umu.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Espaillat, Akbar, master
Biography [eng]

The goal of my doctoral project is to explore the role of peptidoglycan accessory activities present in different bacteria and understand their implications on the bacterial lifestyle. This cell wall modifying activities could be potentially good clinical targets in case they could be implicated in the adaptation of some pathogen to the host.

Publications (10 of 13) Show all publications
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
Show others...
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
Espaillat, A. (2019). Uncovering novel cell wall chemistries in gram negative bacteria: from development or dedicated peptidoglycan chemometric tools to functional genomics. (Doctoral dissertation). Umeå: Umeå University
Open this publication in new window or tab >>Uncovering novel cell wall chemistries in gram negative bacteria: from development or dedicated peptidoglycan chemometric tools to functional genomics
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacteria are surrounded by an external cell wall whose main component is a polymeric net-like structure called the peptidoglycan (PG) or murein sacculus. PG plays crucial roles in bacterial physiology (eg morphogenesis, growth fitness and regulation of innate immunity). Based on the characteristics of this macromolecule, bacteria are grouped as gram negative and positive. Gram negatives present a thin PG layer in the periplasmic space, while Gram positive bacteria contain one thick multi-layered sacculus covering the cytoplasmic membrane. Although the PG sacculus is widely conserved between bacteria, variations in its chemical structure (ie sugars and peptide components) have been reported as a coping mechanism to stress. For example, V. choleraeis able to downregulate PG biosynthesis through non-canonical D-amino acids (NCDAAs) cell wall editing when entering stationary phase. NCDAAs production relies on Bsr enzymes, broad spectrum racemases which are expressed in V. cholerae under the control of stress sigma factor RpoS. In this thesis, we present a comprehensive study that allows us to determine the basic structural and biochemical features required for prominent D-amino acid production by Bsr enzymes.

V. cholerae’s PG editing by NCDAAs revealed the existence of previously unappreciated  chemical modification in the cell wall of bacteria. Such an observation made us question whether the latest technology could reveal, otherwise undetectable, novel PG traits and furthermore, revisit the existence of murein in bacteria which were previously defined as PG-less. Finally, these studies would promote a global assessment of the degree of PG-chemical variability at a Kingdom scale.

On the search for novel functional chemistries and associated mechanisms of cell wall regulation, we analysed the cell wall of hundreds of different species. Here, I present two proof of concept studies: i) investigation of the existence of PG in the Plantomycetes Kuenenia stuttgartiensis, a species previously classified as PG-less; and ii) PG chemical diversity within Class Alphaproteobacteria. To do so, we developed and experimentally validated an innovative chemometric pipeline to rapidly analyse large PG datasets. Chemometric analyses revealed 3 PG clusters within Alphaproteobacteria, which included unprecedented PG modifications widely conserved in family Acetobacteria: amidation at the α-(L)-carboxyl of meso-diaminopimelic acid and the presence of (1–3) cross-linked muropeptides between L-Ala and D-(meso)-diaminopimelate residues from adjacent moieties. Fluctuations of the relative abundance of these PG traits were growth phase and media composition dependent. Functional studies demonstrated that Acetobacteria atypical muropeptides enabled cellular protection against Type VI secreted endopeptidases and negatively affected innate immune system recognition suggesting relevant functional roles in the environmental adaptability of these bacteria.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2019. p. 63
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 2027
Keywords
Bacteria, cell wall, peptidoglycan, peptidoglycan variations, D-amino acids
National Category
Microbiology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-157645 (URN)978-91-7855-045-6 (ISBN)
Public defence
2019-04-26, Hörsal d Unod T 9, Umeå University Hospital, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2019-04-05 Created: 2019-03-28 Last updated: 2019-04-05Bibliographically 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
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
Show others...
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
Maciejewska, B., Roszniowski, B., Espaillat, A., Kęsik-Szeloch, A., Majkowska-Skrobek, G., Kropinski, A., . . . Drulis-Kawa, Z. (2017). Klebsiella phages representing a novel clade of viruses with an unknown DNA modification and biotechnologically interesting enzymes. Applied Microbiology and Biotechnology, 101(2), 673-684
Open this publication in new window or tab >>Klebsiella phages representing a novel clade of viruses with an unknown DNA modification and biotechnologically interesting enzymes
Show others...
2017 (English)In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 101, no 2, p. 673-684Article in journal (Refereed) Published
Abstract [en]

