Upload
khangminh22
View
1
Download
0
Embed Size (px)
Citation preview
1
Dear FASEB Journal Author Please DOWNLOAD this PDF to your computer comment using the PDF comments function save all changes and UPLOAD the file back to this site Please read the proofs carefully and
1 Please correct only typographical and factual errors please do not edit your article or note spacing issues as those are handled at issue stage
2 Make sure you have acknowledged all grant support received 3 Review and answer ALL author queries (marked in the margins of the text with Q1 etc) that are listed on the
query sheet(s) 4 Check each name in the author line carefully for correct spelling 5 Proofread the following elements of your article especially carefully
a Non‐English characters and symbols b Tables c Equations and mathematical symbols d Check figure numbering color text labeling caption placement and cropping if elements are missing
from a figure or if your color figure does not appear in color in the PDF and you would like it to please note this on your proofs
6 Review figures carefully and indicate which if any color figures can be presented adequately and accurately in black and white The production office will convert those from color to black and white Color figures have the word ldquoCOLORrdquo in the margins Grayscale (black and white) figures have ldquoBWrdquo in the margins If you wish to change a color figure to black and white include a comment instructing the figure to be published in ldquoBWrdquo
7 If you need to provide the editorial office with a revised figure please indicate this with a comment on the incorrect figure and write NEW FIGURE FILE REQUIRED in the comment and include the new figure as an attachment to your email
8 Publication charges are calculated based on the final version of the article ndash not this proof Publication charges will be calculated based on your changes to this proof Please note that figures are published the same way in the online and print versions of the journal Authors may not publish figures in color online while publishing the same figures in grayscale in print or vice‐versa
The month of final publication is located at the bottom of your proofs If you do not return your corrections by the deadline your article may be rescheduled for a later issue
Fax PUBLICATION FORMS to 1‐240‐407‐4430 Publication forms sent by any other means or faxed to any other number may result in substantial publication delays
NOTE Proofs or publication forms retained by the author for an excessive length of time may not be published online in a timely way and may need to be scheduled for a later print issue
If you have any problems or questions please contact me Always include your article number in all correspondence Sincerely MR CareyJournal Production Coordinator FASEB Office of Publications9650 Rockville Pike Bethesda Maryland 20814 Phone (301) 634-7108 Fax (240) 407-4430 E-mail mrcareyfaseborg
1
1 Update to Adobe Acrobat Reader DCThe screen images in this document were captured on a Windows PC running Adobe Acrobat Reader DC Upgrading to the newest version is not always necessary but it is preferable and these instructions apply only to Adobe Acrobat Reader DC You can also create annotations using any version of Adobe Acrobat Adobe Acrobat Reader DC can be downloaded at no cost from httpgetadobecomreader
2 What are eProofseProof files are self-contained PDF documents for viewing on-screen and for printing They contain all appropriate formatting and fonts to ensure correct rendering on-screen and when printing hardcopy SJS sends eProofs that can be viewed anno-tated and printed using either Adobe Acrobat Reader or Adobe Acrobat
3 Show the Comment ToolbarThe Comment toolbar isnrsquot displayed by default To display it choose View gt Tools gt Comment gt Open
Pilgrim Five Suite 55 Pilgrim Park Road
Waterbury VT 05676
Annotating PDFs using Adobe Acrobat Reader DCVersion 17 June 27 2016
Refer to Page 2 for annotation examples
4 Using the PDF Comments menuTo insert new text place your cursor where you would like to insert the new text and type the desired text To replace text highlight the text you would like to replace and type the desired replacement text To delete text highlight the text you would like to delete and press the Delete key
Acrobat and Reader will display a pop-up note based on the modification (eg inserted text replacement text etc) To format text in pop-up notes highlight the text right click select Text Style and then choose a style A pop-up note can be minimized by selecting the X button inside it When inserting or replacing text a symbol indicates where your comment was inserted and the comment is shown in the Comments List If you do not see the comments list you are editing the live text instead of adding comments and your changes are not being tracked Please make certain to use the Comments feature instead
5 Inserting symbols or special charactersAn insert symbol feature is not available for annotations and copying and pasting symbols or non-keyboard characters from Microsoft Word does not always work Use angle brackets lt gt to indicate these special characters (eg ltalphagt ltbetagt)
6 Editing near watermarks and hyperlinked texteProof documents often contain watermarks and hyperlinked text Selecting characters near these items can be difficult using the mouse To edit an eProof which contains text in these areas do the following
bull Without selecting the watermark or hyperlink place the cursor near the area for editing
bull Use the arrow keys to move the cursor beside the text to be editedbull Hold down the shift key while simultaneously using arrow keys to select the
block of text if necessarybull Insert replace or delete text as needed
7 Reviewing changesTo review all changes open the Comment menu and the Comment List is displayed Note Selecting a correction in the list highlights the corresponding item in the document and vice versa
8 Still have questionsTry viewing our brief training video at httpsauthorcenterdartmouthjournalscomArticlePdfAnnotation
2
A Inserted text
B Replaced text
C Deleted text
D Sticky Note
B
C
D
A
Author Instructions
Copyright Transfer and Publication Costs Approval Form
All authors are required to sign the following copyright transfer and cost
agreement form prior to publication If you have not yet submitted this form to
the editorial office please fax it to 240‐407‐4430 as soon as possible Multiple
forms may be submitted for the same article
The FASEB Journal The Journal of the Federation of American Societies for Experimental Biology
Mandatory Copyright Transfer and Publication Costs Approval Form
Manuscript No
Title
Author Names (Please Print All Names)
Signatures Below Certify Compliance With the Following Statements
Copyright Transfer In consideration of the acceptance of the above work for publication I do herby assign and transfer to the Federation of American Societies for Experimental Biology (FASEB) all rights titles and interest in and to the copyright in The FASEB Journal This includes preliminary displayposting of the abstract of the accepted article in electronic form before publication The journal grants the author permission to provide a copy of the accepted manuscript to NIH upon acceptance for Journal publication with public release in PubMed Central twelve months after final print publication by The FASEB Journal
