Sequencing, phylogenetic and transcriptional analysis of the glyoxylate bypass operon (ace) in the halophilic archaeon Haloferax volcanii

Serrano, Juan Antonio Molina; Bonete, Marı́a José

doi:10.1016/s0167-4781(01)00263-9

Cited by 31 publications

(36 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The sequence of Chlamydomonas ICL shares higher sequence identity with the E. coli enzyme (61%) than with its A. thaliana counterpart (31%). Two major groups can be distinguished in the ICL family, as previously observed (25,26). One corresponds to bacterial-type ICLs and includes the Chlamydomonas enzyme, whereas the second group corresponds to eukaryotic-type ICLs and contains sequences from organisms such as higher plants or yeast.…”

Section: Sequence and Phylogenetic Analysis Of Chlamydomonas Icl-mentioning

confidence: 81%

Regulation by Glutathionylation of Isocitrate Lyase from Chlamydomonas reinhardtii

Bedhomme

Zaffagnini

Marchand

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

Post-translational modification of protein cysteine residues is emerging as an important regulatory and signaling mechanism. We have identified numerous putative targets of redox regulation in the unicellular green alga Chlamydomonas reinhardtii. One enzyme, isocitrate lyase (ICL), was identified both as a putative thioredoxin target and as an S-thiolated protein in vivo. ICL is a key enzyme of the glyoxylate cycle that allows growth on acetate as a sole source of carbon. The aim of the present study was to clarify the molecular mechanism of the redox regulation of Chlamydomonas ICL using a combination of biochemical and biophysical methods. The results clearly show that purified C. reinhardtii ICL can be inactivated by glutathionylation and reactivated by glutaredoxin, whereas thioredoxin does not appear to regulate ICL activity, and no inter-or intramolecular disulfide bond could be formed under any of the conditions tested. Glutathionylation of the protein was investigated by mass spectrometry analysis, Western blotting, and site-directed mutagenesis. The enzyme was found to be protected from irreversible oxidative inactivation by glutathionylation of its catalytic Cys 178 , whereas a second residue, Cys 247 , becomes artifactually glutathionylated after prolonged incubation with GSSG. The possible functional significance of this post-translational modification of ICL in Chlamydomonas and other organisms is discussed.

show abstract

Section: Sequence and Phylogenetic Analysis Of Chlamydomonas Icl-mentioning

confidence: 81%

Regulation by Glutathionylation of Isocitrate Lyase from Chlamydomonas reinhardtii

Bedhomme

Zaffagnini

Marchand

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…On the other hand, in Corynebacterium glutamicum, aceA is clustered with aceB, which is transcribed in the opposite direction (Reinscheid et al, 1994a, b). In addition, in the (Serrano & Bonete, 2001) and Caulobacter crescentus (AE005673)]. However, aceA and aceB of many bacteria are separated from each other.…”

Section: Discussionmentioning

confidence: 99%

The cold-inducible icl gene encoding thermolabile isocitrate lyase of a psychrophilic bacterium, Colwellia maris a aThe GenBank accession number for the sequence reported in this paper is AB066287.

et al. 2002

View full text Add to dashboard Cite

The gene encoding isocitrate lyase (ICL ; EC 4 . 1 . 3 . 1) of a psychrophilic bacterium, Colwellia maris, was cloned and sequenced. The ORF of the gene (icl) was 1584 bp long, and the predicted gene product consisted of 528 aa (molecular mass 58 150 Da) and showed low homology with the corresponding enzymes from other organisms. The analyses of amino acid content and primary structure of the C. maris ICL suggested that it possessed many features of a cold-adapted enzyme. Primer extension and Northern blot analyses revealed that two species of the icl mRNAs with differential lengths of 5'-untranslated regions (TS1 and TS2) were present, of which the 5' end (TS1 and TS2 sites) were G and A, located at 130 and 39 bases upstream of the translation start codon, respectively. The levels of TS1 and TS2 mRNAs were increased by both acetate and low temperature. The induction of icl expression by low temperature took place in the C. maris cells grown on succinate as the carbon source but not acetate. Furthermore, a similar manner of inductions was also found in the levels of the translation and the enzyme activity in cell-free extract. These results suggest that the icl gene, encoding thermolabile isocitrate lyase, of C. maris is important for acetate utilization and cold adaptation.