Lytic bacteriophages and phage-encoded endolysins (peptidoglycan hydrolases) provide a source for the development of novel antimicrobial strategies. In the present study, we focus on the closely related (96 % DNA sequence identity) environmental myoviruses vB_KpnM_KP15 (KP15) and vB_KpnM_KP27 (KP27) infecting multidrug-resistant Klebsiella pneumoniae and Klebsiella oxytoca strains. Their genome organisation and evolutionary relationship are compared to Enterobacter phage phiEap-3 and Klebsiella phages Matisse and Miro. Due to the shared and distinct evolutionary history of these phages, we propose to create a new phage genus BKp15virus^ within the Tevenvirinae subfamily. In silico genome analysis reveals two unique putative homing endonucleases of KP27 phage, probably involved in unrevealed mechanism of DNA modification and resistance to restriction digestion, resulting in a broader host spectrum. Additionally, we identified in KP15 and KP27 a complete set of lysis genes, containing holin, antiholin, spanin and endolysin. By turbidimetric assays on permeabilized Gram-negative strains, we verified the ability of the KP27 endolysin to destroy the bacterial peptidoglycan. We confirmed high stability, absence of toxicity on a human epithelial cell line and the enzymatic specificity of endolysin, which was found to possess endopeptidase activity, cleaving the peptide stem between L-alanine and D-glutamic acid.

Keywords
Bacteriophage, Klebsiella spp., Kp15virus, Thermostable endolysin, DNA modification
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-128279 (URN)10.1007/s00253-016-7928-3 (DOI)000392060500017 ()2-s2.0-84991832942 (Scopus ID)
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2018-06-09Bibliographically approved
Maciejewska, B., Zrubek, K., Espaillat, A., Wisniewska, M., Rembacz, K. P., Cava, F., . . . Drulis-Kawa, Z. (2017). Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue. Scientific Reports, 7, Article ID 14501.
Open this publication in new window or tab >>Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue
Show others...
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 14501Article in journal (Refereed) Published
Abstract [en]

Endolysins are peptidoglycan-degrading enzymes utilized by bacteriophages to release the progeny from bacterial cells. The lytic properties of phage endolysins make them potential antibacterial agents for medical and industrial applications. Here, we present a comprehensive characterization of phage AP3 modular endolysin (AP3gp15) containing cell wall binding domain and an enzymatic domain (DUF3380 by BLASTP), both widespread and conservative. Our structural analysis demonstrates the low similarity of an enzymatic domain to known lysozymes and an unusual catalytic centre characterized by only a single glutamic acid residue and no aspartic acid. Thus, our findings suggest distinguishing a novel class of muralytic enzymes having the activity and catalytic centre organization of DUF3380. The lack of amino acid sequence homology between AP3gp15 and other known muralytic enzymes may reflect the evolutionary convergence of analogous glycosidases. Moreover, the broad antibacterial spectrum, lack of cytotoxic effect on human cells and the stability characteristics of AP3 endolysin advocate for its future application development.

National Category
Biocatalysis and Enzyme Technology
Identifiers
urn:nbn:se:umu:diva-142247 (URN)10.1038/s41598-017-14797-9 (DOI)000414415000001 ()
Available from: 2017-12-11 Created: 2017-12-11 Last updated: 2018-06-09Bibliographically approved
Kumar, K., Espaillat, A. & Cava, F. (2017). PG-metrics: a chemometric-based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability. PLoS ONE, 12(10), Article ID e0186197.
Open this publication in new window or tab >>PG-metrics: a chemometric-based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability
2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 10, article id e0186197Article in journal (Refereed) Published
Abstract [en]

Bacteria cells are protected from osmotic and environmental stresses by an exoskeleton-like polymeric structure called peptidoglycan ( PG) or murein sacculus. This structure is fundamental for bacteria's viability and thus, the mechanisms underlying cell wall assembly and how it is modulated serve as targets for many of our most successful antibiotics. Therefore, it is now more important than ever to understand the genetics and structural chemistry of the bacterial cell walls in order to find new and effective methods of blocking it for the treatment of disease. In the last decades, liquid chromatography and mass spectrometry have been demonstrated to provide the required resolution and sensitivity to characterize the fine chemical structure of PG. However, the large volume of data sets that can be produced by these instruments today are difficult to handle without a proper data analysis work-flow. Here, we present PG-metrics, a chemometric based pipeline that allows fast and easy classification of bacteria according to their muropeptide chromatographic profiles and identification of the subjacent PG chemical variability between e.g. bacterial species, growth conditions and, mutant libraries. The pipeline is successfully validated here using PG samples from different bacterial species and mutants in cell wall proteins. The obtained results clearly demonstrated that PG-metrics pipeline is a valuable bioanalytical tool that can lead us to cell wall classification and biomarker discovery.

