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      Evasion of autophagy mediated by Rickettsia surface protein OmpB is critical for virulence

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          SUMMARY

          Rickettsia are obligate intracellular bacteria that evade antimicrobial autophagy in the host cell cytosol by unknown mechanisms. Other cytosolic pathogens block different steps of autophagy targeting, including the initial step of polyubiquitin coat formation. One mechanism of evasion is to mobilize actin to the bacterial surface. Here, we show that actin mobilization is insufficient to block autophagy recognition of the pathogen Rickettsia parkeri. Instead, R. parkeri employs outer membrane protein B (OmpB) to block ubiquitylation of bacterial surface proteins, including OmpA, and subsequent recognition by autophagy receptors. OmpB is also required for the formation of a capsule-like layer. Although OmpB is dispensable for bacterial growth in endothelial cells, it is essential for R. parkeri to block autophagy in macrophages and to colonize mice because of its ability to promote autophagy evasion in immune cells. Our results indicate that OmpB acts as a protective shield to obstruct autophagy recognition, revealing a distinctive bacterial mechanism to evade antimicrobial autophagy.

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          Most cited references60

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          A ubiquitin-like system mediates protein lipidation.

          Autophagy is a dynamic membrane phenomenon for bulk protein degradation in the lysosome/vacuole. Apg8/Aut7 is an essential factor for autophagy in yeast. We previously found that the carboxy-terminal arginine of nascent Apg8 is removed by Apg4/Aut2 protease, leaving a glycine residue at the C terminus. Apg8 is then converted to a form (Apg8-X) that is tightly bound to the membrane. Here we report a new mode of protein lipidation. Apg8 is covalently conjugated to phosphatidylethanolamine through an amide bond between the C-terminal glycine and the amino group of phosphatidylethanolamine. This lipidation is mediated by a ubiquitination-like system. Apg8 is a ubiquitin-like protein that is activated by an E1 protein, Apg7 (refs 7, 8), and is transferred subsequently to the E2 enzymes Apg3/Aut1 (ref. 9). Apg7 activates two different ubiquitin-like proteins, Apg12 (ref. 10) and Apg8, and assigns them to specific E2 enzymes, Apg10 (ref. 11) and Apg3, respectively. These reactions are necessary for the formation of Apg8-phosphatidylethanolamine. This lipidation has an essential role in membrane dynamics during autophagy.
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            The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria.

            Cell-autonomous innate immune responses against bacteria attempting to colonize the cytosol of mammalian cells are incompletely understood. Polyubiquitylated proteins can accumulate on the surface of such bacteria, and bacterial growth is restricted by Tank-binding kinase (TBK1). Here we show that NDP52, not previously known to contribute to innate immunity, recognizes ubiquitin-coated Salmonella enterica in human cells and, by binding the adaptor proteins Nap1 and Sintbad, recruits TBK1. Knockdown of NDP52 and TBK1 facilitated bacterial proliferation and increased the number of cells containing ubiquitin-coated salmonella. NDP52 also recruited LC3, an autophagosomal marker, and knockdown of NDP52 impaired autophagy of salmonella. We conclude that human cells utilize the ubiquitin system and NDP52 to activate autophagy against bacteria attempting to colonize their cytosol.
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              The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy.

              Autophagy is a bulk degradation process in eukaryotic cells; autophagosomes enclose cytoplasmic components for degradation in the lysosome/vacuole. Autophagosome formation requires two ubiquitin-like conjugation systems, the Atg12 and Atg8 systems, which are tightly associated with expansion of autophagosomal membrane. Previous studies have suggested that there is a hierarchy between these systems; the Atg12 system is located upstream of the Atg8 system in the context of Atg protein organization. However, the concrete molecular relationship is unclear. Here, we show using an in vitro Atg8 conjugation system that the Atg12-Atg5 conjugate, but not unconjugated Atg12 or Atg5, strongly enhances the formation of the other conjugate, Atg8-PE. The Atg12-Atg5 conjugate promotes the transfer of Atg8 from Atg3 to the substrate, phosphatidylethanolamine (PE), by stimulating the activity of Atg3. We also show that the Atg12-Atg5 conjugate interacts with both Atg3 and PE-containing liposomes. These results indicate that the Atg12-Atg5 conjugate is a ubiquitin-protein ligase (E3)-like enzyme for Atg8-PE conjugation reaction, distinctively promoting protein-lipid conjugation.
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                Author and article information

                Journal
                101674869
                44774
                Nat Microbiol
                Nat Microbiol
                Nature microbiology
                2058-5276
                19 September 2019
                14 October 2019
                December 2019
                14 April 2020
                : 4
                : 12
                : 2538-2551
                Affiliations
                [1 ]Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
                [2 ]Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
                [3 ]QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, CA 94720, USA
                [4 ]Present address: Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
                [5 ]Lead Contact.
                Author notes

                AUTHOR CONTRIBUTIONS

                P.E. and M.D.W. conceived the study. P.E. performed all work with infections of tissue culture cells and imaging, with assistance from N.I. P.E. and T.P.B. performed the mouse studies. P.E., T.P.B., and G.M. generated BMDMs. G.G. bred mice. M.D.W., G.M., K.G.M., M. R., and J.S.C. provided resources and protocol assistance. A.T.I. conducted mass spectrometry analysis. P.E. and M.D.W. drafted the initial manuscript and all authors provided editorial feedback. P.E., M.D.W., G.M., A.T.I., K.G.M., M.R. and J.S.C. obtained funding.

                Article
                NIHMS1539630
                10.1038/s41564-019-0583-6
                6988571
                31611642
                d7bb83f6-bf10-4d72-85f3-271055569297

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                Categories
                Article

                rickettsia,ompb,ompa,polyubiquitylation,autophagic recognition,antimicrobial autophagy,intracellular pathogens,innate immunity

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