1
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Rashan EH, Bartlett AK, Khana DB, Zhang J, Jain R, Smith AJ, Baker ZN, Cook T, Caldwell A, Chevalier AR, Pfleger BF, Yuan P, Amador-Noguez D, Simcox JA, Pagliarini DJ. ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574893. [PMID: 38260250 PMCID: PMC10802472 DOI: 10.1101/2024.01.09.574893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Fatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)-fatty acids hydroxylated at the 4 (γ) position-which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs-conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
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Affiliation(s)
- Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Abigail K. Bartlett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daven B. Khana
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Raghav Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J. Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Zakery N. Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Taylor Cook
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Alana Caldwell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Autumn R. Chevalier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel Amador-Noguez
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith A. Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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2
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Hernandez Garcia A, Nair SK. Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase. ACS CENTRAL SCIENCE 2023; 9:1944-1956. [PMID: 37901177 PMCID: PMC10604976 DOI: 10.1021/acscentsci.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/31/2023]
Abstract
In bacteria, Ser/Thr protein kinase-like sequences are found as part of large multidomain polypeptides that biosynthesize lanthipeptides, a class of natural products distinguished by the presence of thioether cross-links. The kinase domain phosphorylates Ser or Thr residues in the peptide substrates. Subsequent β-elimination by a lyase domain yields electrophilic dehydroamino acids, which can undergo cyclase domain-catalyzed cyclization to yield conformationally restricted, bioactive compounds. Here, we reconstitute the biosynthetic pathway for a class III lanthipeptide from Bacillus thuringiensis NRRL B-23139, including characterization of a two-component protease for leader peptide excision. We also describe the first crystal structures of a class III lanthipeptide synthetase, consisting of the lyase, kinase, and cyclase domains, in various states including complexes with its leader peptide and nucleotide. The structure shows interactions between all three domains that result in an active conformation of the kinase domain. Biochemical analysis demonstrates that the three domains undergo movement upon binding of the leader peptide to establish interdomain allosteric interactions that stabilize this active form. These studies inform on the regulatory mechanism of substrate recognition and provide a framework for engineering of variants of biotechnological interest.
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Affiliation(s)
- Andrea Hernandez Garcia
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
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3
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Saleh A, Noguchi Y, Aramayo R, Ivanova ME, Stevens KM, Montoya A, Sunidhi S, Carranza NL, Skwark MJ, Speck C. The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer. Nat Commun 2022; 13:2915. [PMID: 35614055 PMCID: PMC9133112 DOI: 10.1038/s41467-022-30576-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022] Open
Abstract
The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. Using cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6. In summary, our work provides fundamental insights into DDK structure, control and selective activation of the MCM2-7 helicase during DNA replication. Importantly, these insights can be exploited for development of novel DDK inhibitors.
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Affiliation(s)
- Almutasem Saleh
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Yasunori Noguchi
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Ricardo Aramayo
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Marina E Ivanova
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Kathryn M Stevens
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
| | - Alex Montoya
- Proteomics and Metabolomics Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - S Sunidhi
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK
| | | | | | - Christian Speck
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.
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4
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The expanding world of protein kinase-like families in bacteria: forty families and counting. Biochem Soc Trans 2021; 48:1337-1352. [PMID: 32677675 DOI: 10.1042/bst20190712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022]
Abstract
The protein kinase-like clan/superfamily is a large group of regulatory, signaling and biosynthetic enzymes that were historically regarded as typically eukaryotic proteins, although bacterial members have also been known for a long time. In this review, we explore the diversity of bacterial protein kinase like families, and discuss functional versatility of these enzymes, both the ones acting within the bacterial cell, and those acting within eukaryotic cells as effectors during infection. We focus on novel bacterial kinase-like families discovered in the last five years. A bioinformatics perspective is held here, hence sequence and structure comparison overview is presented, and also a comparison of genomic neighbourhoods of the families. We perform a phylum-level census of the families. Also, we discuss apparent pseudokinases that turned out to perform alternative catalytic functions by repurposing their atypical kinase-like active sites. We also highlight some 'unpopular' kinase-like families that await characterisation.
