Class I and class II lysyl‐tRNA synthetase mutants and the genetic encoding of pyrrolysine in Methanosarcina spp.

  title={Class I and class II lysyl‐tRNA synthetase mutants and the genetic encoding of pyrrolysine in Methanosarcina spp.},
  author={Anirban Mahapatra and Gayathri Rajaram Srinivasan and Kerstin Richter and Andrew Meyer and Tanja Lienard and Jun Kai Zhang and Gang Zhao and Patrick T. Kang and Michael K. Chan and Gerhard Gottschalk and William W. Metcalf and Joseph Adrian Krzycki},
  journal={Molecular Microbiology},
Methanosarcina spp. begin methanogenesis from methylamines with methyltransferases made via the translation of UAG as pyrrolysine. In vitro evidence indicates two possible routes to pyrrolysyl‐tRNAPyl. PylS ligates pyrrolysine to tRNAPyl. Alternatively, class I and class II lysyl‐tRNA synthetases (LysRS1 and LysRS2) together form lysyl‐tRNAPyl, a potential intermediate to pyrrolysyl‐tRNAPyl. The unusual possession of both LysRS1 and LysRS2 by Methanosarcina spp. may also reflect differences in… 

Translation of UAG as Pyrrolysine

Pyrrolysine incorporation appears to occur to some extent by amber suppression on a genome-wide basis in methanogenic Archaea, and some methanogen genomes encode additional homologs of elongation and release factors, however, their limited distribution suggests at best a nonessential role in enhancing UAG translation as pyrrolesine.

Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs.

Structural diversity and protein engineering of the aminoacyl-tRNA synthetases.

A suggested general approach to rational design is presented, which should yield insight into the identities of the protein-RNA motifs at the heart of the genetic code, while also offering a basis for improving the catalytic properties of engineered tRNA synthetases emerging from genetic selections.

Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNASec)

The anti-codon table of the plant tRNA will enable to understand the synonymous codon usage of the plants kingdom and can be very helpful to understand which codon is preferred over other during the translation.

Genetic manipulation of Methanosarcina spp.

An overview of methods for genetic manipulation of Methanosarcina spp.

Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea

This paper summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales.

This review presents the advantages and disadvantages of working with each archaeal group, gives an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

An updated genome-scale metabolic model of M. acetivorans is introduced that is capable of correctly predicting the knockout outcomes for 27 out of 28 gene-protein-reaction associations and establishing improved predictions of growth yields on native substrates.

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

This model represents the most comprehensive up-to-date effort to catalogue methanogenic metabolism and correctly recapitulates metabolic pathway usage patterns of M. acetivorans such as the indispensability of flux through methanogenesis for growth on acetate and methanol and the unique biochemical characteristics under growth on carbon monoxide.

Top-down proteomics reveals novel protein forms expressed in methanosarcina acetivorans



Characterization of a Methanosarcina acetivorans mutant unable to translate UAG as pyrrolysine

The phenotype of ΔppylT reveals the deficiency in methylamine metabolism expected of a Methanosarcina species unable to decode UAG codons as pyrrolysine, but also indicates that loss of pylT does not compromise growth on other substrates.

Divergence in Noncognate Amino Acid Recognition between Class I and Class II Lysyl-tRNA Synthetases*

Differences in resistance to naturally occurring noncognate amino acids suggest the distribution of LysRS1 and LysRS2 contributes to quality control during protein synthesis.

A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases.

The proposed amino acid sequence is similar to open reading frames of unassigned function in both Methanobacterium thermoautotrophicum and Methanococcus jannaschii but is unrelated to canonical LysRS proteins reported in eubacteria, eukaryotes, and the crenarchaeote Sulfolobus solfataricus.

Context-dependent anticodon recognition by class I lysyl-tRNA synthetases.

Competition between unrelated aminoacyl-tRNA synthetases for overlapping anticodon sequences is a determinant of the phylogenetic distribution of extant synthetase families, and patterns of competition provide a basis for the two separate horizontal gene transfer events hypothesized in the evolution of the class I lysyl-t RNA synthetased.

Substrate recognition by class I lysyl-tRNA synthetases: a molecular basis for gene displacement.

Genes encoding both an archaeal and a bacterial class I enzyme were able to rescue an Escherichia coli strain deficient in LysRS, indicating their ability to functionally substitute for a class II LysRS in vivo.

Functional Annotation of Class I Lysyl-tRNA Synthetase Phylogeny Indicates a Limited Role for Gene Transfer

Results suggest that despite its comparative rarity the distribution of class I LysRS conforms to the canonical archaeal-bacterial division, and the only exception appears to be the horizontal transfer of classI LysRS from a pyrococcal progenitor to a limited number of bacteria.

Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code

Diversity of the aminoacyl-tRNA synthetases prevents infiltration of the genetic code by noncanonical amino acids, thereby providing a natural reservoir of potential antibiotic resistance.

Discrimination of cognate and noncognate substrates at the active site of class I lysyl-tRNA synthetase.

Several of the LysRS1 variants were found to be more specific than the wild type with respect to noncognate amino acid recognition but less efficient in cognate aminoacylation, in contrast to LysRS2 which is considerably more effective in catalysis but is less specific than its class I counterpart.

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms

A phylogenetic approach was applied for determining the extent and origin of LGT in prokaryotic LysRS, and the likely origins of the laterally transferred genes of LysRS1 and LysRS2 were evaluated.