Australia declared its second innings at 401-7 late on day three and Ryan Harris and Johnson took early wickets before Cook and Kevin Pietersen combined to lift England to 24-2 at stumps.
England's third-wicket pair survived the first hour Sunday but Johnson broke through two balls after the first drinks break when he had Pietersen (26) caught behind deep square leg by substitute fielder Chris Sabburg, who had only been on the field for two minutes.
Cook, who had scored an unbeaten 235 here in 2010 in the drawn first test at the Gabba, continued in a 58-run partnership with Bell and the pair showed signs of being capable of batting for a long time.
But Peter Siddle got an important breakthrough as the storm clouds gathered, getting feint edge off Bell to wicketkeeper Brad Haddin to reduce England to 130-4.
With Cook and Root as the last recognized batsmen, England is in danger of losing a test to Australia for the first time since 2010. Bell had dominated the Australian bowlers in England's 3-0 series win in the last northern summer and his dismissal gives the home team high hopes of starting the five-test series with a comprehensive victory.
A slow outfield caused by recent resurfacing work and rain could make batting conditions even more difficult as the match progresses.
No team has scored more than 418 in the fourth innings to win a test match, although there have been bigger fourth innings totals in draws or losses.
England's batsmen were unnerved by the bounce in the Gabba pitch in the first innings and were skittled for 136 including a collapse of six wickets for nine runs in a horrible 58-ball stretch.
Johnson took four wickets in the first innings, troubling England with his pace and controlled short-pitch bowling, and has continued to bother them in the second innings.
He has 2-36 so far. He also contributed 64 to an innings-salvaging 114-run stand with Brad Haddin (94) after Australia had slipped to 100-5 after winning the toss and batting. That helped Australia get to 295 which, despite the criticism at the time, became an apparently decent total compared with the England first innings.
David Warner (124) and Michael Clarke (113) scored centuries in the second innings and Haddin added another half century as Australia tried to bat a loss out of the equation before declaring and sending England in for an hour and then six sessions.
Australia hasn't lost a test match at the Gabba in 25 years, and hasn't lost a test to England in Brisbane since 1986.
England is in Australia aiming to win the Ashes for a fourth consecutive series, something it hasn't achieved since the 1800s.
-AP
