Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis

Wenhong Zhu, Claudia I. Reich, Gary J. Olsen, Carol S. Giometti, John R. Yates

Research output: Contribution to journalArticle

Abstract

Methanococcus jannaschii is an autotrophic hyperthermophilic archaeon isolated from an oceanic hydrothermal vent. Its primary pathway for energy production is methanogenesis from H2 and CO2. High-throughput Multidimensional Protein Identification Technology based on microcapillary LC/LC/ MS/MS was used to investigate the proteome of M. jannaschii and the methanogenesis pathway in cells grown in complex medium with high H2 supply. A total of 963 proteins have been unambiguously identified. The identified proteins represent ∼54% of the whole genome of M. jannaschii. About 44% of the identified proteins are either conserved hypothetical or hypothetical proteins. We identified 83-95% of the proteins predicted to be involved in amino acid biosynthesis, cellular processes, central intermediary metabolism, energy metabolism, protein synthesis, transcription, and purine, pyridine, nucleoside, and nucleotide synthesis. Over 40% of these proteins have better than 50% sequence coverage. Approximately 90% of the predicted methanogenesis proteins were detected. In contrast, only 27-37% of predicted hypothetical proteins, proteins involved in transport and binding, and proteins with regulatory functions were identified. High peptide number, spectrum count, and sequence coverage have been used as indicators of high expression levels and are in good agreement with codon bias analysis. Predicted intein peptides were detected in MJ1043 (DMA-directed RNA polymerase, subunit A″), MJ0542 (phosphoenolpyruvate synthase), MJ0782 (transcription initiation factor IIB), and MJ1422 (putative replication factor C subunit). New peptides created by protein splicing were detected in MJ0885 (DNA dependent DNA polymerase), MJ0542, and MJ0782. The methanogenesis pathway and the enzymes involved are also discussed.

Original languageEnglish (US)
Pages (from-to)538-548
Number of pages11
JournalJournal of Proteome Research
Volume3
Issue number3
DOIs
StatePublished - May 1 2004

Fingerprint

Methanocaldococcus
Firearms
Proteomics
Proteins
water dikinase pyruvate
Transcription
Peptides
Carrier Proteins
Replication Protein C
Transcription Factor TFIIB
Hydrothermal Vents
Inteins
Protein Splicing
Purine Nucleosides
Purine Nucleotides
Peptide Initiation Factors
Archaea
DNA-Directed DNA Polymerase
DNA-Directed RNA Polymerases
Proteome

Keywords

  • Archaea
  • Intein
  • LC/LC/MS/MS
  • Mass spectrometry
  • Methanococcus jannaschii
  • Methanogenesis
  • MudPIT
  • Proteomics
  • SEQUEST

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. / Zhu, Wenhong; Reich, Claudia I.; Olsen, Gary J.; Giometti, Carol S.; Yates, John R.

In: Journal of Proteome Research, Vol. 3, No. 3, 01.05.2004, p. 538-548.

Research output: Contribution to journalArticle

Zhu, Wenhong ; Reich, Claudia I. ; Olsen, Gary J. ; Giometti, Carol S. ; Yates, John R. / Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. In: Journal of Proteome Research. 2004 ; Vol. 3, No. 3. pp. 538-548.
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