Escherichia coli transcription termination factor Rho binds and hydrolyzes ATP using a single class of three sites.

Escherichia coli transcription termination factor Rho uses the energy of ATP hydrolysis to travel 5' --> 3' along RNA. We previously showed that the hexameric Rho protein binds three molecules of ATP in active sites and that hydrolysis of the three bound ATP molecules upon RNA binding is sequential. Other models of Rho ATP hydrolysis activity have arisen from reports of additional ATP binding sites on Rho. Here we present further evidence from binding, isotope partitioning, and rapid mix/chemical quench experiments, in support of the presence of only three equivalent ATP binding sites on Rho that are catalytic sites and that fire sequentially. These results are incorporated into a proposed mechanism for directional Rho tracking along RNA.

Instability of pUC19 in Escherichia coli transcription termination factor mutant, rho026.

The higher copy number of pUC19, compared to its parent plasmid pBR322, is known to be due to deletion of rop, also known as rom, and to an ori mutation that impedes RNAI:RNAII interaction. pUC19, unlike pBR322, fails to transform E. coli rho mutant rho026 cells. Here we identify two features of pUC19 that contribute to this transformation defect. (1) The pUCori mutation is involved because replacing the pUCori with that of pBR322 restored transformation. (2) Transcription from the lac promoter in pUC19 is important, since deletion or inversion of the promoter or insertion of a transcription terminator (lambdat0) downstream of it restored transformation. Host RNase E activity is responsible for the transformation defect because introduction of an rne-1 allele into rho026 cells suppressed this defect, indicating that RNAI instability due to RNase E is aggravated in the rho026 strain. We suggest that in rho026 cells pUC19 RNAI:RNAII interaction is more impeded than in rho+ cells and Rop/Rom may confer stability by protecting RNAI against RNase E activity because expression of a rom gene inserted into pUC19 restored transformation.

Sequential hydrolysis of ATP molecules bound in interacting catalytic sites of Escherichia coli transcription termination protein Rho.

Escherichia coli transcription termination protein Rho, an RNA-dependent ATPase, disrupts transcription complexes, releasing RNA and allowing RNA polymerase to recycle. Homohexameric Rho binds three molecules of MgATP in a single class of catalytically competent sites. In rapid mix chemical quench experiments, when Rho saturated with ATP was mixed with RNA and the reaction was quenched after various times, hydrolysis of the three bound ATP molecules was not simultaneous. A hydrolysis burst of one molecule of ATP per hexamer occurred at >300 s-1, followed by steady-state hydrolysis at 30 s-1 per hexamer. The burst also shows that a step following ATP hydrolysis is rate-limiting for overall catalysis and requires communication among the three catalytic sites during net ATP hydrolysis. The rate of hydrolysis of radiolabeled ATP when one labeled and two unlabeled ATP molecules are bound indicates a sequential pattern of hydrolysis. Positive cooperativity of catalysis occurs among the catalytic sites of Rho; when only one ATP molecule is bound per hexamer, ATP hydrolysis upon addition of RNA is 30-fold slower than when ATP is saturating. These behaviors are comparable to those of F1-type ATPases, with which Rho shares a number of structural features.

Effects on mRNA degradation by Escherichia coli transcription termination factor Rho and pBR322 copy number control protein Rop.

Mutants in Escherichia coli transcription termination factor Rho, termed rho(nusD), were previously isolated based on their ability to block the growth of bacteriophage T4. Here we show that rho(nusD) strains have decreased average half-lives for bulk cellular mRNA. Decreased E. coli message lifetimes could be because of increased ribonuclease activity in the rho mutant cells: if a Rho-dependent terminator precedes a ribonuclease gene, weaker termination in the rho mutants could lead to nuclease overexpression. However, inactivation of ribonuclease genes in rho026 cells did not relieve the defective phage growth. Unexpectedly, expression of the pBR322 Rop protein, a structure-specific, sequence-independent RNA-binding protein, in rho(nusD) cells restored the ability of T4 to grow and prolonged cellular message half-life in both the wild-type and the rho026 mutant. These results suggest that it is the RNA-binding ability of Rho rather than its transcription termination function that is important for the inhibition of bacteriophage growth and the shorter bulk mRNA lifetime. We propose that altered interaction of the mutant Rho with mRNA could make the RNA more susceptible to degradation. The inability of the RNA-binding proteins SrmB and DeaD to reverse the rho mutant phenotype when each is overexpressed implies that the required RNA interactions are specific. The results show novel roles for Rho and Rop in mRNA stability.

