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Title: Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410

Authors:
; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Photosynthetic Antenna Research Center (PARC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1387919
DOE Contract Number:  
SC0001035
Resource Type:
Journal Article
Journal Name:
Photosynthesis Research
Additional Journal Information:
Journal Volume: 129; Journal Issue: 2; Related Information: PARC partners with Washington University in St. Louis (lead); University of California, Riverside; University of Glasgow, UK; Los Alamos National Laboratory; University of New Mexico; New Mexico Corsortium; North Carolina State University; Northwestern University; Oak Ridge National Laboratory; University of Pennsylvania; Sandia National Laboratories; University of Sheffield, UK; Journal ID: ISSN 0166-8595
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
solar (fuels), photosynthesis (natural and artificial), biofuels (including algae and biomass), bio-inspired, charge transport, membrane, synthesis (novel materials), synthesis (self-assembly)

Citation Formats

Yoneda, Aki, Wittmann, Bruce J., King, Jeremy D., Blankenship, Robert E., and Dantas, Gautam. Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. United States: N. p., 2016. Web. doi:10.1007/s11120-016-0279-1.
Yoneda, Aki, Wittmann, Bruce J., King, Jeremy D., Blankenship, Robert E., & Dantas, Gautam. Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. United States. doi:10.1007/s11120-016-0279-1.
Yoneda, Aki, Wittmann, Bruce J., King, Jeremy D., Blankenship, Robert E., and Dantas, Gautam. Thu . "Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410". United States. doi:10.1007/s11120-016-0279-1.
@article{osti_1387919,
title = {Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410},
author = {Yoneda, Aki and Wittmann, Bruce J. and King, Jeremy D. and Blankenship, Robert E. and Dantas, Gautam},
abstractNote = {},
doi = {10.1007/s11120-016-0279-1},
journal = {Photosynthesis Research},
issn = {0166-8595},
number = 2,
volume = 129,
place = {United States},
year = {2016},
month = {6}
}

Works referenced in this record:

Multiplexed Illumina sequencing libraries from picogram quantities of DNA
journal, January 2013


Expanding the solar spectrum used by photosynthesis
journal, August 2011


The Synechococcus Strain PCC 7942 glnN Product (Glutamine Synthetase III) Helps Recovery from Prolonged Nitrogen Chlorosis
journal, October 2000


Reduction of arsenate to arsenite by the ArsC protein of the arsenic resistance operon of Staphylococcus aureus plasmid pI258.
journal, October 1992

  • Ji, G.; Silver, S.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 20
  • DOI: 10.1073/pnas.89.20.9474

Structure of Chlorophyll f
journal, March 2013

  • Willows, Robert D.; Li, Yaqiong; Scheer, Hugo
  • Organic Letters, Vol. 15, Issue 7
  • DOI: 10.1021/ol400327j

Mechanism and Catalytic Diversity of Rieske Non-Heme Iron-Dependent Oxygenases
journal, September 2013

  • Barry, Sarah M.; Challis, Gregory L.
  • ACS Catalysis, Vol. 3, Issue 10
  • DOI: 10.1021/cs400087p

Multiple Types of 8-Vinyl Reductases for (Bacterio)Chlorophyll Biosynthesis Occur in Many Green Sulfur Bacteria
journal, July 2011


IsdG and IsdI, Heme-degrading Enzymes in the Cytoplasm of Staphylococcus aureus
journal, October 2003

  • Skaar, Eric P.; Gaspar, Andrew H.; Schneewind, Olaf
  • Journal of Biological Chemistry, Vol. 279, Issue 1
  • DOI: 10.1074/jbc.M307952200

The CopRS Two-Component System Is Responsible for Resistance to Copper in the Cyanobacterium Synechocystis sp. PCC 6803
journal, June 2012

  • Giner-Lamia, Joaquín; López-Maury, Luis; Reyes, José C.
  • Plant Physiology, Vol. 159, Issue 4
  • DOI: 10.1104/pp.112.200659

Chlorophyll d in an Epiphytic Cyanobacterium of Red Algae
journal, March 2004


Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium
journal, February 2015

  • Behrendt, Lars; Brejnrod, Asker; Schliep, Martin
  • The ISME Journal, Vol. 9, Issue 9
  • DOI: 10.1038/ismej.2015.14

Structure and Chemistry of Cytochrome P450
journal, June 2005

  • Denisov, Ilia G.; Makris, Thomas M.; Sligar, Stephen G.
  • Chemical Reviews, Vol. 105, Issue 6
  • DOI: 10.1021/cr0307143

Chlorophyll d as a major pigment
journal, October 1996

  • Miyashita, Hideaki; Ikemoto, Hisato; Kurano, Norihide
  • Nature, Vol. 383, Issue 6599
  • DOI: 10.1038/383402a0

Chromatic photoacclimation extends utilisable photosynthetically active radiation in the chlorophyll d-containing cyanobacterium, Acaryochloris marina
journal, July 2009

  • Duxbury, Zane; Schliep, Martin; Ritchie, Raymond J.
  • Photosynthesis Research, Vol. 101, Issue 1
  • DOI: 10.1007/s11120-009-9466-7

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013


Nitrogen Starvation-Induced Chlorosis in Synechococcus PCC 7942. Low-Level Photosynthesis As a Mechanism of Long-Term Survival
journal, May 2001

  • Sauer, Jörg; Schreiber, Ulrich; Schmid, Roland
  • Plant Physiology, Vol. 126, Issue 1
  • DOI: 10.1104/pp.126.1.233

