Phylogenetic distribution of extracellular guanyl-preferring ribonucleases renews taxonomic status of two <i>Bacillus</i> strains

Abstract

† The GenBank accession number for the 16S rRNA gene sequence of Bacillus altitudinis B-388 is JX129389, for the rpoB gene sequence of Bacillus altitudinis B-388 is JX129391, for the 16S rRNA gene sequence of Bacillus pumilus 7P is JX129390 and for the rpoB gene sequence of Bacillus pumilus 7P is JX129392 correspondingly.None of the authors of this manuscript has any financial or personal relationship with other people or organizations that could inappropriately influence their work. IntroductionBarnase, an extracellular alkaline guanyl-preferring ribonuclease first isolated from Bacillus amyloliquefaciens (Hartley and Rogerson, 1972), was shown to possess a wide range of biological activities and is of special interest for research and practical applications in biotechnology and medicine (Kempe et al., 2014;Spång et al., 2012;Sreenivasan et al., 2013;Ulyanova et al., 2011). Ribonucleases similar to barnase (UniProtKB/Swiss-Prot accession number P00648) were purified from B. intermedius 7P (P00649), B. circulans BCF-256 (P35078), B. pumilus KMM-62 (P48068), B. coagulans BCF-247 (P37203), and B. thuringiensis var. subtoxicus B-388 (Q9R5D7, GenBank acc No. AAB28984.1). B. intermedius RNase referred to as binase is as well studied as barnase. Its antitumor and antiviral properties are documented (Mironova et al., 2013;Mitkevich et al., 2014;Shah Mahmud and Ilinskaya, 2013;Ulyanova et al., 2011) while the strain itself is an undescribed taxon which is The potential of microbial ribonucleases as promising antitumor and antiviral agents, determines today's directions of their study. One direction is connected with biodiversity of RNases. We have analyzed completed and drafted Bacillus genomes deposited in GenBank for the presence of coding regions similar to the gene of an extracellular guanyl-preferring RNase of Bacillus amyloliquefaciens (barnase). Orthologues of the barnase gene were detected in 9 species out of 83. All of these belong to "B. subtilis" group within the genus. B. subtilis itself, as well as some other species within this group, lack such types of RNases. RNases similar to barnase were also found in species of "B. cereus" group as a part of plasmid-encoded S-layer toxins. It was also found that taxonomic states of culture collection strains, which were initially described based on a limited set of phenotypic characteristics, can be misleading and need to be confirmed. Using several approaches such as matrix-assisted laser desorption ionizationtime of flight mass spectrometry (MALDI-TOF MS), sequencing of genes for 16S ribosomal RNA and RNA polymerase subunit beta followed by reconstruction of phylogenetic trees, we have re-identified two RNase-secreting Bacillus strains: B. thuringiensis B-388 which should be assigned as B. altitudinis B388 and B. intermedius 7P which should be renamed as B. pumilus 7P. Therefore, small secreted guanyl-preferring RNases are the feature of "B. subtilis" group only, which is characterized by distinctive lifestyle and adaptation strategies to environment.

Ribonuclease fromBacillusActs as an Antiviral Agent against Negative- and Positive-Sense Single Stranded Human Respiratory RNA Viruses

“…In Figure 4, we have shown a scheme reflecting different possible mechanisms of a binase effect on influenza A viral functional ribonucleoprotein (RNP) complex gene expression using a vRNA-like Pol1-transcript encoding a reporter gene (GFP) step by step starting from internalization of binase (steps A and B) to the step of blocking of viral translation (steps C, D). Steps depicting production of reporter mRNA (7)(8) and transcription of viral RNP mRNA (4-5) can be inhibited by binase.…”

“…Isolation. Binase (EC 3.1.27.3; bacterial extracellular guanyl-preferring ribonuclease) was collected from the culture medium of Bacillus pumilus B3073 (the former name is B. intermedius B3073 [7]). The cultures were grown in a 1 L conical flask containing 1/5 flask volume of the phosphate deficient liquid medium (2.0% low phosphate peptone, 1.0% glucose, 1.0% CaCl 2 , 0.3% NaCl, 0.03% MgSO 4 × 7H 2 O, and 0.01% MnSO 4 , pH 8.5) with 200 rpm in a Multitron shaking incubator (INFORS HT, Switzerland) at 37 ∘ C until the beginning of the stationary phase of bacterial growth.…”

“…In contrast, bacterial RNases are not inhibited by RI and can retain their catalytic activity in mammalian tissues. One of the wellstudied bacterial RNases is binase, the guanyl-preferring low molecular weight RNase secreted by Bacillus pumilus [7].…”

Endophytic Bacillus bacteria with RNase activity in the resistance of potato plants to viruses

“…Endophytic Bacillus bacteria with RNase activity in the resistance of potato plants to viruses and balifases, respectively (Ulyanova et al, 2011(Ulyanova et al, , 2016. Recent studies demonstrated that B. subtilis and B. thuringiensis contain bacterial RNases effectively inactivate RNA-containing viruses -baRNase and binase (Ulyanova et al, 2011).…”

“…A lot of Bacillus species can inhabit internal plant tissues (Burkhanova et al, 2017) and produce ribonucleases (Ulyanova et al, 2016;Ilinskaya et al, 2018). Thus, 73 % of Bacillus which were isolated from Cucurbitaceae produce nucleases (Khalaf, Raizada, 2018).…”