Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.

Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.

Spin splitting of dopant edge state in magnetic zigzag graphene nanoribbons.

Spin-ordered electronic states in hydrogen-terminated zigzag nanographene give rise to magnetic quantum phenomena1,2 that have sparked renewed interest in carbon-based spintronics3,4. Zigzag graphene nanoribbons (ZGNRs)-quasi one-dimensional semiconducting strips of graphene bounded by parallel zigzag edges-host intrinsic electronic edge states that are ferromagnetically ordered along the edges of the ribbon and antiferromagnetically coupled across its width1,2,5. Despite recent advances in the bottom-up synthesis of GNRs featuring symmetry protected topological phases6-8 and even metallic zero mode bands9, the unique magnetic edge structure of ZGNRs has long been obscured from direct observation by a strong hybridization of the zigzag edge states with the surface states of the underlying support10-15. Here, we present a general technique to thermodynamically stabilize and electronically decouple the highly reactive spin-polarized edge states by introducing a superlattice of substitutional N-atom dopants along the edges of a ZGNR. First-principles GW calculations and scanning tunnelling spectroscopy reveal a giant spin splitting of low-lying nitrogen lone-pair flat bands by an exchange field (~850 tesla) induced by the ferromagnetically ordered edge states of ZGNRs. Our findings directly corroborate the nature of the predicted emergent magnetic order in ZGNRs and provide a robust platform for their exploration and functional integration into nanoscale sensing and logic devices15-21.

DNA-Mediated Peptide Assembly into Protein Mimics.

The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.

Topological band engineering of graphene nanoribbons.

Topological insulators are an emerging class of materials that host highly robust in-gap surface or interface states while maintaining an insulating bulk1,2. Most advances in this field have focused on topological insulators and related topological crystalline insulators3 in two dimensions4-6 and three dimensions7-10, but more recent theoretical work has predicted the existence of one-dimensional symmetry-protected topological phases in graphene nanoribbons (GNRs)11. The topological phase of these laterally confined, semiconducting strips of graphene is determined by their width, edge shape and terminating crystallographic unit cell and is characterized by a [Formula: see text] invariant12 (that is, an index of either 0 or 1, indicating two topological classes-similar to quasi-one-dimensional solitonic systems13-16). Interfaces between topologically distinct GNRs characterized by different values of [Formula: see text] are predicted to support half-filled, in-gap localized electronic states that could, in principle, be used as a tool for material engineering11. Here we present the rational design and experimental realization of a topologically engineered GNR superlattice that hosts a one-dimensional array of such states, thus generating otherwise inaccessible electronic structures. This strategy also enables new end states to be engineered directly into the termini of the one-dimensional GNR superlattice. Atomically precise topological GNR superlattices were synthesized from molecular precursors on a gold surface, Au(111), under ultrahigh-vacuum conditions and characterized by low-temperature scanning tunnelling microscopy and spectroscopy. Our experimental results and first-principles calculations reveal that the frontier band structure (the bands bracketing filled and empty states) of these GNR superlattices is defined purely by the coupling between adjacent topological interface states. This manifestation of non-trivial one-dimensional topological phases presents a route to band engineering in one-dimensional materials based on precise control of their electronic topology, and is a promising platform for studies of one-dimensional quantum spin physics.

Genome-wide role of codon usage on transcription and identification of potential regulators.

Codon usage bias is a fundamental feature of all genomes and plays an important role in determining gene expression levels. The codon usage was thought to influence gene expression mainly due to its impact on translation. Recently, however, codon usage was shown to affect transcription of fungal and mammalian genes, indicating the existence of a gene regulatory phenomenon with unknown mechanism. In Neurospora, codon usage biases strongly correlate with mRNA levels genome-wide, and here we show that the correlation between codon usage and RNA levels is maintained in the nucleus. In addition, codon optimality is tightly correlated with both total and nuclear RNA levels, suggesting that codon usage broadly influences mRNA levels through transcription in a translation-independent manner. A large-scale RNA sequencing-based genetic screen in Neurospora identified 18 candidate factors that when deleted decreased the genome-wide correlation between codon usage and RNA levels and reduced the codon usage effect on gene expression. Most of these factors, such as the H3K36 methyltransferase, are chromatin regulators or transcription factors. Together, our results suggest that the transcriptional effect of codon usage is mediated by multiple transcriptional regulatory mechanisms.

IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains.

