Taxobox image Synechococcus PCC 7002 DIC.jpg image width 200px image caption Synechococcus PCC 7002 cells ... genus Synechococcus genus authority Karl Wilhelm von N geli N geli , 1849 subdivision ranks Species subdivision See text Synechococcus from the Greek synechos in succession and the Greek kokkos ... cells per millilitre . Many fresh water freshwater species of Synechococcus have also been described. The genome of Synechococcus elongatus strain PCC7002 has a size of 2.7 base pair Mbp , Citation needed date May 2010 that of the oceanic strain WH8102 is 2.4 Mbp. Introduction Synechococcus ... journal Society for General Microbiology volume 111 pages 1 61 ref This definition of the genus Synechococcus ... based on the presence of the accessory pigment phycoerythrin . The marine forms of Synechococcus ... F. O. Perkins, L. W. Haas, D. E. Phillips & K. L. Webb year 1981 title Ultrastructure of a marine Synechococcus ... or even chemoheterotrophic growth, all marine Synechococcus strains appear to be obligate photoautotrophs ... Synechococcus journal Canadian Bulletin of Fisheries and Aquatic Sciences volume 214 pages ... cases urea as a sole nitrogen source. Marine Synechococcus are traditionally not thought to fix nitrogen This perception may be changing . Pigments The main photosynthetic pigment in Synechococcus ... annurev.mi.31.100177.001301 pmid 410354 ref In addition Synechococcus also contains zeaxanthin but no diagnostic ... Phylogenetic description of Synechococcus is difficult. Isolates are Morphology biology morphologically ... that Synechococcus is composed of at least several species. Bergey s Manual Herdman et al. 2001 now divides Synechococcus into five clusters equivalent to genera based on morphology, physiology ... phycoerythrin lacking marine Synechococcus that are euryhaline i.e. capable of growth in both marine ... clusters of Synechococcus . These cells are truly marine and have been isolated from both the coastal ... anhydrases. Ecology and distribution Synechococcus has been observed to occur at concentrations ranging ... more details
chembox verifiedrevid 265849003 ImageFile phycourobilin.png ImageSize 200px IUPACName 3 2 Z 3 2 carboxyethyl 5 2R 4 ethyl 3 methyl 5 oxo 1,2 dihydropyrrol 2 yl methyl 4 methyl 2 pyrrolylidene methyl 5 2S 3 ethyl 4 methyl 5 oxo 1,2 dihydropyrrol 2 yl methyl 4 methyl 1H pyrrol 3 yl propanoic acid OtherNames Section1 Chembox Identifiers CASNo 61932 71 6 PubChem 5289229 SMILES CCC1 C C O N C H 1CC2 C C C N2 C C 3 C C C N3 C C H 4C C C O N4 CC C C CCC O O CCC O O C C Section2 Chembox Properties Formula C sub 33 sub H sub 42 sub N sub 4 sub O sub 6 sub MolarMass 590.71 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Phycourobilin is a tetrapyrrole orange molecule involved in photosynthesis in cyanobacteria and red algae. This chromophore is bound to the phycobiliprotein phycoerythrin , the distal component of the light harvesting system of cyanobacteria and red algae phycobilisome . When bound to phycoerythrin , phycourobilin shows an absorption maximum around 495 nm. This chromophore is always a donor chromophore of phycoerythrin s, since their acceptor chromophore is always phycoerythrobilin . It can also be linked to the linker polypeptides of the phycobilisome , in which its precise role remains unclear. Phycourobilin is found in marine phycobilisome containing organisms, allowing them to efficiently absorb blue green light. In the ubiquitous marine cyanobacteria Synechococcus , the amount of phycourobilin in the phycobilisome s is correlated to the ecological niche the cells inhabit offshore Synechococcus are quite phycourobililin rich, while coastal Synechococcus contain very little or no phycourobilin. This represents a remarkable adaptation of the cyanobacterial light harvesting system, as oceanic waters are relatively richer in blue light than onshore waters. References reflist Tetrapyrroles Category Photosynthesis Category Tetrapyrroles Category Chemical compounds found in cyanobacteria ... more details
