Machine gets Gene in trouble (6)
I believe the answer is:
engine
'machine' is the definition.
(engine is a kind of machine)
'gene in trouble' is the wordplay.
'trouble' is an anagram indicator.
'gene'+'in'='genein'
'genein' is an anagram of 'ENGINE'.
'gets' is the link.
(Other definitions for engine that I've seen before include "Machine that converts energy into motion" , "Motor" , "Machine doing work" , "Mallard, perhaps" , "eg Nine (anag.)" .)