1
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Jeong KH, Son SB, Ko JH, Lee M, Lee JY. Structural insights into BirA from Haemophilus influenzae, a bifunctional protein as a biotin protein ligase and a transcriptional repressor. Biochem Biophys Res Commun 2024; 733:150601. [PMID: 39213703 DOI: 10.1016/j.bbrc.2024.150601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Biotin is an essential coenzyme involved in various metabolic processes across all known organisms, with biotinylation being crucial for the activity of carboxylases. BirA from Haemophilus influenzae is a bifunctional protein that acts as a biotin protein ligase and a transcriptional repressor. This study reveals the crystal structures of Hin BirA in both its apo- and holo-(biotinyl-5'-AMP bound) forms. As a class II BirA, it consists of three domains: N-terminal DNA binding domain, central catalytic domain, and C-terminal SH3-like domain. The structural analysis shows that the biotin-binding loop forms an ordered structure upon biotinyl-5'-AMP binding. This facilitates its interaction with the ligand and promotes protein dimerization. Comparative studies with other BirA homologs from different organisms indicate that the residues responsible for binding biotinyl-5'-AMP are highly conserved. This study also utilized AlphaFold2 to model the potential heterodimeric interaction between Hin BirA and biotin carboxyl carrier protein, thereby providing insights into the structural basis for biotinylation. These findings enhance our understanding of the structural and functional characteristics of Hin BirA, highlighting its potential as a target for novel antibiotics that disrupt the bacterial biotin synthesis pathways.
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Affiliation(s)
- Kang Hwa Jeong
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Su Bin Son
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Ji Hyuk Ko
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Minho Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
| | - Jae Young Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
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2
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Cronan JE. Lipoic acid attachment to proteins: stimulating new developments. Microbiol Mol Biol Rev 2024; 88:e0000524. [PMID: 38624243 PMCID: PMC11332335 DOI: 10.1128/mmbr.00005-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
SUMMARYLipoic acid-modified proteins are essential for central metabolism and pathogenesis. In recent years, the Escherichia coli and Bacillus subtilis lipoyl assembly pathways have been modified and extended to archaea and diverse eukaryotes including humans. These extensions include a new pathway to insert the key sulfur atoms of lipoate, several new pathways of lipoate salvage, and a novel use of lipoic acid in sulfur-oxidizing bacteria. Other advances are the modification of E. coli LplA for studies of protein localization and protein-protein interactions in cell biology and in enzymatic removal of lipoate from lipoyl proteins. Finally, scenarios have been put forth for the evolution of lipoate assembly in archaea.
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Affiliation(s)
- John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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3
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Purtov YA, Ozoline ON. Neuromodulators as Interdomain Signaling Molecules Capable of Occupying Effector Binding Sites in Bacterial Transcription Factors. Int J Mol Sci 2023; 24:15863. [PMID: 37958845 PMCID: PMC10647483 DOI: 10.3390/ijms242115863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Hormones and neurotransmitters are important components of inter-kingdom signaling systems that ensure the coexistence of eukaryotes with their microbial community. Their ability to affect bacterial physiology, metabolism, and gene expression was evidenced by various experimental approaches, but direct penetration into bacteria has only recently been reported. This opened the possibility of considering neuromodulators as potential effectors of bacterial ligand-dependent regulatory proteins. Here, we assessed the validity of this assumption for the neurotransmitters epinephrine, dopamine, and norepinephrine and two hormones (melatonin and serotonin). Using flexible molecular docking for transcription factors with ligand-dependent activity, we assessed the ability of neuromodulators to occupy their effector binding sites. For many transcription factors, including the global regulator of carbohydrate metabolism, CRP, and the key regulator of lactose assimilation, LacI, this ability was predicted based on the analysis of several 3D models. By occupying the ligand binding site, neuromodulators can sterically hinder the interaction of the target proteins with the natural effectors or even replace them. The data obtained suggest that the direct modulation of the activity of at least some bacterial transcriptional factors by neuromodulators is possible. Therefore, the natural hormonal background may be a factor that preadapts bacteria to the habitat through direct perception of host signaling molecules.
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Affiliation(s)
- Yuri A. Purtov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Olga N. Ozoline
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia
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4
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Tanabe TS, Grosser M, Hahn L, Kümpel C, Hartenfels H, Vtulkin E, Flegler W, Dahl C. Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes. PLoS Biol 2023; 21:e3002177. [PMID: 37368881 DOI: 10.1371/journal.pbio.3002177] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martina Grosser
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lea Hahn
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hanna Hartenfels
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Evelyn Vtulkin
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wanda Flegler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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5
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Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. Nat Methods 2023; 20:908-917. [PMID: 37188954 PMCID: PMC10539039 DOI: 10.1038/s41592-023-01880-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. 'LOV-Turbo' works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.
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Affiliation(s)
- Song-Yi Lee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Joleen S Cheah
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Boxuan Zhao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Charles Xu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heegwang Roh
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Christina K Kim
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Neuroscience and Department of Neurology, University of California, Davis, CA, USA
| | - Kelvin F Cho
- Department of Genetics, Stanford University, Stanford, CA, USA
- Amgen Research, South San Francisco, CA, USA
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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6
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Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531939. [PMID: 36945504 PMCID: PMC10028978 DOI: 10.1101/2023.03.09.531939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions, and function with light. We integrated optogenetic control into proximity labeling (PL), a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the PL enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. "LOV-Turbo" works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffick between endoplasmic reticulum, nuclear, and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by BRET from luciferase, enabling interaction-dependent PL. Overall, LOV-Turbo increases the spatial and temporal precision of PL, expanding the scope of experimental questions that can be addressed with PL.
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7
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Samanta R, Sanghvi N, Beckett D, Matysiak S. Emergence of allostery through reorganization of protein residue network architecture. J Chem Phys 2023; 158:085104. [PMID: 36859102 PMCID: PMC9974213 DOI: 10.1063/5.0136010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Despite more than a century of study, consensus on the molecular basis of allostery remains elusive. A comparison of allosteric and non-allosteric members of a protein family can shed light on this important regulatory mechanism, and the bacterial biotin protein ligases, which catalyze post-translational biotin addition, provide an ideal system for such comparison. While the Class I bacterial ligases only function as enzymes, the bifunctional Class II ligases use the same structural architecture for an additional transcription repression function. This additional function depends on allosterically activated homodimerization followed by DNA binding. In this work, we used experimental, computational network, and bioinformatics analyses to uncover distinguishing features that enable allostery in the Class II biotin protein ligases. Experimental studies of the Class II Escherichia coli protein indicate that catalytic site residues are critical for both catalysis and allostery. However, allostery also depends on amino acids that are more broadly distributed throughout the protein structure. Energy-based community network analysis of representative Class I and Class II proteins reveals distinct residue community architectures, interactions among the communities, and responses of the network to allosteric effector binding. Bioinformatics mutual information analyses of multiple sequence alignments indicate distinct networks of coevolving residues in the two protein families. The results support the role of divergent local residue community network structures both inside and outside of the conserved enzyme active site combined with distinct inter-community interactions as keys to the emergence of allostery in the Class II biotin protein ligases.
