Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH 8501

The unicellular cyanobacterium Crocosphaera watsonii is an important nitrogen fixer in oligotrophic tropical and subtropical oceans. Metabolic, energy and cellular processes in cyanobacteria are regulated by the circadian mechanism, and/or follow the rhythmicity of light–dark cycles. The temporal separation of metabolic processes is especially essential for nitrogen fixation because of inactivation of the nitrogenase by oxygen. Using a microarray approach, we analyzed gene expression in cultures of Crocosphaera watsonii WH 8501 (C. watsonii) over a 24-h period and compared the whole-genome transcription with that in Cyanothece sp. ATCC 51142 (Cyanothece), a unicellular diazotroph that inhabits coastal marine waters. Similar to Cyanothece, regulation at the transcriptional level in C. watsonii was observed for all major metabolic and energy processes including photosynthesis, carbohydrate and amino acid metabolisms, respiration, and nitrogen fixation. Increased transcript abundance for iron acquisition genes by the end of the day appeared to be a general pattern in the unicellular diazotrophs. In contrast, genes for some ABC transporters (for example, phosphorus acquisition), DNA replication, and some genes encoding hypothetical proteins were differentially expressed in C. watsonii only. Overall, C. watsonii showed a higher percentage of genes with light–dark cycling patterns than Cyanothece, which may reflect the habitats preferences of the two cyanobacteria. This study represents the first whole-genome expression profiling in cultivated Crocosphaera, and the results will be useful in determining the basal physiology and ecology of the endemic Crocosphaera populations.

[1]  J. Gallon.  Reconciling the incompatible: N2 fixation And O2 , 2006 .

[2]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[3]  C. Johnson,et al.  Circadian programming in cyanobacteria. , 2001, Seminars in cell & developmental biology.

[4]  L. Sherman,et al.  Microarray Analysis of the Genome-Wide Response to Iron Deficiency and Iron Reconstitution in the Cyanobacterium Synechocystis sp. PCC 68031[w] , 2003, Plant Physiology.

[5]  Rajeev Aurora,et al.  The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle , 2008, Proceedings of the National Academy of Sciences.

[6]  J. Mcdermott,et al.  TRANSCRIPTIONAL ANALYSIS OF THE UNICELLULAR, DIAZOTROPHIC CYANOBACTERIUM CYANOTHECE SP. ATCC 51142 GROWN UNDER SHORT DAY/NIGHT CYCLES 1 , 2009, Journal of phycology.

[7]  E. Leitão,et al.  Analysis of the hupSL Operon of the Nonheterocystous Cyanobacterium Lyngbya majuscula CCAP 1446/4: Regulation of Transcription and Expression under a Light-Dark Regimen , 2005, Applied and Environmental Microbiology.

[8]  S. Dyhrman,et al.  Phosphorus Scavenging in the Unicellular Marine Diazotroph Crocosphaera watsonii , 2006, Applied and Environmental Microbiology.

[9]  Julie LaRoche,et al.  Importance of the diazotrophs as a source of new nitrogen in the ocean , 2005 .

[10]  Brian A. Whitton,et al.  The Ecology of Cyanobacteria , 2002, Springer Netherlands.

[11]  P. Fay.  Oxygen relations of nitrogen fixation in cyanobacteria. , 1992, Microbiological reviews.

[12]  E. Carpenter,et al.  Growth kinetics of marine unicellular N2-fixing cyanobacterial isolates in continuous culture in relation to phosphorus and temperature , 2005 .

[13]  C. M. Short,et al.  Temporal Patterns of Nitrogenase Gene (nifH) Expression in the Oligotrophic North Pacific Ocean , 2005, Applied and Environmental Microbiology.

[14]  H. Hayashi,et al.  Histidine kinases play important roles in the perception and signal transduction of hydrogen peroxide in the cyanobacterium, Synechocystis sp. PCC 6803. , 2007, The Plant journal : for cell and molecular biology.

[15]  Himadri B. Pakrasi,et al.  Differential Transcriptional Analysis of the Cyanobacterium Cyanothece sp. Strain ATCC 51142 during Light-Dark and Continuous-Light Growth , 2008, Journal of bacteriology.

