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. WHY ALGAE (IN GENERAL) AND CHLAMYDOMONAS (SPECIFICALLY)? Algae represent a very large and diverse polyphyletic group of photosynthetic eukaryotes (Blaby-Haas and Merchant, 2019). They occupy all possible ecological niches on the planet, and therefore constitute a potential reservoir of untapped functional capabilities for adaptation to the environment. Algae are primary producers that contribute ;50% of total carbon fixation worldwide (Field et al., 1998), which makes their study fundamental to our understanding of global primary production and carbon flux. They also offer a low-cost option for the large-scale production of high-value molecules, since algae only require water, salts, air, and light. Unicellular algae such as the ciliated green alga Chlamydomonas reinhardtii offer high signal-to-noise during experiments due to the ease of growth in controlled medium and environments (temperature and light regimes) and the homogenous nature of the cultures, and they grow much more rapidly than classic plant models. With its haploid genome, C. reinhardtii is well suited for classical genetics, as loss-of-function mutations are immediately expressed and more likely lead to observable phenotypes compared with diploid organisms. C. reinhardtii not only responds to light, but it also anticipates environmental transitions like dawn and dusk under the supervision of a circadian system, which coordinates cell division, photosynthesis, and cilia biogenesis, representing three fundamental research topics (Noordally and Millar, 2015). Other topics of research using C. reinhardtii include t...

Site-Specific Gene Knock-Out and On-Site Heterologous Gene Overexpression in Chlamydomonas reinhardtii via a CRISPR-Cas9-Mediated Knock-in Method

“…Chlamydomonas reinhardtii is widely used as a model organism and considered to be a potential cell factory to produce value-added compounds (Khan et al, 2018;Salomé and Merchant, 2019). Production of compounds such as zeaxanthin, sesquiterpene, bio-hydrogen, and human epidermal growth factor, have been reported in C. reinhardtii (Torzillo and Seibert, 2013;Lauersen et al, 2016;Baek et al, 2018;Baier et al, 2018a).…”

A recombineering pipeline to clone large and complex genes in Chlamydomonas

“…Figure 1F shows that Chlamydomonas has a higher proportion of long genes and fewer short genes than the three other genomes tested, along with a considerably higher average gene size for Chlamydomonas (5322 bp versus 1430 bp for yeast, 2187 bp for Arabidopsis and 3521 bp for chromosome-assigned genes in wheat). Unlike wheat, Arabidopsis and yeast, Chlamydomonas genes show a trend of increasing complexity per kilobase for longer genes ( Figure 1F), potentially in line with an increase in average UTR length as gene length increases (Salomé and Merchant, 2019).…”

“…The unicellular alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) is a widely used model organism for studying photosynthesis, biofuel production, ciliopathies, flagella-powered motility and cell cycle control (Salomé and Merchant, 2019). Its nuclear, chloroplast and mitochondrial genomes are sequenced, well annotated and transformable, and a variety of genetic resources are available to any institution including a close-to-genome-saturating mutant library (Li et al, 2019), extensive -omics based data and a wealth of molecular tools developed over decades by a dedicated research community (Salomé and Merchant, 2019). These collections, data and tools are a vital resource for studies that aim to understand fundamental biological processes, to guide engineering efforts such as improved photosynthetic efficiency and to enable efficient biomolecule production.…”

What’s so special about Giardia ventral flagella? Interspecies cross-reacting monoclonal antibody againstPneumocystis jirovecireacts with cilia and sparks questions on host-pathogen interactions

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