Polycomb Group (PcG) proteins are part of an epigenetic cell memory system that plays essential roles in multicellular development, stem cell biology, X chromosome inactivation, and cancer. In animals, plants, and many fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to assemble transcriptionally repressed facultative heterochromatin. PRC2 is structurally and functionally conserved in the model fungus Neurospora crassa, and recent work in this organism has generated insights into PRC2 control and function. To identify components of the facultative heterochromatin pathway, we performed a targeted screen of Neurospora deletion strains lacking individual ATP-dependent chromatin remodeling enzymes. We found the Neurospora homolog of IMITATION SWITCH (ISW) is critical for normal transcriptional repression, nucleosome organization, and establishment of typical histone methylation patterns in facultative heterochromatin domains. We also found that stable interaction between PRC2 and chromatin depends on ISW. A functional ISW ATPase domain is required for gene repression and normal H3K27 methylation. ISW homologs interact with accessory proteins to form multiple complexes with distinct functions. Using proteomics and molecular approaches, we identified three distinct Neurospora ISW-containing complexes. A triple mutant lacking three ISW accessory factors and disrupting multiple ISW complexes led to widespread up-regulation of PRC2 target genes and altered H3K27 methylation patterns, similar to an ISW-deficient strain. Taken together, our data show that ISW is a key component of the facultative heterochromatin pathway in Neurospora, and that distinct ISW complexes perform an apparently overlapping role to regulate chromatin structure and gene repression at PRC2 target domains.

Genome-wide association study of bacterial blight resistance in soybean.

Bacterial blight caused by Pseudomonas syringae pv. glycines (Psg) is a widespread foliar disease. Although four Resistance to Pseudomonas syringae pv. glycinea (Rpg) 1 ~ 4 (Rpg1~4) genes that have been observed to segregate in a Mendelian pattern have been reported to confer resistance to Psg in soybean, the genetic basis of quantitative resistance to bacterial blight in soybean remains unclear. In the present study, the Psg resistance of two soybean association panels consisting of 573 and 213 lines, respectively, were phenotyped in multiple environments in 2014 - 2016. Genome-wide association study (GWAS) were performed using 2 models FarmCPU and BLINK to identify Psg resistance loci. A total of 40 soybean varieties with high level of Psg resistance were identified, and 14 quantitative trait loci (QTLs) were detected on 12 soybean chromosomes. These QTLs were identified for the first time. The majority of the QTLs were only detected in one or the other association panels, while qRPG-18-1 was detected in both association panels for at least one growing season. A total of 46 candidate Psg resistance genes were identified from the qRpg_13_1, qRPG-15-1, and qRPG-18-1 loci based on gene function annotation. In addition, we found the genomic region covering rpg1-b and rpg1-r harbored the synteny with a genomic region on chromosome 15, and identified 16 nucleotide binding site - leucine-rich repeat (NBS-LRR) genes as the candidate Psg resistance genes from the synteny blocks. This study provides new information for dissecting the genetic control of Psg resistance in soybean.

Trap-Assisted Auger-Meitner Recombination from First Principles.

Trap-assisted nonradiative recombination is known to limit the efficiency of optoelectronic devices, but the conventional multiphonon emission (MPE) process fails to explain the observed loss in wide-band-gap materials. Here, we highlight the role of trap-assisted Auger-Meitner (TAAM) recombination and present a first-principles methodology to determine TAAM rates due to defects or impurities in semiconductors or insulators. We assess the impact on efficiency of light emitters in a recombination cycle that may include both TAAM and carrier capture via MPE. We apply the formalism to the technologically relevant case study of a calcium impurity in InGaN, where a Shockley-Read-Hall recombination cycle involving MPE alone cannot explain the experimentally observed nonradiative loss. We find that, for band gaps larger than 2.5 eV, the inclusion of TAAM results in recombination rates that are orders of magnitude larger than recombination rates based on MPE alone, demonstrating that TAAM can be a dominant nonradiative process in wide-band-gap materials. Our computational formalism is general and can be applied to the calculation of TAAM rates in any semiconducting or insulating material.

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding.

Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy, and protein folding based on the assumption that codon usage affects translation dynamics. The roles of codon usage in translation, however, are not clear and have been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the preferred codons enhance the rate of translation elongation, whereas non-optimal codons slow elongation. Codon usage also controls ribosome traffic on mRNA. These conclusions were supported by ribosome profiling results in vitro and in vivo with template mRNAs designed to increase the signal-to-noise ratio. Finally, we demonstrate that codon usage regulates protein function by affecting co-translational protein folding. These results resolve a long-standing fundamental question and suggest the existence of a codon usage code for protein folding.

Synthesis of the Hypoxia-Inducible Factor-2α (HIF-2α) Inhibitor, 3-[(1S,2S,3R)-2,3-Difluoro-1-hydroxy-7-methylsulfonylindan-4-yl]oxy-5-fluorobenzonitrile (PT2977, Belzutifan); Efficient Replication of Established Approaches.