Open Access Acknowledgment I understand and agree that (1) I other authors or third parties may elect to pay the Open Access Option fee and without notification to any authors have the article and its contents assigned a Creative Commons (or other) license effectively making the article ldquoOpen Accessrdquo (2) when an article is made Open Access by authors or third parties copyright ownership will revert to the authors who become responsible for enforcing and monitoring of the articlersquos particular copyright licensing terms (3) an Open Access license is assigned on a ldquofirst-come-first-servedrdquo basis meaning that the journal will honor the first Open Access request it receives and will assign the appropriate license for that request once payment has been received (4) Creative Commons and other Open Access licenses are permanent and may not be changed removed or retracted and (5) in the event a conflict among between authors and or third parties is brought to the attention of the journal or FASEB regarding a specific copyright license or the assignment of a specific copyright license the journal andor FASEB reserves the right to withhold any action until the dispute is settled fully before an appropriate authority including but not limited to presiding courts arbitrators author institution(s) etc (6) FASEB or The FASEB Journal will not investigate or settle copyright license disputes among authors their representatives funding agencies institutions or other interested parties
This Form Must Be Signed by All Authors If any changes in authorship (order deletions or additions) occur after the manuscript is submitted agreement by all authors for such changes must be on file with FASEB An authorrsquos name may only be removed at hisher own request and with written consent from all of the other authors as well as final approval by the Editor-in-Chief Material prepared by employees of the US Government in the course of their official duties cannot be copyrighted work prepared by employees of the British or British Commonwealth government in the course of their official duties is subject to Crown Copyright and cannot be transferred to FASEB Nevertheless authors must sign the form to indicate acceptance of all terms other than copyright transfer
Please check if this article was written as part of the official duties of an employee of the US government
Please check if this article was written as part of the official duties of an employee of the British or British Commonwealth government
Authorship Responsibilities I attest that (1) the manuscript is not currently under consideration in press or published elsewhere and the research reported will not be submitted for publication elsewhere until a final decision has been made as to its acceptability by The FASEB Journal (posting of submitted material on a web site or by any other electronic means may be considered prior publicationmdashnote this in your cover letter) (2) the manuscript is truthful original work without fabrication fraud or plagiarism (3) I have made an important scientific contribution to the study and am thoroughly familiar with the primary data and(4) I have read the complete manuscript and take responsibility for the content and completeness of the manuscript and understand that I share responsibility if the paper or part of the paper is found to be faulty or fraudulent
Conflict of Interest Disclosure All funding sources supporting the work and all institutional or corporate affiliations of mine are acknowledged Except as disclosed on a separate attachment I certify that I have no commercial associations (eg consultancies stock ownership equity interests patent-licensing arrangements etc) that might pose a conflict of interest in connection with the submitted article and that I accept full responsibility for the conduct of the trial had full access to all the data and controlled the decision to publish
Author Fees I agree to pay $199 per printed page and $199 per supplemental unit (maximum of 4 units) All amounts are in US dollars
Author Signatures For more than 10 authors use an extra sheet Multiple forms are acceptable
1 Print Name
Signature Date
2 Print Name
Signature Date
3 Print Name
Signature Date
4 Print Name
Signature Date
5 Print Name
Signature Date
6 Print Name
Signature Date
7 Print Name
Signature Date
8 Print Name
Signature Date
9 Print Name
Signature Date
10 Print Name
Signature Date
Signed forms should be faxed to 240-407-4430 or scanned and emailed to journalformsfaseborg
THE
JOURNAL bull RESEARCH bull wwwfasebjorg
Trehalose 6-phosphate phosphataAQ1 seAQ2
s ofAQ3 Pseudomonas aeruginosa
Megan Cross1 Sonja Biberacherdagger1 Suk-Youl ParkDagger1 Siji Rajan Pasi Korhonensect Robin B Gassersect
Jeong-Sun Kim Mark J Coster and Andreas Hofmannsectk2
Griffith Institute for Drug Discovery Griffith University Nathan Queensland Australia daggerDepartment of Biology Friedrich-AlexanderUniversity Erlangen-Nuremberg Erlangen Germany DaggerPohang Accelerator Laboratory Pohang University of Science and TechnologyPohang Gyeongbuk South Korea sectDepartment of Veterinary Biosciences Melbourne Veterinary School The University of MelbourneParkville Victoria Australia Department of Chemistry Chonnam National University Gwangju South Korea and kQueensland TropicalHealth Alliance Smithfield Queensland Australia
ABSTRACT The opportunistic bacterium Pseudomonas aeruginosahas been recognized as an important pathogen ofclinical relevance and is a leading cause of hospital-acquired infections The presence of a glycolytic enzyme inPseudomonaswhichisknowntobe inhibitedby trehalose6-phosphate (T6P) inotherorganisms suggests that thesebacteria may be vulnerable to the detrimental effects of intracellular T6P accumulation In the present study weexplored the structural and functional properties of trehalose 6-phosphate phosphatase (TPP) in P aeruginosa insupport of future target-baseddrugdiscoveryAsurveyofgenomes revealed theexistenceof2TPPgeneswitheitherchromosomal or extrachromosomal location Both TPPs were produced as recombinant proteins and character-ization of their enzymatic properties confirmed specific magnesium-dependent catalytic hydrolysis of T6P The 3-dimensional crystal structure of the chromosomal TPP revealed a protein dimer arising through b-sheet expansionof the individualmonomerswhichpossess theoverall foldofhalo-aciddehydrogenasesmdashCrossMBiberacherSPark S-Y Rajan S Korhonen P Gasser R B Kim J-S Coster M J Hofmann A Trehalose 6-phosphatephosphatases of Pseudomonas aeruginosa FASEB J 32 000ndash000 (2018) wwwfasebjorg
KEY WORDS drug discovery bull enzyme activity bull halo-acid dehydrogenase bull multidrug resistance bull proteinstructurendashfunction
Pseudomonas aeruginosa is a gram-negative multihostopportunistic bacterium that infects humans (1) livestock(2 3) plants (4) rodents insects (5) and nematodes (6) Inhealthyhumans the innate immunesystemcaneffectivelycounteract infection by P aeruginosa however patientswith compromised host defenses in particular burn vic-tims and patients who are immunocompromisedmechanically ventilated or have cystic fibrosis are par-ticularly susceptible to infection with this pathogen (1) Inthe recent past an increase in the occurrence of drug-resistant P aeruginosa strains has been observed (7) and
the lackof effective antibiotics results in apressingneed fornew therapeutics to treat infections with this pathogen
The nonreducing disaccharide trehalose belongs to agroup of so-called compatible solutes which function asosmoprotectants and thus contribute to the protection oforganisms against osmotic stress (8 9) it is also requiredfor survival at temperatures above 37degC in stress-tolerantpathogens (10) In P aeruginosa strain PA14 trehalose hasbeen identified as a virulence factor for pathogenesis inplants but not in metazoan hosts (mice flies nematodes)(11) Trehalose biosynthesis in PA14 occurs in the treYZpathway whereby oligomaltodextrins (eg glycogen) areconverted into trehalose in a 2-step reaction by maltooli-gosyl trehalose synthase (treY) and maltooligosyl treha-lose trehalohydrolase (treZ)