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Affiliation(s)
- Riya Samanta
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - Neel Sanghvi
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
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8
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Abstract
![]()
Proximity
labeling can be defined as an enzymatic “in-cell”
chemical reaction that catalyzes the proximity-dependent modification
of biomolecules in live cells. Since the modified proteins can be
isolated and identified via mass spectrometry, this method has been
successfully utilized for the characterization of local proteomes
such as the sub-mitochondrial proteome and the proteome at membrane
contact sites, or spatiotemporal interactome information in live cells,
which are not “accessible” via conventional methods.
Currently, proximity labeling techniques can be applied not only for
local proteome mapping but also for profiling local RNA and DNA, in
addition to showing great potential for elucidating spatial cell–cell
interaction networks in live animal models. We believe that proximity
labeling has emerged as an essential tool in “spatiomics,”
that is, for the extraction of spatially distributed biological information
in a cell or organism. Proximity labeling is a multidisciplinary
chemical technique. For
a decade, we and other groups have engineered it for multiple applications
based on the modulation of enzyme chemistry, chemical probe design,
and mass analysis techniques that enable superior mapping results.
The technique has been adopted in biology and chemistry. This “in-cell”
reaction has been widely adopted by biologists who modified it into
an in vivo reaction in animal models. In our laboratory, we conducted
in vivo proximity labeling reactions in mouse models and could successfully
obtain the liver-specific secretome and muscle-specific mitochondrial
matrix proteome. We expect that proximity reaction can further contribute
to revealing tissue-specific localized molecular information in live
animal models. Simultaneously, chemists have also adopted the
concept and employed
chemical “photocatalysts” as artificial enzymes to develop
new proximity labeling reactions. Under light activation, photocatalysts
can convert the precursor molecules to the reactive species via electron
transfer or energy transfer and the reactive molecules can react with
proximal biomolecules within a definite lifetime in an aqueous solution.
To identify the modified biomolecules by proximity labeling, the modified
biomolecules should be enriched after lysis and sequenced using sequencing
tools. In this analysis step, the direct detection of modified residue(s)
on the modified proteins or nucleic acids can be the proof of their
labeling event by proximal enzymes or catalysts in the cell. In this
Account, we introduce the basic concept of proximity labeling and
the multidirectional advances in the development of this method. We
believe that this Account may facilitate further utilization and modification
of the method in both biological and chemical research communities,
thereby revealing unknown spatially distributed molecular or cellular
information or spatiome.
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Affiliation(s)
- Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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9
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Chen R, Zhang N, Zhou Y, Jing J. Optical Sensors and Actuators for Probing Proximity-Dependent Biotinylation in Living Cells. Front Cell Neurosci 2022; 16:801644. [PMID: 35250484 PMCID: PMC8890125 DOI: 10.3389/fncel.2022.801644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/13/2022] [Indexed: 01/09/2023] Open
Abstract
Proximity-dependent biotinylation techniques have been gaining wide applications in the systematic analysis of protein-protein interactions (PPIs) on a proteome-wide scale in living cells. The engineered biotin ligase TurboID is among the most widely adopted given its enhanced biotinylation efficiency, but it faces the background biotinylation complication that might confound proteomic data interpretation. To address this issue, we report herein a set of split TurboID variants that can be reversibly assembled by using light (designated “OptoID”), which enable optogenetic control of biotinylation based proximity labeling in living cells. OptoID could be further coupled with an engineered monomeric streptavidin that permits real-time monitoring of biotinylation with high temporal precision. These optical actuators and sensors will likely find broad applications in precise proximity proteomics and rapid detection of biotinylation in living cells.
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Affiliation(s)
- Rui Chen
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ningxia Zhang
- Laboratory of Cancer Biology, Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yubin Zhou
- Department of Translational Medical Sciences, Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, United States
- *Correspondence: Yubin Zhou,
| | - Ji Jing
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Ji Jing,
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10
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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11
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Sternicki LM, Nguyen S, Pacholarz KJ, Barran P, Pendini NR, Booker GW, Huet Y, Baltz R, Wegener KL, Pukala TL, Polyak SW. Biochemical characterisation of class III biotin protein ligases from Botrytis cinerea and Zymoseptoria tritici. Arch Biochem Biophys 2020; 691:108509. [PMID: 32717225 DOI: 10.1016/j.abb.2020.108509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Biotin protein ligase (BPL) is an essential enzyme in all kingdoms of life, making it a potential target for novel anti-infective agents. Whilst bacteria and archaea have simple BPL structures (class I and II), the homologues from certain eukaryotes such as mammals, insects and yeast (class III) have evolved a more complex structure with a large extension on the N-terminus of the protein in addition to the conserved catalytic domain. The absence of atomic resolution structures of any class III BPL hinders structural and functional analysis of these enzymes. Here, two new class III BPLs from agriculturally important moulds Botrytis cinerea and Zymoseptoria tritici were characterised alongside the homologue from the prototypical yeast Saccharomyces cerevisiae. Circular dichroism and ion mobility-mass spectrometry analysis revealed conservation of the overall tertiary and secondary structures of all three BPLs, corresponding with the high sequence similarity. Subtle structural differences were implied by the different thermal stabilities of the enzymes and their varied Michaelis constants for their interactions with ligands biotin, MgATP, and biotin-accepting substrates from different species. The three BPLs displayed different preferences for fungal versus bacterial protein substrates, providing further evidence that class III BPLs have a 'substrate validation' activity for selecting only appropriate proteins for biotinylation. Selective, potent inhibition of these three BPLs was demonstrated despite sequence and structural homology. This highlights the potential for targeting BPL for novel, selective antifungal therapies against B. cinerea, Z. tritici and other fungal species.
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Affiliation(s)
- Louise M Sternicki
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Stephanie Nguyen
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole R Pendini
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Yoann Huet
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Rachel Baltz
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia.
