Table 1.
A summary of omics studies on plant autophagy
| Study | Species/tissue | Experimental condition |
Platform | Key points of interest |
|---|---|---|---|---|
| Transcriptomics | ||||
| Contento et al., (2004) [35] | A.thaliana suspension culture cells | Sucrose starvation | Microarray | An ATG8 gene was up-regulated under sucrose starvation conditions. |
| Caldana et al., (2011) [36] | A.thaliana leaf | Carbon starvation (Dark treatment) | Microarray | Several ATG genes were up-regulated under dark conditions |
| Buchanan-Wollaston et al., (2005) [37] | A.thaliana leaf | Natural senescence | Microarray | Five ATG genes were identified as up-regulated during leaf senescence. |
| van der Graaff et al., (2006) [38] | A.thaliana leaf | Natural senescence, DIS and DET | Microarray | 19 ATG genes were found to be transcriptionally activated in all three senescence conditions. |
| Breeze et al., (2011) [39] | A.thaliana leaf | Natural senescence | Microarray | 15 ATG genes were transcriptionally up-regulated during leaf senescence with nine of them increasing their expression levels in still-expanding leaves. |
| Álvarez et al., (2012) [47] | A.thaliana leaf | Growth with exogenous sulfide | Microarray | Transcriptome studies confirm the role of sulfide as a repressor of autophagy. |
| Caldana et al., (2013) [48] | A.thaliana leaf | Normal growth conditions | Microarray | Transcriptome studies confirm the role of TOR as a negative regulator of autophagy. |
| Masclaux-Daubresse et al., (2014) [50] | A.thaliana leaf | Short day, low or high nitrogen | Microarray | Genes involved in flavonoid biosynthesis are down-regulated, and pathways for glutathione, methionine, raffinose and galacturonate are altered, in atg mutants. |
| Garapati et al., (2015) [49] | A.thaliana leaf | Normal growth conditions | Microarray | Transcription factor ATAF1 is identified by gene-expression profiling as a potential repressor of autophagy under carbon starvation conditions. |
| Li et al., (2015) [24] | Z. mays leaf, endosperm | Normal growth conditions | RNA-seq | A large set of ATG genes are transcriptionally up-regulated during leaf senescence and in developing endosperm. |
| Pérez-Martín et al., (2015) [46] | C. reinhardtii | Heavy metal toxicity | RNA-seq | Autophagy activity is up-regulated upon heavy metal treatment, and such up-regulation is independent of CRR1. |
| Williams et al., (2015) [44] | T. loliiformis leaf | Desiccation | RNA-seq | 13 ATG genes are up-regulated throughout dehydration and desiccation. |
| Zhu et al., (2015) [45] | B. hygrometrica leaf | Rapid dehydration, slow dehydration, and rapid dehydration after acclimation | RNA-seq | Autophagy activity is up-regulated by slow dehydration and rapid dehydration after acclimation but not in rapid dehydration. |
| Minina et al., (2018) [51] | A.thaliana leaf | Natural senescence | Microarray | Transcriptional changes found in plants over-expressing ATG genes are the opposite of those seen in autophagy-defective mutants. |
| Proteomics | ||||
| Avin-Wittenberg et al., (2015) [57] | A.thaliana seedling | Carbon starvation (etiolated seedlings grown without sugar) | SDS-PAGE MS | Several proteins accumulate in atg mutants. |
| Wang et al., (2018) [58] | A.thaliana leaf | V. dahliae infection | iTRAQ | 780 proteins were identified through iTRAQ to be differentially abundant in wild-type versus atg mutant plants; most are involved in defense responses, oxidative stress responses, phenylpropanoid and lignin metabolism, and mitochondrial function. |
| Havé et al., (2018) [59] | A. thaliana leaf | Short day, low or high nitrogen | LC-MS/MS | Chloroplast protease abundance was reduced and levels of proteasome subunits and some cysteine proteases were increased in atg mutants. |
| Metabolomics | ||||
| Izumi et al., (2013) [65] | A.thaliana leaf | Carbon starvation (short day-grown starchless mutants harvested at the end of the night) | CE-TOFMS | The release of branched-chain amino acids (BCAAs) and aromatic amino acids (AAAs) through protein degradation are partially impaired in starchless atg double mutants. |
| Kurusu et al., (2014) [67] | O. sativa mature anther | Normal growth conditions | LC-MS | PC editing and lipid desaturation during pollen maturation are compromised in an atg mutant. |
| Masclaux-Daubresse et al., (2014) [50] | A.thaliana leaf | Short day, low or high nitrogen | GC-MS; LC-MS; starch assay kit | Reduced levels of starch, hexoses and anthocyanins, but higher levels of several amino acids, were detected in atg mutants. |
| Avin-Wittenberg et al., (2015) [57] | A.thaliana seedling | Carbon starvation (etiolated seedlings grown without sugar) | GC-MS; LC-MS | Reduced levels of free amino acids and altered lipid composition are observed in carbon-starved atg mutants. |
| Barros et al., (2017) [66] | A.thaliana leaf | Carbon starvation (extended darkness) | GC-MS | The release of many amino acids during protein degradation is partially impaired in dark-treated atg mutants. |
Abbreviations are DIS: darkening-induced senescence of individual leaves attached to the plant; DET: senescence in dark-incubated detached leaves; iTRAQ: isobaric tags for relative and absolute quantification; GC-MS: gas chromatography mass spectrometry; CE-TOF MS: capillary electrophoresis time-of-flight mass spectrometry; MS: Mass Spectrometry; LC-MS: liquid chromatography-mass spectrometry; PC: Phosphatidylcholine.