Biology subjects

Burman, N.

Publications and source records attributed to Burman, N..

5 recordsLinked to original sources

bioRxiv2025

A census of anti-CRISPR proteins reveals AcrIE9 as an inhibitor of Escherichia coli K12 Type IE CRISPR-Cas system

CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins. The Type IE CRISPR-Cas of Escherichia coli K12 has been a model for structural and functional studies and is a part of the species core genome. However, this system is transcriptionally silent, which has fueled questions about its true biological function. To clarify the role of this system in defense, we carried out a census of Acr proteins found in Enterobacterales and identified AcrIE9 as a potent inhibitor of the E. coli K12 Type IE CRISPR-Cas system. While sharing little sequence identity, AcrIE9 proteins from Pseudomonas and Escherichia both interact with the Cas7 subunit of the Cascade complex, thus preventing its binding to DNA. We further show that AcrIE9 is genetically linked to AcrIE10, forming the most widespread anti-CRISPR cluster in Enterobacterales, and this module often co-occurs with a novel HTH-like protein with unusual architecture.

microbiology↗

bioRxiv2025

Structural basis of antiphage defense by an ATPase-associated reverse transcriptase

Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses and retrotransposons. However, recent evidence suggests that RTs have been conscripted by cells for diverse roles in antiviral defense. Here we determine structures of a type I-A retron, which explain how RNA, DNA, RT, HNH-nuclease and four molecules of an SMC-family ATPase assemble into a 364 kDa complex that provides phage defense. We show that phage-encoded nucleases trigger degradation of the retron-associated DNA, leading to disassembly of the retron and activation of the HNH nuclease. The HNH nuclease cleaves tRNASer, stalling protein synthesis and arresting viral replication. Taken together, these data reveal diverse and paradoxical roles for RTs in the perpetuation and elimination of genetic parasites.

biochemistry↗

bioRxiv2025

Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase

Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation1. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by leveraging DNA synthesis instead2,3. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene, leading to expression of an antiviral effector protein, Neo4,5. It remains unknown whether similar mechanisms of defense are employed by other DRT families. Focusing on DRT9, here we uncover an unprecedented mechanism of DNA homopolymer synthesis, in which viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell to drive abortive infection and population-level immunity. Cryo-EM structures reveal how a conserved noncoding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and RNA-templated poly-dA synthesis. Remarkably, biochemical and functional experiments identify conserved tyrosine residues within the reverse transcriptase itself that prime DNA synthesis, leading to the formation of high-molecular weight protein-DNA covalent adducts. Synthesis of poly-dA in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers of DRT9. Collectively, our work unveils a novel nucleic acid-driven defense system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.

molecular biology↗

bioRxiv2024

Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection

Viruses compete with each other for limited cellular resources, and some viruses deliver defense mechanisms that protect the host from competing genetic parasites. PARIS is a defense system, often encoded in viral genomes, that is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving the host tRNALys. Phage T5 subverts PARIS immunity through expression of a tRNALys variant that prevents PARIS-mediated cleavage, and thereby restores viral infection. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids.

biochemistry↗

bioRxiv2023

Two splice forms of OsbZIP1, a homolog of AtHY5, function to regulate skoto- and photo-morphogenesis in rice

Plants possess well-developed light sensing mechanisms and signal transduction systems for regulating photomorphogenesis. ELONGATED HYOCOTYL 5 (HY5), a basic leucine zipper transcription factor, has been extensively characterized in dicot plants. In this study, we have shown that OsbZIP1 is a functional homolog of Arabidopsis HY5 (AtHY5) and is important for light-mediated regulation of seedling and mature plant development in rice. Ectopic expression of OsbZIP1 in rice reduces plant height and leaf length without affecting plant fertility, which is in contrast to OsbZIP48, another HY5 homolog we characterised earlier. OsbZIP1 is alternatively spliced and the isoform OsbZIP1.2 lacking COP1 binding domain regulates seedling development in dark; this is unique since AtHY5 lacking COP1 binding domain does not display such a phenotype. Rice seedlings overexpressing OsbZIP1 were found to be shorter than vector control under white and monochromatic light conditions whereas RNAi seedlings displayed completely opposite phenotype. While OsbZIP1.1 is light regulated, OsbZIP1.2 shows similar protein profile in both light and dark conditions. Due to its interaction with OsCOP1, OsbZIP1.1 undergoes degradation via 26S proteasome under dark conditions. Also, OsbZIP1.1 interacts with CASEIN KINASE 2 (OsCK2[a]3) and consequently undergoes phosphorylation. In comparison, OsbZIP1.2 did not show any interaction with COP1 and OsCK2[a]3. We propose that OsbZIP1.1 most likely works under low fluence of blue light (15 mol/m{superscript 2}/s) while OsbZIP1.2 becomes dominant as the fluence is increased to 30 mol/m{superscript 2}/s. Data presented in this study reveal that AtHY5 homologs in rice have undergone neofunctionalization and alternative splicing (AS) of OsbZIP1 has increased the repertoire of its functions. One sentence summaryAlternative spliced forms of OsbZIP1, an AtHY5 homolog in rice, regulate seedling development in response to light and dark

plant biology↗