scholarly journals Codon Usage and Amino Acid Identity Are Major Determinants of MRNA Stability in Humans

2018 ◽  
Author(s):  
Megan E. Forrest ◽  
Ashrut Narula ◽  
Thomas J. Sweet ◽  
Daniel Arango ◽  
Gavin Hanson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Mrna Stability ◽  
Amino Acid Identity ◽  
Acid Identity

scholarly journals Codon usage and amino acid identity are major determinants of mRNA stability in humans

2018 ◽  
Author(s):  
Megan E. Forrest ◽  
Ashrut Narula ◽  
Thomas J Sweet ◽  
Daniel Arango ◽  
Gavin Hanson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Mrna Stability ◽  
Protein Sequence ◽  
Synonymous Codon ◽  
Amino Acid Identity ◽  
Mrna Degradation ◽  
Model Organisms ◽  
Mrna Levels ◽  
Acid Identity

mRNA degradation is a critical, yet poorly understood, aspect of gene expression. Previous studies demonstrate that codon content acts as a major determinant of mRNA stability in model organisms. In humans, the importance of open reading frame (ORF)-mediated regulation remains unclear. Here, we globally analyzed mRNA stability for both endogenous and human ORFeome collection mRNAs in human cells. Consistent with previous studies, we observed that synonymous codon usage impacts human mRNA decay. Unexpectedly, amino acid identity also acts as a driver of translation-dependent decay, meaning that primary protein sequence dictates overall mRNA levels and, consequently, protein abundance. Both codon usage and amino acid identity affect translational elongation rate to varying degrees in distinct organisms, with the net result being sensed by mRNA degradation machinery. In humans, interplay between ORF- and UTR-mediated control of mRNA stability may be critical to offset this fundamental relationship between protein sequence and mRNA abundance.

scholarly journals Translation elongation and mRNA stability are coupled through the ribosomal A-site

2018 ◽  
Author(s):  
Gavin Hanson ◽  
Najwa Alhusaini ◽  
Nathan Morris ◽  
Thomas Sweet ◽  
Jeff Coller
Keyword(s):  
Amino Acid ◽  
Mrna Stability ◽  
Transcript Level ◽  
Amino Acid Identity ◽  
Elongation Rate ◽  
Ribosome Profiling ◽  
Translation Elongation ◽  
Acid Identity ◽  
Optimal Codons ◽  
A Site

AbstractMessenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in eukaryotic cells. Previous work by us and others has shown that codon identity exerts a powerful influence on mRNA stability. In Saccharomyces cerevisiae, studies using a handful of reporter mRNAs show that optimal codons increase translation elongation rate, which in turn increase mRNA stability. However, a direct link between elongation rate and mRNA stability has not been established across the entire yeast transcriptome. In addition, there is evidence from work in higher eukaryotes that amino acid identity influences mRNA stability, raising the question as to whether the impact of translation elongation on mRNA decay is at the level of tRNA decoding, amino acid incorporation, or some combination of each. To address these questions, we performed ribosome profiling of wildtype yeast. In good agreement with other studies, our data showed faster codon-specific elongation over optimal codons and faster transcript-level elongation correlating with transcript optimality. At both the codon-level and transcript-level, faster elongation correlated with increased mRNA stability. These findings were reinforced by showing increased translation efficiency and kinetics for a panel of 11 HIS3 reporter mRNAs of increasing codon optimality. While we did observe that elongation measured by ribosome profiling is composed of both amino acid identity and synonymous codon effects, further analyses of these data establish that A-site tRNA decoding rather than other steps of translation elongation is driving mRNA decay in yeast.

scholarly journals A50 Whole-genome sequencing of African swine fever isolates from Sardinia

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
C Torresi ◽  
F Granberg ◽  
L Bertolotti ◽  
A Oggiano ◽  
B Colitti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Temporal Distribution ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Genotype I ◽  
Acid Identity ◽  
Wide Range ◽  
Intergenic Sequences ◽  
Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

Characterization and Induction of Two Cytochrome P450 Genes, CYP6AE28 and CYP6AE30, in Cnaphalocrocis medinalis: Possible Involvement in Metabolism of Rice Allelochemicals

2010 ◽  
Vol 65 (11-12) ◽  
pp. 719-725 ◽  
Author(s):  
Xiaoli Liu ◽  
Jun Chen ◽  
Zhifan Yang
Keyword(s):  
Amino Acid ◽  
Rice Variety ◽  
Amino Acid Identity ◽  
Cnaphalocrocis Medinalis ◽  
Amino Acid Residues ◽  
Acid Identity ◽  
Rice Leaf Folder ◽  
Cytochrome P450 Genes ◽  
Molecular Masses ◽  
Lepidoptera Pyralidae

Two cDNAs specific for P450 genes, CYP6AE28 and CYP6AE30, have been isolated from the rice leaf folder Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae). Both cDNApredicted proteins have 504 amino acid residues in length, but with molecular masses of 60177 Dalton for CYP6AE28 and 60020 Dalton for CYP6AE30, and theoretical pI values of 8.49 for CYP6AE28 and 8.56 for CYP6AE30, respectively. Both putative proteins contain the conserved structural and functional domains characteristic of all CYP6 members. CYP6AE28 and CYP6AE30 show 52% amino acid identity to each other; both of them have 49 - 56% identities with CYP6AE1, Cyp6ae12, and CYP6AE14. Phylogenetic analysis showed that the two P450s are grouped in the lineage containing some of the CYP6AE members, CYP6B P450s and CYP321A1. The transcripts of CYP6AE28 and CYP6AE30 were found to be induced in response to TKM-6, a rice variety with high resistance to C. medinalis. The results suggest that the two P450s may play important roles in adaptation to the host plant rice. This is the first report of P450 genes cloned in C. medinalis

scholarly journals PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Laurent Poirel ◽  
Mattia Palmieri ◽  
Michael Brilhante ◽  
Amandine Masseron ◽  
Vincent Perreten ◽  
...  
Keyword(s):  
Amino Acid ◽  
Pseudomonas Fluorescens ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Chicken Meat ◽  
The Novel ◽  
Content Type ◽  
Acid Identity ◽  
Carbapenem Resistant ◽  
Encoding Genes

ABSTRACT A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola. The blaPFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.

