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Asplund-Samuelsson, Johannes
Publications (4 of 4) Show all publications
Janasch, M., Asplund-Samuelsson, J., Steuer, R. & Hudson, E. P. (2019). Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation. Journal of Experimental Botany, 70(3), 973-983
Open this publication in new window or tab >>Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation
2019 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 3, p. 973-983Article in journal (Refereed) Published
Abstract [en]

Biological fixation of atmospheric CO2 via the Calvin-Benson-Bassham cycle has massive ecological impact and offers potential for industrial exploitation, either by improving carbon fixation in plants and autotrophic bacteria, or by installation into new hosts. A kinetic model of the Calvin-Benson-Bassham cycle embedded in the central carbon metabolism of the cyanobacterium Synechocystis sp. PCC 6803 was developed to investigate its stability and underlying control mechanisms. To reduce the uncertainty associated with a single parameter set, random sampling of the steady-state metabolite concentrations and the enzyme kinetic parameters was employed, resulting in millions of parameterized models which were analyzed for flux control and stability against perturbation. Our results show that the Calvin cycle had an overall high intrinsic stability, but a high concentration of ribulose 1,5-bisphosphate was associated with unstable states. Low substrate saturation and high product saturation of enzymes involved in highly interconnected reactions correlated with increased network stability. Flux control, that is the effect that a change in one reaction rate has on the other reactions in the network, was distributed and mostly exerted by energy supply (ATP), but also by cofactor supply (NADPH). Sedoheptulose 1,7-bisphosphatase/fructose 1,6-bisphosphatase, fructose-bisphosphate aldolase, and transketolase had a weak but positive effect on overall network flux, in agreement with published observations. The identified flux control and relationships between metabolite concentrations and system stability can guide metabolic engineering. The kinetic model structure and parameterizing framework can be expanded for analysis of metabolic systems beyond the Calvin cycle.

Place, publisher, year, edition, pages
NLM (Medline), 2019
National Category
Other Engineering and Technologies not elsewhere specified
Identifiers
urn:nbn:se:kth:diva-244198 (URN)10.1093/jxb/ery382 (DOI)000459350700022 ()30371804 (PubMedID)2-s2.0-85061144018 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20190218

Available from: 2019-02-18 Created: 2019-02-18 Last updated: 2019-03-15Bibliographically approved
Klemencic, M., Asplund-Samuelsson, J., Dolinar, M. & Funk, C. (2019). Phylogenetic distribution and diversity of bacterial pseudo-orthocaspases underline their putative role in photosynthesis. Frontiers in Plant Science, 10, Article ID 293.
Open this publication in new window or tab >>Phylogenetic distribution and diversity of bacterial pseudo-orthocaspases underline their putative role in photosynthesis
2019 (English)In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, article id 293Article in journal (Refereed) Published
Abstract [en]

Orthocaspases are prokaryotic caspase homologs – proteases, which cleave their substrates after positively charged residues using a conserved histidine – cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.

Place, publisher, year, edition, pages
FRONTIERS MEDIA SA, 2019
Keywords
orthocaspase, metacaspase, photosynthesis, pseudo-enzyme, cyanobacteria
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-248072 (URN)10.3389/fpls.2019.00293 (DOI)000461133100001 ()2-s2.0-85064233837 (Scopus ID)
Note

QC 20190509

Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-09Bibliographically approved
Karlsen, J., Asplund-Samuelsson, J., Thomas, Q., Jahn, M. & Hudson, E. P. (2018). Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation. MSYSTEMS, 3(5), Article ID e00126-18.
Open this publication in new window or tab >>Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation
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2018 (English)In: MSYSTEMS, ISSN 2379-5077, Vol. 3, no 5, article id e00126-18Article in journal (Refereed) Published
Abstract [en]

Cyanobacteria experience both rapid and periodic fluctuations in light and inorganic carbon (C-i) and have evolved regulatory mechanisms to respond to these, including extensive posttranscriptional gene regulation. We report the first genome-wide ribosome profiling data set for cyanobacteria, where ribosome occupancy on mRNA is quantified with codon-level precision. We measured the transcriptome and translatome of Synechocystis during autotrophic growth before (high carbon [HC] condition) and 24 h after removing CO2 from the feedgas (low carbon [LC] condition). Ribosome occupancy patterns in the 5' untranslated region suggest that ribosomes can assemble there and slide to the Shine-Dalgarno site, where they pause. At LC, total translation was reduced by 80% and ribosome pausing was increased at stop and start codons and in untranslated regions, which may be a sequestration mechanism to inactivate ribosomes in response to rapid C-i depletion. Several stress response genes, such as thioredoxin M (sll1057), a putative endonuclease (slr0915), protease HtrA (slr1204), and heat shock protein HspA (sll1514) showed marked increases in translational efficiency at LC, indicating translational control in response to Ci depletion. Ribosome pause scores within open reading frames were mostly constant, though several ribosomal proteins had significantly altered pause score distributions at LC, which might indicate translational regulation of ribosome biosynthesis in response to Ci depletion. We show that ribosome profiling is a powerful tool to decipher dynamic gene regulation strategies in cyanobacteria. IMPORTANCE Ribosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium Synechocystis were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when cyanobacteria are cultivated in poorly mixed bioreactors or engineered to be product-secreting cell factories. A small fraction of genes (<200), including stress response genes, showed changes in translational efficiency during carbon starvation, indicating condition-dependent translation-level regulation. We observed ribosome occupancy in untranslated regions, possibly due to an alternative translation initiation mechanism in Synechocystis. The higher proportion of ribosomes residing in untranslated regions during carbon starvation may be a mechanism to quickly inactivate superfluous ribosomes. This work provides the first ribosome profiling data for cyanobacteria and reveals new regulation strategies for coping with nutrient limitation.

Place, publisher, year, edition, pages
American Society for Microbiology, 2018
Keywords
cyanobacteria, gene regulation, light stress, translational control
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:kth:diva-239499 (URN)10.1128/mSystems.00126-18 (DOI)000449523700015 ()
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council Formas, 2015-939Swedish Foundation for Strategic Research , RBP14-0013Swedish Research Council, 2016-06160 2016-06160
Note

QC 20181128

Available from: 2018-11-28 Created: 2018-11-28 Last updated: 2018-11-28Bibliographically approved
Cengic, I., Asplund-Samuelsson, J. & Hudson, E. P.Indications of differential transcriptional regulation of fatty acid synthesis in the model cyanobacteria Synechocystis sp. Strain PCC 6803 and Synechococcus elongatus PCC 7942.
Open this publication in new window or tab >>Indications of differential transcriptional regulation of fatty acid synthesis in the model cyanobacteria Synechocystis sp. Strain PCC 6803 and Synechococcus elongatus PCC 7942
(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-249932 (URN)
Note

QC 20190521

Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-05-21Bibliographically approved
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