Temperature‐dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii

Abstract

Methanococcoides burtonii is a member of the Archaea that was isolated from Ace Lake in Antarctica and is a valuable model for studying cold adaptation. Low temperature transcriptional regulation of global gene expression, and the arrangement of transcriptional units in cold-adapted archaea has not been studied. We developed a microarray for determining which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Approximately 55% of genes were found to be arranged in operons that range in length from 2 to 23 genes, and mRNA abundance tended to increase with operon length. Analysing microarray data previously obtained by others for Halobacterium salinarum revealed a similar correlation between operon length and mRNA abundance, suggesting that operons may play a similar role more broadly in the Archaea. More than 500 genes were differentially expressed at levels up to ≈ 24-fold. A notable feature was the upregulation of genes involved in maintaining RNA in a state suitable for translation in the cold. Comparison between microarray experiments and results previously obtained using proteomics indicates that transcriptional regulation (rather than translation) is primarily responsible for controlling gene expression in M. burtonii. In addition, certain genes (e.g. involved in ribosome structure and methanogenesis) appear to be regulated post-transcriptionally. This is one of few experimental studies describing the genome-wide distribution and regulation of operons in archaea.

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

“…Remarkably, 84 genes in R15 possessed cold-responsive selection of gTSSs and promoters and would be expected to transcribe different mRNA isoforms with alternative 5′ UTRs at different temperatures, like the Hsp20 genes. Though a number of transcriptomic studies on prokaryotes have indicated that many genes are differentially expressed in the cold, a conserved motif or cold box has not been found proximal to the prompters23410. Therefore, it is believed that post-transcriptional regulation, including mRNA stability and translation efficiency, make major contributions to cold adaptation of living organisms7.…”

“…However, the mechanisms of cold adaptation used by these psychrophilic Archaea have not been well studied except for the Antarctic Methanococcoides burtonii 234, probably because only a few cold-adaptive Archaea have been cultured. In this study, a domesticated psychrophilic methanogen Methanolobus psychrophilus R15 isolated from the cold Zoige wetland on Tibetan Plateau5, was used to explore archaeal cold adaptation mechanisms.…”

Psychrophilic Enzymes: From Folding to Function and Biotechnology

“…More specifically, the synthesis of ribosomal proteins and of RNA chaperones [96, 97] appears to be stimulated at low temperature [43, 55, 75, 78–81, 84]. In the archaeon M. burtonii , a notable feature is the upregulation of genes involved in maintaining RNA in a state suitable for translation and for enabling translation initiation [86]. At the genome level, an interesting observation is the relatively high number of rRNA genes and of tRNA genes (up to 106 genes, sometimes organized in long runs of repeated sequences), at least in P. haloplanktis [39], C. psychrerythraea [40], and P. ingrahamii [42].…”

Metabolomic Analysis of Cold Acclimation of Arctic Mesorhizobium sp. Strain N33

“…Most cold adaptation comprehensive studies were mainly performed by applying high-throughput genome sequencing [4], [5], [11] and other omics technologies such as proteomics [13], [14] and transcriptomics [15]. In E. coli , it has been shown that under different perturbations (cold, heat, lactose diauxie, and oxidative stress) the metabolite profiles are much more stress-specific when compared with transcriptomic changes [16].…”