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12
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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13
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Cho KF, Branon TC, Rajeev S, Svinkina T, Udeshi ND, Thoudam T, Kwak C, Rhee HW, Lee IK, Carr SA, Ting AY. Split-TurboID enables contact-dependent proximity labeling in cells. Proc Natl Acad Sci U S A 2020; 117:12143-12154. [PMID: 32424107 PMCID: PMC7275672 DOI: 10.1073/pnas.1919528117] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proximity labeling catalyzed by promiscuous enzymes, such as TurboID, have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein-protein interaction or membrane-membrane apposition. At endoplasmic reticulum-mitochondria contact sites, reconstituted TurboID catalyzed spatially restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to endoplasmic reticulum-mitochondria contacts. We validated eight candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially specific proximity labeling in cells.
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Affiliation(s)
- Kelvin F Cho
- Cancer Biology Program, Stanford University, Stanford, CA 94305
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sanjana Rajeev
- Department of Genetics, Stanford University, Stanford, CA 94305
| | | | | | - Themis Thoudam
- Research Institute of Aging and Metabolism, Kyungpook National University, 37224 Daegu, South Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, 08826 Seoul, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, 44919 Ulsan, South Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, 08826 Seoul, South Korea
- School of Biological Sciences, Seoul National University, 08826 Seoul, South Korea
| | - In-Kyu Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, 37224 Daegu, South Korea
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, 41944 Daegu, South Korea
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University, 41944 Daegu, South Korea
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA 94305;
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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14
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Hayes AJ, Satiaputra J, Sternicki LM, Paparella AS, Feng Z, Lee KJ, Blanco-Rodriguez B, Tieu W, Eijkelkamp BA, Shearwin KE, Pukala TL, Abell AD, Booker GW, Polyak SW. Advanced Resistance Studies Identify Two Discrete Mechanisms in Staphylococcus aureus to Overcome Antibacterial Compounds that Target Biotin Protein Ligase. Antibiotics (Basel) 2020; 9:antibiotics9040165. [PMID: 32268615 PMCID: PMC7235819 DOI: 10.3390/antibiotics9040165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biotin protein ligase (BPL) inhibitors are a novel class of antibacterial that target clinically important methicillin-resistant Staphylococcus aureus (S. aureus). In S. aureus, BPL is a bifunctional protein responsible for enzymatic biotinylation of two biotin-dependent enzymes, as well as serving as a transcriptional repressor that controls biotin synthesis and import. In this report, we investigate the mechanisms of action and resistance for a potent anti-BPL, an antibacterial compound, biotinyl-acylsulfamide adenosine (BASA). We show that BASA acts by both inhibiting the enzymatic activity of BPL in vitro, as well as functioning as a transcription co-repressor. A low spontaneous resistance rate was measured for the compound (<10−9) and whole-genome sequencing of strains evolved during serial passaging in the presence of BASA identified two discrete resistance mechanisms. In the first, deletion of the biotin-dependent enzyme pyruvate carboxylase is proposed to prioritize the utilization of bioavailable biotin for the essential enzyme acetyl-CoA carboxylase. In the second, a D200E missense mutation in BPL reduced DNA binding in vitro and transcriptional repression in vivo. We propose that this second resistance mechanism promotes bioavailability of biotin by derepressing its synthesis and import, such that free biotin may outcompete the inhibitor for binding BPL. This study provides new insights into the molecular mechanisms governing antibacterial activity and resistance of BPL inhibitors in S. aureus.
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Affiliation(s)
- Andrew J. Hayes
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Louise M. Sternicki
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Ashleigh S. Paparella
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Zikai Feng
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Kwang J. Lee
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Beatriz Blanco-Rodriguez
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - William Tieu
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Bart A. Eijkelkamp
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Keith E. Shearwin
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Tara L. Pukala
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Andrew D. Abell
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Grant W. Booker
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Steven W. Polyak
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
- Correspondence: ; Tel.: +61883021603
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15
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Wang J, Samanta R, Custer G, Look C, Matysiak S, Beckett D. Tuning Allostery through Integration of Disorder to Order with a Residue Network. Biochemistry 2020; 59:790-801. [PMID: 31899864 DOI: 10.1021/acs.biochem.9b01006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In allostery, a signal from one site in a protein is transmitted to a second site to alter its function. Due to its ubiquity in biology and the potential for its exploitation in drug and protein design, the molecular basis of allosteric communication continues to be the subject of intense research. Although allosterically coupled sites are frequently characterized by disorder, how communication between disordered segments occurs remains obscure. Allosteric activation of Escherichia coli BirA dimerization occurs via coupled distant disorder-to-order transitions. In this work, combined structural and computational studies reveal an extensive residue network in BirA. Substitution of several network residues yields large perturbations to allostery. Force distribution analysis reveals that disruptions to the disorder-to-order transitions through amino acid substitution are manifested in shifts in the energy experienced by network residues as well as alterations in packing of an α-helix that plays a critical role in allostery. The combined results reveal a highly distributed allosteric mechanism that is robust to sequence change.
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Affiliation(s)
- Jingheng Wang
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Riya Samanta
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Gregory Custer
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Christopher Look
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
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16
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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17
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Satiaputra J, Sternicki LM, Hayes AJ, Pukala TL, Booker GW, Shearwin KE, Polyak SW. Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus. Sci Rep 2019; 9:2767. [PMID: 30808984 PMCID: PMC6391492 DOI: 10.1038/s41598-019-39398-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022] Open
Abstract
An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli, but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA (EcBirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA (SaBirA). We identify a mechanism that differs from that of EcBirA, wherein SaBirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the SaBirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.
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Affiliation(s)
- Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Harry Perkins Institute of Medical Research, Shenton Park, Western Australia, 6008, Australia
| | - Louise M Sternicki
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Andrew J Hayes
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Faculty of Health and Medical Sciences, Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Keith E Shearwin
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5001, Australia.
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18
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Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol 2018; 36:880-887. [PMID: 30125270 PMCID: PMC6126969 DOI: 10.1038/nbt.4201] [Citation(s) in RCA: 1195] [Impact Index Per Article: 170.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. Enzyme-catalyzed proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, current PL methods require over 18 h of labeling time or utilize chemicals with limited cell permeability or high toxicity. We used yeast display-based directed evolution to engineer two promiscuous mutants of biotin ligase, TurboID and miniTurbo, which catalyze PL with much greater efficiency than BioID or BioID2, and enable 10-min PL in cells with non-toxic and easily deliverable biotin. Furthermore, TurboID extends biotin-based PL to flies and worms.
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Affiliation(s)
- Tess C. Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
| | - Justin A. Bosch
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ariana D. Sanchez
- Department of Biology, Stanford University, Stanford, California, USA
| | | | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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19
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He C, Custer G, Wang J, Matysiak S, Beckett D. Superrepression through Altered Corepressor–Activated Protein:Protein Interactions. Biochemistry 2018; 57:1119-1129. [DOI: 10.1021/acs.biochem.7b01122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chenlu He
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory Custer
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jingheng Wang
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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20
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Rodionova IA, Vetting MW, Li X, Almo SC, Osterman AL, Rodionov DA. A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res 2017; 45:3785-3799. [PMID: 28073944 PMCID: PMC5397151 DOI: 10.1093/nar/gkw1331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022] Open
Abstract
Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro. The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea.