In addition to the treYZ pathway another 4 additionalpathways of trehalose biosynthesis have been observed inprokaryotes plants fungi and nonvertebrate animalsAmong those other pathways the so-called osmoticallyregulated trehalose synthesis (ots)AB pathway has attrac-ted particular attention as a target of interest for thera-peutic intervention in infectious diseases [reviewed inCross et al (12)] because accumulation of the metabolitetrehalose 6-phosphate (T6P) results in a lethal phenotype
ABBREVIATIONS chTPP chromosomal trehalose 6-phosphate phospha-tase ecTPP extrachromosomal trehalose 6-phosphate phosphatase GBGenBank HAD haloacid dehydrogenase MD molecular dynamics otsosmotically regulated trehalose synthesis PDB Protein Data Bank PEGpolyethylene glycol PGDB Pseudomonas Genome Database T6P treha-lose 6-phosphate TLS translationlibrationscrew TPP trehalose 6-phosphate phosphatase treY maltooligosyl trehalose synthase treZmaltooligosyl trehalose trehalohydrolase UDP uridine diphosphate1 These authors contributed equally to this work2 Correspondence Griffith University N75 Don Young Rd Nathan QLD4111 Australia E-mail ahofmanngriffitheduau
doi 101096fj201800500RThis article includes supplemental data Please visit httpwwwfasebjorgto obtain this information
0892-6638180032-0001 copy FASEB 1
in Caenorhabditis elegans and Mycobacterium tuberculosis(13 14)
The central steps of the otsAB trehalose biosyntheticpathway involve formation of T6P from uridinediphosphate-glucose and glucose-6-phosphate by the en-zymeT6P synthase (otsA EC24115 InternationalUnionof Biochemistry and Molecular Biology Calgary ABCanada) and subsequent hydrolysis of T6P by trehalose6-phosphate phosphatase (TPP otsB EC 31312 In-ternational Union of Biochemistry and Molecular Bi-ology) yielding trehalose and ortho-phosphate (15 16) Incontrast to fungi which employ cooperativemultienzymecomplexes (17) T6P synthase and TPP operate as func-tionally isolated enzymes in bacteria albeit the expressionof the corresponding genes otsA and otsB appears tightlyregulated (18 19) In Pseudomonas the otsAB pathway andits gene products have previously been investigated in thesolvent-tolerant strain Pseudomonas sp BCNU 106 (19) Inaccordance with the expected link between the otsABpathway and osmoprotection BCNU 106 displayedtoluene-induced overexpression of the genes otsA andotsB resulting in high levels of intracellular trehalose
As part of our ongoing studies of pathogen TPPs asinfectious disease targets we identified and investigatedTPP sequences from P aeruginosa as chromosomal andextrachromosomal genes With a view toward structure-based discovery of potential T6P inhibitors we investi-gated the 3-dimensional crystal structure of chromosomalPaer-TPP and characterized the enzyme activity of chro-mosomal and extrachromosomal Paer-TPP
MATERIALS AND METHODS AQ4
Mining of databases and secondarystructurendashbased alignment
Amino acid sequences of putative P aeruginosa TPPs wereidentified by database mining using the protein BLAST(BLASTp National Center for Biotechnology InformationBethesda MD USA) algorithm (20) with the sequence of Steno-trophomonasmaltophiliaTPP [CCH13862GenBank (GB)NationalCenter for Biotechnology Information] as well as a key-wordsearch for ldquotrehalose phosphataserdquo in the GB database (httpncbinlmnihgovGenbank) and Pseudomonas Genome Database(PGDB httpPseudomonascom) Secondary structure elementsfor each amino acid sequence were predicted by the softwarePSIPRED (21) installed in house A secondary structurendashbasedsequence alignment was generated automatically with the soft-ware SBAL (22) visually inspected and manually adjusted(Fig 1)
Protein expression and purification
The codon-optimized expression constructs of the chromosomal[GB NZ_JTMO01000001 (7065971417) GB WP_043516570strain AZPAE15058 (whole-genome shotgun sequence] and ex-trachromosomal [GB KC543497 (5846759225) GB WP_010792510 strain PA96 plasmid pOZ176] TPP genes of P aeru-ginosaweresynthesizedbyGenScript (PiscatawayTownshipNJUSA) and ligated into the vector p11 (The Biodesign InstituteArizona State University Tempe AZ USA) via NdeI and BamHIrestrictionsites resulting inprotein constructswithanN-terminalfusion peptide (MGSSH6SSGRENLYFQGH) Expression andpurification including proteolytic cleavage of the N-terminal
COLOR
Figure 1 Conservation of bacterial TPP sequences Structure-based amino acid sequence alignment of 18 bacterial TPP enzymesshows conservation of the characteristic HAD motifs IndashIV with key residues in bold as well as the P aeruginosandashspecific b2b3hairpin (flap-like motif) and connector helix (a3) The coloring of topological elements in line 2 is consistent with theillustration of the Paer-chTPP crystal structure shown in Fig 2 Secondary structure elements (experimentally observed for Paer-chTPP and predicted for all others) for individual sequences are mapped with green (a helix) and red (b strand) backgroundcysteine residues are highlighted in yellow GB accession numbers of TPP genes are as follows Pseudomonas aeruginosachromosomal (GB WP_043516570) and extrachromosomal (GB WP_010792510) and Arthrobacter aurescens (GB WP_011773668) Renibacterium salmoninarum (GB WP_012243900) Mycobacterium smegmatis (GB YP_890267) Thermoplasmaacidophilum (GB WP_010901616) Thermoplasma volcanium (GB WP_010917513) Acinetobacter baumannii (GB EGU03169)Escherichia coli (GB KJJ47768) Escherichia coli O157 (GB EGD67586) Shigella boydii (GB ACD06494) Shigella flexneri (GBKFZ97274) Vibrio parahaemolyticus (GB KKY41738) Shigella dysenteriae (GB WP_024250312) Shigella sonnei (GB AMG15538)Citrobacter koseri (GB WP_047464023) Salmonella enterica (GB WP_000840115) and Stenotrophomonas maltophilia (GBCCH13862) Figure prepared with PSIPRED (21) SBAL (22) and Inkscape (87)
2 Vol 32 October 2018 CROSS ET ALThe FASEB Journal x wwwfasebjorg
fusion tag was performed according to the protocol publishedpreviously by Cross et al (23)
Selenomethionine-labeled chromosomal TPP was expressedin the auxotrophicEscherichia coli strain834(DE3)with SelenoMetmedium (Anatrace Maumee OH USA) Briefly a 2-L pro-duction culture was grown for 3 h at 37degC and induced withisopropyl b-D-1-thiogalactopyranoside (1 mM final concentra-tion) after lowering the temperature 20degC incubation at thattemperature was continued for another 20 h
The purified protein samples were dialyzed against 100 mMNaCl 1 mM MgCl2 1 mM DTT and 20 mM Tris (pH 80) andwere concentrated by ultrafiltration with an Amicon Ultracartridge (Merck Kenilworth NJ USA) with a 10-kDa cutoffAll stages of protein purificationweremonitored by SDS-PAGEconfirming the expected molecular mass of 28 kDa (Supple-mental Fig S6) The final purified nontagged proteins weresubjected to nanoliquid chromatographyndashtandem mass spec-trometry fingerprinting confirming their identity with a totalcoverage of 25 of the amino acid sequence (SupplementalTable S1AQ5 )
Determination of quaternary structure in solution
