Well then. According to Maiocco (as seen in this Chronicle article), Tarell Brown will start at left cornerback opposite Shawntae Spencer. Big thanks to kezarvet for mentioning this in the Pro Bowl Voting FanPost. I hadn't even noticed it yet.
According to the Chronicle article, Nate Clements will likely shift inside to a slot position when the 49ers are in their nickel defense, with Dre Bly now being the fourth corner. According to Maiocco this is a one-week demotion of Clements based on the belief that Brown provides a better matchup against the Colts big receivers.
Even if this is a one-week thing, it's still pretty huge news. Brown stated that it was a coincidence that this came just after he signed his contract extension, and I'm definitely willing to believe him. After all, if this was a money thing, Clements would still be the #1 guy this week. Instead the team is dipping their toe in the water with Brown in a pretty big game. Prior to his training camp injury Brown was making big strides, but was set back by that injury.
Given that the team will likely be in their nickel defense much of the game, I'd imagine Clements will still see plenty of playing time. Of course now, instead of facing Reggie Wayne, Clements will be covering Pierre Garcon or Austin Collie much of the time. This could be particularly interesting in the punting game as well. The team mentioned that Nate Clements (and Brandon Jones) could see some time returning punts, so why not go with Clements now that he's not going to be the #1 cornerback?
For those wondering, Clements does have a decent history as a punt returner, with two returned for touchdowns. His most prolific season was in 2004 when he returned 35 punts for 327 yards and a touchdown. Since then he's never returned more than 8.