Cloning and sequencing of the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences

Abstract

The gene ginA encoding glutamine synthetase I (GSI) from the archaeum Pyrococcus woesei was cloned and sequenced with the Sudfolobus solfataricus ginA gene as the probe. An operon reading frame of 448 amino acids was identified within a DNA segment of 1,528 bp. The encoded protein was 49%o identical with the GSI of Methanococcus voltae and exhibited conserved regions characteristic of the GSI family. The P. woesei GSI was aligned with available homologs from other archaea (S. soifataricus, M. voitae) and with representative sequences from cyanobacteria, proteobacteria, and gram-positive bacteria. Phylogenetic trees were constructed from both the amino acid and the nucleotide sequence alignments. In accordance with the sequence similarities, archaeal and bacterial sequences did not segregate on a phylogeny. On the basis of sequence signatures, the GSI trees could be subdivided into two ensembles. One encompassed the GSI of cyanobacteria and proteobacteria, but also that of the high-G+C gram-positive bacterium Streptomyces coelicolor (all of which are regulated by the reversible adenylylation of the enzyme subunits); the other embraced the GSI of the three archaea as well as that of the low-G+C gram-positive bacteria (Clostridium acetobutilycum, Bacillus subtilis) and Thermotoga maritima (none of which are regulated by subunit adenylylation). The GSIs of the Thermotoga and the Bacilus-Clostridium lineages shared a direct common ancestor with that of P. woesei and the methanogens and were unrelated to their homologs from cyanobacteria, proteobacteria, and S. coelicolor.The possibility is presented that the GSI gene arose among the archaea and was then laterally transferred from some early methanogen to a Thermotoga-like organism. However, the relationship of the cyanobacterial-proteobacterial GSIs to the Thermotoga GSI and the GSI of low-G+C gram-positive bacteria remains unexplained.Glutamine synthetase (GS) catalyzes the ATP-dependent synthesis of glutamine from glutamate and ammonium (NH4+). The enzyme is a multimer found in at least two forms that are only distantly related to one another (15 to 19% sequence identity) (43, 56). One of these forms (GSI), composed of 12 identical subunits (443 to 474 amino acids each), occurs in bacteria and archaea. A second form (GSII), composed of eight identical subunits (332 to 378 amino acids each), occurs in eukarya but also in members of the family Rhizobiaceae (12, 23, 53) and in certain actinomycetes (4, 18, 34, 49); these last two groups harbor both a GSI and a GSII-like enzyme. A third form of the enzyme (GSIII), composed of six identical subunits (729 amino acids each), whose sequence is unrelated to both GSI and GSII, is harbored by Bacteroides fragilis (29).Because GSI is a relatively long polypeptide chain containing both semiconserved and highly conserved regions, and because it is ubiquitous in prokaryotes, GSI subunit sequences are suited, in principle, to trace the evolution of the bacterial and the archaeal lineages.A large inventory of (eu)bacterial GSI sequ...

What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram‐positive bacteria? A new proposal for the classification of prokaryotic organisms

“…For Gln I sequences, the species T. maritima again lacked the insert present in various Gram-negative bacteria, supporting its classification as a Gram-positive bacteria (Brown et al, 1994). In phylogenetic trees based on Gln I sequences, archaebacteria and Gram-positive bacteria show a paraphyletic branching (Tiboni et al, 1993;Brown et al, 1994;Golding and Gupta, 1995) similar to that seen for Hsp70 sequences. The distinctness of Grampositive bacteria from Gram-negative bacteria is also supported by signature sequences in a number of additional proteins, including GroEL (Hsp60) (Gupta, 1995a;Gupta et al, 1997), and acetolactate synthase (unpublished data).…”

Characterization of the locus encoding the [Ni-Fe] sulfhydrogenase from the archaeon Pyrococcus furiosus: evidence for a relationship to bacterial sulfite reductases

“…This is a feature in common with many other archaeal genes Tiboni et al, 1993;Uemori e t al., 1993;Zwickl e t al., 1990).…”

Evolution of the chaperonin families (HSP60, HSP 10 and TCP‐1) of proteins and the origin of eukaryotic cells

“…Hsp70, glutamate dehydrogenase, giutamine synthetase), the close relationship between these two groups of organisms was retained and still observed (Benachenhou-Lahfa et al. 1993;Gupta and Golding, 1993;Tiboni et al, 1993;Golding and Gupta, 1995), In the period that followed (during which the environment changed from predominantly anaerobic to aerobic) other groups of archaebactena and eubactei ia (including the Gram-tiegative group) are postulated to have evolved from these ancestral groups. The evolulion of archaebacteria!…”