Thequaternary structureofPaer-TPPs [chromosomal trehalose 6-phosphate phosphatase (chTPP) 110 mgml extrachromo-somal trehalose 6-phosphate phosphatase (ecTPP) 104 mgml]with His-tag fusion peptides removed was assessed by size-exclusion chromatography with a buffer consisting of 100 mMNaCl and20mM4-(2-hydroxyethyl)-1-piperazineethanesulfonicacid (HEPES pH80) for isocratic elution of a Superose 12 10300GL column (GEHealthcare Life Sciences Little Chalfont St GilesBuckinghamshire United Kingdom) mounted on a DuoFlowHPLC system (Bio-Rad Laboratories Hercules CA USA) Thechromatogramswereanalyzedwith the softwareSDAR(24) andmolecularmasseswereestimated for the eluting species basedoncomparison with elution times of proteins of known molecularmass (see Supplemental Data S1)
Crystallization
The purified recombinant proteins were subjected to initialcrystallization screening (sitting drop vapor diffusion) using ourlarge in-house factorial collection with 1300 preformulatedconditions For Paer-chTPP crystals with a shape reminiscent ofarsendescloizite (25) were obtained from a range of conditionscontaining 20 polyethylene glycol (PEG PEG 3000ndash6000) andpH values between 6 and 8 within 1ndash2 wk The largest crystals(03 mm 3 1 mm) with the best diffraction properties wereobtained in hanging-drop experiments from 02 M MgCl2 20PEG 6000 01 M 2-(N-morpholino)ethane sulfonic acid (pH 6)Crystalswere cryoprotectedby flash soaking inbuffer containing25 ethylene glycol and frozen immediately in liquid nitrogenDespite extensive efforts no crystals could be obtained for Paer-ecTPP
Diffraction data collection crystal structuresolution and refinement
X-ray diffraction data from Paer-chTPP collected at the in-housediffractometer (MicroMax-007 HF R-Axis IV++ detector OxfordCryosystems 800 equipment T = 100 K Rigaku Tokyo Japan)were limited to 3 A presumably because crystals were verysensitive to the ambient humidity Diffraction data obtained atthe Pohang Accelerator Laboratory (Pohang Gyeongbuk Re-public of Korea) extended up to 19 A resolution Data sets wereindexedwithXDS(26) andscaling truncationandanalysiswere
performedwith programs from the CCP4 suite (27) Attempts tosolve the crystal structure by molecular replacement (using alibrary of 24models derived frompublished TPP structures) andheavy atom derivatization using soaking procedures were un-successful Therefore the anomalous data obtained from crystalsof selenomethionine derivatized protein were used for structuresolution Theprotocol for structure solutionby single anomalousdiffraction as implemented in Auto-Rickshaw (28) (beamtimemode EMBL-EBI European Molecular Biology LaboratoryndashEuropean Bioinformatics Institute Hinxton United Kingdom)was used to initiate substructure determination and initial phasecalculation for data set TPP022 at a resolution of 37 A AQ6with theSHELXCDE set of programs (29) Sixteen heavy-atom siteswere found and the correct hand for the substructure was de-termined using the programs ABS (30) and SHELXE The occu-pancy of all substructure atoms was refined using the programBP3 (31) The 2-fold noncrystallographic-symmetry operatorwas found with the RESOLVE program (32) Density modifica-tion phase extension and noncrystallographic symmetryndashaveragingwere performedwith theprogramDMfrom theCCP4suite resulting in the localizationof 22heavy-atomsitesApartiala-helical model was produced with ARPwARP (33) and ex-panded by iterative rounds of manual model building andcomputational refinement Once the backbone of 470 of 508 res-idues (93) had been traced and a reasonable number of aminoacid side chains had been built the model was used to solve thestructure of data set TPP023 by molecular replacement Furtheriterative cycles ofmanualmodel adjustments and computationalrefinement enabled buildingof amodel for all but the last residue(Glu252) in both molecules of the asymmetric unit Analysis ofpossible rigid-body displacements in themodel with anisotropicB-factors with the TLSMD server (34) allowed identification ofthe top 3 groups of translationlibrationscrew (TLS) motionsper monomer which were included in the computational re-finement All manual model building was performed with Coot(35) and O (36) and computational refinement of atomic posi-tions atomic displacement factors and TLS groups was donewith Phenix (37) For data collection phasing and refinementstatistics (see Table 2 AQ7) The dimer interface was analyzed usingthe PISA web service (EMBL-EBI) (38) Structure factors andatomic coordinates of the refined structure of Paer-chTPP (dataset TPP023) have been deposited with the Protein Data Base(PDB accession number 6cj0)
Modeling of substrate-bound Paer-chTPP
The substrate-bound structure of Paer-chTPP was modeled bymanually docking T6P into active site of the protein using thecrystal structure described in this study Force field parametersfor T6P were generated with the PRODRG2 server and a mo-lecular dynamics simulation of the solvated complex was per-formed with Gromacs 465 the Gromos 43a1 force field and aTIP3P water model (39) To ensure charge-neutrality and anelectrolyte concentration of 100 mM sodium and chloride ionswere added to the octahedral cell by replacing solventmoleculesAfter an energy-minimization step a position-restrained dy-namic simulationof 20pswasperformed tograduallyequilibratethe solvated complex at 300 K and 1 bar Periodic boundaryconditions were applied in all 3 dimensions Long-range inter-actionsweremodeledusing theparticlemeshEwaldmethod (40)and a grid spacing of 12 A the cutoff for computation of short-range electrostatic interactionswas10 A andwas 14 A forvanderWaals interactions The temperature was controlled with theV-rescale thermostat (41) and the pressure was controlled withthe Parrinello-Rahman barostat (42) bonds were constrainedwith the LINCS algorithm (43) The final molecular dynamics(MD) simulation was performed for 30 ns with a time step of0002 ps The simulationwas performed on a custom-built server
TPP OF PSEUDOMONAS AERUGINOSA 3
with a Xeon E5-1650 6 Core (35 GHz Intel Santa Clara CAUSA) and 32 GB random access memory (RAM) Analyses wereperformed with Gromacs tools and automated plots were gen-erated with Grace (44)
Chemicals
T6P was synthesized in house as published previously byCross et al (23) and was purchased from Santa Cruz Bio-technology (Dallas TX USA) Trehalose 6-sulfate was syn-thesized in house following the published procedure of Farelliet al (45) Flavomycin ADP and phosphosaccharides wereobtained from MilliporeSigma (Billerica MA USA) and uri-dine diphosphate (UDP) and UDP-glucose were purchasedfrom Abcam (Cambridge United Kingdom) All otherchemicals were resourced from MilliporeSigma unless oth-erwise stated
Enzyme kinetics assays
Phosphatase activity of purified recombinant Paer-TPPs wasassessed at a final enzyme concentration of 10 mM in a buffersolution containing 100 mM NaCl and 20 mM Tris (pH 75) aswell asvaryingconcentrationsofT6P (0ndash40mM)Reactionswereset up in a total volume of 180 ml in 96-well plates (CorningCorning NY USA MilliporeSigma) at room temperature star-ted by the addition of the enzyme and stopped at 30-s to 1-minintervals by transferring 25ndash50 ml of reaction mix into 200 mlBiomol Green reagent (Enzo Life Sciences Farmingdale NYUSA) After incubation for 15min the absorbance at 620 nmwasmeasured using a plate reader (BioTek Instruments WinooskiVT USA) All reactions were set up in triplicate and controlexperiments in the absence of enzyme were used to correct forbackground absorbance The corrected data were converted tomolar concentration of phosphate using a calibration functionthat was determined for every new batch of Biomol Green Afterassessment of the raw data with SDAR (24) we concluded thatmodeling of burst-like kinetics (if present) was not feasible be-cause of the lowmagnitude of the observed spectroscopic signalDatawere thus analyzed by extracting initial rateswith linear fitsof the raw data using R software (R Foundation for StatisticalComputing Wien Austria) (46)
