Abstract The degree to which codon usage can be explained by tRNA abundance in bacterial species is often inadequate, partly because differential approximated copy numbers. To better understand the coevolution between and usage, we provide a estimate of profiling mapped reads (tRNA tpm) using publicly available RNA Sequencing data. emphasize feasibility our approach, demonstrate that tpm consistent with abundances derived from fingerprinting experiments Escherichia coli , Bacillus subtilis...

Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade immune responses is important the effort control spread of infection. Two AVPs may shape viral genomes are zinc finger protein (ZAP) and apolipoprotein B mRNA editing enzyme-catalytic polypeptide-like 3 (APOBEC3). The former binds CpG dinucleotides facilitate degradation transcripts while latter frequently deaminates C into U...

Bacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in 5' UTR of mRNA and anti-SD (aSD) at free 3' end 16S rRNA (3' TAIL) due to: 1) SD/aSD binding location 2) affinity. In order to understand what makes an interaction optimal, we must define: terminus TAIL extent core aSD within TAIL. Our approach characterize these components Escherichia coli Bacillus subtilis involves mapping boundary mature using high-throughput RNA sequencing...

The 3' end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved selection and binding mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream codon an anti-SD (aSD) at ssu rRNA. Consequently, rRNA (3'TAIL) strongly conserved among bacterial species because change region may impact many protein-coding genes. Escherichia coli Bacillus subtilis differ their ends rRNA, being GAUCACCUCCUUA3' E....

ABSTRACT Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade immune responses is important the effort control spread of COVID-19. Two AVPs may shape viral genomes are zinc finger protein (ZAP) and apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (APOBEC3). The former binds CpG dinucleotides facilitate degradation transcripts while latter deaminates C into U...

We present an RNA-Seq based approach to map 3' end sequences of mature 16S rRNA (3' TAIL) in bacteria with single-base specificity. Our results show that TAILs are heterogeneous among species; they contain the core CCUCC anti-Shine-Dalgarno motif, but vary downstream lengths. Importantly, our findings rectify mis-annotated rRNAs 11 out 13 bacterial species studied herein (covering Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria, Tenericutes, and Spirochaetes). Furthermore,...