A distinct LHCI arrangement is recruited to photosystem I in Fe-starved green algae

Abstract

Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron microscopy to reveal a unique Fe starvation-dependent arrangement of light-harvesting chlorophyll (LHC) proteins where Fe starvation-induced TIDI1 is found in an additional tetramer of LHC proteins associated with PSI in Dunaliella tertiolecta and Dunaliella salina. These cosmopolitan green algae are resilient to poor Fe nutrition. TIDI1 is a distinct LHC protein that co-occurs in diverse algae with flavodoxin (an Fe-independent replacement for the Fe-containing ferredoxin). The antenna expansion in eukaryotic algae we describe here is reminiscent of the iron-starvation induced (isiA-encoding) antenna ring in cyanobacteria, which typically co-occurs with isiB, encoding flavodoxin. Our work showcases the convergent strategies that evolved after the Great Oxidation Event to maintain PSI capacity.

Keywords: TIDI; iron homeostasis; iron starvation–induced protein A (isiA); phytoplankton; structural biology.

Fig. 1.

Uneven response of Dunaliella spp. LHCA subunits in Fe-starved medium. (A) Geographic distribution of TIDI-encoding algae of either D. salina (orange), D. tertiolecta (green), Chro. zofingiensis (dark blue), T. deserticola (purple), F. rotunda (yellow), and S. NREL 46B-D3 (light blue) modified from Davidi et al. (8). The strains used in this work are D. tertiolecta UTEX LB999 and D. salina Bardawil UTEX LB 2538. (B) A species tree showing the relationship between TIDI1 and non-TIDI1 encoding species from Chlorophyceae (green) and Trebouxiophyceae (salmon). The tree is based on the concatenated polypeptide sequences of universal single-copy orthologs (USCOs) shared among all 9 species. Filled squares signifies the presence of at least one homolog of the indicated protein (FDX1, ferredoxin; FLD1, flavodoxin; LHCA3; TIDI1). Square color describes proteins that are either present (gray), present and binds Fe (cyan), present and binds flavin (green), or absent (white). (C and D) The log₂ fold changes (fc) of protein abundances in the Fe-replete (15 µM Fe) and Fe-starved (0.15 µM Fe) condition detected by at least two spectral counts encoding components of PSII, LHCII, Cyt b₆f, PSI, LHCI, and CF_OCF₁ (ATP synthase) for D. salina (C) and D. tertiolecta (D). For a complete list of protein subunits and their abundances, see Dataset S2. (E and F) The PSI (PSA) and LHCI (LHCA) subunits of PDB:6SL5 (stromal view) colored by its log₂ fold changes (fc) of protein abundances (red, increase; blue, decrease) for D. salina (E) and D. tertiolecta (F). Gray values indicate not detected (<2 spectral counts).

Fig. 2.

Comparison of the Fe-replete and Fe-starved Dunaliella PSI-LHCI supercomplexes. Stromal view (Top) or side view (Bottom) of the PSI-LHCI supercomplexes from D. salina (A and B) and D. tertiolecta (C and D). (A) Fe-replete DsPSI-LHCI₁ supercomplex and (C) Fe-replete DtPSI–LHCI₁ supercomplex in ribbon mode. (B and D) Fe-starved DsPSI–LHCI₂ supercomplex (B) and DtPSI–LHCI₂ supercomplex (D) in ribbon mode (Left) and the composite cryo-EM density map (Right). Subunits are shown in different colors and labeled. Membrane-extrinsic subunits PsaC, PSAD, and PSAE are labeled only in the side view. Black dashed lines indicated the membrane-spanning region of the PSI-LHCI supercomplexes.

Fig. 3.

The interactions between the inner LHCI tetramer and the outer LHCI tetramer in the DsPSI–LHCI₂ and DtPSI–LHCI₂ supercomplexes. (A–H) Top: The interaction regions between the inner and outer LHCI tetramers in the overall DsPSI–LHCI₂ (A–D) and DtPSI–LHCI₂ (E–H) supercomplexes. Boxed areas are enlarged in the indicated panels. Bottom: protein–protein, pigment–pigment, and protein–pigment interactions between: LHCA8a and LHCA1b (A and E), LHCA7a and LHCA1b (B and F), LHCA3 and LHCA7b (C and G), LHCA3 and TIDI1 (D and H). The residues involved in the interactions are highlighted as yellow stick representations.

Fig. 4.

The extended BC loop of DsTIDI1 differently positions Chl 607. (A) Cartoon representation of DsTIDI1. Chls are shown as cyan stick representation, with the central Mg atoms shown as spheres and numbered according to the conserved sites in spinach LHCII (PDB: 1RWT). Carotenoids are shown as yellow-colored stick representation. (B) Interactions between DsTIDI1 and DsLHCA7b in the outer LHCI tetramer are colored in orange. Residues involved in the interaction are shown as orange sticks. (C) Comparison of Chl a607_TIDI1 (magenta) position against position of a607_LHCA3 (light blue) from D. salina on the lumenal side. Distance between molecules is shown as dashed lines. (D) Comparison of DsTIDI1 Chl positions against Chl positions of DsLHCA1, DsLHCA2, DsLHCA3, DsLHCA7, DsLHCA8, and DsLHCA9 from D. salina on the stromal (Top) and lumenal side (Bottom). (E) Side view of D. salina a607_TIDI1 (magenta) and its distance shown as dashed lines to a614_LHCA3 (light blue).

Fig. 5.

Fe-nutrition responsive modification of PSI-LHCI antenna in Dunaliella spp (A-D). (A and C) PSI-LHCI supercomplexes in Fe-replete cells have a single LHCI tetramer (dark green) composed of four subunits in D. salina (A) and D. tertiolecta (C). When cells become Fe-starved, the PSI-LHCI supercomplexes have an additional LHCI tetramer (dark green) also composed of four subunits with the novel, Fe starvation–induced chlorophyll-binding protein, TIDI1 (pink), in D. salina (B) and D. tertiolecta (D). The PSI core subunits are colored in light green. The DtPSI–LHCI₂ does not include the PSAO1, PSAG1, PSAH1, LHCA2, and LHCA9 subunits when compared to those from D. salina cells. Fe-starved D. tertiolecta samples include a small fraction of DtPSI–LHCI₁ supercomplexes, as shown.