The coenzyme thiamine pyrophosphate inhibits the self-splicing of the group I intron

Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas

CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) and/or exogenous expression of recombinases. In this study, we mitigated these constraints by developing a simple and widely applicable genome engineering tool for bacteria which we termed SIBR-Cas (Self-splicing Intron-Based Riboswitch-Cas). SIBR-Cas was generated from a mutant library of the theophylline-dependent self-splicing T4 td intron that allows for tight and inducible control over CRISPR-Cas counter-selection. This control delays CRISPR-Cas counter-selection, granting more time for the editing event (e.g. by homologous recombination) to occur. Without the use of exogenous recombinases, SIBR-Cas was successfully applied to knock-out several genes in three wild-type bacteria species (Escherichia coli MG1655, Pseudomonas putida KT2440 and Flavobacterium IR1) with poor homologous recombination systems. Compared to other genome engineering tools, SIBR-Cas is simple, tightly regulated and widely applicable for most (non-model) bacteria. Furthermore, we propose that SIBR can have a wider application as a simple gene expression and gene regulation control mechanism for any gene or RNA of interest in bacteria.

Insights into functional modulation of catalytic RNA activity

RNA molecules play critical roles in cell biology, and novel findings continuously broaden their functional repertoires. Apart from their well-documented participation in protein synthesis, it is now apparent that several noncoding RNAs (i.e., micro-RNAs and riboswitches) also participate in the regulation of gene expression. The discovery of catalytic RNAs had profound implications on our views concerning the evolution of life on our planet at a molecular level. A characteristic attribute of RNA, probably traced back to its ancestral origin, is the ability to interact with and be modulated by several ions and molecules of different sizes. The inhibition of ribosome activity by antibiotics has been extensively used as a therapeutical approach, while activation and substrate-specificity alteration have the potential to enhance the versatility of ribozyme-based tools in translational research. In this review, we will describe some representative examples of such modulators to illustrate the potential of catalytic RNAs as tools and targets in research and clinical approaches.

Analysis of group I intron splicing in the presence of naturally occurring methylxanthines

BACKGROUND

Recent advances in the understanding of RNA structure-function, intricate folding and its affinity to bind small molecules have led to the proposal that RNA can be a fastidious target for drug design. The revelation that RNA can act as enzymes as in group I intron and that has been recognized by small molecule ligands targeting the catalytic activity has necessitated our focus on group I intron as target for RNA binders.

METHODS

We studied the group I intron splicing of Tetrahymena in the presence of naturally occurring methylxanthines (theophylline, theobromine and caffeine) at 5-200 micromol/l concentration, and analyzed the spliced out products. For the first time the interference of splicing was ascertained on the basis of pre-rRNA accumulation.

RESULTS

The gel mobility shift showed the binding of methylxanthines with group I intron RNA in a dose dependent manner. The densitometric analysis of pre-rRNA accumulation showed 50% of splicing interference at 200 micromol/l of theophylline and theobromine, whereas the structurally similar molecule caffeine does not alter splicing.

CONCLUSION

The splicing interference measured from the accumulation of pre-rRNA in group I intron splicing is considered to be an uncomplicated or simple denominator for calculating the splicing interference or relative splicing activity in the presence of above RNA binders or splicing modulators.

Novobiocin inhibits the self-splicing of the primary transcripts of T4 phage thymidylate synthase gene

Effects of the antibiotic novobiocin on the self-splicing of primary transcripts of the phage T4 thymidylate synthase gene (td) have been investigated. Novobiocin at 10 mM concentration inhibited the splicing by about 5% but at 40 mM concentration the splicing rate was inhibited by about 50%. The novobiocin inhibition of the self-splicing reaction was not reversed even at a high concentration (200 microM) of guanosine. However, increasing the Mg(2+) ion concentrations up to 20 mM almost fully restored the splicing activity to the normal splicing level. The double reciprocal plot analysis demonstrated that novobiocin acts as a mixed noncompetitive inhibitor for the td intron RNA with a K (i) of 90 mM. The splicing inhibition by novobiocin was strongly dependent on Mg(2+) ion concentration, indicating electrostatic interactions with the td intron RNA. It is likely that the antibiotic novobiocin may interfere with the catalytic actions of Mg(2+) ion in the splicing reaction of the td intron RNA.

Pyridoxal phosphate inhibits the group I intron splicing

The coenzyme pyridoxal phosphate and its analogs were tested for inhibition of the self-splicing of primary transcripts of the phage T4 thymidylate synthase gene (td). Of all compounds examined, the pyridoxal phosphate was the most potent inhibitor and the order of inhibitory efficiency for compounds tested was as follows: pyridoxal phosphate > pyridoxal > pyridoxine > pyridoxamine > pyridoxic acid. Increasing Mg2+ concentration up to 14 mM overcame the suppression of self-splicing by pyridoxal phosphate up to 95% of the level of normal splicing, implying its interference with effective catalysis of Mg2+. The kinetic analysis demonstrated that pyridoxal phosphate acts as a mixed type noncompetitive inhibitor for the td intron RNA with a K(i) of 11.8 mM. The specificity of the splicing inhibition by pyridoxal phosphate is predominantly due to increases in K(m) and decreases in V(max) values.

Inhibition of the group I ribozyme splicing by NADP+

The coenzyme NADP+ (nicotinamide adenine dinucleotide phosphate) and its analogs were tested for inhibition of the self-splicing of primary transcripts of the phage T4 thymidylate synthase gene (td). Of all compounds examined, the 3'-NADP was the most potent inhibitor and the order of inhibitory efficiency for compounds tested was as follows: 3'-NADP+ > NADP+ > NADP(+)-dialdehyde > NADPH > 1,N6-etheno-NADP+. Increasing guanosine concentration up to 40 microM overcame the suppression of self-splicing by NADP+ up to 76% of the level of normal splicing but didn't recover the full splicing activity. Similarly, Mg2+ also served to restore the splicing activity by about 90% at 25 mM concentration above which the splicing started to decline. The kinetic analysis showed that NADP+ acts as a mixed type non-competitive inhibitor for the td intron RNA with a Ki of 4.1 mM. The specificity of the splicing inhibition by NADP+ is predominantly due to increases in Km and decreases in kcat values. The results indicate that the inhibition by NADP+ was guanosine and Mg2+ dependent.