A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism

Abstract

The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.

Figure 1.

Taxonomic Basis of Chlamydomonas and Volvox. Ehrenberg’s drawings of Chlamydomonas and Volvox cells, published in 1838. Cells that belong to the same species are indicated by Roman numerals in the right panel. Reproduced with permission, Museum für Naturkunde, Berlin. I, Gonium pectorale; II, Gonium punctatum; III, Gonium tranquillum; IV, Gonium hyalinum; V, Gonium glaucum; VI, Eudorina elegans; VII, Syncrypta volvox; VIII, Sphaerosira volvox; IX, Synura uvella; X, Chlamidomonas pulvisculus; XI, Uroglena volvox. The species was identified as Chlamidomonas pulvisculus but renamed Chlamydomonas reinhardtii in 1888.

Figure 2.

Chlamydomonas Anatomy. (A) Transmission electron micrograph (TEM) of a cell. Originally published by Ohad et al. (Ohad et al., 1967) and made available on the Cell Image Library website ( CIL:37252, C reinhardtii. CIL. Data set: https://doi.org/doi:10.7295/W9CIL37252). (B) Drawing of a C. reinhardtii cell based on the TEM image in (A). (C) and (D) Another TEM of a C. reinhardtii cell, showing a complete basal body (white box, enlarged in [D]), nucleus, and pyrenoid. Image courtesy of Dr. William Dentler (University of Kansas). (E) Scanning electron micrograph of C. reinhardtii cells. Note the two cilia per cell. (F) TEM of a cross section through isolated axonemes. The images in (E) and (F) were generated at the Dartmouth College Rippel Electron Microscope Facility by Louisa Howard, Elizabeth Smith, and Erin Dymek (Smith and Lefebvre, 1996).

Figure 3.

Chlamydomonas Life Cycles. (A) The sexual and vegetative cycles of C. reinhardtii. See text for details. Adapted from a figure originally drawn by Karen VanWinkle-Swift and published in The Chlamydomonas Sourcebook, Volume 1 (Harris, 2008). (B) Genes involved in gamete differentiation, agglutination, fusion, and zygote development as a function of mating type. SAD1, SAG1, FUS1, and HAP2 encode glycoproteins critical for gamete mating type recognition, while GSP1 and GSM1 encode transcription factors (TFs) important for zygote development. MT-linked genes are indicated by asterisks. Adapted from Joo et al. (2017).

Figure 4.

Chlamydomonas Culture and Transformation. (A) Chlamydomonas growing on agar plates, slants, and liquid medium. (B) Example of negative phototaxis. The white arrow represents directed strong white light. After 30 min, most cells have swum away. (C) Transformation of C. reinhardtii by electroporation or glass beads. Cultures are grown to a cell density of 1 to 2 × 10⁶ cells/mL and concentrated by light centrifugation before agitation with glass beads or electroporation. After recovery in fresh medium for 8 to 16 h, the cells are plated onto selective plates, and colonies derived from individual transformants develop within 7 to 10 d.

Figure 5.

Genome Sizes and Chromosome Numbers in Bacteria, Green Algae, Plants, Yeast, and Humans. (A) Nuclear genomes. All chromosomes were drawn to scale and ordered by their assigned number. Chromosomes in C. zofingiensis were sorted by length (Roth et al., 2017). The human X and Y chromosomes were drawn for reference. (B) Genome size versus gene space, showing the number of predicted protein-coding loci as a function of nuclear genome size. (C) The mitochondrial genome is a linear molecule (with inverted repeats at each end for replication) in C. reinhardtii, C. zofingiensis, and rice. (D) The plastid genome is a circular molecule in green algae and plants. A portion of the single chromosome from Synechococcus elongatus PCC7942 is shown as a reference for the genome size of the cyanobacterium ancestor that gave rise to modern-day chloroplasts. A.th, Arabidopsis thaliana; B.d, Brachypodium distachyon; C.re, Chlamydomonas reinhardtii; C.zof, Chromochloris zofingiensis; H.s, Homo sapiens; O.s, Oryza sativa; S.c, Saccharomyces cerevisiae; V.car, Volvox carteri; Z.m, Zea mays. (E) Similarities among the genomes of selected strains, represented within the context of the full genome. Haplotype 1 blocks are shown in blue, and haplotype 2 blocks are shown in yellow. (F) and (G) Comparison of gene family sizes between Arabidopsis and Chlamydomonas (F) and poplar (G). The number of genes associated with each gene family was extracted from Guo (2013).