Ribocentre-switch: a database of riboswitches.

Riboswitches are regulatory elements found in the untranslated regions (UTRs) of certain mRNA molecules. They typically comprise two distinct domains: an aptamer domain that can bind to specific small molecules, and an expression platform that controls gene expression. Riboswitches work by undergoing a conformational change upon binding to their specific ligand, thus activating or repressing the genes downstream. This mechanism allows gene expression regulation in response to metabolites or small molecules. To systematically summarise riboswitch structures and their related ligand binding functions, we present Ribocentre-switch, a comprehensive database of riboswitches, including the information as follows: sequences, structures, functions, ligand binding pockets and biological applications. It encompasses 56 riboswitches and 26 orphan riboswitches from over 430 references, with a total of 89 591 sequences. It serves as a good resource for comparing different riboswitches and facilitating the identification of potential riboswitch candidates. Therefore, it may facilitate the understanding of RNA structural conformational changes in response to ligand signaling. The database is publicly available at https://riboswitch.ribocentre.org.

Ribocentre: a database of ribozymes.

Ribozymes are excellent systems in which to study 'sequence - structure - function' relationships in RNA molecules. Understanding these relationships may greatly help structural modeling and design of functional RNA structures and some functional structural modules could be repurposed in molecular design. At present, there is no comprehensive database summarising all the natural ribozyme families. We have therefore created Ribocentre, a database that collects together sequence, structure and mechanistic data on 21 ribozyme families. This includes available information on timelines, sequence families, secondary and tertiary structures, catalytic mechanisms, applications of the ribozymes together with key publications. The database is publicly available at https://www.ribocentre.org.

Pseudomonas Stutzeri may alter the environmental fate of polystyrene nanoplastics by trapping them with increasing extracellular polymers.

Pseudomonas Stutzeri (P. stutzeri) is a denitrifying bacterium that is essential in biological nitrogen removal. To study the interaction between P. stutzeri and polystyrene nanoplastics (PS-NPs), the effects of PS-NPs posed on P. stutzeri were evaluated in terms of bacterial growth, physiology, denitrification function and extracellular polymers (EPS) secretion. Results of confocal laser scanning microscopy (LCSM), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and flow cytometry confirmed that PS-NPs were trapped by P. stutzeri. Exposure to PS-NPs inhibited bacterial growth and expression of denitrification-related genes, but unaffected the denitrifying enzyme activities. The enhanced secretion of EPS caused PS-NPs and bacterial aggregation. And the enzyme activity of SOD in P. stutzeri was increased while that of CAT was decreased. The results of flow cytometry showed that high concentrations of PS-NPs increased the complexity of P. stutzeri cells. These results reveal that P. stutzeri may be affected after trapping PS-NPs and alter their environmental fate as well. SYNOPSIS: This study contributes to the understanding of the possible effect of P. stutzeri on the distribution of PS-NPs and illustrates the potential impact of PS-NPs on P. stutzeri.

Mangrove plants are promising bioindicator of coastal atmospheric microplastics pollution.

Plastics are commonly used by society and their break down into millimeter-sized bits known as microplastics (MPs). Due to the possibility of exposure, reports of them in atmospheric deposition, indoor, and outdoor air have sparked worry for public health. In tropical and subtropical regions all throughout the world, mangroves constitute a distinctive and significant type of coastal wetlands. Mangrove plants are considered to have the effect of accumulating sediment MPs, but the sedimentation of atmospheric MPs has not been reported. In this study, we illustrated the characteristics, abundance and spatial distribution of MPs in different species of mangrove leaves along the Seagull Island in Guangzhou. MPs samples from leaves in five species showed various shapes, colors, compositions, sizes and abundance. Acanthus ilicifolius had an average fallout rate of 1223 items/m2/day which has the highest abundance of MPs in all samples. Four shapes of MPs were found in all leaves surfaces including fiber, fragment, pellet, and film, with fiber is the most. The dominant types of MPs in all leaves were cellulose and rayon. Most of the total MPs size were smaller than 2 mm. Clearly, the microstructures of each species leaf surfaces had an impact on its ability to retain MPs. The plants rough blade surfaces and big folds or gullies caused more particles to accumulate and had a higher MPs retention capacity. Overall, our study contributes to a better knowledge of the condition of MPs pollution in atmosphere and the connection between leaves structure and the retention of MPs, which indicates that mangrove plants are promising bioindicator of coastal atmospheric MPs pollution.

Biological Degradation of Plastics and Microplastics: A Recent Perspective on Associated Mechanisms and Influencing Factors.

Plastic and microplastic pollution has caused a great deal of ecological problems because of its persistence and potential adverse effects on human health. The degradation of plastics through biological processes is of great significance for ecological health, therefore, the feasibility of plastic degradation by microorganisms has attracted a lot of attention. This study comprises a preliminary discussion on the biodegradation mechanism and the advantages and roles of different bacterial enzymes, such as PET hydrolase and PCL-cutinase, in the degradation of different polymers, such as PET and PCL, respectively. With a particular focus on their modes of action and potential enzymatic mechanisms, this review sums up studies on the biological degradation of plastics and microplastics related to mechanisms and influencing factors, along with their enzymes in enhancing the degradation of synthetic plastics in the process. In addition, biodegradation of plastic is also affected by plastic additives and plasticizers. Plasticizers and additives in the composition of plastics can cause harmful impacts. To further improve the degradation efficiency of polymers, various pretreatments to improve the efficiency of biodegradation, which can cause a significant reduction in toxic plastic pollution, were also preliminarily discussed here. The existing research and data show a large number of microorganisms involved in plastic biodegradation, though their specific mechanisms have not been thoroughly explored yet. Therefore, there is a significant potential for employing various bacterial strains for efficient degradation of plastics to improve human health and safety.

Combined effects of microplastics and antibiotic-resistant bacteria on Daphnia magna growth and expression of functional genes.

Microplastics could act as vectors for the transport of harmful bacteria, such as pathogens and antibiotic resistance bacteria (ARB), but their combined effects have not been reported yet. Here, ARB Shigella flexneri with sulfonamides resistance and micro-polystyrene (micro-PS) were used to investigate their possible combined effects on the growth and expression of functional genes in Daphnia magna. Results showed that micro-PS colonized with S. flexneri were ingested by D. magna and blocked in their intestine after 24 h exposure. Changes were observed in the life history and morphology of D. magna, as well as the expression of functional genes in all treatments, but with no difference in the survival rate. We also determined the expression of six functional genes involved in energy and metabolism (arginine kinase, AK) and oxidative stress response (thioredoxin reductase, TRxR, catalase, CAT, and glutathione S-transferases, GSTs), as well as in growth, development and reproduction (vitellogenin, Vtg1 and ecdysone receptor, EcR). AK and Vtg1 did not show significant differences, however, EcR was down-regulated and the other three genes (TRxR, CAT, GSTs) were up-regulated in the combined-treated group. Antibiotic resistance gene (ARGs) sul1 was detected when exposed to micro-PS colonized with S. flexneri., suggesting that D. magna could acquire resistance genes through microplastic biofilms. These results indicated that MPs could act as a carrier of ARB to transfer ARGs into D. magna, and affect the life history, morphology, and the expression of related functional genes of D. magna, to adapt to the stress caused by MPs and ARB.