Retrograde signaling in plants: from simple to complex scenarios

The concept of retrograde signaling posits that signals originating from chloroplasts or mitochondria modulate the expression of nuclear genes. A popular scenario assumes that signaling factors are generated in, and exported from the organelles, then traverse the cytosol, and act in the nucleus. In this scenario, which is probably over-simplistic, it is tacitly assumed that the signal is transferred by passive diffusion and consequently that changes in nuclear gene expression (NGE) directly reflect changes in the total cellular abundance of putative retrograde signaling factors. Here, this notion is critically discussed, in particular in light of an alternative scenario in which a signaling factor is actively exported from the organelle. In this scenario, NGE can be altered without altering the total concentration of the signaling molecule in the cell as a whole. Moreover, the active transport scenario would include an additional level of complexity, because the rate of the export of the signaling molecule has to be controlled by another signal, which might be considered as the real retrograde signal. Additional alternative scenarios for retrograde signaling pathways are presented, in which the signaling molecules generated in the organelle and the factors that trigger NGE are not necessarily identical. Finally, the diverse consequences of signal integration within the organelle or at the level of NGE are discussed. Overall, regulation of NGE at the nuclear level by independent retrograde signals appears to allow for more complex regulation of NGE than signal integration within the organelle

Alternative electron pathways in photosynthesis: strength in numbers

Electrons supplied by photosystem I (PSI) can have various fates, serving to regenerate NADPH during linear electron flow (LEF), or entering any of several minor ‘alternative electron pathways’ (AEPs). AEPs are thought to play a role in the regulation of photosynthesis and the alleviation of PSI photoinhibition (reviewed in Allahverdiyeva et al., 2015; Yamori & Shikanai, 2016; Alboresi et al., 2019). Several AEPs have been described, including two modes of cyclic electron flow (CEF), one involving the NADH dehydrogenase-like (NDH) complex (NDH-CEF), the other employing the two proteins PGR5 and PGRL1 (PGR5-CEF) (Fig. 1). Pseudo-cyclic electron flow (PCEF) results in the reduction of oxygen to water – by the Mehler reaction (Mehler-PCEF) during which reactive oxygen species (ROS) are generated and scavenged (reviewed in Leister, 2019), or by the direct reduction of oxygen to water catalysed by flavodiiron proteins (FLVs) (FLV-PCEF) (reviewed in Alboresi et al., 2019) (Fig. 1). These four AEPs are not uniformly distributed across all phylogenetic groups of photosynthetic organisms, but the moss Physcomitrella patens harbours all of them, and is, therefore, ideally suited for investigations of their functional overlaps. In this issue of New Phytologist, Storti et al. (2020; pp. 1316–1326) have extended their previous study on AEPs in P. patens and combined and analysed mutations in three AEPs – the two CEF pathways and FLV-CEF. They found that P. patens tolerates the simultaneous loss of both CEF pathways, but becomes severely impaired even under very low light intensities if FLV-PCEF is inactivated as well. This demonstrates that any one of the three AEPs is dispensable, but each one makes a contribution to the maintenance of PSI function even under nonstressful conditions

Towards understanding the evolution and functional diversification of DNA-containing plant organelles:[version 1; referees: 3 approved]

Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA)

NUMTs in Sequenced Eukaryotic Genomes

Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called nuclear mitochondrial DNA (NUMT). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabditis, Plasmodium, Drosophila, and Fugu to more than 500 in human, rice, and Arabidopsis. The average size is between 62 (baker’s yeast) and 647 bps (Neurospora), respectively. A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, such as the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation

NUPTs in Sequenced Eukaryotes and Their Genomic Organization in Relation to NUMTs

NUPTs (nuclear plastid DNA) derive from plastid-to-nucleus DNA transfer and exist in various plant species. Experimental data imply that the DNA transfer is an ongoing, highly frequent process, but for the interspecific diversity of NUPTs, no clear explanation exists. Here, an inventory of NUPTs in the four sequenced plastid-bearing species and their genomic organization is presented. Large genomes with a predicted low gene density contain more NUPTs. In Chlamydomonas and Plasmodium, DNA transfer occurred but was limited, probably because of the presence of only one plastid per cell. In Arabidopsis and rice, NUPTs are frequently organized as clusters. Tight clusters can contain both NUPTs and NUMTs (nuclear mitochondrial DNA), indicating that preNUPTs and preNUMTs might have concatamerized before integration. The composition of such a hypothetical preNUPT-preNUMT pool seems to be variable, as implied by substantially different NUPTs:NUMTs ratios in different species. Loose clusters can span several dozens of kbps of nuclear DNA, and they contain markedly more NUPTs or NUMTs than expected from a random genomic distribution of nuclear organellar DNA. The level of sequence similarity between NUPTs/NUMTs and plastid/mitochondrial DNA correlates with the size of the integrant. This implies that original insertions are large and decay over evolutionary time into smaller fragments with diverging sequences. We suggest that tight and loose clusters represent intermediates of this decay process

Complexities and protein complexes in the antimycin A-sensitive pathway of cyclic electron flow in plants

22013 LEI 1openInternationalInternational coauthor/editorAntimycin A-sensitive cyclic electron flow (AA-sensitive CEF) was discovered by Arnon and co-workers more than 50 years ago and serves to recycle electrons from ferredoxin (Fd) to plastoquinone (PQ). A role in AA-sensitive CEF has been attributed to the two thylakoid proteins PGR5 and PGRL1 ever since their identification, but this assignment remains controversial. While current technical limitations have prevented unequivocal clarification of their precise function in CEF in vivo, recent biochemical experiments have implied that PGRL1/PGR5 complexes possess Fd-PQ reductase (FQR) activity in vitro. Consequently, PGRL1-PGR5 complexes in flowering plants appear to shuttle between photosystem I (PSI) and the cytochrome (Cyt) b6f complex, whereas in the green alga Chlamydomonas PGRL1 (but not PGR5) has been detected in a PSI-Cyt b6f supercomplex that has intrinsic CEF activityopenLeister, D.; Shikanai, T.Leister, D.M.; Shikanai, T

Evidence that cyanobacterial Sll1217 functions analogously to PGRL1 in enhancing PGR5-dependent cyclic electron flow

In plants and cyanobacteria, the PGR5 protein contributes to cyclic electron flow around photosystem I. In plants, PGR5 interacts with PGRL1 during cyclic electron flow, but cyanobacteria appear to lack PGRL1 proteins. We have heterologously expressed the PGR5 and PGRL1 proteins from the plant Arabidopsis in various genetic backgrounds in the cyanobacterium Synechocystis. Our results show that plant PGR5 suffices to re-establish cyanobacterial cyclic electron flow (CEF), albeit less efficiently than the cyanobacterial PGR5 or the plant PGR5 and PGRL1 proteins together. A mutation that inactivates Arabidopsis PGR5 destabilises the protein in Synechocystis. Furthermore, the Synechocystis protein Sll1217, which exhibits weak sequence similarity with PGRL1, physically interacts with both plant and cyanobacterial PGR5 proteins, and stimulates CEF in Synechocystis. Therefore, Sll1217 partially acts as a PGRL1 analogue, the mode of action of PGR5 and PGRL1/Sll1217 proteins is similar in cyanobacteria and plants, and PGRL1 could have evolved from a cyanobacterial ancestor