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Affiliation(s)
- Irina A Rodionova
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiaoqing Li
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrei L Osterman
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051 Russia
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21
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Wang J, Custer G, Beckett D, Matysiak S. Long Distance Modulation of Disorder-to-Order Transitions in Protein Allostery. Biochemistry 2017; 56:4478-4488. [PMID: 28718281 DOI: 10.1021/acs.biochem.7b00496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the Escherichia coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP. The effector acts by promoting BirA dimerization, which is a prerequisite for sequence-specific binding to the biotin biosynthetic operon operator sequence. A 30 Å distance separates the effector binding and dimerization surfaces in BirA, and previous studies indicate that allostery is mediated, in part, by disorder-to-order transitions on the two coupled sites. In this work, combined experimental and computational methods have been applied to investigate the molecular basis of allosteric communication in BirA. Double-mutant cycle analysis coupled with thermodynamic measurements indicates functional coupling between residues in disordered loops on the two distant surfaces. All atom molecular dynamics simulations reveal that this coupling occurs through long distance reciprocal modulation of the structure and dynamics of disorder-to-order transitions on the two surfaces.
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Affiliation(s)
- Jingheng Wang
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gregory Custer
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Dorothy Beckett
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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22
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Wang J, Beckett D. A conserved regulatory mechanism in bifunctional biotin protein ligases. Protein Sci 2017; 26:1564-1573. [PMID: 28466579 DOI: 10.1002/pro.3182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 11/10/2022]
Abstract
Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization. Like E. coli BirA (EcBirA), Staphylococcus aureus, and Bacillus subtilis BirA (Sa and BsBirA) repress transcription in vivo in a biotin-dependent manner. In this work, sedimentation equilibrium measurements were performed to investigate the molecular basis of this biotin-responsive transcription regulation. The results reveal that, as observed for EcBirA, Sa, and BsBirA dimerization reactions are significantly enhanced by bio-5'-AMP binding. Thus, the molecular mechanism of the Biotin Regulatory System is conserved in the biotin repressors from these three organisms.
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Affiliation(s)
- Jingheng Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
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23
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Mechanisms Governing Precise Protein Biotinylation. Trends Biochem Sci 2017; 42:383-394. [DOI: 10.1016/j.tibs.2017.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/25/2017] [Accepted: 02/03/2017] [Indexed: 12/26/2022]
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24
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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25
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Bond TEH, Sorenson AE, Schaeffer PM. Functional characterisation of Burkholderia pseudomallei biotin protein ligase: A toolkit for anti-melioidosis drug development. Microbiol Res 2017; 199:40-48. [PMID: 28454708 DOI: 10.1016/j.micres.2017.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/17/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis. The bacterium is responsible for 20% of community-acquired sepsis cases and 40% of sepsis-related mortalities in northeast Thailand, and is intrinsically resistant to aminoglycosides, macrolides, rifamycins, cephalosporins, and nonureidopenicillins. There is no vaccine and its diagnosis is problematic. Biotin protein ligase (BirA) which is essential for fatty acid synthesis has been proposed as a drug target in bacteria. Very few bacterial BirA have been characterized, and a better understanding of these enzymes is necessary to further assess their value as drug targets. BirA within the Burkholderia genus have not yet been investigated. We present for the first time the cloning, expression, purification and functional characterisation of the putative Bp BirA and orthologous B. thailandensis (Bt) biotin carboxyl carrier protein (BCCP) substrate. A GFP-tagged Bp BirA was produced and applied for the development of a high-throughput (HT) assay based on our differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP) principle as well as an electrophoretic mobility shift assay. Our biochemical data in combination with the new HT DSF-GTP and biotinylation activity assay could facilitate future drug screening efforts against this drug-resistant organism.
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Affiliation(s)
- Thomas E H Bond
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Alanna E Sorenson
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Patrick M Schaeffer
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia.
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A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. J Bacteriol 2017; 199:JB.00743-16. [PMID: 27920295 DOI: 10.1128/jb.00743-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 11/28/2016] [Indexed: 01/15/2023] Open
Abstract
Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the Crenarchaeota phylum as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by in vitro DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon Metallosphaera yellowstonensis MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition. IMPORTANCE Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.
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Biotin Protein Ligase Is a Target for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5030026. [PMID: 27463729 PMCID: PMC5039522 DOI: 10.3390/antibiotics5030026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
Abstract
There is a desperate need for novel antibiotic classes to combat the rise of drug resistant pathogenic bacteria, such as Staphylococcus aureus. Inhibitors of the essential metabolic enzyme biotin protein ligase (BPL) represent a promising drug target for new antibacterials. Structural and biochemical studies on the BPL from S. aureus have paved the way for the design and development of new antibacterial chemotherapeutics. BPL employs an ordered ligand binding mechanism for the synthesis of the reaction intermediate biotinyl-5′-AMP from substrates biotin and ATP. Here we review the structure and catalytic mechanism of the target enzyme, along with an overview of chemical analogues of biotin and biotinyl-5′-AMP as BPL inhibitors reported to date. Of particular promise are studies to replace the labile phosphoroanhydride linker present in biotinyl-5′-AMP with alternative bioisosteres. A novel in situ click approach using a mutant of S. aureus BPL as a template for the synthesis of triazole-based inhibitors is also presented. These approaches can be widely applied to BPLs from other bacteria, as well as other closely related metabolic enzymes and antibacterial drug targets.
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Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway. Microbiol Mol Biol Rev 2016; 80:429-50. [PMID: 27074917 DOI: 10.1128/mmbr.00073-15] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although the structure of lipoic acid and its role in bacterial metabolism were clear over 50 years ago, it is only in the past decade that the pathways of biosynthesis of this universally conserved cofactor have become understood. Unlike most cofactors, lipoic acid must be covalently bound to its cognate enzyme proteins (the 2-oxoacid dehydrogenases and the glycine cleavage system) in order to function in central metabolism. Indeed, the cofactor is assembled on its cognate proteins rather than being assembled and subsequently attached as in the typical pathway, like that of biotin attachment. The first lipoate biosynthetic pathway determined was that of Escherichia coli, which utilizes two enzymes to form the active lipoylated protein from a fatty acid biosynthetic intermediate. Recently, a more complex pathway requiring four proteins was discovered in Bacillus subtilis, which is probably an evolutionary relic. This pathway requires the H protein of the glycine cleavage system of single-carbon metabolism to form active (lipoyl) 2-oxoacid dehydrogenases. The bacterial pathways inform the lipoate pathways of eukaryotic organisms. Plants use the E. coli pathway, whereas mammals and fungi probably use the B. subtilis pathway. The lipoate metabolism enzymes (except those of sulfur insertion) are members of PFAM family PF03099 (the cofactor transferase family). Although these enzymes share some sequence similarity, they catalyze three markedly distinct enzyme reactions, making the usual assignment of function based on alignments prone to frequent mistaken annotations. This state of affairs has possibly clouded the interpretation of one of the disorders of human lipoate metabolism.
