Peer Review #1 of "Exploring regulatory networks in plants: transcription factors of starch metabolism (v0.1)"

Abstract

14Biological networks are complex (non-linear), redundant (cyclic) and compartmentalized at the 15 subcellular level. Rational manipulation of plant metabolism may have failed due to inherent 16 difficulties of a comprehensive understanding of regulatory loops. We first need to identify key 17 factors controlling the regulatory loops of primary metabolism. The paradigms of plant networks 18 are revised in order to highlight the differences between metabolic and transcriptional networks. 19 Comparison between animal and plant transcription factors (TFs) reveal some important 20 differences. Plant transcriptional networks function at a lower hierarchy compared to animal 21 regulatory networks. Plant genomes contain more TFs than animal genomes, but plant proteins 22 are smaller and have less domains as animal proteins which are often multifunctional. We briefly 23 summarize mutant analysis and co-expression results pinpointing some TFs regulating starch 24 enzymes in plants. Detailed information is provided about biochemical reactions, TFs and cis 25 regulatory motifs involved in sucrose-starch metabolism, in both source and sink tissues. 26 Examples about coordinated responses to hormones and environmental cues in different tissues 27 and species are listed. Further advancements require combined data from single-cell 28 transcriptomic and metabolomic approaches. Cell fractionation and subcellular inspection may 29 provide valuable insights. We propose that shuffling of promotorpromoter elements might be a 30 promising strategy to improve in the near future starch content, crop yield or food quality. 31 32 33 Introduction 34 Plant cells are autotrophic organisms fully exposed to many environmental signals. While plants 35 must cope with a wide range of conditions (e.g. light, temperature, water availability, etc.), 36 animals enjoy more stable environments since they are able to escape from danger and to migrate 37 searching for food. Plants are totipotent while animal cells are non-totipotent due to regulatory 38 restrictions by cytosolic and nuclear factors. Photosynthesis in plants leads to sucrose and starch 39 providing food for heterotrophic organisms. This review summarizes what we know about 40 transcriptional regulation of starch metabolism in flowering plants. Most genes of starch 41 synthesis and degradation have been widely studied due to their importance for plant physiology 42 and growth (Zhang et al. 2012). The expression of key enzymes and their regulatory mechanism 43 at different levels have been investigated (Sakulsingharoj et al. 2004; Li et al. 2011c; Gámez-44 Arjona et al. 2011)).. However, their regulation at transcriptional level is still unclear (Kötting et 45 al. 2010; Geigenberger 2011). The difficulty may arise by the great number of genes (isozymes) 46 that catalyze the main key biochemical reactions in autotrophic organisms (Tiessen et al. 2013; 47 Huang et al. 2014). This review starts by listing relevant enzymes and then proceeds to clarify 48 some paradigms of biological networks...