Inactivation of mitochondrial complex IV in Physcomitrium patens reveals the essential role of respiration in coordinating plants metabolism.
Photosynthetic organisms use sunlight as energy source but rely on respiration during the night and in non-photosynthetic tissues. Respiration is also active in photosynthetically active cells, where its role is still unclear due to a lack of viable mutants. We previously isolated plants lacking a functional complex I (ndufa5). Plants lacking cytochrome c oxidase (complex IV) activity are generally lethal but were here isolated exploiting the possibility of generating knockout lines through vegetative propagation in the moss Physcomitrium patens.  ndufa5 plants showed alterations in carbon and nitrogen metabolism that are consistent with those reported in other Complex I mutants in vascular plants. One of the general features of Complex I-deficient plants, that was observed also in ndufa5, is the induction of the alternative oxidase (AOX). We found the metabolic alterations and the AOX induction in ndufa5 to be more severe by the end of the night than during day. The transcriptome of ndufa5 plants suggests that mitochondria-to-nucleus retrograde signalling pathways are strongly induced by the end of the night, which are probably mediated by a homolog of the transcription factor ANAC017, described in vascular plants.  cox11 mutants showed severely impaired growth, with an altered composition of the respiratory apparatus and increased electron transfer through the alternative oxidase. The light phase of photosynthesis remained largely unaffected while the efficiency of carbon fixation was moderately reduced. Transcriptomic and metabolomic analyses showed that the disruption of the cytochrome pathway had broad consequences for carbon and nitrogen metabolism. A major alteration in nitrogen assimilation was observed with a general reduction in amino acid abundance. A partial rescue of the growth could be obtained by growing the plants with an external supply of amino acids but not with sugars, demonstrating that respiration in plant photosynthetic cells plays an essential role at the interface between carbon and nitrogen metabolism and a key role in providing carbon skeletons for amino acid biosynthesis. Overall design: To investigate the role of respiration, we generated NDUFA5 KO and COX11 KO  lines by exploiting homologous recombination in P. patens. A segment of the NDUFA5 or COX11 gene was disrupted by an antibiotic resistance cassette. Two independent NDUFA5 KO and two independent COX11 KO lines were used in this experiment. The transcriptome of WT, NDUFA5 KO and COX11 KO plants was studied at three different zeitgeber times (ZT0, ZT2, ZT6).