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Goyal L, Kaur M, Mandal M, Panda D, Karmakar S, Molla KA, Bhatia D. Potential gene editing targets for developing haploid inducer stocks in rice and wheat with high haploid induction frequency. 3 Biotech 2024; 14:14. [PMID: 38111612 PMCID: PMC10725411 DOI: 10.1007/s13205-023-03857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023] Open
Abstract
Doubled haploid (DH) breeding is a powerful technique to ensure global food security via accelerated crop improvement. DH can be produced in planta by employing haploid inducer stock (HIS). Widely used HIS in maize is known to be governed by ZmPLA, ZmDMP, ZmPLD3, and ZmPOD65 genes. To develop such HIS in rice and wheat, we have identified putative orthologs of these genes using in silico approaches. The OsPLD1; TaPLD1, and OsPOD6; TaPOD8 were identified as putative orthologs of ZmPLD3 and ZmPOD65 in rice and wheat, respectively. Despite being closely related to ZmPLD3, OsPLD1 and TaPLD1 have shown higher anther-specific expression. Similarly, OsPOD6 and TaPOD8 were found closely related to the ZmPOD65 based on both phylogenetic and expression analysis. However, unlike ZmPLD3 and ZmPOD65, two ZmDMP orthologs have been found for each crop. OsDMP1 and OsDMP2 in rice and TaDMP3 and TaDMP13 in wheat have shown similarity to ZmDMP in terms of both sequence and expression pattern. Furthermore, analogs to maize DMP proteins, these genes possess four transmembrane helices making them best suited to be regarded as ZmDMP orthologs. Modifying these predicted orthologous genes by CRISPR/Cas9-based genome editing can produce a highly efficient HIS in both rice and wheat. Besides revealing the genetic mechanism of haploid induction, the development of HIS would advance the genetic improvement of these crops. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03857-9.
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Affiliation(s)
- Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
| | - Mehardeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
| | - Meghna Mandal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Subhasis Karmakar
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | | | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141 004 India
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Vu HN, Situ AJ, Ulmer TS. Isothermal Titration Calorimetry of Membrane Proteins. Methods Mol Biol 2021; 2302:69-79. [PMID: 33877623 DOI: 10.1007/978-1-0716-1394-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The ability to quantify protein-protein interactions without adding labels to protein has made isothermal titration calorimetry (ITC) a preferred technique to study proteins in aqueous solution. Here, we describe the application of ITC to the study of protein-protein interactions in membrane mimics using the association of integrin αIIb and β3 transmembrane domains in phospholipid bicelles as an example. A higher conceptual and experimental effort compared to water-soluble proteins is required for membrane proteins and rewarded with rare thermodynamic insight into this central class of proteins.
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Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D. Characterisation of denatured states of sensory rhodopsin II by solution-state NMR. J Mol Biol 2019; 431:2790-2809. [PMID: 31071327 DOI: 10.1016/j.jmb.2019.04.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022]
Abstract
Sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis, is a novel model system for membrane protein folding studies. Recently, the SDS-denatured states and the kinetics for reversible unfolding of pSRII have been investigated, opening the door to the first detailed characterisation of denatured states of a membrane protein by solution-state nuclear magnetic resonance (NMR) using uniformly 15N-labelled pSRII. SDS denaturation and acid denaturation of pSRII both lead to fraying of helix ends but otherwise small structural changes in the transmembrane domain, consistent with little changes in secondary structure and disruption of the retinal-binding pocket and tertiary structure. Widespread changes in the backbone amide dynamics are detected in the form of line broadening, indicative of μs-to-ms timescale conformational exchange in the transmembrane region. Detailed analysis of chemical shift and intensity changes lead to high-resolution molecular insights on structural and dynamics changes in SDS- and acid-denatured pSRII, thus highlighting differences in the unfolding pathways under the two different denaturing conditions. These results will form the foundation for furthering our understanding on the folding and unfolding pathways of retinal-binding proteins and membrane proteins in general, and also for investigating the importance of ligand-binding in the folding pathways of other ligand-binding membrane proteins, such as GPCRs.
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Affiliation(s)
- Yi Lei Tan
- Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, CB2 1GA, United Kingdom
| | - James Mitchell
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Judith Klein-Seetharaman
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Daniel Nietlispach
- Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, CB2 1GA, United Kingdom.
