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Cava, Felipe
Publications (10 of 82) Show all publications
Jacquier, N., Yadav, A. K., Pillonel, T., Viollier, P. H., Cava, F. & Greub, G. (2019). A SpoIID Homolog Cleaves Glycan Strands at the Chlamydial Division Septum. mBio, 10(4), Article ID e01128-19.
Open this publication in new window or tab >>A SpoIID Homolog Cleaves Glycan Strands at the Chlamydial Division Septum
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2019 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, article id e01128-19Article in journal (Refereed) Published
Abstract [en]

Chlamydiales species are obligate intracellular bacteria lacking a classical peptidoglycan sacculus but relying on peptidoglycan synthesis for cytokinesis. While septal peptidoglycan biosynthesis seems to be regulated by MreB actin and its membrane anchor RodZ rather than FtsZ tubulin in Chlamydiales, the mechanism of peptidoglycan remodeling is poorly understood. An amidase conserved in Chlamydiales is able to cleave peptide stems in peptidoglycan, but it is not clear how peptidoglycan glycan strands are cleaved since no classical lytic transglycosylase is encoded in chlamydial genomes. However, a protein containing a SpoIID domain, known to possess transglycosylase activity in Bacillus subtilis, is conserved in Chiamydiales. We show here that the SpoIID homologue of the Chlamydia-related pathogen Waddlia chondrophila is a septal peptidoglycan-binding protein. Moreover, we demonstrate that SpoIID acts as a lytic transglycosylase on peptidoglycan and as a muramidase on denuded glycan strands in vitro. As SpoIID-like proteins are widespread in nonsporulating bacteria, SpoIID might commonly be a septal peptidoglycan remodeling protein in bacteria, including obligate intracellular pathogens, and thus might represent a promising drug target. IMPORTANCE Chlamydiales species are obligate intracellular bacteria and important human pathogens that have a minimal division machinery lacking the proteins that are essential for bacterial division in other species, such as FtsZ. Chlamydial division requires synthesis of peptidoglycan, which forms a ring at the division septum and is rapidly turned over. However, little is known of peptidoglycan degradation, because many peptidoglycan-degrading enzymes are not encoded by chlamydial genomes. Here we show that an homologue of SpoIID, a peptidoglycan-degrading enzyme involved in sporulation of bacteria such as Bacillus subtilis, is expressed in Chlamydiales, localizes at the division septum, and degrades peptidoglycan in vitro, indicating that SpoIID is not only involved in sporulation but also likely implicated in division of some bacteria.

Place, publisher, year, edition, pages
American Society for Microbiology (ASM), 2019
Keywords
Chlamydiales, Waddlia chondrophila, cell division, peptidoglycan, sporulation
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-162887 (URN)10.1128/mBio.01128-19 (DOI)000481617000036 ()31311880 (PubMedID)
Available from: 2019-09-04 Created: 2019-09-04 Last updated: 2019-09-04Bibliographically approved
Fleurie, A., Zoued, A., Alvarez, L., Hines, K. M., Cava, F., Xu, L., . . . Waldor, M. K. (2019). A Vibrio cholerae BolA-Like Protein Is Required for Proper Cell Shape and Cell Envelope Integrity. mBio, 10(4), Article ID e00790-19.
Open this publication in new window or tab >>A Vibrio cholerae BolA-Like Protein Is Required for Proper Cell Shape and Cell Envelope Integrity
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2019 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, article id e00790-19Article in journal (Refereed) Published
Abstract [en]

