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  1. Article: A Survey of Bacterial Microcompartment Distribution in the Human Microbiome.

    Asija, Kunica / Sutter, Markus / Kerfeld, Cheryl A

    Frontiers in microbiology

    2021  Volume 12, Page(s) 669024

    Abstract: Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs ... ...

    Abstract Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs have been bioinformatically identified based on the encapsulated enzymes and shell proteins encoded in genomic loci. BMCs are found across bacterial phyla. The organisms that contain them, rather than strictly correlating with specific lineages, tend to reflect the metabolic landscape of the environmental niches they occupy. From our recent comprehensive bioinformatic survey of BMCs found in genome sequence data, we find many in members of the human microbiome. Here we survey the distribution of BMCs in the different biotopes of the human body. Given their amenability to be horizontally transferred and bioengineered they hold promise as metabolic modules that could be used to probiotically alter microbiomes or treat dysbiosis.
    Language English
    Publishing date 2021-05-13
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.669024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Hydrophobic Network: Intersubunit and Intercapsomer Interactions Stabilizing the Bacteriophage P22 Capsid.

    Asija, Kunica / Teschke, Carolyn M

    Journal of virology

    2019  Volume 93, Issue 14

    Abstract: Double-stranded DNA (dsDNA) tailed phages and herpesviruses assemble their capsids using coat proteins that have the ubiquitous HK97 fold. Though this fold is common, we do not have a thorough understanding of the different ways viruses adapt it to ... ...

    Abstract Double-stranded DNA (dsDNA) tailed phages and herpesviruses assemble their capsids using coat proteins that have the ubiquitous HK97 fold. Though this fold is common, we do not have a thorough understanding of the different ways viruses adapt it to maintain stability in various environments. The HK97-fold E-loop, which connects adjacent subunits at the outer periphery of capsomers, has been implicated in capsid stability. Here, we show that in bacteriophage P22, residue W61 at the tip of the E-loop plays a role in stabilizing procapsids and in maturation. We hypothesize that a hydrophobic pocket is formed by residues I366 and W410 in the P domain of a neighboring subunit within a capsomer, into which W61 fits like a peg. In addition, W61 likely bridges to residues A91 and L401 in P-domain loops of an adjacent capsomer, thereby linking the entire capsid together with a network of hydrophobic interactions. There is conservation of this hydrophobic network in the distantly related P22-like phages, indicating that this structural feature is likely important for stabilizing this family of phages. Thus, our data shed light on one of the varied elegant mechanisms used in nature to consistently build stable viral genome containers through subtle adaptation of the HK97 fold.
    MeSH term(s) Bacteriophage P22/chemistry ; Bacteriophage P22/genetics ; Hydrophobic and Hydrophilic Interactions ; Protein Domains ; Protein Folding ; Protein Structure, Secondary ; Viral Proteins/chemistry ; Viral Proteins/genetics
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2019-06-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.00727-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Of capsid structure and stability: The partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein.

    Asija, Kunica / Teschke, Carolyn M

    Virology

    2019  Volume 534, Page(s) 45–53

    Abstract: Tailed dsDNA bacteriophages and herpesviruses form capsids using coat proteins that have the HK97 fold. In these viruses, the coat proteins first assemble into procapsids, which subsequently mature during DNA packaging. Generally interactions between the ...

    Abstract Tailed dsDNA bacteriophages and herpesviruses form capsids using coat proteins that have the HK97 fold. In these viruses, the coat proteins first assemble into procapsids, which subsequently mature during DNA packaging. Generally interactions between the coat protein E-loop of one subunit and the P-domain of an adjacent subunit help stabilize both capsomers and capsids. Based on a recent 3.3 Å cryo-EM structure of the bacteriophage P22 virion, E-loop amino acids E52, E59 and E72 were suggested to stabilize the capsid through intra-capsomer salt bridges with the P-domain residues R102, R109 and K118. The glutamic acid residues were each mutated to alanine to test this hypothesis. The substitutions resulted in a WT phenotype and did not destabilize capsids; rather, the alanine substituted coat proteins increased the stability of procapsids and virions. These results indicate that different types of interactions must be used between the E-loop and P-domain to stabilize phage P22 procapsids and virions.
    MeSH term(s) Bacteriophage P22/chemistry ; Bacteriophage P22/genetics ; Bacteriophage P22/metabolism ; Bacteriophage P22/ultrastructure ; Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Models, Molecular ; Protein Domains ; Protein Stability ; Virion/chemistry ; Virion/genetics ; Virion/metabolism
    Chemical Substances Capsid Proteins
    Language English
    Publishing date 2019-06-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2019.05.021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Lessons from bacteriophages part 1

    Kunica Asija / Carolyn M Teschke

    PLoS Pathogens, Vol 14, Iss 5, p e

    Deriving utility from protein structure, function, and evolution.

    2018  Volume 1006971

    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2018-05-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Lessons from bacteriophages part 2

    Kunica Asija / Carolyn M Teschke

    PLoS Pathogens, Vol 14, Iss 5, p e

    A saga of scientific breakthroughs and prospects for their use in human health.

    2018  Volume 1006970

    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2018-05-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Lessons from bacteriophages part 2: A saga of scientific breakthroughs and prospects for their use in human health.

    Asija, Kunica / Teschke, Carolyn M

    PLoS pathogens

    2018  Volume 14, Issue 5, Page(s) e1006970

    MeSH term(s) Bacterial Infections/drug therapy ; Bacterial Infections/microbiology ; Bacterial Infections/therapy ; Bacteriophages/genetics ; Bacteriophages/physiology ; Evolution, Molecular ; Host Specificity ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/physiology ; Humans ; Phage Therapy/methods ; Phage Therapy/trends ; Precision Medicine/methods ; Precision Medicine/trends
    Language English
    Publishing date 2018
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7366
    ISSN (online) 1553-7374
    ISSN 1553-7366
    DOI 10.1371/journal.ppat.1006970
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Lessons from bacteriophages part 1: Deriving utility from protein structure, function, and evolution.

    Asija, Kunica / Teschke, Carolyn M

    PLoS pathogens

    2018  Volume 14, Issue 5, Page(s) e1006971

    MeSH term(s) Animals ; Bacteriophages/genetics ; Bacteriophages/immunology ; Bacteriophages/physiology ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/physiology ; Evolution, Molecular ; Genome, Viral ; Humans ; Models, Molecular ; Protein Conformation ; Vaccines, Virus-Like Particle/chemistry ; Vaccines, Virus-Like Particle/genetics ; Vaccines, Virus-Like Particle/immunology ; Virus Assembly/genetics ; Virus Assembly/physiology
    Chemical Substances Capsid Proteins ; Vaccines, Virus-Like Particle
    Language English
    Publishing date 2018
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7366
    ISSN (online) 1553-7374
    ISSN 1553-7366
    DOI 10.1371/journal.ppat.1006971
    Database MEDical Literature Analysis and Retrieval System OnLINE

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