Ilya Borovok

Ilya Borovok
The George S. Wise Faculty of Life Sciences, Tel Aviv University · The Shmunis School of Biomedicine and Cancer Research

PhD

About

137
Publications
21,220
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
3,613
Citations
Education
September 1986 - May 1991
Institute of Agricultural Biotechnology
Field of study
  • Molecular Biology
September 1974 - June 1979
Lomonosov Moscow State University
Field of study
  • Genetics

Publications

Publications (137)
Article
Full-text available
Listeria monocytogenes strain 10403S harbors two phage elements in its chromosome; one produces infective virions and the other tailocins. It was previously demonstrated that induction of the two elements is coordinated, as they are regulated by the same anti-repressor. In this study, we identified AriS as another phage regulator that controls the...
Article
Full-text available
Bacterial pathogens sense the repertoire of metabolites in the mammalian niche and use this information to shift into the pathogenic state to accomplish a successful infection. Glutathione is a virulence-activating signal that is synthesized by L. monocytogenes during infection of mammalian cells.
Article
Full-text available
The 54 kb GC-rich prophage region of Mycoplasma bovirhinis HAZ141_2 contains three structural ‘compartments’, one of which is a highly transmittable cluster of three genes, aadE-like (aadE*), sat4, and aphA-3. In this study, we characterized recombination events and their consequences occurred within the aadE*-sat4-aphA-3 containing region. Analysi...
Preprint
Full-text available
Listeria monocytogenes ( Lm ) is a saprophyte and a human intracellular pathogen. Upon invasion into mammalian cells, it senses multiple metabolic and environmental signals that collectively trigger its transition to the pathogenic state. One of these signals is the tripeptide glutathione, which acts as an allosteric activator of Lm ’s master virul...
Article
Full-text available
Bioproduction of renewable chemicals is considered as an urgent solution for fossil energy crisis. However, despite tremendous efforts, it is still challenging to generate microbial strains that can produce target biochemical to high levels. Here, we report an example of biosynthesis of high-value and easy-recoverable derivatives built upon natural...
Article
Full-text available
Infection of mammalian cells by Listeria monocytogenes (Lm) was shown to be facilitated by its phage elements. In a search for additional phage remnants that play a role in Lm’s lifecycle, we identified a conserved locus containing two XRE regulators and a pair of genes encoding a secreted metzincin protease and a lipoprotein structurally similar t...
Article
Full-text available
Recently, a complete genome of Mycoplasma bovirhinis HAZ141_2 has been published showing presence of 54-kB prophage-like region. Bioinformatic analysis revealed that this region has a more than 40-% GC content and a chimeric organization with three structural elements – a prophage continuous region, a restriction-modification cassette, and a highly...
Article
Full-text available
Some Listeria monocytogenes (Lm) strains harbor a prophage within the comK gene, which renders it inactive. During Lm infection of macrophage cells, the prophage turns into a molecular switch, promoting comK gene expression and therefore Lm intracellular growth. During this process, the prophage does not produce infective phages or cause bacterial...
Article
Full-text available
Background: Clostridium saccharoperbutylacetonicum N1-4 (HMT) is a strictly anaerobic, spore-forming Gram-positive bacterium capable of hyper-butanol production through the well-known acetone-butanol-ethanol fermentation process. Recently, five putative RRNPP-type QSSs (here designated as QSS1 to QSS5) were predicted in this bacterial strain, each...
Preprint
Full-text available
Endproduct toxicity is a key bottleneck for biofuel/biochemical production. Biosynthesis of high-value derivatives that can easily separate would alleviate such toxicity and thus enhance bioproduction efficiency. As a proof of principle, biosynthesis (along with in-line extractive recovery) of fatty acid esters using clostridia was investigated in...
Article
Full-text available
Background: Mycoplasma bovis is an important etiologic agent of bovine mycoplasmosis affecting cattle production and animal welfare. In the past in Israel, M. bovis has been most frequently associated with bovine respiratory disease (BRD) and was rarely isolated from mastitis. This situation changed in 2008 when M. bovis-associated mastitis emerge...
Article
Full-text available
Bacterial pathogens often carry multiple prophages and other phage-derived elements within their genome, some of which can produce viral particles in response to stress. Listeria monocytogenes 10403S harbors two phage elements in its chromosome, both of which can trigger bacterial lysis under stress: an active prophage (ϕ10403S) that promotes the v...
Conference Paper
Listeria monocytogenes (Lm) is a saprophyte and intracellular pathogen. Transition to the pathogenic state relies on sensing of host-derived metabolites, yet it remains unclear how these are recognized and how they mediate virulence gene regulation. We previously found that low availability of isoleucine signals Lm to activate the virulent state. T...
Conference Paper
Full-text available
