Tree begins autumn pruning, putting leaves everywhere (5)
I believe the answer is:
Here is my best explanation:
'tree' is the definition.
(apple is a kind of tree)
'begins autumn pruning putting leaves everywhere' is the subsidiary indication.
'begins' indicates taking the first letters.
The initial letters of 'autumn pruning putting leaves everywhere' is 'apple'.
(Other definitions for apple that I've seen before include "eg Cox, Bramley", "US computer company", "Tree of the rose family", "Fruit of the rose family", "Common fruit", "'An . . . . . a day keeps the doctor away'", "Pink Lady, for example", "Firm round fruit", "Fruit with firm white flesh" and "A fruit".)