[Identification of 2',3'-cGMP as an intermediate of RNA catalytic cleavage by binase and evaluation of its biological action]

Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics

Unpredictable influenza pandemics, annual epidemics, and sporadic poultry-to-human avian influenza virus infections with high morbidity and mortality rates dictate a need to develop new antiviral approaches. Targeting cellular pathways and processes is a promising antiviral strategy shown to be effective regardless of viral subtypes or viral evolution of drug-resistant variants. Proteomics-based searches provide a tool to reveal the druggable stages of the virus life cycle and to understand the putative antiviral mode of action of the drug(s). Ribonucleases (RNases) of different origins not only demonstrate antiviral effects that are mediated by the direct RNase action on viral and cellular RNAs but can also exert their impact by signal transduction modulation. To our knowledge, studies of the RNase-affected cell proteome have not yet been performed. To reveal cellular targets and explain the mechanisms underlying the antiviral effect employed by the small extra-cellular ribonuclease of Bacillus pumilus (binase) both in vitro and in vivo, qualitative shotgun and quantitative targeted proteomic analyses of the influenza A virus (IAV) H1N1pdm09-infected A549 cells upon binase treatment were performed. We compared proteomes of mock-treated, binase-treated, virus-infected, and virus-infected binase-treated cells to determine the proteins affected by IAV and/or binase. In general, IAV demonstrated a downregulating strategy towards cellular proteins, while binase had an upregulating effect. With the help of bioinformatics approaches, coregulated cellular protein sets were defined and assigned to their biological function; a possible interconnection with the progression of viral infection was conferred. Most of the proteins downregulated by IAV (e.g., AKR1B1, AKR1C1, CCL5, PFN1, RAN, S100A4, etc.) belong to the processes of cellular metabolism, response to stimulus, biological regulation, and cellular localization. Upregulated proteins upon the binase treatment (e.g., AKR1B10, CAP1, HNRNPA2B1, PFN1, PPIA, YWHAB, etc.) are united by the processes of biological regulation, cellular localization, and immune and metabolic processes. The antiviral activity of binase against IAV was expressed by the inversion of virus-induced proteomic changes, resulting in the inhibition of virus-associated processes, including nuclear ribonucleoprotein export (NCL, NPM1, Nup205, and Bax proteins involved) and cytoskeleton remodeling (RDX, PFN1, and TUBB) induced by IAV at the middle stage of single-cycle infection in A549 cells. Modulation of the immune response could be involved as well. Overall, it seems possible that binase exerts its antiviral effects in multiple ways.

Fluorescent determination of micro-quantities of RNA using Hoechst 33258 and binase

Detection of small amounts of RNA in various biological samples is an important applied task. Using fluorescence spectroscopy, the hydrolysis by binase of rRNA and tRNA, stained with Hoechst 33258, in aqueous solutions was investigated. The binding constant of Hoechst with rRNA is 10⁶ M^-1. Specific hydrolysis of rRNA and tRNA by binase during 1-2 min at room temperature leads to a multiple decrease in fluorescence of the dye. This rapid hydrolysis goes to large polynucleotide fragments, but not to short oligonucleotides. The binding constant of binase with rRNA is about of 2.5 × 10⁶ M^-1, which is several dozen times higher than with oligonucleotides. The susceptibility to binase attack depends on the secondary structure of RNA, determined by non-canonical ribonucleotides. The developed highly sensitive fluorescent method can be used for the rapid selective detection of trace amounts of rRNA or tRNA, as well as for studying the physicochemical properties of these RNAs. Using the proposed method, one can confidently detect RNA from 10^-7 M.

