1
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Karlowski WM, Varshney D, Zielezinski A. Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences. Genome Biol Evol 2023; 15:7039703. [PMID: 36790099 PMCID: PMC10003748 DOI: 10.1093/gbe/evad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Taxonomically restricted genes (TRGs) are unique for a defined group of organisms and may act as potential genetic determinants of lineage-specific, biological properties. Here, we explore the TRGs of highly diverse and economically important Bacillus bacteria by examining commonly used TRG identification parameters and data sources. We show the significant effects of sequence similarity thresholds, composition, and the size of the reference database in the identification process. Subsequently, we applied stringent TRG search parameters and expanded the identification procedure by incorporating an analysis of noncoding and non-syntenic regions of non-Bacillus genomes. A multiplex annotation procedure minimized the number of false-positive TRG predictions and showed nearly one-third of the alleged TRGs could be mapped to genes missed in genome annotations. We traced the putative origin of TRGs by identifying homologous, noncoding genomic regions in non-Bacillus species and detected sequence changes that could transform these regions into protein-coding genes. In addition, our analysis indicated that Bacillus TRGs represent a specific group of genes mostly showing intermediate sequence properties between genes that are conserved across multiple taxa and nonannotated peptides encoded by open reading frames.
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Affiliation(s)
- Wojciech M Karlowski
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Deepti Varshney
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, Poznan, Poland
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2
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Xie J, DiMaio D. Traptamer screening: a new functional genomics approach to study virus entry and other cellular processes. FEBS J 2022; 289:355-362. [PMID: 33604985 PMCID: PMC8371075 DOI: 10.1111/febs.15775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/17/2021] [Indexed: 01/03/2023]
Abstract
Historically, the genetic analysis of mammalian cells entailed the isolation of randomly arising mutant cell lines with altered properties, followed by laborious genetic mapping experiments to identify the mutant gene responsible for the phenotype. In recent years, somatic cell genetics has been revolutionized by functional genomics screens, in which expression of every protein-coding gene is systematically perturbed, and the phenotype of the perturbed cells is determined. We outline here a novel functional genomics screening strategy that differs fundamentally from commonly used approaches. In this strategy, we express libraries of artificial transmembrane proteins named traptamers and select rare cells with the desired phenotype because, by chance, a traptamer specifically perturbs the expression or activity of a target protein. Active traptamers are then recovered from the selected cells and can be used as tools to dissect the biological process under study. We also briefly describe how we have used this new strategy to provide insights into the complex process by which human papillomaviruses enter cells.
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Affiliation(s)
- Jian Xie
- Department of Genetics, Yale School of Medicine, New Haven, CT USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT USA
- Yale Cancer Center, New Haven, CT USA
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3
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Petti LM, Koleske BN, DiMaio D. Activation of the PDGF β Receptor by a Persistent Artificial Signal Peptide. J Mol Biol 2021; 433:167223. [PMID: 34474086 DOI: 10.1016/j.jmb.2021.167223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/25/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Most eukaryotic transmembrane and secreted proteins contain N-terminal signal peptides that mediate insertion of the nascent translation products into the membrane of the endoplasmic reticulum. After membrane insertion, signal peptides typically are cleaved from the mature protein and degraded. Here, we tested whether a small hydrophobic protein selected for growth promoting activity in mammalian cells retained transforming activity while also acting as a signal peptide. We replaced the signal peptide of the PDGF β receptor (PDGFβR) with a previously described 29-residue artificial transmembrane protein named 9C3 that can activate the PDGFβR in trans. We showed that a modified version of 9C3 at the N-terminus of the PDGFβR can function as a signal peptide, as assessed by its ability to support high level expression, glycosylation, and cell surface localization of the PDGFβR. The 9C3 signal peptide retains its ability to interact with the transmembrane domain of the PDGFβR and cause receptor activation and cell proliferation. Cleavage of the 9C3 signal peptide from the mature receptor is not required for these activities. However, signal peptide cleavage does occur in some molecules, and the cleaved signal peptide can persist in cells and activate a co-expressed PDGFβR in trans. Our finding that a hydrophobic sequence can display signal peptide and transforming activity suggest that some naturally occurring signal peptides may also display additional biological activities by interacting with the transmembrane domains of target proteins.
