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Ribosomal RNA Processing Sites
Published in S. K. Dutta, DNA Systematics, 2019
Robert J. Crouch, Jean-Pierre Bachellerie
In the pre-rRNA, extensive base pairing is possible for sequences flanking 16S rRNA.24 Such double-stranded RNA regions may then be cleaved by RNase III. Transcripts that terminate in the 5′ half of the 16S rRNA sequences are not cleaved in vitro,28 even though they possess the primary sequence cleaved by RNase III. This is taken as evidence to suggest that both regions flanking the 16S rRNA are required for RNase III cleavage. Extensive base pairing is also possible between sequences flanking 23S rRNA in pre-rRNA.25 However, its involvement as a signal for RNase III action remains to be established. Using results obtained from SI nuclease mapping analysis, King and Schlessinger29 conclude that the 5′ end of 23S rRNA can be cleaved by RNase III before the 3′ end of the same molecule is synthesized. They suggest two interpretations of these results: (1) the newly synthesized 23S 5′ end could hybridize to the 3′ end of a separate pre-rRNA (i.e., an intermolecular reaction) or (2) RNase III recognition sites are present at each end of the 23S rRNA sequences. It is possible to determine if there are independent sites by making transcripts containing each end separately and asking if RNase III cleaves the transcripts. Intermolecular vs. intramolecular RNase III sites might be more difficult to test.
Regulation of Synthesis of the β & β′ Subunits of RNA Polymerase of Escherichia Coli
Published in James F. Kane, Multifunctional Proteins: Catalytic/Structural and Regulatory, 2019
Rudolph Spangler, Geoffrey Zubay
Attenuators in λ and E. coli biosynthetic operons are modulated by specific regulatory factors. There is some evidence for modulation of the β operon attenuator, but it is not clear by what mechanism this modulation could be carried out.13 The function of the RNAse III cleavage site is even less clear. RNAse III cleavage sites were found in λ and T7 phage messengers and in bacterial ribosomal RNAs but never before in a host messenger.14 Possibly this “trimming” operation increases the efficiency of translation of the rpoBC part of the mRNA by removing RNA which could hinder entering ribosomes. This trimming operation has been shown not to be necessary for translation of most T7 phage messengers.15 An important exception is the 0.3 protein of T7, the synthesis of which is greatly stimulated both in vivo and in vitro with RNAse III+ strains. Possibly there is some compensating mechanism which cuts the other mRNAs but which does not cut the mRNA for the 0.3 protein. Alternatively, the other mRNAs do not have to be cut for translation to proceed whereas the mRNA for the 0.3 protein does have to be cut for translation to proceed. A summary of the gross structure of the nascent and processed transcripts believed to be synthesized in vivo from the β operon is given in Figure 1.
Exopolysaccharides metabolism and cariogenesis of Streptococcus mutans biofilm regulated by antisense vicK RNA
Published in Journal of Oral Microbiology, 2023
Yuting Sun, Hong Chen, Mengmeng Xu, Liwen He, Hongchen Mao, Shiyao Yang, Xin Qiao, Deqin Yang
Degradation of RNA is a crucial mechanism for regulating gene expression in organisms. Rnc, located upstream of vicR/K/X, affects vicR/K/X gene at the post-transcriptional level [19]. In previous studies, we found that rnc gene regulates carbohydrate transport and metabolism of S. mutans by regulating the expression of ncRNAs (ASvicR and msRNA1657). In addition, RNAse III, encoded by rnc, is a widespread endoribonuclease that binds and cleaves dsRNA. AsRNA allows precise control of the regulatory circuit, which is the key for bacteria to quickly adapt to environmental changes [26,27]. Plenty of studies have confirmed that the virulence factors and adaptability of S. mutans can be regulated by asRNAs, indicating the feasibility of regulating protein function by asRNAs to affect its cariogenesis [28,29].
Exosomes derived from HeLa cells break down vascular integrity by triggering endoplasmic reticulum stress in endothelial cells
Published in Journal of Extracellular Vesicles, 2020
Yinuo Lin, Chi Zhang, Pingping Xiang, Jian Shen, Weijian Sun, Hong Yu
Growing evidence indicated that exosomal components, especially microRNAs, can suppress the expression of TJ proteins in ECs [14,19]. Our exosomal microRNA sequencing data show that there are several exosomal miRNA(s) in ExoHeLa that may directly or indirectly modulate the expression of TJ proteins. However, we found that the corresponding miRNA inhibitors cannot neutralize the down-regulation effect of ExoHeLa on TJ proteins (Figure 4(c)), indicating that exosomal miRNAs may not be responsible for the decrease of TJ proteins. This was further approved by our Dicer knock-down experiment. It has been approved that RNase III protein, Dicer, is required for the process of microRNA [35]. When we knocked down Dicer in HeLa cells by siRNA, the miRNAs in exosomes were dramatically reduced (Figure 4(f)). However, when these exosomes (ExoHeLa Dicer KD) were used to treat ECs, the TJ proteins in ECs were still decreased (Figure 4(g)). All these results suggested that exosomal miRNAs are not responsible for the ExoHeLa-induced reduction of TJ proteins. Indeed, this finding is discordant with those previous results. It possibly due to the global protein synthesize arrest caused by eIF2α phosphorylation, which may abrogate the microRNA regulation effects on TJ protein expression.
Recent findings regarding the effects of microRNAs on fibroblast-like synovial cells in rheumatoid arthritis
Published in Immunological Medicine, 2019
Naoki Iwamoto, Atsushi Kawakami
The biogenesis and maturation of miRNAs occurs in multiple steps. First, within the cell nucleus, RNA polymerase II transcribes the genes to the primary microRNA(pri-miRNA), which is characterized by a hairpin. Next, pri-miRNAs are processed by the multimeric protein complex called Drosha and the DiGeorge syndrome critical region protein 8 (DGCR8) into the precursor miRNA(pre-miRNA), which is shorter than pri-miRNA (70–80-nt) [11]. The pre-miRNA is then recognized by exportin 5 and transported to the cytoplasm. Subsequently, in the cytoplasm, Dicer, an endonuclease RNase III, cleaves pre-miRNA to release the miRNA/miRNA* duplex. A mature duplex miRNA is loaded onto argonaute (AGO) proteins, after which the guide strand generates the RNA-induced silencing complex (RISC), which suppresses the expression of target genes by complementary binding to the target mRNAs. In the RISC/mRNA complex, mature miRNA recognizes its target mRNA by the small (6–8-nt) miRNA fragment named the “seed” region. Complementary binding between the seed region and the 3'-UTR of target mRNA leads to translational repression or degradation [12,13]. Through these steps, microRNAs mediate the repression of that target. Each miRNA regulates hundreds to thousands of target genes [14].