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FEBS Journal

Cover image for Vol. 279 Issue 6

March 2012

Volume 279, Issue 6

Pages 893–1144

  1. Minireview Series

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Author index
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      Biogenesis and functions of model integral outer membrane proteins: Escherichia coli OmpA and Pseudomonas aeruginosa OprF (page 893)

      Rosetta N. Reusch

      Article first published online: 10 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08486.x

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      Accompanied by a podcast, listen now. Or listen in iTunes; OmpA of Escherichia coli and OprF of Pseudomonas aeruginosa are paradigms for studies of the biogenesis and functions of outer membrane proteins. Yet despite several decades of investigation there remain many questions regarding the structure, method of assembly, and roles in pathogenesis of these two homologs. The most recent and persuasive information is provided in the following three minireviews.

  2. Minireview

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Author index
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      Insights into the structure and assembly of Escherichia coli outer membrane protein A (pages 894–909)

      Rosetta N. Reusch

      Article first published online: 10 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08484.x

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      Outer membrane protein A (OmpA) of Escherichia coli is a model for the biogenesis of outer membrane proteins. Here I discuss the native conformation of OmpA, the in vitro refolding of OmpA into its native conformation, and the mechanisms by which OmpA is transported to and assembled within the outer membrane in its native conformation in vivo.

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      Alternative folding pathways of the major porin OprF of Pseudomonas aeruginosa (pages 910–918)

      Etsuko Sugawara, Keiji Nagano and Hiroshi Nikaido

      Article first published online: 10 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08481.x

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      Pseudomonas aeruginosa, a nosocomial pathogen, owes its multidrug-resistance phenotype partly to the major porin, OprF, of unusually low permeability. Only a small fraction of this protein folds into an open conformer, whereas the majority folds into a closed conformer. The folding pathway can be influenced by mutating key residues within OprF, or by deleting the periplasmic chaperone Skp.

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      Outer membrane protein A and OprF: versatile roles in Gram-negative bacterial infections (pages 919–931)

      Subramanian Krishnan and Nemani V. Prasadarao

      Article first published online: 10 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08482.x

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      Expression of outer membrane protein A in Escherichia coli K1 is important for the onset of meningitis. Here, we demonstrate that OmpA+ E. coli infection of newborn mice caused gliosis and neutrophil infiltration in white matter. Interestingly, lack of Fc-gamma receptor I (CD64) expression in macrophages renders the mice resistant to E. coli K1 infection and the brain appears normal.

  3. Review Articles

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Author index
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      Evolutionarily conserved protein arginine methyltransferases in non-mammalian animal systems (pages 932–945)

      Yi-Chun Wang and Chuan Li

      Article first published online: 10 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08490.x

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      Homologous protein arginine methyltransferases (PRMTs) of nine human PRMTs in non-mammalian animal species were surveyed. We summarize the basic functions of each PRMT and focus on the PRMTs in the non-mammalian animal models. The studies complement the understanding of the PRMT functions in mammals and provide valuable information for the evolution, critical roles and interplays of the PRMTs.

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      Bacterial acetohydroxyacid synthase and its inhibitors – a summary of their structure, biological activity and current status (pages 946–963)

      Vinayakumar Gedi and Moon-Young Yoon

      Article first published online: 27 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08505.x

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      Acetohydroxyacid synthase (AHAS) is a key regulatory enzyme in the branched chain amino acid biosynthesis pathway. In certain pathogenic bacteria, the inhibition of AHAS has emerged as a potential strategy in developing antimicrobial agents. This review highlights the structural and functional features of bacterial AHASs and then provides a detailed overview of its inhibitors.

  4. Original Articles

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Author index
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      A comparative profile of the microRNA transcriptome in immature and mature porcine testes using Solexa deep sequencing (pages 964–975)

      Chuanjiang Lian, Boxing Sun, Shuling Niu, Runjun Yang, Boyang Liu, Chunyan Lu, Jilun Meng, Zhengyan Qiu, Liying Zhang and Zhihui Zhao

      Article first published online: 10 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08480.x

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      We employed Solexa deep sequencing technology to extend the repertoire of porcine testis miRNAs and compare the expression patterns of the sexually immature (30 days) and mature (180 days) porcine testes. Overall, the two developmental stages had significantly different small RNA compositions. We identified hundreds of porcine miRNAs, and 122 miRNAs were differentially expressed in the immature and mature testes.

