Light Harvesting Complexes

From Purdue Genomics Database Facility

Analyses by Dion G. Durnford (durnford@unb.ca) and Jon Neilson (f5yrn@unb.ca), University of New Brunswick, Canada

The light harvesting complexes (LHCs) are a family of nucleus-encoded genes that are post-translationally targeted to the chloroplast where they assemble with chlorophylls (a and b) and carotenoids and integrate into the thylakoid membrane. In the thylakoids they assemble with either Photosystem I or II and function in the harvesting and dissipation of light energy.

Mining and Analyses: Following BLAST-retrieval of the Selaginella sequences, the sequences were aligned and a dataset composed of 137 characters (amino acids) was used to run a maximum likelihood analysis (PhyML, using the LG substitution matrix and accounting for rate variation using 4 gamma categories and the proportion of invariant amino acids. We also retrieved, clustered and included sequences from various EST projects, including Marchantia polymorpha to include in the analyses of the Selaginella sequences. From this analysis (Figure 1), we were able to assign gene names with high confidence.

Results: In Selaginella there are 13 genes encoding the LHC gene family with little evidence of the gene duplication that we often see in other organisms. The following genes (Protein ID) were annotated in Selaginella:

Photosystem II Associated:

Major LHCII:

Lhcb1-1 (87696), Lhcb1-2 (449573)

Lhcb2-1 (158381), Lhcb2-2 (228506) (incomplete- sequencing gaps),

Lhcb3-1(449574), Lhcb3-2(154910)

Minor LHCII:

Lhcb4-1(149722), Lhcb4-2 (181909): CP29

Lhcb5-1 (444370), Lhcb5-2 (35860): CP26

Lhcb6-1 (271833), Lhcb6-2(229479): CP24

Photosystem I Associated:

LHCI

Lhca1 (423144) (only 1 allele detected)

Lhca2-1 (446130), Lhca2-2 (271845)

Lhca3-1 (160411), Lhca3-2 (163144)

Lhca4-1 (270427), Lhca4-2 (271139)

Lhca5-1 (449571), Lhca5-2 (449584)

Minor Antennae:

Lhcq-1 (104804); Lhcq-2 (181983)

PsbS-1 (449583), PsbS-2 (449586)

Figure 1: Maximum Likelihood tree of the Chlorophyll a/b-binding proteins. Selaginella proteins are indicated with a green background. Strongly supported clades containing Selaginella LHCs are indicated by various coloured branches and labeled to the specific protein (gene) clade indicated to the right. Bootstrap values (500 replicates) are indicated at nodes with >50% support.

Main Conclusions:

(1) The Selaginella antennae system is similar to that of angiosperms in terms of complexity of the LHC gene family and the presence of functional homologs. Thus, the genetic components of the antenna system were well developed early in the evolution of land plants.

(2) The transition to land, as evidenced from the Physcomitrella and Selaginella genomes, and clustered Marchantia polymorpha ESTs, correlated with the appearance of the minor PSII antenna protein CP24 (Lhcb6 gene), which is absent from algae examined to date.

(3) Of particular interest is the lack of the LI818 protein (LhcsR), which was used as an outgroup in Figure 1, from Selaginella. LI818 is present in most photosynthetic eukaryotes, with the exception of angiosperms and now Selaginella. A clear LI818 homolog is present in Physcomitrella and thus lost during the evolution of vascular plants. The LI818 protein was first discovered in Chlamydomonas and was correlated with light stress exposure, thus was predicted to have a function related photoprotection. The lack of LI818 (LhcsR) probably represents a change in photoprotective strategies, toward a classic plant response that likely involves the PsbS protein (present in Selaginella), which has an essential role in the photoprotective mechanism called nonphotochemical quenching (NPQ).

LHC-Relatives:

Selaginella has a diverse collection of proteins that are considered members of the larger LHC superfamily, though structurally they are quite unique. These proteins are predicted to be located in the thylakoid membrane and involved in some aspect of photoprotection based on induction characteristics in other organisms, though for the most part their function is unknown. Number after the “-“ in the protein name refers to an allelic variant.

The “one-helix protein” family (1 MSR): 2 members'

OHP1-1 (174988), OHP1-2 (187474)

OHP2-2 (449588), OHP2-1 (449938)

The “Stress Enhanced Protein” family (2 MSR): 5 members

SEP1-1 (449617), SEP1-2 (449939)

SEP2-2 (449618), SEP2-1 (443121)

SEP3-1 (449619), SEP3-2 (449937)

SEP4-1 (449590), SEP4-2 (449610)

LIL3-1 (449446), LIL3-2 (449444)

The “Early Light Inducible Protein” family (3 MSRs): 2 members

ELIP1-1 (449469), ELIP1-2 (449486)

ELIP2-1 (449942), ELIP2-2 (449620)