Publications by authors named "Alla K Golomidova"

12 Publications

  • Page 1 of 1

Equine Intestinal O-Seroconverting Temperate Coliphage Hf4s: Genomic and Biological Characterization.

Appl Environ Microbiol 2021 10 18;87(21):e0112421. Epub 2021 Aug 18.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.

Tailed bacteriophages constitute the bulk of the intestinal viromes of vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are dominated mostly by temperate phages, while in horse feces virulent phages are more prevalent. To our knowledge, all the previously reported isolates of horse fecal coliphages are virulent. Temperate coliphage Hf4s was isolated from horse feces, from the indigenous equine Escherichia coli 4s strain. It is a podovirus related to the genus (including the well-characterized Salmonella bacteriophage P22). Hf4s recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by the same bacteriophage and also abolishes the adsorption of some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. The relationships between virulent and temperate bacteriophages and their impact on high-density symbiotic microbial ecosystems of animals are not always clear and may vary between species or even between individuals. The horse intestinal virome is dominated by virulent phages, and Hf4s is the first temperate equine intestinal coliphage characterized. It recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. These findings raise questions on the significance of bacteriophage-bacteriophage interactions within the ecology of microbial viruses in mammal intestinal ecosystems.
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http://dx.doi.org/10.1128/AEM.01124-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8516047PMC
October 2021

High-throughput LPS profiling as a tool for revealing of bacteriophage infection strategies.

Sci Rep 2019 02 27;9(1):2958. Epub 2019 Feb 27.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, prosp. 60-letiya Oktyabrya, 7 bld. 2, 117312, Moscow, Russian Federation.

O-antigens of Gram-negative bacteria modulate the interactions of bacterial cells with diverse external factors, including the components of the immune system and bacteriophages. Some phages need to acquire specific adhesins to overcome the O-antigen layer. For other phages, O-antigen is required for phage infection. In this case, interaction of phage receptor binding proteins coupled with enzymatic degradation or modification of the O-antigen is followed by phage infection. Identification of the strategies used by newly isolated phages may be of importance in their consideration for various applications. Here we describe an approach based on screening for host LPS alterations caused by selection by bacteriophages. We describe an optimized LPS profiling procedure that is simple, rapid and suitable for mass screening of mutants. We demonstrate that the phage infection strategies identified using a set of engineered E. coli 4 s mutants with impaired or altered LPS synthesis are in good agreement with the results of simpler tests based on LPS profiling of phage-resistant spontaneous mutants.
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http://dx.doi.org/10.1038/s41598-019-39590-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393563PMC
February 2019

Escherichia coli bacteriophage Gostya9, representing a new species within the genus T5virus.

Arch Virol 2019 Mar 1;164(3):879-884. Epub 2018 Dec 1.

Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Winogradsky Institute of Microbiology, prosp. 60-letiya Oktyabrya, 7/2, 117312, Moscow, Russian Federation.

Escherichia coli bacteriophage Gostya9 (genus T5virus) was isolated from horse feces collected in Moscow, Russia, in 2013. This phage was associated in a single plaque with the previously reported phage 9g and was subsequently purified. Analysis of the complete genomic sequence of Gostya9 revealed that it is closely related to the T5-like bacteriophage DT57C, which had been isolated at the same location in 2007. These two viruses share 79.5% nucleotide sequence identity, which is below the 95% threshold applied currently to demarcate bacteriophage species. The most significant features distinguishing Gostya9 from DT57C include 1) the presence of one long tail fiber protein gene, 122c (ltf), instead of the two genes, ltfA and ltfB, that are present in DT57C; 2) the absence of the gene for the receptor-blocking lytic conversion lipoprotein precursor llp; and 3) the divergence of the receptor-recognition protein, pb5, which is only distantly related at the amino acid sequence level. The observed features of the Gostya9 adsorption apparatus are suggestive of a possible novel specificity for the final receptor and make this phage interesting for possible direct application in phage therapy of E. coli infections or as a source of receptor-recognition protein for engineering new phage specificities.
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http://dx.doi.org/10.1007/s00705-018-4113-2DOI Listing
March 2019

Structure and gene cluster of the O antigen of Escherichia coli F17, a candidate for a new O-serogroup.

Int J Biol Macromol 2019 Mar 15;124:389-395. Epub 2018 Nov 15.

Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation.

