Cyber-Physical Systems (CPSs) combine computation, networking, and physical processes. A CPS consists of various independent subsystem components with different interfaces and protocols defined by vendors. Utilizing different interfaces and protocols with the necessity for flexible, dependable, and extensible CPSs poses new challenges for controlling, communicating, and synchronizing the components. In this paper, we propose a Centralized Control Unit (CCU) for CPSs and the associated Communication Infrastructure that enable the support of subsystem components as "plug-and-play" modules. Our CCU consists of a hardware-software architecture that handles physical signals as well as real-time and non-real-time tasks implemented on a single MPSoC-FPGA. To enforce the dependability and flexibility of the communication between components of different vendors, we model the Communication Infrastructure in layers with communication classes. In addition, we propose three vendor-agnostic application protocols, which are also implemented in the CCU. To validate our work, we have implemented and integrated the CCU with the communication infrastructure into an open-interface Computed Tomography (CT) scanner, where sensors/actuators can be added in a "plug-and-play" fashion. We have also evaluated the effort of integrating an additional detector into our scanner. The CCU runs on an AMD-Xilinx Zynq-7000 XC7Z045, and it uses only 10% of the hardware resources.