Escherichia coli str. K-12 substr. MG1655

Summary

Alias: Escherichia coli MG1655, Escherichia coli str. K12 substr. MG1655, Escherichia coli str. MG1655, Escherichia coli strain MG1655

Top Publications

  1. Li C, Zhang Y, Vankemmelbeke M, Hecht O, Aleanizy F, MacDonald C, et al. Structural evidence that colicin A protein binds to a novel binding site of TolA protein in Escherichia coli periplasm. J Biol Chem. 2012;287:19048-57 pubmed publisher
    ..TA(53-107) binds on the opposite side of TolAIII to that used by g3p, ColN, or TolB, illustrating the flexible nature of TolA as a periplasmic hub protein...
  2. Westra E, van Erp P, Künne T, Wong S, Staals R, Seegers C, et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell. 2012;46:595-605 pubmed publisher
    ..The target is then progressively unwound and cleaved by the joint ATP-dependent helicase activity and Mg(2+)-dependent HD-nuclease activity of Cas3, leading to complete target DNA degradation and invader neutralization...
  3. Gray M, Wholey W, Parker B, Kim M, Jakob U. NemR is a bleach-sensing transcription factor. J Biol Chem. 2013;288:13789-98 pubmed publisher
    ..Little is known about how bacteria sense or respond to reactive chlorine species, such as bleach...
  4. Zheng H, Wisedchaisri G, Gonen T. Crystal structure of a nitrate/nitrite exchanger. Nature. 2013;497:647-51 pubmed publisher
    ..We propose that NarK exchanges nitrate for nitrite by a rocker switch mechanism facilitated by inter-domain hydrogen bond networks...
  5. Morgan J, Vendura K, Stevens S, Riordan J. RcsB determines the locus of enterocyte effacement (LEE) expression and adherence phenotype of Escherichia coli O157 : H7 spinach outbreak strain TW14359 and coordinates bicarbonate-dependent LEE activation with repression of motility. Microbiology. 2013;159:2342-53 pubmed publisher
    ..The results of this study significantly broaden the role for RcsB in enterohaemorrhagic E. coli virulence regulation. ..
  6. Liang W, Deutscher M. Ribosomes regulate the stability and action of the exoribonuclease RNase R. J Biol Chem. 2013;288:34791-8 pubmed publisher
    ..Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis. ..
  7. Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, et al. Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol. 2013;11:e1001731 pubmed publisher
    ..This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features. ..
  8. Sham L, Butler E, Lebar M, Kahne D, Bernhardt T, Ruiz N. Bacterial cell wall. MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis. Science. 2014;345:220-2 pubmed publisher
    ..We combined these approaches to demonstrate that MurJ is the lipid II flippase in Escherichia coli. ..
  9. Nomura T, Cranfield C, Deplazes E, Owen D, Macmillan A, Battle A, et al. Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS. Proc Natl Acad Sci U S A. 2012;109:8770-5 pubmed publisher
    ....
  10. Shimizu Y. ArfA recruits RF2 into stalled ribosomes. J Mol Biol. 2012;423:624-31 pubmed publisher
    ..From the results, I discuss differences of in vivo roles of these two systems in addition to the well-known tmRNA-dependent trans-translation system...

Detail Information

Publications128 found, 100 shown here

  1. Li C, Zhang Y, Vankemmelbeke M, Hecht O, Aleanizy F, MacDonald C, et al. Structural evidence that colicin A protein binds to a novel binding site of TolA protein in Escherichia coli periplasm. J Biol Chem. 2012;287:19048-57 pubmed publisher
    ..TA(53-107) binds on the opposite side of TolAIII to that used by g3p, ColN, or TolB, illustrating the flexible nature of TolA as a periplasmic hub protein...
  2. Westra E, van Erp P, Künne T, Wong S, Staals R, Seegers C, et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell. 2012;46:595-605 pubmed publisher
    ..The target is then progressively unwound and cleaved by the joint ATP-dependent helicase activity and Mg(2+)-dependent HD-nuclease activity of Cas3, leading to complete target DNA degradation and invader neutralization...
  3. Gray M, Wholey W, Parker B, Kim M, Jakob U. NemR is a bleach-sensing transcription factor. J Biol Chem. 2013;288:13789-98 pubmed publisher
    ..Little is known about how bacteria sense or respond to reactive chlorine species, such as bleach...
  4. Zheng H, Wisedchaisri G, Gonen T. Crystal structure of a nitrate/nitrite exchanger. Nature. 2013;497:647-51 pubmed publisher
    ..We propose that NarK exchanges nitrate for nitrite by a rocker switch mechanism facilitated by inter-domain hydrogen bond networks...