Infobox rfam Name Cyano 2 RNA motif image Cyano 2 RNA.svg width 350 caption Consensus secondary structure of Cyano 2 RNAs Symbol Cyano 2 AltSymbols Rfam RF01702 miRBase miRBase family RNA type sRNA Tax domain Synechococcus GO SO The Cyano 2 RNA motif is a conserved RNA structure identified by bioinformatics . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref Cyano 2 RNAs are found in Cyanobacteria l species classified within the genus Synechococcus . Many terminal loops in the two conserved stem loop s contain the nucleotide sequecne GCGA, and these sequences might in some cases form stable GNRA tetraloop s. Since the two stem loops are somewhat distant from one another it is possible that they represent two independent non coding RNA s that are often or always co transcription genetics transcribed . The region one thousand base pair s upstream of predicted Cyano 2 RNAs is usually devoid of annotated features such as RNA or protein coding gene s. This absence of annotated genes within one thousand base pairs is relatively unusual within bacteria . See also Yfr1 Yfr2 Cyano S1 RNA motif References references External links Rfam id RF01702 name Cyano 2 RNA Category Non coding RNA molecular cell biology stub ... more details
that the cyanobacterium Synechococcus sp. RF 1 was exhibiting circadian rhythms, and in a series ... rhythms described above in the same organism, the unicellular freshwater Synechococcus sp. RF 1. ref Huang T C and Grobbelaar N 1995 The circadian clock in the prokaryote Synechococcus RF 1. Microbiology 141 535 540. ref ref Lin R F, and Huang, T C 2009 Circadian rhythm of Cyanothece RF 1 Synechococcus ... BM, and Borgese MB 1989 A circadian rhythm in cell division in a prokaryote, the cyanobacterium Synechococcus ... of a daily rhythm in the marine cyanobacterium, Synechococcus WH7803. Inspired by the research of the aforementioned pioneers, the cyanobacterium Synechococcus elongatus was genetically transformed ... ref Johnson, C.H., and Y. Xu 2009 The Decade of Discovery How Synechococcus elongatus became a model ... entrainment . Thus, the work with various Synechococcus species firmly established that prokaryotic ... transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. Proc ... . Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC ..., Golden SS, LiWang AC 2002 Structure and function from the circadian clock protein KaiA of Synechococcus ... of circadian clock protein KaiA from Synechococcus elongatus. J. Biol. Chem. 279, 20511 20518. ref ... more details
. 1979 Discovery of marine Synechococcus by Waterbury ref name Waterbury 79 Waterbury, J. B. et ... fluorescent pigments such as Synechococcus which possess phycoerythrin . Flow cytometry measures the size ... groups of cells Prochlorococcus , Synechococcus and picoeukaryotes can be distinguished. For example Synechococcus is characterized by the double fluorescence of its pigments orange for phycoerythrin and red for chlorophyll . Flow cytometry also allows to sort out specific populations for example Synechococcus ... Synechococcus of a size of 1 m micrometer were first discovered in 1979 by J. Waterbury ... niche in the oceanic environment. The Synechococcus cyanobacterium is generally abundant in mesotrophic ... States of America 100 10020 5. ref and Synechococcus , ref name Palenik 03 Palenik, B. et al. 2003 . The genome of a motile marine Synechococcus . Nature 424 1037 42. ref and of a strain of Ostreococcus ... JGI CC9605 JGI CC9901 JGI Synechococcus WH8102 JGI WH7803 Genoscope RCC307 G noscope CC9311 The Institute for Genomic Research TIGR ref Palenik, B. et al. 2006 . Genome sequence of Synechococcus CC9311 ... more details