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Abstract
The location of fluorescent groups relative to the lipid bilayer can be evaluated using fluorescence quenchers embedded in the membrane and/or dissolved in aqueous solution. Quenching can be used to define the membrane topography of membrane proteins and individual membrane-embedded hydrophobic helices by combining it with the placement of fluorescent groups, including Trp, at defined sequence positions. This chapter briefly discusses various quenching methods for studies of membrane protein topography, and provides detailed protocols for dual quencher analysis (DQA), a rapid, highly sensitive, and experimentally flexible approach in which the information gained from both a membrane-embedded and aqueous quencher is combined. The advantages of the DQA method include flexibility with regard to the bilayer compositions to which it can be applied, including membranes composed of lipids of varying head group and acyl chain compositions, as well as the ability to identify mixed populations of fluorophores residing at different depths within the bilayer.
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Affiliation(s)
- Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, USA
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
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Lans I, Dalton JAR, Giraldo J. Helix 3 acts as a conformational hinge in Class A GPCR activation: An analysis of interhelical interaction energies in crystal structures. J Struct Biol 2015; 192:545-53. [PMID: 26522273 DOI: 10.1016/j.jsb.2015.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/21/2023]
Abstract
A collection of crystal structures of rhodopsin, β2-adrenergic and adenosine A2A receptors in active, intermediate and inactive states were selected for structural and energetic analyses to identify the changes involved in the activation/deactivation of Class A GPCRs. A set of helix interactions exclusive to either inactive or active/intermediate states were identified. The analysis of these interactions distinguished some local conformational changes involved in receptor activation, in particular, a packing between the intracellular domains of transmembrane helices H3 and H7 and a separation between those of H2 and H6. Also, differential movements of the extracellular and intracellular domains of these helices are apparent. Moreover, a segment of residues in helix H3, including residues L/I3.40 to L3.43, is identified as a key component of the activation mechanism, acting as a conformational hinge between extracellular and intracellular regions. Remarkably, the influence on the activation process of some glutamic and aspartic acidic residues and, as a consequence, the influence of variations on local pH is highlighted. Structural hypotheses that arose from the analysis of rhodopsin, β2-adrenergic and adenosine A2A receptors were tested on the active and inactive M2 muscarinic acetylcholine receptor structures and further discussed in the context of the new mechanistic insights provided by the recently determined active and inactive crystal structures of the μ-opioid receptor. Overall, the structural and energetic analyses of the interhelical interactions present in this collection of Class A GPCRs suggests the existence of a common general activation mechanism featuring a chemical space useful for drug discovery exploration.
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Morrill GA, Kostellow AB, Gupta RK. Computational analysis of the extracellular domain of the Ca²⁺-sensing receptor: an alternate model for the Ca²⁺ sensing region. Biochem Biophys Res Commun 2015; 459:36-41. [PMID: 25701780 DOI: 10.1016/j.bbrc.2015.02.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 02/10/2015] [Indexed: 11/21/2022]
Abstract
The extracellular Ca(2+) sensing receptor (CaSR) belongs to Class C G-protein-coupled receptors (GPCRs) which include receptors for amino acids, γ-aminobutyric acid and glutamate neurotransmitters. CaSR has been described as having an extended sequence containing a Ca(2+) binding pocket within an extracellular amino (N)-terminal domain, called a Venus Fly Trap (VFT) module. CaSR is thought to consist of three domains: 1) a Ca(2+-)sensory domain, 2) a region containing 7 transmembrane (TM) helices, and 3) a carboxy (C)-terminal tail. We find that SPOCTOPUS (a combination of hidden Markov models and artificial neural networks) predicts that Homo sapiens CaSR contains two additional TM helices ((190)D - G(210); (262)S-E(282)), with the second TM helix containing a pore-lining region ((265)K - I(280)). This predicts that the putative Ca(2+) sensory domain is within an extracellular loop, N-terminal to the highly conserved heptahelical bundle. This loop contains both the cysteine-rich domain ((537)V - C(598)) and a 14 residue "linker" sequence ((599)I - F(612)) thought to support signal transmission to the heptahelical bundle. Thus domain 1 may contain a 189 residue N-terminal extracellular region followed successively by TM-1, a short intracellular loop, TM-2 and a 329 residue extracellular loop; rather than the proposed 620 residue VFT module based on crystallography of the N-terminal region of mGluR1. Since the topologies of the two proteins differ, the published CaSR VFT model is questionable. CaSR also contains multiple caveolin-binding motifs and cholesterol-binding (CRAC/CARC) domains, facilitating localization to plasma membrane lipid rafts. Ion sensing may involve combination of pore-lining regions from CaSR dimers and CaSR-bound caveolins to form ion channels capable of monitoring ionized Ca(2+) levels.