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      Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1 (pages 976–986)

      Cahyo Budiman, Takashi Tadokoro, Clement Angkawidjaja, Yuichi Koga and Shigenori Kanaya

      Article first published online: 6 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08483.x

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      We show that Asp137, Arg142, Trp157, and Phe197, which are located at the substrate binding cavity of SIB1 FKBP22 from Shewanella sp. SIB1, are important for peptidyl prolyl cis-trans isomerase (PPIase) activity of this protein. We propose the catalytic mechanism of this protein, and we also show that SIB1 FKBP22 does not require PPIase activity for chaperone function.

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      Mechanistic explanations for counter-intuitive phosphorylation dynamics of the insulin receptor and insulin receptor substrate-1 in response to insulin in murine adipocytes (pages 987–999)

      Elin Nyman, Siri Fagerholm, David Jullesson, Peter Strålfors and Gunnar Cedersund

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08488.x

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      We report a counter-intuitive reversed order of peak values of protein phosphorylation in the early insulin signaling events in murine adipocytes. Using a conclusive modeling framework, we test different hypotheses and are able to draw non-trivial conclusions regarding possible mechanisms behind the reversed order of peaks. We also identify new differences between human and murine insulin signaling.

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      Role of α-synuclein penetration into the membrane in the mechanisms of oligomer pore formation (pages 1000–1013)

      Igor F. Tsigelny, Yuriy Sharikov, Wolfgang Wrasidlo, Tania Gonzalez, Paula A. Desplats, Leslie Crews, Brian Spencer and Eliezer Masliah

      Article first published online: 27 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08489.x

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      We utilized computer modeling and cell-based studies to study α-synuclein (α-syn) oligomerization in membranes. The studies suggest that α-syn penetrates the membrane facilitating the incorporation of additional α-syn monomers to the complex, and subsequent displacement of phospholipids, and formation of annular oligomers in the membrane. This process occurred more rapidly for mutant A53T compared with wild-type α-syn.

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      A non-cold-inducible cold shock protein homolog mainly contributes to translational control under optimal growth conditions (pages 1014–1029)

      Toshiko Tanaka, Ryosuke Mega, Kwang Kim, Akeo Shinkai, Ryoji Masui, Seiki Kuramitsu and Noriko Nakagawa

      Article first published online: 16 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08492.x

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      Cold shock proteins (Csps) include both cold-induced and non-cold-induced proteins. Thermus thermophilus Csp1 (ttCsp1) is a non-cold-induced Csp, whose functions remain unknown. We analyzed the oligonucleotide-binding affinities of ttCsp1, the effects of deleting ttcsp1 on transcriptome and proteome, and determined the crystal structure of ttCsp1. These results suggest that ttCsp1 functions in translation independent of transcription under optimal growth conditions.

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      Short-chain dehydrogenases/reductases in cyanobacteria (pages 1030–1043)

      Anneke Kramm, Michael Kisiela, Rüdiger Schulz and Edmund Maser

      Article first published online: 13 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08494.x

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      Short-chain dehydrogenases/reductases (SDRs) represent a large superfamily of enzymes with a wide substrate spectrum. This bioinformatics approach validated the presence of SDRs in cyanobacteria, the first oxygen producers. It showed sequence identities of up to 60% to homologous proteins in other organisms, remarkably also in human, indicating that SDR proteins are highly conserved during evolution, even after dramatic terrestrial changes.

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      Kinetics of hydrolysis and mutational analysis of N,N-diethyl-m-toluamide hydrolase from Pseudomonas putida DTB (pages 1044–1053)

      Giomar Rivera-Cancel, Jennie M. Sanders and Anthony G. Hay

      Article first published online: 27 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08495.x

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      In this study we determined kinetic parameters, pH dependence, and substrate specificity of DthA, which hydrolyzes the insect repellent N,N-diethyl-m-toluamide (DEET) in Pseudomonas putida DTB. Mutational analysis was used to investigate the role of catalytic, oxyanion hole and substrate-binding residues. The results implicate several hydrophobic residues as part of the DEET binding pocket, of which W214 is critical for activity.

