial RNAP. Our extended analysis also indicates that all obligate intracellular bacteria have ω orthologs. IMPORTANCE Chlamydiae are obligate intracellular bacteria that replicate only inside eukaryotic cells. Previously, it has not been possible to identify a candidate gene encoding the chlamydial RNA polymerase ω subunit, and it has been hypothesized that the chlamydial RNA polymerase ω subunit was lost in the evolutionary process through which Chlamydiae reduced their genome size and proteome sizes to adapt to an obligate intracellular lifestyle. Here, we report the identification of the chlamydial RNA polymerase ω subunit, based on conserved sequence, conserved synteny, AlphaFold-predicted conserved three-dimensional structure, and AlfaFold-Multimer-predicted conserved interactions. Our identification of the previously elusive chlamydial RNA polymerase ω subunit sets the stage for investigation of its roles in regulation of gene expression during chlamydial growth, development, and stress responses, and sets the stage for preparation and study of the intact chlamydial RNA polymerase and its interactions with inhibitors.