Light is necessary for photosynthesis, but its absorption by pigment molecules such as chlorophyll can cause severe oxidative damage and result in cell death. The excess absorption of light energy by photosynthetic pigments has led to the evolution of protective mechanisms that operate on the timescale of seconds to minutes and involve feedback-regulated de-excitation of chlorophyll molecules in photosystem II (qE). Despite the significant contribution of eukaryotic algae to global primary production, little is known about their qE mechanism, in contrast to that in flowering plants. Here we show that a qE-deficient mutant of the unicellular green alga Chlamydomonas reinhardtii, npq4, lacks two of the three genes encoding LHCSR (formerly called LI818). This protein is an ancient member of the light-harvesting complex superfamily, and orthologues are found throughout photosynthetic eukaryote taxa, except in red algae and vascular plants. The qE capacity of Chlamydomonas is dependent on environmental conditions and is inducible by growth under high light conditions. We show that the fitness of the npq4 mutant in a shifting light environment is reduced compared to wild-type cells, demonstrating that LHCSR is required for survival in a dynamic light environment. Thus, these data indicate that plants and algae use different proteins to dissipate harmful excess light energy and protect the photosynthetic apparatus from damage.

Under high-light conditions, photoprotective mechanisms minimize the damaging effects of excess light. A primary photoprotective mechanism is thermal dissipation of excess excitation energy within the light-harvesting complex of photosystem II (LHCII). Although roles for both carotenoids and specific polypeptides in thermal dissipation have been reported, neither the site nor the mechanism of this process has been defined precisely. Here, we describe the physiological and molecular characteristics of the Chlamydomonas reinhardtii npq5 mutant, a strain that exhibits little thermal dissipation. This strain is normal for state transition, high light-induced violaxanthin deepoxidation, and low light growth, but it is more sensitive to photoinhibition than the wild type. Furthermore, both pigment data and measurements of photosynthesis suggest that the photosystem II antenna in the npq5 mutant has one-third fewer light-harvesting trimers than do wild-type cells. The npq5 mutant is null for a gene designated Lhcbm1 , which encodes a light-harvesting polypeptide present in the trimers of the photosystem II antennae. Based on sequence data, the Lhcbm1 gene is 1 of 10 genes that encode the major LHCII polypeptides in Chlamydomonas. Amino acid alignments demonstrate that these predicted polypeptides display a high degree of sequence identity but maintain specific differences in their N-terminal regions. Both physiological and molecular characterization of the npq5 mutant suggest that most thermal dissipation within LHCII of Chlamydomonas is dependent on the peripherally associated trimeric LHC polypeptides.

Chlamydomonas reinhardtii is a valuable model system for defining the structure and function of polypeptides of the photosynthetic apparatus and the dynamic aspects of photosynthesis. Recently, a genome-wide analysis of cDNAs and a draft genome sequence that covers approximately 90% of the genome were made available, providing a clear picture of the composition of specific gene families, the relationships among the gene family members, and the location of each member on the genome. We used the available sequence information to analyze the extensive family of light-harvesting genes in C. reinhardtii. There are nine genes encoding polypeptides of the major light-harvesting complex of photosystem II, two genes encoding the minor light-harvesting polypeptides of photosystem II, and nine genes encoding polypeptides predicted to comprise the photosystem I light-harvesting complex. Furthermore, there are five genes encoding early light-induced proteins and two genes encoding LI818 polypeptides. A candidate for the PsbS gene has also been found in the raw genome sequence data (Niyogi, personal communication), although no genes encoding homologues of the Sep, or Hli polypeptides have been identified. In this manuscript, we identify and classify the family of light-harvesting polypeptides encoded on the C. reinhardtii genome. This is an important first step in designing specific genetic, biochemical, and physiological studies aimed at characterizing the composition, function, and regulation of the light-harvesting complexes.