A concise linear synthesis of hypoxia inducible factor-2α (HIF-2α) inhibitor, belzutifan was achieved by reproducing key components of previous synthetic approaches to this molecule as described in several publications and patents. Belzutifan is an orally bioavailable small-molecule (HIF-2α) inhibitor for the treatment of von Hippel-Lindau (VHL) disease-associated renal cell carcinoma (RCC) that received FDA approval in 2021. Herein, we report a 13-step synthesis of PT2977 that proceeded in good overall yield with high diastereoselectivity. Separation of diastereomeric mixtures at two different stages of the synthesis proved advantageous in ease of separation. The X-ray structure of belzutifan was determined.

Effects of codon usage on gene expression are promoter context dependent.

Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the significance of codon usage effect on gene expression. Here we show that gene-specific regulation reduces the genome-wide codon usage and mRNA correlations: Constitutively expressed genes exhibit much higher genome-wide correlations than differentially expressed genes from fungi to human cells. Using Drosophila S2 cells as a model system, we showed that the effect of codon usage on mRNA expression level is promoter-dependent. Regions downstream of the core promoters of differentially expressed genes can repress the codon usage effects on mRNA expression. An element in the Hsp70 promoter was identified to be necessary and sufficient for this inhibitory effect. The promoter-dependent codon usage effects on mRNA levels are regulated at the transcriptional level through modulation of histone modifications, nucleosome densities and premature termination. Together, our results demonstrate that promoters play a major role in determining whether codon usage influences gene expression and further establish the transcription-dependent codon usage effects on gene expression.

Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed.

Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics.

Identification of Novel Genomic Regions for Bacterial Leaf Pustule (BLP) Resistance in Soybean (Glycine max L.) via Integrating Linkage Mapping and Association Analysis.

Bacterial leaf pustule (BLP), caused by Xanthornonas axonopodis pv. glycines (Xag), is a worldwide disease of soybean, particularly in warm and humid regions. To date, little is known about the underlying molecular mechanisms of BLP resistance. The only single recessive resistance gene rxp has not been functionally identified yet, even though the genotypes carrying the gene have been widely used for BLP resistance breeding. Using a linkage mapping in a recombinant inbred line (RIL) population against the Xag strain Chinese C5, we identified that quantitative trait locus (QTL) qrxp-17-2 accounted for 74.33% of the total phenotypic variations. We also identified two minor QTLs, qrxp-05-1 and qrxp-17-1, that accounted for 7.26% and 22.26% of the total phenotypic variations, respectively, for the first time. Using a genome-wide association study (GWAS) in 476 cultivars of a soybean breeding germplasm population, we identified a total of 38 quantitative trait nucleotides (QTNs) on chromosomes (Chr) 5, 7, 8, 9,15, 17, 19, and 20 under artificial infection with C5, and 34 QTNs on Chr 4, 5, 6, 9, 13, 16, 17, 18, and 20 under natural morbidity condition. Taken together, three QTLs and 11 stable QTNs were detected in both linkage mapping and GWAS analysis, and located in three genomic regions with the major genomic region containing qrxp_17_2. Real-time RT-PCR analysis of the relative expression levels of five potential candidate genes in the resistant soybean cultivar W82 following Xag treatment showed that of Glyma.17G086300, which is located in qrxp-17-2, significantly increased in W82 at 24 and 72 h post-inoculation (hpi) when compared to that in the susceptible cultivar Jack. These results indicate that Glyma.17G086300 is a potential candidate gene for rxp and the QTLs and QTNs identified in this study will be useful for marker development for the breeding of Xag-resistant soybean cultivars.

Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae).

BACKGROUND: Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development in T. ravennae. RESULTS: During the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented in the GO enrichment analyses and tests for differential expression (FDR p-value < 0.05). The differential expression of floral integrators observed in the early phases of inflorescence development diminished prior to inflorescence determinacy regulation. Differential expression analysis did not identify many unique genes at mid-inflorescence development stages, though typical biological processes involved in plant growth and development expressed abundantly. The increase in inflorescence determinacy regulatory elements and putative homeotic floral development unigenes at mid-inflorescence development coincided with the expression of multiple meiosis annotations and multicellular organism developmental processes. Analysis of seed development identified multiple unigenes involved in oxidative-reductive processes. CONCLUSION: Reproduction in grasses is a dynamic system involving the sequential coordination of complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development in T. ravennae. These results provide insights into the molecular regulation of reproductive development and provide a foundation for future investigations and analyses, including genome annotation, functional genomics characterization, gene family evolutionary studies, comparative genomics, and precision breeding.

Topological Phases in Graphene Nanoribbons Tuned by Electric Fields.

