The fast increment in the number of IoT (Internet of Things) devices is accelerating the research on new solutions to make cloud services scalable. In this context, the novel concept of fog computing as well as the combined fog-to-cloud computing paradigm is becoming essential to decentralize the cloud, while bringing the services closer to the end-system. This article surveys e application layer communication protocols to fulfill the IoT communication requirements, and their potential for implementation in fog- and cloud-based IoT systems. To this end, the article first briefly presents potential protocol candidates, including request-reply and publish-subscribe protocols. After that, the article surveys these protocols based on their main characteristics, as well as the main performance issues, including latency, energy consumption, and network throughput. These findings are thereafter used to place the protocols in each segment of the system (IoT, fog, cloud), and thus opens up the discussion on their choice, interoperability, and wider system integration. The survey is expected to be useful to system architects and protocol designers when choosing the communication protocols in an integrated IoT-to-fog-to-cloud system architecture.