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Cava, Felipe
Publications (10 of 73) Show all publications
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
Alvarez, L. & Cava, F. (2018). Bacterial Competition Assay Based on Extracellular D-amino Acid Production. Bio-protocol, 8(7), Article ID e2787.
Open this publication in new window or tab >>Bacterial Competition Assay Based on Extracellular D-amino Acid Production
2018 (English)In: Bio-protocol, E-ISSN 2331-8325, Vol. 8, no 7, article id e2787Article in journal (Refereed) Published
Abstract [en]

Bacteria live in polymicrobial communities under tough competition. To persist in a specific niche many species produce toxic extracellular effectors as a strategy to interfere with the growth of nearby microbes. One of such effectors are the non-canonical D-amino acids. Here we describe a method to test the effect of D-amino acid production in fitness/survival of bacterial subpopulations within a community. Co-cultivation methods usually involve the growth of the competing bacteria in the same container. Therefore, within such mixed cultures the effect on growth caused by extracellular metabolites cannot be distinguished from direct physical interactions between species (e.g., T6SS effectors). However, this problem can be easily solved by using a filtration unit that allows free diffusion of small metabolites, like L- and D-amino acids, while keeping the different subpopulations in independent compartments. With this method, we have demonstrated that D-arginine is a bactericide effector produced by Vibrio cholerae, which strongly influences survival of diverse microbial subpopulations. Moreover, D-arginine can be used as a cooperative instrument in mixed Vibrio communities to protect non-producing members from competing bacteria.

Place, publisher, year, edition, pages
BIO-PROTOCOL, 2018
Keywords
D-amino acid, Competition, Co-cultivation, Viability, D-amino acid oxidase (DAAO) assay
Identifiers
urn:nbn:se:umu:diva-157351 (URN)10.21769/BioProtoc.2787 (DOI)000457929800007 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Kempe Foundations
Available from: 2019-03-15 Created: 2019-03-15 Last updated: 2019-03-15Bibliographically approved
Alvarez, L., Aliashkevich, A., de Pedro, M. A. & Cava, F. (2018). Bacterial secretion of D-arginine controls environmental microbial biodiversity. The ISME Journal, 12(2), 438-450
Open this publication in new window or tab >>Bacterial secretion of D-arginine controls environmental microbial biodiversity
2018 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 2, p. 438-450Article in journal (Refereed) Published
Abstract [en]

Bacteria face tough competition in polymicrobial communities. To persist in a specific niche, many species produce toxic extracellular effectors to interfere with the growth of nearby microbes. These effectors include the recently reported non-canonical D-amino acids (NCDAAs). In Vibrio cholerae, the causative agent of cholera, NCDAAs control cell wall integrity in stationary phase. Here, an analysis of the composition of the extracellular medium of V. cholerae revealed the unprecedented presence of D-Arg. Compared with other D-amino acids, D-Arg displayed higher potency and broader toxicity in terms of the number of bacterial species affected. Tolerance to D-Arg was associated with mutations in the phosphate transport and chaperone systems, whereas D-Met lethality was suppressed by mutations in cell wall determinants. These observations suggest that NCDAAs target different cellular processes. Finally, even though virtually all Vibrio species are tolerant to D-Arg, only a few can produce this D-amino acid. Indeed, we demonstrate that D-Arg may function as part of a cooperative strategy in vibrio communities to protect non-producing members from competing bacteria. Because NCDAA production is widespread in bacteria, we anticipate that D-Arg is a relevant modulator of microbial subpopulations in diverse ecosystems.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:umu:diva-144335 (URN)10.1038/ismej.2017.176 (DOI)000422779100013 ()29028003 (PubMedID)
Available from: 2018-02-08 Created: 2018-02-08 Last updated: 2018-06-09Bibliographically approved
Yadav, A. K., Espaillat, A. & Cava, F. (2018). Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats. Frontiers in Microbiology, 9, Article ID 2064.
Open this publication in new window or tab >>Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats
2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2064Article, review/survey (Refereed) Published
Abstract [en]

