Daily Expression Pattern of Protein-Encoding Genes and Small Noncoding RNAs in Synechocystis sp. Strain PCC 6803

Beck, Christian; Hertel, Stefanie; Rediger, Anne; Lehmann, Robert; Wiegard, Anika; Kölsch, Adrian; Heilmann, Beate; Georg, Jens; Hess, Wolfgang R.; Axmann, Ilka M.

doi:10.1128/aem.01086-14

Cited by 52 publications

(63 citation statements)

References 75 publications

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“…Published transcriptome studies of cyanobacteria typically show global rhythms in gene expression, including a significant reduction of the transcriptional output during the dark period (33,35,36). Although environmental LD cycles are sufficient to drive transcriptional and metabolic rhythms, metabolic rhythms are also influenced by the cyanobacterial circadian clock and persist in (previously entrained) cultures under constant light (9, 37, 38).…”

Section: Resultsmentioning

confidence: 99%

Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

Reimers

Knoop

Bockmayr

et al. 2017

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

100

130

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Cyanobacteria are an integral part of Earth's biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO 2 . Growth and metabolism of cyanobacteria are inherently tied to the diurnal rhythm of light availability. As yet, however, insight into the stoichiometric and energetic constraints of cyanobacterial diurnal growth is limited. Here, we develop a computational framework to investigate the optimal allocation of cellular resources during diurnal phototrophic growth using a genome-scale metabolic reconstruction of the cyanobacterium Synechococcus elongatus PCC 7942. We formulate phototrophic growth as an autocatalytic process and solve the resulting time-dependent resource allocation problem using constraint-based analysis. Based on a narrow and well-defined set of parameters, our approach results in an ab initio prediction of growth properties over a full diurnal cycle. The computational model allows us to study the optimality of metabolite partitioning during diurnal growth. The cyclic pattern of glycogen accumulation, an emergent property of the model, has timing characteristics that are in qualitative agreement with experimental findings. The approach presented here provides insight into the time-dependent resource allocation problem of phototrophic diurnal growth and may serve as a general framework to assess the optimality of metabolic strategies that evolved in phototrophic organisms under diurnal conditions. constraint-based analysis | whole-cell models | bioenergetics | metabolism | circadian clock C yanobacterial photoautotrophic growth requires a highly coordinated distribution of cellular resources to different intracellular processes, including the de novo synthesis of proteins, ribosomes, lipids, and other cellular components. For unicellular organisms, the optimal allocation of limiting resources is a key determinant of evolutionary fitness. Owing to the importance of cellular resource allocation for understanding evolutionary trade-offs in bacterial metabolism, the cellular "protein economy" and its implications for bacterial growth laws have been studied extensively, albeit almost exclusively for heterotrophic organisms under stationary environmental conditions (1-7). For photoautotrophic organisms, including cyanobacteria, growthdependent resource allocation is further subject to diurnal lightdark (LD) cycles that partition cellular metabolism into distinct phases. Recent experimental results have demonstrated the relevance of time-specific synthesis for cellular survival and growth (8-10). Nonetheless, the implications and consequences of a diurnal environment for the cellular resource allocation problem are insufficiently understood, and computational approaches hitherto developed for heterotrophic growth are not straightforwardly applicable to diurnal phototrophic growth (11).Here, we propose a computational framework to quantitatively assess the optimality of diurnal resource allocation for phototrophic growth. We are primarily interested i...

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Section: Resultsmentioning

confidence: 99%

Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

Reimers

Knoop

Bockmayr

et al. 2017

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

100

130

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“…To facilitate this comparison, the prediction of homologous genes in the cyanobacterial clade by Beck and colleagues [108] was used as starting point. We focused first on the set of genes with oscillating expression patterns in all datasets.…”

Section: Resultsmentioning

confidence: 99%

Minimal tool set for a prokaryotic circadian clock

Schmelling

Lehmann

Chaudhury³

et al. 2017

BMC Evol Biol

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BackgroundCircadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.ResultsUsing a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.ConclusionOur analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0999-7) contains supplementary material, which is available to authorized users.

