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Title: RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

ABSTRACT The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA Cysis first acylated with phosphoserine (Sep) byO-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA Cysby Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN,Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“CandidatusParcubacteria” andChloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNA Cysspecies with cysteinein vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS-SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea andChloroflexibacteria. We further discuss possible contributions of the SepRS-SepCysS system formore » sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.« less
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [3] ;  [4]
  1. Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry
  2. Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry; Tokyo Univ. of Science, Chiba (Japan). Dept. of Biological Science and Technology
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry and Dept. of Chemistry
Publication Date:
Grant/Contract Number:
FG02-98ER20311; AC02-05CH11231; R01GM22854; R35GM122560
Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 8; Journal Issue: 3; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Research Org:
Yale Univ., New Haven, CT (United States); Univ. of California, Los Angeles, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Chemical Sciences, Geosciences & Biosciences Division; Japan Society for the Promotion of Science (JSPS); National Institutes of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; biochemistry; bioinformatics; cysteine biosynthesis; genetic code; translation
OSTI Identifier:
1425739