Enzyme end-point assays
Phosphatase end-point assays were used to assess possiblesubstrates of Paer-TPPs as well as inhibitors of T6Pase ac-tivity Enzyme activity was assessed at fixed substrate andenzyme concentrations (500 and 10 mM respectively) in 50-ml reaction mixtures in assay buffer [100 mM NaCl 20 mMTris (pH 75)] Potential inhibitors were added to the enzymeat a final concentration of 1 mM and the mixtures were in-cubated for 5 min before reactions were initiated by the ad-dition of T6P
Reactionswereallowed toproceed for6minbeforequenchingwith 100 ml of BIOMOL Green reagent Absorbance at 620 nmwas determined using a plate reader (BioTek Instruments) afteran incubation period of 15 min for color development All reac-tions were set up in triplicate in 96-well plates and control ex-periments in the absence of enzyme were used to correct forbackground absorbance
RESULTS
Genomic identification of Paer-TPP andsequence comparison with bacterial TPPs
A survey of genomic databases available through GB andthe PGDB showed that P aeruginosa possesses 2 TPPproteins 1 with chromosomal and 1 with extrachromo-somal location (Table 1) Notably the occurrence of bothproteins is mutually exclusive all P aeruginosa strains forwhich informationwas available to date possess either thechromosomal (Paer-chTPP) or the plasmid-encoded (Paer-ecTPP) T6P
Comparisonof thePaer-TPP sequenceswith aminoacidsequences from other bacterial TPPs highlighted the con-servation of the canonical haloacid dehydrogenase (HAD)motifs (IndashIV) and revealed the presence of P aeruginosandashspecific insertions between motifs I and IV as well as thefirst linker region between the core and the cap domain(Fig 1)
TABLE 1 TPP genes in P aeruginosa identified in genomic databases
Chromosomal TPP Extrachromosomal TPP
Strain Accession noIdentity querysequence () Strain Accession no
Identity querysequence ()
AZPAE15058 GB NZ_JTMO01000001 100 PA96 plasmid pOZ176 GB KC5434971 10029785cz GB KY8605721 99 FFUP_PS_37 plasmid pJB37 GB KY4948641 99PA58 GB CP0217751 99 PA121617 plasmid pBM413 GB CP0162151 99
PGDB NZ_CP016215 99E6130952 GB CP0206031 99H47921 GB CP0088611 99
PGDB NZ_CP008861 100VR-14397 GB LK0545031 99NCGM1984 GB AP0146461 99
PGDB NZ_AP014646 100NCGM1900 GB AP0146221 99
PGDB NZ_AP014622 10037308 GB GQ1618471 99PACS171b GB EU5957501 99PA1207 GB CP0220011 9939016 PGDB NZ_CM001020 100
4 Vol 32 October 2018 CROSS ET ALThe FASEB Journal x wwwfasebjorg
Quaternary solution structure of Paer-TPPs
The quaternary solution structure of both Paer-TPPs wasassessed by size-exclusion chromatographyAlthough therecombinant chromosomal TPP eluted exclusively as adimeric species amonomerndashdimermixturewith a ratio of11 was observed for the extrachromosomal TPP
Crystal structure of chromosomal Paer-TPP
The crystal structure of Paer-chTPP (diffraction data andrefinement statistics are summarized in Table 2) showsthat the protein adopts the general fold known from othermembers of the HAD superfamily (InterPro IPR023214EMBL-EBI) of enzymes The overall foldwhich comprises
TABLE 2 Crystallographic data collection and refinement statistics for Paer-chTPP
Se-Met
TPP022 TPP023g
Parameter Total Total Molecule 1 Molecule 2
DatAQ15 a collectionX-ray source PAL MX-7A PAL MX-7ADetector ADSC Q270r ADSC Q270rWavelength (A) 09793 09793Space group P21 P21
Cell dimensionsa b c (A) 748 669 754 749 670 756a b g(deg) 90 1197 90 90 1197 90Resolution (A)a 25ndash23 (242ndash230) 25ndash19 (100ndash190)Unique reflectionsa (n) 28778 (4126) 51243 (5069)Rsym
ab 0057 (0201) 0101 (0527)Rmeas
a 0068 (0234) 0118 (0604)Rpim
a 0025 (0086) 0042 (0219)CC(102)a 0999 (0981) 0997 (0898)Mean IsIa 209 (78) 106 (36)Completenessa 0996 (0989) 0997 (0998)Redundancya 75 (74) 75 (75)Wilson B factor (A2) 378 257
PhasingHeavy atom sites (n) 22Correlation coefficient (all weak)c 298 129Mean figure of merit 0701
RefinementResolution (A) 25ndash19 (197ndash190)Reflections (n) 51236 (5069)Working seta 48676 (4784)Test seta 2560 (285)
Atoms (n)Protein 3954 1977 1977Ligandion 2 Mg2+ 2 CO3
22 1 Mg2+ 1 CO322 1 Mg2+ 1 CO3
22
Water 215Average B-factorsProtein (A2) 419 419 419Ligandion (A2) 274 279 269Water (A2) 324
Root mean square deviationsBond lengths (A) 0007Bond angles (deg) 0979B factor for bonded atoms 586 590 590
MolProbity analysisd
Ramachandran outliers () 04Ramachandran allowed () 28Ramachandran favored () 968Rotamer outliers () 31Cb outliers 0Clash score 421R factorae 0174 (0226)Rfree
af 0218 (0301)
aValues in parentheses are for highest-resolution shell bRsym = S |I ndash I|S Ι where I is the observed intensity and I is the averageintensity obtained from multiple observations of symmetry-related reflections after rejections cDefined in Schneider and Sheldrick (85) dResultsfrom the MolProbity analysis as implemented in Phenix (37) eR-factor = S | |Fo|ndash|Fc| |S |Fo| where Fo and Fc are the observed and calculatedstructure factors respectively fRfree is defined in (86) gPDB accession number 6cj0
TPP OF PSEUDOMONAS AERUGINOSA 5
the core domain with a Rossmann fold and an ab capdomain allows for subtle variations when comparingdifferent members of this protein family AccordinglyHAD proteins can be classified into 3 subtypes based onthe structure and insertion location of the cap domainTwo sites for cap insertion exist 1 in the middle of theb-hairpin formedbyb-strands 2 and3 (C1) and another inthe linker after b-strand 3 of the core domain (C2) thosemembers of the protein family having only small inser-tions at either site are designated as C0 C1 caps may beeither a-helical or assume the unique ab fold associatedwith P-type ATPases whereas C2 caps have a distinctb-sheet core surrounded by ab elements (47ndash49)
The crystal structure of Paer-chTPP confirms the pres-ence of all structural elements defining the HAD foldthe sequence of secondary structure elements is N-bbbababba(abbabb)ababa-C indicating that the pro-tein belongs to the HAD C2 subfamily (brackets indicatethe cap domain the underlined a-helix is a contiguouselement linking the core and cap domain) The coredomain is constituted by a 3-layer aba sandwich withthe central 6-stranded b sheet comprising b12(uarr)-b11(uarr)-b1(uarr)-b4(uarr)-b5(uarr)-b6(darr) The cap domain is situatedjuxtaposed and connected to the core domain by the longbent-helixa3 and a coiled linker segment betweenb10 anda5 Like in otherHADC2 familymembers the capdomainof Paer-chTPP possesses abbabb topology with a4-stranded antiparallel b sheet (b7-b8-b10-b9) flanked by
2 a helices (a3 a4) on the side facing away from the coredomain
Paer-TPPs possess 2 obvious differences and to ourknowledge previously unobserved structural elementscomparedwithotherTPPstructures first thepresenceof ab hairpin comprising b-strands b2 and b3 and second along bent helix (a3) that connects the HAD core with thecap domain (Fig 1)
The crystal structure of Paer-chTPP reveals that the bhairpin extends from the core domain (see Fig 2) andnarrows theaccess to the substrate-bindingpocketCrystalstructures of other bacterial and nematode TPPs (Thermo-plasma acidophilumTPP PDB 1u02BrugiamalayiTPP PDB4ofz 5e0o) confirm the absence of thatb hairpin howevera conserved structural element in that place is common toother HAD family proteins and is known as the ldquoflapmotifrdquo (47)Movement of the flapmotif aswell as a helicalturn situated immediately upstream controls access to theactive site particularly in HADs with immobile cap do-mains (47) An intriguingly novel structural elementrevealed by the crystal structure of Paer-chTPP is the firstconnector between the HAD core and the cap domainAlthough the segments connecting the cap and core do-mains in TPPs are typically short extendedunstructuredloops theN-terminal connector is replaced here by a longbent a-helix (a3) with Trp111 (observed in 2 alternateconformations) at the bending point This connector foldconstitutes a rather rigid attachment of the cap to the core
