RNA Post-transcriptional Modifications of an Early-Stage Large-Subunit Ribosomal Intermediate.

Protein production by ribosomes is fundamental to life, and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all of the ribosome assembly intermediates and on each pathway. There are 26 RNA post-transcriptional modifications in 23S RNA of the mature Escherichia coli (E. coli) large ribosomal subunit. The levels of these modifications have been investigated extensively only for a small number of large subunit intermediates and under a limited number of cellular and environmental conditions. In this study, we determined the level of incorporations of 2-methyl adenosine, 3-methyl pseudouridine, 5-hydroxycytosine, and seven pseudouridines in an early-stage E. coli large-subunit assembly intermediate with a sedimentation coefficient of 27S. The 27S intermediate is one of three large subunit intermediates accumulated in E. coli cells lacking the DEAD-box RNA helicase DbpA and expressing the helicase inactive R331A DbpA construct. The majority of the investigated modifications are incorporated into the 27S large subunit intermediate to similar levels to those in the mature 50S large subunit, indicating that these early modifications or the enzymes that incorporate them play important roles in the initial events of large subunit ribosome assembly.

Learnings from the Relation between the Number of Forward and Reverse Reactions (Transfer Cycles) Required to Converge to Equilibrium and the Ratio of the Forward to the Reverse Rate Constants in Simple Chemical Reactions.

In simple, reversible, chemical reactions of the type A ⇋ B, chemical equilibrium is related to chemical kinetics via the equality between the equilibrium constant and the ratio of the forward to the reverse rate-constant, i.e., K eq = k f/k r, where K eq is the equilibrium constant and k f and k r denote the rate constants for the forward (A → B) and reverse (B → A) reactions, respectively. We review and examine the relation between the number of forward and reverse reactions required to take place for the aforementioned system to reach equilibrium and the ratio of the forward to the reverse rate constant. Each cycle of reactants becoming products and the products becoming reactants is defined as the transfer cycle (TC). Therefore, we underscore the relation between the number of TCs required for the system to equilibrate and k f/k r. We also vary the initial concentrations of the reactants and products to examine their dependency of the relation between the number of TCs required to reach equilibrium and k f/k r. The data reveal a logarithmic growth-type relation between the number of TCs required for the system to achieve equilibrium and k f/k r. The results of this relation are discussed in the context of several scenarios that populate the trajectory. We conclude by introducing students and researchers in the area of chemistry and biochemistry to physical phenomena that relate the initial concentrations of the reactants and products and k f/k r to the number of TCs necessary for the system to equilibrate.