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Bonnett SA, Rosenbloom AB, Ong GT, Conner M, Rininger AB, Newhouse D, New F, Phan CQ, Ilcisin S, Sato H, Lyssand JS, Geiss G, Beechem JM. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles. Cancer Res Commun 2023; 3:763-779. [PMID: 37377888 PMCID: PMC10155752 DOI: 10.1158/2767-9764.crc-22-0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 06/29/2023]
Abstract
A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation of multiple "omes". Here we present the development and implementation of a novel spatial proteogenomic (SPG) assay on the GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables ultra high-plex digital quantitation of proteins (>100-plex) and RNA (whole transcriptome, >18,000-plex) from a single formalin-fixed paraffin-embedded (FFPE) sample. This study highlighted the high concordance, R > 0.85 and <15% change in sensitivity between the SPG assay and the single-analyte assays on various cell lines and tissues from human and mouse. Furthermore, we demonstrate that the SPG assay was reproducible across multiple users. When used in conjunction with advanced cellular neighborhood segmentation, distinct immune or tumor RNA and protein targets were spatially resolved within individual cell subpopulations in human colorectal cancer and non-small cell lung cancer. We used the SPG assay to interrogate 23 different glioblastoma multiforme (GBM) samples across four pathologies. The study revealed distinct clustering of both RNA and protein based on pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared with that of the more common GBM. More importantly, the use of spatial proteogenomics allowed simultaneous interrogation of critical protein posttranslational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods. Significance We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.
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Affiliation(s)
| | | | | | - Mark Conner
- NanoString Technologies, Seattle, Washington
| | | | | | - Felicia New
- NanoString Technologies, Seattle, Washington
| | - Chi Q. Phan
- NanoString Technologies, Seattle, Washington
| | | | - Hiromi Sato
- NanoString Technologies, Seattle, Washington
| | | | - Gary Geiss
- NanoString Technologies, Seattle, Washington
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2
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Ray P, Huggett M, Turner PA, Taylor M, Cleghorn LAT, Early J, Kumar A, Bonnett SA, Flint L, Joerss D, Johnson J, Korkegian A, Mullen S, Moure AL, Davis SH, Murugesan D, Mathieson M, Caldwell N, Engelhart CA, Schnappinger D, Epemolu O, Zuccotto F, Riley J, Scullion P, Stojanovski L, Massoudi L, Robertson GT, Lenaerts AJ, Freiberg G, Kempf DJ, Masquelin T, Hipskind PA, Odingo J, Read KD, Green SR, Wyatt PG, Parish T. Spirocycle MmpL3 Inhibitors with Improved hERG and Cytotoxicity Profiles as Inhibitors of Mycobacterium tuberculosis Growth. ACS Omega 2021; 6:2284-2311. [PMID: 33521468 PMCID: PMC7841955 DOI: 10.1021/acsomega.0c05589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Abstract
With the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, there is a pressing need for new oral drugs with novel mechanisms of action. A number of scaffolds with potent anti-tubercular in vitro activity have been identified from phenotypic screening that appear to target MmpL3. However, the scaffolds are typically lipophilic, which facilitates partitioning into hydrophobic membranes, and several contain basic amine groups. Highly lipophilic basic amines are typically cytotoxic against mammalian cell lines and have associated off-target risks, such as inhibition of human ether-à-go-go related gene (hERG) and IKr potassium current modulation. The spirocycle compound 3 was reported to target MmpL3 and displayed promising efficacy in a murine model of acute tuberculosis (TB) infection. However, this highly lipophilic monobasic amine was cytotoxic and inhibited the hERG ion channel. Herein, the related spirocycles (1-2) are described, which were identified following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis. The novel N-alkylated pyrazole portion offered improved physicochemical properties, and optimization led to identification of a zwitterion series, exemplified by lead 29, with decreased HepG2 cytotoxicity as well as limited hERG ion channel inhibition. Strains with mutations in MmpL3 were resistant to 29, and under replicating conditions, 29 demonstrated bactericidal activity against M. tuberculosis. Unfortunately, compound 29 had no efficacy in an acute model of TB infection; this was most likely due to the in vivo exposure remaining above the minimal inhibitory concentration for only a limited time.
