Flexibility in the Periplasmic Domain of BamA Is Important for Function

Warner, Lisa; Gatzeva-Topalova, P.Z.; Doerner, Pamela A.; Pardi, Arthur; Sousa, Marcelo C.

doi:10.1016/j.str.2016.11.013

Cited by 39 publications

(33 citation statements)

References 58 publications

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“…Additionally, N323 of the BepA TPR, which was cross‐linked to BamD, appears to be too far from BamD to cross‐link. The proposed structural flexibility of the BAM complex, including possible conformational changes in the BamA POTRA domains, might allow these resides to reach their respective cross‐linking partners (Fleming et al ., ; Iadanza et al ., ; Warner et al ., ). Alternatively, BepA might interact with the BAM complex in several different configurations.…”

Section: Discussionmentioning

confidence: 97%

The TPR domain of BepA is required for productive interaction with substrate proteins and the β‐barrel assembly machinery complex

Daimon

Iwama-Masui

Tanaka

et al. 2017

Molecular Microbiology

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BepA (formerly YfgC) is an Escherichia coli periplasmic protein consisting of an N-terminal protease domain and a C-terminal tetratricopeptide repeat (TPR) domain. We have previously shown that BepA is a dual functional protein with chaperone-like and proteolytic activities involved in membrane assembly and proteolytic quality control of LptD, a major component of the outer membrane lipopolysaccharide translocon. Intriguingly, BepA can associate with the BAM complex: the β-barrel assembly machinery (BAM) driving integration of β-barrel proteins into the outer membrane. However, the molecular mechanism of BepA function and its association with the BAM complex remains unclear. Here, we determined the crystal structure of the BepA TPR domain, which revealed the presence of two subdomains formed by four TPR motifs. Systematic site-directed in vivo photo-cross-linking was used to map the protein-protein interactions mediated by the BepA TPR domain, showing that this domain interacts both with a substrate and with the BAM complex. Mutational analysis indicated that these interactions are important for the BepA functions. These results suggest that the TPR domain plays critical roles in BepA functions through interactions both with substrates and with the BAM complex. Our findings provide insights into the mechanism of biogenesis and quality control of the outer membrane.

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Section: Discussionmentioning

confidence: 97%

The TPR domain of BepA is required for productive interaction with substrate proteins and the β‐barrel assembly machinery complex

Daimon

Iwama-Masui

Tanaka

et al. 2017

Molecular Microbiology

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“…This stretch is pivotal for obtaining a functional bacteri-ocin, since a minor shortening (3-amino-acid deletion) results in loss of functionality (21). One possible mechanism of action that is compatible with the overall rigidity imposed by the dual ␤-prism architecture of LlpA may be that this part of LlpAs interferes with the gating dynamics of BamA, hampering insertion of unfolded outer membrane proteins (37,(66)(67)(68)(69). In turn, this may lead to accumulation of unfolded polypeptides in the periplasm and a downstream response.…”

Section: Discussionmentioning

confidence: 99%

Hitting with a BAM: Selective Killing by Lectin-Like Bacteriocins

Ghequire

Swings

Michiels

et al. 2018

mBio

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Lectin-like bacteriocins (LlpAs) are secreted by proteobacteria and selectively kill strains of their own or related species, and they are composed of two B-lectin domains with divergent sequences. In spp., initial binding of these antibacterial proteins to cells is mediated by the carboxy-terminal domain through d-rhamnose residues present in the common polysaccharide antigen of their lipopolysaccharide, whereas the amino-terminal domain accounts for strain selectivity of killing. Here, we show that spontaneous LlpA-resistant mutants carry mutations in one of three surface-exposed moieties of the essential β-barrel outer membrane protein insertase BamA, the core component of the BAM complex. Polymorphism of this loop in different groups is linked to LlpA susceptibility, and targeted cells all share the same signature motif in this loop. Since heterologous expression of such a gene confers LlpA susceptibility upon a resistant strain, BamA represents the primary bacteriocin selectivity determinant in pseudomonads. Contrary to modular bacteriocins that require uptake via the Tol or Ton system, parasitism of BamA as an LlpA receptor advocates a novel bacteriocin killing mechanism initiated by impairment of the BAM machinery. Bacteria secrete a variety of molecules to eliminate microbial rivals. Bacteriocins are a pivotal group of peptides and proteins that assist in this fight, specifically killing related bacteria. In Gram-negative bacteria, these antibacterial proteins often comprise distinct domains for initial binding to a target cell's surface and subsequent killing via enzymatic or pore-forming activity. Here, we show that lectin-like bacteriocins, a family of bacteriocins that lack the prototypical modular toxin architecture, also stand out by parasitizing BamA, the core component of the outer membrane protein assembly machinery. A particular surface-exposed loop of BamA, critical for its function, serves as a key discriminant for cellular recognition, and polymorphisms in this loop determine whether a strain is susceptible or immune to a particular bacteriocin. These findings suggest a novel mechanism of contact-dependent killing that does not require cellular uptake. The evolutionary advantage of piracy of an essential cellular compound is highlighted by the observation that contact-dependent growth inhibition, a distinct antagonistic system, can equally take advantage of this receptor.

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“…This step is likely to require the conformational flexibility of the periplasmic domain of BamA (Fleming et al ., ; Warner et al . ) to accommodate a good portion of the folding β‐barrel domain embracing the linker region (step II). A similar assembly intermediate that precedes membrane integration has been proposed for the β‐barrel protein LptD, which undergoes a significant amount of folding near the BamA‐BamD periplasmic interface (Lee et al ., ).…”

Section: Role Of the Bam Complex In Autotransporter Assemblymentioning

confidence: 99%

Job contenders: roles of the β‐barrel assembly machinery and the translocation and assembly module in autotransporter secretion

Albenne

Ieva

2017

Molecular Microbiology

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SummaryIn Gram-negative bacteria, autotransporters secrete effector protein domains that are linked to virulence. Although they were once thought to be simple and autonomous secretion machines, mounting evidence reveals that multiple factors of the bacterial envelope are necessary for autotransporter assembly. Secretion across the outer membrane of their soluble effector "passenger domain" is promoted by the assembly of an outer membrane-spanning "b-barrel domain". Both reactions require BamA, an essential component of the b-barrel assembly machinery (BAM complex) that catalyzes the final reaction step by which outer membrane proteins are integrated into the lipid bilayer. A large amount of data generated in the last decade has shed key insights onto the mechanistic coordination of autotransporter b-barrel domain assembly and passenger domain secretion. These results, together with the recently solved structures of the BAM complex, offer an unprecedented opportunity to discuss a detailed model of autotransporter assembly. Importantly, some autotransporters benefit from the presence of an additional machinery, the translocation and assembly module (TAM), a two-membrane spanning complex, which contains a BamA-homologous subunit. Although it remains unclear how the BAM complex and the TAM cooperate, it is evident that multiple preparatory steps are necessary for efficient autotransporter biogenesis.

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Flexibility in the Periplasmic Domain of BamA Is Important for Function

Cited by 39 publications

References 58 publications

The TPR domain of BepA is required for productive interaction with substrate proteins and the β‐barrel assembly machinery complex

The TPR domain of BepA is required for productive interaction with substrate proteins and the β‐barrel assembly machinery complex

Hitting with a BAM: Selective Killing by Lectin-Like Bacteriocins

Job contenders: roles of the β‐barrel assembly machinery and the translocation and assembly module in autotransporter secretion

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