Bacterial cells are surrounded by an exoskeleton-like structure, the cell wall, composed primarily of the peptidoglycan (PG) sacculus. This structure is made up of glycan strands cross-linked by short peptides generating a covalent mesh that shapes bacteria and prevents their lysis due to their high internal osmotic pressure. Even though the PG is virtually universal in bacteria, there is a notable degree of diversity in its chemical structure. Modifications in both the sugars and peptides are known to be instrumental for bacteria to cope with diverse environmental challenges. In this review, we summarize and discuss the cell wall strategies to withstand biotic and abiotic environmental insults such as the effect of antibiotics targeting cell wall enzymes, predatory PG hydrolytic proteins, and PG signaling systems. Finally we will discuss the opportunities that species-specific PG variability might open to develop antimicrobial therapies.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
peptidoglycan, lysozyme, antibiotic resistance, innate immunity, plasticity
National Category
Microbiology in the medical area Microbiology
Identifiers
urn:nbn:se:umu:diva-151777 (URN)10.3389/fmicb.2018.02064 (DOI)000443238500001 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationThe Kempe Foundations
Available from: 2018-09-14 Created: 2018-09-14 Last updated: 2018-09-14Bibliographically approved
Kumar, K. & Cava, F. (2018). Integrating network analysis with chromatography: introducing a novel chemometry-chromatography based analytical procedure to classify the bacterial cell wall collection. Analytical Methods, 10(10), 1172-1180
Open this publication in new window or tab >>Integrating network analysis with chromatography: introducing a novel chemometry-chromatography based analytical procedure to classify the bacterial cell wall collection
2018 (English)In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 10, no 10, p. 1172-1180Article in journal (Refereed) Published
Abstract [en]

The present work integrates network analysis with chromatography and proposes a novel analytical procedure to classify the bacterial cell wall collection. The network analysis model can capture the heterogeneity present in the datasets and hence can provide unsupervised classification. The proposed approach is successfully applied for classifying the peptidoglycan samples of certain bacterial collections belonging to the class of Alphaproteobacteria. The obtained classification results are found to correlate well with their relative similarity in the peptidoglycan compositions. In summary, the proposed network analysis approach can be helpful in automatizing the bacterial cell wall analysis. The proposed approach can be useful to accelerate the research related to understanding the morphology of bacterial cell walls, host-pathogen interaction and development of effective antibiotics.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-147835 (URN)10.1039/c7ay02863f (DOI)000430960200007 ()
Available from: 2018-05-18 Created: 2018-05-18 Last updated: 2018-06-09Bibliographically approved
Aliashkevich, A., Alvarez, L. & Cava, F. (2018). New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems. Frontiers in Microbiology, 9, Article ID 683.
Open this publication in new window or tab >>New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems
2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 683Article, review/survey (Refereed) Published
Abstract [en]

In the environment bacteria share their habitat with a great diversity of organisms, from microbes to humans, animals and plants. In these complex communities, the production of extracellular effectors is a common strategy to control the biodiversity by interfering with the growth and/or viability of nearby microbes. One of such effectors relies on the production and release of extracellular D-amino acids which regulate diverse cellular processes such as cell wall biogenesis, biofilm integrity, and spore germination. Non-canonical D-amino acids are mainly produced by broad spectrum racemases (Bsr). Bsr's promiscuity allows it to generate high concentrations of D-amino acids in environments with variable compositions of L-amino acids. However, it was not clear until recent whether these molecules exhibit divergent functions. Here we review the distinctive biological roles of D-amino acids, their mechanisms of action and their modulatory properties of the biodiversity of complex eco-systems.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
D-amino acids, D-methionine, D-arginine, bacteria, cell wall, Vibrio cholerae
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-147303 (URN)10.3389/fmicb.2018.00683 (DOI)000429347700001 ()29681896 (PubMedID)
Available from: 2018-05-28 Created: 2018-05-28 Last updated: 2018-06-09Bibliographically approved
Orrego, A. H., Lopez-Gallego, F., Espaillat, A., Cava, F., Guisan, J. M. & Rocha-Martin, J. (2018). One‐step Synthesis of α‐Keto Acids from Racemic Amino Acids by A Versatile Immobilized Multienzyme Cell‐free System. ChemCatChem, 10(14), 3002-3011
Open this publication in new window or tab >>One‐step Synthesis of α‐Keto Acids from Racemic Amino Acids by A Versatile Immobilized Multienzyme Cell‐free System
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2018 (English)In: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 10, no 14, p. 3002-3011Article in journal (Refereed) Published
Abstract [en]