  5. Morgan J, Vendura K, Stevens S, Riordan J. RcsB determines the locus of enterocyte effacement (LEE) expression and adherence phenotype of Escherichia coli O157 : H7 spinach outbreak strain TW14359 and coordinates bicarbonate-dependent LEE activation with repression of motility. Microbiology. 2013;159:2342-53 pubmed publisher
    ..The results of this study significantly broaden the role for RcsB in enterohaemorrhagic E. coli virulence regulation. ..
  6. Liang W, Deutscher M. Ribosomes regulate the stability and action of the exoribonuclease RNase R. J Biol Chem. 2013;288:34791-8 pubmed publisher
    ..Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis. ..
  7. Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, et al. Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol. 2013;11:e1001731 pubmed publisher
    ..This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features. ..
  8. Sham L, Butler E, Lebar M, Kahne D, Bernhardt T, Ruiz N. Bacterial cell wall. MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis. Science. 2014;345:220-2 pubmed publisher
    ..We combined these approaches to demonstrate that MurJ is the lipid II flippase in Escherichia coli. ..
  9. Nomura T, Cranfield C, Deplazes E, Owen D, Macmillan A, Battle A, et al. Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS. Proc Natl Acad Sci U S A. 2012;109:8770-5 pubmed publisher
    ....
  10. Shimizu Y. ArfA recruits RF2 into stalled ribosomes. J Mol Biol. 2012;423:624-31 pubmed publisher
    ..From the results, I discuss differences of in vivo roles of these two systems in addition to the well-known tmRNA-dependent trans-translation system...
  11. Dai Y, Outten F. The E. coli SufS-SufE sulfur transfer system is more resistant to oxidative stress than IscS-IscU. FEBS Lett. 2012;586:4016-22 pubmed publisher
    ..Mass spectrometry analysis demonstrated that IscS-IscU is more susceptible than SufS-SufE to oxidative modification by H(2)O(2). These important results provide biochemical insight into the stress resistance of the Suf pathway...
  12. Baharoglu Z, Krin E, Mazel D. RpoS plays a central role in the SOS induction by sub-lethal aminoglycoside concentrations in Vibrio cholerae. PLoS Genet. 2013;9:e1003421 pubmed publisher
    ..coli is more of an exception than a paradigm for the physiological response to antibiotics sub-MIC...
  13. Monzel C, Degreif Dünnwald P, Gröpper C, Griesinger C, Unden G. The cytoplasmic PASC domain of the sensor kinase DcuS of Escherichia coli: role in signal transduction, dimer formation, and DctA interaction. Microbiologyopen. 2013;2:912-27 pubmed publisher
    ..The study suggests a novel ON homo-dimer conformation (type IIB) and an OFF conformation for PASC . Type IIB-ON corresponds to the fumarate induced wild-type conformation, representing an interesting target for structural biology. ..
  14. Parker B, Schwessinger E, Jakob U, Gray M. The RclR protein is a reactive chlorine-specific transcription factor in Escherichia coli. J Biol Chem. 2013;288:32574-84 pubmed publisher
    ..These results demonstrate the existence of a widely conserved bacterial regulon devoted specifically to RCS resistance. ..
  15. Salscheider S, Jahn A, Schnetz K. Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli. Nucleic Acids Res. 2014;42:2999-3008 pubmed publisher
    ..Thus, BglJ-RcsB is a pleiotropic transcriptional activator that coordinates regulation with global regulators including CRP, LeuO and HNS. ..
  16. Luo Q, Kumar P, Vickers T, Sheikh A, Lewis W, Rasko D, et al. Enterotoxigenic Escherichia coli secretes a highly conserved mucin-degrading metalloprotease to effectively engage intestinal epithelial cells. Infect Immun. 2014;82:509-21 pubmed publisher
    ..coli and Vibrio cholerae bacteria, suggesting that this mucin-degrading enzyme may represent a shared virulence feature of these important pathogens. ..
  17. Housden N, Hopper J, Lukoyanova N, Rodriguez Larrea D, Wojdyla J, Klein A, et al. Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF. Science. 2013;340:1570-4 pubmed publisher
    ..Thus, an intrinsically disordered protein can tunnel through the narrow pores of an oligomeric porin to deliver an epitope signal to the cell to initiate cell death...
  18. Chen B, Boel G, Hashem Y, Ning W, Fei J, Wang C, et al. EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. Nat Struct Mol Biol. 2014;21:152-9 pubmed publisher
    ....
