Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory Bdellovibrio and Increase Population Fitness
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{"title"=>"Specialized peptidoglycan hydrolases sculpt the intra-bacterial niche of predatory Bdellovibrio and increase population fitness", "type"=>"journal", "authors"=>[{"first_name"=>"Thomas R.", "last_name"=>"Lerner", "scopus_author_id"=>"57200746111"}, {"first_name"=>"Andrew L.", "last_name"=>"Lovering", "scopus_author_id"=>"7006580400"}, {"first_name"=>"Nhat Khai", "last_name"=>"Bui", "scopus_author_id"=>"25633585100"}, {"first_name"=>"Kaoru", "last_name"=>"Uchida", "scopus_author_id"=>"36991736400"}, {"first_name"=>"Shin Ichi", "last_name"=>"Aizawa", "scopus_author_id"=>"57198295086"}, {"first_name"=>"Waldemar", "last_name"=>"Vollmer", "scopus_author_id"=>"7005385294"}, {"first_name"=>"R. Elizabeth", "last_name"=>"Sockett", "scopus_author_id"=>"6701430948"}], "year"=>2012, "source"=>"PLoS Pathogens", "identifiers"=>{"issn"=>"15537366", "scopus"=>"2-s2.0-84860904824", "pui"=>"364799353", "doi"=>"10.1371/journal.ppat.1002524", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "sgr"=>"84860904824", "pmid"=>"22346754"}, "id"=>"7b427a5d-5090-3e29-8eab-9969d78bc0b0", "abstract"=>"Bdellovibrio are predatory bacteria that have evolved to invade virtually all gram-negative bacteria, including many prominent pathogens. Upon invasion, prey bacteria become rounded up into an osmotically stable niche for the Bdellovibrio, preventing further superinfection and allowing Bdellovibrio to replicate inside without competition, killing the prey bacterium and degrading its contents. Historically, prey rounding was hypothesized to be associated with peptidoglycan (PG) metabolism; we found two Bdellovibrio genes, bd0816 and bd3459, expressed at prey entry and encoding proteins with limited homologies to conventional dacB/PBP4 DD-endo/carboxypeptidases (responsible for peptidoglycan maintenance during growth and division). We tested possible links between Bd0816/3459 activity and predation. Bd3459, but not an active site serine mutant protein, bound β-lactam, exhibited DD-endo/carboxypeptidase activity against purified peptidoglycan and, importantly, rounded up E. coli cells upon periplasmic expression. A ΔBd0816 ΔBd3459 double mutant invaded prey more slowly than the wild type (with negligible prey cell rounding) and double invasions of single prey by more than one Bdellovibrio became more frequent. We solved the crystal structure of Bd3459 to 1.45 Å and this revealed predation-associated domain differences to conventional PBP4 housekeeping enzymes (loss of the regulatory domain III, alteration of domain II and a more exposed active site). The Bd3459 active site (and by similarity the Bd0816 active site) can thus accommodate and remodel the various bacterial PGs that Bdellovibrio may encounter across its diverse prey range, compared to the more closed active site that \"regular\" PBP4s have for self cell wall maintenance. Therefore, during evolution, Bdellovibrio peptidoglycan endopeptidases have adapted into secreted predation-specific proteins, preventing wasteful double invasion, and allowing activity upon the diverse prey peptidoglycan structures to sculpt the prey cell into a stable intracellular niche for replication.", "link"=>"http://www.mendeley.com/research/specialized-peptidoglycan-hydrolases-sculpt-intrabacterial-niche-predatory-bdellovibrio-increase-pop", "reader_count"=>37, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>9, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>9, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>28, "Neuroscience"=>1, "Physics and Astronomy"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/685104"], "description"=>"<p>*Values in parentheses are for highest-resolution shell.