Place, publisher, year, edition, pages
Public library science, 2017
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-141817 (URN)10.1371/journal.pone.0186197 (DOI)000413167500024 ()29040278 (PubMedID)
Available from: 2017-11-27 Created: 2017-11-27 Last updated: 2019-03-28Bibliographically approved
Ghssein, G., Brutesco, C., Ouerdane, L., Fojcik, C., Izaute, A., Wang, S., . . . Arnoux, P. (2016). Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus. Science, 352(6289), 1105-1109
Open this publication in new window or tab >>Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus
Show others...
2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6289, p. 1105-1109Article in journal (Refereed) Published
Abstract [en]

Metal acquisition is a vital microbial process in metal-scarce environments, such as inside a host. Using metabolomic exploration, targeted mutagenesis, and biochemical analysis, we discovered an operon in Staphylococcus aureus that encodes the different functions required for the biosynthesis and trafficking of a broad-spectrum metallophore related to plant nicotianamine (here called staphylopine). The biosynthesis of staphylopine reveals the association of three enzyme activities: a histidine racemase, an enzyme distantly related to nicotianamine synthase, and a staphylopine dehydrogenase belonging to the DUF2338 family. Staphylopine is involved in nickel, cobalt, zinc, copper, and iron acquisition, depending on the growth conditions. This biosynthetic pathway is conserved across other pathogens, thus underscoring the importance of this metal acquisition strategy in infection.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-123368 (URN)10.1126/science.aaf1018 (DOI)000376480800040 ()27230378 (PubMedID)
Available from: 2016-07-05 Created: 2016-07-01 Last updated: 2019-03-28Bibliographically approved
Espaillat, A., Forsmo, O., El Biari, K., Björk, R., Lemaitre, B., Trygg, J., . . . Cava, F. (2016). Chemometric Analysis of Bacterial Peptidoglycan Reveals Atypical Modifications That Empower the Cell Wall against Predatory Enzymes and Fly Innate Immunity. Journal of the American Chemical Society, 138(29), 9193-9204
Open this publication in new window or tab >>Chemometric Analysis of Bacterial Peptidoglycan Reveals Atypical Modifications That Empower the Cell Wall against Predatory Enzymes and Fly Innate Immunity
Show others...
2016 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, no 29, p. 9193-9204Article in journal (Refereed) Published
Abstract [en]

Peptidoglycan is a fundamental structure for most bacteria. It contributes to the cell morphology and provides cell wall integrity against environmental insults. While several studies have reported a significant degree of variability in the chemical composition and organization of peptidoglycan in the domain Bacteria, the real diversity of this polymer is far from fully explored. This work exploits rapid ultraperformance liquid chromatography and multivariate data analysis to uncover peptidoglycan chemical diversity in the Class Alphaproteobacteria, a group of Gram negative bacteria that are highly heterogeneous in terms of metabolism, morphology and life-styles. Indeed, chemometric analyses revealed novel peptidoglycan structures conserved in Acetobacteria: amidation at the alpha-(L)-carboxyl of meso-diaminopimelic acid and the presence of muropeptides cross-linked by (1-3) L-Ala-D-(meso)diaminopimelate cross-links. Both structures are growth-controlled modifications that influence sensitivity to Type VI secretion system peptidoglycan endopeptidases and recognition by the Drosophila innate immune system, suggesting relevant roles in the environmental adaptability of these bacteria. Collectively our findings demonstrate the discriminative power of chemometric tools on large cell wall-chromatographic data sets to discover novel peptidoglycan structural properties in bacteria.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Chemical Sciences Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-125551 (URN)10.1021/jacs.6b04430 (DOI)000380730000039 ()27337563 (PubMedID)
Available from: 2016-09-16 Created: 2016-09-13 Last updated: 2019-03-28Bibliographically approved
van Teeseling, M. C. F., Mesman, R. J., Kuru, E., Espaillat, A., Cava, F., Brun, Y. V., . . . van Niftrik, L. (2015). Anammox Planctomycetes have a peptidoglycan cell wall. Nature Communications, 6, Article ID 6878.
Open this publication in new window or tab >>Anammox Planctomycetes have a peptidoglycan cell wall
Show others...
2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 6878Article in journal (Refereed) Published
Abstract [en]

Planctomycetes are intriguing microorganisms that apparently lack peptidoglycan, a structure that controls the shape and integrity of almost all bacterial cells. Therefore, the planctomycetal cell envelope is considered exceptional and their cell plan uniquely compartmentalized. Anaerobic ammonium-oxidizing (anammox) Planctomycetes play a key role in the global nitrogen cycle by releasing fixed nitrogen back to the atmosphere as N-2. Here using a complementary array of state-of-the-art techniques including continuous culturing, cryo-transmission electron microscopy, peptidoglycan-specific probes and muropeptide analysis, we show that the anammox bacterium Kuenenia stuttgartiensis contains peptidoglycan. On the basis of the thickness, composition and location of peptidoglycan in K. stuttgartiensis, we propose to redefine Planctomycetes as Gram-negative bacteria. Our results demonstrate that Planctomycetes are not an exception to the universal presence of peptidoglycan in bacteria.

National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-106512 (URN)10.1038/ncomms7878 (DOI)000355526200001 ()25962786 (PubMedID)
Available from: 2015-07-15 Created: 2015-07-14 Last updated: 2019-03-28Bibliographically approved
Organisations

Search in DiVA

Show all publications