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Affiliation(s)
- Peter
C. Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Penelope A. Turner
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Julie Early
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Anuradha Kumar
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Shilah A. Bonnett
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Douglas Joerss
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - James Johnson
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Steven Mullen
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Abraham L. Moure
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan H. Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lisa Massoudi
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne J. Lenaerts
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gail Freiberg
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thierry Masquelin
- Discovery
Chemistry Research, Eli Lilly and Company, Lilly Corporate Centre, MC/87/02/203, G17, Indianapolis, Indiana 46285, United States
| | | | - Joshua Odingo
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
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3
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Punetha A, Ngo HX, Holbrook SYL, Green KD, Willby MJ, Bonnett SA, Krieger K, Dennis EK, Posey JE, Parish T, Tsodikov OV, Garneau-Tsodikova S. Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis. ACS Chem Biol 2020; 15:1581-1594. [PMID: 32421305 DOI: 10.1021/acschembio.0c00184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.
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Affiliation(s)
- Ankita Punetha
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Huy X. Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Shilah A. Bonnett
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
| | - Kyle Krieger
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
- Center for Global Infectious Disease, Seattle Children’s Research Institute, Seattle Children’s Hospital, Seattle, Washington 98145, United States
| | - Emily K. Dennis
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
- Center for Global Infectious Disease, Seattle Children’s Research Institute, Seattle Children’s Hospital, Seattle, Washington 98145, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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4
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Bonnett SA, Ollinger J, Chandrasekera S, Florio S, O’Malley T, Files M, Jee JA, Ahn J, Casey A, Ovechkina Y, Roberts D, Korkegian A, Parish T. A Target-Based Whole Cell Screen Approach To Identify Potential Inhibitors of Mycobacterium tuberculosis Signal Peptidase. ACS Infect Dis 2016; 2:893-902. [PMID: 27642770 PMCID: PMC5215716 DOI: 10.1021/acsinfecdis.6b00075] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Indexed: 12/31/2022]
Abstract
The general secretion (Sec) pathway is a conserved essential pathway in bacteria and is the primary route of protein export across the cytoplasmic membrane. During protein export, the signal peptidase LepB catalyzes the cleavage of the signal peptide and subsequent release of mature proteins into the extracellular space. We developed a target-based whole cell assay to screen for potential inhibitors of LepB, the sole signal peptidase in Mycobacterium tuberculosis, using a strain engineered to underexpress LepB (LepB-UE). We screened 72,000 compounds against both the Lep-UE and wild-type (wt) strains. We identified the phenylhydrazone (PHY) series as having higher activity against the LepB-UE strain. We conducted a limited structure-activity relationship determination around a representative PHY compound with differential activity (MICs of 3.0 μM against the LepB-UE strain and 18 μM against the wt); several analogues were less potent against the LepB overexpressing strain. A number of chemical modifications around the hydrazone moiety resulted in improved potency. Inhibition of LepB activity was observed for a number of compounds in a biochemical assay using cell membrane fraction derived from M. tuberculosis. Compounds did not increase cell permeability, dissipate membrane potential, or inhibit an unrelated mycobacterial enzyme, suggesting a specific mode of action related to the LepB secretory mechanism.
