Data_Sheet_1_Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia.docx

The ability of Mycobacterium tuberculosis to infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5′-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organism Mycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense, or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that like M. tuberculosis, M. smegmatis can initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. To our knowledge, this represents the first report of a transcriptome-wide RNA cleavage site map in mycobacteria. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Taken together, our data provide a foundation for further study of both transcriptional and posttranscriptional regulation in mycobacteria.</p

Table_1_Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia.xlsx

The ability of Mycobacterium tuberculosis to infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5′-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organism Mycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense, or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that like M. tuberculosis, M. smegmatis can initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. To our knowledge, this represents the first report of a transcriptome-wide RNA cleavage site map in mycobacteria. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Taken together, our data provide a foundation for further study of both transcriptional and posttranscriptional regulation in mycobacteria.</p

Effect of Nanopillars on the Wetting State and Adhesion Characteristics of Molten Aluminum Droplets

To solve the adhesion problem between molten aluminum and vacuum ladle liner during the electrolytic aluminum production process, the wetting state and adhesion properties of molten aluminum droplets on substrate surfaces with different nanopillars are investigated based on molecular dynamics. The results show that the adhesion strength of molten aluminum droplets in different wetting states has the pattern Young state > Wenzel state > Cassie state. Effects of increasing nanopillar height or interval are poles apart in the wetting state and adhesion characteristics of aluminum molten droplets. The critical height and critical interval of the nanopillar where the wetting state transition occurs are obtained. The increase of the nanopillar width can induce the wetting state transition from the Cassie state to the Wenzel state. In addition, the phantom wall method is applied to study the variation of the separation force. It is found that a peak in the separation force curve occurs when the molten droplet separates from the bottom of the nanopillar interval or the top of the nanopillar. The separation force curves of the droplets in the Young state and the Cassie state have single peaks, while the droplets in the Wenzel state have double peaks

Sonogashira Couplings on the Surface of Montmorillonite-Supported Pd/Cu Nanoalloys

To explore the true identity of palladium-catalyzed Sonogashira coupling reaction, montmorillonite (MMT)-supported transition metal nanoparticles (MMT@M, M = Pd, Cu, Fe, and Ni) were prepared, characterized, and evaluated systematically. Among all MMT@M catalysts, MMT@Pd/Cu showed the highest activity, and it was successfully extended to 20 examples with 57%–97% yields. The morphology characterization of MMT@Pd/Cu revealed that the crystalline bimetallic particles were dispersed on a MMT layer as nanoalloy with diameters ranged from 10 to 11 nm. In situ IR analysis using CO as molecular probe and XPS characterization found that the surface of Pd/Cu particles consisted of both catalytic active sites of Pd(0) and Cu­(I). The experiments on the catalytic activities of MMT@M found that Pd/Cu catalyst system exhibited high activity only in nanoalloy form. Therefore, the Pd/Cu nanoalloy was identified as catalyst, on which the interatom Pd/Cu transmetalation between surfaces was proposed to be responsible for its synergistic activity

Regulating CO and H₂ Ratios in Syngas Produced from Photocatalytic CO₂/H₂O Reduction by Cu and Co Dual Active Centers on Carbon Nitride Hollow Nanospheres

For photocatalytic CO2 reduction to produce syngas, there are challenges in achieving a high catalytic efficiency and precise control over the product ratio. In this study, two non-noble metal complexes Cobpy and Cubpy (bpy = 2,2′-bipyridine) as cocatalysts for CO2 reduction and hydrogen evolution, respectively, were in situ supported on carbon nitride hollow nanospheres to construct a hybrid system for photocatalytic syngas production. The resulting CO/H2 ratio can be precisely regulated within a wide range of 0:1–9:1 by accurately controlling the content of the two complexes. The presence of the two complexes promotes the migration of photogenerated electrons of the carbon nitride. CO2 can be reduced to CO on the photoreduced species Co(bpy)2+ of Cobpy on CNHS, and H+ can be reduced to H2 on the photoreduced species Cu(bpy)2+ of Cubpy. Furthermore, this method is also applicable to other photocatalysts, such as CdS and TiO2 for generating syngas and regulating product ratios

Transforming Racemic Compounds into Two New Enantioenriched Chiral Products via Intermediate Kinetic Resolution

Converting racemic compounds to enantioenriched products is an important and economic approach for accessing enantioenriched chiral molecules. A common method is kinetic resolution. Herein, we present a mode of kinetic resolution that transforms racemic compounds into enantioenriched products, in which the kinetic resolution of reaction intermediates is the key. Catalyzed by a single Ru complex, racemic allylic alcohols are shown to react with a glycine-derived Schiff base to afford two chiral compounds, a δ-carbonyl product and a δ-hydroxy variant, with good yields and stereoselectivities (up to >20:1 dr, 99% ee, 920 s factor). Mechanistic studies suggest that multiple hydrogen transfer events exist in the reaction: a dehydrogenative coupling process, which leads to a pair of racemic intermediates, and a transfer hydrogenation-enabled kinetic resolution process that resolves the intermediates, alongside H2 release at the catalyst