</p>", "links"=>[], "tags"=>["refinement"], "article_id"=>355593, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_collection_and_refinement_statistics_/355593", "title"=>"Data collection and refinement statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-09 01:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/684727"], "description"=>"<p>Time-lapse microscopy of <i>E. coli</i> TOP10 cells containing either wild type (WT) or active site variant (S70A) Bd3459 protein being overexpressed from an L-arabinose inducible plasmid by addition of arabinose at 0 hours. Cells were immobilised on a YT-agarose pad (YT) or osmotically stabilised M-medium-agarose pad (M), containing 0.2% (v/v) L-arabinose and development over 6 hours is shown. A = Bd3459 (WT) on YT; B = Bd3459 (S70A) on YT; C = Bd3459 (WT) on M; D = Bd3459 (S70A) on M. Osmotically unsupported <i>E. coli</i> expressing WT Bd3459 lyse and osmotically supported <i>E. coli</i> round up. <i>E. coli</i> expressing the S70A protein variant continues to grow normally. Also see Videos S13, S14, S15, S16.</p>", "links"=>[], "tags"=>["full-length", "bd3459", "s70a", "causes"], "article_id"=>355207, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_full_length_Bd3459_protein_alone_but_not_a_S70A_active_site_variant_causes_rounding_lysis_of_E_coli_/355207", "title"=>"Expression of full-length Bd3459 protein alone, but not a S70A active site variant, causes rounding/lysis of <i>E. coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:26:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/348717", "https://ndownloader.figshare.com/files/348753", "https://ndownloader.figshare.com/files/348783", "https://ndownloader.figshare.com/files/348810", "https://ndownloader.figshare.com/files/348849", "https://ndownloader.figshare.com/files/348874", "https://ndownloader.figshare.com/files/348904", "https://ndownloader.figshare.com/files/348925", "https://ndownloader.figshare.com/files/348950", "https://ndownloader.figshare.com/files/349047", "https://ndownloader.figshare.com/files/349081", "https://ndownloader.figshare.com/files/349112", "https://ndownloader.figshare.com/files/349150", "https://ndownloader.figshare.com/files/349184", "https://ndownloader.figshare.com/files/349220", "https://ndownloader.figshare.com/files/349257", "https://ndownloader.figshare.com/files/349291", "https://ndownloader.figshare.com/files/349324", "https://ndownloader.figshare.com/files/349363", "https://ndownloader.figshare.com/files/349401", "https://ndownloader.figshare.com/files/349439", "https://ndownloader.figshare.com/files/349464", "https://ndownloader.figshare.com/files/349485", "https://ndownloader.figshare.com/files/349510", "https://ndownloader.figshare.com/files/349539"], "description"=>"<div><p><em>Bdellovibrio</em> are predatory bacteria that have evolved to invade virtually all Gram-negative bacteria, including many prominent pathogens. Upon invasion, prey bacteria become rounded up into an osmotically stable niche for the <em>Bdellovibrio</em>, preventing further superinfection and allowing <em>Bdellovibrio</em> to replicate inside without competition, killing the prey bacterium and degrading its contents. Historically, prey rounding was hypothesized to be associated with peptidoglycan (PG) metabolism; we found two <em>Bdellovibrio</em> genes, <em>bd0816</em> and <em>bd3459</em>, expressed at prey entry and encoding proteins with limited homologies to conventional <em>dacB</em>/PBP4 DD-endo/carboxypeptidases (responsible for peptidoglycan maintenance during growth and division). We tested possible links between Bd0816/3459 activity and predation. Bd3459, but not an active site serine mutant protein, bound β-lactam, exhibited DD-endo/carboxypeptidase activity against purified peptidoglycan and, importantly, rounded up <em>E. coli</em> cells upon periplasmic expression. A ΔBd0816 ΔBd3459 double mutant invaded prey more slowly than the wild type (with negligible prey cell rounding) and double invasions of single prey by more than one <em>Bdellovibrio</em> became more frequent. We solved the crystal structure of Bd3459 to 1.45 Å and this revealed predation-associated domain differences to conventional PBP4 housekeeping enzymes (loss of the regulatory domain III, alteration of domain II and a more exposed active site). The Bd3459 active site (and by similarity the Bd0816 active site) can thus accommodate and remodel the various bacterial PGs that <em>Bdellovibrio</em> may encounter across its diverse prey range, compared to the more closed active site that “regular” PBP4s have for self cell wall maintenance. Therefore, during evolution, <em>Bdellovibrio</em> peptidoglycan endopeptidases have adapted into secreted predation-specific proteins, preventing wasteful double invasion, and allowing activity upon the diverse prey peptidoglycan structures to sculpt the prey cell into a stable intracellular niche for replication.