BolA family proteins are conserved in Gram-negative bacteria and many eukaryotes. While diverse cellular phenotypes have been linked to this protein family, the molecular pathways through which these proteins mediate their effects are not well described. Here, we investigated the roles of BolA family proteins in Vibrio cholerae, the cholera pathogen. Like Escherichia coli, V. cholerae encodes two BolA proteins, BolA and IbaG. However, in marked contrast to E. coli, where bolA is linked to cell shape and ibaG is not, in V. cholerae, bolA mutants lack morphological defects, whereas ibaG proved critical for the generation and/or maintenance of the pathogen's morphology. Notably, the bizarre-shaped, multipolar, elongated, and wide cells that predominated in exponential-phase Delta ibaG V. cholerae cultures were not observed in stationary-phase cultures. The V. cholerae Delta ibaG mutant exhibited increased sensitivity to cell envelope stressors, including cell wall-acting antibiotics and bile, and was defective in intestinal colonization. Delta ibaG V. cholerae had reduced peptidoglycan and lipid II and altered outer membrane lipids, likely contributing to the mutant's morphological defects and sensitivity to envelope stressors. Transposon insertion sequencing analysis of ibaG's genetic interactions suggested that ibaG is involved in several processes involved in the generation and homeostasis of the cell envelope. Furthermore, copurification studies revealed that IbaG interacts with proteins containing iron-sulfur clusters or involved in their assembly. Collectively, our findings suggest that V. cholerae IbaG controls cell morphology and cell envelope integrity through its role in biogenesis or trafficking of iron-sulfur cluster proteins. IMPORTANCE BolA-like proteins are conserved across prokaryotes and eukaryotes. These proteins have been linked to a variety of phenotypes, but the pathways and mechanisms through which they act have not been extensively characterized. Here, we unraveled the role of the BolA-like protein IbaG in the cholera pathogen Vibrio cholerae. The absence of IbaG was associated with dramatic changes in cell morphology, sensitivity to envelope stressors, and intestinal colonization defects. IbaG was found to be required for biogenesis of several components of the V. cholerae cell envelope and to interact with numerous iron-sulfur cluster-containing proteins and factors involved in their assembly. Thus, our findings suggest that IbaG governs V. cholerae cell shape and cell envelope homeostasis through its effects on iron-sulfur proteins and associated pathways. The diversity of processes involving ironsulfur-containing proteins is likely a factor underlying the range of phenotypes associated with BolA family proteins.

Place, publisher, year, edition, pages
American Society for Microbiology (ASM), 2019
Keywords
BolA, IbaG, Vibrio cholerae, cell envelope, cell shape, iron-sulfur cluster
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-162888 (URN)10.1128/mBio.00790-19 (DOI)000481617000011 ()31289173 (PubMedID)
Available from: 2019-09-03 Created: 2019-09-03 Last updated: 2019-09-03Bibliographically approved
Howell, M., Aliashkevich, A., Sundararajan, K., Daniel, J. J., Lariviere, P. J., Goley, E. D., . . . Brown, P. J. B. (2019). Agrobacterium tumefaciens divisome proteins regulate the transition from polar growth to cell division. Molecular Microbiology, 111(4), 1074-1092
Open this publication in new window or tab >>Agrobacterium tumefaciens divisome proteins regulate the transition from polar growth to cell division
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2019 (English)In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 111, no 4, p. 1074-1092Article in journal (Refereed) Published
Abstract [en]

The mechanisms that restrict peptidoglycan biosynthesis to the pole during elongation and re-direct peptidoglycan biosynthesis to mid-cell during cell division in polar-growing Alphaproteobacteria are largely unknown. Here, we explore the role of early division proteins of Agrobacterium tumefaciens including three FtsZ homologs, FtsA and FtsW in the transition from polar growth to mid-cell growth and ultimately cell division. Although two of the three FtsZ homologs localize to mid-cell, exhibit GTPase activity and form co-polymers, only one, FtsZ(AT), is required for cell division. We find that FtsZ(AT) is required not only for constriction and cell separation, but also for initiation of peptidoglycan synthesis at mid-cell and cessation of polar peptidoglycan biosynthesis. Depletion of FtsZ(AT) in A. tumefaciens causes a striking phenotype: cells are extensively branched and accumulate growth active poles through tip splitting events. When cell division is blocked at a later stage by depletion of FtsA or FtsW, polar growth is terminated and ectopic growth poles emerge from mid-cell. Overall, this work suggests that A. tumefaciens FtsZ makes distinct contributions to the regulation of polar growth and cell division.

