1
|
Grishin SY, Dzhus UF, Selivanova OM, Balobanov VA, Surin AK, Galzitskaya OV. Comparative Analysis of Aggregation of Thermus thermophilus Ribosomal Protein bS1 and Its Stable Fragment. BIOCHEMISTRY (MOSCOW) 2021; 85:344-354. [PMID: 32564739 DOI: 10.1134/s0006297920030104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Functionally important multidomain bacterial protein bS1 is the largest ribosomal protein of subunit 30S. It interacts with both mRNA and proteins and is prone to aggregation, although this process has not been studied in detail. Here, we obtained bacterial strains overproducing ribosomal bS1 protein from Thermus thermophilus and its stable fragment bS1(49) and purified these proteins. Using fluorescence spectroscopy, dynamic light scattering, and high-performance liquid chromatography combined with mass spectrometric analysis of products of protein limited proteolysis, we demonstrated that disordered regions at the N- and C-termini of bS1 can play a key role in the aggregation of this protein. The truncated fragment bS1(49) was less prone to aggregation compared to the full-size bS1. The revealed properties of the studied proteins can be used to obtain protein crystals for elucidating the structure of the bS1 stable fragment.
Collapse
Affiliation(s)
- S Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - U F Dzhus
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.,Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| |
Collapse
|
2
|
Giraud P, Créchet JB, Uzan M, Bontems F, Sizun C. Resonance assignment of the ribosome binding domain of E. coli ribosomal protein S1. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:107-111. [PMID: 24682851 DOI: 10.1007/s12104-014-9554-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 03/15/2014] [Indexed: 06/03/2023]
Abstract
Ribosomal protein S1 is an essential actor for protein synthesis in Escherichia coli. It is involved in mRNA recruitment by the 30S ribosomal subunit and recognition of the correct start codon during translation initiation. E. coli S1 is a modular protein that contains six repeats of an S1 motif, which have distinct functions despite structural homology. Whereas the three central repeats have been shown to be involved in mRNA recognition, the two first repeats that constitute the N-terminal domain of S1 are responsible for binding to the 30S subunit. Here we report the almost complete (1)H, (13)C and (15)N resonance assignment of two fragments of the 30S binding region of S1. The first fragment comprises only the first repeat. The second corresponds to the entire ribosome binding domain. Since S1 is absent from all high resolution X-ray structures of prokaryotic ribosomes, these data provide a first step towards atomic level structural characterization of this domain by NMR. Chemical shift analysis of the first repeat provides evidence for structural divergence from the canonical OB-fold of an S1 motif. In contrast the second domain displays the expected topology for an S1 motif, which rationalizes the functional specialization of the two subdomains.
Collapse
Affiliation(s)
- Pierre Giraud
- CNRS UPR 2301, Institut de Chimie des Substances Naturelles, 91190, Gif-sur-Yvette, France
| | | | | | | | | |
Collapse
|
3
|
Chen D, Norris D, Ventikos Y. Chemosignalling, mechanotransduction and ciliary behaviour in the embryonic node: Computational evaluation of competing theories. Proc Inst Mech Eng H 2014; 228:465-476. [PMID: 24727590 DOI: 10.1177/0954411914531117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Precise specification of left-right asymmetry is essential for patterning the internal organs of vertebrates. Within the embryonic node, posteriorly polarised cilia rotate, causing a leftward fluid flow (nodal flow) that establishes left-right asymmetry. The mechanism by which an embryo senses nodal flow remains uncertain. Existing hypotheses argue that either nodal flow carries morphogen(s) or lipid-bounded vesicles towards the left, thereby generating an asymmetric signal, and/or that mechano-sensory cilia sense this unidirectional flow, stimulating left-sided intracellular calcium signalling. To date, direct and definitive evidence supporting these hypotheses has been lacking. In this study, we conduct a multi-scale study to simulate the nodal cilia and the fluidic environment, analysing left-right signal transmission. By employing computational simulation techniques and solving the relevant three-dimensional unsteady transport equations, we study the flow pattern produced by the rotation of active cilia. By importing dilute species and particles into the computational domain, we investigate the transport of morphogens and nodal vesicular parcels, respectively. Furthermore, by extending the analysis to include the solid mechanics of passive deformable cilia and the coupling of their structural behaviour with the emerging fluid mechanics, we study the response of passive cilia to the nodal flow. Our results reproduce the unidirectional nodal flow, allowing us to evaluate the plausibility of both chemo- and mechano-sensing hypotheses. The quantitative measurements of the flow rate, the molecular transport and distribution provide guidance regarding the necessary morphogen molecular weights to break signalling symmetry. The passive sensory ciliary deformation gives indications regarding the plausibility of this mechano-signalling mechanism.