Most bacterial pathogens carry phage DNA within their genome. Listeria monocytogenes strain 10403S (Lm), a Gram-positive intracellular pathogen, carries two phage elements, one encodes the formation of infective virions (iPE) and the other encodes the formation of bacteriocins (cPE). Both elements encode for Holin and Endolysin proteins that have t...
Conference Paper
Full-text available
The current access to thousands of Listeria monocytogenes genomes provides opportunities for comprehensive analysis of their structure organization and prediction of novel genomic elements not yet discussed. It is known that Listeria genomes contain several types of mobile elements including lysogenic and cryptic prophages, classic insertion sequen...
Article
Full-text available
Cellulolytic clostridia use a highly efficient cellulosome system to degrade polysaccharides. To regulate genes encoding enzymes of the multi‐enzyme cellulosome complex, certain clostridia contain alternative sigma I (σI) factors that have cognate membrane associated anti‐σI factors (RsgIs) which act as polysaccharide sensors. In this work, we anal...
Article
Full-text available
Background and aims: The pathogenesis of pouch inflammation may involve epithelial barrier disruption. We investigated whether faecal proteolytic activity is increased during pouchitis and results in epithelial barrier dysfunction through protease activating receptor [PAR] activation, and assessed whether the intestinal microbiome may be the sourc...
Article
Full-text available
Background Pouchitis in ulcerative colitis (UC) patients is thought to occur due to disruption of the epithelial barrier resulting in an abnormal immune response to a dysbiotic microbiota. We aimed to examine whether faecal proteolytic activity is increased during pouchitis and results in epithelial barrier dysfunction and explore the pathways invo...
Article
Full-text available
Listeria monocytogenes (Lm) is a saprophyte and intracellular pathogen. Transition to the pathogenic state relies on sensing of host-derived metabolites, yet it remains unclear how these are recognized and how they mediate virulence gene regulation. We previously found that low availability of isoleucine signals Lm to activate the virulent state. T...
Data
Supporting information by Moran Brenner et al (PLoS Genetics 2018): Figures S1-S4, Tables S1 and S2.
Article
Full-text available
Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-con...
Article
Full-text available
The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species,...
Article
Full-text available
Background Bioethanol production processes involve enzymatic hydrolysis of pretreated lignocellulosic biomass into fermentable sugars. Due to the relatively high cost of enzyme production, the development of potent and cost-effective cellulolytic cocktails is critical for increasing the cost-effectiveness of bioethanol production. In this context,...
Data
Additional files by Shahar Yoav et al (Biotechnology for Biofuels 2017).
Working Paper
Full-text available
Ribonucleotide reductases (RNRs) are key enzymes in DNA synthesis and repair, with sophisticated allosteric mechanisms controlling both substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the AT...
Article
Bacteriophages are ubiquitous and affect most facets of life, from evolution of bacteria, through ecology and global biochemical cycling to human health. The interactions between phages and bacteria often lead to biological novelty and an important milestone in this process is the ability of phages to regulate their host’s behavior. In this review...
Article
Full-text available
Cellulosomes are considered to be one of the most efficient systems for the degradation of plant cell wall polysaccharides. The central cellulosome component comprises a large, noncatalytic protein subunit called scaffoldin. Multiple saccharolytic enzymes are incorporated into the scaffoldins via specific high-affinity cohesin-dockerin interactions...
Article
Full-text available
Protein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrad...
Article
Full-text available
We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
Article
Full-text available
Importance: Data presented in this study show a high prevalence of diverse ISs within the M. bovis rrn locus resulting in intraspecies variability and diversity. Such abundance of IS elements near or within the rrn locus may offer a selective advantage to M. bovis Moreover, the fact that expression of the rrs genes as well as the number of viable...
Conference Paper
Full-text available
Despite intensive genomic studies of Mycoplasma species, little is known regarding conserved transcriptional mechanisms of these bacteria including the contribution of RNA polymerase (RNAP) sigma factors. It was believed that Mycoplasma species have mainly one sigma factor resembling RpoD subunit, while only a minor number of species have an altern...
Article
Full-text available
The Gram-positive, anaerobic, cellulolytic, thermophile Clostridium (Ruminiclostridium) thermocellum, secretes a multi-enzyme system called the cellulosome to solubilize plant cell wall polysaccharides. During the saccharolytic process, the enzymatic composition of the cellulosome is modulated according to the type of polysaccharide(s) present in t...
Article
Full-text available
We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens . The bacterium produces a particularly elaborate cellulosome system, wherein the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I int...
Article
Full-text available