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Mechanisms of biotin-regulated gene expression in microbes. Synth Syst Biotechnol 2016; 1:17-24. [PMID: 29062923 PMCID: PMC5640590 DOI: 10.1016/j.synbio.2016.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/08/2016] [Accepted: 01/10/2016] [Indexed: 12/23/2022] Open
Abstract
Biotin is an essential micronutrient that acts as a co-factor for biotin-dependent metabolic enzymes. In bacteria, the supply of biotin can be achieved by de novo synthesis or import from exogenous sources. Certain bacteria are able to obtain biotin through both mechanisms while others can only fulfill their biotin requirement through de novo synthesis. Inability to fulfill their cellular demand for biotin can have detrimental consequences on cell viability and virulence. Therefore understanding the transcriptional mechanisms that regulate biotin biosynthesis and transport will extend our knowledge about bacterial survival and metabolic adaptation during pathogenesis when the supply of biotin is limited. The most extensively characterized protein that regulates biotin synthesis and uptake is BirA. In certain bacteria, such as Escherichia coli and Staphylococcus aureus, BirA is a bi-functional protein that serves as a transcriptional repressor to regulate biotin biosynthesis genes, as well as acting as a ligase to catalyze the biotinylation of biotin-dependent enzymes. Recent studies have identified two other proteins that also regulate biotin synthesis and transport, namely BioQ and BioR. This review summarizes the different transcriptional repressors and their mechanism of action. Moreover, the ability to regulate the expression of target genes through the activity of a vitamin, such as biotin, may have biotechnological applications in synthetic biology.
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Cressman WJ, Beckett D. Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation. Biochemistry 2015; 55:243-52. [PMID: 26678378 DOI: 10.1021/acs.biochem.5b00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allosteric coupling in proteins is ubiquitous but incompletely understood, particularly in systems characterized by coupling over large distances. Binding of the allosteric effector, bio-5'-AMP, to the Escherichia coli biotin protein ligase, BirA, enhances the protein's dimerization free energy by -4 kcal/mol. Previous studies revealed that disorder-to-order transitions at the effector binding and dimerization sites, which are separated by 33 Å, are integral to functional coupling. Perturbations to the transition at the ligand binding site alter both ligand binding and coupled dimerization. Alanine substitutions in four loops on the dimerization surface yield a range of energetic effects on dimerization. A glycine to alanine substitution at position 142 in one of these loops results in a complete loss of allosteric coupling, disruption of the disorder-to-order transitions at both functional sites, and a decreased affinity for the effector. In this work, allosteric communication between the effector binding and dimerization surfaces in BirA was further investigated by performing isothermal titration calorimetry measurements on nine proteins with alanine substitutions in three dimerization surface loops. In contrast to BirAG142A, at 20 °C all variants bind to bio-5'-AMP with free energies indistinguishable from that measured for wild-type BirA. However, the majority of the variants exhibit altered heat capacity changes for effector binding. Moreover, the ΔCp values correlate with the dimerization free energies of the effector-bound proteins. These thermodynamic results, combined with structural information, indicate that allosteric activation of the BirA monomer involves formation of a network of intramolecular interactions on the dimerization surface in response to bio-5'-AMP binding at the distant effector binding site.
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Affiliation(s)
- William J Cressman
- Center for Biomolecular Structure and Organization, Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Dorothy Beckett
- Center for Biomolecular Structure and Organization, Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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31
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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32
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
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33
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Eginton C, Cressman WJ, Bachas S, Wade H, Beckett D. Allosteric coupling via distant disorder-to-order transitions. J Mol Biol 2015; 427:1695-704. [PMID: 25746672 DOI: 10.1016/j.jmb.2015.02.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/12/2015] [Accepted: 02/26/2015] [Indexed: 10/23/2022]
Abstract
Intrinsic disorder provides a means of maximizing allosteric coupling in proteins. However, the mechanisms by which the disorder functions in allostery remain to be elucidated. Small ligand, bio-5'-AMP, binding and dimerization of the Escherichia coli biotin repressor are allosterically coupled. Folding of a disordered loop in the allosteric effector binding site is required to realize the full coupling free energy of -4.0 ± 0.3 kcal/mol observed in the wild-type protein. Alanine substitution of a glycine residue on the dimerization surface that does not directly contribute to the dimerization interface completely abolishes this coupling. In this work, the structure of this variant, solved by X-ray crystallography, reveals a monomeric corepressor-bound protein. In the structure loops, neither of which contains the alanine substitution, on both the dimerization and effector binding surfaces that are folded in the corepressor-bound wild-type protein are disordered. The structural data combined with functional measurements indicate that allosteric coupling between ligand binding and dimerization in BirA (E. coli biotin repressor/biotin protein ligase) is achieved via reciprocal communication of disorder-to-order transitions on two distant functional surfaces.
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Affiliation(s)
- Christopher Eginton
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - William J Cressman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Sharrol Bachas
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Herschel Wade
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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34
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Tieu W, Polyak SW, Paparella AS, Yap MY, Soares da Costa TP, Ng B, Wang G, Lumb R, Bell JM, Turnidge JD, Wilce MCJ, Booker GW, Abell AD. Improved Synthesis of Biotinol-5'-AMP: Implications for Antibacterial Discovery. ACS Med Chem Lett 2015; 6:216-20. [PMID: 25699152 DOI: 10.1021/ml500475n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/11/2014] [Indexed: 11/30/2022] Open
Abstract
An improved synthesis of biotinol-5'-AMP, an acyl-AMP mimic of the natural reaction intermediate of biotin protein ligase (BPL), is reported. This compound was shown to be a pan inhibitor of BPLs from a series of clinically important bacteria, particularly Staphylococcus aureus and Mycobacterium tuberculosis, and kinetic analysis revealed it to be competitive against the substrate biotin. Biotinol-5'-AMP also exhibits antibacterial activity against a panel of clinical isolates of S. aureus and M. tuberculosis with MIC values of 1-8 and 0.5-2.5 μg/mL, respectively, while being devoid of cytotoxicity to human HepG2 cells.