</p> </div>", "links"=>[], "tags"=>["specialized", "peptidoglycan", "hydrolases", "sculpt", "intra-bacterial", "niche", "predatory"], "article_id"=>128945, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002524.s001", "https://dx.doi.org/10.1371/journal.ppat.1002524.s002", "https://dx.doi.org/10.1371/journal.ppat.1002524.s003", "https://dx.doi.org/10.1371/journal.ppat.1002524.s004", "https://dx.doi.org/10.1371/journal.ppat.1002524.s005", "https://dx.doi.org/10.1371/journal.ppat.1002524.s006", "https://dx.doi.org/10.1371/journal.ppat.1002524.s007", "https://dx.doi.org/10.1371/journal.ppat.1002524.s008", "https://dx.doi.org/10.1371/journal.ppat.1002524.s009", "https://dx.doi.org/10.1371/journal.ppat.1002524.s010", "https://dx.doi.org/10.1371/journal.ppat.1002524.s011", "https://dx.doi.org/10.1371/journal.ppat.1002524.s012", "https://dx.doi.org/10.1371/journal.ppat.1002524.s013", "https://dx.doi.org/10.1371/journal.ppat.1002524.s014", "https://dx.doi.org/10.1371/journal.ppat.1002524.s015", "https://dx.doi.org/10.1371/journal.ppat.1002524.s016", "https://dx.doi.org/10.1371/journal.ppat.1002524.s017", "https://dx.doi.org/10.1371/journal.ppat.1002524.s018", "https://dx.doi.org/10.1371/journal.ppat.1002524.s019", "https://dx.doi.org/10.1371/journal.ppat.1002524.s020", "https://dx.doi.org/10.1371/journal.ppat.1002524.s021", "https://dx.doi.org/10.1371/journal.ppat.1002524.s022", "https://dx.doi.org/10.1371/journal.ppat.1002524.s023", "https://dx.doi.org/10.1371/journal.ppat.1002524.s024", "https://dx.doi.org/10.1371/journal.ppat.1002524.s025"], "stats"=>{"downloads"=>30, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Specialized_Peptidoglycan_Hydrolases_Sculpt_the_Intra_bacterial_Niche_of_Predatory_Bdellovibrio_and_Increase_Population_Fitness/128945", "title"=>"Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory <em>Bdellovibrio</em> and Increase Population Fitness", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-09 02:29:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/685020"], "description"=>"<p>Comparison of <i>E. coli</i> PBP4 (coloured yellow, active site serine S62, only selected residues shown) and Bd3459 (coloured white, active site serine S70) active sites. The additional hairpin domain of Bd3459 is shown from N292–N303. Despite the more accessible conformation shown in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002524#ppat-1002524-g008\" target=\"_blank\">Figure 8</a>, Bd3459 retains the conserved catalytic apparatus of PBP4 enzymes, in a productive (predicted active) conformation (tallying with the activity assays, and observance of a covalent adduct). Insert (right) shows the refined density for the sulphonyl linkage to S70 (1.2σ, 1.45 Å resolution).</p>", "links"=>[], "tags"=>["overlapping", "residues", "bd3459", "pbp4"], "article_id"=>355505, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g009", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_comparison_detail_of_overlapping_active_site_residues_SXXK_SXN_KTG_and_extra_hairpin_domain_of_Bd3459_versus_E_coli_housekeeping_PBP4_protein_/355505", "title"=>"Structural comparison detail of overlapping active site residues (SXXK, SXN, KTG) and extra “hairpin” domain of Bd3459 versus <i>E. coli</i> “housekeeping” PBP4 protein.