Fine-tuning Translation Research Articles

Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO.

Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.

Cytosolic RGG RNA-binding proteins are temperature sensitive flowering time regulators in Arabidopsis.

mRNA translation is tightly regulated by various classes of RNA-binding proteins (RBPs) during development and in response to changing environmental conditions. In this study, we characterize the arginine-glycine-glycine (RGG) motif containing RBP family of Arabidopsis thaliana representing homologues of the multifunctional translation regulators and ribosomal preservation factors Stm1 from yeast (ScStm1) and human SERBP1 (HsSERBP1). The Arabidopsis genome encodes three RGG proteins named AtRGGA, AtRGGB and AtRGGC. While AtRGGA is ubiquitously expressed, AtRGGB and AtRGGC are enriched in dividing cells. All AtRGGs localize almost exclusively to the cytoplasm and bind with high affinity to ssRNA, while being capable to interact with most nucleic acids, except dsRNA. A protein-interactome study shows that AtRGGs interact with ribosomal proteins and proteins involved in RNA processing and transport. In contrast to ScStm1, AtRGGs are enriched in ribosome-free fractions in polysome profiles, suggesting additional plant-specific functions. Mutant studies show that AtRGG proteins differentially regulate flowering time, with a distinct and complex temperature dependency for each AtRGG protein. In conclusion, we suggest that AtRGGs function in fine-tuning translation efficiency to control flowering time and potentially other developmental processes in response to environmental changes.

An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis

Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyze the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identify large decreases in N2-methyladenosine (m2A) in both 23 S ribosomal RNA and transfer RNA. This we determine to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gives rise to a proteome that mimics the oxidative stress response, with an increase in levels of superoxide dismutase and decrease in virulence proteins. While tRNA modifications were established to be dynamic for fine-tuning translation, here we report the discovery of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to a model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, adding a different paradigm in which RNA modifications can directly regulate the proteome.

Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis.

Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.

RNA-binding proteins and their role in translational regulation in plants.

Translation is a fundamental process for life that needs to be finely adapted to the energetical, developmental and environmental conditions; however, the molecular mechanisms behind such adaptation are not yet fully understood. By directly recognizing and binding to cis-elements present in their target mRNAs, RBPs govern all post-transcriptional regulatory processes. They orchestrate the balance between mRNA stability, storage, decay, and translation of their client mRNAs, playing a crucial role in the modulation of gene expression. In the last years exciting discoveries have been made regarding the roles of RBPs in fine-tuning translation. In this review, we focus on how these RBPs recognize their targets and modulate their translation, highlighting the complex and diverse molecular mechanisms implicated. Since the repertoire of RBPs keeps growing, future research promises to uncover new fascinating means of translational modulation, and thus, of gene expression.

Innovation and Integration Development of the Cultural Industry Based on Mapping Knowledge Domains.

In view of the less current user data of the cultural industry, its classification and presentation form are complex. This paper constructs the MKD of the cultural industry integration through the RDF graph model and realizes the distributed vector representation of cultural project semantic information by using the fine-tuning translation distance model TransH. The semantic information of cultural industry fusion is mapped to a continuous vector space, and the distributed vector representation of cultural projects is realized. The results show that it is helpful to accurately express the correlation between different regions and cultural types and to explore the data association and implicit relationship of innovation and integration development in the cultural industry.

A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics

ABSTRACT Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited for allowing a swift response to changing environments and are therefore considered pivotal during the first wave of stress adaptation. Previously, we identified an mRNA-derived 18 nucleotides long rancRNA (rancRNA_18) in Saccharomyces cerevisiae that rapidly downregulates protein synthesis during hyperosmotic stress. However, the molecular mechanism of action remained enigmatic. Here, we combine biochemical, genetic, transcriptome-wide and structural evidence, thus revealing rancRNA_18 as global translation inhibitor by targeting the E-site region of the large ribosomal subunit. Ribosomes carrying rancRNA_18 possess decreased affinity for A-site tRNA and impaired structural dynamics. Cumulatively, these discoveries reveal the mode of action of a rancRNA involved in modulating protein biosynthesis at a thus far unequalled precision.

Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution

Hepatitis E virus (HEV) is present in different species and ecological niches. It has been divided into 4 major mammalian genotypes. In this study, 3 new full-length genomes of swine HEV were sequenced and the results did not reveal any particular host determinant in comparison with human isolates belonging to the same genotype. Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution. Peculiar nucleotide bias was observed for A and C nucleotides in all HEV genotypes. Apart from the ORF1 hypervariable region and the ORF2/3 overlapping region, no nucleotide bias was observed between the 3 codon positions. CpG dinucleotides were also shown to be under-represented in HEV as in most RNA viruses. The effective number of codon used in HEV genome was high, indicating a lack of codon bias. Correspondence analysis of the relative synonymous codon usage was performed and demonstrated that evolution of HEV is not driven by geographical or host factors, but is representative of HEV phylogeny. These results confirm that HEV genome evolution is mainly based on mutational pressure. Natural selection, for instance involving fine-tuning translation kinetics and escape from the host immune system, may also play a role in shaping the HEV genome, particularly in the ORF1 hypervariable region and the ORF2/3 overlapping region. These regions might be involved in host restriction. Finally this study revealed the need to re-evaluate the possible subtyping classification.

A detailed comparative analysis on the overall codon usage patterns in Hepatitis A virus

Hepatitis A virus (HAV) is a hepatotropic member of the family Picornaviridae. HAV has several unique biological characteristics that distinguish it from other members of this family. Recent and previous studies revealed that codon usage plays a key role in HAV replication and evolution. In this study, the patterns of synonymous codon usage in HAV have been studied through multivariate statistical methods on 30 complete open reading frames (ORFs) from the available 30 full-length HAV sequences. Effective number of codons (ENC) indicates that the overall extent of codon usage bias in HAV genomes is significant. The relative dinucleotide abundances suggest that codon usage in HAV can also be strongly influenced by underlying biases in dinucleotide frequencies. These factors strongly correlated with the first major axis of correspondence analysis (COA) on relative synonymous codon usage (RSCU). The distribution of the HAV ORFs along the plane defined by the first two major axes in COA showed that different genotypes are located at different places in the plane, suggesting that HAV codon usage is also reflecting an evolutionary process. It has been very recently described that fine-tuning translation kinetics selection also contributes to codon usage bias of HAV. The results of these studies suggest that HAV genomic biases are the result of the co-evolution of genome composition, controlled translation kinetics and probably the ability to escape the antiviral cell responses.

How the Sequence of a Gene Can Tune Its Translation

Sixty-one codons specify 20 amino acids, offering cells many options for encoding a polypeptide sequence. Two new studies (Cannarrozzi et al., 2010; Tuller et al., 2010) now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning translation to increase the efficiency of protein synthesis.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.