Endosymbiosis Research Areas – Bhattacharya Lab

Endosymbiotic Origin of Photosynthetic Organelles

**Light microscopic images of *Paulinella* strain NZ134.** This image shows a newly formed test with one daughter cell moving into the new test. Chromatophore and host cell division are synchronized.

Motivation: The Great Oxygenation Event (GOE) occurred ca. 2.4 billion years ago (Ga) and forced a major redox transition in the history of life. It was driven primarily by the spread of oxygenic photosynthesis in cyanobacteria and set in motion major changes in cellular metabolism and catalytic conversions in response to rising oxygen (O₂) levels. Oxygenic photosynthesis entered the eukaryotic domain through cyanobacterial primary endosymbiosis over a billion years ago in the common ancestor of the eukaryotic “supergroup” Archaeplastida (red, green, and glaucophyte algae and land plants). The red and green algae gave rise, through subsequent serial endosymbioses, to a vast array of other unicellular and multicellular algae such as diatoms, dinoflagellates, and kelps that are critical to aquatic ecosystems and to global carbon cycles. The GOE and increasing prominence of photosynthetic eukaryotes created conditions that favored the evolution of complex, multicellular life. Specifically, the use of O₂ as a terminal electron acceptor in respiration greatly increased the energy yield of glycolysis, and oxygenic photosynthesis fostered the evolution of multicellular photosynthetic organisms and colonization of non-aquatic environments by emerging advanced life forms.

Plastid endosymbiosis is undoubtedly one of the most important innovations in the history of our planet. Therefore, a massive effort has been expended to elucidate plastid origin, function, biogenesis, diversity and its impacts on global primary productivity and geochemical cycles. What past work on members of the Archaeplastida and other algal models cannot provide however, due to the ancient derivation of their plastid, are insights into earlier stages of organellogenesis. During this critical phase, biotic interactions and genetic innovations evolved to stabilize, integrate and regulate the association between the host and the O₂-evolving, potentially toxic (because of the production of reactive O₂ species [ROS]) endosymbiont that was compromised by gene loss due to Muller’s ratchet. In this project, we fill a wide gap in knowledge of the evolution of early life by studying the origin of primary plastids in the only non-Archaeplastida model available. This model is a thecate amoeba (rhizarians), Paulinella, which acquired its plastid (referred to as the chromatophore) ca. 100 million years ago from an a-cyanobacterium. Our goals are to: 1) using omics and physiology, generate an understanding of the light response in Paulinella micropora. 2) Generate a genome-scale metabolic network (GEM) model for P. micropora in order to gain a systems-level understanding of chromatophore integration. 3) Using a heterologous expression system (Synechocystis sp. PCC 6803, among others), to study the functions of P. micropora stress-related genes.

Major Partners: PIs: Arthur R. Grossman (Carnegie Institution, Stanford), Hwan Su Yoon (Sungkyunkwan University, Korea), Cheong Xin Chan (University of Queensland, Australia), Eva Nowack (Heinrich-Heine University, Germany), postdocs Timothy Stephens, JunMo Lee, graduate students Arwa Gabr, Julia Van Etten.

Example Research Outcomes

**Key landmarks of plastid endosymbiosis in photosynthetic *Paulinella*.** Bacterial internalization in phagotrophic *Paulinella* (step 1). This event is followed by endosymbiont genome reduction, whereby the chromatophore genome loses genes outright or genes are transferred to the host nuclear genome through endosymbiotic gene transfer (EGT) (steps 1-2). Translation occurs of chromatophore-destined gene products on cytosolic ribosomes and these are translocated into the organelle where they express their function (step 2-3). Metabolic rewiring takes place as the crosstalk between the host and chromatophore is established, leading to endosymbiont integration (step 4).

**Gene co-expression analysis of *Paulinella micropora* KR01 cultures treated with control (10 μmol photons m−² s−¹) and high (120 μmol photons m−² s−¹) white light.** Left: Individual gene expression patterns in gene co-expression module 22 under control (blue lines) and high light stress (yellow lines) conditions. Right: Gene co-expression network of module 22. Each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a co-expression similarity between them. Annotation of a subset of the nodes is shown.

Representative Publications

Gabr A, Grossman AR, Bhattacharya D. 2020. Paulinella, a model for understanding plastid primary endosymbiosis. Journal of Phycology Apr 14. doi:10.1111/jpy.13003.
Lhee D, Ha J-S, Kim S, Park MG, Bhattacharya D, Yoon HS. 2019. Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species. Scientific Reports 9(1):2560.
Bhattacharya D, Price DC. 2020. The algal tree of life from a genomics perspective. In: Photosynthesis in Algae: Biochemical and Physiological Mechanisms. Eds: Larkum AWD, Grossmann AR, Raven JA. Springer International Publishing. DOI 10.1007/978-3-030-33397-3_2.
Lee J, Kim D, Bhattacharya D, Yoon HS. 2019. Expansion of phycobilisome linker gene families in mesophilic red algae. Nature Communications 10:4823.
Price DC, Goodenough UW, Roth R, Lee J-H, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D. 2019. Analysis of an improved Cyanophora paradoxa genome assembly. DNA Research 26(4):287–299.
Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price DC, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M. 2019. Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nature Communications 10:737.
Zhang R, Nowack ECM, Price DC, Bhattacharya D, Grossman AR. 2017. Impact of light intensity and quality on chromatophore and nuclear gene expression in Paulinella chromatophora, an amoeba with nascent photosynthetic organelles. Plant Journal 90(2):221-234.
Nowack EC, Price DC, Bhattacharya D, Singer A, Melkonian M, Grossman AR. 2016. Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora. Proceedings of the National Academy of Sciences USA 113:12214-9.