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  1. Article ; Online: Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM.

    Wu, Runrun / Bakelar, Jeremy W / Lundquist, Karl / Zhang, Zijian / Kuo, Katie M / Ryoo, David / Pang, Yui Tik / Sun, Chen / White, Tommi / Klose, Thomas / Jiang, Wen / Gumbart, James C / Noinaj, Nicholas

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 7131

    Abstract: In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in ... ...

    Abstract In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in nanodiscs, prepared using polar lipids and native membranes, where we observe an outward-open state. Mutations in the barrel domain of BamA reveal that plasticity in BAM is essential, particularly along the lateral seam of the barrel domain, which is further supported by molecular dynamics simulations that show conformational dynamics in BAM are modulated by the accessory proteins. We also report the structure of BAM in complex with EspP, which reveals an early folding intermediate where EspP threads from the underside of BAM and incorporates into the barrel domain of BamA, supporting a hybrid-barrel budding mechanism in which the substrate is folded into the membrane sequentially rather than as a single unit.
    MeSH term(s) Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Outer Membrane Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Lipids ; Molecular Dynamics Simulation ; Mutation ; Protein Folding
    Chemical Substances Bacterial Outer Membrane Proteins ; BamA protein, E coli ; Escherichia coli Proteins ; Lipids
    Language English
    Publishing date 2021-12-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-27449-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Crystal structures of S-HPCDH reveal determinants of stereospecificity for R- and S-hydroxypropyl-coenzyme M dehydrogenases.

    Bakelar, Jeremy W / Sliwa, Dariusz A / Johnson, Sean J

    Archives of biochemistry and biophysics

    2013  Volume 533, Issue 1-2, Page(s) 62–68

    Abstract: R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases (R- and S-HPCDH) are stereospecific enzymes that are central to the metabolism of propylene and epoxide in Xanthobacter autotrophicus. The bacterium produces R- and S-HPCDH simultaneously to facilitate ...

    Abstract (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases (R- and S-HPCDH) are stereospecific enzymes that are central to the metabolism of propylene and epoxide in Xanthobacter autotrophicus. The bacterium produces R- and S-HPCDH simultaneously to facilitate transformation of R- and S-enantiomers of epoxypropane to a common achiral product 2-ketopropyl-CoM (2-KPC). Both R- and S-HPCDH are highly specific for their respective substrates as each enzyme displays less than 0.5% activity with the opposite substrate isomer. In order to elucidate the structural basis for stereospecificity displayed by R- and S-HPCDH we have determined substrate bound crystal structures of S-HPCDH to 1.6Å resolution. Comparisons to the previously reported product-bound structure of R-HPCDH reveal that although the placement of catalytic residues within the active site of each enzyme is nearly identical, structural differences in the surrounding area provide each enzyme with a distinct substrate binding pocket. These structures demonstrate how chiral discrimination by R- and S-HPCDH results from alternative binding of the distal end of substrates within each substrate binding pocket.
    MeSH term(s) Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Mesna/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases/chemistry ; Oxidoreductases/metabolism ; Protein Multimerization ; Protein Structure, Quaternary ; Stereoisomerism ; Substrate Specificity ; Xanthobacter/enzymology
    Chemical Substances Oxidoreductases (EC 1.-) ; Mesna (NR7O1405Q9)
    Language English
    Publishing date 2013-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 523-x
    ISSN 1096-0384 ; 0003-9861
    ISSN (online) 1096-0384
    ISSN 0003-9861
    DOI 10.1016/j.abb.2013.02.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Rapid evolution in response to introduced predators II: the contribution of adaptive plasticity.

    Latta, Leigh C / Bakelar, Jeremy W / Knapp, Roland A / Pfrender, Michael E

    BMC evolutionary biology

    2007  Volume 7, Page(s) 21

    Abstract: Background: Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic responses of ... ...

    Abstract Background: Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic responses of Daphnia populations to recent introductions of non-native fish to assess the relative roles of phenotypic plasticity versus genetic change in causing the observed patterns. The Daphnia community in alpine lakes throughout the Sierra Nevada of California (USA) is ideally suited for investigation of rapid adaptive evolution because there are multiple lakes with and without introduced fish predators. We conducted common-garden experiments involving presence or absence of chemical cues produced by fish and measured morphological and life-history traits in Daphnia melanica populations collected from lakes with contrasting fish stocking histories. The experiment allowed us to assess the degree of population differentiation due to fish predation and examine the contribution of adaptive plasticity in the response to predator introduction.
    Results: Our results show reductions in egg number and body size of D. melanica in response to introduced fish. These phenotypic changes have a genetic basis but are partly due to a direct response to chemical cues from fish via adaptive phenotypic plasticity. Body size showed the largest phenotypic change, on the order of nine phenotypic standard deviations, with approximately 11% of the change explained by adaptive plasticity. Both evolutionary and plastic changes in body size and egg number occurred but no changes in the timing of reproduction were observed.
    Conclusion: Native Daphnia populations exposed to chemical cues produced by salmonid fish predators display adaptive plasticity for body size and fecundity. The magnitude of adaptive plasticity was insufficient to explain the total phenotypic change, so the realized change in phenotypic means in populations exposed to introduced fish may be the result of a combination of initial plasticity and subsequent genetic adaptation. Our results suggest that immediately following the introduction of fish predators, adaptive plasticity may reduce the impact of selection through "Baldwin/Bogert effects" by facilitating the movement of populations toward new fitness optima. Our study of the response of a native species to an introduced predator enhances our understanding of the conditions necessary for rapid adaptive evolution and the relationship between rapid evolution and adaptive phenotypic plasticity.
    MeSH term(s) Adaptation, Physiological ; Animals ; Biological Evolution ; California ; Clutch Size ; Daphnia/genetics ; Daphnia/physiology ; Fertility ; Food Chain ; Genetic Variation ; Oncorhynchus mykiss/physiology ; Phenotype
    Language English
    Publishing date 2007-02-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1471-2148
    ISSN (online) 1471-2148
    DOI 10.1186/1471-2148-7-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Rapid evolution in response to introduced predators II

