Branding the mark of the Decepticons into one's structure is more significant than wearing the Autobrand or the simple inks that humans paint upon themselves. It weaves its way into the body, taking hold of vital circuits until it makes its way the Transformer's very spark. And once the branding is done, it is not easy to remove...
Dreamwave Generation One comics
After sufficient (and painful) modifications to the structure, a newly recruited Decepticon would then be branded with the mark of the Decepticons. Starscream once claimed that it was all part of Megatron's way of controlling them.
Later, after the creation of Alpha Quintesson's planets, Megatron rebranded Scorponok, going even further than the last time. After this, he captured Inferno and branded him, causing a mental battle within Inferno over whether or not he was an Autobot. The dilemma only ended with his death.
Once the Constructicons had completed the space bridge, Megatron then initiated them into the ranks of the Decepticons. After the pair recited the oath of loyalty, Megatron then branded them with the Decepticon seal, painfully. The two Constructicons suffered some serious discomfort, but also got a color change of their exostructures and optics.