Translation initiation site of mRNA is selected through dynamic interaction with the ribosome.

Initiation of protein synthesis from the correct start codon of messenger RNA (mRNA) is crucial to translation fidelity. In bacteria, the start codon is usually preceded by a 4- to 6-mer adenosine/guanosine-rich Shine­Dalgarno (SD) sequence. Both the SD sequence and the start codon comprise the core ribosome-binding site (RBS), to which the 30S ribosomal subunit binds to initiate translation. How the rather short and degenerate information inside the RBS can be correctly accommodated by the ribosome is not well understood. Here, we used single-molecule techniques to tackle this long-standing issue. We found that the 30S subunit initially binds to mRNA through the SD sequence, whereas the downstream RBS undergoes dynamic motions, especially when it forms structures. The mRNA is either dissociated or stabilized by initiation factors, such as initiation factor 3 (IF3). The initiator transfer RNA (tRNA) further helps the 30S subunit accommodate mRNA and unwind up to 3 base pairs of the RBS structure. Meanwhile, the formed complex of the 30S subunit with structured mRNA is not stable and tends to disassociate. IF3 promotes dissociation by dismissing the bound initiator tRNA. Thus, initiation factors may accelerate the dynamic assembly­disassembly process of 30S­mRNA complexes such that the correct RBS can be preferentially selected. Our study provides insights into how the bacterial ribosome identifies a typical translation initiation site from mRNA.

Global fitness landscapes of the Shine-Dalgarno sequence.

Shine-Dalgarno sequences (SD) in prokaryotic mRNA facilitate protein translation by pairing with rRNA in ribosomes. Although conventionally defined as AG-rich motifs, recent genomic surveys reveal great sequence diversity, questioning how SD functions. Here, we determined the molecular fitness (i.e., translation efficiency) of 49 synthetic 9-nt SD genotypes in three distinct mRNA contexts in Escherichia coli We uncovered generic principles governing the SD fitness landscapes: (1) Guanine contents, rather than canonical SD motifs, best predict the fitness of both synthetic and endogenous SD; (2) the genotype-fitness correlation of SD promotes its evolvability by steadily supplying beneficial mutations across fitness landscapes; and (3) the frequency and magnitude of deleterious mutations increase with background fitness, and adjacent nucleotides in SD show stronger epistasis. Epistasis results from disruption of the continuous base pairing between SD and rRNA. This "chain-breaking" epistasis creates sinkholes in SD fitness landscapes and may profoundly impact the evolution and function of prokaryotic translation initiation and other RNA-mediated processes. Collectively, our work yields functional insights into the SD sequence variation in prokaryotic genomes, identifies a simple design principle to guide bioengineering and bioinformatic analysis of SD, and illuminates the fundamentals of fitness landscapes and molecular evolution.

Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates.

Programmed -1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands.

Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi-C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.

Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot.

Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes. We found that the first ribosome target stem was resistant to unwinding when the neighboring loop was confined along the stem; such constrained conformation was dependent on the presence of consecutive adenosines in this loop. Mutations that disrupted the distal base triples abolished all remaining tertiary base pairs. Changes in frameshifting efficiency correlated with the stem unwinding resistance. Our results demonstrate that various tertiary base pairs are coordinated inside a highly efficient frameshift-stimulating RNA pseudoknot and suggest a mechanism by which mechanical resistance of the pseudoknot may persistently act on translocating ribosomes.

Enhanced Photocatalytic Degradation of Indoor Low Concentration Gaseous Formaldehyde by Asymmetric Silveriodate Composited with 2D or 3D Bismuth Oxybromide.