enzyme Name nitrate transmembrane transporting ATPase EC number 3.6.3.26 CAS number IUBMB EC number 3 6 3 26 GO code 0015414 image width caption In enzymology , a nitrate transporting ATPase EC number 3.6.3.26 is an enzyme that catalysis catalyzes the chemical reaction ATP H sub 2 sub O nitrateout math rightleftharpoons math ADP phosphate nitratein The 3 substrate biochemistry substrates of this enzyme are adenosine triphosphate ATP , water H sub 2 sub O , and nitrate , whereas its 3 product chemistry products are adenosine diphosphate ADP , phosphate , and nitrate . This enzyme belongs to the family of hydrolase s, specifically those acting on acid anhydrides to catalyse transmembrane movement of substances. The systematic name of this enzyme class is ATP phosphohydrolase nitrate importing . References reflist 1 cite journal author Omata T year 1995 title Structure, function and regulation of the nitrate transport system of the cyanobacterium Synechococcus sp. PCC7942 journal Plant. Cell. Physiol. volume 36 pages 207&ndash 13 pmid 7767600 issue 2 cite journal author Kuan G, Dassa E, Saurin W, Hofnung M, Saier MH Jr year 1995 title Phylogenetic analyses of the ATP binding constituents of bacterial extracytoplasmic receptor dependent ABC type nutrient uptake permeases journal Res. Microbiol. volume 146 pages 271&ndash 8 pmid 7569321 issue 4 doi 10.1016 0923 2508 96 81050 3 cite journal author Saier MH Jr year 1998 title Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya journal Adv. Microb. Physiol. volume 40 pages 81&ndash 136 pmid 9889977 doi 10.1016 S0065 2911 08 60130 7 cite journal author Griffiths JK and Sansom CE date title The Transporter Factsbook, Academic Press, San Diego, 1998 journal volume pages Category EC 3.6.3 Category Enzymes of unknown structure hydrolase stub ... more details
Orphan date August 2008 Infobox rfam Name ATPC RNA motif image ATPC secondary structure.jpg width caption Predicted secondary structure and sequence conservation of ATPC Symbol ATPC AltSymbols Rfam RF01067 miRBase miRBase family RNA type Gene Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The ATPC RNA motif is a conserved RNA structure found in certain cyanobacteria . ref cite journal author Weinberg Z, Barrick JE, Yao Z, et al. title Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline journal Nucleic Acids Res. volume 35 issue 14 pages 4809 19 year 2007 pmid 17621584 pmc 1950547 doi 10.1093 nar gkm487 url ref It is apparently ubiquitous in Prochlorococcus marinus , and is present in many species in the genus Synechococcus . The RNA is always found within an operon encoding subunits of ATP synthase , and it is always located downstream of the gene encoding the A subunit of ATP synthase, and upstream of the ATP synthase subunit C C subunit gene. This location is consistent with a cis regulatory element , but also with a non coding RNA that is transcribed with the ATP synthase genes. Simple RNA structures called stem loop s have been reported in the ATP synthase operons of various cyanobacteria, ref cite journal author Curtis SE title Structure, organization and expression of cyanobacterial ATP synthase genes journal Photosynth. Res. volume 18 pages 223 244 year 1988 doi 10.1007 BF00042986 ref but not structures such as the 3 stem junction that is the main feature of the ATPC RNA motif. References references External links Rfam id RF01067 name ATPC RNA motif DEFAULTSORT Atpc Rna Motif Category Cis regulatory RNA elements Category Non coding RNA molecular cell biology stub ... more details
