Structural analysis of the plastid transcriptional complex and study of functional regulations through plastid-nucleus cross-talk during the rise of photosynthesis in angiosperms – PEPPAPnetworks

The assembly of the photosynthetic apparatus (PS) in plastids requires specific transcription of the photosynthesis associated plastid genes (PhAPGs) and of photosynthesis associated nuclear genes (PhANGs). In angiosperms, upon perception of light, plastids differentiate into chloroplasts with strong coordination of PhAPGs and PhANGs transcription involving anterograde signals from nucleus to plastids, retrograde signals from plastids to the nucleus, both supported by protein trafficking between the organelles. Among all, redox signals play an essential role in the operational buildup of the PS.
Although the plastid genome is very small, it remains essential for autotrophic plant development. Its expression requires a eukaryotic-type and prokaryotic-type expression machinery. In plastids, the PhAPGs (type I genes such as rbcl, psaA and psbA) are transcribed by the plastidial RNA-polymerase (PEP), a machinery of unknown 3D structure at the center stage of this proposal. The PEP catalytic core comprises four plastid-encoded prokaryotic subunits that assemble in plastids. Upon light-induced chloroplast development, in angiosperms, the PEP catalytic core is reshaped with addition of 12 nuclear-encoded subunits called PEP-associated proteins (PAPs) translocated into plastids via recognition of a N-terminal chloroplast transit peptide (cTP). The PAPs, of various functions, are co-expressed in mesophyll cells exposed to light. The PEP is therefore a multi-subunit complex mixing domains of plastid- and nuclear-encoded proteins. The PAPs are indissociably essential to transcribe PhAPGs. As a regulon, the PAP genes exhibit similar co-expression profiles. Their expression in the dark is specific to epidermal cells of the cotyledons while light rapidly induces transcription in mesophyll cells through the phytochrome-mediated light regulation network. Although PAPs expression may be regulated by skotomorphogenetic and photomorphogenetic factors (PIFs and HY5-related transcription factors), the dark-light switch in the expression pattern is not well understood. Moreover, at least four PAPs display a functional nuclear localization signal and are dually-localized into the nucleus and chloroplast, triggering the question of nuclear sub-complexes coordinating plastid and nuclear functions. From their protein domain assignments, the function of nuclear PAPs may directly relate to nucleic acid metabolism, gene expression and chromatin state regulation. Dually-localized PAPs may carry several signals to the nucleus to regulate the PhANGs transcription by interacting with nuclear proteins involved in the control of the nuclear transcription. To date, little is known about the PAPs trafficking from the chloroplast to the nucleus, the compositions of PAPs-containing nuclear complexes as well as their role in nuclear functions. Little is also known about the precise role of all PAPs within the PEP complex as well as the 3D structures of the full complex. To understand the functions of the PAPs in both organelles, we want to characterize:
- the control of nuclear transcription by the dually-localized PAPs,
- the role of PAPs and other proteins in regulating the PEP activity in chloroplast,
- the PEP 3D structures at the atomic resolution.
Plastid transcription has been an important hub for growth competition and adaptation during evolution; it has been an important target for plant growth control in agriculture, and it is still hiding so many secrets in link to the great success of the green lineage in our biosphere to justify the effort in studying the structure-function relationships of the PEP/PAPs complexes.