Comparative sequence analysis of morbillivirus receptors and its implication in host range expansion

2019 ◽  
Vol 65 (11) ◽  
pp. 783-794
Author(s):  
Ajay Kumar Yadav ◽  
Kaushal Kishor Rajak ◽  
Mukesh Bhatt ◽  
Ashok Kumar ◽  
Soumendu Chakravarti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Host Range ◽  
Range Expansion ◽  
Small Ruminants ◽  
Amino Acid Identity ◽  
Amino Acid Residues ◽  
Binding Region ◽  
Acid Identity ◽  
Host Range Expansion ◽  
High Amino Acid

SLAM (CD150) and nectin-4 are the major morbillivirus receptors responsible for virus pathogenesis and host range expansion. Recently, morbillivirus infections have been reported in unnatural hosts, including endangered species, posing a threat to their conservation. To understand the host range expansion of morbilliviruses, we generated the full-length sequences of morbillivirus receptors (goat, sheep, and dog SLAM, and goat nectin-4) and tried to correlate their role in determining host tropism. A high level of amino acid identity was observed between the sequences of related species, and phylogenetic reconstruction showed that the receptor sequences of carnivores, marine mammals, and small ruminants grouped separately. Analysis of the ligand binding region (V region; amino acid residues 52–136) of SLAM revealed high amino acid identity between small ruminants and bovine SLAMs. Comparison of canine SLAM with ruminants and non-canids SLAM revealed appreciable changes, including charge alterations. Significant differences between feline SLAM and canine SLAM have been reported. The binding motifs of nectin-4 genes (FPAG motif and amino acid residues 60, 62, and 63) were found to be conserved in sheep, goat, and dog. The differences reported in the binding region may be responsible for the level of susceptibility or resistance of a species to a particular morbillivirus.

scholarly journals Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Sara Kleindienst ◽  
Karuna Chourey ◽  
Gao Chen ◽  
Robert W. Murdoch ◽  
Steven A. Higgins ◽  
...  
Keyword(s):  
Amino Acid ◽  
Reductive Dechlorination ◽  
Bond Cleavage ◽  
Amino Acid Identity ◽  
Methyl Group ◽  
Acid Identity ◽  
Group Transfer ◽  
Degrading Bacterium ◽  
Chlorine Bond ◽  
Methyl Group Transfer

ABSTRACTDichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader “CandidatusDichloromethanomonas elyunquensis” strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM’s genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase ofDehalococcoides mccartyistrain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase ofDehalobactersp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCENaturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader “CandidatusDichloromethanomonas elyunquensis” strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacteriumDehalobacterium formicoaceticumand “CandidatusDichloromethanomonas elyunquensis” strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.

scholarly journals Genome of Lumpy Skin Disease Virus

2001 ◽  
Vol 75 (15) ◽  
pp. 7122-7130 ◽  
Author(s):  
E. R. Tulman ◽  
C. L. Afonso ◽  
Z. Lu ◽  
L. Zsak ◽  
G. F. Kutish ◽  
...  
Keyword(s):  
Amino Acid ◽  
Host Range ◽  
Disease Virus ◽  
Skin Disease ◽  
Amino Acid Identity ◽  
Lower Percentage ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus ◽  
Acid Identity ◽  
Viral Virulence

ABSTRACT Lumpy skin disease virus (LSDV), a member of the capripoxvirus genus of the Poxviridae, is the etiologic agent of an important disease of cattle in Africa. Here we report the genomic sequence of LSDV. The 151-kbp LSDV genome consists of a central coding region bounded by identical 2.4 kbp-inverted terminal repeats and contains 156 putative genes. Comparison of LSDV with chordopoxviruses of other genera reveals 146 conserved genes which encode proteins involved in transcription and mRNA biogenesis, nucleotide metabolism, DNA replication, protein processing, virion structure and assembly, and viral virulence and host range. In the central genomic region, LSDV genes share a high degree of colinearity and amino acid identity (average of 65%) with genes of other known mammalian poxviruses, particularly suipoxvirus, yatapoxvirus, and leporipoxviruses. In the terminal regions, colinearity is disrupted and poxvirus homologues are either absent or share a lower percentage of amino acid identity (average of 43%). Most of these differences involve genes and gene families with likely functions involving viral virulence and host range. Although LSDV resembles leporipoxviruses in gene content and organization, it also contains homologues of interleukin-10 (IL-10), IL-1 binding proteins, G protein-coupled CC chemokine receptor, and epidermal growth factor-like protein which are found in other poxvirus genera. These data show that although LSDV is closely related to other members of the Chordopoxvirinae, it contains a unique complement of genes responsible for viral host range and virulence.

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