Graphene nanoribbons (GNRs) possess distinct symmetry-protected topological phases. We show, through first-principles calculations, that by applying an experimentally accessible transverse electric field, certain boron and nitrogen periodically codoped GNRs have tunable topological phases. The tunability arises from a field-induced band inversion due to an opposite response of the conduction- and valence-band states to the electric field. With a spatially varying applied field, segments of GNRs of distinct topological phases are created, resulting in a field-programmable array of topological junction states, each may be occupied with charge or spin. Our findings not only show that electric field may be used as an easy tuning knob for topological phases in quasi-one-dimensional systems, but also provide new design principles for future GNR-based quantum electronic devices through their topological characters.

eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons.

Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and plays an important role in regulating gene expression levels. A major role of codon usage is thought to regulate protein expression levels by affecting mRNA translation efficiency, but the underlying mechanism is unclear. By analyzing ribosome profiling results, here we showed that codon usage regulates translation elongation rate and that rare codons are decoded more slowly than common codons in all codon families in Neurospora. Rare codons resulted in ribosome stalling in manners both dependent and independent of protein sequence context and caused premature translation termination. This mechanism was shown to be conserved in Drosophila cells. In both Neurospora and Drosophila cells, codon usage plays an important role in regulating mRNA translation efficiency. We found that the rare codon-dependent premature termination is mediated by the translation termination factor eRF1, which recognizes ribosomes stalled on rare sense codons. Silencing of eRF1 expression resulted in codon usage-dependent changes in protein expression. Together, these results establish a mechanism for how codon usage regulates mRNA translation efficiency.

Covalent C-N Bond Formation through a Surface Catalyzed Thermal Cyclodehydrogenation.

The integration of substitutional dopants at predetermined positions along the hexagonal lattice of graphene-derived polycyclic aromatic hydrocarbons is a critical tool in the design of functional electronic materials. Here, we report the unusually mild thermally induced oxidative cyclodehydrogenation of dianthryl pyrazino[2,3-g]quinoxalines to form the four covalent C-N bonds in tetraazateranthene on Au(111) and Ag(111) surfaces. Bond-resolved scanning probe microscopy, differential conductance spectroscopy, along with first-principles calculations unambiguously confirm the structural assignment. Detailed mechanistic analysis based on ab initio density functional theory calculations reveals a stepwise mechanism featuring a rate determining barrier of only ΔE⧧ = 0.6 eV, consistent with the experimentally observed reaction conditions.

Efficient optical parameter mapping based on time-domain radiative transfer equation combined with parallel programming.

A two-dimensional optical parameter mapping based on the time-domain radiative transfer equation (TD-RTE) is studied in this work. The finite element method with structured and unstructured grids is employed to solve TD-RTE and OpenMP parallel technology is employed to improve the computing efficiency. The sequential quadratic programming algorithm is used as a powerful optimization method to reconstruct absorption and scattering parameter fields and the maximum a posteriori estimation is employed by introducing the regularization term into the objective function to improve the ill-posed inverse problem. In addition, the effects of measurement errors on reconstruction accuracy are investigated thoroughly. All the simulation results demonstrate that the reconstructed scheme we developed is accurate and efficient in optical parameter mapping based on TD-RTE.

Early-life lactoferrin intervention modulates the colonic microbiota, colonic microbial metabolites and intestinal function in suckling piglets.

This study reports the effects of early-life lactoferrin (LF) intervention on the colonic microbiota, intestinal function and mucosal immunity in suckling piglets. A total of 60 Duroc × Landrace × Yorkshire suckling piglets from six sows were assigned to the control (CON) and LF groups in litters. The LF group piglets were fed 0.5 g/kg body weight of LF solution per day, and the CON group piglets were fed the same dose of physiological saline for a week. Six piglets from the two groups were randomly chosen and euthanised on days 8 and 21. The LF group piglets had higher ACE and Chao1 indices of colonic microbiota than the CON group piglets (P < 0.05). In addition, the LF group piglets had a higher abundance of Roseburia (P < 0.05) and a lower abundance of Escherichia-Shigella (P < 0.05) in the colonic digesta. The LF group piglets also had a higher concentration of butyrate (P < 0.05) in the colonic digesta. Moreover, the LF group piglets had a higher gene expression of occludin (P < 0.05) in the colonic mucosa. In addition, the gene expression of MUC4 was upregulated in the LF group piglets compared with that in the CON group on day 21 (P < 0.05), and the lower gene expression of TLR-4 was found in the LF group compared with the CON group on day 8 (P < 0.05). Furthermore, the concentration of IL-10 was increased in the LF group on day 8 (P < 0.05), while the LF group piglets had a higher concentration of sIgA and lower concentrations of IL-1α and IL-1ß (P < 0.05) in the colonic mucosa. These results suggest that early-life LF intervention can modulate the composition of colonic microbiota and improve the intestinal function in suckling piglets.Key Points• Early-life LF intervention significantly modulated colon microbiota.• Early-life LF intervention can improve the colon health.• The colon microbiota plays an important role in host health.