COLOR
Figure 2 The crystal structureof Paer-chTPP A) Stereo figureof a cartoon representation ofthe dimer in the X-ray crystalstructure The HAD core do-main with the characteristicRossmann fold is blue and theHAD cap domain is teal Theb2b3 hairpin (flap-like motif)is highlighted in yellow and thebent helix (a3) connectingcore and cap domain is shownin turquoise The location ofHAD motifs IndashIV is shown inorange (I II) and green (IIIIV) and magnesium ions arerendered as magenta spheresB) Stereo figure of the 2FondashFc(contoured at 1 s) electrondensity in the active site show-ing the octahedral coordinationof the protein-bound magne-sium ion (magenta sphere)Coordination is provided by theside-chain carboxylate groups ofAsp11 Asp14 and Asp220 thebackbone carbonyl of Asp13 2water molecules (red spheres)and a bound ligand modeled ascarbonate Figure prepared withPyMOL (88) and Inkscape (87)
6 Vol 32 October 2018 CROSS ET ALThe FASEB Journal x wwwfasebjorg
domain because of the inherent directional stability of thehelical fold
Notably the crystal structure of Paer-chTPP reveals ahomodimer inwhich 2monomersmake contact through apredominantly hydrophobic interface around b12 andb129 In the dimer the centralb sheet of the core domain isthus extended to a 12-stranded b sheet and the dimerinterface is further expanded by the formation of a 4-helixbundle comprising a6 a7 a69 and a79 (Fig 2)
T6P-bound structure of chromosomal Paer-TPP
To gain insights into the molecular interactions betweenthe substrate and the enzyme we docked T6P into theactive site of Paer-chTPP and subjected the hydratedcomplex to a molecular-dynamic simulation of 30000 psduration The simulation revealed that a stable-bindingpose of the substrate in the active site can be obtained (seeSupplemental Fig S1 and Table 3)
TheMDsimulationhighlighted substantial flexibilityofthe b2b3 hairpin with respect to the core domain Thatflexibility is illustrated by the highly variable distance be-tween the hairpin tip and the end-cap residue of helix a1(see Supplemental Fig S1AQ8 ) A comparison of the confor-mationof theb2b3hairpin in the crystal structureand theMD simulation at 30000 ps (Fig 3A B) shows that thehairpin closes over the active site when the substrate isbound Notably the distance between the centers ofgravity of the cap and core domains remained ratherconstant (between 21 and 23 A see Supplemental Fig S1)throughout the duration of the simulation thereby in-dicating that the openingclosingmovement between thecap and core domains as observed in other TPPs is likelyabsent in the P aeruginosa enzymes (Fig 3A B)
In the active site the substrate adopts a curved-conformation wound around a ldquolockrdquo between the coreand the cap domain formed by the side chains of Asp14and Asn182 (Fig 3B and Supplemental Fig S1) The T6Pgroup coordinated the protein-boundmagnesium ion andmaintained a stable contact with the side chain hydroxylgroup of Ser221 (Supplemental Fig S1) Although the 3-hydroxy group of T6P was engaged in a hydrogen bondwith the backbone carbonyl of Asn185 from early onduring the simulation the hydroxy groups of the second
glucose moiety formed interactions with the protein onlyat times beyond 25000 ps specifically hydrogen bondswere observed between the 29-hydroxy group and thebackbone amine of Asp14 the 49-hydroxy group and theside chain hydroxy group of Thr19 and the 69-hydroxygroup and the side chain carbonyl of Asn185 (Supple-mental Fig S1)
Compared with the crystal structure in which themagnesium ion was coordinated by the side-chain car-boxylates of Asp11 and Asp220 as well as 2 water mole-cules anda carbonate ion (Fig 2) themetal ion relocated inthe simulation of the T6P-bound protein and remainedstably coordinated by the T6P group the side chain car-boxylates ofAsp220 and 2watermolecules The side chainofAsp11 appeared not involved in direct interactionswiththe substrate
Enzyme activity of Paer-TPPs
Phosphatase activity of both recombinant Paer-TPPs wasassessed with T6P and a panel of phosphocarbohydratesThe panel consisted of the nucleoside phosphates ADPUDP and UDP-glucose as well as glucose 6-phosphatesucrose 6-phosphate galactose 6-phosphate fructose 16-bisphosphate glucose 16-bisphosphate and T6P Amongthe compounds tested notable phosphatase activity wasobserved only for T6P (Fig 4) Enzymatic activity of bothPaer-TPPs relies on the presence of magnesium ions withanoptimumpHof65ndash7 notably aplot of enzymeactivityagainst pH yields bell-shaped curves for both enzymes(Supplemental Fig S2) in agreement with the expectedinvolvement of 2 catalytically active aspartate residues inthe enzymatic mechanism of HAD enzymes The experi-mentally determined pKa values for the catalytic residueswere615and71 forPaer-chTPPand645and725 forPaer-ecTPP (Supplemental Fig S2) Those values are muchhigher than the pKa value for the side chain of free asparticacid However such an increase in pKa values for acidiccatalytic residues is frequently observed and is a conse-quence of the particular environment within a foldedprotein (50 51)
The T6Pase kinetics of both proteins revealedMichaelis-Menten behavior (Fig 5) albeit with low effi-ciency and large KM values (Table 4) Notably despite
TABLE 3 Ligandndashprotein interactions in simulated Paer-chTPPT6P complex
Ligand Protein Distance (A)a
PO4-OAX Mg2+ 18PO4-OAY Mg2+ 18PO4-OAY (SOL-4233 SOL-3507) rarr D11-OD1 26 29 rarr (28 27)PO4-OAX D220-OD2 33PO4-OAY D220-OD1 30PO4-OAX S221-OG 30PO4-OAY S221-OG 253-OH N185-CO 3329-OH D14-NH 3349-OH T19-OG 3269-OH N185-OD1 36
aAt simulation time t = 30000 ps
TPP OF PSEUDOMONAS AERUGINOSA 7
Paer-chTPP forming a dimeric species no cooperativitywas observed in the plot of the initial rate vs the substrateconcentrationAlthoughother bacterial andnematodeTPPshave previously been shown to possess burst-like kinetics(52) a clear conclusion to that effect cannot be made for the2 Paer-TPPs because of the low turnaround of substratewhich resulted in a spectroscopic signal of lowmagnitude
To assess susceptibility of Paer-TPPs to common phos-phatase inhibitors and probe molecules a panel of 8commercially available compounds and the in-house
synthesized sulfate analog of T6P trehalose 6-sulfatewere tested at a concentration of 1 mM in competitiveinhibition assays against T6P as the substrate (Fig 6) In-hibitors that act by restricting access to the catalytic metalion showed no substantial effects on the T6Pase activity ofthe 2 Paer-TPPs In contrast the presence of the divalentmetal chelatorEDTAor the sulfateanalogofT6P trehalose6-sulfate led to significant reduction in enzymatic activityby 70ndash80 Notably the antibiotic Flavomycin increasedphosphatase activity
COLOR
Figure 3 Docking of T6P into the crystal structure of Paer-chTPP T6P was docked into the crystal structure of Paer-chTPP andthe hydrated complex was subjected to MD simulation Comparison of the surface representations of the crystal structure (A) anda snapshot from the MD simulation at t = 30000 ps (B) shows that the relative orientation of core (blue) and cap (gray) domainsdo not change The notable conformational changes upon substrate binding include a closing of the active-site cleft by the b2b3hairpin (cyan) and the formation of a ldquolockrdquo by the side chains of Asp14 and Asn182 C) Cut-away view of the active-site cleft withT6P rendered as a stick model and magnesium shown as a magenta sphere direct interactions between substrate and protein areindicated (see also Table 3) Figure prepared with PyMOL (88) and Inkscape (87)