Place, publisher, year, edition, pages
Wiley-Blackwell Publishing Inc., 2019
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-158586 (URN)10.1111/mmi.14212 (DOI)000464655800015 ()30693575 (PubMedID)
Available from: 2019-05-27 Created: 2019-05-27 Last updated: 2019-05-27Bibliographically approved
Chauhan, D., Srivastava, P. A., Ritzl, B., Yennamalli, R. M., Cava, F. & Priyadarshini, R. (2019). Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1. Frontiers in Microbiology, 10, Article ID 1449.
Open this publication in new window or tab >>Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1
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2019 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, article id 1449Article in journal (Refereed) Published
Abstract [en]

Deinococcus radiodurans exhibits growth medium-dependent morphological variation in cell shape, but there is no evidence whether this phenomenon is observed in other members of the Deinococcaceae family. In this study, we isolated a red-pigmented, aerobic, Deinococcus indicus strain DR1 from Dadri wetland, India. This D. indicus strain exhibited cell-morphology transition from rod-shaped cells to multi-cell chains in a growth-medium-dependent fashion. In response to addition of 1% casamino acids in the minimal growth medium, rod-shaped cells formed multi-cell chains. Addition of all 20 amino acids to the minimal medium was able to recapitulate the phenotype. Specifically, a combination of L-methionine, L-lysine, L-aspartate, and L-threonine caused morphological alterations. The transition from rod shape to multi-cell chains is due to delay in daughter cell separation after cell division. Minimal medium supplemented with L-ornithine alone was able to cause cell morphology changes. Furthermore, a comparative UPLC analysis of PG fragments isolated from D. indicus cells propagated in different growth media revealed alterations in the PG composition. An increase in the overall cross-linkage of PG was observed in muropeptides from nutrient-rich TSB and NB media versus PYE medium. Overall our study highlights that environmental conditions influence PG composition and cell morphology in D. indicus.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
Deinococcus indicus, morphological alterations, amino acids, cell wall, muropeptides
National Category
Microbiology Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-161695 (URN)10.3389/fmicb.2019.01449 (DOI)000473576800001 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Kempe Foundations
Available from: 2019-08-05 Created: 2019-08-05 Last updated: 2019-08-05Bibliographically approved
Kumar, K. & Cava, F. (2019). Chromatographic analysis of peptidoglycan samples with the aid of a chemometric technique: introducing a novel analytical procedure to classify bacterial cell wall collection. Analytical Methods, 11(12), 1671-1679
Open this publication in new window or tab >>Chromatographic analysis of peptidoglycan samples with the aid of a chemometric technique: introducing a novel analytical procedure to classify bacterial cell wall collection
2019 (English)In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 11, no 12, p. 1671-1679Article in journal (Refereed) Published
Abstract [en]

The technical development of liquid chromatography has provided the necessary sensitivity to characterise peptidoglycan samples. However, the analysis of large numbers of complex chromatographic data sets without the aid of a proper chemometric technique is a laborious task, carrying a high risk of losing important biochemical information. The present work describes the development of a simple analytical procedure using self-organising map (SOM) analysis to analyse the large number of complex chromatographic data sets from bacterial peptidoglycan samples. SOM analysis essentially maps the samples to a hexagonal sheet based on their compositional similarity, and thus provides an approach to classify the bacterial cell wall collection in an unsupervised manner. The utility of the proposed approach was successfully validated by analysing peptidoglycan samples belonging to the Alphaproteobacterium class. The classification results achieved with SOM analysis were found to correlate well with their relative similarity in peptidoglycan compositions. In summary, the SOM analysis-based analytical procedure is shown to be useful towards automatising the analyses of chromatographic data sets of peptidoglycan samples from bacterial collections.

National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-158380 (URN)10.1039/c8ay02501k (DOI)000463892500011 ()
Available from: 2019-04-29 Created: 2019-04-29 Last updated: 2019-04-29Bibliographically approved
Bernardo-Garcia, N., Sánchez-Murcia, P. A., Espaillat, A., Martínez-Caballero, S., Cava, F., Hermoso, J. A. & Gago, F. (2019). Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Organic and biomolecular chemistry, 17(17), 4350-4358
Open this publication in new window or tab >>Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase
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2019 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 17, no 17, p. 4350-4358Article in journal (Refereed) Published
Abstract [en]

Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound to an active-site lysine to form an internal aldimine. The crystal structure of BsAlaR grown in the presence of Tris lacks this covalent linkage and the PLP cofactor appears deformylated. However, loss of activity in a Tris buffer only occurred after the solution was frozen prior to carrying out the enzymatic assay. This evidence strongly suggests that Tris can access the active site at subzero temperatures and behave as an alternate racemase substrate leading to mechanism-based enzyme inactivation, a hypothesis that is supported by additional X-ray structures and theoretical results from QM/ MM calculations. Taken together, our findings highlight a possibly underappreciated role for a common buffer component widely used in biochemical and biophysical experiments.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2019
National Category
Organic Chemistry Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-159052 (URN)10.1039/c9ob00223e (DOI)000465953500024 ()30977502 (PubMedID)
Available from: 2019-05-21 Created: 2019-05-21 Last updated: 2019-05-21Bibliographically approved
Murphy, S. G., Alvarez, L., Adams, M. C., Liu, S., Chappie, J. S., Cava, F. & Dorr, T. (2019). Endopeptidase Regulation as a Novel Function of the Zur-Dependent Zinc Starvation Response. mBio, 10(1), Article ID e02620-18.
Open this publication in new window or tab >>Endopeptidase Regulation as a Novel Function of the Zur-Dependent Zinc Starvation Response
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2019 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 1, article id e02620-18Article in journal (Refereed) Published
Abstract [en]

The cell wall is a strong, yet flexible, meshwork of peptidoglycan (PG) that gives a bacterium structural integrity. To accommodate a growing cell, the wall is remodeled by both PG synthesis and degradation. Vibrio cholerae encodes a group of three nearly identical zinc-dependent endopeptidases (EPs) that are predicted to hydrolyze PG to facilitate cell growth. Two of these (ShyA and ShyC) are conditionally essential housekeeping EPs, while the third (ShyB) is not expressed under standard laboratory conditions. To investigate the role of ShyB, we conducted a transposon screen to identify mutations that activate shyB transcription. We found that shyB is induced as part of the Zur-mediated zinc starvation response, a mode of regulation not previously reported for cell wall lytic enzymes. In vivo, ShyB alone was sufficient to sustain cell growth in low-zinc environments. In vitro, ShyB retained its D, D-endopeptidase activity against purified sacculi in the presence of the metal chelator EDTA at concentrations that inhibit ShyA and ShyC. This insensitivity to metal chelation is likely what enables ShyB to substitute for other EPs during zinc starvation. Our survey of transcriptomic data from diverse bacteria identified other candidate Zur-regulated EPs, suggesting that this adaptation to zinc starvation is employed by other Gram-negative bacteria. IMPORTANCE Bacteria encode a variety of adaptations that enable them to survive during zinc starvation, a condition which is encountered both in natural environments and inside the human host. In Vibrio cholerae, the causative agent of the diarrheal disease cholera, we have identified a novel member of this zinc starvation response, a cell wall hydrolase that retains function and is conditionally essential for cell growth in low-zinc environments. Other Gram-negative bacteria contain homologs that appear to be under similar regulatory control. These findings are significant because they represent, to our knowledge, the first evidence that zinc homeostasis influences cell wall turnover. Anti-infective therapies commonly target the bacterial cell wall; therefore, an improved understanding of how the cell wall adapts to host-induced zinc starvation could lead to new antibiotic development. Such therapeutic interventions are required to combat the rising threat of drug-resistant infections.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2019
Keywords
Gram-negative, Vibrio cholerae, cell wall, hydrolase, metalloproteins, peptidoglycan, zinc starvation
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-157540 (URN)10.1128/mBio.02620-18 (DOI)000460314300056 ()30782657 (PubMedID)
Available from: 2019-04-01 Created: 2019-04-01 Last updated: 2019-04-01Bibliographically approved
Hsu, Y.-P., Hall, E., Booher, G., Murphy, B., Radkov, A. D., Yablonowski, J., . . . VanNieuwenhze, M. S. (2019). Fluorogenic D-amino acids enable real-time monitoring of peptidoglycan biosynthesis and high-throughput transpeptidation assays. Nature Chemistry, 11(4), 335-341
Open this publication in new window or tab >>Fluorogenic D-amino acids enable real-time monitoring of peptidoglycan biosynthesis and high-throughput transpeptidation assays
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2019 (English)In: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 11, no 4, p. 335-341Article in journal (Refereed) Published
Abstract [en]

