Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2.

It has been shown that phages have evolved anti-CRISPR (Acr) proteins to inhibit host CRISPR-Cas systems. Most acr genes are located upstream of anti-CRISPR-associated (aca) genes, which is instrumental for identifying these acr genes. Thus far, eight Aca families (Aca1-Aca8) have been identified, all proteins of which share low sequence homology and bind to different target DNA sequences. Recently, Aca1 and Aca2 proteins were discovered to function as repressors by binding to acr-aca promoters, thus implying a potential anti-anti-CRISPR mechanism. However, the structural basis for the repression roles of Aca proteins is still unknown. Here, we elucidated apo-structures of Aca1 and Aca2 proteins and their complex structures with their cognate operator DNA in two model systems, the Pseudomonas phage JBD30 and the Pectobacterium carotovorum template phage ZF40. In combination with biochemical and cellular assays, our study unveils dimerization and DNA-recognition mechanisms of Aca1 and Aca2 family proteins, thus revealing the molecular basis for Aca1-and Aca2-mediated anti-CRISPR repression. Our results also shed light on understanding the repression roles of other Aca family proteins and autoregulation roles of acr-aca operons.

Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide.

Phytopathogenic bacteria belonging to the Pectobacterium and Dickeya genera (soft-rot Pectobacteriaceae) are in the focus of agriculture-related microbiology because of their diversity, their substantial negative impact on the production of potatoes and vegetables, and the prospects of bacteriophage applications for disease control. Because of numerous amendments in the taxonomy of P. carotovorum, there are still a few studied sequenced strains among this species. The present work reports on the isolation and characterization of the phage infectious to the type strain of P. carotovorum. The phage Arno 160 is a lytic Podovirus representing a potential new genus of the subfamily Autographivirinae. It recognizes O-polysaccahride of the host strain and depolymerizes it in the process of infection using a rhamnosidase hydrolytic mechanism. Despite the narrow host range of this phage, it is suitable for phage control application.

Complete genome sequence of the Pectobacterium carotovorum subsp. carotovorum virulent bacteriophage PM1.

PM1, a novel virulent bacteriophage that infects Pectobacterium carotovorum subsp. carotovorum, was isolated. Its morphological features were examined by electron microscopy, which indicated that this phage belongs to the family Myoviridae. It has a 55,098-bp genome, including a 2,665-bp terminal repeat. A total of 63 open reading frames (ORFs) were predicted, but only 20 ORFs possessed homology with functional proteins. There is one tRNA coding region, and the GC-content of the genome is 44.9 %. Most ORFs in bacteriophage PM1 showed high homology to enterobacteria phage ΦEcoM-GJ1 and Erwinia phage νB EamM-Y2. Like these bacteriophages, PM1 encodes an RNA polymerase, which is a hallmark of T7-like phages. There is no integrase or repressor, suggesting that PM1 is a virulent bacteriophage.

Biocontrol of Pectobacterium carotovorum subsp. carotovorum using bacteriophage PP1.

Pectobacterium carotovorum subsp. carotovorum (formerly Erwinia carotovora subsp. carotovora) is a plant pathogen that causes soft rot and stem rot diseases in several crops, including Chinese cabbage, potato, and tomato. To control this bacterium, we isolated a bacteriophage, PP1, with lytic activity against P. carotovorum subsp. carotovorum. Transmission electron microscopy revealed that the PP1 phage belongs to the Podoviridae family of the order Caudovirales, which exhibit icosahedral heads and short non-contractile tails. PP1 phage showed high specificity for P. carotovorum subsp. carotovorum, and several bacteria belonging to different species and phyla were resistant to PP1. This phage showed rapid and strong lytic activity against its host bacteria in liquid medium and was stable over a broad range of pH values. Disease caused by P. carotovorum subsp. carotovorum was significantly reduced by PP1 treatment. Overall, PP1 bacteriophage effectively controls P. carotovorum subsp. carotovorum.

