A Novel Repressor of Nif and glnA Expression in the Methanogenic Archaeon Methanococcus Maripaludis

Mol Microbiol. 2003 Jan;47(1):235-46. doi: 10.1046/j.1365-2958.2003.03293.x.


Nitrogen assimilation in the methanogenic archaeon Methanococcus maripaludis is regulated by transcriptional repression involving a palindromic 'nitrogen operator' repressor binding sequence. Here we report the isolation of the nitrogen repressor, NrpR, from M. maripaludis using DNA affinity purification. Deletion of the nrpR gene resulted in loss of nitrogen operator binding activity in cell extracts and loss of repression of nif (nitrogen-fixation) and glnA (glutamine synthetase) gene expression in vivo. Genetic complementation of the nrpR mutation restored all functions. NrpR contained a putative N-terminal winged helix-turn-helix motif followed by two mutually homologous domains of unknown function. Comparison of the migration of NrpR in gel-filtration chromatography with its subunit molecular weight (60 kDa) suggested that NrpR was a tetramer. Several lines of evidence suggested that the level of NrpR itself is not regulated, and the binding affinity of NrpR to the nitrogen operator is controlled by an unknown mechanism. Homologues of NrpR were found only in certain species in the kingdom Euryarchaeota. Full length homologues were found in Methanocaldococcus jannaschii and Methanothermobacter thermoautotrophicus, and homologues lacking one or more of the three polypeptide domains were found in Archaeoglobus fulgidus, Methanopyrus kandleri, Methanosarcina acetivorans, and Methanosarcina mazei. NrpR represents a new family of regulators unique to the Euryarchaeota.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Blotting, Northern
  • DNA, Archaeal / genetics
  • Gene Expression Regulation, Archaeal*
  • Gene Expression Regulation, Enzymologic
  • Genes, Archaeal
  • Glutamate-Ammonia Ligase / genetics*
  • Glycoproteins / genetics*
  • Helminth Proteins / genetics*
  • Membrane Proteins*
  • Methanococcus / enzymology
  • Methanococcus / genetics*
  • Molecular Sequence Data
  • Nitrogen Fixation / genetics
  • Nitrogen Fixation / physiology
  • Operator Regions, Genetic
  • Repressor Proteins / genetics
  • Repressor Proteins / isolation & purification
  • Repressor Proteins / physiology*
  • Sequence Alignment


  • DNA, Archaeal
  • Glycoproteins
  • Helminth Proteins
  • Membrane Proteins
  • Repressor Proteins
  • NIF protein, Ancylostoma caninum
  • glutamine synthetase I
  • Glutamate-Ammonia Ligase