  19. Boel G, Smith P, Ning W, Englander M, Chen B, Hashem Y, et al. The ABC-F protein EttA gates ribosome entry into the translation elongation cycle. Nat Struct Mol Biol. 2014;21:143-51 pubmed publisher
    ..These studies demonstrate that an ABC-F protein regulates protein synthesis via a new mechanism sensitive to cellular energy status. ..
  20. Ramrath D, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, et al. The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Nature. 2012;485:526-9 pubmed publisher
    ....
  21. Gagnon M, Lin J, Bulkley D, Steitz T. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Science. 2014;345:684-7 pubmed publisher
    ..The structure is consistent with EF4 functioning either as a back-translocase or a ribosome sequester...
  22. Tchigvintsev A, Tchigvintsev D, Flick R, Popović A, Dong A, Xu X, et al. Biochemical and structural studies of conserved Maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides. Chem Biol. 2013;20:1386-98 pubmed publisher
    ..Thus, pyrophosphatase activity of Maf proteins toward canonical and modified nucleotides might provide the molecular mechanism for a dual role of these proteins in cell division arrest and house cleaning. ..
  23. Uhlich G, Chen C, Cottrell B, Irwin P, Phillips J. Peroxide resistance in Escherichia coli serotype O157 : H7 biofilms is regulated by both RpoS-dependent and -independent mechanisms. Microbiology. 2012;158:2225-34 pubmed publisher
    ..05) katG, ahpC and katP expression in biofilm cells, suggesting that peroxide induction of the OxyR-dependent resistance genes may contribute to the RpoS-independent protection in Shiga toxin-producing E. coli biofilms. ..
  24. Reidy M, Miot M, Masison D. Prokaryotic chaperones support yeast prions and thermotolerance and define disaggregation machinery interactions. Genetics. 2012;192:185-93 pubmed publisher
    ..Our results define cooperative interactions among these components that are specific or interchangeable across life kingdoms and imply Hsp100 family disaggregases possess intrinsic amyloid remodeling activity. ..
  25. Ude S, Lassak J, Starosta A, Kraxenberger T, Wilson D, Jung K. Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches. Science. 2013;339:82-5 pubmed publisher
    ....
  26. Qi R, Sarbeng E, Liu Q, Le K, Xu X, Xu H, et al. Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP. Nat Struct Mol Biol. 2013;20:900-7 pubmed publisher
    ..These conformational changes, together with our biochemical assays, provide a structural explanation for allosteric coupling in Hsp70 activity. ..
  27. Stouf M, Meile J, Cornet F. FtsK actively segregates sister chromosomes in Escherichia coli. Proc Natl Acad Sci U S A. 2013;110:11157-62 pubmed publisher
    ..Our data are consistent with a model in which FtsK acts to release the MatP-mediated cohesion and/or interaction with the division apparatus of the terminus region in a KOPS-oriented manner. ..
  28. Buss J, Coltharp C, Huang T, Pohlmeyer C, Wang S, Hatem C, et al. In vivo organization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy. Mol Microbiol. 2013;89:1099-120 pubmed publisher
    ..Our results suggest that the main function of ZapA and ZapB in vivo may not be to promote the association of individual protofilaments but to align FtsZ clusters that consist of multiple FtsZ protofilaments. ..
  29. Nesta B, Valeri M, Spagnuolo A, Rosini R, Mora M, Donato P, et al. SslE elicits functional antibodies that impair in vitro mucinase activity and in vivo colonization by both intestinal and extraintestinal Escherichia coli strains. PLoS Pathog. 2014;10:e1004124 pubmed publisher
    ..Taken together, these data strongly support the importance of SslE in E. coli colonization of mucosal surfaces and reinforce the use of this antigen as a component of a broadly protective vaccine against pathogenic E. coli species. ..
  30. Vaisman A, Kuban W, McDonald J, Karata K, Yang W, Goodman M, et al. Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity. Nucleic Acids Res. 2012;40:6144-57 pubmed
    ....
  31. Cheng Z, Caillet A, Ren B, Ding H. Stimulation of Escherichia coli DNA damage inducible DNA helicase DinG by the single-stranded DNA binding protein SSB. FEBS Lett. 2012;586:3825-30 pubmed publisher
    ..coli wild-type SSB stimulates the DinG DNA helicase via specific protein-protein interaction. ..
  32. Sun L, Zeng X, Yan C, Sun X, Gong X, Rao Y, et al. Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature. 2012;490:361-6 pubmed publisher
    ..The structural and biochemical information reported here constitutes an important framework for mechanistic understanding of glucose transporters and sugar porters in general. ..
