scholarly journals Two essential regions for tRNA recognition in Bacillus subtilis tryptophanyl-tRNA synthetase

2002 ◽  
Vol 365 (3) ◽  
pp. 749-756 ◽  
Author(s):  
Jie JIA ◽  
Feng XU ◽  
Xianglong CHEN ◽  
Li CHEN ◽  
Youxin JIN ◽  
...  

Bacillus subtilis tryptophanyl-tRNA synthetase (TrpRS) is a homodimeric enzyme. A model for its ability to recognize tRNATrp in B. subtilis was proposed by using computer modelling. This was based on the the fact that there is high homology among bacterial TrpRSs [Chen, Jiang, Jin and Wang (2001) Acta Biochim. Biophys. Sinica 33, 687–690], in which the enzyme dimer binds to two tRNATrp molecules and each tRNATrp is bound to two different domains across the surface of the dimer. In this work, three deletion mutants of TrpRS were constructed and their products were purified. After determining the kinetic parameters of the mutants in the two-step reaction, it was found that the relative activities of wild-type and mutant enzymes had changed little in the ATP-pyrophosphate exchange reaction. In contrast, the activities of three mutant proteins were much decreased in the tRNATrp aminoacylation assay. Deletion of residues 108–122 and residues 234–238 caused 44% and 80% reductions in the activity, respectively. When both regions were deleted, the aminoacylation activity of the TrpRS mutant was too low to be determined using tRNATrp at the limiting concentration. Gel-retardation assays showed that the acceptor minihelix and the anticodon microhelix were recognized by the domains of TrpRS spanning residues 108–122 and residues 234–238 respectively. In addition, the deletion of amino acids 234–238 affected the normal induced expression of TrpRS at 37°C. In conclusion, residues 108–122 and 234–238 were found essential for tRNATrp recognition.

2009 ◽  
Vol 284 (44) ◽  
pp. 30643-30651 ◽  
Author(s):  
Jelena Jaric ◽  
Silvija Bilokapic ◽  
Sonja Lesjak ◽  
Ana Crnkovic ◽  
Nenad Ban ◽  
...  

1998 ◽  
Vol 180 (17) ◽  
pp. 4760-4763 ◽  
Author(s):  
Dean A. Rowe-Magnus ◽  
Mario Mencía ◽  
Fernando Rojo ◽  
Margarita Salas ◽  
George B. Spiegelman

ABSTRACT In vitro transcription from the spoIIG promoter byBacillus subtilis RNA polymerase reconstituted with wild-type alpha subunits and with C-terminal deletion mutants of the alpha subunit was equally stimulated by the response regulator Spo0A. Some differences in the structure of open complexes formed by RNA polymerase containing alpha subunit mutants were noted, although the wild-type and mutant polymerases appeared to use the same initiation mechanism.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1211-1211
Author(s):  
Jasper C. Lin ◽  
Jason T. Schuman ◽  
Shannon L. Meeks ◽  
John F. Healey ◽  
Arthur R. Thompson ◽  
...  