[16]  L. Stal,et al.  Nitrogenase activity in cyanobacteria measured by the acetylene reduction assay: a comparison between batch incubation and on-line monitoring. , 2001, Environmental microbiology.

[17]  Edward J. Carpenter,et al.  Trichodesmium, a Globally Significant Marine Cyanobacterium , 1997 .

[18]  David M. Karl,et al.  Dinitrogen fixation in the world's oceans , 2002 .

[19]  Paula Tamagnini,et al.  Hydrogenases and Hydrogen Metabolism of Cyanobacteria , 2002, Microbiology and Molecular Biology Reviews.

[20]  T. A. Villareal,et al.  Marine Nitrogen-Fixing Diatom-Cyanobacteria Symbioses , 1992 .

[21]  M. Kanehisa,et al.  Positive Regulation of Sugar Catabolic Pathways in the Cyanobacterium Synechocystis sp. PCC 6803 by the Group 2 σ Factor SigE* , 2005, Journal of Biological Chemistry.

[22]  L. Stal,et al.  Cyanobacterial nitrogen fixation in the ocean : diversity, regulation and ecology , 2008 .

[23]  R. Howarth,et al.  Nitrogen fixation in freshwater, estuarine, and marine ecosystems. 1. Rates and importance1 , 1988 .

[24]  J. Zehr,et al.  GROWTH AND NITROGEN FIXATION OF THE DIAZOTROPHIC FILAMENTOUS NONHETEROCYSTOUS CYANOBACTERIUM TRICHODESMIUM SP. IMS 101 IN DEFINED MEDIA: EVIDENCE FOR A CIRCADIAN RHYTHM 1 , 1996 .

[25]  F. Cipriano,et al.  Diversity of Diazotrophic Unicellular Cyanobacteria in the Tropical North Atlantic Ocean , 2002, Applied and Environmental Microbiology.

[26]  E. Carpenter,et al.  Marine pelagic cyanobacteria : Trichodesmium and other diazotrophs , 1992 .

[27]  Minoru Kanehisa,et al.  Global Analysis of Circadian Expression in the Cyanobacterium Synechocystis sp. Strain PCC 6803 , 2005, Journal of bacteriology.

[28]  E. Delong,et al.  Low genomic diversity in tropical oceanic N2-fixing cyanobacteria , 2007, Proceedings of the National Academy of Sciences.

[29]  R. Beinart,et al.  In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii , 2009, The ISME Journal.

[30]  F. Cipriano,et al.  N2 Fixation by Unicellular Bacterioplankton from the Atlantic and Pacific Oceans: Phylogeny and In Situ Rates , 2004, Applied and Environmental Microbiology.

[31]  Michael B. Jenkins,et al.  Nitrogen Fixation, 3rd Edition , 2000 .

[32]  J. LaRoche,et al.  Diazotrophic Diversity and Distribution in the Tropical and Subtropical Atlantic Ocean , 2005, Applied and Environmental Microbiology.

[33]  M. Potts,et al.  Introduction to the Cyanobacteria , 2012 .

[34]  Miguel Vicente,et al.  Septum Enlightenment: Assembly of Bacterial Division Proteins , 2006, Journal of bacteriology.

[35]  C. M. Short,et al.  Experiments linking nitrogenase gene expression to nitrogen fixation in the North Pacific subtropical gyre , 2007 .

[36]  L. Sherman,et al.  Role of Sigma Factors in Controlling Global Gene Expression in Light/Dark Transitions in the Cyanobacterium Synechocystis sp. Strain PCC 6803 , 2007, Journal of bacteriology.

[37]  Andrew Hansen,et al.  Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean , 2001, Nature.

[38]  N. Straus,et al.  Characterization of a cyanobacterial iron stress-induced gene similar to psbC , 1988, Journal of bacteriology.

[39]  Stephen D. Bay,et al.  EXAMINATION OF DIEL CHANGES IN GLOBAL TRANSCRIPT ACCUMULATION IN SYNECHOCYSTIS (CYANOBACTERIA) 1 , 2006 .

[40]  Rajeev Aurora,et al.  Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes , 2008, Proceedings of the National Academy of Sciences.

