The Linker Region of AraC Protein

Overview

Journal J Bacteriol

Publisher American Society for Microbiology

Specialty Microbiology

Date 1996 Dec 1

PMID 8955380

Citations 7

Authors

R J Eustance

R F Schleif

Affiliations

Soon will be listed here.

Abstract

AraC protein, a transcriptional regulator of the L-arabinose operon in Escherichia coli, is dimeric. Each monomer consists of a domain for DNA binding plus transcription activation and a domain for dimerization plus arabinose binding. These are connected to one another by a linker region of at least 5 amino acids. Here we have addressed the question of whether any of the amino acids in the linker region play active, specific, and crucial structural roles or whether these amino acids merely serve as passive spacers between the functional domains. We found that all but one of the linker amino acids can be changed to other amino acids individually and in small groups without substantially affecting the ability of AraC protein to activate transcription when arabinose is present. When, however, the entire linker region is replaced with linker sequences from other proteins, the functioning of AraC is impaired.

Citing Articles

Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes.

Picard H, Schwingen K, Green L, Shis D, Egan S, Bennett M Proteins. 2021; 90(1):186-199.

PMID: 34369028 PMC: 8671227. DOI: 10.1002/prot.26206.

Arabinose Alters Both Local and Distal H-D Exchange Rates in the Escherichia coli AraC Transcriptional Regulator.

Tischer A, Brown M, Schleif R, Auton M Biochemistry. 2019; 58(26):2875-2882.

PMID: 31199144 PMC: 11747938. DOI: 10.1021/acs.biochem.9b00389.

Active role of the interdomain linker of AraC.

Seedorff J, Schleif R J Bacteriol. 2011; 193(20):5737-46.

PMID: 21840981 PMC: 3187213. DOI: 10.1128/JB.05339-11.

Linker regions of the RhaS and RhaR proteins.

Kolin A, Jevtic V, Swint-Kruse L, Egan S J Bacteriol. 2006; 189(1):269-71.

PMID: 17071764 PMC: 1797203. DOI: 10.1128/JB.01456-06.

In vivo DNA-binding and oligomerization properties of the Shigella flexneri AraC-like transcriptional regulator VirF as identified by random and site-specific mutagenesis.

Porter M, Dorman C J Bacteriol. 2001; 184(2):531-9.

PMID: 11751832 PMC: 139584. DOI: 10.1128/JB.184.2.531-539.2002.

References

Schnarr M . Spacing requirements between LexA operator half-sites can be relaxed by fusing the LexA DNA binding domain with some alternative dimerization domains. J Mol Biol. 1993; 229(1):1-7. DOI: 10.1006/jmbi.1993.1001. View

Tobin J, Schleif R . Positive regulation of the Escherichia coli L-rhamnose operon is mediated by the products of tandemly repeated regulatory genes. J Mol Biol. 1987; 196(4):789-99. DOI: 10.1016/0022-2836(87)90405-0. View

Sander C, Schneider R . Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991; 9(1):56-68. DOI: 10.1002/prot.340090107. View

Gubler M, Bickle T . Increased protein flexibility leads to promiscuous protein--DNA interactions in type IC restriction-modification systems. EMBO J. 1991; 10(4):951-7. PMC: 452739. DOI: 10.1002/j.1460-2075.1991.tb08029.x. View

Lobell R, Schleif R . DNA looping and unlooping by AraC protein. Science. 1990; 250(4980):528-32. DOI: 10.1126/science.2237403. View

Argos P . An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J Mol Biol. 1990; 211(4):943-58. DOI: 10.1016/0022-2836(90)90085-Z. View

Martin K, Huo L, Schleif R . The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. Proc Natl Acad Sci U S A. 1986; 83(11):3654-8. PMC: 323581. DOI: 10.1073/pnas.83.11.3654. View

Moult J, Sussman F, James M . Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution. J Mol Biol. 1985; 182(4):555-66. DOI: 10.1016/0022-2836(85)90241-4. View

Dunn T, Hahn S, Ogden S, Schleif R . An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. Proc Natl Acad Sci U S A. 1984; 81(16):5017-20. PMC: 391628. DOI: 10.1073/pnas.81.16.5017. View

10.

STONER C, Schleif R . The araE low affinity L-arabinose transport promoter. Cloning, sequence, transcription start site and DNA binding sites of regulatory proteins. J Mol Biol. 1983; 171(4):369-81. DOI: 10.1016/0022-2836(83)90035-9. View

11.

Sauer R, Ross M, Ptashne M . Cleavage of the lambda and P22 repressors by recA protein. J Biol Chem. 1982; 257(8):4458-62. View

12.

ENGLESBERG E, Squires C, Meronk Jr F . The L-arabinose operon in Escherichia coli B-r: a genetic demonstration of two functional states of the product of a regulator gene. Proc Natl Acad Sci U S A. 1969; 62(4):1100-7. PMC: 223620. DOI: 10.1073/pnas.62.4.1100. View

13.

ENGLESBERG E, Irr J, Power J, Lee N . Positive control of enzyme synthesis by gene C in the L-arabinose system. J Bacteriol. 1965; 90(4):946-57. PMC: 315760. DOI: 10.1128/jb.90.4.946-957.1965. View

14.

Astromoff A, Ptashne M . A variant of lambda repressor with an altered pattern of cooperative binding to DNA sites. Proc Natl Acad Sci U S A. 1995; 92(18):8110-4. PMC: 41105. DOI: 10.1073/pnas.92.18.8110. View

15.

Eustance R, Bustos S, Schleif R . Reaching out. Locating and lengthening the interdomain linker in AraC protein. J Mol Biol. 1994; 242(4):330-8. DOI: 10.1006/jmbi.1994.1584. View

16.

Horii T, Ogawa T, Nakatani T, Hase T, Matsubara H, Ogawa H . Regulation of SOS functions: purification of E. coli LexA protein and determination of its specific site cleaved by the RecA protein. Cell. 1981; 27(3 Pt 2):515-22. DOI: 10.1016/0092-8674(81)90393-7. View

17.

Reece R, Ptashne M . Determinants of binding-site specificity among yeast C6 zinc cluster proteins. Science. 1993; 261(5123):909-11. DOI: 10.1126/science.8346441. View

18.

Bustos S, Schleif R . Functional domains of the AraC protein. Proc Natl Acad Sci U S A. 1993; 90(12):5638-42. PMC: 46776. DOI: 10.1073/pnas.90.12.5638. View

19.

Reeder T, Schleif R . AraC protein can activate transcription from only one position and when pointed in only one direction. J Mol Biol. 1993; 231(2):205-18. DOI: 10.1006/jmbi.1993.1276. View

20.

Carra J, Schleif R . Variation of half-site organization and DNA looping by AraC protein. EMBO J. 1993; 12(1):35-44. PMC: 413173. DOI: 10.1002/j.1460-2075.1993.tb05629.x. View