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Affiliation(s)
- William Tieu
- School
of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Steven W. Polyak
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ashleigh S. Paparella
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y. Yap
- School
of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Tatiana P. Soares da Costa
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Belinda Ng
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Geqing Wang
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Richard Lumb
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | - Jan M. Bell
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | - John D. Turnidge
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | | | - Grant W. Booker
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- School
of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
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35
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Eginton C, Naganathan S, Beckett D. Sequence-function relationships in folding upon binding. Protein Sci 2014; 24:200-11. [PMID: 25407143 DOI: 10.1002/pro.2605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/13/2014] [Indexed: 11/08/2022]
Abstract
Folding coupled to binding is ubiquitous in biology. Nevertheless, the relationship of sequence to function for protein segments that undergo coupled binding and folding remains to be determined. Specifically, it is not known if the well-established rules that govern protein folding and stability are relevant to ligand-linked folding transitions. Upon small ligand biotinoyl-5'-AMP (bio-5'-AMP) binding the Escherichia coli protein BirA undergoes a disorder-to-order transition that results in formation of a network of packed hydrophobic side chains. Ligand binding is also allosterically coupled to protein association, with bio-5'-AMP binding enhancing the dimerization free energy by -4.0 kcal/mol. Previous studies indicated that single alanine replacements in a three residue hydrophobic cluster that contributes to the larger network disrupt cluster formation, ligand binding, and allosteric activation of protein association. In this work, combined equilibrium and kinetic measurements of BirA variants with alanine substitutions in the entire hydrophobic network reveal large functional perturbations resulting from any single substitution and highly non-additive effects of multiple substitutions. These substitutions also disrupt ligand-linked folding. The combined results suggest that, analogous to protein folding, functional disorder-to-order linked to binding requires optimal packing of the relevant hydrophobic side chains that contribute to the transition. The potential for many combinations of residues to satisfy this requirement implies that, although functionally important, segments of homologous proteins that undergo folding linked to binding can exhibit sequence divergence.
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Affiliation(s)
- Christopher Eginton
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland, 20742
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36
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Sittiwong W, Cordonier EL, Zempleni J, Dussault PH. β-Keto and β-hydroxyphosphonate analogs of biotin-5'-AMP are inhibitors of holocarboxylase synthetase. Bioorg Med Chem Lett 2014; 24:5568-5571. [PMID: 25466176 DOI: 10.1016/j.bmcl.2014.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 11/15/2022]
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent attachment of biotin to cytoplasmic and mitochondrial carboxylases, nuclear histones, and over a hundred human proteins. Nonhydrolyzable ketophosphonate (β-ketoP) and hydroxyphosphonate (β-hydroxyP) analogs of biotin-5'-AMP inhibit holocarboxylase synthetase (HLCS) with IC50 values of 39.7 μM and 203.7 μM. By comparison, an IC50 value of 7 μM was observed with the previously reported biotinol-5'-AMP. The Ki values, 3.4 μM and 17.3 μM, respectively, are consistent with the IC50 results, and close to the Ki obtained for biotinol-5'-AMP (7 μM). The β-ketoP and β-hydroxyP molecules are competitive inhibitors of HLCS while biotinol-5'-AMP inhibited HLCS by a mixed mechanism.
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Affiliation(s)
- Wantanee Sittiwong
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Elizabeth L Cordonier
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA.
| | - Patrick H Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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37
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Tieu W, Jarrad AM, Paparella AS, Keeling KA, Soares da Costa TP, Wallace JC, Booker GW, Polyak SW, Abell AD. Heterocyclic acyl-phosphate bioisostere-based inhibitors of Staphylococcus aureus biotin protein ligase. Bioorg Med Chem Lett 2014; 24:4689-4693. [DOI: 10.1016/j.bmcl.2014.08.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/07/2014] [Accepted: 08/11/2014] [Indexed: 01/17/2023]
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38
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Henke SK, Cronan JE. Successful conversion of the Bacillus subtilis BirA Group II biotin protein ligase into a Group I ligase. PLoS One 2014; 9:e96757. [PMID: 24816803 PMCID: PMC4016012 DOI: 10.1371/journal.pone.0096757] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Group II biotin protein ligases (BPLs) are characterized by the presence of an N-terminal DNA binding domain that allows transcriptional regulation of biotin biosynthetic and transport genes whereas Group I BPLs lack this N-terminal domain. The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties. We report evidence that B. subtilis BirA is a Group II BPL that regulates transcription at three genomic sites: bioWAFDBI, yuiG and yhfUTS. Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function. This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.
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Affiliation(s)
- Sarah K. Henke
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
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39
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Ma Q, Akhter Y, Wilmanns M, Ehebauer MT. Active site conformational changes upon reaction intermediate biotinyl-5'-AMP binding in biotin protein ligase from Mycobacterium tuberculosis. Protein Sci 2014; 23:932-9. [PMID: 24723382 DOI: 10.1002/pro.2475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/07/2022]
Abstract
Protein biotinylation, a rare form of post-translational modification, is found in enzymes required for lipid biosynthesis. In mycobacteria, this process is essential for the formation of their complex and distinct cell wall and has become a focal point of drug discovery approaches. The enzyme responsible for this process, biotin protein ligase, substantially varies in different species in terms of overall structural organization, regulation of function and substrate specificity. To advance the understanding of the molecular mechanism of biotinylation in Mycobacterium tuberculosis we have biochemically and structurally characterized the corresponding enzyme. We report the high-resolution crystal structures of the apo-form and reaction intermediate biotinyl-5'-AMP-bound form of M. tuberculosis biotin protein ligase. Binding of the reaction intermediate leads to clear disorder-to-order transitions. We show that a conserved lysine, Lys138, in the active site is essential for biotinylation.
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Affiliation(s)
- Qingjun Ma
- European Molecular Biology Laboratory, EMBL-Hamburg, c/o DESY, Building 25A, Notkestrasse 85, 22603, Hamburg, Germany
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40
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Pendini NR, Yap MY, Traore DAK, Polyak SW, Cowieson NP, Abell A, Booker GW, Wallace JC, Wilce JA, Wilce MCJ. Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Protein Sci 2013; 22:762-73. [PMID: 23559560 DOI: 10.1002/pro.2262] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 11/06/2022]
Abstract
The essential metabolic enzyme biotin protein ligase (BPL) is a potential target for the development of new antibiotics required to combat drug-resistant pathogens. Staphylococcus aureus BPL (SaBPL) is a bifunctional protein, possessing both biotin ligase and transcription repressor activities. This positions BPL as a key regulator of several important metabolic pathways. Here, we report the structural analysis of both holo- and apo-forms of SaBPL using X-ray crystallography. We also present small-angle X-ray scattering data of SaBPL in complex with its biotin-carboxyl carrier protein substrate as well as the SaBPL:DNA complex that underlies repression. This has revealed the molecular basis of ligand (biotinyl-5'-AMP) binding and conformational changes associated with catalysis and repressor function. These data provide new information to better understand the bifunctional activities of SaBPL and to inform future strategies for antibiotic discovery.