Peptidoglycan is an essential cell wall component that maintains the morphology and viability of nearly all bacteria. Its biosynthesis requires periplasmic transpeptidation reactions, which construct peptide crosslinkages between polysaccharide chains to endow mechanical strength. However, tracking the transpeptidation reaction in vivo and in vitro is challenging, mainly due to the lack of efficient, biocompatible probes. Here, we report the design, synthesis and application of rotor-fluorogenic D-amino acids (RfDAAs), enabling real-time, continuous tracking of transpeptidation reactions. These probes allow peptidoglycan biosynthesis to be monitored in real time by visualizing transpeptidase reactions in live cells, as well as real-time activity assays of D,D- and L,D-transpeptidases and sortases in vitro. The unique ability of RfDAAs to become fluorescent when incorporated into peptidoglycan provides a powerful new tool to study peptidoglycan biosynthesis with high temporal resolution and prospectively enable high-throughput screening for inhibitors of peptidoglycan biosynthesis.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-157944 (URN)10.1038/s41557-019-0217-x (DOI)000462046600011 ()30804500 (PubMedID)
Available from: 2019-04-18 Created: 2019-04-18 Last updated: 2019-04-18Bibliographically approved
Irazoki, O., Hernandez, S. B. & Cava, F. (2019). Peptidoglycan Muropeptides: Release, Perception, and Functions as Signaling Molecules. Frontiers in Microbiology, 10, Article ID 500.
Open this publication in new window or tab >>Peptidoglycan Muropeptides: Release, Perception, and Functions as Signaling Molecules
2019 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, article id 500Article, review/survey (Refereed) Published
Abstract [en]

Peptidoglycan (PG) is an essential molecule for the survival of bacteria, and thus, its biosynthesis and remodeling have always been in the spotlight when it comes to the development of antibiotics. The peptidoglycan polymer provides a protective function in bacteria, but at the same time is continuously subjected to editing activities that in some cases lead to the release of peptidoglycan fragments (i.e., muropeptides) to the environment. Several soluble muropeptides have been reported to work as signaling molecules. In this review, we summarize the mechanisms involved in muropeptide release (PG breakdown and PG recycling) and describe the known PG-receptor proteins responsible for PG sensing. Furthermore, we overview the role of muropeptides as signaling molecules, focusing on the microbial responses and their functions in the host beyond their immunostimulatory activity.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
peptidoglycan, PG cleaving enzymes, PG recycling, PG receptors, signaling functions, bacterial interactions
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-158090 (URN)10.3389/fmicb.2019.00500 (DOI)000462687700001 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationThe Kempe Foundations
Available from: 2019-04-15 Created: 2019-04-15 Last updated: 2019-04-15Bibliographically approved
Bueno, E., Sit, B., Waldor, M. K. & Cava, F. (2018). Anaerobic nitrate reduction divergently governs population expansion of the enteropathogen Vibrio cholerae [Letter to the editor]. Nature Microbiology, 3(12), 1346-1353
Open this publication in new window or tab >>Anaerobic nitrate reduction divergently governs population expansion of the enteropathogen Vibrio cholerae
2018 (English)In: Nature Microbiology, E-ISSN 2058-5276, Vol. 3, no 12, p. 1346-1353Article in journal, Letter (Refereed) Published
Abstract [en]

To survive and proliferate in the absence of oxygen, many enteric pathogens can undergo anaerobic respiration within the host by using nitrate (NO3-) as an electron acceptor(1,2). In these bacteria, NO3- is typically reduced by a nitrate reductase to nitrite (NO2-), a toxic intermediate that is further reduced by a nitrite reductase(3). However, Vibrio cholerae, the intestinal pathogen that causes cholera, lacks a nitrite reductase, leading to NO2- accumulation during nitrate reduction 4(.) Thus, V. cholerae is thought to be unable to undergo NO3-(-)dependent anaerobic respiration(4). Here, we show that during hypoxic growth, NO3- reduction in V. cholerae divergently affects bacterial fitness in a manner dependent on environmental pH. Remarkably, in alkaline conditions, V. cholerae can reduce NO3- to support population growth. Conversely, in acidic conditions, accumulation of NO2- from NO3- reduction simultaneously limits population expansion and preserves cell viability by lowering fermentative acid production. Interestingly, other bacterial species such as Salmonella typhimurium, enterohaemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium also reproduced this pH-dependent response, suggesting that this mechanism might be conserved within enteric pathogens. Our findings explain how a bacterial pathogen can use a single redox reaction to divergently regulate population expansion depending on the fluctuating environmental pH.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-154339 (URN)10.1038/s41564-018-0253-0 (DOI)000451259600007 ()30275512 (PubMedID)
Available from: 2018-12-18 Created: 2018-12-18 Last updated: 2018-12-18Bibliographically approved
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