The phycobilisome is primarily bound to the thylakoid membrane via the LCM subunit that penetrates into the reaction centers of PSII. A typical phycobilisome thus provides the absorptive power of more than 600 chromophores to a single PSII dimer . Taking into account the number of chlorophyll a molecules attached to PSII, this brings the total antenna potential for energy absorption to more than 350 chromophores per reaction center. This can be compared to about 100 chlorophylls per cyanobacterial Photosystem I ( PSI ) monomer  . In plant and green algae systems, the number of chromophores is also large , but still smaller than that provided by the phycobilisome. The result of this enlarged antenna allows many cyanobacterial species to increase the ratio of PSI/ PSII to between three and six , as opposed to the green algae and plant situation, where the ratio is close to one )94] ) Lowering the amount of PSII may be physiologically beneficial due to the well known requirement of PSII to replace the D1 protein under normal illumination conditions. Under extreme conditions, high light stress or a combination of light and temperature stress, the cells can be photoinhibited, leading to cell death [82, 96]. One method of prevention of photoinhibition can be achieved by rapid replacement of the PSII D1 subunit, something that can be achieved more efficiently by lowering the total amount of PSII.
An additional protective route would be via disconnection of the phycobilisome from PSII, leading to increased fluorescence. Indeed, the phycobilisome has been shown to have the potential to become disconnected from PSII and to functionally associate with Photosystem I (PSI) (see Chapter 2). A brief period of heat treatment also has the effect of disconnecting the phycobilisome from PSII, without direct damage to either complex . Direct measurements using confocal microscopy have indicated that the phycobilisome is quite mobile in vivo, much more than the photosystems [98, 99]. indicating that the association between antenna and photosystems in cyanobacteria my be much looser than in other systems. Recent experiments performed on cyanobacterial cells in vivo show that the mobility of the phycobilisome and its disconnection from PSII is light dependent . Disconnection occurs rapidly and thus this phenomenon has been equated to state 1-state 2 transition in plants that occurs via the phosphorylation-induced disconnection of LHCII from PSII. In this study, the product of the gene rpaC was found to be required for the occurrence of the state transition at very low light intensities. rpaC deletion mutants exhibited no state transitions, but were unaffected in comparison to wild-type cells, at high light. Thus, multiple mechanisms for protection of PSII may exist.
Many reports exist showing the ability of the phycobilisome to transfer energy to PSI in vitro  and in vivo ; however, whether binding to PSI is mediated by specific interactions or by transient association is unclear . Heat treatment appears not to affect the phycobilisome - PSI functional interaction in the same manner as it does the phycobilisome-PSII interaction . The report by Rakhim-berdieva and coworkers  on Spirulina cells indicates that most of the phycobilisome is functionally connected to PSI, both trimers and monomers, and not to PSII. This could correlate with the fact that, while there is a PSI : PSII ratio of ~6, electron micrographs of thylakoid membranes appear to show almost complete coverage of the stromal side of the thylakoid membrane with phycobilisome complexes [15, 25]. Since LCM has been indicated as the source of phycobilisome-PSII binding, it would be unlikely that phycobilisome-PSI binding would occur via the same mechanism. Indeed, there are indications that the phycobilisome binds to PSI via interactions of rod PBPs, mostly PC, with the ferredoxin-NADP+ oxidore-ductase (FNR) subunit of PSI . It is certainly possible that these auxiliary-like phycobilisome units not connected to PSII loosely interact with PSI, both structurally and functionally, with the potential to increase its potential for both linear and cyclic electron transfer.
This auxiliary population of phycobilisomes could have a second physiological role, in addition to light absorption. The phycobilisome has been identified as an emergency source of nutrients to be used in the case of nitrogen, sulfur, or carbon starvation [83, 84, 105]. Use of the phycobilisome as a nutrient source requires its ordered disassembly, as described in Section 11.3.2.
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