  33. Fried L, Behr S, Jung K. Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli. J Bacteriol. 2013;195:807-15 pubmed publisher
    ..Finally, we characterized the pattern of yhjX expression and identified extracellular pyruvate as a stimulus for the YpdA/YpdB system. It is suggested that YpdA/YpdB contributes to nutrient scavenging before entry into stationary phase. ..
  34. Miyauchi K, Kimura S, Suzuki T. A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol. 2013;9:105-11 pubmed publisher
    ..ct(6)A was involved in promoting decoding efficiency. Structural modeling suggests that ct(6)A recognizes the first adenine base of ANN codon at the ribosomal A site. ..
  35. Ashenberg O, Keating A, Laub M. Helix bundle loops determine whether histidine kinases autophosphorylate in cis or in trans. J Mol Biol. 2013;425:1198-209 pubmed publisher
    ..These findings suggest that histidine kinases are under selective pressure to maintain their mode of autophosphorylation, but they can do so with a wide range of sequences. ..
  36. Zhang D, Qin Y. The paradox of elongation factor 4: highly conserved, yet of no physiological significance?. Biochem J. 2013;452:173-81 pubmed publisher
    ..Lastly, we present a hypothesis for back-translocation and discuss the directions future EF4 research should focus on. ..
  37. Bell J, Plank J, Dombrowski C, Kowalczykowski S. Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Nature. 2012;491:274-8 pubmed publisher
    ..We further demonstrate that the recombination mediator protein pair, RecOR (RecO and RecR), accelerates both RecA nucleation and filament growth, and that the introduction of RecF further stimulates RecA nucleation. ..
  38. Joshi M, Magnan D, Montminy T, Lies M, Stepankiw N, Bates D. Regulation of sister chromosome cohesion by the replication fork tracking protein SeqA. PLoS Genet. 2013;9:e1003673 pubmed publisher
    ..Lastly, reducing cohesion by genetic manipulation of Topo IV or SeqA resulted in dramatically slowed sister locus separation and poor nucleoid partitioning, indicating that cohesion has a prominent role in chromosome segregation. ..
  39. Dickey S, Baker R, Cho S, Urban S. Proteolysis inside the membrane is a rate-governed reaction not driven by substrate affinity. Cell. 2013;155:1270-81 pubmed publisher
    ..These properties are unlike those of other studied proteases or membrane proteins but are strikingly reminiscent of one subset of DNA-repair enzymes, raising important mechanistic and drug-design implications. ..
  40. Volbeda A, Amara P, Darnault C, Mouesca J, Parkin A, Roessler M, et al. X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli. Proc Natl Acad Sci U S A. 2012;109:5305-10 pubmed publisher
    ..The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O(2) reduction, located near the active site. ..
  41. Wang X, Lord D, Cheng H, Osbourne D, Hong S, Sanchez Torres V, et al. A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol. 2012;8:855-61 pubmed
    ..Hence, GhoT-GhoS is to our knowledge the first type V toxin-antitoxin system where a protein antitoxin inhibits the toxin by cleaving specifically its mRNA. ..
  42. Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, et al. A tightly regulated molecular toggle controls AAA+ disaggregase. Nat Struct Mol Biol. 2012;19:1338-46 pubmed publisher
    ..Our results underline the vital nature of tight ClpB activity control and elucidate a regulated M-domain toggle control mechanism. ..
  43. Yakhnin A, Baker C, Vakulskas C, Yakhnin H, Berezin I, Romeo T, et al. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage. Mol Microbiol. 2013;87:851-66 pubmed publisher
    ..Data from mRNA decay studies and quantitative primer extension assays support a model in which bound CsrA activates flhDC expression by inhibiting the 5' end-dependent RNase E cleavage pathway. ..
  44. Witan J, Bauer J, Wittig I, Steinmetz P, Erker W, Unden G. Interaction of the Escherichia coli transporter DctA with the sensor kinase DcuS: presence of functional DctA/DcuS sensor units. Mol Microbiol. 2012;85:846-61 pubmed publisher
    ..In DcuS, deletion and mutation of the cytoplasmic PAS(C) domain affected the interaction between DctA and DcuS. It is concluded that DctA forms a functional unit or sensor complex with DcuS through specific interaction sites. ..
  45. Shyp V, Tankov S, Ermakov A, Kudrin P, English B, Ehrenberg M, et al. Positive allosteric feedback regulation of the stringent response enzyme RelA by its product. EMBO Rep. 2012;13:835-9 pubmed publisher
    ..By integrating the output of individual RelA molecules and ppGpp degradation pathways, this regulatory circuit contributes to a fast and coordinated transition to stringency. ..