Structure-function relationships in Escherichia coli transcription termination protein Rho revealed by radiation target analysis.

High-energy electrons were used to measure the target sizes for inactivation of the RNA-dependent ATPase activity of Escherichia coli transcription termination factor Rho, for its ATP binding ability, and for its physical destruction. SDS-PAGE analysis of irradiated samples indicated that the target size for polypeptide destruction in the homohexameric enzyme is the dimer, indicating that energy transfer must occur from a hit subunit to one other subunit, although the subunits are not known to be linked by any covalent bonds. The ATP binding ability of Rho also inactivates as a dimer, a result that is consistent with the physical destruction target size. However, a single subunit as the ATP binding entity is not excluded. The RNA-dependent ATPase activity of Rho inactivates with the apparent target size of trimer to tetramer, indicating that interactions among the subunits of Rho are required for ATP hydrolysis. Rho hexamers are known to exchange subunits, although the identity of the exchanging unit is not known. Models in which this property of Rho is taken into account indicate that the closest fit to the experimental data is for an ATPase target size of a hexamer with dimers as the exchanging units, consistent with earlier chemical inactivation studies.

In vitro characterization of transcription termination factor Rho from Escherichia coli rho(nusD) mutants.

Escherichia coli nusD strains are bacteria that carry mutations in rho, the gene for transcription termination factor Rho, that block the growth of phages T4 and lambdar32. We have identified the rho mutation in six independent nusD strains, and although five of the strains have different mutations, with one exception the mutations are in the proposed RNA-binding domain of Rho. We overexpressed, purified, and characterized the five different mutant Rho proteins. All show substantial RNA-dependent ATPase activity with several homoribopolymers or the lambda cro message as cofactor. At the lambda tR1 Rho-dependent terminator in vitro, all mutant Rho proteins show decreased termination compared with wild-type, and all also terminate within cro at a new terminator, tRE, with endpoints 5' to tR1 at 170, 200, 245 and 260 nucleotides 3' from the transcription start. The mutant Rho proteins are proposed to interfere with bacteriophage T4 growth through indirect effects on host gene expression.

The mechanism of early transcription termination by Rho026.

We previously found that nusD-type mutations in Escherichia coli transcription termination factor Rho enhance in vitro transcription termination at four points within the lambdacro gene. Here we show that the early termination points are part of one Rho-dependent termination site, tRE, with properties like those of previously characterized Rho-dependent sites lamda tR1 and trpt'. The early termination points are all RNA polymerase pause sites, and by deletion analysis and oligonucleotide blocking experiments, a common 5' Rho entry site for the early termination points (rutE) is identified. We show that both Rho026 and Rho+ can use rutE as an entry point for termination, but that Rho026 is more efficient in releasing the nascent RNA at tRE. The RNA-dependent ATPase activities of wild-type and mutant Rhos are similar, as are their abilities to bind free RNA and to use (rC)10 oligomers for ATPase activation. We therefore suggest that Rho-RNA polymerase interactions that define the site of RNA 3' end formation are altered in NusD Rho mutants. NusD Rho mutants are less dependent on, but still responsive to, the transcription termination factor NusG. However, addition of NusG to in vitro termination assays allows Rho+ to terminate more efficiently at tRE. These results suggest that NusG aids in the 3' end formation process. The decreased dependence on NusG for termination by the mutant Rhos in vitro provides an explanation for poorer lambda growth in rho(nusD) cells by interference with lamdaN-mediated antitermination at Rho-dependent sites.

Escherichia coli NusG protein stimulates transcription elongation rates in vivo and in vitro.

The rate of transcription elongation in Escherichia coli was reduced when cells were depleted of NusG. In a purified in vitro system, NusG accelerated the transcription elongation rate. The stimulation of the rate of transcription elongation by NusG appears to result from the suppression of specific transcription pause sites.

8-Azido-ATP inactivation of Escherichia coli transcription termination factor Rho. Modification of one subunit inactivates the hexamer.

