Biology subjects

Qimron, U.

Publications and source records attributed to Qimron, U..

7 recordsLinked to original sources

bioRxiv2026

Pantoea agglomerans T6SS effectors reside in hotspots with combinatorial offensive and defensive arsenals

Gram-negative bacteria deploy type VI secretion systems (T6SSs) to mediate interbacterial competition. Although numerous T6SS effectors have been identified, their pan-genomic repertoires and evolutionary dynamics remain poorly understood. Here, we combine proteomics and comparative genomics to map the T6SS effector landscape across Pantoea agglomerans, a diverse species that includes pathogenic and beneficial strains. We uncover an extensive pan-genomic arsenal in which most effectors are encoded outside the main T6SS gene cluster, within highly dynamic hotspots distributed across the chromosome and megaplasmids. Analysis of these hotspots reveals multilayered, combinatorial arrangements of shuffled genetic cargo. Remarkably, these loci act as versatile "genomic armories" that co-localize offensive antibacterial weapons with protective anti-phage defense systems. By investigating uncharacterized genes within these variable regions, we discovered and validated a novel T6SS effector and a previously unknown anti-phage defense system, named Juno. Collectively, our findings demonstrate that bacterial warfare arsenals are highly modular and reside in dynamic genomic hubs that alternate or combine interbacterial aggression with viral defense. This evolutionary association reveals a functional blurring between offensive and defensive strategies within the bacterial accessory genome. Our findings further highlight orphan effector-associated variable regions as promising leads in the search for unrecognized bacterial conflict and defense systems.

microbiology↗

bioRxiv2025

Phage-encoded homing endonucleases attenuate bacterial immunity

The arms race between bacteria and bacteriophages (phages) gave rise to multiple layers of antagonistic mechanisms, many of which remain unexplored. Here, we investigated the anti-phage defense system GAPS4 and showed that it is a non-selective DNase triggered by sensing DNA breaks. We further demonstrated that this activation mechanism renders GAPS4 a double-edged sword, sensitizing bacteria to various forms of antibacterial antagonism. Using comparative genomics, we found that phage-encoded homing endonucleases, long considered selfish mobile genetic elements, enhance phage fitness by attenuating GAPS4-mediated immunity. Our findings shed light on the evolutionary advantage provided by these ubiquitous mobile elements to their host phages, and on the intricate evolutionary cross-talk between bacteria and their predators.

microbiology↗

bioRxiv2023

Engineering mice for female-biased progeny without impacting genetic integrity and litter size

The ability to influence the sex ratio of mammalian offspring has applications in agriculture and animal welfare. Here we describe a genetic system in mice that produces predominantly female progeny, reaching approximately ninety percent, without affecting litter size or introducing genetic modifications into the offspring. The system consists of a doxycycline-regulated cassette inserted into the Y chromosome, encoding dCas9 and RNA guides intended to impair the function of Y bearing sperm. While the cassette was originally intended to repress a spermatid maturation gene, our analyses did not detect meaningful changes in gene expression or sperm function that would account for the phenotype. Nevertheless, male mice carrying the cassette consistently produced female biased litters, and the effect was reversed by doxycycline, confirming that it depends on cassette expression. Similar female bias was observed following in vitro fertilization using sperm from transgenic males. These findings demonstrate a reproducible, genetically confined, and conditionally regulated system for sex ratio bias in mice. The strategy may prove adaptable across species, even without a complete mechanistic understanding. Graphical AbstractA single line genetic system producing female biased, genetically unmodified progeny in mice by conditionally impairing Y bearing sperm. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/568055v4_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@5f23b3org.highwire.dtl.DTLVardef@20ed2corg.highwire.dtl.DTLVardef@1b3007dorg.highwire.dtl.DTLVardef@e54cf6_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryY chromosome manipulation yields mostly female mice, preserving litter size without genetic alteration in females. Significance statementThis study describes a genetic approach for producing predominantly female offspring in mice without altering litter size or transmitting genetic modifications to the progeny. A cassette inserted into the Y chromosome of males induces a strong female bias in offspring through a mechanism that remains unclear. The female offspring do not inherit the transgene and are genetically unmodified. This system provides a simple and conditional platform for sex ratio control in mammals, with potential applications in animal breeding and welfare.

bioengineering↗

bioRxiv2023

A widespread bacterial mobile genetic element encodes weapons against phages, bacteria, and eukaryotes