Bacterioplankton refers to the bacterium bacterial component of the plankton that drifts in the water column. The name comes from the Ancient Greek word lang grc lang grc Latn planktos , meaning wanderer or drifter Thurman, 1997 , and lang la bacterium , a Latin neologism coined in the 19th century by Christian Gottfried Ehrenberg . They are found in both seawater and freshwater . Bacterioplankton occupy a range of ecological niche s in aquatic systems. Many are saprotroph ic, and obtain energy by consuming organic material produced by other organisms. This material may be Dissolved Organic Carbon dissolved in the medium and taken directly from there, or bacteria may live and grow in association with particulate material such as marine snow . Many other bacterioplankton species are autotroph ic, and derive energy from either photosynthesis or chemosynthesis . The former are often categorised as phytoplankton picophytoplankton , and include cyanobacteria l groups such as Prochlorococcus and Synechococcus . Bacterioplankton also play roles in ecological pathways such as nitrogen fixation , nitrification , denitrification , remineralisation and methanogen esis. Like other small plankton, the bacterioplankton are predation preyed upon by zooplankton usually protozoa ns , and their numbers are also controlled through infection by bacteriophage s. See also Cyanobacteria Pelagibacter Phytoplankton Plankton Zooplankton References cite book last Thurman first H. V. year 1997 title Introductory Oceanography publisher Prentice Hall College location New Jersey, USA isbn 0 13 262072 3 External links http thalassa.cbl.umces.edu MO2006 Typical Marine bacterioplankton http thalassa.cbl.umces.edu MO2006 marbac.html A list of Seawater Bacteria http halia.hik.se mbd start.jsp Marine Bacterioplankton Database plankton Category Biological oceanography Category Planktology Category Aquatic ecology ar de Bakterio und Virioplankton et Bakterioplankton fr Bact rioplan ... more details
Taxobox name Chironomidae image image width image caption regnum Animal ia phylum Arthropod a subphylum Hexapoda classis Insect a ordo Fly Diptera subordo Nematocera superfamilia Chironomoidea familia Chironomidae genus Cardiocladius genus authority Kieffer, 1911 ref Kieffer 1911. Bull. Soc. Metz, 27 42. Nomenclator Zoologicus ref For the algae Synechococcus Lauterbornia is a genus of midges in the bloodworm family Chironomidae . Members of this genus live in cold water lakes in stenothermic stenothermal or limited temperature change areas. ref Cite book author Adams, William J. Chapman, Gary Landis, Wayne G., editors authorlink coauthors title Aquatic Toxicology and Hazard Assessment 10th Volume date 1988 publisher ASTM, 1988. location isbn 978 0 8031 0978 0 pages 78 ref ref name Bliss cite book last Bliss first L. C. authorlink coauthors title Truelove Lowland, Devon Island, Canada A High Arctic Ecosystem publisher University of Alberta Press date 1987 location pages url doi id isbn 9780888641212 ref Lauterbornia coracin is known for inhabiting oligotrophic or nutrient depleted cold lake waters in the Northern Hemisphere . ref cite journal title An investigation of the profundal and sublittoral fauna of Windermere journal Journal of Animal Ecology date 1936 first Carmel last Humphries coauthors volume 5 issue 1 pages 29 52 id url format doi 10.2307 1090 ref ref name Bliss References reflist Chironomidae stub Category Chironomidae ... more details
Infobox rfam Name Downstream peptide RNA image Downstream peptide RNA.svg width caption Consensus secondary structure of Downstream peptide RNAs Symbol Downstream peptide AltSymbols Rfam RF01704 miRBase miRBase family RNA type Cis regulatory element Tax domain Prochlorococcus and Synechococcus GO SO The Downstream peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacteria l genus genera Synechococcus and Prochlorococcus and one phage that infects such bacteria . