Codon usage bias regulates gene expression and protein conformation in yeast expression system P. pastoris.

BACKGROUND: Protein synthesis is one of the extremely important anabolic pathways in the yeast expression system Pichia pastoris. Codon optimization is a commonly adopted strategy for improved protein expression, although unexpected failures did appear sometimes waiting for further exploration. Recently codon bias has been studied to regulate protein folding and activity in many other organisms. RESULTS: Here the codon bias profile of P. pastoris genome was examined first and a direct correlation between codon translation efficiency and usage frequency was identified. By manipulating the codon choices of both endogenous and heterologous signal peptides, secretion abilities of N-terminal signal peptides were shown to be tolerant towards codon changes. Then two gene candidates with different levels of structural disorder were studied, and full-length codon optimization was found to affect their expression profiles differentially. Finally, more evidences were provided to support possible protein conformation change brought by codon optimization in structurally disordered proteins. CONCLUSION: Our results suggest that codon bias regulates gene expression by modulating several factors including transcription and translation efficiency, protein folding and activity. Because of sequences difference, the extent of affection may be gene specific. For some genes, special codon optimization strategy should be adopted to ensure appropriate expression and conformation.

Codon usage bias affects α-amylase mRNA level by altering RNA stability and cytosine methylation patterns in Escherichia coli.

Codon usage bias exists in almost every organism and is reported to regulate protein translation efficiency and folding. Besides translation, the preliminary role of codon usage bias on gene transcription has also been revealed in some eukaryotes such as Neurospora crassa. In this study, we took as an example the α-amylase-coding gene (amyA) and examined the role of codon usage bias in regulating gene expression in the typical prokaryote Escherichia coli. We confirmed the higher translation efficiency on codon-optimized amyA RNAs and found that the RNA level itself was also affected by codon optimization. The decreased RNA level was caused at least in part by altered mRNA stability at the post-transcriptional level. Codon optimization also altered the number of cytosine methylation sites. Examination on dcm knockouts suggested that cytosine methylation may be a minor mechanism adopted by codon bias to regulate gene RNA levels. More studies are required to verify the global effect of codon usage and to reveal its detailed mechanism on transcription.

Whole-course application of dexmedetomidine as an adjuvant to spinal-epidural anesthesia for cesarean section: A randomized, controlled trial.

Background: Dexmedetomidine is known to prolong the analgesic duration of spinal anesthesia, but it can be challenging to achieve further extension without opioids. Therefore, this study aimed to investigate a novel analgesic strategy using dexmedetomidine as an adjuvant to spinal-epidural anesthesia for elective cesarean surgery. Methods: The study was a randomized, double-blind, controlled trial conducted at a single center. Sixty parturients who underwent elective cesarean were randomly assigned to either group C or group D. Group D received an intrathecal injection of 12.5 mg ropivacaine and 5 µg dexmedetomidine followed by continuous epidural patient-controlled analgesia (PCA) infusion with a total volume of 100 ml, containing 0.2 % ropivacaine and 0.5 µg/kg dexmedetomidine. Group C received an intrathecal injection of 12.5 mg ropivacaine with an equivalent saline placebo followed by a similar PCA infusion, containing 0.2 % ropivacaine and an equivalent saline placebo. Results: The primary outcome was visual analog scale score on movement at 24 h after surgery. The results showed that the rest and motion pain scores in group D were significantly lower than those in group C at 6 h, 12 h, and 24 h after surgery (P < 0.05), with the differences at 24 h were 5.0 (5.0, 5.0)in group D versus 5.0 (5.0, 6.0) in group C (P = 0.04). Additionally, the time to the first PCA in group D was significantly longer than that in group C (P < 0.05), as well as the time of sensory and motor recovery. Conclusions: Whole-course application of dexmedetomidine as an adjuvant to spinal-epidural anesthesia could effectively extend the analgesic duration of ropivacaine to 24 h following elective cesarean surgery.

Dome-Conformal Electrode Strategy for Enhancing the Sensitivity of BaTiO3-Doped Flexible Self-powered Triboelectric Pressure Sensor.

A microstructured surface has been applied in self-powered triboelectric pressure sensors to increase the charge-carrying sites and enhance the output performance. However, the microstructure increases the distance between the electrode and the triboelectric layer, and its influence on the output performance is unknown. Herein, we proposed a dome-conformal electrode strategy for a self-powered triboelectric nanogenerator (TENG) pressure sensor. With a simple reverse-dome adsorption process, an ultrathin triboelectric layer and Ag electrode can be made conformal to the dome PDMS structure. The TENG sensor is constructed with paper as a positive triboelectric layer. Compared with the device based on nonconformal structure, the conformal design strategy endows the device with a faster charge transfer and enhanced output voltage. By doping with BaTiO3, the outermost triboelectric layer can be easily modified to improve its ability of sustaining charge, and an ultrathin PDMS layer is coated on the triboelectric layer to expand the triboelectric polarity difference between two triboelectric layers so as to enhance the output voltage. The synergistic effects enable the optimized TENG sensor with a sensitivity of 0.75 V/kPa in the low-pressure region (0-26 kPa) and 0.19 V/kPa in the high-pressure range (26-120 kPa). Its application in human motion detection, grabbing water beakers, and noncontact distance testing has been demonstrated. This work provides a route such as a conformal structure design strategy to enhance the output performance of a microstructure-based TENG sensor.

Strong negative correlation between codon usage bias and protein structural disorder impedes protein expression after codon optimization.

As a common phenomenon existing in almost all genomes, codon usage bias has been studied for a long time. Codon optimization is a frequently used strategy to accelerate protein synthesis rate. Besides regulating protein translation speed, codon usage bias has also be reported to affect co-translation folding and transcription. P. pastoris is a well-developed expression system, whose efficiency is tightly correlated with commercial value. However, few studies focus on the role of codon usage bias in affecting protein expression in P. pastoris. Besides, many genes in P. pastoris genome show significant negative correlation between codon usage bias and protein structural disorder tendency. It's not known whether this feature is important for their expression. In order to answer these questions, we picked 4P. pastoris gene candidates with strong negative correlation between codon usage bias and protein structural disorder. We then performed full-length codon optimization which completely eliminated the correlation. Protein and RNA assays were then used to compare protein and mRNA levels before and after codon optimization. As a result, codon optimization failed to elevate their protein expression levels, and even resulted in a decrease. As represented by the trypsin sensitivity assays, codon optimization also altered the protein structure of 0616 and 0788. Besides protein, codon optimization also affected mRNA levels. Shown by in vitro and in vivo RNA degradation assays, the mRNA stability of 0616, 0788 and 0135 were also altered by codon optimization. For each gene, the detailed effect may be related with its specific sequence and protein structure. Our results suggest that codon usage bias is an important factor to regulate gene expression level, as well as mRNA and protein stabilities in P. pastoris. "Extreme" codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored. Compromised strategies should be tried if expression is not successful. Besides, codon optimization may affect protein structural conformation more severely in structural disordered proteins.