Assistant ultimately in charge is occupied by work matter (5)
I believe the answer is:
topic
'matter' is the definition.
('topic' can be a synonym of 'matter')
'assistant ultimately in charge is occupied by work' is the wordplay.
'ultimately' says to take the final letters.
'in charge' becomes 'ic'.
'is occupied by' indicates putting letters inside.
'work' becomes 'op' (abbreviation for opus).
The last letter of 'assistant' is 't'.
't'+'ic'='tic'
'tic' enclosing 'op' is 'TOPIC'.
(Other definitions for topic that I've seen before include "Theme (of, eg, a talk)" , "Subject (of a talk, etc)" , "one discussed" , "Content of argument" , "might this be hot?" .)