Influence of Temperature on tRNA Modification in Archaea: Methanococcoides burtonii (Optimum Growth Temperature [ T _opt ], 23°C) and Stetteria hydrogenophila ( T _opt , 95°C)

Abstract

We report the first study of tRNA modification in psychrotolerant archaea, specifically in the archaeon Methanococcoides burtonii grown at 4 and 23°C. For comparison, unfractionated tRNA from the archaeal hyperthermophile Stetteria hydrogenophila cultured at 93°C was examined. Analysis of modified nucleosides using liquid chromatography-electrospray ionization mass spectrometry revealed striking differences in levels and identities of tRNA modifications between the two organisms. Although the modification levels in M. burtonii tRNA are the lowest in any organism of which we are aware, it contains more than one residue per tRNA molecule of dihydrouridine, a molecule associated with maintenance of polynucleotide flexibility at low temperatures. No differences in either identities or levels of modifications, including dihydrouridine, as a function of culture temperature were observed, in contrast to selected tRNA modifications previously reported for archaeal hyperthermophiles. By contrast, S. hydrogenophila tRNA was found to contain a remarkable structural diversity of 31 modified nucleosides, including nine methylated guanosines, with eight different nucleoside species methylated at O-2 of ribose, known to be an effective stabilizing motif in RNA. These results show that some aspects of tRNA modification in archaea are strongly associated with environmental temperature and support the thesis that posttranscriptional modification is a universal natural mechanism for control of RNA molecular structure that operates across a wide temperature range in archaea as well as bacteria.The posttranscriptional processing of tRNA produces a diverse wealth of modified nucleotides (29,30,41), most of which occur at conserved RNA sequence locations in all three phylogenetic domains (4, 45). Many of the functional roles of these modifications, in addition to other factors, such as G-C and metal ion content, are associated with their influence on secondary and tertiary structures in RNA (1, 14, 43). Thus, RNA modifications offer an important means of mediation of RNA structure across the entire temperature range of natural habitats for microorganisms: in low-temperature organisms, a degree of conformational flexibility in tRNA must be maintained during translation, while in the case of thermophiles, protection against environmental temperatures which may exceed the melting point of unmodified base-paired stems is required (27, 50). For example, it has been shown with increases in growth temperature for a single species (2, 27, 51) or through comparison of closely related organisms growing optimally at different temperatures (32) that selected stabilizing tRNA modifications are associated with increased culture temperature. By contrast, in bacterial psychrophiles, low levels of modification have been reported, with the exception of dihydrouridine (10), a modified tRNA nucleoside which is associated with enhancement and maintenance of molecular flexibility at low temperatures (12).From a phylogenetic perspective, it is interesting t...

The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs

“…Dihydrouridine is known to cause increased flexibility in loops that contain it because of the propensity of dihydrouridine residues to adopt the C2Ј-endo conformation (38). Consistent with this increased flexibility, dihydrouridine is found in high levels in cold-adapted (psychrophilic) bacteria and archaea but not in thermophilic archaea (4,39). Dihydrouridine modification of tRNA also causes less efficient hybridization of oligonucleotides to regions of tRNA with dihydrouridine (16).…”

“…Consistent with its abundance, dihydrouridine is found widely in tRNAs of eubacteria and eukaryotes (3), although it is less common in archaebacteria (4). Furthermore, dihydrouridines are found at one or more of multiple different positions in tRNA, the vast majority of which are in the D loop at positions 16, 17, 20, 20a, and 20b and at the base of the variable arm at position 47.…”

Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures

“…Given the abundance and diversity of Archaea in cold environments (Karner et al 2001;Feller & Gerday 2003), especially in the oceans, our understanding of the genetics and physiology of coldadapted Archaea is surprisingly scarce . Some insights have been obtained on the level of protein structure and function (Schleper et al 1997;Thomas et al 2001;Siddiqui et al 2002), gene regulation (Lim et al 2000;DasSarma 2006), tRNA modification (Noon et al 2004), membrane lipid composition (Nichols et al 2004 ;Gibson et al 2005), proteomics (Goodchild et al 2004a(Goodchild et al , b, 2005Saunders et al 2005) and genomics (Saunders et al 2003) by studying coldadapted Archaea.…”

Biosynthesis of 4-Thiouridine in tRNA in the Methanogenic Archaeon Methanococcus maripaludis

“…The presence of s 4 U in archaeal tRNAs has been demonstrated in Thermoproteus neutrophilus (40) and a number of methanogenic archaea, including Methanococcus vannielii, Methanococcus maripaludis, Methanothermococcus thermolithotrophicus, Methanocaldococcus igneus, Methanocaldococcus jannaschii, and Methanococcoides burtonii (41)(42)(43). However, some fundamental questions remain about the mechanism of sulfur transfer to generate s 4 U in archaea.…”