Explore the vast range of titles available.

Tyrosinases (TYRs) are type‐3 copper proteins that are widely distributed in nature. They can hydroxylate and oxidize phenolic molecules and are mostly known for producing melanins that confer protection against photo induced damage. TYRs are also thought to play an important role in the ‘latch mechanism’, where high concentrations of phenolic compounds inhibit oxidative decomposition of organic biomass and subsequent CO2 release, especially relevant in wetland environments. In the present study, we describe two TYRs, HcTyr1 and HcTyr2, from halophilic bacterium Hahella sp. CCB MM4 previously isolated at Matang mangrove forest in Perak, Malaysia. The structure of HcTyr1 was determined by X‐ray crystallography at a resolution of 1.9 Å and represents an uncharacterized group of prokaryotic TYRs as demonstrated by a sequence similarity network analysis. The genes encoding the enzymes were cloned, expressed, purified and thoroughly characterized by biochemical methods. HcTyr1 was able to self‐cleave its lid‐domain (LID) in a protease independent manner, whereas the LID of HcTyr2 was essential for activity and stability. Both enzymes showed variable activity in the presence of different metals, surfactants and NaCl, and were able to oxidize lignin constituents. The high salinity tolerance of HcTyr1 indicates that the enzyme can be an efficient catalyst in the habitat of the host. Drying marshes, swamps and peatlands comprise wetland environments and huge carbon deposits where organic matter rich in phenolic compounds accumulates. If these environments dry and are exposed to atmospheric oxygen, TYR activity will increase, breaking down the accumulated phenolic compounds. As a result, aerobic respiration and hydrolytic processes are enhanced, leading to higher CO2 emissions into the atmosphere.

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2′-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5′ leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

Rigid polyurethane foam (RPUF) is widely utilized in construction and rail transportation due to its lightweight properties and low thermal conductivity, contributing to energy conservation and emission reduction. However, the inherent flammability of RPUF presents significant challenges. Delaying the time to ignition and preventing flame spread post-combustion is crucial for ensuring sufficient evacuation time in the event of a fire. Based on this principle, this study explores the efficacy of using potassium salts as a catalyst to promote the self-cleavage of RPUF, generating substantial amounts of CO2, thereby reducing the local oxygen concentration and delaying ignition. Additionally, the inclusion of a reactive flame retardant (DFD) facilitates the release of phosphorus-oxygen free radicals during combustion, disrupting the combustion chain reaction and thus mitigating flame propagation. Moreover, potassium salt-induced catalytic carbonization and phosphorus derivative cross-linking enhance the condensed phase flame retardancy. Consequently, the combined application of potassium salts and DFD increases the limiting oxygen index (LOI) and reduces both peak heat release rate (PHRR) and total heat release (THR). Importantly, the incorporation of these additives does not compromise the compressive strength or thermal insulation performance of RPUF. This integrated approach offers a new and effective strategy for the development of flame retardant RPUF.

A complexity of pathway expression in yeast compared to prokaryotes is the need for separate promoters and terminators for each gene expressed. Single transcript expression and separated protein production is possible via the use of 2A viral peptides, but detailed characterization to assess their suitability and applications is needed. The present work aimed to characterize multiple 2A peptide sequences to determine suitability for metabolic engineering applications in Saccharomyces cerevisiae. We screened 22 peptides placed between fluorescent protein sequences. Cleaving efficiency was calculated by western blot intensity of bands corresponding to the cleaved and uncleaved forms of the reporter. Three out of the 22 sequences showed high cleavage efficiency: 2A peptide from Equine rhinitis B virus (91%), Porcine teschovirus-1 (85%) and Operophtera brumata cypovirus-18 (83%). Furthermore, expression of the released protein was comparable to its monocistronic expression. As a proof-of-concept, the triterpene friedelin was successfully produced in the same yeast strain by expressing its synthase with the truncated form of HMG1 linked by the 2A peptide of ERBV-1, with production titers comparable to monocistronic expression (via separate promoters). These results suggest that these peptides could be suitable for expression and translation of multiple proteins in metabolic engineering applications in S. cerevisiae.

Background Spidroins are well-known for their exceptional mechanical properties, which have inspired extensive research and applications across various fields. Large-scale production of spidroin continues to face major challenges due to the complexity involved in inducing host organisms to express full-length spidroins. This process requires advanced techniques and has issues such as plasmid instability and potential misfolding. Results In this study, we developed a novel expression system by combining a fusion tag with a self-cleavage intein, enabling the convenient expression of three chimeric spidroins with varying numbers of repetitive units. After optimising expression conditions, NT2RepCT, NT4RepCT and NT6RepCT spidroins were obtained in soluble form, with yields of 266, 135 and 125 mg/L, respectively. All three spidroins exhibited an increased β-sheet content with increased numbers of repetitive units during transition from soluble to dry state. In terms of nanofibril morphologies, the self-assemblies of NT4RepCT and NT6RepCT closely resemble those of native silk proteins. Conclusion This study can serve as a reference for preparation of high-performance spider silk materials and soluble expression of proteins, such as collagen, and as a foundation for preparation of other structurally complex polymer materials.

