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Jahn, Michael
Publications (2 of 2) Show all publications
Jahn, M., Vialas, V., Karlsen, J., Maddalo, G., Edfors, F., Forsström, B., . . . Hudson, E. P. (2018). Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins. Cell reports, 25(2), 478-+
Open this publication in new window or tab >>Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins
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2018 (English)In: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 25, no 2, p. 478-+Article in journal (Refereed) Published
Abstract [en]

Cyanobacteria must balance separate demands for energy generation, carbon assimilation, and biomass synthesis. We used shotgun proteomics to investigate proteome allocation strategies in the model cyanobacterium Synechocystis sp. PCC 6803 as it adapted to light and inorganic carbon (C-i) limitation. When partitioning the proteome into seven functional sectors, we find that sector sizes change linearly with growth rate. The sector encompassing ribosomes is significantly smaller than in E. coli, which may explain the lower maximum growth rate in Synechocystis. Limitation of light dramatically affects multiple proteome sectors, whereas the effect of C-i limitation is weak. Carbon assimilation proteins respond more strongly to changes in light intensity than to C-i. A coarse-grained cell economy model generally explains proteome trends. However, deviations from model predictions suggest that the large proteome sectors for carbon and light assimilation are not optimally utilized under some growth conditions and may constrain the proteome space available to ribosomes.

Place, publisher, year, edition, pages
et al., 2018
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-237095 (URN)10.1016/j.celrep.2018.09.040 (DOI)000446691400020 ()30304686 (PubMedID)2-s2.0-85054193580 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council Formas, 2015-939Swedish Research CouncilSwedish Foundation for Strategic Research , RBP14-0013
Note

QC 20181029

Available from: 2018-10-29 Created: 2018-10-29 Last updated: 2019-10-07Bibliographically 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
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