Enzyme dimension of the ribosomal protein S4 across plant and animal kingdoms

Sudhamalla, Babu; Kumar, Mahesh; Kumar, Rajesh; Sashi, Pulikallu; Yasin, U. Mahammad; Ramakrishna, Dasari; Rao, P. Nageswara; Bhuyan, Abani K.

doi:10.1016/j.bbagen.2013.06.010

Cited by 6 publications

(8 citation statements)

References 22 publications

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“…We have previously reviewed evidence for autologous regulation of most ribosomal proteins of their own translation by means of binding directly to their own mRNA [7], and they include only a summary of that information in Table 3, Table 4, Table 5 and Table 6. The majority of ribosomal proteins, both in prokaryotes and eukaryotes, play additional roles in cellular metabolism, ranging from DNA repair, control of transcription and replication, and histone binding to the regulation of various enzymes and mRNA splicing as summarized in Table 3, Table 4, Table 5 and Table 6 [81,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112]. The degree to which these extra-ribosomal functions are integrated into cellular functions is exemplified by the participation of riboprotein L13a into the GAIT complex in eukaryotes.…”

Section: Resultsmentioning

confidence: 99%

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

Root‐Bernstein

2019

IJMS

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We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.

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Section: Resultsmentioning

confidence: 99%

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

Root‐Bernstein

2019

IJMS

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“…The substrate concentration in these experiments was 20 μM, which is nearly equal to the reported K m value of 19.8 μM. 44 Experiments at a later stage were also performed using 40 μM substrate. The appearance of the profile for the solvent viscosity dependence of the initial velocity (v 0 ) for the substrate cleavage by hS4 at a constant enzyme:substrate ratio (Figure 3) is similar to that for the viscosity dependence of cytochrome c unfolding (Figure 1), and the same Kramers-like empirical relation (eq 2) fits the data best.…”

Section: ■ Resultsmentioning

confidence: 68%

“…In this set of experiments, human ribosomal protein S4 (hS4) that has been recently described as a cysteine protease , was allowed to cleave the synthetic substrate Z-FR↓-AMC (N-CBZ-Phe-Arg-aminomethylcoumarin) at different glycerol contents in 20 mM Tris-HCl and 100 mM NaCl (pH 7.6) at 37 °C. The substrate concentration in these experiments was 20 μM, which is nearly equal to the reported K m value of 19.8 μM . Experiments at a later stage were also performed using 40 μM substrate.…”

Section: Resultsmentioning

confidence: 99%

“…An earlier study at 25% glycerol and 283 K (3.4 cP) also did not find any considerable effect of viscogen-induced stability on the folding rate of cytochrome c. 21 Higher Overdamping in the Cysteine Protease Activity of Ribosomal Protein S4. In this set of experiments, human ribosomal protein S4 (hS4) that has been recently described as a cysteine protease 44,50 was allowed to cleave the synthetic substrate Z-FR↓-AMC (N-CBZ-Phe-Arg-aminomethylcoumarin) at different glycerol contents in 20 mM Tris-HCl and 100 mM NaCl (pH 7.6) at 37 °C. The substrate concentration in these experiments was 20 μM, which is nearly equal to the reported K m value of 19.8 μM.…”

Section: ■ Resultsmentioning

confidence: 99%

“…Human S4 Enzyme Kinetics. Recombinant human S4 (hS4) was produced as described previously, 44 and the steadystate kinetic experiments involved measurement of the initial velocity of hS4-catalyzed cleavage of the cysteine protease synthetic substrate analogue Z-FR↓-AMC (N-CBZ-Phe-Argaminomethylcoumarin) by detecting the level of AMC released with time. A typical reaction was initiated by injecting a 5 μL stock solution of Z-FR↓-AMC (1 mg/mL) into 400 μL of a 3 μM hS4 solution prepared in 20 mM Tris-HCl and 100 mM NaCl (pH 7.6) containing glycerol (v/v).…”

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confidence: 99%

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Viscosity Dependence of Some Protein and Enzyme Reaction Rates: Seventy-Five Years after Kramers

Sashi

Bhuyan

2015

Biochemistry

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Kramers rate theory is a milestone in chemical reaction research, but concerns regarding the basic understanding of condensed phase reaction rates of large molecules in viscous milieu persist. Experimental studies of Kramers theory rely on scaling reaction rates with inverse solvent viscosity, which is often equated with the bulk friction coefficient based on simple hydrodynamic relations. Apart from the difficulty of abstraction of the prefactor details from experimental data, it is not clear why the linearity of rate versus inverse viscosity, k ∝ η(-1), deviates widely for many reactions studied. In most cases, the deviation simulates a power law k ∝ η(-n), where the exponent n assumes fractional values. In rate-viscosity studies presented here, results for two reactions, unfolding of cytochrome c and cysteine protease activity of human ribosomal protein S4, show an exceedingly overdamped rate over a wide viscosity range, registering n values up to 2.4. Although the origin of this extraordinary reaction friction is not known at present, the results indicate that the viscosity exponent need not be bound by the 0-1 limit as generally suggested. For the third reaction studied here, thermal dissociation of CO from nativelike cytochrome c, the rate-viscosity behavior can be explained using Grote-Hynes theory of time-dependent friction in conjunction with correlated motions intrinsic to the protein. Analysis of the glycerol viscosity-dependent rate for the CO dissociation reaction in the presence of urea as the second variable shows that the protein stabilizing effect of subdenaturing amounts of urea is not affected by the bulk viscosity. It appears that a myriad of factors as diverse as parameter uncertainty due to the difficulty of knowing the exact reaction friction and both mode and consequences of protein-solvent interaction work in a complex manner to convey as though Kramers rate equation is not absolute.

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A Molecular Switch‐Integrated Nanoplatform Enables Photo‐Unlocked Antibacterial Drug Delivery for Synergistic Abscess Therapy

Yan

Liu

et al. 2023

Adv Healthcare Materials

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Drug delivery systems (DDSs) capable of sequential multistage drug release are urgently needed for antibacterial applications. Herein, a molecular switch‐integrated, photo‐responsive nanoplatform is reported based on hollow mesoporous silica nanospheres (HMSN) loaded with silver nanoparticles (Ag NPs), vancomycin (Van), and hemin (HAVH) for bacteria elimination and abscess therapy. Upon near‐infrared (NIR) light irradiation, the molecular switch, hemin, can effuse from the mesopores of HMSN, triggering the release of pre‐loaded Ag+ and Van, which enables photothermal‐modulated drug release and synergistic photothermal‐chemo therapy (PTT‐CHT). The HAVH_NIR irreversibly disrupts the bacterial cell membrane, facilitating the penetration of Ag+ and Van. It is found that these compounds restrain the transcription and translation of ribosomes and lead to rapid bacterial death. Furthermore, hemin can effectively inhibit excessive inflammatory responses associated with the treatment, promoting accelerated wound healing in a murine abscess model. This work presents a new strategy for antibacterial drug delivery with high controllability and extendibility, which may benefit the development of smart multifunctional nanomedicine for diseases not limited to bacterial infections.

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Enzyme dimension of the ribosomal protein S4 across plant and animal kingdoms

Cited by 6 publications

References 22 publications

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

Viscosity Dependence of Some Protein and Enzyme Reaction Rates: Seventy-Five Years after Kramers

A Molecular Switch‐Integrated Nanoplatform Enables Photo‐Unlocked Antibacterial Drug Delivery for Synergistic Abscess Therapy

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