  46. Burmann B, Knauer S, Sevostyanova A, Schweimer K, Mooney R, Landick R, et al. An α helix to β barrel domain switch transforms the transcription factor RfaH into a translation factor. Cell. 2012;150:291-303 pubmed publisher
    ..As a consequence, RfaH-CTD binding to S10 is enabled and translation of RfaH-controlled operons is strongly potentiated. PAPERFLICK: ..
  47. Benítez Páez A, Villarroya M, Armengod M. The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA. 2012;18:1783-95 pubmed publisher
    ....
  48. Punekar A, Shepherd T, Liljeruhm J, Forster A, Selmer M. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Nucleic Acids Res. 2012;40:10507-20 pubmed publisher
    ..A continuous surface of conserved positive charge indicates that RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate. ..
  49. Tan B, Bogdanov M, Zhao J, Dowhan W, Raetz C, Guan Z. Discovery of a cardiolipin synthase utilizing phosphatidylethanolamine and phosphatidylglycerol as substrates. Proc Natl Acad Sci U S A. 2012;109:16504-9 pubmed publisher
    ..Unlike eukaryotic Cls (that use PG and CDP-diacylglycerol as substrates) or ClsA, the combined YmdB-ClsC used PE as the phosphatidyl donor to PG to form CL, which demonstrates a third and unique mode for CL synthesis. ..
  50. Zhuravleva A, Clerico E, Gierasch L. An interdomain energetic tug-of-war creates the allosterically active state in Hsp70 molecular chaperones. Cell. 2012;151:1296-307 pubmed publisher
    ..The resulting energetic tension underlies Hsp70 functional properties and enables them to be modulated by ligands and cochaperones and "tuned" through evolution. ..
  51. Kim M, Shin I, Cho S, Lee J, Rhee S. Structural and functional insights into (S)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization. PLoS ONE. 2012;7:e52066 pubmed publisher
    ..Other residues conserved in the active sites of this novel l-sulfolactate dehydrogenase-like family also play essential roles in catalysis. ..
  52. Chintakayala K, Singh S, Rossiter A, Shahapure R, Dame R, Grainger D. E. coli Fis protein insulates the cbpA gene from uncontrolled transcription. PLoS Genet. 2013;9:e1003152 pubmed publisher
    ..Disruption of the cbpA gene prompts dramatic changes in DNA topology. Thus, our work identifies a novel role for Fis and incorporates CbpA into the growing network of factors that mediate bacterial chromosome structure. ..
  53. Arias Palomo E, O Shea V, Hood I, Berger J. The bacterial DnaC helicase loader is a DnaB ring breaker. Cell. 2013;153:438-48 pubmed publisher
    ....
  54. Wessel S, Marceau A, Massoni S, Zhou R, Ha T, Sandler S, et al. PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein. J Biol Chem. 2013;288:17569-78 pubmed publisher
    ..These data lead to a model in which PriC interaction with SSB remodels SSB/DNA structures at abandoned DNA replication forks to create a DNA structure that is competent for DnaB loading. ..
  55. Tonthat N, Milam S, Chinnam N, Whitfill T, Margolin W, Schumacher M. SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid. Proc Natl Acad Sci U S A. 2013;110:10586-91 pubmed publisher
    ....
  56. Pulk A, Cate J. Control of ribosomal subunit rotation by elongation factor G. Science. 2013;340:1235970 pubmed publisher
    ..These structures suggest that EF-G controls the translocation reaction by cycles of conformational rigidity and relaxation before and after GTP hydrolysis. ..
  57. Peil L, Starosta A, Lassak J, Atkinson G, Virumae K, Spitzer M, et al. Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P. Proc Natl Acad Sci U S A. 2013;110:15265-70 pubmed publisher
    ..These findings provide mechanistic insight into how the characteristics of the specific amino acid substrates influence the fundamentals of peptide bond formation. ..
  58. Tripathi A, Dewan P, Siddique S, Varadarajan R. MazF-induced growth inhibition and persister generation in Escherichia coli. J Biol Chem. 2014;289:4191-205 pubmed publisher
    ..The MazF-mediated persistence phenotype was found to be independent of RecA and dependent on the presence of the ClpP and Lon proteases. This study confirms the role of MazEF in reversible growth inhibition and persistence. ..
  59. Hochstrasser M, Taylor D, Bhat P, Guegler C, Sternberg S, Nogales E, et al. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A. 2014;111:6618-23 pubmed publisher
    ..Together, these data show that the CasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage. ..
  60. Gagnon M, Seetharaman S, Bulkley D, Steitz T. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome. Science. 2012;335:1370-2 pubmed publisher
    ..This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes. ..
  61. Papakostas K, Frillingos S. Substrate selectivity of YgfU, a uric acid transporter from Escherichia coli. J Biol Chem. 2012;287:15684-95 pubmed publisher
    ....
