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

Ricardo Z. N. Vêncio,Amr Galal Abd El-Raheem Ibrahim,Tie Koide,Alan P. R. Lorenzetti

doi:10.3390/genes12071018

Ricardo Z. N. Vêncio, Amr Galal Abd El-Raheem Ibrahim + Show 2 more

Open Access

https://doi.org/10.3390/genes12071018

Copy DOI

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.

Highlights

Post-transcriptional processing of mRNAs is an important regulatory mechanism of gene expression [1,2]
We identified transcript processing sites (TPS) in H. salinarum NRC-1 and H. volcanii
Since H. salinarum and H. volcanii are organisms that show important lifestyle differSince H. salinarum and H. volcanii are organisms that show important lifestyle ences, we evaluated the orthologous genes with internal TPS present in one but not differences, we evaluated the orthologous genes with internal TPS present in one but in the other, with special attention to salt homeostasis related genes, which may indicate not in the other, with special attention to salt homeostasis related genes, which may differential post-transcriptional regulatory strategies

Summary

Introduction

Post-transcriptional processing of mRNAs is an important regulatory mechanism of gene expression [1,2]. Decay and turnover rates have been measured at the systems-level [5], there are no comprehensive genome-wide maps of processing sites comparable to that available for the methanogenic psychrophilic archaeon Methanolobus psychrophilus [6] or the hyperthermophile Pyrococcus furiosus [7], which would address the problem from the RNA perspective. Halophile research would benefit from the availability of such processing site maps for its two main model organisms, Halobacterium salinarum and Haloferax volcanii. Halobacterium salinarum is a photosynthesizing archaeon that does not rely on either chlorophyll or bacteriochlorophyll [8]. It shows no turgor pressure and uses the “salt-in”

Results

Discussion

Conclusion