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:31:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/684841"], "description"=>"<p>(<b>A</b>) Pentapeptide-rich peptidoglcyan was incubated with Bd3459, Bd3459 pre-incubated with ampicillin, Bd3459 (S70A) or no enzyme, followed by digestion with cellosyl, reduction with sodium borohydride and analysis of the resulting muropeptides by HPLC. Muropeptides: 4, Tetra; 5, Penta; 44, TetraTetra; 45, TetraPenta. Peaks originating from ampicillin are indicated by a star. Bd3459, but not Bd3459 (S70A) or ampicillin-blocked Bd3459, digested Penta and TetraPenta to Tetra indicative of a DD-endo/carboxypeptidase activity. (<b>B</b>) Structures of the reduced muropeptides. GlcNAc, N-acetylglucosamine; MurNAc(r), N-acetylmuramitol; L-Ala, L-alanine; D-iGlu, D-isoglutamic acid; <i>m</i>-Dap, <i>meso</i>-diaminopimelic acid; D-Ala, D-alanine. (<b>C</b>) Bd3459 and Bd3459 (S70A) were incubated with or without ampicillin, followed by labelling with Bocillin-FL and SDS-polyacrylamide gel electrophoresis. Bocillin-FL was detected by fluorescence (Bocillin-FL); total protein was visualized by staining with Coomassie Blue. Bocillin-FL-binding of Bd3459 was greatly inhibited by pre-incubation with ampicillin; Bd3459 (S70A) bound substantially less Bocillin-FL than Bd3459. Thus, Bd3459 is a penicillin-binding protein and degrades isolated cell wall material.</p>", "links"=>[], "tags"=>["bd3459", "inhibition"], "article_id"=>355325, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g007", "stats"=>{"downloads"=>1, "page_views"=>43, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Activity_of_Bd3459_and_its_inhibition_by_ampicillin_/355325", "title"=>"Activity of Bd3459 and its inhibition by ampicillin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/684201"], "description"=>"<p>RNA was isolated at the indicated time points during one round of synchronous <i>Bdellovibrio</i> infection of <i>E. coli</i> host cells, and primers specific to the genes <i>bd3244</i> (<i>dacB</i>), <i>bd0816</i> and <i>bd3459</i> (<i>dacB</i>-like) were used to amplify an approximately 100 bp internal fragment from each transcript if present. <i>bd3244</i> expression shows constitutive expression across the <i>Bdellovibrio</i> lifecycle, (including 2–3 hour septation period) as would be expected for a “peptidoglycan-housekeeping” gene. <i>bd0816</i> and <i>bd3459</i> show a strong peak of expression at 15 minutes post-infection, when <i>Bdellovibrio</i> has attached to prey cells and is beginning to invade. The expression diminishes rapidly at the 45 minute to 1 hour time point once invasion is complete and the prey bdelloplast is formed, and before septation. This is indicative of predation-specific expression. AP = Attack phase (free-swimming <i>Bdellovibrio</i>); 15, 30, 45 = minutes since start of infection (attachment to and rounding of <i>E. coli</i> host cell into a bdelloplast structure); 1 h, 2 h, 3 h, 4 h = hours since start of infection (host cell resources being degraded and used for <i>Bdellovibrio</i> growth into a filament, followed by septation into multiple progeny and eventually lysis from host cell); Ec = <i>E. coli</i> S17-1 RNA (no <i>Bdellovibrio</i> control); gen = <i>B. bacteriovorus</i> HD100 genomic DNA (positive control); NT = No template control; L = NEB 100 bp DNA ladder, arrowed is 100 bp.</p>", "links"=>[], "tags"=>["pcr", "transcriptional", "hd100"], "article_id"=>354687, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reverse_transcriptase_PCR_showing_relative_transcriptional_expression_of_the_three_B_bacteriovorus_HD100_dacB_homologues_/354687", "title"=>"Reverse-transcriptase PCR showing relative transcriptional expression of the three <i>B. bacteriovorus</i> HD100 <i>dacB</i> homologues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:18:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/684484"], "description"=>"<p>Time-lapse microscopy was used to observe invasions when two <i>Bdellovibrio</i> cells were seen to attach to a single prey cell for longer than 10 minutes (longer than the usual ‘recognition’ period) and was taken to be an ‘attempted invasion’ by both cells. The outcomes of invasions (N = 42 for HD100 WT, N = 40 for both HD100 Δ<i>bd0816</i> and HD100 <i>Δbd3459</i>, N = 44 for HD100 Δ<i>bd0816</i> Δ<i>bd3459</i>) were tallied into one of three categories; i) ‘single infection’ (black bars; just one <i>Bdellovibrio</i> successfully invades); ii) ‘synchronous infection’ (grey bars; both invade successfully at the same time); or iii) ‘tailgating