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“…Unfortunately, such tools often do not function as expected in cyanobacteria (15,16). This is due to differences in the transcription (17) and translation (18) machinery, cyanobacterial traits such as polyploidy (19), an efficient recombination system (20), and a circadian rhythm (21,22), and other features that distinguish cyanobacteria from their heterotrophic cousins. Repositories of biological parts, such as the Registry of Standard Biological Parts, have only recently begun to include information and parts for cyanobacteria.…”

mentioning

confidence: 99%

Fine-Tuning of Photoautotrophic Protein Production by Combining Promoters and Neutral Sites in the Cyanobacterium Synechocystis sp. Strain PCC 6803

Berla

Pakrasi

2015

Appl Environ Microbiol

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Cyanobacteria are photosynthetic cell factories that use solar energy to convert CO 2 into useful products. Despite this attractive feature, the development of tools for engineering cyanobacterial chassis has lagged behind that for heterotrophs such as Escherichia coli or Saccharomyces cerevisiae. Heterologous genes in cyanobacteria are often integrated at presumptively "neutral" chromosomal sites, with unknown effects. We used transcriptome sequencing (RNA-seq) data for the model cyanobacterium Synechocystis sp. strain PCC 6803 to identify neutral sites from which no transcripts are expressed. We characterized the two largest such sites on the chromosome, a site on an endogenous plasmid, and a shuttle vector by integrating an enhanced yellow fluorescent protein (EYFP) expression cassette expressed from either the P cpc560 or the P trc1O promoter into each locus. Expression from the endogenous plasmid was as much as 14-fold higher than that from the chromosome, with intermediate expression from the shuttle vector. The expression characteristics of each locus correlated predictably with the promoters used. These findings provide novel, characterized tools for synthetic biology and metabolic engineering in cyanobacteria.C yanobacteria are oxygenic photosynthetic prokaryotes that use solar energy to fix CO 2 , converting it into biomass and valuable products. Since these organisms do not require fixed carbon feedstocks, they have great potential for synthetic biology and metabolic engineering applications (1-4). Several strains of cyanobacteria have been engineered to act as microbial cellular factories for the production of fuels and chemicals, such as isobutanol, 2,3-butanediol, free fatty acids, and D-lactate (5-7). Despite these advances, none of these engineered strains has been able to achieve industrially relevant levels of productivity. A lack of effective and well-characterized tools for synthetic biology in cyanobacteria has limited progress relative to that with other established microbial chassis, such as Escherichia coli or Saccharomyces cerevisiae (1). Synechocystis sp. strain PCC 6803 is a naturally transformable cyanobacterial chassis for synthetic biology. This strain carries several endogenous plasmids in addition to its single chromosome (8-11). Since there are a limited number of self-replicating exogenous plasmids for the expression of heterologous genes in Synechocystis PCC 6803 (12) and other cyanobacteria, these endogenous plasmids may prove to be attractive parts for synthetic biology (13). Additionally, these plasmids increase their copy numbers during the transition from the exponential-growth phase to the stationary phase (14). Thus, we have hypothesized that the expression of heterologous genes from sites in these plasmids could be autoinduced by such a growth transition. This induction could be advantageous in a production system that first yields a dense culture of light-harvesting cyanobacteria and later uses those microbial cell factories to churn out a product of interest.One strat...

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Daily Expression Pattern of Protein-Encoding Genes and Small Noncoding RNAs in Synechocystis sp. Strain PCC 6803

Cited by 52 publications

References 75 publications

Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

Minimal tool set for a prokaryotic circadian clock

Fine-Tuning of Photoautotrophic Protein Production by Combining Promoters and Neutral Sites in the Cyanobacterium Synechocystis sp. Strain PCC 6803

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