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AIMS Neuroscience

2020, Volume 7, Issue 3: 299-310. doi: 10.3934/Neuroscience.2020016
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Review

mRNA localization and local translation in neurons

  • 1.
    Lincoln College, University of Oxford, Turl Street, Oxford, OX1 3DR, United Kingdom
  • 2.
    Merton College, University of Oxford, Merton Street, Oxford, OX1 4DJ, United Kingdom
  • 3.
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
  • The spatial and temporal regulation of gene expression in neurons is an important step in creating functional and structural neuronal networks. The complexity of neurons require differential expression of various proteins in different compartments. Highly polarised cells, such as neurons, respond rapidly to different external stimuli by changing their local protein abundance and composition. Neurons can have extensions up to a meter away from their cell body in humans, so it is easy to envisage why they need to manage the synthesis of new proteins locally and on-demand. Recent research has demonstrated that neurons can control the expression of different proteins by localising translationally silent mRNAs, followed by subsequent translation. Neurons use mRNA localization and local translation to achieve different purposes during their life cycle. While developing neurons rely on mRNA localization for axon guidance and synaptogenesis, mature neurons can use mRNA localization for maintenance of essential physiological processes. mRNA localization also plays a role in response to neuron injury to regenerate and restore neuronal connections. Recent microscopic imaging techniques such as live imaging of fluorescently tagged molecules combined with genetic and biochemical studies in neurons have illustrated evolutionarily conserved mechanisms for targeting mRNAs into their correct compartments. This review provides an overview of mRNA localization and local translation in vertebrate and invertebrate neurons and discusses the mechanism by which mRNAs are trafficked into axons. Furthermore, the role of mRNA localization in synaptic activation, as well as axonal injury is explored.

    Citation: Mohammad Mofatteh. mRNA localization and local translation in neurons[J]. AIMS Neuroscience, 2020, 7(3): 299-310. doi: 10.3934/Neuroscience.2020016

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  • The spatial and temporal regulation of gene expression in neurons is an important step in creating functional and structural neuronal networks. The complexity of neurons require differential expression of various proteins in different compartments. Highly polarised cells, such as neurons, respond rapidly to different external stimuli by changing their local protein abundance and composition. Neurons can have extensions up to a meter away from their cell body in humans, so it is easy to envisage why they need to manage the synthesis of new proteins locally and on-demand. Recent research has demonstrated that neurons can control the expression of different proteins by localising translationally silent mRNAs, followed by subsequent translation. Neurons use mRNA localization and local translation to achieve different purposes during their life cycle. While developing neurons rely on mRNA localization for axon guidance and synaptogenesis, mature neurons can use mRNA localization for maintenance of essential physiological processes. mRNA localization also plays a role in response to neuron injury to regenerate and restore neuronal connections. Recent microscopic imaging techniques such as live imaging of fluorescently tagged molecules combined with genetic and biochemical studies in neurons have illustrated evolutionarily conserved mechanisms for targeting mRNAs into their correct compartments. This review provides an overview of mRNA localization and local translation in vertebrate and invertebrate neurons and discusses the mechanism by which mRNAs are trafficked into axons. Furthermore, the role of mRNA localization in synaptic activation, as well as axonal injury is explored.


    1.   Introduction

    Photocatalytic water splitting using semiconductor materials provides a way to produce clean hydrogen fuel [1,2,3,4]. A photocatalytic water splitting has to be proper band positions, i.e., the valence band maximum VBM should be more positive than the water oxidation potential and the conduction band minimum CBM must be more negative than the hydrogen reduction potential, the SrTiO3 has benne a most stability and an abundance of raw materials, and thus it is a promising photocatalyst for producing hydrogen from water using solar energy [5,6]. SrTiO3 is a cubic perovskite structure material [7]. However, SrTiO3 use at range of applications in many fields such as, photocatalysis [8,9,10], energy storage [11,12], sensing [13], micro wave devices[14], anode material for lithium-ion batteries [15], H2S solar cells [16], and random access memories[17]. Can be synthesize SrTiO3 by several methods such as sol-gel [18], treatment hydrothermal [8,10,13,19,20], solid state reaction [15], polymeric precursor method [9], pulsed laser decomposition [21,22], co-precipitation/solvo-thermal [15], and electro-spinning [23]. And many studies have been done about metal-doped SrTiO3, such as Fe, La and Mn [24,25,26].

    In this work, the structural and electronic properties of both SrTiO3 and SrNi0.125Ti0.875O3 were calculated by using the full potential augmented plane wave plus local orbital (FP-(APW + lo)) method based on density functional theory (DFT) [27]. This is implemented in wien2k code to solve Kohn Sham equation within Full Potential Linearized Augmented Plane Wave (FP-LAPW) method. This method is one of the best methods for appropriate computation of electronic states of various crystalline solids. For structural optimization and the electronic properties the exchange correlation approximation is treated with Perdew-Burke-Ernzerhof Generalized Gradient Approximation (PBE-GGA) Trans-Blaha modified Becke-Johnson (TB-mBJ) potential is employed [28,29,30,31].

