Lydi_00010 Lydi_00010   Lydi_00030 Lydi_00030

Lydi_00020 : CDS information

close this sectionLocation

Organism
StrainTP-A0598 (=NBRC 110027)
Entry nameLydicamycin
Contig
Start / Stop / Direction3,223 / 6,012 / + [in whole cluster]
3,223 / 6,012 / + [in contig]
Location3223..6012 [in whole cluster]
3223..6012 [in contig]
TypeCDS
Length2,790 bp (929 aa)
Click on the icon to see Genetic map.

close this sectionAnnotation

Category4.1 transcriptional regulator
Productputative LuxR family transcriptional regulator
Product (GenBank)putative LuxR family transcriptional regulator
GeneTPA0598_03_00660
Gene (GenBank)
EC number
Keyword
Note
Note (GenBank)
Reference
ACC
PmId
[26380643] Draft genome sequence of marine-derived Streptomyces sp. TP-A0598, a producer of anti-MRSA antibiotic lydicamycins. (Stand Genomic Sci. , 2015)
comment
Streptomyces sp. TP-A0598におけるputative lydicamycin biosynthetic gene clusterの報告。
このclusterが実際にlydicamycin産生に関わるかどうかの実験的な確認はされていない。

TPA0598_03_00660(929aa): LuxR family transcriptional regulator

本文中にコメントなし。
Related Reference
ACC
Q9ZGI0
NITE
Pikro_00180
PmId
[11344155] Characterization and analysis of the PikD regulatory factor in the pikromycin biosynthetic pathway of Streptomyces venezuelae. (J Bacteriol. , 2001)
[18245260] Enhanced heterologous production of desosaminyl macrolides and their hydroxylated derivatives by overexpression of the pikD regulatory gene in Streptomyces venezuelae. (Appl Environ Microbiol. , 2008)
[26608164] Interspecies Complementation of the LuxR Family Pathway-Specific Regulator Involved in Macrolide Biosynthesis. (J Microbiol Biotechnol. , 2016)
comment
BLAST id38%
Streptomyces venezuelae_pikD
[DoBISCUIT]LuxR family transcriptional regulator

--
[PMID: 11344155](2001)
pikDは抗生物質産生に必須。pikD deletionによる抗生物質非産生は、plasmidによる相補で回復する。
PikDによって行使される調節のレベルを、pathway中間体の変換と、xylE reporter systemを使ったpromoter probingで見ている。
PikDが媒介する転写調節は、pikRII, pikAI, and desI の発現を調節するpromotersで起こるが、pikRI or pikCを調節するpromotersでは起こらない。

---
[PMID: 18245260](2008)
S.venezuelae ATCC 15439のPKS genes deletion mutantにtylosin PKS genesを導入した株と、さらにpikDの追加コピーを入れた株での産物解析。
pikD追加があるとdesosaminyl tylactone産生が増えるので、PikDはdesosamine生合成gene clusterの発現をupregulateすると示唆される。また、2つのhydroxylate型desosaminyl tylactoneが新たにこの株から検出され、P450 hydroxylaseをコードするpikCの発現がPikDによって増加したためであると考えられた。

RT-PCRによる遺伝子発現解析と、10-deoxymethynolide, narbonolide, and TL→対応するdesosaminyl macrolidesへの生物変換実験によっても、PikDがdes and pikC genesのpositive regulatorであることを確かめている。

[PMID: 11344155]との矛盾点はxylE assayでのせいであり、RT-PCRと生物変換実験を使った結果のほうが直接的な証拠であると言っている。

---
[PMID: 26608164](2016)
pikDの過剰発現はpikromycin産生を拡大し、pikD deletion mutantはrapHとfkbNで補完することができる。

