Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

Schriek S, Rückert C, Staiger D, Pistorius EK, Michel K-P (2007)
BMC Genomics 8(1).

Download
OA
Journal Article | Published | English
Author
; ; ; ;
Abstract
BACKGROUND:So far very limited knowledge exists on L-arginine catabolism in cyanobacteria, although six major L-arginine-degrading pathways have been described for prokaryotes. Thus, we have performed a bioinformatic analysis of possible L-arginine-degrading pathways in cyanobacteria. Further, we chose Synechocystis sp. PCC 6803 for a more detailed bioinformatic analysis and for validation of the bioinformatic predictions on L-arginine catabolism with a transcript analysis.RESULTS:We have evaluated 24 cyanobacterial genomes of freshwater or marine strains for the presence of putative L-arginine-degrading enzymes. We identified an L-arginine decarboxylase pathway in all 24 strains. In addition, cyanobacteria have one or two further pathways representing either an arginase pathway or L-arginine deiminase pathway or an L-arginine oxidase/dehydrogenase pathway. An L-arginine amidinotransferase pathway as a major L-arginine-degrading pathway is not likely but can not be entirely excluded. A rather unusual finding was that the cyanobacterial L-arginine deiminases are substantially larger than the enzymes in non-photosynthetic bacteria and that they are membrane-bound. A more detailed bioinformatic analysis of Synechocystis sp. PCC 6803 revealed that three different L-arginine-degrading pathways may in principle be functional in this cyanobacterium. These are (i) an L-arginine decarboxylase pathway, (ii) an L-arginine deiminase pathway, and (iii) an L-arginine oxidase/dehydrogenase pathway. A transcript analysis of cells grown either with nitrate or L-arginine as sole N-source and with an illumination of 50 mumol photons m-2 s-1 showed that the transcripts for the first enzyme(s) of all three pathways were present, but that the transcript levels for the L-arginine deiminase and the L-arginine oxidase/dehydrogenase were substantially higher than that of the three isoenzymes of L-arginine decarboxylase.CONCLUSION:The evaluation of 24 cyanobacterial genomes revealed that five different L-arginine-degrading pathways are present in the investigated cyanobacterial species. In Synechocystis sp. PCC 6803 an L-arginine deiminase pathway and an L-arginine oxidase/dehydrogenase pathway represent the major pathways, while the L-arginine decarboxylase pathway most likely only functions in polyamine biosynthesis. The transcripts encoding the enzymes of the two major pathways were constitutively expressed with the exception of the transcript for the carbamate kinase, which was substantially up-regulated in cells grown with L-arginine.
Publishing Year
ISSN
PUB-ID

Cite this

Schriek S, Rückert C, Staiger D, Pistorius EK, Michel K-P. Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803. BMC Genomics. 2007;8(1).
Schriek, S., Rückert, C., Staiger, D., Pistorius, E. K., & Michel, K. - P. (2007). Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803. BMC Genomics, 8(1).
Schriek, S., Rückert, C., Staiger, D., Pistorius, E. K., and Michel, K. - P. (2007). Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803. BMC Genomics 8.
Schriek, S., et al., 2007. Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803. BMC Genomics, 8(1).
S. Schriek, et al., “Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803”, BMC Genomics, vol. 8, 2007.
Schriek, S., Rückert, C., Staiger, D., Pistorius, E.K., Michel, K.-P.: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803. BMC Genomics. 8, (2007).
Schriek, Sarah, Rückert, Christian, Staiger, Dorothee, Pistorius, Elfriede K., and Michel, Klaus-Peter. “Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803”. BMC Genomics 8.1 (2007).
Main File(s)
Access Level
OA Open Access
Last Uploaded
2012-03-23 08:21:18

This data publication is cited in the following publications:
This publication cites the following data publications:

9 Citations in Europe PMC

Data provided by Europe PubMed Central.

Advances in detection methods of L-amino acid oxidase activity.
Yu Z, Wang Y, Zhou N, Zhao M, Qiu J, Lin J., Appl. Biochem. Biotechnol. 174(1), 2014
PMID: 24903958
A new arsenate reductase involved in arsenic detoxification in Anabaena sp. PCC7120.
Pandey S, Shrivastava AK, Singh VK, Rai R, Singh PK, Rai S, Rai LC., Funct. Integr. Genomics 13(1), 2013
PMID: 23086594
Hydrogenosome-localization of arginine deiminase in Trichomonas vaginalis.
Morada M, Smid O, Hampl V, Sutak R, Lam B, Rappelli P, Dessi D, Fiori PL, Tachezy J, Yarlett N., Mol. Biochem. Parasitol. 176(1), 2011
PMID: 21074581
Detection of an L-amino acid dehydrogenase activity in Synechocystis sp. PCC 6803.
Schriek S, Kahmann U, Staiger D, Pistorius EK, Michel KP., J. Exp. Bot. 60(3), 2009
PMID: 19213808
Amino acid availability determines the ratio of microcystin variants in the cyanobacterium Planktothrix agardhii.
Tonk L, van de Waal DB, Slot P, Huisman J, Matthijs HC, Visser PM., FEMS Microbiol. Ecol. 65(3), 2008
PMID: 18616588
Transcript profiling indicates that the absence of PsbO affects the coordination of C and N metabolism in Synechocystis sp. PCC 6803
Schriek S, Aguirre-von-Wobeser E, Nodop A, Becker A, Ibelings BW, Bok J, Staiger D, Matthijs HCP, Pistorius EK, Michel KP., Physiol Plant 133(3), 2008
PMID: IND44069758
Transcript profiling indicates that the absence of PsbO affects the coordination of C and N metabolism in Synechocystis sp. PCC 6803.
Schriek S, Aguirre-von-Wobeser E, Nodop A, Becker A, Ibelings BW, Bok J, Staiger D, Matthijs HC, Pistorius EK, Michel KP., Physiol Plant 133(3), 2008
PMID: 18419737

65 References

Data provided by Europe PubMed Central.

Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method.
Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A., Protein Eng. 10(6), 1997
PMID: 9278280
TMbase - A database of membrane-spanning protein segments
Hofmann K, Stoffel W., 1993
Polyamines of Anacystis nidulans and metabolism of exogenous spermidine and spermine.
Ramakrishna S, Guarino L, Cohen SS., J. Bacteriol. 134(3), 1978
PMID: 96100
The aerobic respiratory chain of
Anraku Y, Gennis RB., 1987
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG., Nucleic Acids Res. 25(24), 1997
PMID: 9396791

Maciukenas M., 0
Web Services at the European Bioinformatics Institute
Labarga A, Valentin F, Andersson M, Lopez R., 2007

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 18045455
PubMed | Europe PMC

Search this title in

Google Scholar