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Affiliation(s)
- Shilah A. Bonnett
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Juliane Ollinger
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Susantha Chandrasekera
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Stephanie Florio
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Theresa O’Malley
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Megan Files
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Jo-Ann Jee
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - James Ahn
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Allen Casey
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Yulia Ovechkina
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - David Roberts
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
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5
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Kancharla P, Bonnett SA, Reynolds KA. Stenotrophomonas maltophilia OleC-Catalyzed ATP-Dependent Formation of Long-Chain Z-Olefins from 2-Alkyl-3-hydroxyalkanoic Acids. Chembiochem 2016; 17:1426-9. [PMID: 27238740 DOI: 10.1002/cbic.201600063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Indexed: 12/21/2022]
Abstract
The bacterial pathway of olefin biosynthesis starts with OleA catalyzed "head-to-head" condensation of two CoA-activated long-chain fatty acids to generate (R)-2-alkyl-3-ketoalkanoic acids. A subsequent OleD-catalyzed reduction generates (2R,3S)-2-alkyl-3-hydroxyalkanoic acids. We now show that the final step in the pathway is an OleC-catalyzed ATP-dependent decarboxylative dehydration to form the corresponding Z olefins. Higher kcat /Km values were seen for substrates with longer alkyl chains. All four stereoisomers of 2-hexyl-3-hydroxydecanoic acid were shown to be substrates, and GC-MS and NMR analyses confirmed that the product in each case was (Z)-pentadec-7-ene. LC-MS analysis supported the formation of AMP adduct as an intermediate. The enzymatic and stereochemical course of olefin biosynthesis from long-chain fatty acids by OleA, OleD and OleC is now established.
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Affiliation(s)
- Papireddy Kancharla
- Department of Chemistry, Portland State University, Portland, OR, 97201-3203, USA
| | - Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, OR, 97201-3203, USA
| | - Kevin A Reynolds
- Department of Chemistry, Portland State University, Portland, OR, 97201-3203, USA.
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6
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Bonnett SA, Whicher JR, Papireddy K, Florova G, Smith JL, Reynolds KA. Structural and stereochemical analysis of a modular polyketide synthase ketoreductase domain required for the generation of a cis-alkene. ACTA ACUST UNITED AC 2014; 20:772-83. [PMID: 23790488 DOI: 10.1016/j.chembiol.2013.04.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
Abstract
The formation of an activated cis-3-cyclohexylpropenoic acid by Plm1, the first extension module of the phoslactomycin polyketide synthase, is proposed to occur through an L-3-hydroxyacyl-intermediate as a result of ketoreduction by an A-type ketoreductase (KR). Here, we demonstrate that the KR domain of Plm1 (PlmKR1) catalyzes the formation of an L-3-hydroxyacyl product. The crystal structure of PlmKR1 revealed a well-ordered active site with a nearby Trp residue characteristic of A-type KRs. Structural comparison of PlmKR1 with B-type KRs that produce D-3-hydroxyacyl intermediates revealed significant differences. The active site of cofactor-bound A-type KRs is in a catalysis-ready state, whereas cofactor-bound B-type KRs are in a precatalytic state. Furthermore, the closed lid loop in substrate-bound A-type KRs restricts active site access from all but one direction, which is proposed to control the stereochemistry of ketoreduction.
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Affiliation(s)
- Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, OR. 97201
| | - Jonathan R Whicher
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109
| | | | - Galina Florova
- Department of Chemistry, Portland State University, Portland, OR. 97201
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Kevin A Reynolds
- Department of Chemistry, Portland State University, Portland, OR. 97201
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7
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Yan J, Hazzard C, Bonnett SA, Reynolds KA. Functional modular dissection of DEBS1-TE changes triketide lactone ratios and provides insight into Acyl group loading, hydrolysis, and ACP transfer. Biochemistry 2012; 51:9333-41. [PMID: 23116287 DOI: 10.1021/bi300830q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DEBS1-TE fusion protein is comprised of the loading module, the first two extension modules, and the terminal TE domain of the Saccharopolyspora erythraea 6-deoxyerythronolide B synthase. DEBS1-TE produces triketide lactones that differ on the basis of the starter unit selected by the loading module. Typical fermentations with plasmid-based expression of DEBS1-TE produce a 6:1 ratio of propionate to isobutyrate-derived triketide lactones. Functional dissection of the loading module from the remainder of DEBS1-TE results in 50% lower titers of triketide lactone and a dramatic shift in the production to a 1:4 ratio of propionate to isobutyrate-derived products. A series of radiolabeling studies of the loading module has shown that transfer from the AT to the ACP occurs much faster for propionate than for isobutyrate. However, the equilibrium occupancy of the AT favors isobutyrate such that propionate is outcompeted for ACP occupancy. Thus, propionyl-ACP is the kinetic product, while isobutyryl-ACP is the thermodynamic product. A slowed transfer from the loading domain ACP to first-extension module KS due to functional dissection of DEBS1-TE allows this isobutyryl-ACP-favored equilibrium to be realized and likely accounts for the observed shift in triketide lactone products.
