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

Mahapatra, Anirban; Srinivasan, Gayathri; Richter, Kerstin B.; Meyer, A.W.; Lienard, Tanja; Zhang, Jun Kai; Zhao, Gang; Kang, Patrick T.; Chan, Michael K.; Gottschalk, Gerhard; Metcalf, William W.; Krzycki, Joseph A.

doi:10.1111/j.1365-2958.2007.05740.x

Cited by 16 publications

(9 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A striking feature in Methanosarcina is that the methylamine methyltransferases contain pyrrolysine, the 22nd genetically encoded amino acid. Genetic studies have helped determine the function of a dedicated tRNA and aminoacyl-tRNA synthetase in pyrrolysyl-tRNA synthesis (Mahapatra et al, 2006(Mahapatra et al, , 2007. Genetic studies in Methanococcus have addressed a wide range of questions.…”

Section: Discoveries and Recent Progressmentioning

confidence: 99%

Model organisms for genetics in the domain Archaea: methanogens, halophiles,ThermococcalesandSulfolobales

et al. 2011

View full text Add to dashboard Cite

The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.

show abstract

Section: Discoveries and Recent Progressmentioning

confidence: 99%

Model organisms for genetics in the domain Archaea: methanogens, halophiles,ThermococcalesandSulfolobales

et al. 2011

View full text Add to dashboard Cite

show abstract

“…Both ideas proved incorrect. Loss of the genes encoding one or the other LysRS from Methanosarcina acetivorans does not affect UAG translation as pyrrolysine [105], and the substrate of PylS is not lysine, but pyrrolysine itself [106]. Quite unexpected by analogy to selenocysteine, pyrrolysine is not made on tRNA Pyl , but as a free amino acid which is directly ligated to the tRNA (Figure 4).…”

Section: Pyrrolysine Synthesis and Incorporation Is Different Frommentioning

confidence: 99%

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

Rother

Krzycki

2010

Archaea

Self Cite

View full text Add to dashboard Cite

Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and 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.

show abstract

“…While not the only methanogenic archaeon, it is arguably one of the most metabolically diverse, with a large genome of 5.7 Mb harboring three distinct methanogenesis pathways [5]. Furthermore, M. acetivorans also contain pyrrolysine in methyltransferases [6, 7]. This 22nd amino acid was discovered first in a similar methanogen, Methanosarcina barkeri [8].…”

mentioning

confidence: 99%

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

Ferguson

Wenger

Metcalf

et al. 2009

J. Am. Soc. Mass Spectrom.

Self Cite

View full text Add to dashboard Cite

Using both automated nanospray and online liquid chromatography mass spectrometry LC-MS strategies, 99 proteins have been newly identified by top-down tandem mass spectrometry (MS/MS) in Methanosarcina acetivorans, the methanogen with the largest known genome [5.7 mega base pairs (Mb)] for an Archaeon. Because top-down MS/MS was used, 15 proteins were detected with mispredicted start sites along with an additional five from small open reading frames (SORFs). Beyond characterization of these more common discrepancies in genome annotation, one SORF resulted from a rare start codon (AUA) as the initiation site for translation of this protein. Also, a methylation on a 30S ribosomal protein (MA1259) was localized to Pro59 -Val69, contrasting sharply from its homologue in Escherichia coli (rp S12) known to harbor an unusual ␤-thiomethylated aspartic acid residue. C omprising one of the three domains of life, the Archaea utilize unique metabolic pathways to survive in seemingly inhospitable environments such as high salt or extremes of temperature and pH [1,2]. Archaea share many similarities to both bacteria and eukaryotes, but are a separate form of life based on now classic studies of 16S rRNA [3]. The Archaea are an important component of the biosphere, in part due to the production of methane as a byproduct that contributes to the global carbon cycle and has been used in commercial energy-producing applications [2,4,5]. Methanosarcina acetivorans is an especially diverse methanogen in its ability to use several substrates (mono-, di-, trimethyl amines, methanol, carbon monoxide, and acetate) for energy with methane generated as the byproduct. As long as M. acetivorans is supplied with a suitable anaerobic environment, the organism can generate all necessary amino acids solely from its food source. While not the only methanogenic archaeon, it is arguably one of the most metabolically diverse, with a large genome of 5.7 Mb harboring three distinct methanogenesis pathways [5]. Furthermore, M. acetivorans also contain pyrrolysine in methyltransferases [6,7]. This 22nd amino acid was discovered first in a similar methanogen, Methanosarcina barkeri [8].Several approaches have been undertaken to characterize the M. acetivorans proteome. A bottom-up twodimensional (2D) gel approach by Ferry and coworkers resulted in 422 identified proteins from 968 spots [9].

show abstract

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

Abstract: SummaryMethanosarcina spp. begin methanogenesis from methylamines with methyltransferases made via the translation of UAG as pyrrolysine. In vitro evidence indicates two possible routes to pyrrolysyl-tRNA

Cited by 16 publications

References 58 publications

Model organisms for genetics in the domain Archaea: methanogens, halophiles,ThermococcalesandSulfolobales

Model organisms for genetics in the domain Archaea: methanogens, halophiles,ThermococcalesandSulfolobales

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

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

Contact Info

Product

Resources

About