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5
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Oliver MR, Horne CR, Shrestha S, Keown JR, Liang LY, Young SN, Sandow JJ, Webb AI, Goldstone DC, Lucet IS, Kannan N, Metcalf P, Murphy JM. Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix. Nat Commun 2021; 12:1002. [PMID: 33579933 PMCID: PMC7881018 DOI: 10.1038/s41467-021-21191-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
The life cycle of Baculoviridae family insect viruses depends on the viral protein kinase, PK-1, to phosphorylate the regulatory protein, p6.9, to induce baculoviral genome release. Here, we report the crystal structure of Cydia pomenella granulovirus PK-1, which, owing to its likely ancestral origin among host cell AGC kinases, exhibits a eukaryotic protein kinase fold. PK-1 occurs as a rigid dimer, where an antiparallel arrangement of the αC helices at the dimer core stabilizes PK-1 in a closed, active conformation. Dimerization is facilitated by C-lobe:C-lobe and N-lobe:N-lobe interactions between protomers, including the domain-swapping of an N-terminal helix that crowns a contiguous β-sheet formed by the two N-lobes. PK-1 retains a dimeric conformation in solution, which is crucial for catalytic activity. Our studies raise the prospect that parallel, side-to-side dimeric arrangements that lock kinase domains in a catalytically-active conformation could function more broadly as a regulatory mechanism among eukaryotic protein kinases. The viral Protein Kinase-1 (PK-1) phosphorylates the regulatory protein p6.9, which facilitates baculoviral genome release. Here, the authors combine X-ray crystallography with biophysical and biochemical analyses as well as molecular dynamics simulations to characterize Cydia pomenella granulovirus PK-1, which forms a dimer with a parallel side-to-side arrangement of the kinase domains and furthermore, they provide insights into its catalytic mechanism and evolutionary relationships with other kinases.
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Affiliation(s)
- Michael R Oliver
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jeremy R Keown
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Peter Metcalf
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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6
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Shrestha S, Katiyar S, Sanz-Rodriguez CE, Kemppinen NR, Kim HW, Kadirvelraj R, Panagos C, Keyhaninejad N, Colonna M, Chopra P, Byrne DP, Boons GJ, van der Knaap E, Eyers PA, Edison AS, Wood ZA, Kannan N. A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily. Sci Signal 2020; 13:13/639/eaax6313. [PMID: 32636308 DOI: 10.1126/scisignal.aax6313] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aberrant regulation of metabolic kinases by altered redox homeostasis substantially contributes to aging and various diseases, such as diabetes. We found that the catalytic activity of a conserved family of fructosamine-3-kinases (FN3Ks), which are evolutionarily related to eukaryotic protein kinases, is regulated by redox-sensitive cysteine residues in the kinase domain. The crystal structure of the FN3K homolog from Arabidopsis thaliana revealed that it forms an unexpected strand-exchange dimer in which the ATP-binding P-loop and adjoining β strands are swapped between two chains in the dimer. This dimeric configuration is characterized by strained interchain disulfide bonds that stabilize the P-loop in an extended conformation. Mutational analysis and solution studies confirmed that the strained disulfides function as redox "switches" to reversibly regulate the activity and dimerization of FN3K. Human FN3K, which contains an equivalent P-loop Cys, was also redox sensitive, whereas ancestral bacterial FN3K homologs, which lack a P-loop Cys, were not. Furthermore, CRISPR-mediated knockout of FN3K in human liver cancer cells altered the abundance of redox metabolites, including an increase in glutathione. We propose that redox regulation evolved in FN3K homologs in response to changing cellular redox conditions. Our findings provide insights into the origin and evolution of redox regulation in the protein kinase superfamily and may open new avenues for targeting human FN3K in diabetic complications.
