Accumulation of Cyanobacterial Photosystem II Containing the 'Rogue' D1 Subunit Is Controlled by FtsH Protease and Synthesis of the Standard D1 Protein.

Unicellular diazotrophic cyanobacteria contribute significantly to the photosynthetic productivity of the ocean and the fixation of molecular nitrogen, with photosynthesis occurring during the day and nitrogen fixation during the night. In species like Crocosphaera watsonii WH8501, the decline in photosynthetic activity in the night is accompanied by the disassembly of oxygen-evolving photosystem II (PSII) complexes. Moreover, in the second half of the night phase, a small amount of rogue D1 (rD1), which is related to the standard form of the D1 subunit found in oxygen-evolving PSII, but of unknown function, accumulates but is quickly degraded at the start of the light phase. We show here that the removal of rD1 is independent of the rD1 transcript level, thylakoid redox state and trans-thylakoid pH but requires light and active protein synthesis. We also found that the maximal level of rD1 positively correlates with the maximal level of chlorophyll (Chl) biosynthesis precursors and enzymes, which suggests a possible role for rogue PSII (rPSII) in the activation of Chl biosynthesis just before or upon the onset of light, when new photosystems are synthesized. By studying strains of Synechocystis PCC 6803 expressing Crocosphaera rD1, we found that the accumulation of rD1 is controlled by the light-dependent synthesis of the standard D1 protein, which triggers the fast FtsH2-dependent degradation of rD1. Affinity purification of FLAG-tagged rD1 unequivocally demonstrated the incorporation of rD1 into a non-oxygen-evolving PSII complex, which we term rPSII. The complex lacks the extrinsic proteins stabilizing the oxygen-evolving Mn4CaO5 cluster but contains the Psb27 and Psb28-1 assembly factors.

Improving microalgae for biotechnology--From genetics to synthetic biology.

Microalgae have traditionally been used in many biotechnological applications, where each new application required a different species or strain expressing the required properties; the challenge therefore is to isolate or develop, characterize and optimize species or strains that can express more than one specific property. In agriculture, breeding of natural variants has been successfully used for centuries to improve production traits in many existing plant and animal species. With the discovery of the concepts of classical genetics, these new ideas have been extensively used in selective breeding. However, many biotechnologically relevant algae do not possess the sexual characteristics required for traditional breeding/crossing, although they can be modified by chemical and physical mutagens. The resulting mutants are not considered as genetically modified organisms (GMOs) and their cultivation is therefore not limited by legislation. On the other hand, mutants prepared by random or specific insertion of foreign DNA are considered to be GMOs. This review will compare the effects of two genetic approaches on model algal species and will summarize their advantages in basic research. Furthermore, we will discuss the potential of mutagenesis to improve microalgae as a biotechnological resource, to accelerate the process from specific strain isolation to growth optimization, and discuss the production of new products. Finally, we will explore the potential of algae in synthetic biology.

The rice word landscape: a detailed catalogue of the rice motif content in the non-coding regions.

Among the different areas of molecular biology concerning the detailed study of different parts of the cell, such as genomics, proteomics, and metabolomics, different new areas of study are emerging which entail the analysis of different parts of the genome, such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study was to construct and analyze a catalogue of all statistically relevant putative functional octamer words or motifs (which we have termed the "motifome" of a given organism) found within first introns, promoters, the 5' and 3' untranslated regions (UTRs), and the entire genome of japonica rice, and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of non-coding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. While common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.

The rice word landscape--a detailed catalog of the rice motif content in the noncoding regions.

Among the different areas of molecular biology concerning the detailed study of different parts of the cell such as genomics, proteomics, or metabolomics, different new areas of study are emerging that entail the analysis of different parts of the genome such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study is to draw up and analyze a catalog of all statistically relevant putative functional octamer words or motifs found within first introns, promoters, the 5' and 3' UTRs, and the entire genome of japonica rice and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of noncoding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. Although common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.

Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis.

Plants undergo an extensive change in gene regulation during abiotic stress. It is of great agricultural importance to know which genes are affected during stress response. The genome sequence of a number of plant species has been determined, among them Arabidopsis and Oryza sativa, whose genome has been annotated most completely as of yet, and are well-known organisms widely used as experimental systems. This paper applies a statistical algorithm for predicting new stress-induced motifs and genes by analyzing promoter sets co-regulated by abiotic stress in the previously mentioned two species. After identifying characteristic putative regulatory motif sequence pairs (dyads) in the promoters of 125 stress-regulated Arabidopsis genes and 87 O. sativa genes, these dyads were used to screen the entire Arabidopsis and O. sativa promoteromes to find related stress-induced genes whose promoters contained a large number of these dyads found by our algorithm. We were able to predict a number of putative dyads, characteristic of a large number of stress-regulated genes, some of them newly discovered by our algorithm and serve as putative transcription factor binding sites. Our new motif prediction algorithm comes complete with a stand-alone program. This algorithm may be used in motif discovery in the future in other species. The more than 1,200 Arabidopsis and 1,700 Orzya sativa genes found by our algorithm are good candidates for further experimental studies in abiotic stress.

Overproduction of a rice aldo-keto reductase increases oxidative and heat stress tolerance by malondialdehyde and methylglyoxal detoxification.

The accumulation of toxic compounds generated by the interaction between reactive oxygen species and polyunsaturated fatty acids of membrane lipids can significantly damage plant cells. A plethora of enzymes act on these reactive carbonyls, reducing their toxicity. Based on the chromosomal localization and on their homology with other stress-induced aldo-keto reductases (AKRs) we have selected three rice AKR genes. The transcription level of OsAKR1 was greatly induced by abscisic acid and various stress treatments; the other two AKR genes tested were moderately stress-inducible. The OsAKR1 recombinant protein exhibited a high nicotinamide adenine dinucleotide phosphate-dependent catalytic activity to reduce toxic aldehydes including glycolysis-derived methylglyoxal (MG) and lipid peroxidation-originated malondialdehyde (MDA). The function of this enzyme in MG detoxification was demonstrated in vivo in E. coli and in transgenic plants overproducing the OsAKR1 protein. Heterologous synthesis of the OsAKR1 enzyme in transgenic tobacco plants resulted in increased tolerance against oxidative stress generated by methylviologen (MV) and improved resistance to high temperature. In these plants lower levels of MDA were detected both following MV and heat treatment due to the activity of the OsAKR1 enzyme. The transgenic tobaccos also exhibited higher AKR activity and accumulated less MG in their leaves than the wild type plants; both in the presence and absence of heat stress. These results support the positive role of OsAKR1 in abiotic stress-related reactive aldehyde detoxification pathways and its use for improvement of stress tolerance in plants.