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Botelho SC, Enquist K, von Heijne G, Draheim RR. Differential repositioning of the second transmembrane helices from E. coli Tar and EnvZ upon moving the flanking aromatic residues. Biochim Biophys Acta 2014; 1848:615-21. [PMID: 25445668 DOI: 10.1016/j.bbamem.2014.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/29/2014] [Accepted: 11/17/2014] [Indexed: 01/04/2023]
Abstract
Aromatic tuning, i.e. repositioning aromatic residues found at the cytoplasmic end of transmembrane (TM) domains within bacterial receptors, has been previously shown to modulate signal output from the aspartate chemoreceptor (Tar) and the major osmosensor EnvZ of Escherichia coli. In the case of Tar, changes in signal output consistent with the vertical position of the native Trp-Tyr aromatic tandem within TM2 were observed. In contrast, within EnvZ, where a Trp-Leu-Phe aromatic triplet was repositioned, the surface that the triplet resided upon was the major determinant governing signal output. However, these studies failed to determine whether moving the aromatic residues was sufficient to physically reposition the TM helix within a membrane. Recent coarse-grained molecular dynamics (CG-MD) simulations predicted displacement of Tar TM2 upon moving the aromatic residues at the cytoplasmic end of the helix. Here, we demonstrate that repositioning the Trp-Tyr tandem within Tar TM2 displaces the C-terminal boundary of the helix relative to the membrane. In a similar analysis of EnvZ, an abrupt initial displacement of TM2 was observed but no subsequent movement was seen, suggesting that the vertical position of TM2 is not governed by the location of the Trp-Leu-Phe triplet. Our results also provide another set of experimental data, i.e. the resistance of EnvZ TM2 to being displaced upon aromatic tuning, which could be useful for subsequent refinement of the initial CG-MD simulations. Finally, we discuss the limitations of these methodologies, how moving flanking aromatic residues might impact steady-state signal output and the potential to employ aromatic tuning in other bacterial membrane-spanning receptors.
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Affiliation(s)
- Salomé C Botelho
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Karl Enquist
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Roger R Draheim
- Division of Pharmacy, Durham University, Queen's Campus, Stockton-on-Tees TS17 6BH, England, UK; Wolfson Research Institute for Health and Wellbeing, Durham University, Queen's Campus, Stockton-on-Tees, TS17 6BH, England, UK.
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Nagarathnam B, Sankar K, Dharnidharka V, Balakrishnan V, Archunan G, Sowdhamini R. TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences. Bioinformation 2011; 7:214-21. [PMID: 22125389 PMCID: PMC3218415 DOI: 10.6026/97320630007214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 10/21/2011] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Multiple sequence alignments become biologically meaningful only if conserved and functionally important residues and secondary structural elements preserved can be identified at equivalent positions. This is particularly important for transmembrane proteins like G-protein coupled receptors (GPCRs) with seven transmembrane helices. TM-MOTIF is a software package and an effective alignment viewer to identify and display conserved motifs and amino acid substitutions (AAS) at each position of the aligned set of homologous sequences of GPCRs. The key feature of the package is to display the predicted membrane topology for seven transmembrane helices in seven colours (VIBGYOR colouring scheme) and to map the identified motifs on its respective helices /loop regions. It is an interactive package which provides options to the user to submit query or pre-aligned set of GPCR sequences to align with a reference sequence, like rhodopsin, whose structure has been solved experimentally. It also provides the possibility to identify the nearest homologue from the available inbuilt GPCR or Olfactory Receptor cluster dataset whose association is already known for its receptor type. AVAILABILITY The database is available for free at mini@ncbs.res.in.
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Affiliation(s)
| | - Kannan Sankar
- Birla Institute of Technology and Science, Pilani, India; Presently in: Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
| | - Varadhan Dharnidharka
- R.V. College of Engineering, Mysore Road, Bangalore, India; Presently in: Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, USA
| | - Veluchamy Balakrishnan
- Department of Biotechnology, K.S.Rangasamy College of Technology, KSR. Kalvi Nagar, Tiruchengode - 637215, Tamilnadu, India
| | - Govindaraju Archunan
- Department of Animal Science, Bharathidasan University,Trichirapalli, Tamil Nadu, 620 024, India
| | - Ramanathan Sowdhamini
- National Center for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
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