Abstract The most troublesome clinical complication that can afflict hemophilia A patients who receive factor VIII (FVIII) infusions as replacement therapy is the development of an anti-FVIII immune response, in which antibodies bind to functionally important FVIII surfaces, thereby blocking the pro-coagulant function of this important plasma protein cofactor. These antibodies, commonly referred to as “FVIII inhibitors”, bind primarily to the FVIII A2 and C2 domains and to the C-terminal region of the C1 domain, and inhibitors mapping to other regions have also been seen. There are multiple epitopes on the FVIII C2 domain, reflecting both its immunogenicity/antigenicity and its diverse roles in mediating interactions between FVIII and other molecules. For example, the C2 domain is essential for binding of FVIII to its carrier protein von Willebrand factor (VWF). Proteolytic activation to FVIIIa causes its release from VWF and subsequent binding to negatively charged membrane surfaces, e.g. on activated platelets, whereupon a region that overlaps the VWF binding site contacts the membrane. The C2 domain also interacts with thrombin and factor Xa, which both can activate FVIII. To better understand the basis for FVIII inhibition, and to better delineate functionally important FVIII surfaces, a panel of 56 murine anti-C2 monoclonal antibodies was generated. Competition ELISAs and functional assays were used to classify the antibodies into five groups corresponding to distinct regions on the C2 surface, which comprised a larger number of distinct epitopes (Meeks et al., Blood110, 4234–42, 2007). The present study is a high-resolution mapping of the epitopes recognized by six representative antibodies (2-77, 2-117, 3D12, 3E6, I109 and I54) using surface plasmon resonance (SPR). Each antibody was immobilized covalently via amine coupling to a CM5 chip or was captured by a rat anti-mouse IgG attached covalently to a CM5 chip. Referring to the FVIII C2 domain crystal structure (Pratt et al., Nature402, 439–42, 1999), surface-exposed amino acids were selected for mutagenesis using the Stratagene Quik-Change system, and C2 constructs with single substitutions to alanine or amino acids that were structurally similar to the wild-type residues were generated. Forty-five of these proteins were expressed in E. coli and purified; their purity and structural integrity were confirmed by SDS-PAGE and Western blot analysis. The on- and off-rates for binding of these proteins to the six monoclonal antibodies were determined using a Biacore T100 instrument. Mutations that affected binding significantly were analyzed by measuring association and dissociation constants over a temperature gradient (10–40°C), yielding estimates of changes in antibody-binding energy (ΔΔGº) of these mutant proteins compared to wild-type C2. Van’t Hoff analysis was carried out to determine the relative contributions of enthalpy and entropy to the binding energies. Interestingly, C2 binding to each antibody was abrogated by 1–5 of the 45 amino acid substitutions tested. Each of these C2 mutants bound to other antibodies with affinities similar to that of wild-type C2, indicating that this was not an artifact due to protein misfolding. The following substitutions resulted in little or no binding, as evidenced by a completely abated signal (very low Rmax compared to the wild-type C2 protein): L2273A (2-77, 2-117), R2220A (3D12, I109), Q2231A (I54) and T2272A (I109). Additional mutant proteins with reduced binding to inhibitor(s) displayed markedly higher dissociation constants and sometimes less pronounced differences in association constants compared to wild-type C2. Although several FVIII residues contributed to more than one epitope, each antibody had a unique epitope map profile. Our results suggest that a limited number of amino acid substitutions could produce a modified FVIII protein capable of eluding immunodominant inhibitors. This approach could eventually find clinical application as a novel strategy to achieve hemostasis in patients with an established FVIII inhibitor.


2004 ◽  
Vol 186 (7) ◽  
pp. 1999-2005 ◽  
Author(s):  
Shonna McBride ◽  
W. G. Haldenwang

ABSTRACT σE, a sporulation-specific sigma factor of Bacillus subtilis, is formed from an inactive precursor (pro-σE) by a developmentally regulated processing reaction that removes 27 amino acids from the proprotein's amino terminus. A sigE variant (sigE335) lacking 15 amino acids of the prosequence is not processed into mature σE but is active without processing. In the present work, we investigated the sporulation defect in sigE335-expressing B. subtilis, asking whether it is the bypass of proprotein processing or a residual inhibition of σE activity that is responsible. Fluorescence microscopy demonstrated that sigE335-expressing B. subtilis progresses further into sporulation (stage III) than do strains lacking σE activity (stage II). Consistent with its stage III phenotype, and a defect in σE activity rather than its timing, the sigE335 allele did not disturb early sporulation gene expression but did inhibit the expression of late sporulation genes (gerE and sspE). The Spo− phenotype of sigE335 was found to be recessive to wild-type sigE. In vivo assays of σE activity in sigE, sigE335, and merodiploid strains indicate that the residual prosequence on σE335, still impairs its activity to function as a transcription factor. The data suggest that the 11-amino-acid extension on σE335 allows it to bind RNA polymerase and direct the resulting holoenzyme to σE-dependent promoters but reduces the enzyme's ability to initiate transcription initiation and/or exit from the promoter.