Escherichia coli F17 isolated from horse feces was studied in respect to the O antigen (O polysaccharide) structure and genetics. The lipopolysaccharide was isolated by phenol-water extraction of bacterial cells and cleaved by mild acid hydrolysis to yield the O polysaccharide, which was studied by sugar analysis and selective solvolysis with CFCOH along with one- and two-dimensional H and C NMR spectroscopy. The O polysaccharide was found to have a branched pentasaccharide repeat (O-unit) containing one residue each of d-galactose, d-mannose, l-rhamnose, d-glucuronic acid, and N-acetyl-d-glucosamine; about 2/3 units bear a side-chain glucose residue. To our knowledge, the F17 O-polysaccharide structure established is unique among known bacterial polysaccharide structures. The O-antigen gene cluster of E. coli F17 between the conserved genes galF and gnd was sequenced and found to be 99% identical to that of E. coli 102,755 assigned to a novel OgN8 genotype (A. Iguchi, S. Iyoda, K. Seto, H. Nishii, M. Ohnishi, H. Mekata, Y. Ogura, T. Hayashi, Front. Microbiol. 7 (2016) 765). Genes in the cluster were annotated taking into account the F17 O-polysaccharide structure. The data obtained confirm that E. coli F17 and E. coli strains belonging to the OgN8 genotype can be considered as a candidate to a new E. coli O-serogroup. The O antigen of this novel type was demonstrated to make for an effective shield protecting the intimate outer membrane surface of bacteria from direct interaction with bacteriophages.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.11.149DOI Listing
March 2019

Corrigendum to "Structure of the O-polysaccharide of Escherichia coli O87" [Carbohydr. Res. 412 (2015) 15-18].

Carbohydr Res 2018 07 25;464. Epub 2018 May 25.

N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russia.

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http://dx.doi.org/10.1016/j.carres.2018.04.013DOI Listing
July 2018

Complete Genome Sequence of Bacteriophage PGT2.

Genome Announc 2018 Jan 18;6(3). Epub 2018 Jan 18.

Winogradsky Institute of Microbiology, RC Biotechnology RAS, Moscow, Russia

Bacteriophage PGT2 was isolated from horse feces by using an uncharacterized strain, 7s, isolated from the same sample as the host. Bacteriophage PGT2 and a related phage, phiKT, which was previously isolated from the same source, are likely to represent a new genus within the subfamily of the family of viruses.
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http://dx.doi.org/10.1128/genomeA.01370-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773715PMC
January 2018

Complete Genome Sequence of Bacteriophage St11Ph5, Which Infects Uropathogenic Strain up11.

Genome Announc 2018 Jan 11;6(2). Epub 2018 Jan 11.

Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russian Federation

Bacteriophage St11Ph5 was isolated from a sewage sample on a particularly phage-resistant uropathogenic (UPEC) up11 host strain. It appeared to be closely related to bacteriophage G7C, isolated from horse feces; however, it carries a highly divergent host recognition module.
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http://dx.doi.org/10.1128/genomeA.01371-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764931PMC
January 2018

Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis.

Viruses 2016 Jan 21;8(1). Epub 2016 Jan 21.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, build. 2, Moscow 119071, Russia.

The T5-like siphoviruses DT57C and DT571/2, isolated from horse feces, are very closely related to each other, and most of their structural proteins are also nearly identical to T5 phage. Their LTFs (L-shaped tail fibers), however, are composed of two proteins, LtfA and LtfB, instead of the single Ltf of bacteriophage T5. In silico and mutant analysis suggests a possible branched structure of DT57C and DT571/2 LTFs, where the LtfB protein is connected to the phage tail via the LtfA protein and with both proteins carrying receptor recognition domains. Such adhesin arrangement has not been previously recognized in siphoviruses. The LtfA proteins of our phages are found to recognize different host O-antigen types: E. coli O22-like for DT57C phage and E. coli O87 for DT571/2. LtfB proteins are identical in both phages and recognize another host receptor, most probably lipopolysaccharide (LPS) of E. coli O81 type. In these two bacteriophages, LTF function is essential to penetrate the shield of the host's O-antigens. We also demonstrate that LTF-mediated adsorption becomes superfluous when the non-specific cell protection by O-antigen is missing, allowing the phages to bind directly to their common secondary receptor, the outer membrane protein BtuB. The LTF independent adsorption was also demonstrated on an O22-like host mutant missing O-antigen O-acetylation, thus showing the biological value of this O-antigen modification for cell protection against phages.
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http://dx.doi.org/10.3390/v8010026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728585PMC
January 2016

Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces.

Arch Virol 2015 Dec 9;160(12):3133-7. Epub 2015 Sep 9.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave 33, build. 2, Moscow, 119071, Russia.