Transforming Racemic Compounds into Two New Enantioenriched Chiral Products via Intermediate Kinetic Resolution

Converting racemic compounds to enantioenriched products is an important and economic approach for accessing enantioenriched chiral molecules. A common method is kinetic resolution. Herein, we present a mode of kinetic resolution that transforms racemic compounds into enantioenriched products, in which the kinetic resolution of reaction intermediates is the key. Catalyzed by a single Ru complex, racemic allylic alcohols are shown to react with a glycine-derived Schiff base to afford two chiral compounds, a δ-carbonyl product and a δ-hydroxy variant, with good yields and stereoselectivities (up to >20:1 dr, 99% ee, 920 s factor). Mechanistic studies suggest that multiple hydrogen transfer events exist in the reaction: a dehydrogenative coupling process, which leads to a pair of racemic intermediates, and a transfer hydrogenation-enabled kinetic resolution process that resolves the intermediates, alongside H2 release at the catalyst

Asymmetric Hydrogenation of Racemic Allylic Alcohols via an Isomerization–Dynamic Kinetic Resolution Cascade

Prochiral racemic allylic alcohols are converted to enantioenriched chiral alcohols bearing adjacent stereocenters catalyzed by a diamine diphosphine Ru complex in the presence of tBuOK. The protocol features a broad substrate scope (56 examples) and high diastereo- and enantioselectivities (up to >99:1 dr, >99% ee) and could be applied to the synthesis of enantioenriched chromane and indane compounds. Mechanistic studies suggest that the reaction proceeds via tBuOK-promoted allylic alcohol isomerization followed by Ru-catalyzed hydrogenative dynamic kinetic resolution

Privilege Ynone Synthesis via Palladium-Catalyzed Alkynylation of “Super-Active Esters”

A neat palladium-catalyzed alkynylation reaction was developed with “super-active ester” as the carbonyl electrophile, which provides a clean and efficient synthetic protocol for a broad array of ynone compounds under CO-, Cu-, ligand-, and base-free conditions. The superior activity of triazine ester was rationalized by the strong electron-withdrawing ability and the unique affinity of triazine on palladium. A mechanistic experiment clearly demonstrated that the N–Pd coordination of triazine plays a crucial role for the highly efficient C–O activation

Synthesis and Optical Properties of Donor–Acceptor-Type 1,3,5,9-Tetraarylpyrenes: Controlling Intramolecular Charge-Transfer Pathways by the Change of π‑Conjugation Directions for Emission Color Modulations

In dipolar organic π-conjugated molecules, variable photophysical properties can be realized through efficient excited-state intramolecular charge transfer (ICT), which essentially depends on the π-conjugation patterns. Herein, we report a controllable regioselective strategy for synthesis and optical properties of two donor–acceptor (DA)-type 1,3,5,9-tetraarylpyrenes (i.e., 1,3-A/5,9-D (4b) and 1,3-D/5,9-A (4c)) by covalently integrating two phenyl rings and two p-OMe/CHO-substituted phenyl units into the 2-tert-butylpyrene building block, in which the two phenyl rings substituted at the 1,3-positions act as acceptors for 4b or as donors for 4c and the two p-OMe or p-CHO-substituted phenyl moieties substituted at the K-region of 5,9-positions act as donors for 4b or as acceptors for 4c, respectively. Density functional theory calculations on their frontier molecular orbitals and UV–vis absorption of S0 → S1 transition theoretically predicted that the change of π-conjugation directions in the two DA pyrenes could be realized through a variety of substitution patterns, implying that the dissimilar ground-state and excited-state electronic structures exist in each molecule. Their single-crystal X-ray analysis reveal their highly twisted conformations that are beneficial for inhibiting the π-aggregations, which are strikingly different from the normal 1,3,5,9-tetraphenylpyrenes (4a) and related 1,3,6,8-tetraarylpyrenes. Indeed, experimental investigations on their optical properties demonstrated that the excited-state ICT pathways can be successfully controlled by the change of π-conjugation directions through the variety of substitution positions, resulting in the modulations of emission color from deep-blue to green in solution. Moreover, for the present DA pyrenes, highly fluorescent emissions with moderate-to-high quantum yields both in the thin film and in the doped poly­(methyl methacrylate) film were obtained, suggesting them as promising emitting materials for the fabrication of organic light-emitting diodes