Conflicts between bacteria and their rivals led to an evolutionary arms race and the development of bacterial immune systems. Although diverse immunity mechanisms were recently identified, many remain unknown, and their dissemination within bacteria is poorly understood. Here, we describe a widespread genetic element, defined by the presence of the Gamma-Mobile-Trio (GMT) proteins, that serves as a bacterial survival kit. We show that GMT-containing genomic islands are active mobile elements with cargo comprising various anti-phage defense systems, in addition to antibacterial type VI secretion system (T6SS) effectors and antibiotic resistance genes. We identify four new anti-phage defense systems encoded within GMT islands. A thorough investigation of one system reveals that it is triggered by a phage capsid protein to induce cell dormancy. Our findings underscore the need to broaden the concept of defense islands to include also antibacterial offensive tools, such as T6SS effectors, as they share the same mobile elements as defensive tools for dissemination.

microbiology↗

bioRxiv2023

An efficient, scarless, selection-free technology for phage engineering

Many phage engineering technologies, mainly based on the CRISPR-Cas system, have been recently developed. Here we present a method to genetically engineer the Escherichia coli phages T5, T7, and P1 by adapting a technology, called pORTMAGE, developed for engineering bacterial genomes. The technology comprises of E. coli harboring a plasmid encoding a potent recombinase and a gene transiently silencing a repair system. Oligonucleotides with the desired phage mutation are electroporated into E. coli followed by infection of the target bacteriophage. The high efficiency of this technology, ranging from 1-14% of desired recombinants, allows low-throughput screening for the desired mutant. We demonstrated the use of this technology for single-base substitutions, for deletions of 50 bases, for insertions of 20 bases, and for three different phages. The technology may be adjusted for use across many bacterial and phage strains.

molecular biology↗

bioRxiv2019

A genetic system for generating single-sex progeny in mice

The ability to preselect the sex of livestock is economically beneficial and significantly increases the welfare and proper use of animals. In the poultry industry, for example, almost all males are brutally and unnecessarily killed shortly after hatching. The labor and associated costs of separation of females from males, as well as the massive killing of males, could be reduced by using a system that biases the sex of the progeny. Here, we provide a first proof of concept for such a system by crossing two genetically engineered mouse lines. The maternal line encodes a functional Cas9 protein on an autosomal chromosome, whereas the paternal line encodes guide RNAs on the Y chromosome targeting vital mouse genes. After fertilization, the presence of both the Y-encoded guide RNAs from the paternal sperm and the Cas9 protein from the maternal egg target the vital genes in males. We show that this breeding consequently self-destructs solely the males. Our results pave the way for a biased sex production of livestock, thus saving labor, costs, and eliminating substantial animal suffering.

developmental biology↗

bioRxiv2018

A T7 phage factor required for managing RpoS in Escherichia coli

T7 development in Escherichia coli requires the inhibition of the housekeeping form of the bacterial RNA polymerase (RNAP), E{sigma}70, by two T7 proteins: Gp2 and Gp5.7. While the biological role of Gp2 is well understood, that of Gp5.7 remains to be fully deciphered. Here, we present results from functional and structural analyses to reveal that Gp5.7 primarily serves to inhibit E{sigma}S, the predominant form of the RNAP in the stationary phase of growth, which accumulates in exponentially growing E. coli as a consequence of buildup of guanosine pentaphosphate ((p)ppGpp) during T7 development. We further demonstrate a requirement of Gp5.7 for T7 development in E. coli cells in the stationary phase of growth. Our finding represents a paradigm for how some lytic phages have evolved distinct mechanisms to inhibit the bacterial transcription machinery to facilitate phage development in bacteria in the exponential and stationary phases of growth.\n\nSignificance statementVirus that infect bacteria (phages) represent the most abundant living entities on the planet and many aspects of our fundamental knowledge of phage-bacteria relationships have been derived in the context of exponentially growing bacteria. In the case of the prototypical Escherichia coli phage T7, specific inhibition of the housekeeping form of the RNA polymerase (E{sigma}70) by a T7 protein, called Gp2, is essential for the development of viral progeny. We now reveal that T7 uses a second specific inhibitor that selectively inhibits the stationary phase RNAP (E{sigma}S), which enables T7 to develop well in exponentially growing and stationary phase bacteria. The results have broad implications for our understanding of phage-bacteria relationships and therapeutic application of phages.

microbiology↗