Abstract:NanoRNase (Nrn) specifically degrades nucleoside 3′,5′-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn2+ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables… Show more
“…3B ). Similar conformational variations are seen in the structures of the DHH family enzymes RecJ and PPase, and also in homologous nanoRNases, where it has been suggested that the C-terminal domain is dynamic and may play a role in bringing substrate to the N-terminal catalytic domain within an individual monomer 7 , 22 , 24 , 25 , 28 . Figure 3 Mobility of the NrnA DHHA1 substrate binding domain.…”
Section: Resultsmentioning
confidence: 55%
“…Similar GG motifs are present in other proteins with DHHA1 domains such as AlaRS and RecJ (Fig. 1B ), but it has been suggested that exonucleases in this family (RecJ and NrnA) may extend this motif to terminate with a histidine (H284 in B. subtilis NrnA) for substrate recognition 7 , 22 , 24 – 26 . Bacillus type NrnA homologs also contain an R-x-R-x-R motif (R262, 264, and 266 in B. subtilis NrnA) that is only partially conserved in other DHHA1 domains (only the arginine equivalent to R266 is conserved in RecJ; Fig.…”
Section: Resultsmentioning
confidence: 55%
“…Bacillus nrnA complements both an E. coli orn ts mutant and a deletion of cysQ , a gene responsible for pAp turnover 16 . However, NrnA is homologous to RecJ, a 5′ → 3′ DHH family DNase, and it has been suggested that NrnA is a 5′ → 3′ exonuclease based on mass spectrum analysis of in vitro generated reaction products 23 , 24 . Structures of nanoRNases from Bacteroides fragilis 24 , Mycobacterium smegmatis 25 , and Mycobacterium tuberculosis 7 have yielded important insights into the 2-metal ion mechanism of the DHH domain and the nucleotide binding pocket of the DHHA1 domain, but have not cleared up confusion regarding the polarity of NrnA.…”
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3′ → 5′ exonuclease, but we show here that NrnA is bidirectional, degrading 2–5 nucleotide long RNA oligomers from the 3′ end, and longer RNA substrates from the 5′ end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5′ → 3′ DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3′ → 5′ activity.
“…3B ). Similar conformational variations are seen in the structures of the DHH family enzymes RecJ and PPase, and also in homologous nanoRNases, where it has been suggested that the C-terminal domain is dynamic and may play a role in bringing substrate to the N-terminal catalytic domain within an individual monomer 7 , 22 , 24 , 25 , 28 . Figure 3 Mobility of the NrnA DHHA1 substrate binding domain.…”
Section: Resultsmentioning
confidence: 55%
“…Similar GG motifs are present in other proteins with DHHA1 domains such as AlaRS and RecJ (Fig. 1B ), but it has been suggested that exonucleases in this family (RecJ and NrnA) may extend this motif to terminate with a histidine (H284 in B. subtilis NrnA) for substrate recognition 7 , 22 , 24 – 26 . Bacillus type NrnA homologs also contain an R-x-R-x-R motif (R262, 264, and 266 in B. subtilis NrnA) that is only partially conserved in other DHHA1 domains (only the arginine equivalent to R266 is conserved in RecJ; Fig.…”
Section: Resultsmentioning
confidence: 55%
“…Bacillus nrnA complements both an E. coli orn ts mutant and a deletion of cysQ , a gene responsible for pAp turnover 16 . However, NrnA is homologous to RecJ, a 5′ → 3′ DHH family DNase, and it has been suggested that NrnA is a 5′ → 3′ exonuclease based on mass spectrum analysis of in vitro generated reaction products 23 , 24 . Structures of nanoRNases from Bacteroides fragilis 24 , Mycobacterium smegmatis 25 , and Mycobacterium tuberculosis 7 have yielded important insights into the 2-metal ion mechanism of the DHH domain and the nucleotide binding pocket of the DHHA1 domain, but have not cleared up confusion regarding the polarity of NrnA.…”
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3′ → 5′ exonuclease, but we show here that NrnA is bidirectional, degrading 2–5 nucleotide long RNA oligomers from the 3′ end, and longer RNA substrates from the 5′ end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5′ → 3′ DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3′ → 5′ activity.
“…In biological systems, phosphoesterase plays a vital role in DNA fragmentation, RNA replication, human body medicine, metabolism, chemotherapy, and bioremediation [23,24]. In the present results, the phosphoesterase protein (point 36) that corresponded with the transcriptome genes phosphoesterase (TRINITY_DN431_c0_g2) was downregulated.…”
Section: Castellote Et Al Investigated the Molecular Expression Ofsupporting
Antagonistic yeasts can inhibit fungal growth. In our previous research, Meyerozyma guilliermondii, one of the antagonistic yeasts, exhibited antagonistic activity against Penicillium expansum. However, the mechanisms, especially the molecular mechanisms of inhibiting activity of M. guilliermondii, are not clear. In this study, the protein expression profile and transcriptome characterization of P. expansum induced by M. guilliermondii were investigated. In P. expansum induced by M. guilliermondii, 66 proteins were identified as differentially expressed, among them six proteins were upregulated and 60 proteins were downregulated, which were associated with oxidative phosphorylation, ATP synthesis, basal metabolism, and response regulation. Simultaneously, a transcriptomic approach based on RNA-Seq was applied to annotate the genome of P. expansum and then studied the changes of gene expression in P. expansum treated with M. guilliermondii. The results showed that differentially expressed genes such as HEAT, Phosphoesterase, Polyketide synthase, ATPase, and Ras-association were significantly downregulated, in contrast to Cytochromes P450, Phosphatidate cytidylyltransferase, and Glutathione S-transferase, which were significantly upregulated. Interestingly, the downregulated differentially expressed proteins and genes have a corresponding relationship; these results revealed that these proteins and genes were important in the growth of P. expansum treated with M. guilliermondii.
“…A Phyre2 structural model of the GdpP DHH-DHHA1 domain shows remarkable resemblance to the NrnA crystal structures and the DhhP structure of M. smegmatis
( Fig. 2A ) [4,5]. Among these proteins, the amino-terminal DHH subunit and the carboxy-terminal DHHA1 subunit are connected by a flexible loop to form a cleft.…”
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