The elevated value of α‐keto acids has pushed scientists to explore more efficient and less expensive alternatives for their synthesis. In this work, an immobilized tri‐enzyme system that produced α‐keto acids in “one‐pot” from l‐ or racemic mixtures of diverse amino acids was presented. The system combined a broad‐spectrum amino acid racemase (BsrV), a d‐amino acid oxidase (DAAO) and catalase (CAT). BsrV racemized l‐amino acids into their d‐enantiomers, DAAO catalyzed the stereospecific oxidative deamination of the d‐amino acids into their corresponding α‐keto acids, ammonium ion, and H2O2. Finally, CAT converted the inactivating H2O2 into H2O and O2, which can be reused by the oxidase reaction. BsrV thermal stability was improved 3,300‐fold by immobilizing the enzyme on glyoxyl‐activated agarose beads. DAAO and CAT were co‐immobilized on agarose beads functionalized with glutaraldehyde groups for enhancing their stabilities and eliminating H2O2 in a much more effective way. To show the versatility of this system, racemic mixtures of amino acids were converted in their corresponding α‐keto acids. The coupling of the three immobilized enzymes permitted conversions of approximately 99 % through a dynamic kinetic resolution process. This system conserved 100 % of its initial effectiveness after 8 reaction cycles. Collectively, our innovative tri‐enzyme system for the synthesis of α‐keto acids opens the door for a cheapening in the production of many pharmaceutical and cosmetics.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2018
Keywords
biocatalysis, dynamic kinetic resolution, immobilization, PLP-dependent enzymes, alpha-keto acids
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-150721 (URN)10.1002/cctc.201800359 (DOI)000439756600010 ()
Available from: 2018-08-29 Created: 2018-08-29 Last updated: 2018-08-29Bibliographically approved
Kumar, K. & Cava, F. (2018). Principal coordinate analysis assisted chromatographic analysis of bacterial cell wall collection: a robust classification approach. Analytical Biochemistry, 550, 8-14
Open this publication in new window or tab >>Principal coordinate analysis assisted chromatographic analysis of bacterial cell wall collection: a robust classification approach
2018 (English)In: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 550, p. 8-14Article in journal (Refereed) Published
Abstract [en]

In the present work, Principal coordinate analysis (PCoA) is introduced to develop a robust model to classify the chromatographic data sets of peptidoglycan sample. PcoA captures the heterogeneity present in the data sets by using the dissimilarity matrix as input. Thus, in principle, it can even capture the subtle differences in the bacterial peptidoglycan composition and can provide a more robust and fast approach for classifying the bacterial collection and identifying the novel cell wall targets for further biological and clinical studies. The utility of the proposed approach is successfully demonstrated by analysing the two different kind of bacterial collections. The first set comprised of peptidoglycan sample belonging to different subclasses of Alphaproteobacteria. Whereas, the second set that is relatively more intricate for the chemometric analysis consist of different wild type Vibrio Cholerae and its mutants having subtle differences in their peptidoglycan composition. The present work clearly proposes a useful approach that can classify the chromatographic data sets of chromatographic peptidoglycan samples having subtle differences. Furthermore, present work clearly suggest that PCoA can be a method of choice in any data analysis workflow.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Principal coordinate analysis, Classification, Peptidoglycans, Chromatography, Principal component analysis, Data heterogeneity
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-150872 (URN)10.1016/j.ab.2018.04.008 (DOI)000436056600002 ()29649471 (PubMedID)2-s2.0-85045282388 (Scopus ID)
Available from: 2018-08-31 Created: 2018-08-31 Last updated: 2018-08-31Bibliographically approved
Chahlafi, Z., Alvarez, L., Cava, F. & Berenguer, J. (2018). The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus. Environmental Microbiology, 20(10), 3851-3861
Open this publication in new window or tab >>The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus
2018 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 10, p. 3851-3861Article in journal (Refereed) Published
Abstract [en]