close this sectionSequence

selected fasta
>putative LuxR family transcriptional regulator [putative LuxR family transcriptional regulator]
MGLVEREAVMSELRAALSDSAKGCGKVAVIRGGIASGKTALLRAFEEHAVAAGATLLRAS
GAPGEQSLRFGVIEQFLSGATTPPGATESLSHLAGLTTPQVGSEAPSSALSGTRAAHDLC
VGLLELSRQGPLVITVDDHQFADSASLQVLTYLQHRIGTARVMLLLSQGTEPPSELVAEV
LRQPYSRQFTLSPLSPEGVGQLLAQRLDSSVAVQQAPGSYAVTGGNPLLTHALIDDSLAP
DQEAAAGAAVEPVAGQAFTRAVLAILRRGGPQLLRTARAVAVLGEFAAPALLARFLDVRP
SVVGGALETLELAGLTTDAQFRYHGTRTAVLDELTPEERSALNRRAAELLHHDGVAPSDV
VGYLLAAGEADEPWAARVLHAAADQALAHAEQALAGGKVAEAVQYLEFASRSCGDEHKRA
MLTARLAWVQWTISPAAATRHHGPLQTALEKELLSSREVMRLVRSLAWHGRPEEAVRALQ
SLGSLPEGDGSRDPAERRLTRQWLARWYPQIFAQVERHAAMAEPMSSPGPVRRPHPAVLP
RGTANVPAVDGPEQVLQRARVRETPLASVLSALHELLAAERFERAMYWCNELLQKAEGQH
AAAWRGVLLDTRAAVSLRLGDLADAERDASSALTALSARSWGVAIGSPLSHAIHAATMRG
HFDRAEAFLHQMIPQSMMDTRYGLQYRTARGHFHLATDRPHAALEDFEAVGDLVVKWKLD
HPMTLPWRGDLAQALVRVGQTDRARELIKDQLRMIGPDSTRMRGISLGILASVSDLKQRL
PLLGEVVDLLQAGGDRYQLAQAFVELGQVWQILGKLDRAQLIRRRALQLAKSCHAEQLSH
QLLATREPLNSEPATSQWEDAEGMAVLSEAERRVAALAALGRTNREIGRKLHITVSTVEQ
HLTRVYRKLNIKRRADLPVGLPADIADIA
selected fasta
>putative LuxR family transcriptional regulator [putative LuxR family transcriptional regulator]
ATGGGGTTAGTGGAACGAGAAGCAGTGATGTCGGAGCTACGCGCCGCATTGAGCGACAGC
GCCAAAGGGTGCGGCAAGGTAGCGGTGATACGAGGGGGAATCGCCAGCGGTAAGACGGCC
CTGCTCAGGGCGTTCGAGGAGCATGCGGTGGCGGCCGGCGCCACGCTGTTGCGGGCCTCG
GGCGCGCCCGGTGAGCAATCGCTCCGCTTCGGTGTGATCGAGCAGTTCCTCAGCGGGGCG
ACCACCCCGCCGGGAGCCACCGAGTCGCTGTCCCACCTGGCCGGCCTGACCACGCCCCAG
GTGGGGAGCGAGGCGCCCTCTTCTGCGCTGTCCGGGACCAGGGCCGCGCACGACCTGTGC
GTCGGGCTGCTCGAACTGAGCAGGCAGGGGCCATTGGTGATCACCGTGGACGATCACCAG
TTCGCTGACAGCGCCTCGCTGCAAGTGCTGACCTACCTCCAGCACCGGATCGGCACCGCA
CGGGTGATGCTGCTGCTCAGCCAGGGGACCGAACCGCCGTCCGAGCTGGTCGCCGAGGTG
CTCAGGCAGCCGTACTCCCGGCAGTTCACGCTGTCCCCGCTGTCCCCGGAAGGGGTCGGG
CAGCTTCTCGCGCAGCGGCTGGACTCCTCGGTCGCCGTTCAGCAGGCACCCGGCAGTTAC
GCCGTGACCGGTGGCAATCCCCTGCTGACGCACGCCCTGATCGACGACAGTCTGGCCCCC
GACCAGGAAGCGGCCGCCGGAGCGGCGGTCGAACCGGTCGCCGGGCAGGCCTTCACCAGG
GCCGTGCTGGCGATCCTGCGTCGCGGCGGCCCGCAACTGCTGCGGACGGCGCGAGCGGTC
GCGGTGCTCGGCGAGTTCGCCGCCCCCGCGCTGCTGGCCCGATTCCTGGACGTCCGGCCG
TCGGTCGTGGGCGGTGCGCTGGAAACCCTGGAACTGGCGGGGCTGACCACCGACGCCCAG
TTCCGCTACCACGGCACACGGACCGCCGTACTGGACGAACTCACGCCCGAGGAGCGTTCC
GCACTGAACCGCCGCGCGGCCGAGCTGCTGCACCACGACGGCGTGGCACCCTCGGACGTG
GTGGGCTACCTGCTGGCCGCCGGCGAGGCCGACGAGCCCTGGGCCGCCCGGGTGCTGCAT
GCCGCCGCCGACCAGGCGCTGGCCCACGCGGAGCAGGCGCTGGCGGGCGGCAAGGTGGCG
GAGGCCGTGCAGTACCTGGAGTTCGCCAGCCGTTCCTGCGGCGACGAGCACAAGCGCGCC
ATGCTCACCGCCCGGCTCGCCTGGGTGCAGTGGACGATCAGCCCCGCGGCCGCGACCCGG
CACCACGGGCCCTTGCAGACGGCGCTGGAGAAGGAGTTGCTCAGCTCCCGTGAGGTGATG
CGGCTGGTCCGTTCGCTGGCATGGCACGGCCGCCCCGAGGAAGCGGTGCGCGCGCTGCAA
AGCCTGGGCTCCCTGCCCGAGGGCGACGGCTCCCGCGATCCGGCTGAACGGAGACTGACC
CGCCAGTGGCTCGCCCGCTGGTATCCGCAGATCTTCGCCCAGGTCGAACGGCACGCCGCG
ATGGCCGAACCCATGAGTTCCCCGGGCCCGGTGCGCCGGCCACACCCCGCCGTCCTTCCT
CGTGGCACCGCAAACGTCCCGGCCGTGGACGGACCCGAGCAGGTGCTGCAAAGGGCCCGG
GTCCGGGAGACCCCGCTGGCATCCGTGCTCTCCGCGCTCCATGAACTCCTCGCTGCCGAG
CGGTTCGAGCGCGCGATGTACTGGTGCAATGAGCTGCTCCAGAAGGCCGAGGGCCAGCAT
GCCGCCGCATGGCGCGGTGTGCTGCTGGACACCAGGGCCGCGGTCAGCCTCCGGCTCGGT
GATCTCGCCGATGCGGAACGGGACGCTTCCAGCGCTTTGACGGCCCTCTCCGCACGGAGC
TGGGGCGTGGCGATCGGTTCACCGCTGTCGCACGCGATACACGCCGCGACGATGCGCGGC
CACTTCGACCGGGCCGAGGCATTCCTCCACCAGATGATCCCGCAGTCCATGATGGACACC
CGTTACGGGCTCCAGTACCGGACGGCGCGGGGGCATTTCCATCTCGCGACGGACCGGCCG
CATGCCGCGCTGGAGGATTTCGAGGCCGTGGGCGATCTCGTGGTCAAGTGGAAGCTCGAT
CACCCGATGACGCTGCCCTGGCGCGGGGACCTGGCCCAGGCCCTGGTGCGGGTGGGGCAG
ACCGACCGGGCCAGGGAGCTCATCAAGGATCAACTACGCATGATCGGGCCGGACTCCACC
CGGATGCGCGGGATCTCCCTCGGCATCCTCGCCTCGGTCAGCGACCTCAAACAACGACTG
CCGCTGCTCGGCGAGGTGGTCGATCTGTTGCAGGCCGGCGGGGACCGCTACCAGCTGGCC
CAGGCGTTCGTCGAACTCGGTCAGGTCTGGCAGATCCTCGGCAAACTGGACCGGGCCCAG
CTGATCCGGCGCCGGGCGCTGCAACTCGCCAAGAGCTGCCATGCCGAGCAGTTGTCCCAT
CAGCTGCTCGCCACCAGGGAGCCGCTGAACAGTGAGCCGGCCACGAGCCAGTGGGAGGAC
GCCGAGGGCATGGCCGTGCTGAGCGAGGCCGAGCGCCGGGTGGCCGCGCTCGCCGCGCTG
GGGCGGACGAACCGGGAGATCGGCCGGAAGCTGCACATCACCGTGAGCACCGTGGAACAG
CACCTGACGAGGGTGTACCGGAAGCTGAACATCAAGCGCCGGGCGGATCTGCCGGTCGGG
CTCCCGGCGGATATCGCGGATATCGCCTGA