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Affiliation(s)
- Lisa M Petti
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
| | - Benjamin N Koleske
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA; Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208024, New Haven, CT 06520-8024, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA; Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208024, New Haven, CT 06520-8024, USA; Department of Therapeutic Radiology, Yale School of Medicine, PO Box 208040, New Haven, CT 06520-8040, USA; Yale Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA.
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4
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Affiliation(s)
- Xianxun Sun
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of Sciences Wuhan 430071 China
- College of Life ScienceJiang Han University Wuhan 430056 China
| | - Zongqiang Cui
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of Sciences Wuhan 430071 China
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5
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Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun 2020; 11:781. [PMID: 32034123 PMCID: PMC7005711 DOI: 10.1038/s41467-020-14500-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/20/2019] [Indexed: 11/14/2022] Open
Abstract
Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast. Disruption of emerging sequences is generally inconsequential for fitness in the laboratory and in natural populations. Overexpression of emerging sequences, however, is enriched in adaptive fitness effects compared to overexpression of established genes. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich non-genic regions and subsequently accumulate changes molded by natural selection. There is increasing evidence that protein-coding genes can emerge de novo from noncoding genomic regions. Vakirlis et al. propose that sequences encoding transmembrane polypeptides can emerge de novo in thymine-rich genomic regions and provide organisms with fitness benefits.
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Affiliation(s)
- Nikolaos Vakirlis
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, 2, Ireland
| | - Omer Acar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Brian Hsu
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - S Branden Van Oss
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Kate Medetgul-Ernar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - Ray W Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States
| | - Cameron P Hines
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - John Iannotta
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Saurin Bipin Parikh
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, 2, Ireland
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Allyson F O'Donnell
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States. .,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States.
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States.
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States. .,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.
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6
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Willemsen A, Félez-Sánchez M, Bravo IG. Genome Plasticity in Papillomaviruses and De Novo Emergence of E5 Oncogenes. Genome Biol Evol 2019; 11:1602-1617. [PMID: 31076746 PMCID: PMC6557308 DOI: 10.1093/gbe/evz095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2019] [Indexed: 02/06/2023] Open
Abstract
The clinical presentations of papillomavirus (PV) infections come in many different flavors. While most PVs are part of a healthy skin microbiota and are not associated to physical lesions, other PVs cause benign lesions, and only a handful of PVs are associated to malignant transformations linked to the specific activities of the E5, E6, and E7 oncogenes. The functions and origin of E5 remain to be elucidated. These E5 open reading frames (ORFs) are present in the genomes of a few polyphyletic PV lineages, located between the early and the late viral gene cassettes. We have computationally assessed whether these E5 ORFs have a common origin and whether they display the properties of a genuine gene. Our results suggest that during the evolution of Papillomaviridae, at least four events lead to the presence of a long noncoding DNA stretch between the E2 and the L2 genes. In three of these events, the novel regions evolved coding capacity, becoming the extant E5 ORFs. We then focused on the evolution of the E5 genes in AlphaPVs infecting primates. The sharp match between the type of E5 protein encoded in AlphaPVs and the infection phenotype (cutaneous warts, genital warts, or anogenital cancers) supports the role of E5 in the differential oncogenic potential of these PVs. In our analyses, the best-supported scenario is that the five types of extant E5 proteins within the AlphaPV genomes may not have a common ancestor. However, the chemical similarities between E5s regarding amino acid composition prevent us from confidently rejecting the model of a common origin. Our evolutionary interpretation is that an originally noncoding region entered the genome of the ancestral AlphaPVs. This genetic novelty allowed to explore novel transcription potential, triggering an adaptive radiation that yielded three main viral lineages encoding for different E5 proteins, displaying distinct infection phenotypes. Overall, our results provide an evolutionary scenario for the de novo emergence of viral genes and illustrate the impact of such genotypic novelty in the phenotypic diversity of the viral infections.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS IRD Uni Montpellier), Centre National de la Recherche Scientique (CNRS), Montpellier, France