COLOR
Figure 4 The phosphatase activity of recombinant Paer-TPPs is specific for T6P Comparison of corrected absorbance data (l =620 nm) obtained in endpoint assays of recombinant Paer-chTPP (blue) and Paer-ecTPP (red) with nucleoside phosphates (left)and other carbohydrate phosphates (right) Data shown represent the means of 3 technical repeats error bars indicate the SEFigure were generated with R software (46) and Inkscape (87) Left) The nucleoside phosphates ADP UDP and UDP-glucosewere tested at 200 mM concentration in endpoint assays containing 25 mM enzyme For comparison activity observed with calfalkaline intestine phosphatase (CIP M0290 New England BioLabs Ipswich MA USA) is shown in green Right) Thecarbohydrates glucose 6-phosphate sucrose 6-phosphate galactose 6-phosphate glucose 16-bisphosphate and fructose 16-bisphosphate were tested at 500 mM concentration in endpoint assays containing 10 mM enzyme
8 Vol 32 October 2018 CROSS ET ALThe FASEB Journal x wwwfasebjorg
DISCUSSION
P aeruginosa possesses a chromosomal andan extrachromosomal TPP
A survey of genomic databases revealed that P aeruginosastrains possess genes coding for 2 different TPPs Theamino acid sequences of the 2 TPP gene products share93 identity Although 1 of the 2 TPPs originated from agene that hadbeenmapped on the chromosome the otherTPP gene was located on a plasmid Interestingly in all Paeruginosa strains with available genome information theexistence of either chromosomal or extrachromosomalTPP is exclusive
The dynamic pathogenicity and impressive adaptabil-ity of the Pseudomonas species has been attributed to theirmosaic genomic structure which comprises a conservedldquocorerdquo genome and a variable ldquoaccessoryrdquo genome (53)The accessory genome varies widely among strains and isassociated with the bacteriumrsquos genetic plasticity andsurvival in specific environmental niches (53 54) Becausethose advantageous genes are believed to be acquiredthrough horizontal gene transfer they have been dubbedldquogenomic islandsrdquo and may take the form of plasmidsconjugative transposons nonreplicative elements orcryptic prophages (55) The transfer of plasmids from Ecoli toP aeruginosahaspreviously beendemonstrated (56)and the presence of an otsB gene in different genomic lo-cales in P aeruginosa suggests that it may have been ac-quired by different strains when required to confer afitness advantage Many Pseudomonas species express thetreP phosphotransferase subunit and the treA trehalasewhich allow the importation and use of environmentaltrehalose as an energy source (57 58) respectively and
treA has been annotated in the P aeruginosa genome(UniProt Q9I165) Building on this existing component ofthe trehalose catabolism the ability to synthesize this di-saccharide could provide additional benefits such as os-moregulation and abiotic stress tolerance to P aeruginosaas in other bacteria (10)
Theenclosedarea in thedimer interfaceofPaer-chTPP is1350 A2 and thus11of the total solvent-accessible areaof 1 monomer suggesting that the dimer observed in thecrystal structure may be of physiologic significance (59)This hypothesis is further supported by data from size-exclusion chromatography which revealed a 66 kDa (di-mer) species as the predominant form of the protein insolution at pH 8 (Supplemental Fig S3) Although the di-mer formation with the characteristic motif of b-sheet ex-pansion has not been observed so far with TPPs thatbelong to the HAD C2 subfamily (see above) there isprecedence for this type of homo-oligomerization withinthe larger HAD family of proteins In particular somesubtype C1 HAD members exhibit similar dimers in-cluding the cytosolic 59-(39)-deoxyribonucleotidase (PDB2jar) mitochondrial 59-(39)-deoxyribonucleotidase (PDB2jaw) and soluble epoxide hydrolase 2 (PDB 5ai0)
Although the sequences of both TPPs differ by only 18aa substitutions (Fig 7) those variations result in a changein the quaternary structure in solution Although Paer-chTPP exists exclusively as a dimeric species in solutionPaer-ecTPP forms a roughly equimolar mixture of mono-mers and dimers (Supplemental Fig S3) This hetero-dispersive behavior in solution may be one reason for thefailure to obtain crystals of Paer-ecTPP Analysis of thedimer interface (mainly around the C-terminal b strandand a helix) shows that none of the amino acid substitu-tions in the plasmid-encoded TPP as compared with thechromosomal TPP are located in that area The only var-iable amino acids in the dimer interface comprise Ile247(Val in ecTPP) andGly229 (Asp in ecTPP) neither ofwhichis engaged in particularly significant interactions In-triguingly 3 of the variation hotspots in the P aeruginosaTPPs are involved in the crystal contacts of thedimer in thecrystal structure of Paer-chTPP Ser53 (Asn in ecTPP)Lys108 (Glu in ecTPP) and Arg126 (Gln in ecTPP) areinvolved in lattice contacts with Thr30 Trp111 andGlu247 respectively Of those 3 contacts the 1 most likelyto be perturbed by the amino acid variation betweenchromosomal and plasmid-encoded TPP is Lys108Trp111 Formation of a hydrogen bond between the sidechain amino group of Lys108 and the aromatic system ofTrp111 is not possible if the lysine is replaced with a glu-tamate residue
COLOR
Figure 5 Steady-state Paer-TPP enzyme kinetics follow Michae-lis-Menten behavior A plot of initial rates of phosphataseactivity of Paer-chTPP (blue enzyme concentration 5 mM) andPaer-ecTPP (red enzyme concentration 10 mM) at varying T6Pconcentrations reveals Michaelis-Menten behavior The solidlines represent the fits of the Michaelis-Menten equation usingR software (46) Numerical fitting results are listed in Table 4
TABLE 4 Michaelis-Menten parameters for T6Pase activity ofPaer-TPPs
Parameter Paer-chTPP Paer-ecTPP
Km 32 mM 42 mMkcat 006s 006sh = kcatKm 19sM 14sM
KM and kcat were obtained from fitting the Michaelis-Mentenequation to the data shown in Fig 5
TPP OF PSEUDOMONAS AERUGINOSA 9
Enzyme activity of P aeruginosa TPPs highsubstrate specificity but moderate efficiency
From a panel of 8 metabolically relevant phosphocarbo-hydrates phosphatase activity was observed only withT6P (Fig 4) confirming the anticipated function of the 2 Paeruginosa enzymes as TPPs and the high substrate speci-ficity of those enzymes Compared with the enzymatic
activities of all other known TPPs Paer-TPPs possess thelowest efficiency so far with h values of 10ndash20sM(Table 4) which is 1 order of magnitude less than the ef-ficiency observed for TPP from Stenotrophomonas malto-philia (52)
The low enzyme efficiency arises for 2 reasons a ratherhighKMand an extremely low catalytic rate constant (kcat)The unusually low turnover rate is a consequence of thespecific structural fabric of the enzyme Particularly thepresence of a flap-like element in the form of the b2b3-hairpin provides spatial restrictions at the entry to thesubstrate binding site Additionally the rigid attachmentof the cap to the core domain by means of helix a3 mayprevent conformational movements between the 2 do-mains (ie ldquoopeningrdquo and ldquoclosingrdquo) and thus force a veryspecific entryexit trajectory for reactants and productsThis hypothesis is supported by the absence of domainmovements in the MD simulation of substrate-bound Paeruginosa TPP