Identification of the major proteins of the virions of bacteriophage ZF40 Pectobacterium carotovorum.

The vast variety of bacteriophages and the uniqueness of their individual representatives dictate to perform the detailed study of the actual phage-cell interactions, the virion morphogenesis and morphopoiesis in particular. An analysis of the complete genome sequence of the temperate phage ZF40 Pectobacterium carotovorum has shown that it is a representative of a unique group of phages of the Myoviridae family [Comeau A. M, Tremblay D., Moineau S., Rattei T., Kushkina A. I, Tovkach F I., H.M. Krisch, H.W. Ackermann Phage Morphology Recapitulates Phylogeny: The Comparative Genomics of a New Group of Myoviruses // PLoS ONE.--July 2012. - 7. - N 7. - e40102]. Characteristic features of these viruses are a small length of the tail compared with the diameter of the capsid and a complicated pattern of the tail sheath, leading to its criss-cross striation. In the presented article the major proteins were identified by means of the SDS-PAGE method: the head proteins (mp2: 33.9 kDa), the sheath (mp1: 39.2 kDa) and the tail tube ones (mp3: 19.9 kDa). It was proved that the mp2 molecular weight is the same with the gp46, the putative major capsid protein derived from the results of the genome sequencing. Therefore, it is still not determined whether the gp46 (mp2) of the virulent mutant 421 of the phage ZF40 is exposed to post-translational modification in the course of the phage particle maturation during its development in the cells of the strain M2-4/50RI P. carotovorum. To study the morphogenetic development pathways it was proposed to use the phage variants that form an excess of individual components of the virion: capsids, procapsids and separate tails propagated on different hosts.

Complete genome sequence of Pectobacterium carotovorum subsp. carotovorum bacteriophage My1.

Pectobacterium carotovorum subsp. carotovorum, a member of the Enterobacteriaceae family, is an important plant-pathogenic bacterium causing significant economic losses worldwide. P. carotovorum subsp. carotovorum bacteriophage My1 was isolated from a soil sample. Its genome was completely sequenced and analyzed for the development of an effective biological control agent. Sequence and morphological analyses revealed that phage My1 is a T5-like bacteriophage and belongs to the family Siphoviridae. To date, there is no report of a Pectobacterium-targeting siphovirus genome sequence. Here, we announce the complete genome sequence of phage My1 and report the results of our analysis.

Complete genome sequence of phytopathogenic Pectobacterium carotovorum subsp. carotovorum bacteriophage PP1.

Pectobacterium carotovorum subsp. carotovorum is a phytopathogen causing soft rot disease on diverse plant species. To control this plant pathogen, P. carotovorum subsp. carotovorum-targeting bacteriophage PP1 was isolated and its genome was completely sequenced to develop a novel biocontrol agent. Interestingly, the 44,400-bp genome sequence does not encode any gene involved in the formation of lysogen, suggesting that this phage may be very useful as a biocontrol agent because it does not make lysogen after host infection. This is the first report on the complete genome sequence of the P. carotovorum subsp. carotovorum-targeting bacteriophage, and it will enhance our understanding of the interaction between phytopathogens and their targeting bacteriophages.

Characteristics of defective phage particles of Pectobacterium carotovorum ZM1.

It is shown for the first time that the expression products of defective prophages are typical of defective lysogenic systems of phytopathogenic Pectobacterium carotovorum. It is established that virus-like particles (LP) such as phage capsids are packing bacterial DNA which size is determined by pulse field gel electrophoresis separation. Based on data about capsid structures which are formed by the virulent mutant ZF40/421, there is made a suggestion about the forming mechanism of defective virions of P carotovorum.

[Dissociation of Pectobacterium carotovorum subsp. carotovorumrelated to the changes in the cell wall lipopolysaccharide].