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Affiliation(s)
- Nicole R Pendini
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
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41
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Soares da Costa TP, Yap MY, Perugini MA, Wallace JC, Abell AD, Wilce MCJ, Polyak SW, Booker GW. Dual roles of F123 in protein homodimerization and inhibitor binding to biotin protein ligase fromStaphylococcus aureus. Mol Microbiol 2013; 91:110-20. [DOI: 10.1111/mmi.12446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | - Min Y. Yap
- School of Biomedical Science; Monash University; Victoria 3800 Australia
| | - Matthew A. Perugini
- Department of Biochemistry; La Trobe Institute for Molecular Science; La Trobe University; Victoria 3086 Australia
| | - John C. Wallace
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- School of Chemistry and Physics; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | | | - Steven W. Polyak
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | - Grant W. Booker
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
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42
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Chakravartty V, Cronan JE. The wing of a winged helix-turn-helix transcription factor organizes the active site of BirA, a bifunctional repressor/ligase. J Biol Chem 2013; 288:36029-39. [PMID: 24189073 DOI: 10.1074/jbc.m113.525618] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The BirA biotin protein ligase of Escherichia coli belongs to the winged helix-turn-helix (wHTH) family of transcriptional regulators. The N-terminal BirA domain is required for both transcriptional regulation of biotin synthesis and biotin protein ligase activity. We addressed the structural and functional role of the wing of the wHTH motif in both BirA functions. A panel of N-terminal deletion mutant proteins including a discrete deletion of the wing motif were unable to bind DNA. However, all the N-terminal deletion mutants weakly complemented growth of a ΔbirA strain at low biotin concentrations, indicating compromised ligase activity. A wing domain chimera was constructed by replacing the BirA wing with the nearly isosteric wing of the E. coli OmpR transcription factor. Although this chimera BirA was defective in operator binding, it was much more efficient in complementation of a ΔbirA strain than was the wing-less protein. The enzymatic activities of the wing deletion and chimera proteins in the in vitro synthesis of biotinoyl-5'-AMP differed greatly. The wing deletion BirA accumulated an off pathway compound, ADP, whereas the chimera protein did not. Finally, we report that a single residue alteration in the wing bypasses the deleterious effects caused by mutations in the biotin-binding loop of the ligase active site. We believe that the role of the wing in the BirA enzymatic reaction is to orient the active site and thereby protect biotinoyl-5'-AMP from attack by solvent. This is the first evidence that the wing domain of a wHTH protein can play an important role in enzymatic activity.
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43
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Eginton C, Beckett D. A large solvent isotope effect on protein association thermodynamics. Biochemistry 2013; 52:6595-600. [PMID: 23984950 DOI: 10.1021/bi400952m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Solvent reorganization can contribute significantly to the energetics of protein-protein interactions. However, our knowledge of the magnitude of the energetic contribution is limited, in part, by a dearth of quantitative experimental measurements. The biotin repressor forms a homodimer as a prerequisite to DNA binding to repress transcription initiation. At 20 °C, the dimerization reaction, which is thermodynamically coupled to binding of a small ligand, bio-5'-AMP, is characterized by a Gibbs free energy of -7 kcal/mol. This modest net dimerization free energy reflects underlying, very large opposing enthalpic and entropic driving forces of 41 ± 3 and -48 ± 3 kcal/mol, respectively. The thermodynamics have been interpreted as indicating coupling of solvent release to dimerization. In this work, this interpretation has been investigated by measuring the effect of replacing H2O with D2O on the dimerization thermodynamics. Sedimentation equilibrium measurements performed at 20 °C reveal a solvent isotope effect of -1.5 kcal/mol on the Gibbs free energy of dimerization. Analysis of the temperature dependence of the reaction in D2O indicates enthalpic and entropic contributions of 28 and -37 kcal/mol, respectively, considerably smaller than the values measured in H2O. These large solvent isotope perturbations to the thermodynamics are consistent with a significant contribution of solvent release to the dimerization reaction.
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Affiliation(s)
- Christopher Eginton
- Department of Chemistry and Biochemistry, College of Computer, Mathematical and Natural Sciences, University of Maryland , College Park, Maryland 20742, United States
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44
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Adikaram PR, Beckett D. Protein:protein interactions in control of a transcriptional switch. J Mol Biol 2013; 425:4584-94. [PMID: 23896299 DOI: 10.1016/j.jmb.2013.07.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 12/01/2022]
Abstract
Protein partner exchange plays a key role in regulating many biological switches. Although widespread, the mechanisms dictating protein partner identity and, therefore, the outcome of a switch have been determined for a limited number of systems. The Escherichia coli protein BirA undergoes a switch between posttranslational biotin attachment and transcription repression in response to cellular biotin demand. Moreover, the functional switch reflects formation of alternative mutually exclusive protein:protein interactions by BirA. Previous studies provided a set of alanine-substituted BirA variants with altered kinetic and equilibrium parameters of forming these interactions. In this work, DNase I footprinting measurements were employed to investigate the consequences of these altered properties for the outcome of the BirA functional switch. The results support a mechanism in which BirA availability for DNA binding and, therefore, transcription repression is controlled by the rate of the competing protein:protein interaction. However, occupancy of the transcriptional regulatory site on DNA by BirA is exquisitely tuned by the equilibrium constant governing its homodimerization.
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Affiliation(s)
- Poorni R Adikaram
- Department of Chemistry and Biochemistry, College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, MD 20742, USA
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45
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Saracino GAA, Gelain F. Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides. J Biomol Struct Dyn 2013; 32:759-75. [PMID: 23730849 DOI: 10.1080/07391102.2013.790848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the increasing use and development of peptide-based scaffolds in different fields including that of regenerative medicine, the understanding of the factors governing the self-assembly process and the relationship between sequence and properties have not yet been fully understood. BMHP1-derived self-assembling peptides (SAPs) have been developed and characterized showing that biotinylation at the N-terminal cap corresponds to better performing assembly and scaffold biomechanics. In this study, the effects of biotinylation on the self-assembly dynamics of seven BMHP1-derived SAPs have been investigated by molecular dynamics simulations. We confirmed that these SAPs self-assemble into β-structures and that proline acts as a β-breaker of the assembled aggregates. In biotinylated peptides, the formation of ordered β-structured aggregates is triggered by both the establishment of a dense and dynamic H-bonds network and the formation of a 'hydrophobic wall' available to interact with other peptides. Such conditions result from the peculiar chemical composition of the biotinyl-cap, given by the synergic cooperation of the uracil function of the ureido ring with the high hydrophobic portion consisting of the thiophenyl ring and valeryl chain. The inbuilt propensity of biotinylated peptides towards the formation of ordered small aggregates makes them ideal precursors of higher hierarchically organized self-assembled nanostructures as experimentally observed.