Formaldehyde is one of the most hazardous and typical indoor VOCs air pollutants. Asymmetric AgIO3 was respectively composited with 3D hierarchically structured BiOBr and 2D BiOBr nanosheets to photodegrade gas-phase formaldehyde. Ag/AgIO3 /BiOBr(CMC) demonstrated better photocatalytic performance than Ag/AgIO3 /BiOBr owning to the role of biomass solvent sodium carboxymethyl cellulose in increasing the specific surface area, reducing the band gap and changing the dominant facets. Moreover, Ag nanoparticles coming from the reduction in AgIO3 were confirmed by XRD, SEM and XPS. The surface plasma resonance effect of Ag NPs improved the efficiency of the light quantum. Besides, different exposed facets of {010} in BiOBr(CMC) and {001} in BiOBr resulted in distinct oxygen vacancy structures. O 2 2 - could be generated via a two-electron transfer pathway on the {010} dominant facets surface in AABR-CMC, leading to the change in photolysis pathway and facilitating more · OH produced by AABR-CMC. Compared with pure AgIO3 and BiOBr or BiOBr(CMC), the photocatalytic efficiency of the composites was improved significantly. Optimal photodegradation efficiency for HCHO was achieved for AABR-75 and AABR-CMC50.

Varying characteristics and driving mechanisms of antibiotic resistance genes in farmland soil amended with high-density polyethylene microplastics.

The differential effects of microplastics and phthalates released from microplastics on antibiotic resistance genes in soil remain unknown. This study aims to analyze the varying characteristics and driving mechanisms of antibiotic resistance genes in soils amended with high-density polyethylene microplastics (with and without phthalates) through a 60-day microcosm experiment. The results indicate that the amended high-density polyethylene microplastics (containing phthalates) enhanced the abundance of antibiotic resistance genes in the soil, a phenomenon that markedly increased with the amendment period. Nevertheless, the addition of high-density polyethylene microplastics (without phthalates) mitigated the abundance of antibiotic resistance genes, which was less significant with increasing amendment period. Furthermore, addition of high-density polyethylene microplastics altered the soil properties, especially porosity. The phthalates released from high-density polyethylene microplastics and the changes in the soil properties transformed soil bacterial communities, resulting in increased abundance of bacterial hosts harboring antibiotic resistance genes (Calditrichaeota, Candidate division CPR1, Candidatus Delongbacteria, Candidatus Kapabacteria, Candidatus Spechtbacteria, Candidatus Wildermuthbacteria, and Ignavibacteriae), thereby enhancing the abundance of antibiotic resistance genes. These findings suggest that compared to microplastics, the phthalates released from microplastics considerably affect the antibiotic resistance genes in soils, thereby promoting the propagation of antibiotic resistance genes in agricultural environments.

Bouveret syndrome: A case report.

BACKGROUND: Bouveret syndrome is a rare complication of cholelithiasis, with only 315 cases reported in the literature between 1967 and 2016. Delay in diagnosis is associated with a high mortality rate. Diagnosis is based upon clinical manifestations, gastroscopy, and imaging studies such as abdominal computed tomography and magnetic resonance cholan-giopancreatography. Endoscopic stone extraction or lithotripsy is the preferred choice for treatment as it is safe and minimally invasive with few complications. However, if endoscopy fails, surgery is required. CASE SUMMARY: A 61-year-old female patient presented with recurrent epigastric pain for more than 6 mo. On endoscopy, a large amount of food residue was present in the stomach with multiple stones and ulcers in the antro-pyloric region. Based on these findings, a diagnosis of gastrolithiasis was made. However, computed tomography of the abdomen revealed the correct diagnosis of Bouveret syndrome. Initially, endoscopic treatment was attempted but it failed. Later, she was successfully managed by cholecystectomy with duodenal stone extraction and fistula repair (one-step method). At the last follow-up 6 mo after surgery, the patient was symptom-free. CONCLUSION: Bouveret syndrome is a rare complication of gallstones that requires prompt endoscopic or surgical treatment to prevent mortality.

[Dynamics of and relationship between fat accumulation and enzyme activities of precocious walnut]. / æ—©å®žæ ¸æ¡ƒè„‚è‚ªç§¯ç´¯ä¸Žé ¶æ´»æ€§åŠ¨æ€åŠå ¶ç›¸å ³æ€§.

