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Transcript analysis of the extended hyp-operon in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133 英文论文文献.doc 12页
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Transcript analysis of the extended hyp-operon in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133 英文论文文献
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Holmqvistetal.BMCResearchNotes
http://www.biomedcentral.com//186
SHORT REPORT
OpenAccess
Transcriptanalysisoftheextendedhyp-operonin
thecyanobacteriaNostocsp.strainPCC7120and
NostocpunctiformeATCC29133
MarieHolmqvist,PiaLindberg?,?saAgervald?,KarinStensj?andPeterLindblad*
Background:Cyanobacteriaharbortwo[NiFe]-typehydrogenasesconsistingofalargeandasmallsubunit,the
Hup-andHox-hydrogenase,respectively.Insertionofligandsandcorrectfoldingofnickel-ironhydrogenases
requireassistanceofaccessorymaturationproteins(encodedbythehyp-genes).Theintergenicregionbetween
thestructuralgenesencodingtheuptakehydrogenase(hupSL)andtheaccessorymaturationproteins(hypgenes)
inthecyanobacteriaNostocPCC7120andN.punctiformewereanalysedusingmolecularmethods.
Findings:ThefiveORFs,locatedinbetweentheuptakehydrogenasestructuralgenesandthehyp-genes,can
formatranscriptwiththehyp-genes.AnidenticalgenomiclocalizationoftheseORFsarefoundinother
filamentous,N2-fixingcyanobacterialstrains.InN.punctiformeandNostocPCC7120theORFsupstreamofthehyp-
genesshowedsimilartranscriptlevelprofilesashupS(hydrogenasestructuralgene),nifD(nitrogenasestructural
gene),hypCandhypF(accessoryhydrogenasematurationgenes)afternitrogendepletion.Insilicoanalyzesshowed
thattheseORFsinN.punctiformeharborthesameconservedregionsastheirhomologuesinNostocPCC7120
andthatthey,liketheirhomologuesinNostocPCC7120,canbetranscribedtogetherwiththehyp-genesforming
alargerextendedhyp-operon.DNAbindingstudiesshowedinteractionsofthetranscriptionalregulatorsCalAand
CalBtothepromoterregionsoftheextendedhyp-operoninN.punctiformeandNostocPCC7120.
Conclusions:ThefiveORFsupstreamofthehyp-genesinseveralfilamentousN2-fixingcyanobacteriahavean
identicalgenomiclocalization,inbetweenthegenesencodingtheuptakehydrogenaseandthematuration
proteingenes.InN.punctiformeandNostocPCC7120theyaretranscribedasoneoperonandmayform
transcriptstogetherwiththehyp-genes.TheexpressionpatternofthefiveORFswithintheextendedhyp-operon
inbothNostocpun
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the omega subunit of the rna polymerase core directs transcription efficiency in.
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内容提示：the omega subunit of the rna polymerase core directs transcription efficiency in cyanobacteria
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the omega subunit of the rna polymerase core dir
关注微信公众号Gene Ontology[IEA]ipr2go
Biological Process: DNA modification ()
Molecular Function: DNA binding ()
Genomic context
complement
Genomic context
Transcript
Nucleotide sequence
Length1395 nt
Sequence retrieving
Initial position:
Terminal position:
Translated sequence
Length464 AA.
Protein families, domains and functional sites
Graphical view
Table view
Transmembrane regions predicted by SOSUI
Not detected.
Protein-Protein Interaction experiments
Homology search results (Blast2)
CyanoBase Ortholog table (blast reciprocal best hit pairs)
References
External links
Sequence databases
Gene annotation databases
KEGG/GENES
-- EC, KO, Codon usage
related MeSH terms.
Protein databases
in Protein Knowledgebase (UniProtKB)
3D structure databases
-- Genomes TO Protein structures and functions.
Ortholog/paralog cluster databases
-- Phylogenetic classification of ortholog.
-- The automated construction of orthologous groups.
-- trans-kingdom classification of proteins.
Phenotype database
-- The Cyanobacterial Chlorophyll Fluorescence Database.
-- DNA sequence in fasta format.
-- Amino acids sequence in fasta format.
-- Reference list.
Homology: Blast hits
-- TableView.
Orthologs: Blast hit ortholog pairs
-- TableView.
InterProScan matches
-- TableView.
-- PNG image.Nucleic Acids Res
CyanoBase: a large-scale update on its 2...
Nucleic Acids Res &2016,
1.Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan.
2.Department of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan.
3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601 Japan.
4.Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan.
5.NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
6.Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
7.Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8503, Japan.
8.Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510 Japan.
9.Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami Osawa, Hachioji, Tokyo 192-0397, Japan.
10.Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan.
11.Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan yn@nig.ac.jp.
The first ever cyanobacterial genome sequence was determined two decades ago and
CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research.}