show abstract

“…Interestingly, the H. volcanii malate synthase falls into a distinct class separate from the previously known sequence-based classes (A and G) (45). However, this class may not be typical of the archaea, as the P. aerophilum putative malate synthase falls clearly within class A, sharing 30% amino acid identity (BLAST Expect ϭ e…”

Section: Nucleotide Excision Repair (Ner)mentioning

confidence: 98%

Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum

Fitz‐Gibbon

Ladner

Kim

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

200

128

View full text Add to dashboard Cite

We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum aerophilum, a facultatively aerobic nitratereducing hyperthermophilic (T opt ‫؍‬ 100°C) crenarchaeon. Clues were found suggesting explanations of the organism's surprising intolerance to sulfur, which may aid in the development of methods for genetic studies of the organism. Many interesting features worthy of further genetic studies were revealed. Whole genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps all crenarchaea) lack 5 untranslated regions in their mRNAs and thus appear not to use a ribosome-binding site (Shine-Dalgarno)-based mechanism for translation initiation at the 5 end of transcripts. Inspection of the lengths and distribution of mononucleotide repeattracts revealed some interesting features. For instance, it was seen that mononucleotide repeat-tracts of Gs (or Cs) are highly unstable, a pattern expected for an organism deficient in mismatch repair. This result, together with an independent study on mutation rates, suggests a ''mutator'' phenotype. P yrobaculum aerophilum is a hyperthermophilic (T max ϭ 104°C, T opt ϭ 100°C) and metabolically versatile member of the crenarchaea ( Fig. 1), which are predominantly anaerobic respirers. Unlike most hyperthermophiles, P. aerophilum can withstand the presence of oxygen, growing efficiently in microaerobic conditions, thus making it relatively easy to work with in the laboratory. Unlike most of its phylogenetic neighbors, the growth of P. aerophilum is inhibited by the presence of elemental sulfur, but it grows well anaerobically using nitrate reduction (1). Here we have determined the complete genome sequence of P. aerophilum IM2, which was isolated from a boiling marine water hole at Maronti Beach, Italy (1). We obtained the sequence by a low coverage random shotgun sequencing strategy, with gap closure and resolution of ambiguities aided by the creation of a genomic fosmid map (2). We present an overview of the features and content of the genome, including a possible explanation of the organism's intolerance to sulfur and evidence of a possible lack of mismatch repair activity. Studies of the genus Pyrobaculum provide important opportunities for understanding the boundaries of life in extreme habitats. In a recent molecular sampling of a deep subsurface geothermal water pool, the only organisms detected were hyperthermophilic archaeal members closely related to Pyrobaculum (3).The P. aerophilum IM2 genome has 2,222,430 base pairs, 51% G ϩ C. Two thousand five hundred and eight-seven proteincoding regions were designated, with an average length of 759 amino acids, covering 88% of the genome (Table 1). Circular and linear maps of genome features, including many features discussed below, are published as supporting information (Figs. 4 and 5) on the PNAS web site, www.pnas.org. MethodsFosmid and pUC18 libraries were constructed as described (2). Approximately 26,000 sequences were obtained from Ϸ14,000 pUC18 clones by using both ...

show abstract

Sequencing, phylogenetic and transcriptional analysis of the glyoxylate bypass operon (ace) in the halophilic archaeon Haloferax volcanii

Cited by 31 publications

References 30 publications

Regulation by Glutathionylation of Isocitrate Lyase from Chlamydomonas reinhardtii

Regulation by Glutathionylation of Isocitrate Lyase from Chlamydomonas reinhardtii

The cold-inducible icl gene encoding thermolabile isocitrate lyase of a psychrophilic bacterium, Colwellia maris a aThe GenBank accession number for the sequence reported in this paper is AB066287.

Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum

Contact Info

Product

Resources

About