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      Comprehensive analysis of differential genes and miRNA profiles for discovery of topping-responsive genes in flue-cured tobacco roots (pages 1054–1070)

      Yuancheng Qi, Hongxiang Guo, Ke Li and Weiqun Liu

      Article first published online: 20 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08497.x

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      One hundred and twenty-nine differently expressed genes were acquired by SSH, and high-throughput sequencing of two sRNA libraries revealed 15 differential miRNAs whose target genes were identical to some differential genes identified by SSH, suggesting that miRNAs play a critical role in post-transcriptional gene regulation in the response of flue-cured tobacco to topping. A miRNAs mediated model in response to topping was proposed.

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      Response of midgut epithelial cells to Cry1Aa is toxin-dependent and depends on the interplay between toxic action and the host apoptotic response (pages 1071–1079)

      Shiho Tanaka, Yasutaka Yoshizawa and Ryoichi Sato

      Article first published online: 13 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08499.x

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      To elucidate the mechanisms of cell/individual death and healing in the midgut epithelium, Bombyx mori larva were administered with Bacilllus thuringiensis Cry1Aa and sections from the midgut were examined by TUNEL staining. Our data suggested the reaction, which occurs in the midgut of intoxicated insects, is determined by the interplay between passive toxic action and the active host healing response.

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      Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity (pages 1080–1092)

      Ritesh Kumar, Varatharajan Sabareesh, Asish K. Mukhopadhyay and Desirazu N. Rao

      Article first published online: 16 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08502.x

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      HpyAVIBM codes for a C5– cytosine MTase from H. pylori. It was observed that expression of M.HpyAVIB in E. coli enhanced the mutation rate. hpyAVIBM itself was mutated to give rise to different variants. Purified MTase variants showed relaxed substrate specificity. Thus, hpyAVIBM presents an interesting example of allelic variations in H. pylori where changes in the nucleotide sequence result in proteins with new properties.

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      Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members (pages 1093–1105)

      Przemyslaw J. Porebski, Maria Klimecka, Maksymilian Chruszcz, Robert A. Nicholls, Krzysztof Murzyn, Marianne E. Cuff, Xiaohui Xu, Marcin Cymborowski, Garib N. Murshudov, Alexei Savchenko, Aled Edwards and Wladek Minor

      Article first published online: 27 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08506.x

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      We determined structures of DBTS from H. pylori (hpDTBS) bound with cofactors and a substrate analog. We have shown that the C-terminal region of DTBSes, which contains two nucleotide-recognition motifs, greatly differs among DTBSes. hpDTBS is characterized by a unique mode of nucleotide recognition–it does not contain a C-terminal region containing one of the motifs, but it is ATP specific.

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      Contribution of active site glutamine to rate enhancement in ubiquitin C-terminal hydrolases (pages 1106–1118)

      David A. Boudreaux, Joseph Chaney, Tushar K. Maiti and Chittaranjan Das

      Article first published online: 27 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08507.x

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      The conserved active-site glutamine contributes to rate enhancement in ubiquitin carboxy terminal hydrolases perhaps through a C—H•••O hydrogen bonding interaction with the catalytic histidine.

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      Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators (pages 1119–1130)

      Shwe L. Chin, Ian M. Marcus, Robert R. Klevecz and Caroline M. Li

      Article first published online: 27 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08508.x

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      Time-resolved microarray data revealed genome-wide transcriptional oscillation in a yeast continuous culture system with ∼ 2 and ∼ 4 h periods. Transcripts are ordered and coupled to each other through time and concentration space. Gene transcripts appear to be coordinated with metabolic functions and the cell division cycle.

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      A recurrent D-strand association interface is observed in β-2 microglobulin oligomers (pages 1131–1143)

      Matteo Colombo, Matteo de Rosa, Vittorio Bellotti, Stefano Ricagno and Martino Bolognesi

      Article first published online: 23 FEB 2012 | DOI: 10.1111/j.1742-4658.2012.08510.x

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      β-2 microglobulin (β2m) is an amyloidogenic protein whose early aggregation stages are poorly understood. Here we present structural and biochemical data on two amyloidogenic disulphide-linked β2m dimers, which share a common non-covalent interface in their higher order aggregation. Such dimers trigger wild-type β2m amyloid aggregation in the absence of fibril seeds.

  5. Author index

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Author index
    1. You have free access to this content
      Author index (page 1144)

      Article first published online: 12 MAR 2012 | DOI: 10.1111/j.1742-4658.2011.08326.x

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