Escherichia coli transcription termination factor Rho (EC 3.6.1.3) releases nascent RNA from transcription complexes in a reaction which requires ATP hydrolysis. To understand the structure of the ATPase active site, we employed an analog of ATP, 8-azidoadenosine 5'-triphosphate (8-azido-ATP) as a photoaffinity labeling agent. 8-Azido-ATP interacts nearly normally with the active site of Rho. It binds to 3 sites per Rho hexamer with a 100 microM KD and is a substrate with a Vmax 5% that of ATP and a Km of 18 microM. Under UV irradiation, 8-azido-ATP makes covalent bonds with Rho, inactivating its ATPase. Rho is protected from this inactivation by the presence of ATP. We used [alpha-32P]8-azido-ATP to label the active site and identify residues involved in ATP binding. Labeled tryptic peptides of the modified Rho were purified by Fe(3+)-iminodiacetic acid affinity chromatography and reverse-phase C18 column high performance liquid chromatography. We identified a single peptide, Gly174-Lys184, that is labeled by 8-azido-ATP and protected from labeling in the presence of ATP. The modified amino acid is Lys181, whose conservative replacement by Gln181 gives rise to a poorly active enzyme (Dombroski, A. J., Brennan, C. A., Spear, P., and Platt, T. (1988a) J. Biol. Chem. 263, 18802-18809). Lys181 probably participates in binding the phosphoryl groups of ATP. Incorporation of one 8-azido-ATP per Rho hexamer is sufficient to cause inactivation, a result that indicates that the active sites of Rho interact in RNA-dependent ATP hydrolysis.

Impaired expression of certain prereplicative bacteriophage T4 genes explains impaired T4 DNA synthesis in Escherichia coli rho (nusD) mutants.

The Escherichia coli rho 026 mutation that alters the transcription termination protein Rho prevents growth of wild-type bacteriophage T4. Among the consequences of this mutation are delayed and reduced T4 DNA replication. We show that these defects can be explained by defective synthesis of certain T4 replication-recombination proteins. Expression of T4 gene 41 (DNA helicase/primase) is drastically reduced, and expression of T4 genes 43 (DNA polymerase), 30 (DNA ligase), 46 (recombination nuclease), and probably 44 (DNA polymerase-associated ATPase) is reduced to a lesser extent. The compensating T4 mutation goF1 partially restores the synthesis of these proteins and, concomitantly, the synthesis of T4 DNA in the E. coli rho mutant. From analyzing DNA synthesis in wild-type and various multiply mutant T4 strains, we infer that defective or reduced synthesis of these proteins in rho 026-infected cells has several major effects on DNA replication. It impairs lagging-strand synthesis during the primary mode of DNA replication; it delays and depresses recombination-dependent (secondary mode) initiation; and it inhibits the use of tertiary origins. All three T4 genes whose expression is reduced in rho 026 cells and whose upstream sequences are known have a palindrome containing a CUUCGG sequence between the promoter(s) and ribosome-binding site. We speculate that these palindromes might be important for factor-dependent transcription termination-antitermination during normal T4 development. Our results are consistent with previous proposals that the altered Rho factor of rho 026 may cause excessive termination because the transcription complex does not interact normally with a T4 antiterminator encoded by the wild-type goF gene and that the T4 goF1 mutation restores this interaction.

Escherichia coli transcription termination protein rho has three hydrolytic sites for ATP.

We have determined that 3 mol of ATP or other adenine nucleotide can bind to Escherichia coli transcription termination protein rho, in the presence or absence of the RNA cofactor that is required for activation of rho's ATPase activity. Isotope trap experiments show that the three molecules of ATP bound/rho hexamer in the absence of RNA are hydrolyzed upon addition of RNA and are therefore correctly and productively bound at active sites. These results imply that rho acts as a trimer of dimers and that either the ATPase active sites are at the interface between head-to-head protein monomers, or that ATP binding induces asymmetry among rho subunits and results in the formation of functional dimers within the hexamer. We show that ATP is efficiently hydrolyzed by rho only upon RNA binding. We have measured KD values for ATP, ADP, and Pi binding to rho and have constructed a minimal kinetic mechanism for ATP hydrolysis by the enzyme.