The steady-state kinetic parameters obtained for the Paeruginosa TPPs are very different from the kinetically su-preme enzymes typically portrayed in textbooks withtheoretical considerations suggesting an upper limit forkcat of 10
6ndash107s (60) (the upper limit for rates of diffusion-controlled reactions is 108ndash109Ms) Notably it has pre-viously been suggested that low enzyme efficiencies mayreflect the searchof a rare enzymeconformation thatyieldsthe catalytically competent substrate-bound state (61 62)Furthermore in contrast to the broadly held view thatenzymes have evolved to maximize their efficiency otherhypotheses have been presented including the idea thatevolution forges the KM value of an enzyme to suit thephysiologic substrate concentration (63) In that context asurvey of some 1000 enzymes demonstrated that moder-ate enzyme efficiencies are rather common and not anexception the kinetic parameters of the ldquoaveragerdquo enzyme
COLOR
Figure 6 The T6Pase activity of recombinant Paer-TPPs isinhibited by EDTA and trehalose 6-sulfate Comparison of therelative phosphatase activity of 10 mM of recombinant Paer-chTPP (blue) and Paer-ecTPP (red) with 500 mM T6P as thesubstrate in the presence of 1 mM of generic phosphataseinhibitors as well as Flavomycin and trehalose 6-sulfate Datashown were obtained from endpoint assays and represent themeans of 3 technical repeats error bars indicate the SE Figuregenerated with R software (46) and Inkscape (87)
COLOR
Figure 7 Structural mapping of amino acid sequence differences between Paer-TPPs Amino acid differences betweenchromosomal and extrachromosomal TPPs are mapped onto the structure of the Paer-chTPP monomer shown as cartoonrepresentation in stereo The 2 sequences are 93 identical and differ in 18 residues of 251 (7)AQ14 Figure created with PyMOL(88) and Inkscape (87)
10 Vol 32 October 2018 CROSS ET ALThe FASEB Journal x wwwfasebjorg
adopt much lower values than the upper limit and globalanalysis yieldedanaverageof kcat of10sandanaverageefficiency of 105Ms (64) Such large deviations fromthe maximum possible performance indicate that thoseenzymes are under much weaker evolutionary-selectionpressure than enzymes with high-performance parame-ters Fulfilling roles in the secondary metabolism theweaker selectionpressure facedbyTPPs fromP aeruginosaand other bacterial organisms may be due to their limitedcontributions to the fitness of the entire organism or in-deed because their activity is only required under specificconditions andor for limitedperiods iewith lowoverallturnaround (64)
Inhibition of P aeruginosa TPPenzyme activity
The inhibition profile of a panel of generic phosphataseinhibitors observed with P aeruginosa TPPs is strikinglysimilar to that observed with S maltophilia (52) AlthoughPaer-chTPP is largely unaffected generic phosphatase in-hibitors exert only minor effects on the activity of Paer-ecTPP (Fig 6) In the presence of themetal chelator EDTAhowever the enzymatic activity of both P aeruginosa en-zymes is strongly suppressedbecauseof theremovalof thecatalytic metal ion
Because synthetic carbohydrate chemistry is challeng-ing the development of substratemimics that can be usedas probe molecules and for structure-based inhibitor de-sign is slow but some progress has been made (65) Tre-halose 6-sulfate has previously been shown to marginallylimit the enzymatic activity of TPP from the nematodeBrugia malayi (45) In contrast to other nematode and bac-terial TPPs fromour in-house panel (52) thePaer-TPPs aresusceptible to trehalose 6-sulfate with the remaining ac-tivities between 20 and 30 (Fig 6)
The antibiotic complex consisting of moenomycins Aand C known as Flavomycin has previously been testedas effectors ofmycobacterial TPPs (66)We thus includedFlavomycin in the panel of potential inhibitors in the cur-rent study Similar to the observations of the TPP fromMycobacterium tuberculosis which displayed increasedT6Pase activity in the presence of up to 60mMFlavomycin(66) we found that the presence of 1 mM Flavomycin in-creased the enzymatic phosphatase activity of both Paeruginosa TPPs2- to 5-fold (Fig 6)
CONCLUSIONS
A BLAST search with the P aeruginosa b2b3-hairpin se-quence identified ldquotrehalose phosphataserdquo and ldquohypo-theticalrdquo enzymes with a very high degrees of identityfrom various Pseudomonas and Burkholderia species Asan example the amino acid sequence alignment of Paer-chTPP with trehalose phosphatase of Burkholderiaubonensis (UniProt WP_0717619711) both share the b2b3-hairpin sequence with 100 identity revealing 79identity overall (Supplemental Fig S4) Like PseudomonasBurkholderia spp are opportunistic bacteria and includethe human pathogens Burkholderia cepacia (causing
pulmonary infections) and Burkholderia pseudomallei(causing melioidosis) Intriguingly both genera make useof genomic islands for pathogenicity (67) are susceptibleto the same phage-transfer mechanisms (68) and are eachcapable of influencinggene expression in theother (69 70)MoreoverBurkholderia spppossess a full suite of trehalosemetabolismgenes including trehalasewhichsignificantlyaffects virulence and biofilm formationwhen it is knockeddown (71) This suggests an important role for trehalosemetabolism in Burkholderia [as discussed by Schwarz andVanDijck (72)] and thus potentially in Pseudomonas giventhe similarity between the 2 enzymes and the fact that thespecies occupy similar environmental niches
The toxicity of intracellularly accumulating T6P hasbeen attributed directly to its role in regulating energymetabolism and consequent ability to inhibit hexokinase(13 73ndash77) Additionally high intracellular concentrationsof this metabolite induce dysregulation of multiple genesin some cases through inhibition of SNF1-related proteinkinase 1 (14 78ndash80) The P aeruginosa enzyme originallybelieved to be hexokinase (81) was found to be inactivetoward fructose and mannose and has since been reclas-sified as glucokinase (82) Nevertheless it performs thephosphorylation of glucose to glucose 6-phosphate asyeast hexokinase does furthermore it possesses the keyresidues used by yeast hexokinase (83 84) (SupplementalFig S5) Thus although the effects of T6P accumulation inP aeruginosa are unknown the broad functionality of T6Pin signaling and regulation its widespread toxicity andthe presence of a glycolytic enzyme inPseudomonas similarto that which this metabolite is already known to inhibitall suggest that the bacterium may be vulnerable to thedetrimental effects of T6P accumulation (85ndash88) AQ9
ACKNOWLEDGMENTS AQ10
Research in the investigatorsrsquo laboratories was funded bythe Australian Research Council (to AH and RBG) theRebecca L Cooper Medical Research Foundation (to AH)and the Chonnam National University (2015-0597 to J-SK)The Equity Trustees PhD Scholarship and the AustralianGovernment Research Training Program Scholarship (to MC)as well as support by DAA AQ11D RISE and PROMOS scholarships (toSB) are gratefully acknowledged Mass spectrometric analysiswas undertaken at the Australian Proteome Analysis Facility andthe infrastructure was provided by the Australian Governmentthrough the National Collaborative Research InfrastructureStrategy The authors declare no conflicts of interest
AUTHOR CONTRIBUTIONS
M Cross R B Gasser J-S Kim M J Coster and AHofmann designed the research M Cross S BiberacherS-Y Park and S Rajan performed the experiments MCross S Biberacher S-Y Park P Korhonen R B Gasserand A Hofmann analyzed the data and M Cross and AHofmann wrote the paper with critical input from allauthors
TPP OF PSEUDOMONAS AERUGINOSA 11