Two precocious walnut varieties, Lvling and Lvzao were used as materials in this study, the kernel fat contents and 3 related enzyme activities in different development periods after flowe-ring 50 days were analyzed. The key enzymes affecting walnut fat in different periods were illumina-ted. The results showed that the kernel fat accumulation trends of the two varieties were basically the same. The kernel began to solidify 50 days after flowering, and the increase in kernel fat content was rapid 60-90 days after flowering, slowed down 90-120 days after flowering, and stopped 120-130 days after flowering. The Logistic model was used to fit the fat accumulation (P<0.01). Fat content rapid accumulation period was 57.8-85.8 days after flowering for Lvling, and 67.4-92.1 days after flowering for Lvzao. The activities of acetyl-CoA carboxylase (ACCase), 6-phosphate dextrose dehydrogenase (G6PDH) and pyruvate kinase (PK) increased from 50 to 100 days after flowering, and then the activities of enzymes began to decrease. The kernel fat content was positively correlated with the activity of ACCase. The kernel fat accumulation rate was positively correlated with PK enzyme activity. The correlation between fat content and enzyme activity was different at different development stages. The 50-100 days after flowering was the exuberant period of walnut kernel fat synthesis, and at this time the fat content could be improved by strengthening the field cultivation management measures. At the early stage of the walnut fat synthesis, G6PDH was the major enzyme to affect fat content, and PK activity influenced the formation of pyruvic acid, so as to indirectly affect the synthesis of fat. ACCase activity affected the final fat content and ACCase played an important regulating role in every period of fat synthesis. It was speculated that ACCase might be a key enzyme to affect the fat synthesis of walnut kernel.

[Relationship between apoptosis of rat hippocampus cells induced by aluminum and the copy of the bcl-2 as well as bax mRNA].

OBJECTIVE: To explore the effects of aluminum chloride (AlCl3) on the apoptosis of rat hippocampus cells and the relationship between the apoptosis and the expression of the bcl-2 as well as bax mRNA. METHODS: 40 SD rats, adult and healthy, were divided into 4 groups randomly: normal saline, Al3+ 2.5 mg/kg, 5 mg/kg, 10 mg/kg. They were exposed to AlCl, by intraperitioneal injection at the dose of 0.2 ml/d for 60 days. After exposure, the apoptosis of hippocampus cells were measured by method of TUNEL. The expression of bcl-2 mRNA and bax mRNA in rats' hippocampus were measured by RT-PCR. The results were analyzed by the gelatum analyzing system. RESULTS: The rates of apoptosis in hippocampus cells in Al3+ 5 mg/kg group and Al3+ 10 mg/kg group were significantly higher than that of controls (P < 0.05). But Al3+ 2.5 mg/kg group was not significantly higher than that of control (P > 0.05), and was significantly decreased in hippocampus cells in Al3+ 5 mg/kg and 10 mg/kg group compared with the control group (P < 0.05). The expression of bcl-2 mRNA was significantly decreased in every aluminum treatment group compared with the control group (P < 0.05). The expression of bax mRNA was significantly increased in every aluminum treatment group compared with the control group (P < 0.05). There was negative correlation between AI and the expression of Bcl-2 (r = -0.909, P < 0.01). There was positive correlation between Al and the expression of Bax (r = 0.871, P < 0.01). CONCLUSION: Aluminum can induce apoptosis in rat hippocampus cells through the downwards regulation of bcl-2 mRNA, the upwards regulation of bax mRNA expression.

p38 MAPK and NF-kappaB pathways are involved in naphtho[1,2-b] furan-4,5-dione induced anti-proliferation and apoptosis of human hepatoma cells.

Naphtho[1,2-b] furan-4,5-dione (NFD) was investigated for its anti-proliferation effect on human hepatocellular carcinoma (HCC), Hep3B, HepG(2), and Huh-7 cells. The effect of NFD on inhibiting proliferation and apoptosis was correlated with up-regulation of pro-apoptotic protein and down-regulation of pro-survival proteins. Remarkably, we found that NFD inhibited the nuclear translocation of NF-kappaB, likely accounting for the down-regulation of pro-survival Bcl-2 family. Furthermore, suppression of p38 MAPK activity by a specific inhibitor significantly rescued the cell proliferation inhibited by NFD. These findings suggest that signaling imbalance between p38 MAPK and NF-kappaB by NFD results in the proliferative inhibition and apoptosis of HCC tumor cells.