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Affiliation(s)
- Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Samiksha Katiyar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Carlos E Sanz-Rodriguez
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Nolan R Kemppinen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Hyun W Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Renuka Kadirvelraj
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Charalampos Panagos
- Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA 30602, USA
| | - Neda Keyhaninejad
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, GA 30602, USA
| | - Maxwell Colonna
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA 30602, USA
| | - Pradeep Chopra
- Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA 30602, USA
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Geert J Boons
- Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA 30602, USA.,Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, Netherlands
| | - Esther van der Knaap
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, GA 30602, USA.,Department of Horticulture, University of Georgia, Athens, GA 30602, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Arthur S Edison
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA 30602, USA
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. .,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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7
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The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major may be Involved in the Resistance to Drugs such as Paromomycin. Biomolecules 2019; 9:biom9110723. [PMID: 31718000 PMCID: PMC6920834 DOI: 10.3390/biom9110723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
The identification and clarification of the mechanisms of action of drugs used against leishmaniasis may improve their administration regimens and prevent the development of resistant strains. Herein, for the first time, we describe the structure of the putatively essential Ser/Thr kinase LmjF.22.0810 from Leishmania major. Molecular dynamics simulations were performed to assess the stability of the kinase model. The analysis of its sequence and structure revealed two druggable sites on the protein. Furthermore, in silico docking of small molecules showed that aminoglycosides preferentially bind to the phosphorylation site of the protein. Given that transgenic LmjF.22.0810-overexpressing parasites displayed less sensitivity to aminoglycosides such as paromomycin, our predicted models support the idea that the mechanism of drug resistance observed in those transgenic parasites is the tight binding of such compounds to LmjF.22.0810 associated with its overexpression. These results may be helpful to understand the complex machinery of drug response in Leishmania.
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8
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Bradley D, Beltrao P. Evolution of protein kinase substrate recognition at the active site. PLoS Biol 2019; 17:e3000341. [PMID: 31233486 PMCID: PMC6611643 DOI: 10.1371/journal.pbio.3000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase-substrate motif. Kinases have been extensively duplicated throughout evolution, but little is known about when in time new target motifs have arisen. Here, we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity-determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but are not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired around the time of the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
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9
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Hareza A, Bakun M, Świderska B, Dudkiewicz M, Koscielny A, Bajur A, Jaworski J, Dadlez M, Pawłowski K. Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58. PeerJ 2018; 6:e4599. [PMID: 29666759 PMCID: PMC5896498 DOI: 10.7717/peerj.4599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography–tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.
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Affiliation(s)
- Agnieszka Hareza
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Magda Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Bianka Świderska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Alicja Koscielny
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Anna Bajur
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland.,Current affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jacek Jaworski
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
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10
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Neuwald AF, Altschul SF. Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. PLoS Comput Biol 2016; 12:e1005294. [PMID: 28002465 PMCID: PMC5225019 DOI: 10.1371/journal.pcbi.1005294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/10/2017] [Accepted: 12/08/2016] [Indexed: 11/25/2022] Open
Abstract
Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes’ theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu). Protein sequence data, when gathered in great quantity, contain important but implicit biological information manifest as statistical correlations. Here we describe an approach to access this information by comprehensively modeling and characterizing the distribution of sequences belonging to a major protein superfamily. This approach takes as input a large set of unaligned sequences belonging to the superfamily. By applying the minimum description length principle, it seeks the statistical model that best explains the sequences while avoiding over-fitting the data. It concurrently aligns the sequences and, to model evolutionary divergence, partitions them into subgroups that are hierarchically-arranged based upon correlated residue patterns. Auxiliary routines create PyMOL scripts to visualize the locations of correlated residues within available structures. Because these correlations likely arise from structural and biochemical constraints, they can help elucidate protein properties important for functional specificity. Comparing and contrasting sequence and structural features in this way may therefore suggest, in the light of published studies, plausible biological hypotheses for experimental investigation. We illustrate this approach with N-acetyltransferases.