  62. Wada T, Hatamoto Y, Kutsukake K. Functional and expressional analyses of the anti-FlhD4C2 factor gene ydiV in Escherichia coli. Microbiology. 2012;158:1533-42 pubmed publisher
    ..coli cells did not require FliZ for efficient motility development. This indicates that, unlike in Salmonella, the FliZ-YdiV regulatory system does not work in the nutritional control of flagellar gene expression in E. coli. ..
  63. Shanmugham A, Bakayan A, Völler P, Grosveld J, Lill H, Bollen Y. The hydrophobic core of twin-arginine signal sequences orchestrates specific binding to Tat-pathway related chaperones. PLoS ONE. 2012;7:e34159 pubmed publisher
    ..Interestingly, binding of DmsD to its model substrate reduced membrane binding of the pre-protein. This property could link REMP-signal peptide binding to its reported proofreading function. ..
  64. Durand Heredia J, Rivkin E, Fan G, Morales J, Janakiraman A. Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli. J Bacteriol. 2012;194:3189-98 pubmed publisher
    ..Similarly to ZapA, ZapB, and ZapC, ZapD is dispensable for division and therefore belongs to the growing group of FtsZ-associated proteins in E. coli that aid in the overall fitness of the division process. ..
  65. Chadani Y, Ito K, Kutsukake K, Abo T. ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli. Mol Microbiol. 2012;86:37-50 pubmed publisher
    ..In support of this model, the ArfA-RF2 pathway did not act on the SecM-arrested ribosome, which contains an aminoacyl-tRNA in the A-site. ..
  66. Dow J, Gabel F, Sargent F, Palmer T. Characterization of a pre-export enzyme-chaperone complex on the twin-arginine transport pathway. Biochem J. 2013;452:57-66 pubmed publisher
    ..It is possible that correct folding of Domain IV upon cofactor loading is the trigger for TorD release and subsequent export of TorA. ..
  67. Hu L, Chi B, Kuhn M, Filippova E, Walker Peddakotla A, Bäsell K, et al. Acetylation of the response regulator RcsB controls transcription from a small RNA promoter. J Bacteriol. 2013;195:4174-86 pubmed publisher
    ..We propose that acetylation inhibits RcsB activity and that some of this inhibition acts through the acetylation of Lys-154. ..
  68. Robinson K, Orans J, Kovach A, Link T, Brennan R. Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching. Nucleic Acids Res. 2014;42:2736-49 pubmed publisher
    ..TFQ data also demonstrated that the 5'-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus. ..
  69. Kocsis Z, Sarlós K, Harami G, Martina M, Kovacs M. A nucleotide-dependent and HRDC domain-dependent structural transition in DNA-bound RecQ helicase. J Biol Chem. 2014;289:5938-49 pubmed publisher
    ..The results shed light on the nature of conformational changes leading to processive ssDNA translocation and multistranded DNA processing by RecQ helicases. ..
  70. Kaur G, Vora M, Czerwonka C, Rozgaja T, Grimwade J, Leonard A. Building the bacterial orisome: high-affinity DnaA recognition plays a role in setting the conformation of oriC DNA. Mol Microbiol. 2014;91:1148-63 pubmed publisher
    ..We propose a model in which interaction of DnaA molecules at high-affinity sites regulates oriC DNA conformation. ..
  71. Johnson C, Ridley H, Marchetti R, Silipo A, Griffin D, Crawford L, et al. The antibacterial toxin colicin N binds to the inner core of lipopolysaccharide and close to its translocator protein. Mol Microbiol. 2014;92:440-52 pubmed publisher
    ..ColN is, currently, unique among colicins in requiring LPS and, combined with previous data, this implies that the ColN translocon is distinct from those of other known colicins. ..
  72. Espeli O, Borne R, Dupaigne P, Thiel A, Gigant E, Mercier R, et al. A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli. EMBO J. 2012;31:3198-211 pubmed publisher
    ..Our results reveal how segregation of the Ter MD is integrated in the cell-cycle control. ..
  73. Matsuda A, Kurono N, Kawano C, Shirota K, Hirabayashi A, Horino M, et al. Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids. Biochem Biophys Res Commun. 2012;428:445-50 pubmed publisher
    ..Our results suggest that these 55 genes may be involved in repressing plasmid uptake during cell-to-cell plasmid transfer. ..
  74. Shiomi D, Toyoda A, Aizu T, Ejima F, Fujiyama A, Shini T, et al. Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells. Mol Microbiol. 2013;87:1029-44 pubmed publisher
    ..Thus, we found that mutations in domain IA of MreB and in the periplasmic domain of PBP2 and RodA can restore growth and rod shape to ΔrodZ cells, possibly by changing the requirements of MreB in the process. ..