Discovery and Roles of 2',3'-cAMP in Biological Systems

In 2009, investigators using ultra-performance liquid chromatography-tandem mass spectrometry to measure, by selected reaction monitoring, 3',5'-cAMP in the renal venous perfusate from isolated, perfused kidneys detected a large signal at the same m/z transition (330 → 136) as 3',5'-cAMP but at a different retention time. Follow-up experiments demonstrated that this signal was due to a positional isomer of 3',5'-cAMP, namely, 2',3'-cAMP. Soon thereafter, investigative teams reported the detection of 2',3'-cAMP and other 2',3'-cNMPs (2',3'-cGMP, 2',3'-cCMP, and 2',3'-cUMP) in biological systems ranging from bacteria to plants to animals to humans. Injury appears to be the major stimulus for the release of these unique noncanonical cNMPs, which likely are formed by the breakdown of RNA. In mammalian cells in culture, in intact rat and mouse kidneys, and in mouse brains in vivo, 2',3'-cAMP is metabolized to 2'-AMP and 3'-AMP; and these AMPs are subsequently converted to adenosine. In rat and mouse kidneys and mouse brains, injury releases 2',3'-cAMP, 2'-AMP, and 3'-AMP into the extracellular compartment; and in humans, traumatic brain injury is associated with large increases in 2',3'-cAMP, 2'-AMP, 3'-AMP, and adenosine in the cerebrospinal fluid. These findings motivate the extracellular 2',3'-cAMP-adenosine pathway hypothesis: intracellular production of 2',3'-cAMP → export of 2',3'-cAMP → extracellular metabolism of 2',3'-cAMP to 2'-AMP and 3'-AMP → extracellular metabolism of 2'-AMP and 3'-AMP to adenosine. Since 2',3'-cAMP has been shown to activate mitochondrial permeability transition pores (mPTPs) leading to apoptosis and necrosis and since adenosine is generally tissue protective, the extracellular 2',3'-cAMP-adenosine pathway may be a protective mechanism [i.e., removes 2',3'-cAMP (an intracellular toxin) and forms adenosine (a tissue protectant)]. This appears to be the case in the brain where deficiency in CNPase (the enzyme that metabolizes 2',3'-cAMP to 2-AMP) leads to increased susceptibility to brain injury and neurological diseases. Surprisingly, CNPase deficiency in the kidney actually protects against acute kidney injury, perhaps by preventing the formation of 2'-AMP (which turns out to be a renal vasoconstrictor) and by augmenting the mitophagy of damaged mitochondria. With regard to 2',3'-cNMPs and their downstream metabolites, there is no doubt much more to be discovered.

Secretome of Intestinal Bacilli: A Natural Guard against Pathologies

Current studies of human gut microbiome usually do not consider the special functional role of transient microbiota, although some of its members remain in the host for a long time and produce broad spectrum of biologically active substances. Getting into the gastrointestinal tract (GIT) with food, water and probiotic preparations, two representatives of Bacilli class, genera Bacillus and Lactobacillus, colonize epithelium blurring the boundaries between resident and transient microbiota. Despite their minor proportion in the microbiome composition, these bacteria can significantly affect both the intestinal microbiota and the entire body thanks to a wide range of secreted compounds. Recently, insufficiency and limitations of pure genome-based analysis of gut microbiota became known. Thus, the need for intense functional studies is evident. This review aims to characterize the Bacillus and Lactobacillus in GIT, as well as the functional roles of the components released by these members of microbial intestinal community. Complex of their secreted compounds is referred by us as the "bacillary secretome." The composition of the bacillary secretome, its biological effects in GIT and role in counteraction to infectious diseases and oncological pathologies in human organism is the subject of the review.

The Role of Metals in the Reaction Catalyzed by Metal-Ion-Independent Bacillary RNase

Extracellular enzymes of intestinal microbiota are the key agents that affect functional activity of the body as they directly interact with epithelial and immune cells. Several species of the Bacillus genus, like Bacillus pumilus, a common producer of extracellular RNase binase, can populate the intestinal microbiome as a colonizing organism. Without involving metal ions as cofactors, binase depolymerizes RNA by cleaving the 3',5'-phosphodiester bond and generates 2',3'-cyclic guanosine phosphates in the first stage of a catalytic reaction. Maintained in the reaction mixture for more than one hour, such messengers can affect the human intestinal microflora and the human body. In the present study, we found that the rate of 2',3'-cGMP was growing in the presence of transition metals that stabilized the RNA structure. At the same time, transition metal ions only marginally reduced the amount of 2',3'-cGMP, blocking binase recognition sites of guanine at N7 of nucleophilic purine bases.

Purines: forgotten mediators in traumatic brain injury

Recently, the topic of traumatic brain injury has gained attention in both the scientific community and lay press. Similarly, there have been exciting developments on multiple fronts in the area of neurochemistry specifically related to purine biology that are relevant to both neuroprotection and neurodegeneration. At the 2105 meeting of the National Neurotrauma Society, a session sponsored by the International Society for Neurochemistry featured three experts in the field of purine biology who discussed new developments that are germane to both the pathomechanisms of secondary injury and development of therapies for traumatic brain injury. This included presentations by Drs. Edwin Jackson on the novel 2',3'-cAMP pathway in neuroprotection, Detlev Boison on adenosine in post-traumatic seizures and epilepsy, and Michael Schwarzschild on the potential of urate to treat central nervous system injury. This mini review summarizes the important findings in these three areas and outlines future directions for the development of new purine-related therapies for traumatic brain injury and other forms of central nervous system injury. In this review, novel therapies based on three emerging areas of adenosine-related pathobiology in traumatic brain injury (TBI) were proposed, namely, therapies targeting 1) the 2',3'-cyclic adenosine monophosphate (cAMP) pathway, 2) adenosine deficiency after TBI, and 3) augmentation of urate after TBI.