| | - Marta Félez-Sánchez
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Ignacio G Bravo
- Laboratory MIVEGEC (UMR CNRS IRD Uni Montpellier), Centre National de la Recherche Scientique (CNRS), Montpellier, France
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7
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Federman RS, Boguraev AS, Heim EN, DiMaio D. Biologically Active Ultra-Simple Proteins Reveal Principles of Transmembrane Domain Interactions. J Mol Biol 2019; 431:3753-3770. [PMID: 31301406 DOI: 10.1016/j.jmb.2019.07.009] [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: 05/23/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 11/30/2022]
Abstract
Specific interactions between the helical membrane-spanning domains of transmembrane proteins play central roles in the proper folding and oligomerization of these proteins. However, the relationship between the hydrophobic amino acid sequences of transmembrane domains and their functional interactions is in most cases unknown. Here, we use ultra-simple artificial proteins to systematically study the sequence basis for transmembrane domain interactions. We show that most short homopolymeric polyleucine transmembrane proteins containing single amino acid substitutions can activate the platelet-derived growth factor β receptor or the erythropoietin receptor in cultured mouse cells, resulting in cell transformation or proliferation. These proteins displayed complex patterns of activity that were markedly affected by seemingly minor sequence differences in the ultra-simple protein itself or in the transmembrane domain of the target receptor, and the effects of these sequence differences are not additive. In addition, specific leucine residues along the length of these proteins are required for activity, and the positions of these required leucines differ based on the identity and position of the central substituted amino acid. Our results suggest that these ultra-simple proteins use a variety of molecular mechanisms to activate the same target and that diversification of transmembrane domain sequences over the course of evolution minimized off-target interactions.
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Affiliation(s)
- Ross S Federman
- Department of Immunobiology, Yale School of Medicine, PO Box 208011, New Haven, CT 06520-8011, USA
| | - Anna-Sophia Boguraev
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
| | - Erin N Heim
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA; Department of Therapeutic Radiology, Yale School of Medicine, PO Box 208040, New Haven, CT 06520-8040, USA; Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208024, New Haven, CT 06520-8024, USA; Yale Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA.
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8
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Mauro VP, Chappell SA. Considerations in the Use of Codon Optimization for Recombinant Protein Expression. Methods Mol Biol 2018; 1850:275-288. [PMID: 30242693 DOI: 10.1007/978-1-4939-8730-6_18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Codon optimization is a gene engineering approach that is commonly used for enhancing recombinant protein expression. This approach is possible because (1) degeneracy of the genetic code enables most amino acids to be encoded by multiple codons and (2) different mRNAs encoding the same protein can vary dramatically in the amount of protein expressed. However, because codon optimization potentially disrupts overlapping information encoded in mRNA coding regions, protein structure and function may be altered. This chapter discusses the use of codon optimization for various applications in mammalian cells as well as potential consequences, so that informed decisions can be made on the appropriateness of using this approach in each case.
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9
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He L, Steinocher H, Shelar A, Cohen EB, Heim EN, Kragelund BB, Grigoryan G, DiMaio D. Single methyl groups can act as toggle switches to specify transmembrane Protein-protein interactions. eLife 2017; 6:27701. [PMID: 28869036 PMCID: PMC5597333 DOI: 10.7554/elife.27701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/01/2017] [Indexed: 01/13/2023] Open
Abstract
Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively of leucine and isoleucine (called LIL traptamers) that specifically activate the erythropoietin receptor (EPOR) in mouse cells to confer growth factor independence. We discovered that the placement of a single side chain methyl group at specific positions in a traptamer determined whether it associated productively with the TMD of the human EPOR, the mouse EPOR, or both receptors. Association of the traptamers with the EPOR induced EPOR oligomerization in an orientation that stimulated receptor activity. These results highlight the high intrinsic specificity of TMD interactions, demonstrate that a single methyl group can dictate specificity, and define the minimal chemical difference that can modulate the specificity of TMD interactions and the activity of transmembrane proteins.
