ORIGINAL PAPER
Katharina Veit Æ Claudia Ehlers Æ Armin Ehrenreich
Kirsty Salmon Æ Raymond Hovey Æ Robert P. Gunsalus
Uwe Deppenmeier Æ Ruth A. Schmitz
Global transcriptional analysis of
Methanosarcina mazei
strain Go
¨
1
under different nitrogen availabilities
Received: 21 December 2005 / Accepted: 27 February 2006 / Published online: 20 April 2006
Ó Springer-Verlag 2006
Abstract Certain archaeal species can fix molecular
nitrogen under nitrogen limiting conditions although
little is known about this process at either the genetic or
molecular level. To address this on a genome-wide scale,
transcriptional analysis was performed on the model
methanogen Methanosarcina mazei strain Go
¨
1 using
DNA-microarrays. The genomic expression patterns for
cells grown under nitrogen fixing conditions versus
nitrogen sufficiency (10 mM ammonium) revealed that
approximately 5% of all genes are differentially ex-
pressed. Besides a small set of genes previously known to
be up-regulated under nitrogen limitation, 14 additional
genes involved in nitrogen metabolism were identified
plus 10 genes encoding potential transcriptional regula-
tors, 13 genes involved in carbon metabolism, 3 genes in
general stress response, 8 putative transporter genes,
and an additional 21 genes with unknown function.
Quantitative reverse transcriptase PCR experiments
confirmed the differential expression of a subset of these
genes. Promoter analysis revealed a palindromic DNA
motif centered nearby the transcriptional start point for
several genes up-regulated under nitrogen limitation. A
bioinformatics study demonstrated the presence of this
motif in the up-stream region of 52 genes genome-wide,
the majority of which showed nitrogen dependent dif-
ferential transcription. We therefore hypothesize that
this DNA element is involved in nitrogen control in
M. mazei where it may act as a binding site for a
regulatory protein.
Keywords Methanosarcina mazei strain Go
¨
1 Æ
Transcriptional regulation Æ Nitrogen metabolism Æ
Nitrogen fixation Æ GOGAT
Introduction
Methanosarcina mazei strain Go
¨
1 is a representative
methane-producing Archaeon of significant ecological
importance due to its role in biogenic methane produc-
tion in various anaerobic habitats on Earth (Rogers and
Whiteman 1991). Although the biochemical basis of
methanogenesis has been analyzed in considerable detail
(Thauer 1998; Ferry 1999; Deppenmeier 2002), little is
known about either the metabolism or regulation of
nitrogen acquisition in this important group of Archaea,
in contrast to our knowledge of these processes in the
Bacteria. Thus, the goal of this study was to understand
the nitrogen metabolism and its regulation in M. mazei.
The genome sequences of several Methanosarcina
species including M. mazei and its close relatives M.
acetivorans, and M. barkeri have recently become
available (Deppenmeier et al. 2002; Galagan et al. 2002;
http://www.ncbi.nlm.nih.gov). Genome analysis has re-
vealed that the broad substrate spectrum of the order
Methanosarcinales is reflected on the genome level where
these genomes are the largest among the archaea (http://
www.ncbi.nlm.nih.gov/genomes/lproks.cgi).
Electronic Supplementary Material Supplementary material is
available for this article at http://dx.doi.org/10.1007/s00438-006-
0117-9 and is accessible for authorized users.
Communicated by G. Klug
K. Veit Æ C. Ehlers Æ R. A. Schmitz (&)
Institut fu
¨
r Allgemeine Mikrobiologie,
Christian-Albrechts-Universita
¨
t Kiel,
Am Botanischen Garten 1-9, 24118 Kiel, Germany
E-mail: rschmitz@ifam.uni-kiel.de
Tel.: +49-431-8804334
Fax: +49-431-8802194
A. Ehrenreich Æ K. Veit
Institut fu
¨
r Mikrobiologie und Genetik, Universita
¨
tGo
¨
ttingen,
Grisebachstr. 8, 37077 Go
¨
ttingen, Germany
K. Salmon Æ R. P. Gunsalus
Department of Microbiology, Immunology, and Molecular
Genetics, University of California, Los Angeles,
CA 90095-1489, USA
R. Hovey Æ U. Deppenmeier
Department of Biological Sciences,
University of Wisconsin-Milwaukee, P.O. Box 413,
Milwaukee, WI 53201, USA
Mol Gen Genomics (2006) 276: 41–55
DOI 10.1007/s00438-006-0117-9