Transcription factors mediating regulation of photosynthesis

Abstract

Photosynthesis by which plants convert carbon dioxide to sugars using the energy of light is fundamental to life as it forms the basis of nearly all food chains. Surprisingly, our knowledge about its transcriptional regulation remains incomplete. Effort for its agricultural optimization have mostly focused on post-translational regulatory processes1-3 but photosynthesis is regulated at the post-transcriptional4 and the transcriptional level5. Stacked transcription factor mutants remain photosynthetically active5,6 and additional transcription factors have been difficult to identify possibly due to redundancy6 or lethality. Using a random forest decision tree-based machine learning approach for gene regulatory network calculation7 we determined ranked candidate transcription factors and validated five out of five tested transcription factors as controlling photosynthesis in vivo. The detailed analyses of previously published and newly identified transcription factors suggest that photosynthesis is transcriptionally regulated in a partitioned, non-hierarchical, interlooped network.

Natural genetic variation inGLK1-mediated photosynthetic acclimation in response to light

“…1a ). NFY TFs can interact with BBX TFs that have recently been identified as central regulators of photosynthetic gene expression [21, 22]. SPL7 is a regulator of copper signaling that is also required for ROS-detoxifying enzyme activities in plastids [23].…”

Multiple transcription factors mediate acclimation of Chlamydomonas to light stress

“…In eight mutants, LHC and PS genes are inversely regulated compared to PP genes (Figure 3, Figure 5), but no changes in PSI to PSII ratio (Bailey et al, 2001) or a decoupling of LHCs and PS from the CBBc can be observed (Halpape et al, 2023). The observed general reduction of expression for LHCs and PS may ultimately lead to a reduction in light-harvesting capacity and therefore to reduced pressure on PP.…”

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

“…Network inference with the random forest decision tree-based algorithm GENIE3 (Huynh-Thu et al, 2010) was used to infer a gene regulatory network (GRN) in wheat (Ramírez-González et al, 2018) and analyze polyploid evolution (Almeida-Silva and Van de Peer, 2023). Recently, GENIE3 was used for identification and validation of regulators involved in photosynthesis in A. thaliana (Halpape et al, 2023) and in the regulation of photoprotection and the carbon concentrating mechanism in Chlamydomonas reinhardtii (Arend et al, 2023; Wulf et al, 2023) making it a promising candidate to compare gene regulatory networks across species. By performing GRN inference based on expression data comparability of individual samples is not necessary, because transcription factors are examined in relation to all other genes.…”

“…The split between BEP and PACMAD can be roughly dated at 55 million years ago (Christin et al, 2014). By including previously published and validated gene regulatory networks of A. thaliana (Halpape et al, 2023) and C. reinhardii (Wulf et al, 2023) the analysis is extended to dicots and algae to include more distant species at 150 million years between eudicots and monocots and 950 million years between the chlorophyta and the streptophyta (Magallón et al, 2013; Hedges et al, 2004). We hypothesized that the comparison of networks will identify conserved and divergent regulatory events.…”

“…C. reinhardtii , S. bicolor and Z. mays operate a photosynthesis associated pathway, the carbon concentrating mechanism, which eliminates the need for high flux photorespiration (Wang et al, 2015; Mallmann et al, 2014). The photorespiratory pathway is associated with the photosynthetic regulon in C3 plants such as Arabidopsis (Halpape et al, 2023). In C. reinhardtii , CO 2 is converted to H 3 O - and transported into the chloroplast into the pyrenoid, which is structurally made out of a starch shell and condensed RuBisCO (Wang et al, 2015).…”