  75. Raivio T, Leblanc S, Price N. The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity. J Bacteriol. 2013;195:2755-67 pubmed publisher
    ..Altogether, our work suggests new mechanisms of Cpx-mediated envelope stress adaptation and antibiotic resistance. ..
  76. Alcock F, Baker M, Greene N, Palmer T, Wallace M, Berks B. Live cell imaging shows reversible assembly of the TatA component of the twin-arginine protein transport system. Proc Natl Acad Sci U S A. 2013;110:E3650-9 pubmed publisher
    ..In contrast to TatA-YFP, the oligomeric states of TatB-YFP and TatC-YFP fusions are not affected by substrate or the PMF, although TatB-YFP oligomerization does require TatC. ..
  77. Peil L, Starosta A, Virumae K, Atkinson G, Tenson T, Remme J, et al. Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Nat Chem Biol. 2012;8:695-7 pubmed publisher
    ....
  78. Leonard Rivera M, Misra R. Conserved residues of the putative L6 loop of Escherichia coli BamA play a critical role in the assembly of β-barrel outer membrane proteins, including that of BamA itself. J Bacteriol. 2012;194:4662-8 pubmed publisher
    ..Thus, the conserved (641)RGF(643) residues of the BamA L6 loop are important for BamA folding and biogenesis. ..
  79. Seyffer F, Kummer E, Oguchi Y, Winkler J, Kumar M, Zahn R, et al. Hsp70 proteins bind Hsp100 regulatory M domains to activate AAA+ disaggregase at aggregate surfaces. Nat Struct Mol Biol. 2012;19:1347-55 pubmed publisher
    ..Our results uncover a new function for Hsp70: the coupling of substrate targeting to AAA+ chaperone activation at aggregate surfaces. ..
  80. Klein G, Muller Loennies S, Lindner B, Kobylak N, Brade H, Raina S. Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region. J Biol Chem. 2013;288:8111-27 pubmed publisher
    ..This P-EtN modification is essential for resistance to a variety of factors, which destabilize the outer membrane like the addition of SDS or challenge to sublethal concentrations of Zn(2+). ..
  81. Toste Rêgo A, Holding A, Kent H, Lamers M. Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J. 2013;32:1334-43 pubmed publisher
    ....
  82. Zahn M, Berthold N, Kieslich B, Knappe D, Hoffmann R, Strater N. Structural studies on the forward and reverse binding modes of peptides to the chaperone DnaK. J Mol Biol. 2013;425:2463-79 pubmed publisher
    ..Optimal hydrophobic interactions with binding pockets -2 to 0 appear to be the main determinant for the orientation and sequence position of peptide binding. ..
  83. Briegel A, Ames P, GUMBART J, Oikonomou C, Parkinson J, Jensen G. The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state. Mol Microbiol. 2013;89:831-41 pubmed publisher
    ..These findings confirm that chemoreceptor arrays do not undergo large structural changes during signalling, and suggest instead that kinase activity is modulated at least in part by changes in the mobility of key domains. ..
  84. Mahalakshmi S, Sunayana M, SaiSree L, Reddy M. yciM is an essential gene required for regulation of lipopolysaccharide synthesis in Escherichia coli. Mol Microbiol. 2014;91:145-57 pubmed publisher
    ..In summary, this study demonstrates an essential role for YciM in regulation of LPS biosynthesis in E. coli. ..
  85. Söderström B, Skoog K, Blom H, Weiss D, von Heijne G, Daley D. Disassembly of the divisome in Escherichia coli: evidence that FtsZ dissociates before compartmentalization. Mol Microbiol. 2014;92:1-9 pubmed publisher
    ..This observation implies that FtsZ cannot be a force generator during the final stage(s) of envelope constriction in E. coli. ..
  86. Silva M, Nevin P, Ronayne E, Beuning P. Selective disruption of the DNA polymerase III α-β complex by the umuD gene products. Nucleic Acids Res. 2012;40:5511-22 pubmed publisher
    ..We also find that UmuD, but not UmuD', disrupts the α-β complex. We propose that the interaction between α and UmuD contributes to the transition between replicative and TLS polymerases by removing α from the β clamp. ..
  87. Holdsworth S, Law C. Functional and biochemical characterisation of the Escherichia coli major facilitator superfamily multidrug transporter MdtM. Biochimie. 2012;94:1334-46 pubmed publisher
    ..This work provides a firm foundation for structural studies on this class of multidrug transporter protein. ..
