Methylglyoxal (MGO) and glyoxal (GO) are toxic reactive carbonyl species generated as by-products of glycolysis. The pre-emption pathway for detoxification of these products, the glyoxalase (GLX) system, involves two consecutive reactions catalyzed by GLXI and GLXII. In , the GLX system is encoded by three homologs of and three homologs of , from which several predicted GLXI and GLXII isoforms can be derived through alternative splicing. We identified the physiologically relevant splice forms using sequencing data and demonstrated that the resulting isoforms have different subcellular localizations. All three GLXI homologs are functional in vivo, as they complemented a yeast GLXI loss-of-function mutant. Efficient MGO and GO detoxification can be controlled by a switch in metal cofactor usage. MGO formation is closely connected to the flux through glycolysis and through the Calvin Benson cycle; accordingly, expression analysis indicated that GLXI is transcriptionally regulated by endogenous sugar levels. Analyses of Arabidopsis loss-of-function lines revealed that the elimination of toxic reactive carbonyl species during germination and seedling establishment depends on the activity of the cytosolic GLXI;3 isoform. The Arabidopsis GLX system involves the cytosol, chloroplasts, and mitochondria, which harbor individual components that might be used at specific developmental stages and respond differentially to cellular sugar status.

The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.

The Arabidopsis genome annotation include 11 glyoxalase I (GLXI) genes, all encoding for protein members of the vicinal oxygen chelate (VOC) superfamily. The biochemical properties and physiological importance of three Arabidopsis GLXI proteins in the detoxification of reactive carbonyl species has been recently described. Analyses of phylogenetic relationships and conserved GLXI binding sites indicate that the other eight GLXI genes (GLXI-like) do not encode for proteins with GLXI activity. In this perspective article we analyse the structural features of GLXI and GLXI-like proteins, and explore splice forms and transcript abundance under abiotic stress conditions. Finally, we discuss future directions of research on this topic with respect to the substrate identification of GLXI and GLXI-like proteins and the need of reliable quantitative measurements of reactive carbonyl species in plant tissues.

BackgroundGenome reduction in intracellular pathogens and endosymbionts is usually compensated by reliance on the host for energy and nutrients. Free-living taxa with reduced genomes must however evolve strategies for generating functional diversity to support their independent lifestyles. An emerging model for the latter case is the Rhodophyta (red algae) that comprises an ecologically widely distributed, species-rich phylum. Red algae have undergone multiple phases of significant genome reduction, including extremophilic unicellular taxa with limited nuclear gene inventories that must cope with hot, highly acidic environments.ResultsUsing genomic data from eight red algal lineages, we identified 155 spliceosomal machinery (SM)-associated genes that were putatively present in the red algal common ancestor. This core SM gene set is most highly conserved in Galdieria species (150 SM genes) and underwent differing levels of gene loss in other examined red algae (53-145 SM genes). Surprisingly, the high SM conservation in Galdieria sulphuraria coincides with the enrichment of spliceosomal introns in this species (2 introns/gene) in comparison to other red algae (< 0.34 introns/gene). Spliceosomal introns in G. sulphuraria undergo alternatively splicing, including many that are differentially spliced upon changes in culture temperature.ConclusionsOur work reveals the unique nature of G. sulphuraria among red algae with respect to the conservation of the spliceosomal machinery and introns. We discuss the possible implications of these findings in the highly streamlined genome of this free-living eukaryote.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1161-x) contains supplementary material, which is available to authorized users.

Cyanidioschyzon merolae (C. merolae) is an acidophilic red alga growing in a naturally low carbon dioxide (CO) environment. Although it uses a ribulose 1,5-bisphosphate carboxylase/oxygenase with high affinity for CO, the survival of C. merolae relies on functional photorespiratory metabolism. In this study, we quantified the transcriptomic response of C. merolae to changes in CO conditions. We found distinct changes upon shifts between CO conditions, such as a concerted up-regulation of photorespiratory genes and responses to carbon starvation. We used the transcriptome data set to explore a hypothetical CO concentrating mechanism in C. merolae, based on the assumption that photorespiratory genes and possible candidate genes involved in a CO concentrating mechanism are co-expressed. A putative bicarbonate transport protein and two α-carbonic anhydrases were identified, which showed enhanced transcript levels under reduced CO conditions. Genes encoding enzymes of a PEPCK-type C pathway were co-regulated with the photorespiratory gene cluster. We propose a model of a hypothetical low CO compensation mechanism in C. merolae integrating these low CO-inducible components.

Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. sulphuraria , which is 14°C below its optimal growth temperature of 42°C. Cold stress was applied for more than 100 generations to identify components that are critical for conferring thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted samples grew ∼30% faster than the starting population. Whole-genome sequencing revealed 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule nucleation, and transmembrane transport. CpG islands located in the intergenic region accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. We present 20 candidate genes and three putative cis -regulatory elements with various functions most affected by temperature. Our work shows that natural selection toward temperature tolerance is a complex systems biology problem that involves gradual reprogramming of an intricate gene network and deeply nested regulators.

18The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics 19 that impact our understanding regarding the origin of metabolic processes and the role of 20 organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales 21 genomes and determined that 1% of their gene inventory is candidates originated from polyextremophilic prokaryotes that live in similar habitats as the 23Cyanidiales and encodes functions related to polyextremophily. HGT candidates differ from 24 native genes in GC-content, number of splice sites, and gene expression. HGT candidates are 25 more prone to loss, which may explain the nonexistence of a eukaryotic pan-genome. 26Therefore, absence of a pan-genome and cumulative effects fail to provide substantive 27 arguments against our hypothesis of recurring HGT followed by differential loss in 28 eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction 29 underlines the importance of non-endosymbiosis related foreign gene acquisition. 30others. Under this view, there is no eukaryotic pan-genome, there are no cumulative effects 56 (e.g., the evolution of eukaryotic gene structures and accrual of divergence over time), and 57 therefore, mechanisms for the uptake and integration of foreign DNA in eukaryotes are 58 unnecessary. 59 A comprehensive analysis of the frequency of eukaryotic HGT was recently done by 60Ku et al. [13]. These authors reported the absence of eukaryotic HGT candidates sharing over 61 70% protein identity with their putative non-eukaryotic donors (for very recent HGTs, this 62 figure could be as high as 100%). Furthermore, no continuous sequence identity distribution 63 was detected for HGT candidates across eukaryotes and the "the 70% rule" was proposed 64 4 ("Coding sequences in eukaryotic genomes that share more than 70% amino acid sequence 65 identity to prokaryotic homologs are most likely assembly or annotation artifacts.") [13]. 66 However, as noted by others [14, 15], this result was obtained by categorically dismissing all 67 eukaryotic HGT singletons located within non-eukaryotic branches as assembly/annotation 68 artefacts, as well as those remaining that exceeded the 70% threshold. In addition, all genes 69 that were presumed to be of organellar origin were excluded from the analysis, leaving a 70 small dataset extracted from already under-sampled eukaryotic genomes. 71Given these uncertainties, the aim of our work was to systematically analyze 72 eukaryotic HGT using the Cyanidiales as model organisms. The Cyanidiales comprise a 73 monophyletic clade of polyextremopilic, unicellular red algae (Rhodophyta) that thrive in 74 acidic and thermal habitats worldwide (e.g., volcanoes, geysers, acid mining sites, acid rivers, 75 urban wastewaters, geothermal plants) [16]. With a divergence age estimated to be around 76 1.92 -1.37 billion years [17], the Cyanidiales are the earliest split within Rhodophyta and 77 define one of oldest surviving eukaryotic lineages. They are located near ...

12Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. 13 Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional 14 and post-transcriptional mechanisms. Persistent change of the environmental context, however, 15 requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic 16 eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In 17 this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. 18 sulphuraria, which is 14°C below its optimal growth temperature of 42°C. Cold stress was 19 applied for more than 100 generations to identify components that are critical for conferring 20 thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted 21 samples grew ~30% faster than the starting population. Whole-genome sequencing revealed 22 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions 23 involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule 24 nucleation, and transmembrane transport. CpG islands located in the intergenic region 25 accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. 26We present 20 candidate genes and three putative cis-regulatory elements with various 27 functions most affected by temperature. Our work shows that natural selection towards 28 temperature tolerance is a complex systems biology problem that involves gradual 29 reprogramming of an intricate gene network and deeply nested regulators. 30 31 32