We report the complete genome sequencing of two Escherichia coli T5-related bacteriophages, DT57C and DT571/2, isolated from the same specimen of horse feces. These two isolates share 96% nucleotide sequence identity and can thus be considered representatives of the same novel species within the genus T5likevirus. The observed variation in the ltfA gene of these phages, resulting from a recent recombination event, may explain the observed host-range differences, suggesting that a modular mechanism makes a significant contribution to the short-term evolution (or adaptation) of T5-like phage genomes in the intestinal ecosystem. Comparison of our isolates to their closest relative, coliphage T5, revealed high overall synteny of the genomes and high conservation of the sequences of almost all structural proteins as well as of the other proteins with identified functions. At the same time, numerous alterations and non-orthologous replacements of non-structural protein genes (mostly of those with unknown functions) as well as substantial differences in tail fiber locus organization support the conclusion that DT57C and DT571/2 form a species-level group clearly distinct from bacteriophage T5.
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http://dx.doi.org/10.1007/s00705-015-2582-0DOI Listing
December 2015

Structure of the O-polysaccharide of Escherichia coli O87.

Carbohydr Res 2015 Aug 1;412:15-8. Epub 2015 May 1.

N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia.

The following structure of the O-polysaccharide of Escherichia coli HS1/2 serving as a primary receptor for bacteriophage DT57-12 was elucidated by sugar analysis along with 1D and 2D (1)H and (13)C NMR spectroscopy: This structure is shared by E. coli O87 type strain. Putatively assigned functions of genes in the O-antigen gene cluster of E. coli O87 are consistent with the O-polysaccharide structure established.
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http://dx.doi.org/10.1016/j.carres.2015.04.014DOI Listing
August 2015

Genomic sequencing and biological characteristics of a novel Escherichia coli bacteriophage 9g, a putative representative of a new Siphoviridae genus.

Viruses 2014 Dec 19;6(12):5077-92. Epub 2014 Dec 19.

Laboratory of microbial viruses, Winogradsky Institute of Microbiology, Russian Academy of Sciences, prosp. 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia.

Bacteriophage 9 g was isolated from horse feces using Escherichia coli C600 as a host strain. Phage 9 g has a slightly elongated capsid 62 × 76 nm in diameter and a non-contractile tail about 185 nm long. The complete genome sequence of this bacteriophage consists of 56,703 bp encoding 70 predicted open reading frames. The closest relative of phage 9 g is phage PhiJL001 infecting marine alpha-proteobacterium associated with Ircinia strobilina sponge, sharing with phage 9 g 51% of amino acid identity in the main capsid protein sequence. The DNA of 9 g is resistant to most restriction endonucleases tested, indicating the presence of hypermodified bases. The gene cluster encoding a biosynthesis pathway similar to biosynthesis of the unusual nucleoside queuosine was detected in the phage 9 g genome. The genomic map organization is somewhat similar to the typical temperate phage gene layout but no integrase gene was detected. Phage 9 g efficiently forms stable associations with its host that continues to produce the phage over multiple passages, but the phage can be easily eliminated via viricide treatment indicating that no true lysogens are formed. Since the sequence, genomic organization and biological properties of bacteriophage 9 g are clearly distinct from other known Enterobacteriaceae phages, we propose to consider it as the representative of a novel genus of the Siphoviridae family.
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http://dx.doi.org/10.3390/v6125077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276943PMC
December 2014

Variations in O-antigen biosynthesis and O-acetylation associated with altered phage sensitivity in Escherichia coli 4s.

J Bacteriol 2015 Mar 15;197(5):905-12. Epub 2014 Dec 15.

S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia

The O polysaccharide of the lipopolysaccharide (O antigen) of Gram-negative bacteria often serves as a receptor for bacteriophages that can make the phage dependent on a given O-antigen type, thus supporting the concept of the adaptive significance of the O-antigen variability in bacteria. The O-antigen layer also modulates interactions of many bacteriophages with their hosts, limiting the access of the viruses to other cell surface receptors. Here we report variations of O-antigen synthesis and structure in an environmental Escherichia coli isolate, 4s, obtained from horse feces, and its mutants selected for resistance to bacteriophage G7C, isolated from the same fecal sample. The 4s O antigen was found to be serologically, structurally, and genetically related to the O antigen of E. coli O22, differing only in side-chain α-D-glucosylation in the former, mediated by a gtr locus on the chromosome. Spontaneous mutations of E. coli 4s occurring with an unusually high frequency affected either O-antigen synthesis or O-acetylation due to the inactivation of the gene encoding the putative glycosyltransferase WclH or the putative acetyltransferase WclK, respectively, by the insertion of IS1-like elements. These mutations induced resistance to bacteriophage G7C and also modified interactions of E. coli 4s with several other bacteriophages conferring either resistance or sensitivity to the host. These findings suggest that O-antigen synthesis and O-acetylation can both ensure the specific recognition of the O-antigen receptor following infection by some phages and provide protection of the host cells against attack by other phages.
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http://dx.doi.org/10.1128/JB.02398-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325112PMC
March 2015
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