But that said, I would recommend it-ogo's answer as a general model for how to translate "The question is..." -- in Russian, one can often use вопрос в том ("the question [is] in this..."), or in interrogative contexts, в чём вопрос? ("in what [is] the question?..."). If you want an explicit verb, you can often use лежать, "to lie, to be in a horizontal position".

Вопрос лежал в том, какой рыбой представляет собой эта окаменелость -- морской или речной?
The question was, what kind of fish did this fossil represent: sea-dwelling or river dwelling? (Lit., "The question lay in this: What kind of fish...?")

В чём лежит смысл жизни?
What is the meaning of life? (Lit., "In what lies the meaning of life?")

Вопрос в том, кто (из мужиков) круче всех?
The question is, ¿Quién es más macho?