Translation initiation factor 3 families: what are their roles in regulating cyanobacterial and chloroplast gene expression?

Chloroplast proteostasis: A story of birth, life, and death

Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.

Transcriptome and metabolome analyses of response of Synechocystis sp. PCC 6803 to methyl viologen

The toxicity of methyl viologen (MV) to organisms is mainly due to the oxidative stress caused by reactive oxygen species produced from cell response. This study mainly investigated the response of Synechocystis sp. PCC 6803 to MV by combining transcriptomic and metabolomic analyses. Through transcriptome sequencing, we found many genes responding to MV stress, and analyzed them by weighted gene co-expression network analysis (WGCNA). Meanwhile, many metabolites were also found by metabolomic analysis to be regulated post MV treatment. Based on the analysis results of Kyoto encyclopedia of genes and genomes (KEGG) of the differentially expressed genes (DEGs) in the transcriptome and the differential metabolites in the metabolome, the dynamic changes of genes and metabolites involved in ten metabolic pathways in response to MV were analyzed. The results indicated that although the oxidative stress caused by MV was the strongest at 6 h, the proportion of the upregulated genes and metabolites involved in these ten metabolic pathways was the highest. Photosynthesis positively regulated the response to MV-induced oxidative stress, and the regulation of environmental information processing was inhibited by MV. Other metabolic pathways played different roles at different times and interacted with each other to respond to MV. This study comprehensively analyzed the response of Synechocystis sp. PCC 6803 to oxidative stress caused by MV from a multi-omics perspective, with providing key data and important information for in-depth analysis of the response of organisms to MV, especially photosynthetic organisms. KEY POINTS: • Methyl viologen (MV) treatment caused regulatory changes in genes and metabolites. • Proportion of upregulated genes and metabolites was the highest at 6-h MV treatment. • Photosynthesis and environmental information processing involved in MV response.

Adaptive laboratory evolution of the fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for improved solvent tolerance

Cyanobacteria hold promise as cell factories for the photoautotrophic conversion of carbon dioxide to useful chemicals. For the eventual commercial viability of such processes, cyanobacteria need to be engineered for (i) efficient channeling of carbon flux toward the product of interest and (ii) improved product tolerance, the latter being the focus of this study. We chose the recently reported, fast-growing, high light and CO₂ tolerant cyanobacterium Synechococcus elongatus PCC 11801 for adaptive laboratory evolution. In two parallel experiments that lasted over 8400 h of culturing and 100 serial passages, S. elongatus PCC 11801 was evolved to tolerate 5 g/L n-butanol or 30 g/L 2,3-butanediol representing a 100% improvement in concentrations tolerated. The evolved strains retained alcohol tolerance even after being passaged several times without the alcohol stress suggesting that the changes were permanent. Whole genome sequencing of the n-butanol evolved strains revealed mutations in a number of stress responsive genes encoding translation initiation factors, RpoB and an ABC transporter. In 2,3-butanediol evolved strains, genes for ClpC, a different ABC transporter, glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase were found to be mutated. Furthermore, the evolved strains showed significant improvement in tolerance toward several other alcohols. Notably, the n-butanol evolved strain could tolerate up to 32 g/L ethanol, thereby making it a promising host for photosynthetic production of biofuels via metabolic engineering.

Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis

Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light color niches. The recent discoveries of several new CA types suggest that additional CA systems involving additional light colors and molecular mechanisms will be revealed in coming years. Here we provide a comprehensive overview of the currently known types of CA and summarize the molecular details that underpin CA regulation.

Chloroplast Translation Elongation Factor EF-Tu/SVR11 Is Involved in var2-Mediated Leaf Variegation and Leaf Development in Arabidopsis

Chloroplasts are semiautonomous organelles, retaining their own genomes and gene expression apparatuses but controlled by nucleus genome encoded protein factors during evolution. To analyze the genetic regulatory network of FtsH-mediated chloroplast development in Arabidopsis, a set of suppressor mutants of yellow variegated (var2) have been identified. In this research, we reported the identification of another new var2 suppressor locus, SUPPRESSOR OF VARIEGATION11 (SVR11), which encodes a putative chloroplast-localized prokaryotic type translation elongation factor EF-Tu. SVR11 is likely essential to chloroplast development and plant survival. GUS activity reveals that SVR11 is abundant in the juvenile leaf tissue, lateral roots, and root tips. Interestingly, we found that SVR11 and SVR9 together regulate leaf development, including leaf margin development and cotyledon venation patterns. These findings reinforce the notion that chloroplast translation state triggers retrograde signals regulate not only chloroplast development but also leaf development.