Plant Gene and Trait 2025, Vol.16, No.3, 92-103 http://genbreedpublisher.com/index.php/pgt 95 3.2 Transcriptional and post-transcriptional regulation of C4 genes Controlling the expression of these genes is not as simple as “turning them on” or “turning them off”. Take Pdk for example, its 5’ end sequence is like a switchboard, which determines whether it can be efficiently expressed in mesophyll cells. The promoter of its other intron controls the low-level expression in the cytoplasm. The same principle can be seen in Me1-5’ controls “where” the expression is, and 3’ controls “how much expression”. However, this is not all. Some regulatory factors are hidden deeper, such as cis-elements (duons) in exons, which are involved in protein coding on the one hand, and can also affect transcriptional repression in specific cells on the other hand. These “multifunctional elements” are not exclusive to C4 plants, but are retained in many land plants. It is these hidden regulatory clues that may have played an unexpected role in the evolution of C4 function (Reyna-Llorens et al., 2018). 3.3 Role of epigenetics and non-coding RNAs in C4 pathway regulation When it comes to regulation, we cannot ignore epigenetics. Unlike DNA sequences, which are clear at a glance, epigenetic changes are more like adding some “emotions” to the original “score” - especially the acetylation and methylation of histones, which play a quiet but important role in regulating C4 genes. Research on corn has found that there are obvious H3K9 acetylation signals in the upstream regions of some photosynthetic genes and C4-related genes. This phenomenon is particularly concentrated in the so-called R-SUP region (secondary upstream peak), which may be the region that lets genes “know” when to be turned on. Although there are not many studies on sugarcane, from other systems, non-coding RNA, such as “small molecule players” such as miRNA, may also intervene - for example, intervening in chromatin state or controlling the stability of mRNA. In other words, the regulatory network of C4 may be more complicated than we imagined (Perduns et al., 2015; Morselli and Dieci, 2022). 4 Genetic Control of Carbon Fixation and Transport 4.1 Genes involved in Rubisco activity and Calvin cycle regulation It is not an exaggeration to say that the enzyme Rubisco is the “opening remarks” of photosynthesis. Without it, CO₂ cannot enter the cycle. But Rubisco does not fight alone. Its activity is regulated by a whole set of transcriptional and post-translational mechanisms. For crops like sugarcane, the expression of Rubisco and a bunch of Calvin cycle-related genes will change when there is shading or excessive sugar accumulation. This shows that its expression is “mutually sensitive” to sugar concentration and reservoir demand, and there may be some kind of kinase pathway involved in the coordination behind it (Figure 2). In addition to Rubisco, enzymes involved in RuBP regeneration cannot be ignored, such as PRK, RPI and RPE-the regulation of these enzymes is actually very critical. They often respond to environmental pressures through changes in redox or metabolic states to ensure that the entire cycle is not “stuck” (Chen et al., 2022; Meloni et al., 2023). 4.2 Sugar transporter genes and carbon partitioning in source-sink dynamics After carbon fixation, the next question is how to send these sugars to “where they should go”. Once the sugar is synthesized in the leaves of sugarcane, it still depends on sugar transporters to be successfully transported to the roots and stems. Especially when photosynthesis is enhanced and the source-sink ratio is unstable, the expression of such transport genes will be significantly upregulated (McCormick et al., 2008). Taking Arabidopsis as an example, sucrose transporters such as SUC and SWEET are responsible for the loading and unloading of sugars in the phloem. The location, timing and even response of these proteins to the external environment are very particular. It can be said that they regulate the efficiency of the “carbon logistics” in the entire plant-how do leaves supply sugar to the roots? How does the storage area adjust the receiving intensity? Behind it, it is inseparable from the work of these transporters at the cellular level (Durand et al., 2017). 4.3 Genetic factors affecting starch and sucrose biosynthesis Once carbon enters the cell, it is not as simple as converting it on the spot. How the sugar in sugarcane is converted into starch or sucrose depends on the gene expression of the relevant metabolic enzymes. For example, once the source-sink relationship is disrupted, the expression of many metabolic genes will “change accordingly”, especially those core enzyme genes that control starch synthesis or sucrose synthesis. Like HXK (hexokinase), its
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