    Knapp Roland A / Bakelar Jeremy W / Latta Leigh C / Pfrender Michael E

    BMC Evolutionary Biology, Vol 7, Iss 1, p

    the contribution of adaptive plasticity

    2007  Volume 21

    Abstract: Abstract Background Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic ... ...

    Abstract Abstract Background Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic responses of Daphnia populations to recent introductions of non-native fish to assess the relative roles of phenotypic plasticity versus genetic change in causing the observed patterns. The Daphnia community in alpine lakes throughout the Sierra Nevada of California (USA) is ideally suited for investigation of rapid adaptive evolution because there are multiple lakes with and without introduced fish predators. We conducted common-garden experiments involving presence or absence of chemical cues produced by fish and measured morphological and life-history traits in Daphnia melanica populations collected from lakes with contrasting fish stocking histories. The experiment allowed us to assess the degree of population differentiation due to fish predation and examine the contribution of adaptive plasticity in the response to predator introduction. Results Our results show reductions in egg number and body size of D. melanica in response to introduced fish. These phenotypic changes have a genetic basis but are partly due to a direct response to chemical cues from fish via adaptive phenotypic plasticity. Body size showed the largest phenotypic change, on the order of nine phenotypic standard deviations, with approximately 11% of the change explained by adaptive plasticity. Both evolutionary and plastic changes in body size and egg number occurred but no changes in the timing of reproduction were observed. Conclusion Native Daphnia populations exposed to chemical cues produced by salmonid fish predators display adaptive plasticity for body size and fecundity. The magnitude of adaptive plasticity was insufficient to explain the total phenotypic change, so the realized change in phenotypic means in populations exposed to introduced fish may be the result of a combination of initial plasticity and subsequent genetic adaptation. Our results suggest that immediately following the introduction of fish predators, adaptive plasticity may reduce the impact of selection through "Baldwin/Bogert effects" by facilitating the movement of populations toward new fitness optima. Our study of the response of a native species to an introduced predator enhances our understanding of the conditions necessary for rapid adaptive evolution and the relationship between rapid evolution and adaptive phenotypic plasticity.
    Keywords Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Evolution ; QH359-425
    Subject code 590
    Language English
    Publishing date 2007-02-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Crystal structures of S-HPCDH reveal determinants of stereospecificity for R- and S-hydroxypropyl-coenzyme M dehydrogenases

    Bakelar, Jeremy W. / Sliwa, Dariusz A. / Johnson, Sean J.

    Archives of biochemistry and biophysics

    Volume v. 533,, Issue no. 1

    Abstract: R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases (R- and S-HPCDH) are stereospecific enzymes that are central to the metabolism of propylene and epoxide in Xanthobacter autotrophicus. The bacterium produces R- and S-HPCDH simultaneously to facilitate ...

    Abstract (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases (R- and S-HPCDH) are stereospecific enzymes that are central to the metabolism of propylene and epoxide in Xanthobacter autotrophicus. The bacterium produces R- and S-HPCDH simultaneously to facilitate transformation of R- and S-enantiomers of epoxypropane to a common achiral product 2-ketopropyl-CoM (2-KPC). Both R- and S-HPCDH are highly specific for their respective substrates as each enzyme displays less than 0.5% activity with the opposite substrate isomer. In order to elucidate the structural basis for stereospecificity displayed by R- and S-HPCDH we have determined substrate bound crystal structures of S-HPCDH to 1.6Å resolution. Comparisons to the previously reported product-bound structure of R-HPCDH reveal that although the placement of catalytic residues within the active site of each enzyme is nearly identical, structural differences in the surrounding area provide each enzyme with a distinct substrate binding pocket. These structures demonstrate how chiral discrimination by R- and S-HPCDH results from alternative binding of the distal end of substrates within each substrate binding pocket.
    Keywords Xanthobacter autotrophicus ; isomers ; metabolism ; bacteria ; active sites ; crystal structure ; propylene ; enzymes
    Language English
    Document type Article
    ISSN 0003-9861
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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