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The Chlamydomonas genome reveals the evolution of key animal and plant functions.

ABSTRACT: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

SUBMITTER: Merchant SS

PROVIDER: S-EPMC2875087 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Merchant Sabeeha S SS Prochnik Simon E SE Vallon Olivier O Harris Elizabeth H EH Karpowicz Steven J SJ Witman George B GB Terry Astrid A Salamov Asaf A Fritz-Laylin Lillian K LK Maréchal-Drouard Laurence L Marshall Wallace F WF Qu Liang-Hu LH Nelson David R DR Sanderfoot Anton A AA Spalding Martin H MH Kapitonov Vladimir V VV Ren Qinghu Q Ferris Patrick P Lindquist Erika E Shapiro Harris H Lucas Susan M SM Grimwood Jane J Schmutz Jeremy J Cardol Pierre P Cerutti Heriberto H Chanfreau Guillaume G Chen Chun-Long CL Cognat Valérie V Croft Martin T MT Dent Rachel R Dutcher Susan S Fernández Emilio E Fukuzawa Hideya H González-Ballester David D González-Halphen Diego D Hallmann Armin A Hanikenne Marc M Hippler Michael M Inwood William W Jabbari Kamel K Kalanon Ming M Kuras Richard R Lefebvre Paul A PA Lemaire Stéphane D SD Lobanov Alexey V AV Lohr Martin M Manuell Andrea A Meier Iris I Mets Laurens L Mittag Maria M Mittelmeier Telsa T Moroney James V JV Moseley Jeffrey J Napoli Carolyn C Nedelcu Aurora M AM Niyogi Krishna K Novoselov Sergey V SV Paulsen Ian T IT Pazour Greg G Purton Saul S Ral Jean-Philippe JP Riaño-Pachón Diego Mauricio DM Riekhof Wayne W Rymarquis Linda L Schroda Michael M Stern David D Umen James J Willows Robert R Wilson Nedra N Zimmer Sara Lana SL Allmer Jens J Balk Janneke J Bisova Katerina K Chen Chong-Jian CJ Elias Marek M Gendler Karla K Hauser Charles C Lamb Mary Rose MR Ledford Heidi H Long Joanne C JC Minagawa Jun J Page M Dudley MD Pan Junmin J Pootakham Wirulda W Roje Sanja S Rose Annkatrin A Stahlberg Eric E Terauchi Aimee M AM Yang Pinfen P Ball Steven S Bowler Chris C Dieckmann Carol L CL Gladyshev Vadim N VN Green Pamela P Jorgensen Richard R Mayfield Stephen S Mueller-Roeber Bernd B Rajamani Sathish S Sayre Richard T RT Brokstein Peter P Dubchak Inna I Goodstein David D Hornick Leila L Huang Y Wayne YW Jhaveri Jinal J Luo Yigong Y Martínez Diego D Ngau Wing Chi Abby WC Otillar Bobby B Poliakov Alexander A Porter Aaron A Szajkowski Lukasz L Werner Gregory G Zhou Kemin K Grigoriev Igor V IV Rokhsar Daniel S DS Grossman Arthur R AR

Science (New York, N.Y.) 20071001 5848

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying ...[more]

PMID: 17932292

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Project description:The absence of oxygen (O2) is a stress condition for aerobic organisms and requires extensive acclimation responses. Previously, Chlamydomonas reinhardtii has been used as a reference organism for understanding these acclimation responses. In this work, we use RNA-Seq for a whole genome view of the acclimation of the organism to dark-anoxic conditions. To distinguish the responses dependent on the COPPER RESPONSE REGULATOR 1 (CRR1), which is also involved in hypoxic gene regulation, we compared the transcriptome of crr1 mutants to that of complemented strains. Nearly 10% of the genome (~ 1,400 genes) are affected by hypoxia based on pairwise comparisons of all strains and two time-points. Comparing transcript profiles from early (hypoxic) with those from late (anoxic) time-points indicated that the cells activated oxidative energy generation pathways before employing fermentative enzymes. Probable substrates included not only carbohydrates but also amino acids and fatty acids (FAs). Lipid profiling of the C. reinhardtii cells revealed that they degraded FAs but also accumulated triacylglycerols (TAGs). In contrast to N-deprived cells, the TAGs accumulating in hypoxic cells are enriched in desaturated FAs, which distinguishes the contribution of individual pathways for Chlamydomonas TAG accumulation. In crr1 mutants, about 140 genes were aberrantly regulated , re-affirming the importance of CRR1 for the hypoxic response, but indicating also the contribution of additional O2-sensors and signaling strategies to account for the remaining differentially regulated transcripts. We conclude that nitric oxide (NO) dependent signaling cascades, employing both known and novel components, are operative in C. reinhardtii. The transcriptome of four different Chlamydomonas strains (wild type CC-124, crr1 mutant, crr1:CRR1 rescued strain and crr1dCys rescued strain) are profiled by RNA-Seq in the dark at different times after the transition from light-oxic to dark-anoxic conditions

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The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Publications

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

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