Yorke explained that he wrote this lyric in a the period between OK Computer and Kid A where-in he was in a very depressed state. It makes sense because a lemon is very sour and makes a persons face scrunch up when their taste buds sense the acidity and harshness (the same face a person makes when saddened or stressed).

And just like the harshness of a lemon Yorke creates a metaphor where he and the people of the world wake up sad and angered with their face twisted as if they had sucked on a lemon.
Sucking a lemon is also a common UK phrase, it means you look miserable. If life gives you lemons, don’t wake up sucking on one.