infection’ (white bars; one invades followed by the other). The double mutant <i>Bdellovibrio</i> strain showed a much higher proportion of double invasions and therefore decreased predatory population fitness due to self competition in single prey. The absence of Bd3459 has less of an effect on double invasions than the absence of Bd0816 although both single mutant datasets show an intermediate effect between WT and the double mutant. Data were taken from at least two experimental repeats. See <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002524#s4\" target=\"_blank\">Materials and Methods</a> for more information.</p>", "links"=>[], "tags"=>["invasions", "prey", "hd100"], "article_id"=>354968, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_double_invasions_of_E_coli_prey_during_attack_by_B_bacteriovorus_HD100_wild_type_HD100_bd0816_HD100_bd3459_or_B_bacteriovorus_HD100_bd0816_bd3459_DKO_strains_/354968", "title"=>"Frequency of double invasions of <i>E. coli</i> prey during attack by <i>B. bacteriovorus</i> HD100 wild type, HD100 Δ<i>bd0816</i>, HD100 Δ<i>bd3459</i> or <i>B. bacteriovorus</i> HD100 Δ<i>bd0816</i> Δ<i>bd3459</i> (DKO) strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:22:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/684385"], "description"=>"<p>Histograms of mean times for attachment (<b>A</b>) and invasion (<b>B</b>) by <i>B. bacteriovorus</i> HD100 wild type (WT) and Δ<i>bd0816</i> D<i>bd3459</i> (DKO) strains infecting <i>E. coli</i> K-12 MG1655 (black fill) and <i>A. baumannii</i> (grey fill); (Mean attachment time - as measured from initial <i>Bdellovibrio</i> contact with outside of prey cell to the start of traversal through the prey cell wall. Mean invasion time - as measured from the start of traversal through the prey cell wall to not being visible outside the prey cell, i.e. being completely within the prey cell) (N = 50 for all experiments). At least two independent experiments were carried out with error bars showing 95% confidence intervals and statistical analyses shown (ns = not significant; *** = p<0.001). Time-lapse images showing prey rounding relative to invasion for <b>C</b>) <i>E. coli</i> and <b>D</b>) <i>A. baumannii</i> by wild type HD100 <i>Bdellovibrio</i>. Arrowed box shows relative time at which rounding first becomes obvious. <i>E. coli</i> begins to round on average 2.3 minutes before invasion (N = 50), whereas <i>A. baumannii</i> begins to round on average 10.7 minutes before invasion (N = 50). <i>E. coli</i> finishes prey rounding concurrently with the completion of invasion, whereas <i>A. baumannii</i> tends to have its rounding completed earlier. Refer to results section for more information. Scale bar is 2 µm.</p>", "links"=>[], "tags"=>["images", "hd100", "strains", "infecting", "k-12", "mg1655"], "article_id"=>354865, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_and_images_of_B_bacteriovorus_HD100_and_bd0816_bd3459_strains_infecting_E_coli_K_12_MG1655_and_A_baumannii_/354865", "title"=>"Histograms and images of <i>B. bacteriovorus</i> HD100 and Δ<i>bd0816</i> Δ<i>bd3459</i> strains infecting <i>E. coli</i> K-12 MG1655 and <i>A. baumannii</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:21:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/684944"], "description"=>"<p>Bd3459 left hand panel, <i>E. coli</i> PBP4 centre panel, coloured thus: TP domain, white; domain II, yellow; domain III, orange; “insert” hairpin, purple; C-terminal “staple”, red. The active site serine residues of Bd3459 (S70 sulfonyl adduct) and <i>E. coli</i> PBP4 (S62) are shown in stick form. Domain III of <i>E. coli</i> PBP4 acts to functionally constrict the active site (for a more attenuated/regulated self-peptidoglycan metabolism), whereas Bd3459 lacks this and thus may act promiscuously on a range of larger peptidoglycan substrates. This would fit with the predatory role of Bd3459 shown genetically. Right hand panel is composed of Bd3459 (blue, with S70 coloured in red) and <i>E. coli</i> PBP4 (orange) superimposed via their transpeptidase domains, illustrating the relatively more solvent-exposed active site of Bd3459 and respective differences in domains II and III.