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Affiliation(s)
- Li He
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Helena Steinocher
- Department of Biology, Structural and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
| | - Ashish Shelar
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Emily B Cohen
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Erin N Heim
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Birthe B Kragelund
- Department of Biology, Structural and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, United States
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, United States.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, United States.,Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, United States.,Yale Cancer Center, New Haven, United States
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10
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Windisch D, Ziegler C, Grage SL, Bürck J, Zeitler M, Gor'kov PL, Ulrich AS. Hydrophobic Mismatch Drives the Interaction of E5 with the Transmembrane Segment of PDGF Receptor. Biophys J 2016; 109:737-49. [PMID: 26287626 PMCID: PMC4547410 DOI: 10.1016/j.bpj.2015.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 02/05/2023] Open
Abstract
The oncogenic E5 protein from bovine papillomavirus is a short (44 amino acids long) integral membrane protein that forms homodimers. It activates platelet-derived growth factor receptor (PDGFR) β in a ligand-independent manner by transmembrane helix-helix interactions. The nature of this recognition event remains elusive, as numerous mutations are tolerated in the E5 transmembrane segment, with the exception of one hydrogen-bonding residue. Here, we examined the conformation, stability, and alignment of the E5 protein in fluid lipid membranes of substantially varying bilayer thickness, in both the absence and presence of the PDGFR transmembrane segment. Quantitative synchrotron radiation circular dichroism analysis revealed a very long transmembrane helix for E5 of ∼26 amino acids. Oriented circular dichroism and solid-state 15N-NMR showed that the alignment and stability of this unusually long segment depend critically on the membrane thickness. When reconstituted alone in exceptionally thick DNPC lipid bilayers, the E5 helix was found to be inserted almost upright. In moderately thick bilayers (DErPC and DEiPC), it started to tilt and became slightly deformed, and finally it became aggregated in conventional DOPC, POPC, and DMPC membranes due to hydrophobic mismatch. On the other hand, when E5 was co-reconstituted with the transmembrane segment of PDGFR, it was able to tolerate even the most pronounced mismatch and was stabilized by binding to the receptor, which has the same hydrophobic length. As E5 is known to activate PDGFR within the thin membranes of the Golgi compartment, we suggest that the intrinsic hydrophobic mismatch of these two interaction partners drives them together. They seem to recognize each other by forming a closely packed bundle of mutually aligned transmembrane helices, which is further stabilized by a specific pair of hydrogen-bonding residues.
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Affiliation(s)
- Dirk Windisch
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Colin Ziegler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcel Zeitler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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11
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Abstract
We have constructed 26-amino acid transmembrane proteins that specifically transform cells but consist of only two different amino acids. Most proteins are long polymers of amino acids with 20 or more chemically distinct side-chains. The artificial transmembrane proteins reported here are the simplest known proteins with specific biological activity, consisting solely of an initiating methionine followed by specific sequences of leucines and isoleucines, two hydrophobic amino acids that differ only by the position of a methyl group. We designate these proteins containing leucine (L) and isoleucine (I) as LIL proteins. These proteins functionally interact with the transmembrane domain of the platelet-derived growth factor β-receptor and specifically activate the receptor to transform cells. Complete mutagenesis of these proteins identified individual amino acids required for activity, and a protein consisting solely of leucines, except for a single isoleucine at a particular position, transformed cells. These surprisingly simple proteins define the minimal chemical diversity sufficient to construct proteins with specific biological activity and change our view of what can constitute an active protein in a cellular context.
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12
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Abstract
Many viruses encode short transmembrane proteins that play vital roles in virus replication or virulence. Because many of these proteins are less than 50 amino acids long and not homologous to cellular proteins, their open reading frames were often overlooked during the initial annotation of viral genomes. Some of these proteins oligomerize in membranes and form ion channels. Other miniproteins bind to cellular transmembrane proteins and modulate their activity, whereas still others have an unknown mechanism of action. Based on the underlying principles of transmembrane miniprotein structure, it is possible to build artificial small transmembrane proteins that modulate a variety of biological processes. These findings suggest that short transmembrane proteins provide a versatile mechanism to regulate a wide range of cellular activities, and we speculate that cells also express many similar proteins that have not yet been discovered.
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Affiliation(s)
- Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520;
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