Widespread occurrence ofN⁶-methyladenosine in bacterial mRNA

Abstract

N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent discoveries of demethylases and specific binding proteins of m6A as well as m6A methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this RNA modification. Although m6A is present in the ribosomal RNA of bacteria, its occurrence in mRNA still remains elusive. Here, we have employed ultra-high pressure liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QQQ-MS/MS) to calculate the m6A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m6A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m6A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved m6A pattern that is distinct from those in eukaryotes. Most m6A peaks are located inside open reading frames and carry a unique consensus motif of GCCAU. Functional enrichment analysis of bacterial m6A peaks indicates that the majority of m6A-modified genes are associated with respiration, amino acids metabolism, stress response and small RNAs, suggesting potential functional roles of m6A in these pathways.

RNase E and RNase J are needed for S-adenosylmethionine homeostasis in Sinorhizobium meliloti

“…As a control we used RNA from E. coli, for which we determined 0.3 % m 6 A (Fig. 3d), a value very similar to the recently determined m 6 A-content of E. coli mRNA [71]. The presence of m 6 A in S. meliloti was not analysed previously.…”

“…Recently, methylated mRNAs and sRNAs were detected both in Eukarya and in Bacteria, and it was proposed that this may represent an additional level of posttranscriptional gene regulation [71,75]. In contrast to the nucleotide modification at defined tRNA and rRNA positions, only a small portion of the sRNA and mRNA molecules are modified [71]. We speculate that the aberrant electrophoretic behaviour of sRNAs from the mutants is because of uncontrolled methylation due to increased cellular SAM concentrations.…”

“…Nucleotide modifications such as methylation are important for stable secondary and tertiary structures and specific functions of rRNAs and tRNAs [74]. Recently, methylated mRNAs and sRNAs were detected both in Eukarya and in Bacteria, and it was proposed that this may represent an additional level of posttranscriptional gene regulation [71,75]. In contrast to the nucleotide modification at defined tRNA and rRNA positions, only a small portion of the sRNA and mRNA molecules are modified [71].…”

“…(d) Content (in %) of m 6 A in RNA of the indicated strains. E. coli DH5a was used as control [71]. strain 2011rnj (pWBrnj) was first grown without IPTG overnight and diluted to an OD 600 of 0.05.…”

The dual role of N6‐methyladenosine modification of RNAs is involved in human cancers

“…They are N6‐methyladenosine (m 6 A), N7‐methylguanosine, 5‐methylcytosine and N1‐methyladenosine, etc . Recent studies have illustrated that m 6 A modification is a highly abundant and conservative RNA modification in eukaryotic cells 5, 6. In addition, changes in m 6 A modification are observed to be involved in multiple cellular processes, which may have impacts on several human diseases 7, 8.…”