An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State

Chure, Griffin; Cremer, Jonas

doi:10.1101/2022.01.27.477569

Cited by 2 publications

(2 citation statements)

References 102 publications

(344 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ribosomes represent important energy cost and resource allocation for cells, and in bacteria, the number of ribosomes is the result of a trade-off in the use of nutrients between protein synthesis capacity and production of metabolic enzymes (Kim et al, 2020). In bacteria and yeasts, allocation of resources towards ribosome synthesis is tuned to optimize growth (Chure and Cremer, 2022). Photoautotrophic organisms are likely to have similar constrains, especially when it comes to tune ribosomal content devoted to photosynthetic proteins when light is the sole source of energy given the strong turnover rate of photosynthetic proteins (Li et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

A plastidial DEAD box RNA helicase plays a critical role in high light acclimation by modulating ribosome biogenesis inChlamydomonas reinhardtii

Djouani-Tahri

Nellaepalli

Auroy

et al. 2022

Preprint

View full text Add to dashboard Cite

Photosynthetic organisms have developed sophisticated strategies to fine-tune light energy conversion to meet the metabolic demand, thereby optimizing growth in fluctuating light environments. Although mechanisms such as energy dissipation, photosynthetic control, or the photosystem II (PSII) damage and repair have been widely studied, little is known about the regulation of protein synthesis capacity during light acclimation. By screening a Chlamydomonas reinhardtii insertional mutant library using chlorophyll fluorescence imaging, we isolated a high chlorophyll fluorescence mutant (hf0) defected in a gene encoding a putative plastid targeted DEAD-box RNA helicase called CreRH22. CreRH22 is rapidly induced upon illumination and belongs to the GreenCut, a set of proteins specific to photosynthetic organisms. While photosynthesis is slightly affected in the mutant under low light (LL), exposure to high light (HL) induces a marked decrease in both PSII and PSI, and a strong alteration of the light-induced gene expression pattern. These effects are explained by the inability of hf0 to increase plastid ribosome amounts under HL. We conclude that CreRH22, by promoting ribosomal RNA precursor maturation in a light-dependent manner, enables the assembly of extra-ribosomes required to synthesize photosystem subunits at a higher rate, a critical step in the acclimation of algae to HL.

show abstract

Section: Discussionmentioning

confidence: 99%

A plastidial DEAD box RNA helicase plays a critical role in high light acclimation by modulating ribosome biogenesis inChlamydomonas reinhardtii

Djouani-Tahri

Nellaepalli

Auroy

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…[22,23], and as a meta-analysis in Ref. [24]), providing a more concrete understanding of how this important phenomenon is regulated.…”

Section: Reproducibility As a Requirement For Understandingmentioning

confidence: 99%

Be Prospective, Not Retrospective: A Philosophy for Advancing Reproducibility in Modern Biological Research

Chure¹

2022

Preprint

View full text Add to dashboard Cite

The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax, making the data and code often difficult to decipher or practically use. I believe that this is due to the documentation, collation, and validation of code and data only being done in retrospect. In this essay, I reflect on my experience contending with these challenges and present a philosophy for prioritizing reproducibility in modern biological research where balancing computational analysis and wet-lab experiments is commonplace. Modern tools used in scientific workflows (such as GitHub repositories) lend themselves well to this philosophy where reproducibility begins at project inception, not completion. To that end, I present and provide a programming-language agnostic template architecture that can be immediately copied and made bespoke to your next paper, whether your labwork is wet, dry, or somewhere in between.

show abstract

An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State

Cited by 2 publications

References 102 publications

A plastidial DEAD box RNA helicase plays a critical role in high light acclimation by modulating ribosome biogenesis inChlamydomonas reinhardtii

A plastidial DEAD box RNA helicase plays a critical role in high light acclimation by modulating ribosome biogenesis inChlamydomonas reinhardtii

Be Prospective, Not Retrospective: A Philosophy for Advancing Reproducibility in Modern Biological Research

Contact Info

Product

Resources

About