A Complex Little Alga that Lives by the Sea

The Science

Researchers have sequenced and analyzed the genome (the genetic material) of Porphyra umbilicalis. This red alga is thought to be one of the oldest forms of marine life. The team found strong cytoskeletal limitations in Porphyra and most other red algae with sequenced genomes. These results offered a possible explanation for why red algae tend to be small compared to other multicellular eukaryotes. The 50-member team was led by the University of Maine, Carnegie Institution for Science and East Carolina University. They used the Community Science Program of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, to carry out the study.

The Impact

Although red algae are one of the oldest multicellular lineages, only a few have had their genomes sequenced. Porphyra umbilicalis is found in the ocean’s intertidal zone. High and low tides subject the zone to constantly changing conditions. Analyzing the alga’s genome lends insights into how it tolerates stress and how its stress-tolerance mechanisms impact its ability to fix carbon. Because red algae genomes are strongly related to numerous other organisms, understanding the genome impacts aquatic food and oxygen production.

Summary

The intertidal zone is the area between land and sea that is sometimes concealed by high tide or revealed by low tide. As this ecosystem is in constant flux, the organisms that inhabit the area have adapted to thrive under a range of constantly changing environmental conditions. Porphyra and other genera of bangiophyte red algae thrive in the intertidal zones of the northern and southern hemispheres. Their lineage is ancient, and the oldest taxonomically resolved fossil of a multicellular eukaryote, 1.2 billion years old, was also a bangiophyte. The green algae and red algae are both groups of plants that carry out photosynthesis using light-harnessing organelles called chloroplasts, which evolved from cyanobacteria that were engulfed by the ancestral eukaryotic algae. Later, other environmentally important algae such as diatoms, dinoflagellates and haptophytes evolved when other non-photosynthetic eukaryotes captured red algae and integrated the red algal chloroplast and red algal nuclear genes into their genomes. These processes greatly diversified the organisms capable of conducting photosynthesis, and the red algal imprint on global productivity, aquatic food webs, and oxygen production is significant.

As reported in the Proceedings of the National Academy of Sciences, a team sequenced, assembled and annotated the genome of the red alga Porphyra umbilicalis to better understand how it harvests light and nutrients, and how warming oceans might impact its ability to fix carbon. The researchers found that the red alga has previously unrecognized means of tolerating its physically stressful intertidal habitat. For example, Porphyra umbilicalis has multiple strategies to protect cells from being damaged by high light levels, including expanded families of proteins that protect the photosynthetic apparatus from high light. It also has unusual genomic arrangements of the genes that synthesize the mycosporine-like amino acids that protect against ultraviolet light. They also found that the alga has a significantly reduced cytoskeleton and lacks many motors other organisms rely on for intracellular transport. This may explain why red algae, compared to many other multicellular eukaryotes, are smaller and less structurally complex and how they can survive, in the closing words of the publication, “in the pounding waves, baking sun, and drying winds of the high intertidal zone.”

Funding

Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract DE-AC02-05CH11231). This work was also supported by the National Science Foundation, National Oceanic and Atmospheric Administration (NOAA), German Research Foundation, French National Research Agency, U.S. Department of Agriculture/National Institute of Food and Agriculture, Biotechnology and Biological Sciences Research Council and European Union FP7 e Curie Photo.Comm, Connecticut Sea Grant College Program, NOAA National Marine Aquaculture Initiative, National Institutes of Health, United Kingdom Natural Environment Research Council International Opportunities Fund Pump-priming + scheme, The Great Barrier Reef Foundation, Australian Research Council, and a University of Queensland Early Career Researcher grant.

Publications

S. Brawley, N. Blouin, E. Ficko-Blean, G. Wheeler, M. Lohr, H. Goodson, J. Jenkins, C. Blaby-Haas, K. Helliwell, C. Chan, T. Marriage, D. Bhattacharya, A. Klein, Y. Badis, J. Brodie, Y. Cao, J. Collén, S. Dittami, C. Gachon, B. Green, S. Karpowicz, J. Kim, U. Kudahl, S. Lin, G. Michel, M. Mittag, B. Olson, J. Pangilinan, Y. Peng, H. Qiu, S. Shu, J. Singer, A. Smith, B. Sprecher, V. Wagner, W. Wang, Z.Y. Wang, J. Yan, C. Yarish, S. Zäuner-Riek, Y. Zhuang, Y. Zou, E. Lindquist, J. Grimwood, K. Barry, D. Rokhsar, J. Schmutz, J. Stiller, A. Grossman, and S. Prochnik, “Insights into the red algae from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).” Proceedings of the National Academy of Sciences USA 114(31), E6361-6370(2017). [DOI: 10.1073/pnas.1703088114]