1994 ◽  
Vol 14 (1) ◽  
pp. 815-821 ◽  
Author(s):  
P Poullet ◽  
B Lin ◽  
K Esson ◽  
F Tamanoi

Lysine 1423 of neurofibromin (neurofibromatosis type I gene product [NF1]) plays a crucial role in the function of NF1. Mutations of this lysine were detected in samples from a neurofibromatosis patient as well as from cancer patients. To further understand the significance of this residue, we have mutated it to all possible amino acids. Functional assays using yeast ira complementation have revealed that lysine is the only amino acid that produced functional NF1. Quantitative analyses of different mutant proteins have suggested that their GTPase-activating protein (GAP) activity is drastically reduced as a result of a decrease in their Ras affinity. Such a requirement for a specific residue is not observed in the case of other conserved residues within the GAP-related domain. We also report that another residue, phenylalanine 1434, plays an important role in NF1 function. This was first indicated by the finding that defective NF1s due to an alteration of lysine 1423 to other amino acids can be rescued by a second site intragenic mutation at residue 1434. The mutation partially restored GAP activity in the lysine mutant. When the mutation phenylalanine 1434 to serine was introduced into a wild-type NF1 protein, the resulting protein acquired the ability to suppress activated phenotypes of RAS2Val-19 cells. This suppression, however, does not involve Ras interaction, since the phenylalanine mutant does not stimulate the intrinsic GTPase activity of RAS2Val-19 protein and does not have an increased affinity for Ras proteins.


2015 ◽  
Vol 81 (21) ◽  
pp. 7420-7430 ◽  
Author(s):  
Akiko Hida ◽  
Shota Oku ◽  
Takeru Kawasaki ◽  
Yutaka Nakashimada ◽  
Takahisa Tajima ◽  
...  

ABSTRACTSequence analysis has revealed the presence of 22 putative methyl-accepting chemotaxis protein (mcp) genes in theRalstonia pseudosolanacearumGMI1000 genome. PCR analysis and DNA sequencing showed that the highly motileR. pseudosolanacearumstrain Ps29 possesses homologs of all 22R. pseudosolanacearumGMI1000mcpgenes. We constructed a complete collection of singlemcpgene deletion mutants ofR. pseudosolanacearumPs29 by unmarked gene deletion. Screening of the mutant collection revealed thatR. pseudosolanacearumPs29 mutants of RSp0507 and RSc0606 homologs were defective in chemotaxis tol-malate and amino acids, respectively. RSp0507 and RSc0606 homologs were designatedmcpMandmcpA. While wild-typeR. pseudosolanacearumstrain Ps29 displayed attraction to 16 amino acids, themcpAmutant showed no response to 12 of these amino acids and decreased responses to 4 amino acids. We constructedmcpAandmcpMdeletion mutants of highly virulentR. pseudosolanacearumstrain MAFF106611 to investigate the contribution of chemotaxis tol-malate and amino acids to tomato plant infection. Neither single mutant exhibited altered virulence for tomato plants when tested by root dip inoculation assays. In contrast, themcpMmutant (but not themcpAmutant) was significantly less infectious than the wild type when tested by a sand soak inoculation assay, which requires bacteria to locate and invade host roots from sand. Thus, McpM-mediated chemotaxis, possibly reflecting chemotaxis tol-malate, facilitatesR. pseudosolanacearummotility to tomato roots in sand.


1994 ◽  
Vol 14 (1) ◽  
pp. 815-821
Author(s):  
P Poullet ◽  
B Lin ◽  
K Esson ◽  
F Tamanoi

Lysine 1423 of neurofibromin (neurofibromatosis type I gene product [NF1]) plays a crucial role in the function of NF1. Mutations of this lysine were detected in samples from a neurofibromatosis patient as well as from cancer patients. To further understand the significance of this residue, we have mutated it to all possible amino acids. Functional assays using yeast ira complementation have revealed that lysine is the only amino acid that produced functional NF1. Quantitative analyses of different mutant proteins have suggested that their GTPase-activating protein (GAP) activity is drastically reduced as a result of a decrease in their Ras affinity. Such a requirement for a specific residue is not observed in the case of other conserved residues within the GAP-related domain. We also report that another residue, phenylalanine 1434, plays an important role in NF1 function. This was first indicated by the finding that defective NF1s due to an alteration of lysine 1423 to other amino acids can be rescued by a second site intragenic mutation at residue 1434. The mutation partially restored GAP activity in the lysine mutant. When the mutation phenylalanine 1434 to serine was introduced into a wild-type NF1 protein, the resulting protein acquired the ability to suppress activated phenotypes of RAS2Val-19 cells. This suppression, however, does not involve Ras interaction, since the phenylalanine mutant does not stimulate the intrinsic GTPase activity of RAS2Val-19 protein and does not have an increased affinity for Ras proteins.