In many Thermus thermophilus strains, nitrate respiration is encoded in mobile genetic regions, along with regulatory circuits that modulate its expression based on anoxia and nitrate presence. The oxygen‐responsive system has been identified as the product of the dnrST (dnr) operon located immediately upstream of the nar operon (narCGHJIKT), which encodes the nitrate reductase (NR) and nitrate/nitrite transporters. In contrast, the nature of the nitrate sensory system is not known. Here, we analyse the putative nitrate‐sensing role of the bicistronic drp operon (drpAB) present downstream of the nar operon in most denitrifying Thermus spp. Expression of drp was found to depend on the master regulator DnrT, whereas the absence of DrpA or DrpB increased the expression of both DnrS and DnrT and, concomitantly, of the NR. Absence of both proteins made expression from the dnr and nar operons independent of nitrate. Polyclonal antisera allowed us to identify DrpA as a periplasmic protein and DrpB as a membrane protein, with capacity to bind to the cytoplasmic membrane. Here, we propose a role for DrpA/DrpB as nitrate sensors during denitrification.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-153131 (URN)10.1111/1462-2920.14400 (DOI)000447549700029 ()30187633 (PubMedID)2-s2.0-85054313930 (Scopus ID)
Available from: 2018-11-09 Created: 2018-11-09 Last updated: 2018-11-09Bibliographically approved
Castanheira, S., Cestero, J. J., Rico-Perez, G., Garcia, P., Cava, F., Ayala, J. A., . . . Garcia-del Portillo, F. (2017). A Specialized Peptidoglycan Synthase Promotes Salmonella Cell Division inside Host Cells. mBio, 8(6), Article ID e01685-17.
Open this publication in new window or tab >>A Specialized Peptidoglycan Synthase Promotes Salmonella Cell Division inside Host Cells
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2017 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 8, no 6, article id e01685-17Article in journal (Refereed) Published
Abstract [en]

Bacterial cell division has been studied extensively under laboratory conditions. Despite being a key event in the bacterial cell cycle, cell division has not been explored in vivo in bacterial pathogens interacting with their hosts. We discovered in Salmonella enterica serovar Typhimurium a gene absent in nonpathogenic bacteria and encoding a peptidoglycan synthase with 63% identity to penicillin-binding protein 3 (PBP3). PBP3 is an essential cell division-specific peptidoglycan synthase that builds the septum required to separate daughter cells. Since S. Typhimurium carries genes that encode a PBP3 paralog-which we named PBP3(SAL)-and PBP3, we hypothesized that there are different cell division events in host and nonhost environments. To test this, we generated S. Typhimurium isogenic mutants lacking PBP3(SAL) or the hitherto considered essential PBP3. While PBP3 alone promotes cell division under all conditions tested, the mutant producing only PBP3(SAL) proliferates under acidic conditions (pH <= 5.8) but does not divide at neutral pH. PBP3(SAL) production is tightly regulated with increased levels as bacteria grow in media acidified up to pH 4.0 and in intracellular bacteria infecting eukaryotic cells. PBP3(SAL) activity is also strictly dependent on acidic pH, as shown by beta-lactam antibiotic binding assays. Live-cell imaging microscopy revealed that PBP3(SAL) alone is sufficient for S. Typhimurium to divide within phagosomes of the eukaryotic cell. Additionally, we detected much larger amounts of PBP3(SAL) than those of PBP3 in vivo in bacteria colonizing mouse target organs. Therefore, PBP3(SAL) evolved in S. Typhimurium as a specialized peptidoglycan synthase promoting cell division in the acidic intraphagosomal environment. IMPORTANCE During bacterial cell division, daughter cells separate by a transversal structure known as the division septum. The septum is a continuum of the cell wall and therefore is composed of membrane(s) and a peptidoglycan layer. To date, actively growing bacteria were reported to have only a "cell division-specific" peptidoglycan synthase required for the last steps of septum formation and consequently, essential for bacterial life. Here, we discovered that Salmonella enterica has two peptidoglycan synthases capable of synthesizing the division septum. One of these enzymes, PBP3(SAL), is present only in bacterial pathogens and evolved in Salmonella to function exclusively in acidic environments. PBP3(SAL) is used preferentially by Salmonella to promote cell division in vivo in mouse target organs and inside acidified phagosomes. Our data challenge the concept of only one essential cell division-specific peptidoglycan synthase and demonstrate that pathogens can divide in defined host locations using alternative mechanisms.

Keywords
Salmonella, cell division, intracellular pathogens, penicillin-binding proteins, peptidoglycan, LPORTILLO FG, 1990, JOURNAL OF BACTERIOLOGY, V172, P5863 tsenko KA, 2000, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-144122 (URN)10.1128/mBio.01685-17 (DOI)000418889500036 ()
Available from: 2018-01-23 Created: 2018-01-23 Last updated: 2018-06-09Bibliographically approved
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