Collapse
Affiliation(s)
- Duanduan Chen
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing, China
| | | | - Yiannis Ventikos
- Department of Mechanical Engineering, University College London, London, UK
| |
Collapse
|
4
|
Kaul H, Cui Z, Ventikos Y. A multi-paradigm modeling framework to simulate dynamic reciprocity in a bioreactor. PLoS One 2013; 8:e59671. [PMID: 23555740 PMCID: PMC3612085 DOI: 10.1371/journal.pone.0059671] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 02/19/2013] [Indexed: 12/28/2022] Open
Abstract
Despite numerous technology advances, bioreactors are still mostly utilized as functional black-boxes where trial and error eventually leads to the desirable cellular outcome. Investigators have applied various computational approaches to understand the impact the internal dynamics of such devices has on overall cell growth, but such models cannot provide a comprehensive perspective regarding the system dynamics, due to limitations inherent to the underlying approaches. In this study, a novel multi-paradigm modeling platform capable of simulating the dynamic bidirectional relationship between cells and their microenvironment is presented. Designing the modeling platform entailed combining and coupling fully an agent-based modeling platform with a transport phenomena computational modeling framework. To demonstrate capability, the platform was used to study the impact of bioreactor parameters on the overall cell population behavior and vice versa. In order to achieve this, virtual bioreactors were constructed and seeded. The virtual cells, guided by a set of rules involving the simulated mass transport inside the bioreactor, as well as cell-related probabilistic parameters, were capable of displaying an array of behaviors such as proliferation, migration, chemotaxis and apoptosis. In this way the platform was shown to capture not only the impact of bioreactor transport processes on cellular behavior but also the influence that cellular activity wields on that very same local mass transport, thereby influencing overall cell growth. The platform was validated by simulating cellular chemotaxis in a virtual direct visualization chamber and comparing the simulation with its experimental analogue. The results presented in this paper are in agreement with published models of similar flavor. The modeling platform can be used as a concept selection tool to optimize bioreactor design specifications.
Collapse
Affiliation(s)
- Himanshu Kaul
- Institute of Biomedical Engineering and Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Zhanfeng Cui
- Institute of Biomedical Engineering and Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Yiannis Ventikos
- Institute of Biomedical Engineering and Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
5
|
Ashbourn JMA, Geris L, Gerisch A, Young CJS. Numerical simulation of two-dimensional and three-dimensional axisymmetric advection–diffusion systems with complex geometries using finite-volume methods. Proc Math Phys Eng Sci 2010. [DOI: 10.1098/rspa.2009.0527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A finite-volume method has been developed that can deal accurately with complicated, curved boundaries for both two-dimensional and three-dimensional axisymmetric advection–diffusion systems. The motivation behind this is threefold. Firstly, the ability to model the correct geometry of a situation yields more accurate results. Secondly, smooth geometries eliminate corner singularities in the calculation of, for example, mechanical variables and thirdly, different geometries can be tested for experimental applications. An example illustrating each of these is given: fluid carrying a dye and rotating in an annulus, bone fracture healing in mice, and using vessels of different geometry in an ultracentrifuge.
Collapse
Affiliation(s)
- J. M. A. Ashbourn
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - L. Geris
- Division of Biomechanics and Engineering Design, K.U. Leuven, B-3001 Leuven, Belgium
| | - A. Gerisch
- Institut für Mathematik, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - C. J. S. Young
- Magdalen College, University of Oxford, Oxford OX1 4AU, UK
| |
Collapse
|
6
|
Aliprandi P, Sizun C, Perez J, Mareuil F, Caputo S, Leroy JL, Odaert B, Laalami S, Uzan M, Bontems F. S1 ribosomal protein functions in translation initiation and ribonuclease RegB activation are mediated by similar RNA-protein interactions: an NMR and SAXS analysis. J Biol Chem 2008; 283:13289-301. [PMID: 18211890 DOI: 10.1074/jbc.m707111200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosomal protein S1, in Escherichia coli, is necessary for the recognition by the ribosome of the translation initiation codon of most messenger RNAs. It also participates in other functions. In particular, it stimulates the T4 endoribonuclease RegB, which inactivates some of the phage mRNAs, when their translation is no longer required, by cleaving them in the middle of their Shine-Dalgarno sequence. In each function, S1 seems to target very different RNAs, which led to the hypothesis that it possesses different RNA-binding sites. We previously demonstrated that the ability of S1 to activate RegB is carried by a fragment of the protein formed of three consecutive domains (domains D3, D4, and D5). The same fragment plays a central role in all other functions. We analyzed its structural organization and its interactions with three RNAs: two RegB substrates and a translation initiation region. We show that these three RNAs bind the same area of the protein through a set of systematic (common to the three RNAs) and specific (RNA-dependent) interactions. We also show that, in the absence of RNA, the D4 and D5 domains are associated, whereas the D3 and D4 domains are in equilibrium between open (noninteracting) and closed (weakly interacting) forms and that RNA binding induces a structural reorganization of the fragment. All of these results suggest that the ability of S1 to recognize different RNAs results from a high adaptability of both its structure and its binding surface.