close this sectionFeature

BLASTP
Database:UniProtKB:2011_09 		show BLAST table
InterPro
Database:interpro:38.0
IPR000792 Transcription regulator LuxR, C-terminal (Domain)
[864-921] 5.5e-17 SM00421
SM00421   helix_turn_helix, Lux Regulon
[867-881] 2.1e-08 PR00038 [881-897] 2.1e-08 PR00038 [897-909] 2.1e-08 PR00038
PR00038   HTHLUXR
[860-925] 15.773 PS50043
PS50043   HTH_LUXR_2
[881-908] PS00622
PS00622   HTH_LUXR_1
[865-917] 2.3e-11 PF00196
PF00196   GerE
IPR011990 Tetratricopeptide-like helical (Domain)
[731-839] 5.9e-08 G3DSA:1.25.40.10
G3DSA:1.25.40.10   no description
IPR011991 Winged helix-turn-helix transcription repressor DNA-binding (Domain)
[863-917] 2.1e-15 G3DSA:1.10.10.10
G3DSA:1.10.10.10   no description
IPR016032 Signal transduction response regulator, C-terminal effector (Domain)
[845-917] 2.5e-15 SSF46894
SSF46894   C-terminal effector domain of the bipartite response regulators
SignalP No significant hit
TMHMM No significant hit
Lydi_00010 Lydi_00010   Lydi_00030 Lydi_00030
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