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The activity of plasmodesmata are linked to physiological and developmental processes within plants. There is a hormone signaling pathway that relays primary cellular signals to the plasmodesmata. There are also patterns of environmental, physiological, and developmental cues that show relation to plasmodesmata function. An important mechanism of plasmodesmata is the ability to gate its channels. The pore size of plasmodesmata determines the flow of micro and macro molecules through the cells. This allows for cell-to-cell communication and for long distance signaling. Callose levels have been proved to be a method of changing plasmodesmata aperture size. Callose deposits are found at the neck of the plasmodesmata in new cell walls that have been formed. The level of deposits at the plasmodesmata can fluctuate which shows that there are signals that trigger an accumulation of callose at the plasmodesmata and cause plasmodesmata to become gated or more open. Enzyme activities of Beta 1,3-glucan synthase and hydrolases are involved in changes in plasmodesmata cellulose level. Some extracellular signals change transcription of activities of this synthase and hydrolase. Arabidopsis thailana contain callose synthase genes that encode a catalytic subunit of B-1,3-glucan. Gain of function mutants in this gene pool show increased deposition of callose at plasmodesmata and a decrease in macromolecular trafficking as well as a defective root system during development.

Cytoskeletal components of Plasmodesmata
Plasmodesmata link almost every cell within a plant, which can cause negative effects such as the spread of viruses. In order to understand this we must first look at cytoskeletal components, such as actin microfilaments, microtubules, and myosin proteins, and how they are related to cell to cell transport. Actin microfilaments are linked to the transport of viral movement proteins to plasmodesmata which allow for cell to cell transport through the plasmodesmata. Fluorescent tagging for co-expression in tobacco leaves showed that actin filaments are responsible for transporting viral movement proteins to the plasmodesmata. When actin polymerization was blocked it caused a decrease in plasmodesmata targeting of the movement proteins in the tobacco and allowed for 10-kDa (rather than 126-kDa) components to move between tobacco mesophyll cells. This also impacted cell to cell movement of molecules within the tobacco plant.

Viruses
Viruses break down actin filaments within the plasmodesmata channel in order to move within the plant. For example, when the cucumber mosaic virus (CMV) gets into plants it is able to travel through almost every cell through utilization of viral movement proteins to transport themselves through the plasmodesmata. When tobacco leaves are treated with a drug that stabilizes actin filaments, phalloidin, the cucumber mosaic virus movement proteins are unable to increase the plasmodesmata size exclusion limit (SEL).

Myosin
High amounts of myosin proteins are found at the sights of plasmodesmata. These proteins are involved in directing viral cargoes to plasmodesmata. When mutant forms of myosin were tested in tobacco plants, viral protein targeting to plasmodesmata was negatively affected. Permanent binding of myosin to actin, which was induced by a drug, caused a decrease in cell to cell movement. Viruses are also able to selectively bind to myosin proteins.

Microtubules
Microtubules are also are also an important role in cell to cell transport of viral RNA. Viruses use many different methods of transporting themselves from cell to cell, and one of those methods associating the N-terminal domain of its RNA to localize to plasmodesmata through microtubules. Tobacco plants injected with tobacco movement viruses that were kept in high temperatures there was a strong correlation between TMV movement proteins that were attached to GFP with microtubules. This lead to an increase in the spread of viral RNA through the tobacco.