Multiomics resolution of molecular events during a day in the life of Chlamydomonas.
Daniela Strenkert,Stefan Schmollinger,Sean D. Gallaher,Patrice A. Salomé,Samuel O. Purvine,C. Nicora,Tabea Mettler-Altmann,Eric Soubeyrand,Andreas P.M. Weber,Mary S. Lipton,Gilles J. Basset,Sabeeha S. Merchant +11 more
TLDR
It is found that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; and it is proposed that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases.Abstract:
The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.read more
Citations
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A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism
TL;DR: A historical retrospective of the rise of C. reinhardtii is presented to illuminate its past and present and resources for current and future scientists who may wish to expand their studies to the realm of microalgae are presented.
Journal ArticleDOI
PhycoCosm, a comparative algal genomics resource.
Igor V. Grigoriev,Igor V. Grigoriev,Richard D. Hayes,Sara Calhoun,Bishoy Kamel,Alice Wang,Alice Wang,Steven Ahrendt,Sergey Dusheyko,Roman Nikitin,Stephen J Mondo,Asaf Salamov,Igor Shabalov,Alan Kuo +13 more
TL;DR: PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.
Journal ArticleDOI
Multiview learning for understanding functional multiomics.
Nam D. Nguyen,Daifeng Wang +1 more
TL;DR: This review introduces multiview learning—an emerging machine learning field—and envisions its potentially powerful applications to multiomics and discusses the potential applications of each method, including genomics, transcriptomics, and epigenomics, in an aim to discover the functional and mechanistic interpretations across omics.
Journal ArticleDOI
Assembly of the algal CO2-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif.
Moritz T. Meyer,Alan K. Itakura,Alan K. Itakura,Weronika Patena,Lianyong Wang,Shan He,Tom Z. Emrich-Mills,Chun S. Lau,Gary Yates,Luke C. M. Mackinder,Martin C. Jonikas +10 more
TL;DR: It is shown that the Rubisco-binding motif is necessary and sufficient to target proteins to the pyrenoid and that the motif binds to Rubisco, suggesting a mechanism for targeting.
Journal ArticleDOI
When Unity Is Strength: The Strategies Used by Chlamydomonas to Survive Environmental Stresses.
TL;DR: It is shown that despite being a unicellular organism, Chlamydomonas can survive very severe environmental conditions and can range from acclimation to the formation of multicellular structures, or involve programmed cell death.
References
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell,Adam Roberts,Loyal A. Goff,Loyal A. Goff,Loyal A. Goff,Geo Pertea,Daehwan Kim,Daehwan Kim,David R. Kelley,David R. Kelley,Harold Pimentel,Steven L. Salzberg,John L. Rinn,John L. Rinn,Lior Pachter +14 more
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Juan Antonio Vizcaíno,Attila Csordas,Noemi del-Toro,José A. Dianes,Johannes Griss,Ilias Lavidas,Gerhard Mayer,Yasset Perez-Riverol,Florian Reisinger,Tobias Ternent,Qing Wei Xu,Rui Wang,Henning Hermjakob +12 more
TL;DR: The developments in PRIDE resources and related tools are summarized and a brief update on the resources under development 'PRIDE Cluster' and 'PRide Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available inPRIDE Archive are given.
Journal ArticleDOI
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
Sabeeha S. Merchant,Simon E. Prochnik,Olivier Vallon,Elizabeth H. Harris,Steven J. Karpowicz,George B. Witman,Astrid Terry,Asaf Salamov,Lillian K. Fritz-Laylin,Laurence Maréchal-Drouard,Wallace F. Marshall,Liang-Hu Qu,David R. Nelson,Anton A. Sanderfoot,Martin H. Spalding,Vladimir V. Kapitonov,Qinghu Ren,Patrick J. Ferris,Erika Lindquist,Harris Shapiro,Susan Lucas,Jane Grimwood,Jeremy Schmutz,Pierre Cardol,Pierre Cardol,Heriberto Cerutti,Guillaume Chanfreau,Chun-Long Chen,Valérie Cognat,Martin T. Croft,Rachel M. Dent,Susan K. Dutcher,Emilio Fernández,Hideya Fukuzawa,David González-Ballester,Diego González-Halphen,Armin Hallmann,Marc Hanikenne,Michael Hippler,William Inwood,Kamel Jabbari,Ming Kalanon,Richard Kuras,Paul A. Lefebvre,Stéphane D. Lemaire,Alexey V. Lobanov,Martin Lohr,Andrea L Manuell,Iris Meier,Laurens Mets,Maria Mittag,Telsa M. Mittelmeier,James V. Moroney,Jeffrey L. Moseley,Carolyn A. Napoli,Aurora M. Nedelcu,Krishna K. Niyogi,Sergey V. Novoselov,Ian T. Paulsen,Greg Pazour,Saul Purton,Jean-Philippe Ral,Diego Mauricio Riaño-Pachón,Wayne R. Riekhof,Linda A. Rymarquis,Michael Schroda,David B. Stern,James G. Umen,Robert D. Willows,Nedra F. Wilson,Sara L. Zimmer,Jens Allmer,Janneke Balk,Katerina Bisova,Chong-Jian Chen,Marek Eliáš,Karla C Gendler,Charles R. Hauser,Mary Rose Lamb,Heidi K. Ledford,Joanne C. Long,Jun Minagawa,M. Dudley Page,Junmin Pan,Wirulda Pootakham,Sanja Roje,Annkatrin Rose,Eric Stahlberg,Aimee M. Terauchi,Pinfen Yang,Steven G. Ball,Chris Bowler,Carol L. Dieckmann,Vadim N. Gladyshev,Pamela J. Green,Richard A. Jorgensen,Stephen P. Mayfield,Bernd Mueller-Roeber,Sathish Rajamani,Richard T. Sayre,Peter Brokstein,Inna Dubchak,David Goodstein,Leila Hornick,Y. Wayne Huang,Jinal Jhaveri,Yigong Luo,Diego Martinez,Wing Chi Abby Ngau,Bobby Otillar,Alexander Poliakov,Aaron Porter,Lukasz Szajkowski,Gregory Werner,Kemin Zhou,Igor V. Grigoriev,Daniel S. Rokhsar,Daniel S. Rokhsar,Arthur R. Grossman +118 more
TL;DR: Analyses of the Chlamydomonas genome advance the 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.
Journal ArticleDOI
Metabolite profiling for plant functional genomics.
Oliver Fiehn,Joachim Kopka,Peter Dörmann,Thomas Altmann,Richard N. Trethewey,Lothar Willmitzer +5 more
TL;DR: The use of metabolite profiling is described as a new tool for a comparative display of gene function and has the potential not only to provide deeper insight into complex regulatory processes but also to determine phenotype directly.
Journal ArticleDOI
Proteomic analysis of a eukaryotic cilium
TL;DR: This paper used mass spectrometry to identify proteins in purified flagella from the green alga Chlamydomonas reinhardtii and found that flagellum is rich in motor and signal transduction components, and contains numerous proteins with homologues associated with diseases such as cystic kidney disease, male sterility, and hydrocephalus in humans and model vertebrates.
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The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
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