A pair of towers and retail podium would rise above the Massachusetts Turnpike in Back Bay at Samuels & Assoc.’s proposed 550,000-square-foot air rights development on Massachusetts Department of Transportation’s parcel 12.

The developer kicked off permitting Thursday for the 1-acre site, which would be built on an elevated deck above the Turnpike. The towers would contain office space and either residences or a hotel, said Abe Menzin, Samuels’ senior vice president of development.

It’s the second air rights project currently moving ahead in the Back Bay. Boston-based Weiner Ventures received approval in March for a 108-unit condo tower on MassDOT’s parcel 15, which would cover the Turnpike just west of the Prudential Center tunnel.

The Samuels proposal will include 325,000 square feet of office space and 150,000 square feet of residences or hotel space above a 70,000-square-foot retail podium.

“We think this is a unique project in terms of its ability to connect all of these neighborhoods together,” Menzin said. “We’ve come up with some significant improvements to the public infrastructure, which gelled nicely with the timing of the office market being healthy in Boston. This is a really visible sight which comes with a lot of responsibility, but it also means it’s a very marketable site from a retail and office perspective.”

Designs by Elkus Manfredi Architects would improve pedestrian and bicycling access, with the creation of separated bus and bike lanes on the west side of Massachusetts Avenue. A long-dormant pedestrian tunnel beneath Newbury Street would be reactivated, providing new access to the MBTA’s Hynes Convention Center station.

The project would enable the on-ramp to the Massachusetts Turnpike to be moved further west, rather than dipping down immediately past the Massachusetts Avenue intersection. And sidewalks would be widened from 10 to 30 feet on the western side of Massachusetts Avenue, Menzin said.

Cost of the building the roughly half-acre deck above the Turnpike, which has been a sticking point for many air rights projects, has yet to be determined, Menzin said. A detailed project notification form will be filed with the Boston Planning and Development Agency this summer.