The biochemistry of heme biosynthesis
journal, June 2008

  • Heinemann, Ilka U.; Jahn, Martina; Jahn, Dieter
  • Archives of Biochemistry and Biophysics, Vol. 474, Issue 2
  • DOI: 10.1016/j.abb.2008.02.015

Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina
journal, February 2008

  • Swingley, W. D.; Chen, M.; Cheung, P. C.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 6
  • DOI: 10.1073/pnas.0709772105

Redesigning photosynthesis to sustainably meet global food and bioenergy demand
journal, June 2015

  • Ort, Donald R.; Merchant, Sabeeha S.; Alric, Jean
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 28
  • DOI: 10.1073/pnas.1424031112

Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene
journal, January 2005

  • Miller, S. R.; Augustine, S.; Olson, T. L.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 3
  • DOI: 10.1073/pnas.0405667102

Chlorophyll breakdown: Pheophorbide a oxygenase is a Rieske-type iron-sulfur protein, encoded by the accelerated cell death 1 gene
journal, December 2003

  • Pruzinska, A.; Tanner, G.; Anders, I.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 25
  • DOI: 10.1073/pnas.2036571100

Effect of Iron on Growth and Ultrastructure of Acaryochloris marina
journal, December 2005


A cyanobacterium that contains chlorophyll f - a red-absorbing photopigment
journal, July 2012


Extinction coefficient for red-shifted chlorophylls: Chlorophyll d and chlorophyll f
journal, August 2012

  • Li, Yaqiong; Scales, Nicholas; Blankenship, Robert E.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1817, Issue 8
  • DOI: 10.1016/j.bbabio.2012.02.026

Chromatic photoacclimation, photosynthetic electron transport and oxygen evolution in the Chlorophyll d-containing oxyphotobacterium Acaryochloris marina
journal, February 2007

  • Gloag, Rosalyn S.; Ritchie, Raymond J.; Chen, Min
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1767, Issue 2
  • DOI: 10.1016/j.bbabio.2006.11.014

Chlorophyll b to Chlorophyll a Conversion Precedes Chlorophyll Degradation in Hordeum vulgare L.
journal, July 1999


Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light
journal, August 2014


Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina
journal, February 2016

  • Chen, Guangyu E.; Hitchcock, Andrew; Jackson, Philip J.
  • Journal of Bacteriology, Vol. 198, Issue 9
  • DOI: 10.1128/JB.00925-15

Chlorophyll Modifications and Their Spectral Extension in Oxygenic Photosynthesis
journal, June 2014


Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

A Red-Shifted Chlorophyll: Fig. 1
journal, August 2010


Time-resolved Studies of IsdG Protein Identify Molecular Signposts along the Non-canonical Heme Oxygenase Pathway
journal, November 2015

  • Streit, Bennett R.; Kant, Ravi; Tokmina-Lukaszewska, Monika
  • Journal of Biological Chemistry, Vol. 291, Issue 2
  • DOI: 10.1074/jbc.M115.666560

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
journal, January 2011


Discovery of Chlorophyll d in Acaryochloris marina and Chlorophyll f in a Unicellular Cyanobacterium, Strain KC1, Isolated from Lake Biwa
journal, January 2014


Occurrence of Far-Red Light Photoacclimation (FaRLiP) in Diverse Cyanobacteria
journal, December 2014


Dynamics of Gene Duplication in the Genomes of Chlorophyll d-Producing Cyanobacteria: Implications for the Ecological Niche
journal, January 2011

  • Miller, Scott R.; Wood, A. Michelle; Blankenship, Robert E.
  • Genome Biology and Evolution, Vol. 3
  • DOI: 10.1093/gbe/evr060

Chlorophyll biosynthesis: spotlight on protochlorophyllide reduction
journal, November 2010


Copper toxicity and cyanobacteria ecology in the Sargasso Sea
journal, July 2002

  • Mann, Elizabeth L.; Ahlgren, Nathan; Moffett, James W.
  • Limnology and Oceanography, Vol. 47, Issue 4
  • DOI: 10.4319/lo.2002.47.4.0976

Chlorophyll d: the puzzle resolved
journal, August 2005


Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803
journal, September 2010

  • Kato, K.; Tanaka, R.; Sano, S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 38
  • DOI: 10.1073/pnas.1000771107

A new arsenate reductase involved in arsenic detoxification in Anabaena sp. PCC7120
journal, October 2012

  • Pandey, Sarita; Shrivastava, A. K.; Singh, V. K.
  • Functional & Integrative Genomics, Vol. 13, Issue 1
  • DOI: 10.1007/s10142-012-0296-x

18 O Labeling of Chlorophyll d in Acaryochloris marina Reveals That Chlorophyll a and Molecular Oxygen Are Precursors
journal, July 2010

  • Schliep, Martin; Crossett, Ben; Willows, Robert D.
  • Journal of Biological Chemistry, Vol. 285, Issue 37
  • DOI: 10.1074/jbc.M110.146753

The Sequence Alignment/Map format and SAMtools
journal, June 2009


Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a
journal, October 1998

  • Tanaka, A.; Ito, H.; Tanaka, R.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 21
  • DOI: 10.1073/pnas.95.21.12719

The Glutathione/Glutaredoxin System Is Essential for Arsenate Reduction in Synechocystis sp. Strain PCC 6803
journal, March 2009

  • Lopez-Maury, L.; Sanchez-Riego, A. M.; Reyes, J. C.
  • Journal of Bacteriology, Vol. 191, Issue 11
  • DOI: 10.1128/JB.01798-08

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014