Photoaffinity labeling of the TF1-ATPase from the thermophilic bacterium PS3 with 3'-O-(4-benzoyl)benzoyl ADP

3'-O-(4-Benzoyl)benzoyl ADP (BzADP) was used as a photoaffinity label for covalent binding of adenine nucleotide analogs to the nucleotide binding site(s) of the thermophilic bacterium PS3 ATPase (TF1). As with the CF1-ATPase (Bar-Zvi, D. and Shavit, N. (1984) Biochim. Biophys. Acta 765, 340-356) noncovalently bound BzADP is a reversible inhibitor of the TF1-ATPase. BzADP changes the kinetics of ATP hydrolysis from noncooperative to cooperative in the same way as ADP does, but, in contrast to the effect on the CF1-ATPase, it has no effect on the Vmax. In the absence of Mg2+ 1 mol BzADP binds noncovalently to TF1, while with Mg2+ 3 mol are bound. Photoactivation of BzADP results in the covalent binding of the analog to the nucleotide binding site(s) on TF1 and correlates with the inactivation of the ATPase. Complete inactivation of the TF1-ATPase occurs after covalent binding of 2 mol BzADP/mol TF1. Photoinactivation of TF1 by BzADP is prevented if excess of either ADP or ATP is present during irradiation. Analysis by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate of the Bz[3H]ADP-labeled TF1-ATPase shows that all the radioactivity is incorporated into the beta subunit.     

A simple physiologically relevant double-agar-layer method for post-germination treatment of seedlings

Arabidopsis thaliana is frequently grown on semisolid medium in Petri dishes, for various experiments that usually consist of two stages on two distinct growth media. Seedlings are germinated under favorable conditions followed by their transfer to another medium containing the given treatment(s). This often causes secondary effects on seedlings due to root shock, or direct and unavoidable contact of the shoot with the second medium. We have developed a simple and efficient method for the transfer of seedlings grown on semisolid medium with minimal damage. In this double-agar-layer method, seeds are germinated on a thin growth-medium-containing agar layer. Subsequently, medium blocks containing the embedded seedlings are excised and placed on the second semisolid medium supplemented with the treatment agent. Differential agar concentrations allow easy penetration of the roots into the second medium, but do not allow the shoots to come into contact with it. This unique method offers several advantages over others that are in common use, in which the seedlings are individually transferred to the second medium or alternatively grown on transfer-carrier matrices, such as filter paper, mesh and cellophane. In the presented method, the entire root system faces the growth medium, the shoots are surrounded by air at all growth stages and transfer of the seedlings is much easier. In addition, a large number of seedlings can be transferred in a single step, without stressing the plants or damaging the delicate root system. This method can also be applied to other plant species grown on semisolid media.     

Mapping the DNA- and zinc-binding domains of ASR1 (abscisic acid stress ripening), an abiotic-stress regulated plant specific protein

Abscisic acid stress ripening (ASR1) is a highly charged low molecular weight plant specific protein that is regulated by salt- and water-stresses. The protein possesses a zinc-dependent DNA-binding activity (Kalifa et al., Biochem. J. 381 (2004) 373) and overexpression in transgenic plants results in an increased salt-tolerance (Kalifa et al., Plant Cell Environ. 27 (2004) 1459). There are no structure homologs of ASR1, thus the structural and functional domains of the protein cannot be predicted. Here, we map the protein domains involved in the binding of Zn(2+) and DNA. Using mild acid hydrolysis, and a series of ASR1 carboxy-terminal truncations we show that the zinc-dependent DNA-binding could be mapped to the central/carboxy-terminal domain. In addition, using MALDI-TOF-MS with a non-acidic matrix, we show that two zinc ions are bound to the amino-terminal domain. Other zinc ion(s) bind the DNA-binding domain. Binding of zinc to ASR1 induces conformational changes resulting in a decreased sensitivity to proteases.     

Covalent binding of 3'-O-(4-benzoyl)benzoyl adenosine 5'-triphosphate (BzATP) to the isolated alpha and beta subunits and the alpha 3 beta 3 core complex of TF1. Covalent binding of BzATP prevents association of alpha and beta subunits and induces dissociation of the alpha 3 beta 3 core complex.

Binding of the photoreactive ATP analog, 3'-O-(4-benzoyl)benzoyl adenosine 5'-triphosphate (BzATP), to the isolated alpha and beta subunits of TF1 and to the alpha 3 beta 3 "core" complex of the holoenzyme is described. About 1 mol of BzATP/mol of subunit was incorporated to isolated alpha and beta subunits. The incorporation of BzATP was prevented by ATP. Covalent binding of BzATP to the alpha subunit was in general somewhat lower than that observed with the beta subunit. No complex was formed upon mixing of either of the modified subunits with the complementary nontreated subunits. Covalent binding of 3 mol of BzATP/alpha 3 beta 3 complex completely inhibited ATPase activity and resulted in the dissociation of the complex. The labeled nucleotide analog was specifically incorporated into the beta subunit of the complex. The holoenzyme TF1, in contrast to the core complex, did not dissociate to the individual subunits upon covalent binding of BzATP. These results are discussed in relation to the location of the catalytic nucleotide binding site(s) and the conformation stability of the alpha 3 beta 3 core complex of TF1.     

Assembled clathrin in erythrocytes

Clathrin cages were isolated from rat erythrocytes. These structures exist in the intact cell as demonstrated by immunofluorescence and were not formed during the isolation procedure. The cages were largely devoid of membrane but contained the assembly protein complex and both the 50-kDa kinase (pp50) and casein kinase II activities found previously in clathrin-coated vesicles.     

In vivo phosphorylation of clathrin-coated vesicle proteins from rat reticulocytes

We have studied the in vivo phosphorylation of clathrin-coated vesicle proteins from rat reticulocytes. The major 32P-labeled polypeptides of clathrin-coated vesicles isolated from metabolically labeled cells were the the 165-, 100-110-, and 50-kDa polypeptides of the assembly protein, the clathrin beta-light chain, and to a lesser extent the clathrin alpha-light chain. The phosphorylation of the assembled (particulate) and unassembled (soluble) pools of clathrin and assembly protein was compared by immunoprecipitating the respective protein complexes from particulate and soluble cell fractions. Although all the phosphorylated polypeptides were present in both fractions, the extent of labeling was protein and fraction specific: the apparent specific activities of the assembly protein 50-kDa polypeptide and clathrin light chain were higher in the unassembled pool, whereas those of the 100-110-kDa polypeptides were higher in the assembled pool. The amino acids and polypeptide fragments labeled in vivo appeared similar to those labeled in vitro.