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      A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis

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          Abstract

          Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low‐oxygen activated ( lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa‐encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56‐2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild‐type and complement strains but not the Δ usp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.

          Abstract

          A Burkholderia cenocepacia universal stress protein encoded on the BCAM0276 gene (USP76) which is upregulated in chronic infection in people with cystic fibrosis (CF) and by hypoxia, is involved in attachment to human epithelial cells. It is required for growth in conditions associated with the CF lung, including acidic conditions and oxidative stress. Survival of usp76 deletion mutant was impaired in monocyte‐derived macrophages from CF patients, suggesting it is involved in bacterial survival within macrophages, a hallmark of Burkholderia infection.

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          Most cited references61

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          Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

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          The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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            Twilight zone of protein sequence alignments.

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            Sequence alignments unambiguously distinguish between protein pairs of similar and non-similar structure when the pairwise sequence identity is high (>40% for long alignments). The signal gets blurred in the twilight zone of 20-35% sequence identity. Here, more than a million sequence alignments were analysed between protein pairs of known structures to re-define a line distinguishing between true and false positives for low levels of similarity. Four results stood out. (i) The transition from the safe zone of sequence alignment into the twilight zone is described by an explosion of false negatives. More than 95% of all pairs detected in the twilight zone had different structures. More precisely, above a cut-off roughly corresponding to 30% sequence identity, 90% of the pairs were homologous; below 25% less than 10% were. (ii) Whether or not sequence homology implied structural identity depended crucially on the alignment length. For example, if 10 residues were similar in an alignment of length 16 (>60%), structural similarity could not be inferred. (iii) The 'more similar than identical' rule (discarding all pairs for which percentage similarity was lower than percentage identity) reduced false positives significantly. (iv) Using intermediate sequences for finding links between more distant families was almost as successful: pairs were predicted to be homologous when the respective sequence families had proteins in common. All findings are applicable to automatic database searches.
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              CFTR regulates phagosome acidification in macrophages and alters bactericidal activity.

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                Author and article information

                Contributors
                siobhan.mcclean@ucd.ie
                Journal
                Microbiologyopen
                Microbiologyopen
                10.1002/(ISSN)2045-8827
                MBO3
                MicrobiologyOpen
                John Wiley and Sons Inc. (Hoboken )
                2045-8827
                09 December 2022
                February 2023
                : 12
                : 1 ( doiID: 10.1002/mbo3.v12.1 )
                : e1311
                Affiliations
                [ 1 ] School of Biomolecular and Biomedical Sciences University College Dublin Belfield Dublin Ireland
                [ 2 ] UCD Conway Institute of Biomolecular and Biomedical Science Befield Dublin Ireland
                [ 3 ] Cell Screening Laboratory, School of Biology and Environmental Science University College Dublin Belfield Dublin Ireland
                [ 4 ] Department of Microbiology St. Vincent's University Hospital Elm Park Dublin Ireland
                [ 5 ] Institute of Biostructures and Bioimaging National Research Council Naples Italy
                Author notes
                [*] [* ] Correspondence Siobhán McClean, School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland.

                Email: siobhan.mcclean@ 123456ucd.ie

                Author information
                http://orcid.org/0000-0001-6389-2542
                Article
                MBO31311
                10.1002/mbo3.1311
                9733578
                8b5f1a3c-cf04-4be7-a6fc-1e543d1bacd6
                © 2022 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 July 2022
                : 14 March 2022
                : 29 July 2022
                Page count
                Figures: 15, Tables: 4, Pages: 20, Words: 12303
                Funding
                Funded by: European Union
                Funded by: EU COST
                Award ID: BM1003
                Funded by: Science Foundation Ireland , doi 10.13039/501100001602;
                Award ID: 20/FFP‐P/8717
                Funded by: Institute of Technology Tallaght, Dublin
                Funded by: Marie Sklodowska‐Curie
                Award ID: 860325
                Funded by: Government of Ireland
                Award ID: GOIPG/2017/788
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                February 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.2 mode:remove_FC converted:09.12.2022

                Microbiology & Virology
                adaptation,burkholderia cenocepacia,chronic infection,cystic fibrosis,intra‐macrophage survival,respiratory infection,universal stress proteins

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