Unlike lytic phages, temperate phages that enter lysogeny maintain a long-term association with their bacterial host. In this context, mutually beneficial interactions can evolve that support efficient reproduction of both phages and bacteria. Temperate phages are integrated into the bacterial chromosome as large DNA insertions that can disrupt gen...
Article
Full-text available
Importance: In this study 84 putative c-di-GMP binding proteins were identified in B. bacteriovorus, an obligate predatory bacterium whose lifestyle and reproduction are dependent on c-di-GMP signalling, using a c-di-GMP capture compound precipitation approach. This predicted complement covers metabolic, energy, transport, motility and regulatory...
Article
Full-text available
Clostridium thermocellum efficiently degrades crystalline cellulose by a high molecular weight protein complex, the cellulosome. The bacterium regulates its cellulosomal genes using a unique extracellular biomass-sensing mechanism that involves alternative sigma factors and extracellular carbohydrate-binding modules attached to intracellular anti-s...
Article
Full-text available
The cellulolytic bacterium Ruminococcus flavefaciens of the herbivore rumen produces an elaborate cellulosome system, anchored to the bacterial cell wall via the covalently bound scaffoldin ScaE. Dockerin-bearing scaffoldins also bind to an autonomous cohesin of unknown function, called CohG. Here, we demonstrate that CohG binds to the scaffoldin-b...
Article
Full-text available
A cellulolytic fiber-degrading bacterium, Ruminococcus champanellensis, was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R. champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic seg...
Article
Full-text available
Ruminococcus albus, a cellulolytic bacterium, is a critical member of the rumen community. Ruminococcus albus lacks a classical cellulosome complex, but it possesses a unique family 37 carbohydrate-binding module (CBM37), which is integrated into a variety of carbohydrate-active enzymes. We developed a potential molecular tool for functional phylot...
Article
Full-text available
Metabolic adaptations are critical to the ability of bacterial pathogens to grow within host cells and are normally preceded by sensing of host-specific metabolic signals, which in turn can influence the pathogen's virulence state. Previously, we reported that the intracellular bacterial pathogen Listeria monocytogenes responds to low availability...
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
Full-text available
Background A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert ce...
Article
Full-text available
Background: Clostridium clariflavum is an anaerobic, thermophilic, Gram-positive bacterium, capable of growth on crystalline cellulose as a single carbon source. The genome of C. clariflavum has been sequenced to completion, and numerous cellulosomal genes were identified, including putative scaffoldin and enzyme subunits. Results: Bioinformatic an...
Article
Full-text available
Ruminococcus flavefaciens is a cellulolytic bacterium found in the rumen of herbivores and produces one of the most elaborate and variable cellulosome systems. The structure of an R. flavefaciens protein ( Rf CohG, ZP_06142108), representing a freestanding (non-cellulosomal) type III cohesin module, has been determined. A selenomethionine derivativ...
Article
Full-text available
The anaerobic, thermophilic, cellulosome-producing bacterium Clostridium thermocellum relies on a variety of carbohydrate-active enzymes in order to efficiently break down complex carbohydrates into utilizable simple sugars. The regulation mechanism of the cellulosomal genes was unknown until recently, when genomic analysis revealed a set of putati...
Conference Paper
Full-text available
Systematic analysis of available complete genomes of Listeria monocytogenes has revealed a strong relationship between the well-known laboratory strain 10403S and the rabbit isolate SLCC5850 (GenBank accession numbers NC_017544 and NC_018592, respectively). Both strains belong to serovar 1/2a and exhibit almost the same sequence and genome organiza...
Data
Full-text available
Systematic analysis of available complete genomes of Listeria monocytogenes has revealed a strong relationship between the well-known laboratory strain 10403S and the rabbit isolate SLCC5850 (GenBank accession numbers NC_017544 and NC_018592, respectively). Both strains belong to serovar 1/2a and exhibit almost the same sequence and genome organiza...
Article
Full-text available
We report the draft genome sequence of the cellulose-degrading bacterium Clostridium papyrosolvens C7, originally isolated from mud collected below a freshwater pond in Massachusetts. This Gram-positive bacterium grows in a mesophilic anaerobic environment with filter paper as the only carbon source, and it has a simple cellulosome system with mult...
Article
Full-text available
Background Many bacteria efficiently degrade lignocellulose yet the underpinning genome-wide metabolic and regulatory networks remain elusive. Here we revealed the “cellulose degradome” for the model mesophilic cellulolytic bacterium Clostridium cellulolyticum ATCC 35319, via an integrated analysis of its complete genome, its transcriptomes under g...
Article
Full-text available
Background: Ruminococcus flavefaciens is one of the predominant fiber-degrading bacteria found in the rumen of herbivores. Bioinformatic analysis of the recently sequenced genome indicated that this bacterium produces one of the most intricate cellulosome systems known to date. A distinct ORF, encoding for a multi-modular protein, RflaF_05439, was...