    The outline of this paper is as follows: in section computational details, we give the computation details. The results and discussion are presented in section results and discussion. Finally section conclusions concludes the paper.

    2.   Computational details

    All calculations were performed in the framework of the density function theory (DFT) [27] using the WIEN2k package [32], the full-potential Linearized augmented plane-wave method (FP-LAPW) [27] and the generalized-gradient approximation PBE-GGA with the exchange-correlation functional suggested by Perdew, Burke, and Ernzerhof (PBE) [27].

    In these computations, and in order to investigate the structural and electronic properties of SrTiO3 and SrNi0.125Ti0.875O3, the unit cell is separated in two regions, an interstitial region and non-overlapping atomic spheres. In each of these regions, Kohn-Sham wave functions and charge densities as well as electronic potentials are calculated in a different way inside the unit cell. Inside the atomic sphere, they are defined usually by the RMT (radius of muffin tin) around the position of each atom, a spherical harmonic expansion is used, whereas in the interstitial space of the unit cell a plane wave basis set is taken into account. RMT values were chosen as 1.65 a.u. for O, 1.75 a.u. for Ti, 1.8 a.u. for Ni and 2.2 a.u. for Sr. Charge density was Fourier expanded up to Gmax = 12 au−1. The plane wave cut-off Kmax × RMT radius was taken such that RMT × Kmax = 9. For convergence of energy we used a 7 × 7 × 7 k-points grid in the special irreducible Brillouin zone. The self-consistent convergence criteria of total energy calculations of the system were achieved when the total energy stabilized within 10−4 Ry.

    3.   Results and discussion

    3.1.   Structural analysis

    For the calculion of structural and electronic properties of Ni doped SrTiO3, we adopt for the SrTiO3 compound—a cubic structure (space group). Pm3m where atomic positions in the elementary cell as presented in Figure 1a are Sr: (0, 0, 0); O: (0, 1/2, 1/2), (1/2, 1/2, 0), (1/2, 0, 1/2); and Ti: (1/2, 1/2, 1/2) When, for the Ni-doped compound SrNi0.125Ti0.875O3, we build a cubic super-cell having twice the cell parameter of the parent SrTiO3 compound Figure 1b whose atomic positions are listed in Table 1.

    Figure 1.  (a) SrTiO3 perovskite structure, and (b) supercell of SrNi0.125Ti0.875O3 structure.
    DownLoad: Full-Size Img PowerPoint
    Table 1.  Atomic positions for cubic supercell SrNi0.125Ti0.875O3.
    Atom Positions
    Sr (0.75, 0.75, 0.75)(0.25, 0.25, 0.25)(0.25, 0.75, 0.75)(0.75, 0.25, 0.25)(0.25, 0.25, 0.75)(0.75, 0.75, 0.25)(0.75, 0.25, 0.75)(0.25, 0.75, 0.25)
    Ni (0, 0, 0)
    Ti (0.5, 0.0, 0.0)(0.0, 0.5, 0.0)(0.0, 0.0, 0.5)(0.0, 0.5, 0.5)(0.5, 0.0, 0.5)(0.5, 0.5, 0.0)(0.5, 0.5, 0.5)
    O (0.0, 0.0, 0.75)(0.0, 0.0, 0.25)(0.75, 0.0, 0.0)(0.25, 0.0, 0.0)(0.0, 0.75, 0.0)(0.0, 0.25, 0.0)(0.5, 0.0, 0.75)
     | Show Table
    DownLoad: CSV

    All calculations were performed for a 40 atom (5 × 8) super-cell (with a0 = 7.81 Å) (Figure 1b). The optimization of the lattice constants for SrTiO3 and SrNi0.125Ti0.875O3 is made by minimization of the total energy. The calculate lattice parameters, bulk moduli, pressure derivatives B' for SrTiO3 and SrNi0.125Ti0.875O3 were calculated by fitting the total energy E versus volume V data to the non-linear Murnagham equation of state [27]. We present the E (V) relationship of both SrTiO3 and SrNi0.125Ti0.875O3 in Figure 2a, b respectively.

    Figure 2.  Calculated total energy curves as a function of cell volume for (a) SrTiO3 and (b) SrNi0.125Ti0.875O3.
    DownLoad: Full-Size Img PowerPoint

    Table 2 presents the calculate lattice parameters, bulk moduli, their pressure derivatives B' together with available experimental data and other theoretical data for both SrTiO3 and SrNi0.125Ti0.875O3. The value of our calculated lattice constants for both SrTiO3 (3.894 Å) and SrNi0.125Ti0.875O3 (3.877 Å). This is in good agreement with the experiment results [7] that the lattice constant of SrNi0.125Ti0.875O3 films increase after doping. From the values of bulk moduli, we can conclude that the SrNi0.125Ti0.875O3 is slightly less stable than SrTiO3.

