Before Getting Started:
This and the next two posts will be referring to genes and the proteins they code for. Writing the two can be confusing, as they often have the same name! This becomes even more confusing when the qualifying terms ‘protein’ and ‘gene’ are not written alongside the names, as is common in scientific papers written for an expert audience.

For example, the insulin like growth factor 1 (IGF1) protein in humans is encoded by the insulin like growth factor 1 (IGF1) gene. Here is where nomenclature becomes very important, as if I hadn’t used the words ‘protein’ and ‘gene’ you would have had to know that the uppercase, non-italicised ‘IGF1’ denotes the protein, and the uppercase, italicised ‘IGF1’ denotes the gene, in order to be able to follow along.

Mind you, this rule applies to human genes, and nomenclatures differ for other species, and there are specific rules for bacteria, mice, chickens, flies, worms, maize, rice…

Crops such as maize and rice are extensively studied, and it’s understandable that nomenclature standards have evolved within those fields for researchers to communicate unambiguously with each other. But there’s no standard that covers ‘all plants’ — many species haven’t even been genotyped much less studied — and here I’ll simply be using the nomenclature as reported in the literature. You may see uppercase, lowercase, or both.

It is standard to use italics for genes and non-italics for proteins regardless, and please read those as such wherever they occur. I will also use ‘gene’ and ‘protein’ everywhere appropriate for extra clarity!

Dormancy induction is the first stage in the onset of winter dormancy, marked by slowed growth and the shedding of leaves. (And for jujube trees, the shedding of the deciduous fruiting branchlets unique to them.)

The lower temperatures of autumn are detected by the whole plant and helps it develop cold hardiness (cold acclimation) well ahead of the very cold temperatures that are coming. Proteins and lipids become less fluid as temperatures fall, which creates rigidity in the cell membranes. These stiffened membranes enable an influx of calcium ions (Ca²⁺) into the cells as calcium channels are activated. This has flow-on effects to do with hormone and enzyme processes that further affect growth and transpiration.

As plants can’t regulate their temperature, plant metabolism slows as temperature-dependent enzyme reactions also slow or cease as temperatures drop.

Increasing levels of cytokine and decreasing levels of the auxin indole-3-acetic acid (both phytohormones) towards the end of the growing season results in the production of callose, a polysaccharide (a long chain carbohydrate polymer). This begins depositing in the plasmodesmata in response to increasing levels of abscisic acid (another phytohormone), which blocks phloem transport and cell-to-cell communications. Abscisic acid inhibits DNA replication, and is a growth inhibitor and storage promoter.

Phytochromes are photoreceptors in leaves which are sensitive to the red and far-red (just before infra-red) end of the visible light spectrum. These wavelengths are longer than those at the blue/ultraviolet end of the spectrum. The sun’s highest point in the sky becomes lower and lower as the winter solstice approaches, and these longer red wavelengths scatter less through the atmosphere than the blue wavelengths. The phytochromes thus detect more red/far-red light than blue as winter advances.

This detection of change in light stimuli make phytochromes a molecular switch — genetic regulators which trigger the reduced expression of the CONSTANS (CO)/FLOWERING LOCUS T (FT) gene module, which regulates flowering. The CO protein becomes less stable in shorter days, and this leads to decreased FT gene expression. The reduced production of the FT protein in turn decreases production of gibberellin synthesis. These lower amounts of gibberellin set in motion physiological changes within the plant that enable bud formation. The FT protein moves through the phloem to the apices of shoots where the formation of bud scales and embryonic shoots develops.

Leaf senescence and leaf fall ends transpiration, causing xylem flow to come to a halt.

During the growing season, carbohydrates produced in the leaves via photosynthesis were regularly transported from the leaves to ’sinks’ such as stems, fruit and roots. This production slows gradually through autumn and winter until leaf fall, when it ceases altogether. Prior to leaf fall though, nitrogen is removed from the leaves and relocated to the main storage organs — the stems and roots in this case — which reach maximum storage capacity just before leaf fall.

With all these processes in place, the tree is now ready for the endodormancy stage, the subject of our next post!