High-Resolution Cryo-EM Structure of the Pseudomonas Bacteriophage E217

E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4

S1 ribosomal protein and the interplay between translation and mRNA decay

S1 is an ‘atypical’ ribosomal protein weakly associated with the 30S subunit that has been implicated in translation, transcription and control of RNA stability. S1 is thought to participate in translation initiation complex formation by assisting 30S positioning in the translation initiation region, but little is known about its role in other RNA transactions. In this work, we have analysed in vivo the effects of different intracellular S1 concentrations, from depletion to overexpression, on translation, decay and intracellular distribution of leadered and leaderless messenger RNAs (mRNAs). We show that the cspE mRNA, like the rpsO transcript, may be cleaved by RNase E at multiple sites, whereas the leaderless cspE transcript may also be degraded via an alternative pathway by an unknown endonuclease. Upon S1 overexpression, RNase E-dependent decay of both cspE and rpsO mRNAs is suppressed and these transcripts are stabilized, whereas cleavage of leaderless cspE mRNA by the unidentified endonuclease is not affected. Overall, our data suggest that ribosome-unbound S1 may inhibit translation and that part of the Escherichia coli ribosomes may actually lack S1

Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins

Bacillus subtilis pnpA gene product, polynucleotide phosphorylase (PNPase), is involved in double-strand break (DSB) repair via homologous recombination (HR) or non-homologous end-joining (NHEJ). RecN is among the first responders to localize at the DNA DSBs, with PNPase facilitating the formation of a discrete RecN focus per nucleoid. PNPase, which co-purifies with RecA and RecN, was able to degrade single-stranded (ss) DNA with a 3′ → 5′ polarity in the presence of Mn2+ and low inorganic phosphate (Pi) concentration, or to extend a 3′-OH end in the presence dNDP·Mn2+. Both PNPase activities were observed in evolutionarily distant bacteria (B. subtilis and Escherichia coli), suggesting conserved functions. The activity of PNPase was directed toward ssDNA degradation or polymerization by manipulating the Pi/dNDPs concentrations or the availability of RecA or RecN. In its dATP-bound form, RecN stimulates PNPase-mediated polymerization. ssDNA phosphorolysis catalyzed by PNPase is stimulated by RecA, but inhibited by SsbA. Our findings suggest that (i) the PNPase degradative and polymerizing activities might play a critical role in the transition from DSB sensing to end resection via HR and (ii) by blunting a 3′-tailed duplex DNA, in the absence of HR, B. subtilis PNPase might also contribute to repair via NHEJ

Terminazione della trascrizione e maturazione di un RNA antisenso nel sistema di immunita' del batteriofago P4

Dottorato di ricerca in scienze genetiche. 8. ciclo. A.a. 1994-95. Docente guida G. Deho'. Coordinatore G. SironiConsiglio Nazionale delle Ricerche - Biblioteca Centrale - P.le Aldo Moro, 7, Rome; Biblioteca Nazionale Centrale - P.za Cavalleggeri, 1, Florence / CNR - Consiglio Nazionale delle RichercheSIGLEITItal

The RNA processing enzyme polynucleotide phosphorylase negatively controls biofilm formation by repressing poly-<it>N</it>-acetylglucosamine (PNAG) production in <it>Escherichia coli</it> C

<p>Abstract</p> <p>Background</p> <p>Transition from planktonic cells to biofilm is mediated by production of adhesion factors, such as extracellular polysaccharides (EPS), and modulated by complex regulatory networks that, in addition to controlling production of adhesion factors, redirect bacterial cell metabolism to the biofilm mode.</p> <p>Results</p> <p>Deletion of the <it>pnp</it> gene, encoding polynucleotide phosphorylase, an RNA processing enzyme and a component of the RNA degradosome, results in increased biofilm formation in <it>Escherichia coli</it>. This effect is particularly pronounced in the <it>E</it>. <it>coli</it> strain C-1a, in which deletion of the <it>pnp</it> gene leads to strong cell aggregation in liquid medium. Cell aggregation is dependent on the EPS poly-<it>N</it>-acetylglucosamine (PNAG), thus suggesting negative regulation of the PNAG biosynthetic operon <it>pgaABCD</it> by PNPase. Indeed, <it>pgaABCD</it> transcript levels are higher in the <it>pnp</it> mutant. Negative control of <it>pgaABCD</it> expression by PNPase takes place at mRNA stability level and involves the 5’-untranslated region of the <it>pgaABCD</it> transcript, which serves as a <it>cis</it>-element regulating <it>pgaABCD</it> transcript stability and translatability.</p> <p>Conclusions</p> <p>Our results demonstrate that PNPase is necessary to maintain bacterial cells in the planktonic mode through down-regulation of <it>pgaABCD</it> expression and PNAG production.</p

Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli

The exoribonuclease polynucleotide phosphorylase (PNPase, encoded by pnp) is a major player in bacterial RNA decay. In Escherichia coli, PNPase expression is post-transcriptionally regulated at the level of mRNA stability. The primary transcript is very efficiently processed by the endonuclease RNase III at a specific site and the processed pnp mRNA is rapidly degraded in a PNPase-dependent manner. While investigating the PNPase autoregulation mechanism we found, by UV-cross-linking experiments, that the ribosomal protein S1 in crude extracts binds to the pnp-mRNA leader region. We assayed the potential role of S1 protein in pnp gene regulation by modulating S1 expression from depletion to overexpression. We found that S1 depletion led to a sharp decrease of the amount of pnp and other tested mRNAs, as detected by Northern blotting, whereas S1 overexpression caused a strong stabilization of pnp and the other transcripts. Surprisingly, mRNA stabilization depended on PNPase, as it was not observed in a pnp deletion strain. PNPase-dependent stabilization, however, was not detected by chemical decay assay of bulk mRNA. Overall, our data suggest that PNPase exonucleolytic activity may be modulated by the translation potential of the target mRNAs and that, upon ribosomal protein S1 overexpression, PNPase protects from degradation a set of full-length mRNAs. It thus appears that a single mRNA species may be differentially targeted to either decay or PNPase-dependent stabilization, thus preventing its depletion in conditions of fast turnover

Axonal neuropathy due to myelin protein zero mutation misdiagnosed as amyloid neuropathy

In up to 50% of chronic idiopathic axonal neuropathies, an underlying diagnosis may be identified, including hereditary neuropathy. Charcot-Marie-Tooth disease (CMT) is clinically and genetically heterogeneous. Several mutations in the myelin protein zero (MPZ) gene have been associated with different CMT phenotypes, including classical demyelinating CMT1B and the axonal form of the disease. Primary amyloidosis, a rare disease where the amyloid is formed by the N-terminal portion of a monoclonal immunoglobulin light chain, may be complicated by polyneuropathy. We report a patient who was incorrectly diagnosed with amyloid neuropathy, but was found to have axonal CMT1B only after sural nerve biopsy ruled out an acquired amyloid neuropathy