Collapse
Affiliation(s)
- Pascale Aliprandi
- CNRS, Antenne de l'ICSN à l'Ecole Polytechnique, Ecole Polytechnique, 91128 Palaiseau, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Selivanova OM, Fedorova YY, Serduyk IN. Proteolysis of ribosomal protein S1 from Escherichia coli and Thermus thermophilus leads to formation of two different fragments. BIOCHEMISTRY (MOSCOW) 2007; 72:1225-32. [DOI: 10.1134/s0006297907110089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Vimberg V, Tats A, Remm M, Tenson T. Translation initiation region sequence preferences in Escherichia coli. BMC Mol Biol 2007; 8:100. [PMID: 17973990 PMCID: PMC2176067 DOI: 10.1186/1471-2199-8-100] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/31/2007] [Indexed: 11/10/2022] Open
Abstract
Background The mRNA translation initiation region (TIR) comprises the initiator codon, Shine-Dalgarno (SD) sequence and translational enhancers. Probably the most abundant class of enhancers contains A/U-rich sequences. We have tested the influence of SD sequence length and the presence of enhancers on the efficiency of translation initiation. Results We found that during bacterial growth at 37°C, a six-nucleotide SD (AGGAGG) is more efficient than shorter or longer sequences. The A/U-rich enhancer contributes strongly to the efficiency of initiation, having the greatest stimulatory effect in the exponential growth phase of the bacteria. The SD sequences and the A/U-rich enhancer stimulate translation co-operatively: strong SDs are stimulated by the enhancer much more than weak SDs. The bacterial growth rate does not have a major influence on the TIR selection pattern. On the other hand, temperature affects the TIR preference pattern: shorter SD sequences are preferred at lower growth temperatures. We also performed an in silico analysis of the TIRs in all E. coli mRNAs. The base pairing potential of the SD sequences does not correlate with the codon adaptation index, which is used as an estimate of gene expression level. Conclusion In E. coli the SD selection preferences are influenced by the growth temperature and not influenced by the growth rate. The A/U rich enhancers stimulate translation considerably by acting co-operatively with the SD sequences.
Collapse
Affiliation(s)
- Vladimir Vimberg
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia.
| | | | | | | |
Collapse
|
9
|
Timchenko AA, Shiryaev VM, Fedorova YY, Kihara H, Kimura K, Willumeit R, Garamus VM, Selivanova OM. Conformation of Thermus thermophilus ribosomal protein S1 in solution at different ionic strengths. Biophysics (Nagoya-shi) 2007. [DOI: 10.1134/s0006350907020030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
10
|
Agalarov SC, Kalinichenko AA, Kommer AA, Spirin AS. Ribosomal protein S1 induces a conformational change of the 30S ribosomal subunit. FEBS Lett 2006; 580:6797-9. [PMID: 17150214 DOI: 10.1016/j.febslet.2006.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 11/13/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
A comparative study of the 30S ribosomal subunit in the complex with protein S1 and the subunit depleted of this protein has been carried out by the hot tritium bombardment method. Differences in exposure of some ribosomal proteins within the 30S subunit depleted of S1 and within the 30S-S1 complex were found. It was concluded that protein S1 binds in the region of the neck of the 30S ribosomal subunit inducing a conformational change of its structure.
Collapse
Affiliation(s)
- Sultan Ch Agalarov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | | | | | | |
Collapse
|
11
|
Balsera M, Menéndez M, Sáiz JL, de Las Rivas J, Andreu JM, Arellano JB. Structural Stability of the PsbQ Protein of Higher Plant Photosystem II. Biochemistry 2004; 43:14171-9. [PMID: 15518567 DOI: 10.1021/bi048369e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have characterized the stability and folding behavior of the isolated extrinsic PsbQ protein of photosystem II (PSII) from a higher plant, Spinacia oleracea, using intrinsic protein fluorescence emission and near- and far-UV circular dichroism (CD) spectroscopy in combination with differential scanning calorimetry (DSC). Experimental results reveal that both chemical denaturation using guanidine hydrochloride (GdnHCl) and thermal unfolding of PsbQ proceed as a two-state reversible process. The denaturation free-energy changes (DeltaG(D)) at 20 degrees C extrapolated from GdnHCl (4.0 +/- 0.6 kcal mol(-1)) or thermal unfolding (4.4 +/- 0.8 kcal mol(-1)) are very close. Moreover, the far-UV CD spectra of the denatured PsbQ registered at 90 degrees C in the absence and presence of 6.0 M GdnHCl superimpose, leading us to conclude that both denatured states of PsbQ are structurally and energetically similar. The thermal unfolding of PsbQ has been also characterized by CD and DSC over a wide pH range. The stability of PsbQ is at its maximum at pH comprised between 5 and 8, being wider than the optimal pH for oxygen evolution in the lumen of thylakoid membranes. In addition, no significant structural changes were detected in PsbQ between 50 and 55 degrees C in the pH range of 3-8, suggesting that PsbQ behaves as a soluble and stable particle in the lumen when it detaches from PSII under physiological stress conditions such as high temperature (45-50 degrees C) or low pH (<5.0). Sedimentation experiments showed that, in solution at 20 degrees C, the PsbQ protein is a monomer with an elongated shape.
Collapse
Affiliation(s)
- Mónica Balsera
- Instituto de Recursos Naturales y Agrobiología (CSIC), Cordel de Merinas 52, 37008 Salamanca, Spain
| | | | | | | | | | | |
Collapse
|