Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites

Abstract

Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.

A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

“…Next, we compiled orthogonal, genome-wide evidence for putative post-transcriptional regulation. Specifically, we relocated one or more published transcript processing sites (TPS) within at least 966 protein-coding genes (37% of all protein-coding genes) (47), mapped cis-acting asRNAs for 536 genes (46), and determined that 166 genes were differentially expressed upon deletion of one out of 12 RNases predicted within the genome (VNG_2099C; here onwards “RNase_2099C”) (21) (File S2). To characterize the role of SmAP1 (VNG_1496G) in H. salinarum NRC-1, epitope-tagged SmAP1-RNA complexes were co-immunoprecipitated from late-exponential phase cultures from standard growth conditions (Figure S1), and transcriptome-wide binding locations of SmAP1 were mapped by enrichment of sequenced transcripts (RIP-Seq; see Methods).…”

“…Chromosome, pNRC100, and pNRC200 show the replicon location of each gene within the genome. The presence of SmAP1 binding, antisense RNAs (asRNA) (46), and putative endoribonuclease-generated transcript processing sites (TPS) (47) are indicated in corresponding tracks. The 2099 track shows log 2 fold change (LFC) of transcript levels in the RNAse_2099C null mutant (Δ VNG_2099C ) relative to the parent Δ ura3 strain (21).…”

“…We collected antisense RNA (asRNA) data from Table S4 of (46). We obtained transcript processing sites (TPS) from Table S1 of (47).…”

“…However, the transcriptional regulatory network by itself or the half-lives of all transcripts (43) did not fully explain the complex relationship between absolute and relative abundance of transcripts and proteins across different environmental contexts (44, 45), suggesting an important role for post-transcriptional regulation. Indeed, prior studies have uncovered evidence for the potential of extensive post-transcriptional regulation in H. salinarum NRC-1, including the presence of a strikingly large number of regulatory elements within coding sequences (3) that leads to widespread conditional splitting of at least 40% of all operons into multiple overlapping transcriptional units (5), presence of asRNAs for 22% of all genes (46), differential regulation of 23 transcripts in an RNase knockout background (21), and extensive transcript processing sites (TPS) across 43% of all coding sequences (47).…”

“…Through integrated analysis of a new transcriptome-wide map of SmAP1 binding located with RNA immunoprecipitation sequencing (RIP-Seq), global differential regulation of transcripts upon deletion of an RNase (VNG_2099C) implicated in acclimation to salinity change (21), and locations of asRNAs and TPS (46, 47), we have generated a genome-scale atlas that has discovered that 54% of all protein-coding genes in H. salinarum NRC-1 are targeted by multiple mechanisms for putative post-transcriptional regulation. Interestingly, 20% of all protein-coding genes are likely post-transcriptionally regulated in combinatorial schemes involving SmAP1, asRNAs, and RNase.…”