Precise developmental timing control is essential for organism formation and function, but its mechanisms are unclear. In C. elegans , the microRNA lin-4 critically regulates developmental timing by post-transcriptionally downregulating the larval-stage-fate controller LIN-14. However, the mechanisms triggering the activation of lin-4 expression toward the end of the first larval stage remain unknown. We demonstrate that the transmembrane transcription factor MYRF-1 is necessary for lin-4 activation. MYRF-1 is initially localized on the cell membrane, and its increased cleavage and nuclear accumulation coincide with lin-4 expression timing. MYRF-1 regulates lin-4 expression cell-autonomously and hyperactive MYRF-1 can prematurely drive lin-4 expression in embryos and young first-stage larvae. The tandem lin-4 promoter DNA recruits MYRF-1 GFP to form visible loci in the nucleus, suggesting that MYRF-1 directly binds to the lin-4 promoter. Our findings identify a crucial link in understanding developmental timing regulation and establish MYRF-1 as a key regulator of lin-4 expression.

Viroid and viroid-like satellite RNAs are infectious, circular, non-protein coding RNAs reported in plants only so far. Some viroids (family Avsunviroidae) and viroid-like satellite RNAs share self-cleaving activity mediated by hammerhead ribozymes (HHRzs) endowed in both RNA polarity strands. Using a homology-independent method based on the search for conserved structural motifs of HHRzs in reads and contigs from high-throughput sequenced RNAseq libraries, we identified a novel small (550 nt) viroid-like RNA in a library from a Citrus reticulata tree. Such a viroid-like RNA contains a HHRz in both polarity strands. Northern blot hybridization assays showed that circular forms of both polarity strands of this RNA (tentatively named citrus transiently-associated hammerhead viroid-like RNA1 (CtaHVd-LR1)) exist, supporting its replication through a symmetric pathway of the rolling circle mechanism. CtaHVd-LR1 adopts a rod-like conformation and has the typical features of quasispecies. Its HHRzs were shown to be active during transcription and in the absence of any protein. CtaHVd-LR1 was not graft-transmissible, and after its first identification, it was not found again in the original citrus source when repeatedly searched in the following years, suggesting that it was actually not directly associated with the plant. Therefore, the possibility that this novel self-cleaving viroid-like RNA is actually associated with another organism (e.g., a fungus), in turn, transiently associated with citrus plants, is proposed.

Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

A rapid, highly sensitive and selective colorimetric assay is presented for visually detecting L-histidine. It is based on L-histidine-triggered self-cleavage of DNA duplex-induced gold nanoparticle (AuNP) aggregation. The citrate-capped AuNPs easily aggregate in a high concentration of salt environment. However, in the presence of L-histidine aptamers (DNA1 and DNA2), the partial strands of DNA1 and DNA2 hybridize to form a DNA duplex with a swing structure. The swing-like DNA duplexes are adsorbed on the surface of AuNPs to improve the stability of AuNPs, and the AuNPs also are better dispersed in high-salt media. When L-histidine is added to the solutions, it catalyzes the self-cleavage of DNA1 to form many single-stranded DNA (ssDNA) fragments. These ssDNA segments are adsorbed on the AuNPs and weaken the stability of AuNPs. Hence, the AuNPs aggregate in high-salt environment, and this results in a red-to-blue color change. Under the optimized conditions, L-histidine can be determined with a limit of detection of 3.6 nM. In addition, the sensor was successfully applied to the determination of L-histidine in spiked serum samples. Graphical abstract Schematic of a rapid and homogeneous colorimetric L-histidine assay. It combines L-histidine-triggered self-cleavage of the swing-like DNA duplexes and self-cleavage of DNA-induced AuNP aggregation.

Bacterial l-aspartate α-decarboxylase (PanD) specifically catalyzes the decarboxylation of l-aspartic acid to β-alanine. It is translated as an inactive pro-protein, then processed by self-cleavage to form two small subunits with catalytic activity. There is a significant difference in the efficiency of this process among the reported PanDs, while the structural basis remains unclear. More PanDs with known sequences and characterized properties are needed to shed light on the molecular basis of the self-cleavage process. In this study, PanD genes from 33 selected origins were synthesized and expressed; using purified recombinant enzymes, their self-processing properties were characterized and classified. Three classes of PanDs were acquired based on their self-cleavage efficiency. Combined with the phylogenetic analysis and structure comparison, sited-directed mutagenesis was performed to investigate the effects of four mutants on self-processing. In comparison with the wild-type (96.4%), the self-cleavage efficiencies of mutants V23E, I26C, T27A, and E56S were decreased to 90.5, 83.6, 74.4 and 81.2%, respectively. The results indicated that residues of V23, I26, T27 and E56 were critical to the self-cleavage processing of PanDs. This work provided further understanding to the self-cleavage processing of PanDs, which may contribute to protein engineering of the enzyme.