Absence of a phosphorylated intermediate during ATP hydrolysis by Escherichia coli transcription termination protein rho.

We have established the suitability of adenosine 5'-O-(gamma-thio)triphosphate(ATP gamma S) as an analog of ATP for the nucleoside triphosphatase activity of Escherichia coli transcription termination protein rho (EC 3.6.1.3). Steady-state analysis gives a Vmax of 1.5 mumol min-1 mg-1, 9% of the value with MgATP as substrate, and indicates that ATP gamma S binds as tightly (based on Km and Ki versus ATP) to rho as does ATP. (gamma-S)[beta gamma-17O,gamma-17O,gamma-18O]ATP gamma S was used as substrate to produce chiral product inorganic [17O,18O]thiophosphate and determine the stereochemical course of the hydrolysis. The results of this determination, inversion at the thiophosphoryl phosphorus, indicate that the enzymatic hydrolysis of ATP by rho consists of a direct transfer of the phospho group to water without the existence of a phosphoenzyme or phospho-RNA intermediate.

Morphogenesis of bacteriophage phi 6: a presumptive viral membrane precursor.

Bacteriophage phi 6 has a lipid- and protein-containing membrane as its outer covering. Two phi 6-coded proteins are known to be required to produce enveloped phage particles: one is P9, the major phi 6 membrane structural protein, and the other is P12, a nonstructural protein without which membrane fails to assemble around phage nucleocapsids. A particle containing phospholipid, P9, and two minor phi 6 membrane proteins has been found in cells pulse labeled with protein precursors at late times after infection. The P9 particle can be chased into phage and is dependent on active P12 for its formation. Models are presented in which the role of the P9 particle in phi 6 membrane assembly is discussed.

The structure of bacteriophage phi 6: protease digestion of phi 6 virions.

Proteolysis experiments with phi 6 virions show that the adsorption protein, P3, is digested by both trypsin and chymotrypsin. In addition, chymotrypsin also removes P6, a protein thought to be the anchor for P3 in the phi 6 membrane.

Role of the host cell in bacteriophage T4 development. II. Characterization of host mutants that have pleiotropic effects on T4 growth.

Mutant host-defective Escherichi coli that fail to propagate bacteriophage T4 and have a pleiotropic effect on T4 development have been isolated and characterized. In phage-infected mutant cells, specific early phage proteins are absent or reduced in amount, phage DNA synthesis is depressed by about 50%, specific structural phage proteins, including some tail and collar components, are deficient or missing, and host-cell lysis is delayed and slow. Almost all phage that can overcome the host block carry mutantions that map in functionally undefined 'nonessential' regions of the T4 genome, most near gene 39. The mutant host strains are temperature sensitive for growth and show simultaneous reversion of the ts phenotype and the inability to propagate T4+. The host mutations are cotransduced with ilv (83 min) and may lie in the gene for transcription termination factor rho.

Role of the host cell in bacteriophage T4 development. I. Characterization of host mutants that block T4 head assembly.

To study the role of the host cell in bacteriophage T4 infection, we selected more than 600 mutant host-defective bacteria that absorbed and were killed by phage T4+ but were unable to support its growth. The mutants were grouped into seven classes by the growth patterns of T4 phages carrying compensating mutations (go mutants [grows on]), selected on four prototype host-defective strains. Lysis and DNA synthesis experiments indicated that classes A, AD, D, and B (the majority of the host-defective mutants) block T4+ development at an assembly step, class C mutants affect an early stage in phage development, and class F mutants appear to act at more than one stage. Analysis of T4+ infection in the assembly-defective mutants by in vitro complementation, electron microscopy, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the host-defective mutations interfere with T4+ capsid formation at the level of phage gene 31 function, before assembly of any recognizable capsid structure. The mutations map near purA, but at two or possibly three different sites. The go mutant phages able to overcome the host defect carry mutations in either gene 31, as found by others for similar defective hosts, or in the gene for the major capsid protein (gene 23). The gene 23 go mutations do not bypass the requirement for gene 31 function. These results suggest that at least three components must interact to initiate T4 head assembly: gp31, gp23, and one or more host factors. The compensatory effects of mutational alterations in these components are highly allele specific, consistent with the view that phage and host components interact directly in protein complexes.