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| 45. |
- Abdulkarim, Farhad, et al.
(författare)
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Homologous recombination between the tuf genes of Salmonella typhimurium
- 1996
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 260:4, s. 506-522
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Tidskriftsartikel (refereegranskat)abstract
- The genes coding for the translation factor EF-Tu, tufA and tufB are separated by over 700 kb on the circular chromosome of Salmonella typhimurium. The coding regions of these genes have 99% identity at the nucleotide level in spite of the presumed ancient origin of the gene duplication. Sequence comparisons between S. typhimurium and Escherichiacoli suggest that within each species the two tuf genes are evolving inconcert. Here we show that each of the S. typhimurium tuf genes cantransfer genetic information to the other. In our genetic system thetransfers are seen as non-reciprocal, i.e. as gene conversion events.However, the mechanism of recombination could be reciprocal, with sisterchromosome segregation and selection leading to the isolation of aparticular class of recombinant. The amount of sequence informationtransferred in individual recombination events varies, but can be close tothe entire length of the gene. The recombination is RecABCD-dependent,and is opposed by MutSHLU mismatch repair. In the wild-type, this typeof recombination occurs at a rate that is two or three orders of magnitudegreater than the nucleotide substitution rate. The rate of recombinationdiffers by six orders of magnitude between a recA and a mutS strain.Mismatch repair reduces the rate of this recombination 1000-fold. The rateof recombination also differs by one order of magnitude depending onwhich tuf gene is donating the sequence selected for. We discuss threeclasses of model that could, in principle, account for the sequencetransfers: (1) tuf mRNA mediated recombination; (2) non-allelic reciprocalrecombination involving sister chromosomes; (3) non-allelic geneconversion involving sister chromosomes, initiated by a double-strandbreak close to one tuf gene. Although the mechanism remains to bedetermined, the effect on the bacterial cells is tuf gene sequencehomogenisation. This recombination phenomenon can account for theconcerted evolution of the tuf genes.
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| 46. |
- Abdulkarim, Farhad, et al.
(författare)
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Missense substitutions lethal to essential functions of EF-Tu
- 1991
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Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 73:12, s. 1457-1464
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Tidskriftsartikel (refereegranskat)abstract
- We have used a simple selection and screening method to isolate function defective mutants of EF-Tu. From 28 mutants tested, 12 different missense substitutions, individually lethal to some essential function of EF-Tu, were identified by sequencing. In addition we found a new non-lethal missense mutation. The frequency of isolation of unique mutations suggests that this method can be used to easily isolate many more. The lethal mutations occur in all three structural domains of EF-Tu, but most are in domain II. We aim to use these mutants to define functional domains on EF-Tu.
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| 47. |
- Abdulkarim, Farhad, et al.
(författare)
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Mutants of EF-Tu defective in binding aminoacyl-tRNA
- 1996
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Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 382:3, s. 297-303
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Tidskriftsartikel (refereegranskat)abstract
- Five single amino acid substitution variants of EF-Tu from Salmonella typhimurium were tested for their ability to promote poly(U)-translation in vitro. The substitutions are Leu120Gln, Gln124Arg and Tyr160 (Asp or Asn or Cys). They were selected by their kirromycin resistant phenotypes and all substitutions are in domain I at the interface between domains I and III of the EF-Tu · GTP configuration. The different EF-Tu variants exhibit a spectrum of phenotypes. First, k(cat)/K(M) for the interaction between ternary complex and the programmed ribosome is apparently reduced by the substitutions Leu120Gln, Gln124Arg and Tyr160Cys. Second, this reduction is caused by a defect in the interaction between these EF-Tu variants and aminoacyl-tRNA during translation. Third, in four cases out of five the affinity of the complex between EF-Tu · GTP and aminoacyl-tRNA is significantly decreased. The most drastic reduction is observed for the Gln124Arg change, where the association constant is 30-fold lower than in the mild-type case. Fourth, missense errors are increased as well as decreased by the different amino acid substitutions. Finally, the dissociation rate constant (k(d)) for the release of GDP from EF-Tu is increased 6-fold by the Tyr160Cys substitution, but remains unchanged in the four other cases. These results show that the formation of ternary complex is sensitive to many different alterations in the domain I-III interface of EF-Tu.
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| 48. |
- Abdulkarim, Farhad, et al.
(författare)
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Mutations to kirromycin resistance occur in the interface of domains I and III of EF-Tu.GTP
- 1994
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Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 352, s. 118-122
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Tidskriftsartikel (refereegranskat)abstract
- The antibiotic kirromycin inhibits protein synthesis by binding to EF-Tu and preventing its release from the ribosome after GTP hydrolysis.We have isolated and sequenced a collection of kirromycin resistant tuf mutations and identified thirteen single amino acid substitutions at sevendifferent sites in EF-Tu. These have been mapped onto the 3D structures of EF-Tu’GTP and EF-Tu.GDP. In the active GTP form of EF-Tu themutations cluster on each side of the interface between domains I and III. We propose that this domain interface is the binding site for kirromycin.
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| 49. |
- Abdulla, Parosh Aziz, et al.
(författare)
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A general approach to partial order reductions in symbolic verification
- 1998
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Ingår i: Computer Aided Verification. - 9783540646082 - 9783540693390 ; , s. 379-390
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Konferensbidrag (refereegranskat)abstract
- The purpose of partial-order reduction techniques is to avoid exploring several interleavings of independent transitions when model checking the temporal properties of a concurrent system. The purpose of symbolic verification techniques is to perform basic manipulations on sets of states rather than on individual states. We present a general method for applying partial order reductions to improve symbolic verification. The method is equally applicable to the verification of finite-state and infinite-state systems. It considers methods that check safety properties, either by forward reachability analysis or by backward reachability analysis. We base the method on the concept of commutativity (in one direction) between predicate transformers. Since the commutativity relation is not necessarily symmetric, this generalizes those existing approaches to partial order verification which are based on a symmetric dependency relation.We show how our method can be applied to several models of infinite-state systems: systems communicating over unbounded lossy FIFO channels, and unsafe (infinite-state Petri Nets. We show by a simple example how partial order reduction can significantly speed up symbolic backward analysis of Petri Nets.
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| 50. |
- Abdulla, Parosh Aziz, et al.
(författare)
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Handling Global Conditions in Parameterized System Verification
- 1999
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Ingår i: Proc. 11th Int. Conf. on Computer Aided Verification. - Berlin : Springer Verlag. - 3540662022 ; , s. 134-145
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Konferensbidrag (refereegranskat)abstract
- We consider symbolic verification for a class of parameterized systems, where a system consists of a linear array of processes, and where an action of a process may in general be guarded by both local conditions restricting the state of the process about to perform the action, and global conditions defining the context in which the action is enabled. Such actions are present, e.g., in idealized versions of mutual exclusion protocols, such as the bakery and ticket algorithms by Lamport, Burn’s protocol, Dijkstra’s algorithm, and Szymanski’s algorithm. The presence of both local and global conditions makes the parameterized versions of these protocols infeasible to analyze fully automatically, using existing model checking methods for parameterized systems. In all these methods the actions are guarded only by local conditions involving the states of a finite set of processes. We perform verification using a standard symbolic reachability algorithm enhanced by an operation to accelerate the search of the state space. The acceleration operation computes the effect of an arbitrary number of applications of an action, rather than a single application. This is crucial for convergence of the analysis e.g. when applying the algorithm to the above protocols. We illustrate the use of our method through an application to Szymanski’s algorithm.
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