Selenocysteine-independent suppression of UGA codons in the archaeon Methanococcus maripaludis

Seyhan, Deniz; Jehmlich, Nico; Bergen, Martin von; Fersch, Julia; Rother, Michael

doi:10.1016/j.bbagen.2015.07.009

Cited by 11 publications

(6 citation statements)

References 54 publications

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“…Consequently, tRNA ReC genes in bacteria may have originated as an alternative mechanism to recode UGA with Cys. In archaea, near-cognate UGA suppression by Cys-tRNA Cys GCA was observed in selenoprotein translation when tRNA Sec was deleted [22], while E. coli tolerates wobble decoding of UGG by Sec, a process that requires the presence of the SECIS element [23]. Therefore, although Pelotomaculum sp.…”

Section: Discussionmentioning

confidence: 99%

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA^Cysand elongation factor SelB

et al. 2018

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In many organisms, the UGA stop codon is recoded to insert selenocysteine (Sec) into proteins. Sec incorporation in bacteria is directed by an mRNA element, known as the Sec-insertion sequence (SECIS), located downstream of the Sec codon. Unlike other aminoacyl-tRNAs, Sec-tRNA is delivered to the ribosome by a dedicated elongation factor, SelB. We recently identified a series of tRNA-like tRNA genes distributed across Bacteria that also encode a canonical tRNA. These tRNAs contain sequence elements generally recognized by cysteinyl-tRNA synthetase (CysRS). While some of these tRNAs contain a UCA Sec anticodon, most have a GCA Cys anticodon. tRNA with GCA anticodons are known to recode UGA codons. Here we investigate the clostridial Desulfotomaculum nigrificans tRNA-like tRNA, and show that this tRNA is acylated by CysRS, recognized by SelB, and capable of UGA recoding with Cys in Escherichia coli. We named this non-canonical group of tRNA as 'tRNA' (Recoding with Cys). We performed a comprehensive survey of tRNA genes to establish their phylogenetic distribution, and found that, in a particular lineage of clostridial Pelotomaculum, the Cys identity elements of tRNA had mutated. This novel tRNA, which contains a UCA anticodon, is capable of Sec incorporation in E. coli, albeit with lower efficiency relative to Pelotomaculum tRNA. We renamed this unusual tRNA derived from tRNA as 'tRNA' (Recoding with Sec). Together, our results suggest that tRNA and tRNA may serve as safeguards in the production of selenoproteins and - to our knowledge - they provide the first example of programmed codon-anticodon mispairing in bacteria.

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Section: Discussionmentioning

confidence: 99%

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA^Cysand elongation factor SelB

et al. 2018

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“…Genomes of various archaea lacking selenoproteins have been found to contain SelB-like elongation factors . Additionally, several cases of codon and tRNA flexibility have been documented for incorporation of selenocysteine. − Methanogenic archaea exhibit the unique feature of not directly incorporating cysteine but instead relying on SepRS and SepCysS to modify phosphoserine bound to Cys-tRNA. , This could imply that certain archaea use promiscuous tRNAs that can incorporate both selenocysteine and cysteine without the need for a stop codon and Sec-specific tRNAs. ,, A recent observation was made in Escherichia coli, where random selenocysteine “misincorporation” occurred without the UGA codon . In this case, misincorporation was deemed to be random.…”

Section: Resultsmentioning

confidence: 99%

The Selenoproteome as a Dynamic Response Mechanism to Oxidative Stress in Hydrogenotrophic Methanogenic Communities

Kleikamp,

Palacios,

Kofoed

et al. 2024

Environ. Sci. Technol.

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Methanogenesis is a critical process in the carbon cycle that is applied industrially in anaerobic digestion and biogas production. While naturally occurring in diverse environments, methanogenesis requires anaerobic and reduced conditions, although varying degrees of oxygen tolerance have been described. Microaeration is suggested as the next step to increase methane production and improve hydrolysis in digestion processes; therefore, a deeper understanding of the methanogenic response to oxygen stress is needed. To explore the drivers of oxygen tolerance in methanogenesis, two parallel enrichments were performed under the addition of H2/CO2 in an environment without reducing agents and in a redox-buffered environment by adding redox mediator 9,10-anthraquinone-2,7-disulfonate disodium. The cellular response to oxidative conditions is mapped using proteomic analysis. The resulting community showed remarkable tolerance to high-redox environments and was unperturbed in its methane production. Next to the expression of pathways to mitigate reactive oxygen species, the higher redox potential environment showed an increased presence of selenocysteine and selenium-associated pathways. By including sulfur-to-selenium mass shifts in a proteomic database search, we provide the first evidence of the dynamic and large-scale incorporation of selenocysteine as a response to oxidative stress in hydrogenotrophic methanogenesis and the presence of a dynamic selenoproteome.

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“…1 B). Large genome rearrangements are often found between two laboratories working with the same organisms (Periwal and Scaria 2015 ; Guérillot et al 2019 ; Liao et al 2022 ), but to ensure that the ~ 80 kbp deletion was not important for the transformation phenotype we observe, we compared the natural transformation efficiency of KC13 to J901, a variant of the sequenced strain (Seyhan et al 2015 ). After transformation and selection, we observed that both strains were capable of DNA uptake with a similar efficiency (Figure S1), therefore the deletion present in strain KC13 was not considered further.…”

Section: Resultsmentioning

confidence: 99%

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

et al. 2023

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Natural transformation, the process whereby a cell acquires DNA directly from the environment, is an important driver of evolution in microbial populations, yet the mechanism of DNA uptake is only characterized in bacteria. To expand our understanding of natural transformation in archaea, we undertook a genetic approach to identify a catalog of genes necessary for transformation in Methanococcus maripaludis. Using an optimized method to generate random transposon mutants, we screened 6144 mutant strains for defects in natural transformation and identified 25 transformation-associated candidate genes. Among these are genes encoding components of the type IV-like pilus, transcription/translation associated genes, genes encoding putative membrane bound transport proteins, and genes of unknown function. Interestingly, similar genes were identified regardless of whether replicating or integrating plasmids were provided as a substrate for transformation. Using allelic replacement mutagenesis, we confirmed that several genes identified in these screens are essential for transformation. Finally, we identified a homolog of a membrane bound substrate transporter in Methanoculleus thermophilus and verified its importance for transformation using allelic replacement mutagenesis, suggesting a conserved mechanism for DNA transfer in multiple archaea. These data represent an initial characterization of the genes important for transformation which will inform efforts to understand gene flow in natural populations. Additionally, knowledge of the genes necessary for natural transformation may assist in identifying signatures of transformation machinery in archaeal genomes and aid the establishment of new model genetic systems for studying archaea.

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Selenocysteine-independent suppression of UGA codons in the archaeon Methanococcus maripaludis

Cited by 11 publications

References 54 publications

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA^Cysand elongation factor SelB

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA^Cysand elongation factor SelB

The Selenoproteome as a Dynamic Response Mechanism to Oxidative Stress in Hydrogenotrophic Methanogenic Communities

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

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Selenocysteine-independent suppression of UGA codons in the archaeon Methanococcus maripaludis

Cited by 11 publications

References 54 publications

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNACysand elongation factor SelB

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNACysand elongation factor SelB

The Selenoproteome as a Dynamic Response Mechanism to Oxidative Stress in Hydrogenotrophic Methanogenic Communities

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

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Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA^Cysand elongation factor SelB

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA^Cysand elongation factor SelB