2015 ◽  
Vol 197 (9) ◽  
pp. 1632-1639 ◽  
Author(s):  
Sara A. Leiman ◽  
Charles Richardson ◽  
Lucy Foulston ◽  
Alexander K. W. Elsholz ◽  
Eric A. First ◽  
...  

ABSTRACTBacteria produced-amino acids for incorporation into the peptidoglycan and certain nonribosomally produced peptides. However,d-amino acids are toxic if mischarged on tRNAs or misincorporated into protein. Common strains of the Gram-positive bacteriumBacillus subtilisare particularly sensitive to the growth-inhibitory effects ofd-tyrosine due to the absence ofd-aminoacyl-tRNA deacylase, an enzyme that prevents misincorporation ofd-tyrosine and otherd-amino acids into nascent proteins. We isolated spontaneous mutants ofB. subtilisthat survive in the presence of a mixture ofd-leucine,d-methionine,d-tryptophan, andd-tyrosine. Whole-genome sequencing revealed that these strains harbored mutations affecting tRNATyrcharging. Three of the most potent mutations enhanced the expression of the gene (tyrS) for tyrosyl-tRNA synthetase. In particular, resistance was conferred by mutations that destabilized the terminator hairpin of thetyrSriboswitch, as well as by a mutation that transformed a tRNAPheinto atyrSriboswitch ligand. The most potent mutation, a substitution near the tyrosine recognition site of tyrosyl-tRNA synthetase, improved enzyme stereoselectivity. We conclude that these mutations promote the proper charging of tRNATyr, thus facilitating the exclusion ofd-tyrosine from protein biosynthesis in cells that lackd-aminoacyl-tRNA deacylase.IMPORTANCEProteins are composed ofl-amino acids. Mischarging of tRNAs withd-amino acids or the misincorporation ofd-amino acids into proteins causes toxicity. This work reports on mutations that confer resistance tod-amino acids and their mechanisms of action.


2017 ◽  
Vol 30 (12) ◽  
pp. 974-983 ◽  
Author(s):  
Satyanarayana Tatineni ◽  
Christian Elowsky ◽  
Robert A. Graybosch

Previously, we reported that coat protein (CP) of Wheat streak mosaic virus (WSMV) (genus Tritimovirus, family Potyviridae) tolerates deletion of amino acids 36 to 84 for efficient systemic infection of wheat. In this study, we demonstrated that WSMV mutants with deletion of CP amino acids 58 to 84 but not of 36 to 57 induced severe chlorotic streaks and spots, followed by acute chlorosis in wheat, maize, barley, and rye compared with mild to moderate chlorotic streaks and mosaic symptoms by wild-type virus. Deletion of CP amino acids 58 to 84 from the WSMV genome accelerated cell-to-cell movement, with increased accumulation of genomic RNAs and CP, compared with the wild-type virus. Microscopic examination of wheat tissues infected by green fluorescent protein–tagged mutants revealed that infection by mutants lacking CP amino acids 58 to 84 caused degradation of chloroplasts, resulting in acute macroscopic chlorosis. The profile of CP-specific proteins was altered in wheat infected by mutants causing acute chlorosis, compared with mutants eliciting wild-type symptoms. All deletion mutants accumulated CP-specific major protein similarly to that in wild-type virus; however, mutants that elicit acute chlorosis failed to accumulate a 31-kDa minor protein compared with wild-type virus or mutants lacking amino acids 36 to 57. Taken together, these data suggest that deletion of CP amino acids 58 to 84 from the WSMV genome enhanced accumulation of CP and genomic RNA, altered CP-specific protein profiles, and caused severe symptom phenotypes in multiple cereal hosts.


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