Biology subjects

Arend, M.

Publications and source records attributed to Arend, M..

3 recordsLinked to original sources

bioRxiv2022

Estimates of in vivo turnover numbers by simultaneously considering data from multiple conditions improve metabolic predictions

Turnover numbers characterize a key property of enzymes, and their usage in constraint-based metabolic modeling is expected to increase prediction accuracy of diverse cellular phenotypes. In vivo turnover numbers can be obtained by ranking of estimates obtained by integrating reaction rate and enzyme abundance measurements from individual experiments; yet, their contribution to improving predictions of condition-specific cellular phenotypes remains elusive. Here we show that available in vitro and in vivo turnover numbers lead to poor prediction of condition-specific growth rates with protein-constrained models of Escherichia coli and Saccharomyces cerevisiae, particularly in the ultimate test scenario when protein abundances are integrated in the model. We demonstrate that in vivo estimation of turnover number by simultaneous consideration of heterogeneous physiological data leads to improved prediction of condition-specific growth rates. Moreover, the obtained estimates are more precise than the available in vivo turnover numbers. Therefore, our approach provides the means to decrease the bias of in vivo turnover numbers and paves the way towards cataloguing in vivo kcatomes of other organisms.

bioinformatics↗

bioRxiv2022

Widening the landscape of transcriptional regulation of algal photoprotection

Availability of light and CO2, substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO2 Concentrating Mechanism (CCM) under low CO2, to raise intracellular CO2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomics data compendium of Chlamydomonas reinhardtiis responses to different light and carbon supply, we reconstructed a consensus genome-scale gene regulatory network from complementary inference approaches and used it to elucidate transcriptional regulators of photoprotection. We showed that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO2-mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga.

plant biology↗

bioRxiv2021

Photoprotection is regulated by light-independent CO2 availability

Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.

plant biology↗