It is shown for the first time that population heterogeneity of Pectobacterium carotovorum subsp. carotovorum is applicable to a wide range of strains and therefore is a universal characteristic. Using the method of specific selection with the help of carotovoricins which are identical to the phage tails a set of population dissociants of different types was obtained, due to the fact that S-LPS is the part of the cell wall which contains their attachment sites. It was determined that changes in S-lipopolysaccharides lead to the formation of SR-, R-forms of P. carotovorum. A suggestion is made that the changes in the surface structures of dissociants have a significant impact on secretion types II and III--the main pathogenicity factor of some bacteria. The results presented are a prerequisite for studying the direction, the reasons for dissociation process and its impact on the pathogenicity of P. carotovorum.

[Polypeptide content and HPLC-chromatography of the virions of phage ZF40 mutants].

Study of the polypeptide content of erwiniophage ZF40c(5/5) and ZF40-421 virulent mutants has shown that their virions include no less than 10 structural proteins with molecular weights ranging from 16.9 to 96.5 kDa. Three polypeptides belong to a group of major proteins with molecular weights 39.2, 33.1 and 18.5 kDa. They correlate with the polypeptides of phage head, tail sheath and tail core correspondingly. It has been proven that the protein contents of these phages are identical, taking into account that the percent ratio of all polypeptides approaches 1.0. The polypeptide profile of isogenic variant of phage ZF40-421 obtained on EccRC5297 is characterized by another ratio of major proteins. These differences are reflected in the structure of procapsids, that explains low level of stability and viability of the variant. The work shows for the first time the possibility of using HPLC-chromatography for studying native phage particles and their structural components.

[Peculiarities of morphogenetical development of erwiniophage ZF40 virulent mutants ].

The distortion of morphopoiesis or tail attachment to the capsid is a characteristic feature of morphogenetical development not only of a reproductive infection but also of the lysogenic induction of the defective bacteriophage Erwinia carotovora subsp. carotovora (Ecc). A model system for studying morphogenetical development and assembling of the virion was created on the basis of the phage ZF40 and its two virulent mutants ZF40-421 and ZF40(5/5), as well as the indicator culture Ecc M2-4/50 R1 being nontraditional host for these phages. It has helped to establish that the diameter of the phage capsid is not a conservative value. The presence of capsids of two types with the average diameters 60.3 and 65.0 nm is characteristic of the virmutant ZF40c(5/5)/50RI, while in the course of morphogenesis the phage ZF40-421/50RI forms only one type of heads of 65 nm in size. These heads are probably not firmly connected to the tails since the degree of the secondary destruction of the virions of the phage Zf40-421/50RI is considerably higher, than that of the virions of the phage ZF40c(5/5)/50RI. The number of capsids being 60.3 nm in diameter prevails considerably in the latter. The both virulent mutants as a whole are essentially more stable than their isogenic partners obtained on Ecc RC5297 which helps to make a conclusion about considerable influence of specific bacterial proteins of the host-cell on morphogenesis and morphopoiesis.

[Transduction as one of the methods of obtaining genetic information in Erwinia].

Transduction is one of the key processes of horizontal transfer of genes in bacteria. It is known that it is involved in distribution of the main factors of pathogenicity among numerous enterobacteria. It is shown that clear mutants and some variants of the temperate bacteriophage ZF40 Erwinia carotovora subsp. carotovora can perform general transduction of chromosome and plasmid genes of the bacterium E. carotovora. The indicators of chromosome transduction frequencies of the markers--arg+, met+, trp+, ura+ have a broad range of values: 7.10-10(-8) - 1.1-10(-1). The authors have succeeded in increasing the transduction efficiency due to infecting the recipient bacteria on the solid medium LB. Such approach is important for the phages similar to ZF40 in which adsorption is accompanied by re-adsorption of phage particles. The mechanism of transfer of bacterial genes by the type of general transduction is connected with cyclic permutation of phage DNA.

[Detection of bacteriophages of siphoviridae family in Erwinia carotovora subsp. carotovora].