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref It was also detected in marine ocean marine samples of DNA from uncultivated bacteria , which are presumably other species of cyanobacteria. Downstream peptide RNAs are found upstream of short open reading frame s ORFs that are predicted to encode short peptide s usually between 17 and 100 amino acid s . One of the ORFs is apparently down regulated when cells are grown with an insufficient supply of nitrogen sources. ref name Axmann cite journal author Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR title Identification of cyanobacterial non coding RNAs by comparative genome analysis journal Genome Biol. volume 6 issue 9 pages R73 year 2005 pmid 16168080 pmc 1242208 doi 10.1186 gb 2005 6 9 r73 url ref Downstream peptide RNAs overlap a predicted non coding RNA called yfr6 that is over 200 nucleotide s in length, ref name Axmann but it was proposed that only the upstream region corresponding to the Downstream peptide motif functions as an RNA structure. ref name Weinberg2010 A distinct predicted non coding RNA called yfr14 ref cite journal author Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR editor1 last Matic editor1 first Iv ... more details
cultures of Shewanella and Synechococcus have been used to produce long chain hydrocarbons directly ... cultured Synechococcus and Shewanella Produce Hydrocarbons without Cellulosic Feedstock 20100084.aspx url http www.license.umn.edu Products Co cultured Synechococcus and Shewanella Produce Hydrocarbons ... more details
italic title taxobox name Akashiwo sanguinea image akashiwo sanguinea cluster.jpg domain Eukarya regnum Protista phylum Dinoflagellata classis Dinophyceae order Gymnodiniales familia Gymnodiniaceae genus Akashiwo species A. sanguinea binomial Akashiwo sanguinea binomial authority K. Hirasaka Hansen & Moestrup Akashiwo sanguinea is a marine dinoflagellate well known for forming blooms that result in red tides. ref name SMS cite web url http www.sms.si.edu IRLSPEC Akashi sangui.htm title Akashiwo sanguinea work Protists of the Indian River Lagoon author P. E. Hargraves publisher Smithsonian Institution accessdate October 27, 2011 date June 14, 2011 ref The protist is unarmored naked . Therefore, it lacks a thick cellulose wall, the theca , common in other genera of dinoflagellates. Reproduction of the phytoplankton species is primarily asexual. ref cite book author Carol M. Lalli & Timothy R. Parsons year 1993 title Biological Oceanography an Introduction edition 2nd publisher Elsevier Butterworth Heinemann pages 42 45 isbn 0 7506 3384 0 ref Recently recognized as mixotrophic , A. sanguinea is capable of preying on various organisms. ref cite journal author K. R. Bockstahler & D. W. Coats year 1993 title Grazing of the mixotrophic dinoflagellate Gymnodinium sanguineum on ciliate populations of Chesapeake Bay journal Marine Biology journal Marine Biology volume 116 issue 3 pages 477 487 doi 10.1007 BF00350065 ref For example, A. sanguinea is found to be capable of ingesting the cyanobacterium Synechococcus sp. at values comparable to other heterotrophic phytoplankton. This suggests implications it may have on the grazing impact of Synechococcus . ref cite journal author Hae Jin Jeong, Jae Yeon Park, Jae Hoon Nho, Myung Ok Park, Jeong Hyun Ha, Kyeong Ah Seong, Chang Jeng, Chi Nam Seong, Kwang Ya Lee & Won Ho Yih year 2005 title Feeding by red tide dinoflagellates on the cyanobacterium Synechococcus journal Aquatic Microbial Ecology volume 41 issue 2 pages 131 143 doi 10 ... more details