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Affiliation(s)
- Andrew F. Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, Baltimore, MD, United States of America
- * E-mail:
| | - Stephen F. Altschul
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America
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11
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Eyers PA, Keeshan K, Kannan N. Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease. Trends Cell Biol 2016; 27:284-298. [PMID: 27908682 PMCID: PMC5382568 DOI: 10.1016/j.tcb.2016.11.002] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/26/2022]
Abstract
The Tribbles (TRIB) pseudokinases control multiple aspects of eukaryotic cell biology and evolved unique features distinguishing them from all other protein kinases. The atypical pseudokinase domain retains a regulated binding platform for substrates, which are ubiquitinated by context-specific E3 ligases. This plastic configuration has also been exploited as a scaffold to support the modulation of canonical MAPK and AKT modules. In this review, we discuss the evolution of TRIBs and their roles in vertebrate cell biology. TRIB2 is the most ancestral member of the family, whereas the emergence of TRIB3 homologs in mammals supports additional biological roles, many of which are currently being dissected. Given their pleiotropic role in diseases, the unusual TRIB pseudokinase conformation provides a highly attractive opportunity for drug design. Pseudoenzymes are inactive counterparts of classical enzymes and have evolved in all kingdoms of life, where they regulate a vast array of biological processes. The pseudokinases are one of the best-studied families of human pseudoenzymes. Eukaryotic TRIB pseudokinases evolved from a common ancestor (the human TRIB2 homolog), and contain a highly atypical pseudokinase domain fused to a unique docking site in an extended C tail that binds to ubiquitin E3 ligases. TRIB evolution has led to the appearance of three mammalian TRIB pseudokinases, termed TRIB1, TRIB2, and TRIB3, which contain both unique and shared features. In cells, TRIB pseudokinases act as modulators of substrate ubiquitination and as molecular scaffolds for the assembly and regulation of signaling modules, including the C/EBPα transcription factor and AKT and ERK networks. TRIB1 and TRIB2 have potent oncogenic activities in vertebrate cells, and recent evidence also suggests that TRIB2 acts as a tumour suppressor, consistent with the requirement for balanced TRIB signaling in the regulation of transcription, differentiation, proliferation, and apoptosis.
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Affiliation(s)
- Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Karen Keeshan
- Paul O'Gorman Leukemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 0YN, UK.
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJP, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Mol Cell 2016; 63:608-620. [PMID: 27499294 DOI: 10.1016/j.molcel.2016.06.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/27/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesis and an ataxia (ARCA2) through unclear means. We show that mice lacking COQ8A develop a slowly progressive cerebellar ataxia linked to Purkinje cell dysfunction and mild exercise intolerance, recapitulating ARCA2. Interspecies biochemical analyses show that COQ8A and yeast Coq8p specifically stabilize a CoQ biosynthesis complex through unorthodox PKL functions. Although COQ8 was predicted to be a protein kinase, we demonstrate that it lacks canonical protein kinase activity in trans. Instead, COQ8 has ATPase activity and interacts with lipid CoQ intermediates, functions that are likely conserved across all domains of life. Collectively, our results lend insight into the molecular activities of the ancient UbiB family and elucidate the biochemical underpinnings of a human disease.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Floriana Licitra
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Leila Laredj
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Andrew G Reidenbach
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachary A Kemmerer
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anais Grangeray
- Université de Strasbourg, 67081 Strasbourg, France; Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 67084 Strasbourg, France
| | - Tiphaine Jaeg-Ehret
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Catherine E Minogue
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emily M Wilkerson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Deniz Aydin
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiao Guo
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Elyse C Freiberger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laurence Reutenauer
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maya Chergova
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Isabel E Johnson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Danielle C Lohman
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J P Rush
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pankaj K Singh
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Anna I Schlagowski
- Fédération de Medicine Translationnelle de Strasbourg, EA3072, Faculté de Médicine et Faculté des Sciences du Sport, Université de Strasbourg, 67084 Strasbourg, France
| | - Brendan J Floyd
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ulrika Forsman
- University Grenoble Alpes, LCBM, UMR 5249, 38000 Grenoble, France
| | - Pavel J Sindelar
- University Grenoble Alpes, LCBM, UMR 5249, 38000 Grenoble, France; Laboratoire de Chimie des Processus Biologiques, CNRS UMR 8229, Collège de France, 75252 Paris, France
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fabien Pierrel
- University Grenoble Alpes, LCBM, UMR 5249, 38000 Grenoble, France; TIMC-IMAG, CNRS UMR 5525, UFR de Médecine, University Joseph Fourier, 38706 La Tronche, France
| | - Joffrey Zoll
- Fédération de Medicine Translationnelle de Strasbourg, EA3072, Faculté de Médicine et Faculté des Sciences du Sport, Université de Strasbourg, 67084 Strasbourg, France
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Philippe Isope
- Université de Strasbourg, 67081 Strasbourg, France; Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 67084 Strasbourg, France
| | - Hélène Puccio
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France.
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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