The DNA-binding specificity of eubacterial and archaeal FFRPs

被引:28
作者
Suzuki, M [1 ]
机构
[1] Natl Inst Adv Ind Sci & Technol AIST, Tsukuba Ctr 6 10, Tsukuba, Ibaraki 3058566, Japan
来源
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES | 2003年 / 79卷 / 07期
关键词
AsnC DNA-binding; DNA-protein interaction; DNA recognition; FFRP; Lrp transcription factor;
D O I
10.2183/pjab.79B.213
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
In the light of crystal 3D structures of feast/famine regulatory proteins (FFRPs), biochemical and biological experiments characterizing DNA-binding by FFRPs, carried out by other groups, have been reanalyzed. An important conclusion is that the consensus sequences of DNA sites recognized by dimers of types of FFRPs are in the same form of NANBNCNDNETTTNENDNCNBNA, where, e.g., N-A is the base complementary to N-A (e.g., when G is N-A, C is N-A), and N-E is either A or T. The NANBNCND and NDNCNBNA parts are different among FFRPs, and are important for discrimination between DNA promoters. The cluster of four T bases (i.e. the three Ts plus N-E or N-E) in the center appears to be important for bending of the DNA sites, and possibly used as the unit for formation of superstructures. Either 7-8 or similar to18 (i.e. 7-8 plus a helical turn of DNA, similar to10.5) basepairs are inserted between dimer-binding sites in many promoters, e.g. [NANBNCNDNETTTNENDNCNBNA]N1N2N3N4N5N6N7[NANBNCNDNETTTNENDNCNBNA], when dimer-binding sites repeat, most frequently, four times.
引用
收藏
页码:213 / 222
页数:10
相关论文
共 59 条
[11]   THE LEUCINE-RESPONSIVE REGULATORY PROTEIN, A GLOBAL REGULATOR OF METABOLISM IN ESCHERICHIA-COLI [J].
CALVO, JM ;
MATTHEWS, RG .
MICROBIOLOGICAL REVIEWS, 1994, 58 (03) :466-490
[12]   Conjugal transfer of the virulence plasmid of Salmonella enterica is regulated by the leucine-responsive regulatory protein and DNA adenine methylation [J].
Camacho, EM ;
Casadesús, J .
MOLECULAR MICROBIOLOGY, 2002, 44 (06) :1589-1598
[13]   Leucine-regulated self-association of leucine-responsive regulatory protein (Lrp) from Escherichia coli [J].
Chen, S ;
Rosner, MH ;
Calvo, JM .
JOURNAL OF MOLECULAR BIOLOGY, 2001, 312 (04) :625-635
[14]   The putA gene of Agrobacterium tumefaciens is transcriptionally activated in response to proline by an Lrp-like protein and is not autoregulated [J].
Cho, KY ;
Winans, SC .
MOLECULAR MICROBIOLOGY, 1996, 22 (05) :1025-1033
[15]   A CONSENSUS SEQUENCE FOR BINDING OF LRP TO DNA [J].
CUI, YH ;
WANG, Q ;
STORMO, GD ;
CALVO, JM .
JOURNAL OF BACTERIOLOGY, 1995, 177 (17) :4872-4880
[16]   A Pyrococcus homolog of the leucine-responsive regulatory protein, LrpA, inhibits transcription by abrogating RNA polymerase recruitment [J].
Dahlke, I ;
Thomm, M .
NUCLEIC ACIDS RESEARCH, 2002, 30 (03) :701-710
[17]   SITE-DIRECTED MUTAGENESIS OF THE ESCHERICHIA-COLI CHROMOSOME NEAR ORIC - IDENTIFICATION AND CHARACTERIZATION OF ASNC, A REGULATORY ELEMENT IN ESCHERICHIA-COLI ASPARAGINE METABOLISM [J].
DEWIND, N ;
DEJONG, M ;
MEIJER, M ;
STUITJE, AR .
NUCLEIC ACIDS RESEARCH, 1985, 13 (24) :8797-8811
[18]   DNA STRUCTURAL VARIATIONS IN THE ESCHERICHIA-COLI TYRT-PROMOTER [J].
DREW, HR ;
TRAVERS, AA .
CELL, 1984, 37 (02) :491-502
[19]   High resolution contact probing of the Lrp-like DNA-binding protein Ss-Lrp from the hyperthermoacidophilic crenarchaeote Sulfolobus solfataricus P2 [J].
Enoru-Eta, J ;
Gigot, D ;
Glansdorff, N ;
Charlier, D .
MOLECULAR MICROBIOLOGY, 2002, 45 (06) :1541-1555
[20]   Purification and characterization of Sa-lrp, a DNA-binding protein from the extreme thermoacidophilic archaeon Sulfolobus acidocaldarius homologous to the bacterial global transcriptional regulator Lrp [J].
Enoru-Eta, J ;
Gigot, D ;
Thia-Toong, TL ;
Glansdorff, N ;
Charlier, D .
JOURNAL OF BACTERIOLOGY, 2000, 182 (13) :3661-3672