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Affiliation(s)
- Gloria Anna Ada Saracino
- a Center of Nanomedicine and Tissue Engineering A. O. Ospedale Niguarda Ca' Granda , Milan , 20162 Italy
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46
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Post-translational modification in the archaea: structural characterization of multi-enzyme complex lipoylation. Biochem J 2013; 449:415-25. [PMID: 23116157 DOI: 10.1042/bj20121150] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multi-enzyme complexes, is essential for metabolism in aerobic bacteria and eukarya. In Escherichia coli, lipoylation is catalysed by LplA (lipoate protein ligase) or by LipA (lipoic acid synthetase) and LipB [lipoyl(octanoyl) transferase] combined. Whereas bacterial and eukaryotic LplAs comprise a single two-domain protein, archaeal LplA function typically involves two proteins, LplA-N and LplA-C. In the thermophilic archaeon Thermoplasma acidophilum, LplA-N and LplA-C are encoded by overlapping genes in inverted orientation (lpla-c is upstream of lpla-n). The T. acidophilum LplA-N structure is known, but the LplA-C structure is unknown and LplA-C's role in lipoylation is unclear. In the present study, we have determined the structures of the substrate-free LplA-N-LplA-C complex and E2lipD (dihydrolipoyl acyltransferase lipoyl domain) that is lipoylated by LplA-N-LplA-C, and carried out biochemical analyses of this archaeal lipoylation system. Our data reveal the following: (i) LplA-C is disordered but folds upon association with LplA-N; (ii) LplA-C induces a conformational change in LplA-N involving substantial shortening of a loop that could repress catalytic activity of isolated LplA-N; (iii) the adenylate-binding region of LplA-N-LplA-C includes two helices rather than the purely loop structure of varying order observed in other LplA structures; (iv) LplAN-LplA-C and E2lipD do not interact in the absence of substrate; (v) LplA-N-LplA-C undergoes a conformational change (the details of which are currently undetermined) during lipoylation; and (vi) LplA-N-LplA-C can utilize octanoic acid as well as lipoic acid as substrate. The elucidated functional inter-dependence of LplA-N and LplA-C is consistent with their evolutionary co-retention in archaeal genomes.
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47
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Tieu W, Soares da Costa TP, Yap MY, Keeling KL, Wilce MCJ, Wallace JC, Booker GW, Polyak SW, Abell AD. Optimising in situ click chemistry: the screening and identification of biotin protein ligase inhibitors. Chem Sci 2013. [DOI: 10.1039/c3sc51127h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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48
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Bisubstrate adenylation inhibitors of biotin protein ligase from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2012; 18:1432-41. [PMID: 22118677 DOI: 10.1016/j.chembiol.2011.08.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/05/2011] [Accepted: 08/24/2011] [Indexed: 10/15/2022]
Abstract
The mycobacterial biotin protein ligase (MtBPL) globally regulates lipid metabolism in Mtb through the posttranslational biotinylation of acyl coenzyme A carboxylases involved in lipid biosynthesis that catalyze the first step in fatty acid biosynthesis and pyruvate coenzyme A carboxylase, a gluconeogenic enzyme vital for lipid catabolism. Here we describe the design, development, and evaluation of a rationally designed bisubstrate inhibitor of MtBPL. This inhibitor displays potent subnanomolar enzyme inhibition and antitubercular activity against multidrug resistant and extensively drug resistant Mtb strains. We show that the inhibitor decreases in vivo protein biotinylation of key enzymes involved in fatty acid biosynthesis and that the antibacterial activity is MtBPL dependent. Additionally, the gene encoding BPL was found to be essential in M. smegmatis. Finally, the X-ray cocrystal structure of inhibitor bound MtBPL was solved providing detailed insight for further structure-activity analysis. Collectively, these data suggest that MtBPL is a promising target for further antitubercular therapeutic development.
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49
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Adikaram PR, Beckett D. Functional versatility of a single protein surface in two protein:protein interactions. J Mol Biol 2012; 419:223-33. [PMID: 22446587 DOI: 10.1016/j.jmb.2012.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 11/18/2022]
Abstract
The ability of the Escherichia coli protein BirA to function as both a metabolic enzyme and a transcription repressor relies on the use of a single surface for two distinct protein:protein interactions. BirA forms a heterodimer with the biotin acceptor protein of acetyl-coenzyme A carboxylase and catalyzes posttranslational biotinylation. Alternatively, it forms a homodimer that binds sequence-specifically to DNA to repress transcription initiation at the biotin biosynthetic operon. Several surface loops on BirA, two of which exhibit sequence conservation in all biotin protein ligases and the remainder of which are highly variable, are located at the two interfaces. The function of these loops in both homodimerization and biotin transfer was investigated by characterizing alanine-substituted variants at 18 positions of one constant and three variable loops. Sedimentation equilibrium measurements reveal that 11 of the substitutions, which are distributed throughout conserved and variable loops, significantly alter homodimerization energetics. By contrast, steady-state and single-turnover kinetic measurements indicate that biotin transfer to biotin carboxyl carrier protein is impacted by seven substitutions, the majority of which are in the constant loop. Furthermore, constant loop residues that function in biotin transfer also support homodimerization. The results reveal clues about the evolution of a single protein surface for use in two distinct functions.
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Affiliation(s)
- Poorni R Adikaram
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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50
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Soares da Costa TP, Tieu W, Yap MY, Pendini NR, Polyak SW, Sejer Pedersen D, Morona R, Turnidge JD, Wallace JC, Wilce MCJ, Booker GW, Abell AD. Selective inhibition of biotin protein ligase from Staphylococcus aureus. J Biol Chem 2012; 287:17823-17832. [PMID: 22437830 DOI: 10.1074/jbc.m112.356576] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.
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Affiliation(s)
- Tatiana P Soares da Costa
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William Tieu
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y Yap
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Nicole R Pendini
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Steven W Polyak
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Daniel Sejer Pedersen
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John D Turnidge
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; SA Pathology at Women's and Children's Hospital, South Australia 5006, Australia
| | - John C Wallace
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew C J Wilce
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Grant W Booker
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
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