It was established that the polylysogenic phage system of culture Erwinia carotovora subsp. carotovora 91P includes: a) defective bacteriophages of Myoviridae family, which are displayed as macromolecular carotovoricins b) valuable highly unstable temperate phage, which can be attributed to the family Myoviridae, and which, perhaps, is an analogue of phage ZF40 [6], and c) resistant to osmotic shock temperate phage of family Siphoviridae. This phage, called TIRI, consists of isometric head 50 nm in diameter and a rigid tail structure 203 nm long. A characteristic feature of the phage tail is an evident transverse striation, which is also indicative for the tail-like particle of the defective temperate phage of the strain 48A-7/4b. In general, the phage system of E carotovora subsp. carotovora is similar to Pseudomonas aeruginosa with its R- and F-bacteriocins, and phages of the families Myoviridae and Siphoviridae.

Exploitation of a new flagellatropic phage of Erwinia for positive selection of bacterial mutants attenuated in plant virulence: towards phage therapy.

AIMS: To isolate and characterize novel bacteriophages for the phytopathogen, Erwinia carotovora ssp. atroseptica (Eca), and to isolate phage-resistant mutants attenuated in virulence. METHODS AND RESULTS: A novel flagellatropic phage was isolated on the potato-rotting bacterial species, Eca, and characterized using electron microscopy and restriction analysis. The phage, named PhiAT1, has an icosahedral head and a long, contractile tail; it belongs to the Myoviridae family. Partial sequencing revealed the presence of genes with homology to those of coliphages T4, T7 and Mu. Phage-resistant transposon mutants of Eca were isolated and studied in vitro for a number of virulence-related phenotypes; only motility was found to be affected. In vivo tuber rotting assays showed that these mutants were attenuated in virulence, presumably because the infection is unable to spread from the initial site of inoculation. CONCLUSIONS: The Eca flagellum can act as a receptor for PhiAT1 infection, and resistant mutants are enriched for motility and virulence defects. SIGNIFICANCE AND IMPACT OF THE STUDY: PhiAT1 is the first reported flagellatropic phage found to infect Eca and has enabled further study of the virulence of this economically important phytopathogen.

[Abortive infection in Erwinia carotovora, as a source of nanoparticles of phage nature].

A possibility to obtain nanoparticles of phage nature using abortive phage infection was shown for the first time. It was found out that the nonspecific host Erwinia carotovora subsp. carotovora J2 being infected by phage ZF 40-RT80, the cells form a 100-fold surplus of capsid structures. Using the electron microscope the authors have found two types of phage capsids which differ from each other and have different modal diameters--47.5 and 71.5 nm. The found capsids pack the phage DNA which releases them under treatment of the preparations by DNAse I. A simple method of purification of capsid structures from mature virions which are formed in inconsiderable quantity in the process of abortive phage infection is proposed. The obtained results create preconditions for obtaining capsid nanoparticles as well as for studying the stages of morphogenesis and morphopoiesis of phage ZF40 without attracting special phage mutants.

[The characteristic of the colispecific bacteriocins of Erwinia carotovora subsp. carotovora Ec153].

It has been shown for the first time that macromolecular carotovoricins from Erwinia carotovora subsp. carotovora Ec153 strain are active to Escherichia coli and posses endonuclease activity. It has been established that 19.1% of strains isolated from the patients are sensitive to these bacteriocins. The type and the form of these particles have been also determined and they show resemblance with phage objects.

Mutagenesis and functional characterization of the RNA and protein components of the toxIN abortive infection and toxin-antitoxin locus of Erwinia.

Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multiple adaptive resistance mechanisms. These mechanisms include the abortive infection systems, which promote "altruistic suicide" of an infected cell, protecting the clonal population. A cryptic plasmid of Erwinia carotovora subsp. atroseptica, pECA1039, has been shown to encode an abortive infection system. This highly effective system is active across multiple genera of gram-negative bacteria and against a spectrum of phages. Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module. ToxIN is the first member of a new type III class of protein-RNA toxin-antitoxin modules, of which there are multiple homologues cross-genera. We characterized in more detail the abortive infection phenotype of ToxIN using a suite of Erwinia phages and performed mutagenesis of the ToxI and ToxN components. We determined the minimal ToxI RNA sequence in the native operon that is both necessary and sufficient for abortive infection and to counteract the toxicity of ToxN. Furthermore, site-directed mutagenesis of ToxN revealed key conserved amino acids in this defining member of the new group of toxic proteins. The mechanism of phage activation of the ToxIN system was investigated and was shown to have no effect on the levels of the ToxN protein. Finally, evidence of negative autoregulation of the toxIN operon, a common feature of toxin-antitoxin systems, is presented. This work on the components of the ToxIN system suggests that there is very tight toxin regulation prior to suicide activation by incoming phage.

The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair.

Various mechanisms exist that enable bacteria to resist bacteriophage infection. Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population. A highly effective 2-gene Abi system from the phytopathogen Erwinia carotovora subspecies atroseptica, designated ToxIN, is described. The ToxIN Abi system also functions as a toxin-antitoxin (TA) pair, with ToxN inhibiting bacterial growth and the tandemly repeated ToxI RNA antitoxin counteracting the toxicity. TA modules are currently divided into 2 classes, protein and RNA antisense. We provide evidence that ToxIN defines an entirely new TA class that functions via a novel protein-RNA mechanism, with analogous systems present in diverse bacteria. Despite the debated role of TA systems, we demonstrate that ToxIN provides viral resistance in a range of bacterial genera against multiple phages. This is the first demonstration of a novel mechanistic class of TA systems and of an Abi system functioning in different bacterial genera, both with implications for the dynamics of phage-bacterial interactions.

[Destabilization of defective lysogeny as the index of population dissociation of Erwinia carotovora].

The method of quantitative determination of bacteriocinogenicity in Erwinia carotovora dissociants has been suggested. It is based on the application of indicator bacterial mutants that are resistant to nalidixic acid. It has been revealed that population dissociation destabilizes a defective lysogeny of pectolytic Erwinia. In particular, a decrease of cell indicator survivability due to an increase of active bacteriocins yield has been found under lysogenic induction of defective prophages. The reverse dependence between the indicator cell survivability caused by dissociants bacteriocins induction and the reaction of hypersensitivity on leaves of the resistant plant Nicotiana tabacum, has been revealed. Similar dependence has been determined between dissociation and activity of pectate lyase. It has been hypothesized, that viable erwiniophages, being involved in the process of lysogenicity and induction, could play the role of 'switches' of bacterial phenotype raising adaptive phytopathogene reactions. The paper is presented in Russian. K e y w o r d s: Erwinia carotovora, defective lysogeny, population dissociation, reaction of hypersensitivity, activity of pectate lyase.

[Preliminary characteristic of DNA-containing virus-like particles of Erwinia carotovora].

DNA-containing particles formed by the expression of the defect prophages of E. carotovora subsp. carotovora (Ecc) have been revealed for the first time. Two types of virus-like particles (VLP) occur in this phytopathogenic bacterium. Capsides of the first type VLP are weakly identified at agarose electrophoretic separation while DNA released from them are presented by distinct reflexes. Mobility of the second type particles is close to that of separate capsids of the temperate phage ZF40. DNA packed in these VLP are slightly mobile in agarose gels and are, most likely, typologically close to the open ring forms. Molecules of DNA particles of the both types possess the size equal to or more than 50 t.p.n. It is shown that DNA-containing VLP prevail in lysates obtained at lysogenic induction of cells by nalidixic acid, while the induction by mitomycin C is mainly characterized by formation of biologically active tails of defective temperate phages. The obtained result create preconditions for studying molecular-genetic organization of defective prophages and their significance in ecology of the important phytopathogen E. carotovora.