Infobox protein family Symbol Fe S biosyn Name Fe S biosyn image PDB 1s98 EBI.jpg width caption e.coli isca crystal structure to 2.3 a Pfam PF01521 Pfam clan InterPro IPR000361 SMART PROSITE PDOC00887 MEROPS SCOP 1nwb TCDB OPM family OPM protein CAZy CDD In molecular biology, the iron sulfur cluster biosynthesis protein family of includes proteins involved in Iron sulfur cluster Fe S cluster biogenesis iron sulfur cluster insertion protein, Fe S biogenesis protein . This family includes IscA, HesB, YadR and YfhF like protein s. The hesB gene is gene expression expressed only under nitrogen fixation conditions. ref name pmid10217509 cite journal author Huang TC, Lin RF, Chu MK, Chen HM title Organization and expression of nitrogen fixation genes in the aerobic nitrogen fixing unicellular cyanobacterium Synechococcus sp. strain RF 1 journal Microbiology Reading, Engl. volume 145 issue 3 pages 743 53 year 1999 month March pmid 10217509 doi url ref IscA, an 11 kDa member of the hesB family of proteins, Molecular binding bind s iron and 2Fe 2S clusters, and participates in the biosynthesis of iron sulfur protein s. IscA is able to bind at least 2 iron ion s per protein dimer dimer . ref name pmid15050828 cite journal author Cupp Vickery JR, Silberg JJ, Ta DT, Vickery LE title Crystal structure of IscA, an iron sulfur cluster assembly protein from Escherichia coli journal J. Mol. Biol. volume 338 issue 1 pages 127 37 year 2004 month April pmid 15050828 doi 10.1016 j.jmb.2004.02.027 url ref Other members of this family include various hypothetical proteins that also contain the NifU like protein domain domain suggesting that they too are able to bind iron and are involved in Fe S cluster biogenesis. The HesB family are found in species as divergent as Homo sapiens Human and Haemophilus influenzae suggesting that these proteins are involved in basic cellular functions. ref name pmid8875867 cite journal author Hwang DM, Dempsey A, Tan KT, Liew CC title A modular domain of Ni ... more details
events occur in FGL, due to the large Synechococcus population in the lake. ref name Thompson2 Thompson ... 1 , 133 141. ref Calcite precipitates in microenvironments surrounding the Synechococcus and this is believed ... more details
Infobox protein family Symbol 6PGD Name 6PGD image PDB 1pgq EBI.jpg width caption Crystallographic structure of sheep 6 phosphogluconate dehydrogenase complexed with adenosine 2 monophosphate. ref name pmid7922042 PDB 1PGQ cite journal author Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C title Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6 phosphogluconate dehydrogenase implications for NADP specificity and the enzyme mechanism journal Structure volume 2 issue 7 pages 651 68 year 1994 month July pmid 7922042 doi ref Pfam PF00393 Pfam clan CL0106 InterPro IPR006114 SMART PROSITE PDOC00390 MEROPS SCOP 2pgd TCDB OPM family OPM protein CAZy CDD enzyme Name Phosphogluconate dehydrogenase EC number 1.1.1.43 CAS number 9001 82 5 IUBMB EC number 1 1 1 43 GO code 0008114 image width caption protein Name phosphogluconate dehydrogenase caption image width HGNCid 8891 Symbol PGD AltSymbols EntrezGene 5226 OMIM 172200 RefSeq NM 002631 UniProt P52209 PDB ECnumber 1.1.1.43 Chromosome 1 Arm p Band 36.3 LocusSupplementaryData 36.13 Phosphogluconate dehydrogenase is an enzyme in the pentose phosphate pathway . It forms ribulose 5 phosphate from 6 phosphogluconate . It is an oxidative carboxylase that catalysis catalyses the decarboxylating Redox reduction of 6 phosphogluconate into ribulose 5 phosphate in the presence of NADP . This reaction is a component of the hexose mono phosphate shunt and pentose phosphate pathway s PPP . ref name pmid2113917 cite journal author Broedel SE, Wolf RE title Genetic tagging, cloning, and DNA sequence of the Synechococcus sp. strain PCC 7942 gene gnd encoding 6 phosphogluconate dehydrogenase journal J. Bacteriol. volume 172 issue 7 pages 4023 31 year 1990 month July pmid 2113917 pmc 213388 doi url ref ref name pmid6641716 cite journal author Adams MJ, Archibald IG, Bugg CE, Carne A, Gover S, Helliwell JR, Pickersgill RW, White SW title The three dimensional structure of sheep liver 6 phosphogluconate dehydrogen ... more details
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