    Table 2.  Calculated lattice constants, bulk moduli B, pressure derivatives B' and compared to experimental data and other available works for SrTiO3 and SrNi0.125Ti0.875O3.
    Compounds Method Approximation Lattice constant (Å) B (GPa) B' Refs.
    SrTiO3 FP-LAPW PBE-GGA 3.894 184.489 4.41 Present
    Experimental Experimental 3.905 / / [7]
    FP-LAPW GGA-96 3.905 184 / [33]
    3.87 194 / [34]
    SrNi0.125Ti0.875O3 FP-LAPW PBE-GGA 3.877 183.62 4.44 Present
     | Show Table
    DownLoad: CSV

    3.2.   Electronic properties

    3.2.1.   Density of states

    In this section, the electronic structures for both SrTiO3 and SrNi0.125Ti0.875O3 will be studied and compared to each other. Several indicators will be used to detect the effects of Ni doping on the SrTiO3 electronic composition, which is total DOS and states partial density (PDOS). From these tools, some aspects of structural features can be demonstrated. The total DOS and PDOS for SrTiO3 are first calculated for comparison and the results are shown in Figure 3a. For clarity, only the Ti 3d, O 2p and Sr 5p PDOS are shown and this will be evident in the following figures. The top of the valence bands (VBs) mainly consists of O 2p states and the most important vacancy power bands in the lower conduction bands (CBs) mainly consist of Ti 3d states. There is no interference between PDOS between Sr atoms and O atoms, meaning that the Sr-O bonds have a high ion city. Furthermore, the band gap in SrTiO3 is about 2.857 eV, which is less than the experimental value (of about 3.2 eV) [32]. This is naturally underestimated by the DFT [35,36] and by cause the strong self-interaction of the Ti 3d states [37] (Figure 3).The total DOS and PDOS for SrNi0.125Ti0.875O3 are shown in (Figure 3).Where we see the control of both the Ti 3d, Ni 3d, O 2p and Sr 5p PDOS are shown and this will be evident in the following figures. The top of the valence bands (VBs) mainly consists of Ni 3d and O 2p states and the most important vacancy power bands in the lower conduction bands (CBs) mainly consist of Ti 3d states. We also notice no overlap between PDOS Sr atoms and O atoms, meaning that the Sr-O bonds have a high ion. Furthermore, the band gap in SrNi0.125Ti0.875O3 is about 1.078 eV. From all this we conclude that Ni atoms reduce the band gap and improve the effectiveness of SrTiO3.

    Figure 3.  The calculated total and partial density of states for (a) SrTiO3 and (b) SrNi0.125Ti0.875O3.
    DownLoad: Full-Size Img PowerPoint
    3.2.2.   Band structure

    We calculated the band structures of SrTiO3 (Figure 4), and the effect for all doping by nickel metal atoms on the electronic properties of SrTiO3. We found that the SrTiO3 has an indirect gap Γ-M point of Brillouin zone, and our calculated value of this gap (about 2.857 eV) is lower than the experimental value (around 3.2 eV). The largely, due to the well-known shortcoming of exchange-correction functionals in describing, excited states using the PBE-GGA approximation [38,39]. However, the characters of band structures and the relative variation of band gap are reasonable and reliable, so a scissors worker (1.3 eV) was performed to correct the underestimation of the band gaps of doped SrTiO3 [35,36,37,38,39,40]. Figure 4 shows the calculated band structures SrNi0.125Ti0.875O3 and SrTiO3 around band gap states. Because 1.078 eV, which is an indirect gap (Γ-M point of Brillouin zone). Two isolated defect bands crossing the Brillouin zone make a great decrease to the band gap, thus the optical absorption edge towards the visible light region is largely expanded. The defect bands are close to the valence band, which indicates that Ni dopant atoms are the acceptor impurities, leading to the increase of whole concentration [39].

    Figure 4.  Electronic band structure of (a) SrTiO3 and (b) SrNi0.125Ti0.875O3.
    DownLoad: Full-Size Img PowerPoint
    3.2.3.   Charge density

    Figure 5 represents the charge density of SrNi0.125Ti0.875O3 and SrTiO3. The Sr, Ti, and Ni atoms contain more basic electrons, resulting in a higher overall density of charge near the nucleus position, while oxygen atoms are larger with a large number of valence electrons. In the compounds SrTiO3 and SrNi0.125Ti0.875O3, we note a difference in ionic bonds between Ni-O and Ti-O. This is due to the electronic distribution of Ni and Ti atoms.

    Figure 5.  Charge density on the (111) plane for (a) SrTiO3 and (b) SrNi0.125Ti0.875O3.
    DownLoad: Full-Size Img PowerPoint

    4.   Conclusion

    We investigated the structural and electronic properties of Ni-doped SrTiO3 by a first-principles calculation of FP-LAPW method based on DFT. The calculated results the structure of SrNi0.125Ti0.875O3 is less stable than that of pure SrTiO3. The Ni fully acts as an electron donor in SrNi0.125Ti0.875O3 and the Fermi level shifts into the CBs after Ni doping. The DOS of the SrNi0.125Ti0.875O3 system shift toward low energies and the band gap of SrTiO3 is 2.857 eV and reduced by about 1.779 eV for SrNi0.125Ti0.875O3.

    Conflict of interests

    The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.


    Acknowledgments


    The author would like to thank Lincoln College Oxford for a BTG Research Fellowship in Biomedical Sciences.

    Conflict of interest


    The author reports no conflicts of interest.

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