[41]  D. Scanlan,et al.  PCR Analysis of the Distribution of Unicellular Cyanobacterial Diazotrophs in the Arabian Sea , 2004, Applied and Environmental Microbiology.

[42]  J. Zehr,et al.  Characterization of diatom-cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences. , 2006, Environmental microbiology.

[43]  J. Waterbury,et al.  Diel variation of molybdenum and iron in marine diazotrophic cyanobacteria , 2004 .

[44]  P. Falkowski,et al.  Segregation of Nitrogen Fixation and Oxygenic Photosynthesis in the Marine Cyanobacterium Trichodesmium , 2001, Science.

[45]  K. Michel,et al.  Comparative analysis of idiA and isiA transcription under iron starvation and oxidative stress in Synechococcus elongatus PCC 7942 wild-type and selected mutants , 2003, Archives of Microbiology.

[46]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[47]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[48]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[49]  J. Montoya,et al.  High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean , 2004, Nature.

[50]  L. Stal,et al.  Oxygen and the light-dark cycle of nitrogenase activity in two unicellular cyanobacteria. , 2010, Environmental microbiology.

[51]  Paula Tamagnini,et al.  Cyanobacterial hydrogenases: diversity, regulation and applications. , 2007, FEMS microbiology reviews.

[52]  Elena Litchman,et al.  Phytoplankton growth and stoichiometry under multiple nutrient limitation , 2004 .

[53]  G. Tarran,et al.  Nutrient limitation of picophytoplankton photosynthesis and growth in the tropical North Atlantic , 2008 .

[54]  Dmitry A. Los,et al.  The Cyanobacteria: Molecular Biology, Genomics and Evolution , 2008 .

[55]  J. Waterbury,et al.  Phenotypic and genotypic characterization of multiple strains of the diazotrophic cyanobacterium, Crocosphaera watsonii, isolated from the open ocean. , 2009, Environmental microbiology.

[56]  N. Straus,et al.  Isolation, sequence analysis, and transcriptional studies of the flavodoxin gene from Anacystis nidulans R2 , 1988, Journal of bacteriology.

[57]  L. Sherman,et al.  Oscillating behavior of carbohydrate granule formation and dinitrogen fixation in the cyanobacterium Cyanothece sp. strain ATCC 51142 , 1994, Journal of bacteriology.

[58]  Fei-xue Fu,et al.  Interactions between changing pCO2, N2 fixation, and Fe limitation in the marine unicellular cyanobacterium Crocosphaera , 2008 .

[59]  P. Falkowski,et al.  Effects of iron limitation on the expression of metabolic genes in the marine cyanobacterium Trichodesmium erythraeum IMS101. , 2007, Environmental microbiology.

[60]  S. Golden,et al.  Roles for Sigma Factors in Global Circadian Regulation of the Cyanobacterial Genome , 2002, Journal of bacteriology.

[61]  Luke R. Thompson,et al.  Choreography of the Transcriptome, Photophysiology, and Cell Cycle of a Minimal Photoautotroph, Prochlorococcus , 2009, PloS one.

[62]  H. Riethman,et al.  Organization of pigment proteins in the photosystem II complex of the cyanobacterium Anacystis nidulans R2. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[63]  A. Grossman,et al.  Genes Essential to Iron Transport in the Cyanobacterium Synechocystis sp. Strain PCC 6803 , 2001, Journal of bacteriology.

[64]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[65]  E. Webb,et al.  A molecular assessment of the iron stress response in the two phylogenetic clades of Trichodesmium. , 2010, Environmental microbiology.

[66]  J. Zehr,et al.  Circadian Rhythm of Nitrogenase Gene Expression in the Diazotrophic Filamentous Nonheterocystous CyanobacteriumTrichodesmium sp. Strain IMS 101 , 1998, Journal of bacteriology.

[67]  J. Sarmiento,et al.  Inputs, losses and transformations of nitrogen and phosphorus in the pelagic North Atlantic Ocean , 1996 .

[68]  Yi-Wei Tang,et al.  Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology , 2009, Clinical Microbiology Reviews.

[69]  G. Garrity.  Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.