</p>", "links"=>[], "tags"=>["bd3459", "revealing", "predatory", "adaptations", "differing", "pbp4"], "article_id"=>355428, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g008", "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystal_structure_of_B_bacteriovorus_Bd3459_revealing_predatory_adaptations_differing_from_the_PG_housekeeping_PBP4_of_E_coli_/355428", "title"=>"Crystal structure of <i>B. bacteriovorus</i> Bd3459 revealing predatory adaptations differing from the “PG-housekeeping” PBP4 of <i>E. coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:30:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/684282"], "description"=>"<p>Images were taken 90-minutes post-invasion and the roundness of infected prey cells were analysed using ImageJ software. Invasion by <b>A</b>: Wild-type HD100 (100% of bdelloplasts were rounded, N = 25); <b>B</b>: HD100 Δ<i>bd0816</i> (100% of bdelloplasts were rounded, N = 21); <b>C</b>: HD100 Δb<i>d3459</i> (75% of bdelloplasts were rounded, N = 24); <b>D</b>: HD100 Δ<i>bd0816</i> Δ<i>bd3459</i> (DKO) double mutant (<10% bdelloplasts were rounded, N = 53). <b>E</b>: Bar graph showing the average roundness coefficient of the bdelloplasts from EM images with error bars showing 95% confidence intervals and statistical analysis of the means compared to WT (ns = not significant; ** = p<0.005; *** = p<0.001). Data is taken from 4 independent experiments. All displayed images were taken from the same experimental repeat at 80 kV (20,000-fold magnification) and stained with 1% PTA for 1 min. Scale bar is 500 µm.</p>", "links"=>[], "tags"=>["micrographs", "roundness", "knockout-mutant", "infected", "prey"], "article_id"=>354767, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electron_micrographs_and_roundness_analysis_of_wild_type_and_dacB_knockout_mutant_infected_E_coli_prey_cells_/354767", "title"=>"Electron micrographs and roundness analysis of wild type and <i>dacB</i> knockout-mutant infected <i>E. coli</i> prey cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/684563"], "description"=>"<p>The structural elements of the <i>E. coli</i> PBP4 and the Bd3459 proteins are displayed respectively below and above the alignment. The central structural differences between Bd3459/Bd0816 PBP4s and <i>E. coli</i> PBP4/Bd3244 (reflected in missing/altered domains in the structure (see <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002524#ppat-1002524-g008\" target=\"_blank\">Figure 8</a>) can be clearly seen.</p>", "links"=>[], "tags"=>["bd3244", "predatory", "proteins", "housekeeping", "pbp4"], "article_id"=>355039, "categories"=>["Biochemistry"], "users"=>["Thomas R. Lerner", "Andrew L. Lovering", "Nhat Khai Bui", "Kaoru Uchida", "Shin-Ichi Aizawa", "Waldemar Vollmer", "R. Elizabeth Sockett"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002524.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_Bdellovibrio_housekeeping_Bd3244_and_predatory_Bd0816_Bd3549_proteins_versus_housekeeping_PBP4_of_E_coli_/355039", "title"=>"Alignment of <i>Bdellovibrio</i> “housekeeping” Bd3244 and predatory Bd0816/Bd3549 proteins versus housekeeping PBP4 of <i>E. coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-09 01:23:59"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
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  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"14", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"15", "full-text"=>"18", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"16", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"12", "full-text"=>"16", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"12", "full-text"=>"17", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"13", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"13", "full-text"=>"20", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"12", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"9", "full-text"=>"12", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
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Relative Metric

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