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Affiliation(s)
- John Yan
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
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8
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Bonnett SA, Rath CM, Shareef AR, Joels JR, Chemler JA, Håkansson K, Reynolds K, Sherman DH. Acyl-CoA subunit selectivity in the pikromycin polyketide synthase PikAIV: steady-state kinetics and active-site occupancy analysis by FTICR-MS. ACTA ACUST UNITED AC 2012; 18:1075-81. [PMID: 21944746 DOI: 10.1016/j.chembiol.2011.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/23/2011] [Accepted: 07/04/2011] [Indexed: 10/17/2022]
Abstract
Polyketide natural products generated by type I modular polyketide synthases (PKSs) are vital components in our drug repertoire. To reprogram these biosynthetic assembly lines, we must first understand the steps that occur within the modular "black boxes." Herein, key steps of acyl-CoA extender unit selection are explored by in vitro biochemical analysis of the PikAIV PKS model system. Two complementary approaches are employed: a fluorescent-probe assay for steady-state kinetic analysis, and Fourier Transform Ion Cyclotron Resonance-mass spectrometry (FTICR-MS) to monitor active-site occupancy. Findings from five enzyme variants and four model substrates have enabled a model to be proposed involving catalysis based upon acyl-CoA substrate loading followed by differential rates of hydrolysis. These efforts suggest a strategy for future pathway engineering efforts using unnatural extender units with slow rates of hydrolytic off-loading from the acyltransferase domain.
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Affiliation(s)
- Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
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9
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Bonnett SA, Papireddy K, Higgins S, del Cardayre S, Reynolds KA. Functional characterization of an NADPH dependent 2-alkyl-3-ketoalkanoic acid reductase involved in olefin biosynthesis in Stenotrophomonas maltophilia. Biochemistry 2011; 50:9633-40. [PMID: 21958090 DOI: 10.1021/bi201096w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OleD is shown to play a key reductive role in the generation of alkenes (olefins) from acyl thioesters in Stenotrophomonas maltophilia. The gene coding for OleD clusters with three other genes, oleABC, and all appear to be transcribed in the same direction as an operon in various olefin producing bacteria. In this study, a series of substrates varying in chain length and stereochemistry were synthesized and used to elucidate the functional role and substrate specificity of OleD. We demonstrated that OleD, which is an NADP(H) dependent reductase, is a homodimer which catalyzes the reversible stereospecific reduction of 2-alkyl-3-ketoalkanoic acids. Maximal catalytic efficiency was observed with syn-2-decyl-3-hydroxytetradecanoic acid, with a k(cat)/K(m) 5- and 8-fold higher than for syn-2-octyl-3-hydroxydodecanoic acid and syn-2-hexyl-3-hydroxydecanoic acid, respectively. OleD activity was not observed with syn-2-butyl-3-hydroxyoctanoic acid and compounds lacking a 2-alkyl group such as 3-ketodecanoic and 3-hydroxydecanoic acids, suggesting the necessity of the 2-alkyl chain for enzyme recognition and catalysis. Using diastereomeric pairs of substrates and 4 enantiopure isomers of 2-hexyl-3-hydroxydecanoic acid of known stereochemistry, OleD was shown to have a marked stereochemical preference for the (2R,3S)-isomer. Finally, experiments involving OleA and OleD demonstrate the first 3 steps and stereochemical course in olefin formation from acyl thioesters; condensation to form a 2-alkyl-3-ketoacyl thioester, subsequent thioester hydrolysis, and ketone reduction.
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Affiliation(s)
- Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
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