Construction of a functional Photosystem II (PSII) in cyanobacteria and chloroplasts depends on the action of auxiliary factors, which transiently interact with PSII intermediates during assembly. In addition to a common PSII structure and a conserved set of PSII assembly factors, cyanobacteria, and higher plants have evolved additional, clade-specific assembly factors. Most such factors in cyanobacteria and chloroplasts have been identified by “top-down” approaches (forward and reverse genetics), which involved genetic disruption of individual components in the assembly process and subsequent characterization of the ensuing phenotypic effects on the respective mutant lines/strains. In contrast, a “bottom-up” strategy, based on the engineering of a synthetic bacterium with a plant-type PSII, has the potential to identify all assembly factors sufficient to make a functional plant PSII. Photosystem II (PSII) is a water-plastoquinone photo-oxidoreductase, which is found in cyanobacteria and their endosymbiotic descendants, the chloroplasts. Light-driven water splitting and subsequent electron transfer steps are carried out with the assistance of non-proteinaceous cofactors. Thus, the PSII monomer harbors a Mn4CaO5 cluster, chloride, bicarbonate, 1-2 hemes, 1 nonheme iron, 35 chlorophyll a molecules, 2 pheophytins, 11 β-carotenes, and 2 plastoquinones (Umena et al., 2011), all of which are embedded in a shell made up of at least 20 proteins (Shen, 2015) that determine their correct positioning and relative orientation. Several PSII-associated lipids have been identified in crystal structures and might also be important for functionality (Mizusawa and Wada, 2012; Kansy et al., 2014). The structural core of PSII is conserved between chloroplasts and cyanobacteria (Allen et al., 2011). However, the oxygen-evolving complex in cyanobacteria contains subunits U and V, which are replaced by Q, R, P, and Tn in higher plants (Bricker et al., 2012). Furthermore, in contrast to the soluble, peripherally attached phycobilisomes found in cyanobacteria, green photosynthetic eukaryotes have evolved integrated light-harvesting complexes and lack phycobilisomes (Hohmann-Marriott and Blankenship, 2011; Figure ​Figure1A1A). Figure 1 Strategies for identifying auxiliary factors in PSII assembly. (A) Subunit compositions of cyanobacterial (Synechocystis) and plant thylakoid (Arabidopsis) PSII complexes. Components shown in blue or yellow are only found in Synechocystis or Arabidopsis ... In accordance with its structural complexity, the assembly of PSII is an elaborate and highly coordinated process, which depends on the action of a network of assembly factors and the fabrication of distinct metastable modules during the course of assembly (see for reviews on this topic: Nixon et al., 2010; Nickelsen and Rengstl, 2013; and papers in this special issue of Frontiers in Plant Science). Several modules common to cyanobacterial and chloroplast PSII assembly processes have been described and are characterized by transient binding of specific assembly factors. An additional level of complexity arises from the fact that PSII is susceptible to photodamage, with subunit D1 being the primary target (Kato and Sakamoto, 2009), as replacement of damaged D1 entails partial disassembly of PSII and reassembly of a functional complex. This repair mechanism features some distinct intermediates, but otherwise involves steps and assembly factors that are shared with the de novo assembly pathway (Jarvi et al., 2015). It has become increasingly clear in recent years that the set of assembly factors is largely conserved between cyanobacteria and chloroplasts (Nickelsen and Rengstl, 2013). However, higher plants have extended their inventory during evolution, giving rise to new, plant-specific factors, such as the D1 stabilization factor HCF243 (Zhang et al., 2011) or the repair factors PPL1 and LQY1 (Ishihara et al., 2007; Lu et al., 2011; Figure ​Figure1B).1B). Furthermore, the consequences of disruption of conserved auxiliary factors sometimes differ between the two systems. For instance, Arabidopsis PAM68 and its cyanobacterial counterpart (Armbruster et al., 2010), as well as HCF136 (Meurer et al., 1998) and the cyanobacterial homolog YCF48 (Komenda et al., 2008), participate in the early steps of PSII assembly, but their absence has more severe effects on photosynthesis in plants. Thus, to understand the evolutionary diversification of assembly factors, it is crucial to study chloroplast and cyanobacterial PSII assembly in parallel.