  88. Rothe M, Alpert C, Engst W, Musiol S, Loh G, Blaut M. Impact of nutritional factors on the proteome of intestinal Escherichia coli: induction of OxyR-dependent proteins AhpF and Dps by a lactose-rich diet. Appl Environ Microbiol. 2012;78:3580-91 pubmed publisher
    ..Mice fed the lactose-rich diet possibly had a higher intestinal osmolality, leading to the upregulation of OxyR-dependent proteins, which enable intestinal E. coli to better cope with diet-induced osmotic stress. ..
  89. Ogasawara H, Shinohara S, Yamamoto K, Ishihama A. Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli. Microbiology. 2012;158:1482-92 pubmed publisher
    ....
  90. Masuda H, Tan Q, Awano N, Wu K, Inouye M. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol Microbiol. 2012;84:979-89 pubmed publisher
    ..Here we propose to rename YeeU as CbeA for cytoskeleton bundling-enhancing factor A. ..
  91. Badrinarayanan A, Lesterlin C, Reyes Lamothe R, Sherratt D. The Escherichia coli SMC complex, MukBEF, shapes nucleoid organization independently of DNA replication. J Bacteriol. 2012;194:4669-76 pubmed publisher
    ....
  92. Golovina A, Dzama M, Osterman I, Sergiev P, Serebryakova M, Bogdanov A, et al. The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA. RNA. 2012;18:1725-34 pubmed publisher
    ..Only minor changes in the total E. coli proteome could be observed in a cell devoid of the 23S rRNA nucleotide A2030 methylation. ..
  93. Qu X, Lancaster L, Noller H, Bustamante C, Tinoco I. Ribosomal protein S1 unwinds double-stranded RNA in multiple steps. Proc Natl Acad Sci U S A. 2012;109:14458-63 pubmed publisher
    ..Unwinding by multiple small substeps is much less rate limited by thermal breathing than unwinding in a single step. Thus, a multistep scheme greatly expedites S1 unwinding of an RNA structure compared to a single-step mode. ..
  94. Perez Cheeks B, Lee C, Hayama R, Marians K. A role for topoisomerase III in Escherichia coli chromosome segregation. Mol Microbiol. 2012;86:1007-22 pubmed publisher
    ..coli. ..
  95. Peters J, Mooney R, Grass J, Jessen E, Tran F, Landick R. Rho and NusG suppress pervasive antisense transcription in Escherichia coli. Genes Dev. 2012;26:2621-33 pubmed publisher
    ..The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes. ..
  96. Jacob A, Köhrer C, Davies B, Rajbhandary U, Walker G. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell. 2013;49:427-38 pubmed publisher
    ..These key roles in ribosome quality control and maturation indicate why YbeY is a member of the minimal bacterial gene set and suggest that it could be a potential target for antibacterial drugs. ..
  97. Guo Q, Goto S, Chen Y, Feng B, Xu Y, Muto A, et al. Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process. Nucleic Acids Res. 2013;41:2609-20 pubmed publisher
    ..More importantly, this study reveals intriguing similarities and dissimilarities between the in vitro and the in vivo assembly pathways, suggesting that they are in general similar but with subtle differences. ..
  98. Hayama R, Bahng S, Karasu M, Marians K. The MukB-ParC interaction affects the intramolecular, not intermolecular, activities of topoisomerase IV. J Biol Chem. 2013;288:7653-61 pubmed publisher
    ..These data suggest that the MukB-ParC interaction may play a role in chromosome organization rather than in separation of daughter chromosomes. ..
  99. Hor L, Dobson R, Downton M, Wagner J, Hutton C, Perugini M. Dimerization of bacterial diaminopimelate epimerase is essential for catalysis. J Biol Chem. 2013;288:9238-48 pubmed publisher
    ..Our findings offer insight into the development of novel antimicrobial agents targeting the dimeric antibiotic target DAP epimerase. ..
  100. Lee C, Park Y, Kim M, Kim Y, Park S, Peterkofsky A, et al. Reciprocal regulation of the autophosphorylation of enzyme INtr by glutamine and α-ketoglutarate in Escherichia coli. Mol Microbiol. 2013;88:473-85 pubmed publisher
    ..Taken together, our results suggest that the PTS(Ntr) senses nitrogen availability. ..
  101. Sulthana S, Deutscher M. Multiple exoribonucleases catalyze maturation of the 3' terminus of 16S ribosomal RNA (rRNA). J Biol Chem. 2013;288:12574-9 pubmed publisher
    ..These findings, together with the earlier discovery that RNases E and G are the 5'-processing enzymes, completes the catalogue of RNases involved in maturation of Escherichia coli 16S rRNA. ..