Biology subjects

Hsueh, B. Y.

Publications and source records attributed to Hsueh, B. Y..

6 recordsLinked to original sources

bioRxiv2024

pGpG-signaling regulates virulence and global transcriptomic targets in Erwinia amylovora

Cyclic-di-GMP (c-di-GMP) is a critical bacterial second messenger that enables the physiological phase transition in Erwinia amylovora, the phytopathogenic bacterium that causes fire blight disease. C-di-GMP generation is dependent on diguanylate cyclase enzymes while the degradation of c-di-GMP can occur through the action of phosphodiesterase (PDE) enzymes that contain an active EAL and/or a HD-GYP domain. The HD-GYP-type PDEs, which are absent in E. amylovora, can directly degrade c-di-GMP into two GMP molecules. PDEs that contain an active EAL domain, as found in all active PDEs in E. amylovora, degrade c-di-GMP into pGpG. The signaling function of pGpG is not fully understood in bacterial systems. A transcriptomic approach revealed that elevated levels of pGpG in E. amylovora impacted several genes involved in metabolic and regulatory functions including several type III secretion and extracellular appendage related genes. The heterologous overexpression of an EAL or HD-GYP-type PDE in different background E. amylovora strains with varying c-di-GMP levels revealed that in contrast to the generation of pGpG, the direct breakdown of c-di-GMP into GMP by the HD-GYP-type PDE led to an elevation in amylovoran production and biofilm formation despite a decrease in c-di-GMP levels. The breakdown of c-di-GMP into pGpG (as opposed to GTP) also led to a decrease in virulence in apple shoots. The expression of hrpS was significantly increased in response to the breakdown of c-di-GMP into pGpG. Further, our model suggests that a balance in the intracellular ratio of pGpG and c-di-GMP is essential for biofilm regulation in E. amylovora. Importancec-di-GMP is the keystone molecule for regulating the transition from motility to biofilm formation in most bacteria. Interestingly, there are two distinct enzymatic phosphodiesterase (PDE) domains, termed EAL and HD-GYP, that degrade c-di-GMP. EAL domains cleave one bond of the cyclic ring to generate pGpG while HD-GYP enzymes cleave c-di-GMP to two GMP molecules. A central question regarding c-di-GMP signaling is has whether or not pGpG itself functions as a signaling molecule. Here we demonstrate in the plant pathogen Erwinia amylovora that pGpG specifically regulates genes and contributes to biofilm formation and disease progression.

microbiology↗

bioRxiv2023

Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion

A major challenge faced by bacteria is infection by bacteriophage (phage). Abortive infection is one strategy for combating phage in which an infected cell kills itself to limit phage replication, thus protecting neighboring kin. One class of abortive infection systems is the cyclic oligonucleotide based anti-phage signaling system (CBASS) which relies on two core enzymatic activities; an oligo-nucleotide cyclase that is activated following phage infection and a cyclic-oligo-nucleotide sensitive effector whose activity kills the infected cell. However, the mechanisms behind the deployment and activation of these lethal CBASS systems prior-to and following infection have largely remained a mystery. While exploring unique genomic features of the current pandemic Vibrio cholerae biotype El Tor for clues underlying its pandemic success we found its CBASS was spuriously activated by the folate biosynthesis inhibitor sulfamethoxazole, but only after the population had reached a high-cell density. This population density dependent activity revealed that transcription of both the oligo-nucleotide cyclase, dncV, and the CBASS phospholipase effector, capV, is enhanced at high-cell density by quorum sensing. Together, these results demonstrate that the V. cholerae CBASS is deployed when the environment is densely populated and activated in response to a perturbation in folate biosynthesis. SignificanceTo counteract infection with phage, bacteria have evolved a myriad of molecular defense systems. Some of these systems initiate a process called abortive infection, in which the infected cell kills itself to prevent phage propagation. However, such systems must be inhibited in the absence of phage infection to prevent spurious death of the host. Here we show that the cyclic oligonucleotide based anti-phage signaling system (CBASS) accomplishes this by sensing intracellular folate molecules and only expressing this system in a group. These results enhance our understanding of the evolution of the 7th V. cholerae pandemic and more broadly how bacteria defend themselves against phage infection.

microbiology↗

bioRxiv2023

Time to lysis determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system

Toxin-antitoxin (TA) systems are ubiquitous two-gene loci that bacteria use to regulate cellular processes such as phage defense. Here, we demonstrate the mechanism by which a novel type III TA system, avcID, is activated and confers resistance to phage infection. The toxin of the system (AvcD) is a deoxycytidylate deaminase that converts deoxycytidines (dC) to dexoyuridines (dU), while the RNA antitoxin (AvcI) inhibits AvcD activity. We have shown that AvcD deaminated dC nucleotides upon phage infection, but the molecular mechanism that activated AvcD was unknown. Here we show that the activation of AvcD arises from phage-induced shutoff of host transcription, leading to degradation of the labile AvcI. AvcD activation and nucleotide depletion not only decreases phage replication but also increases the formation of defective phage virions. Surprisingly, infection of phages such as T7 that are not inhibited by AvcID also lead to AvcI RNA antitoxin degradation and AvcD activation, suggesting that depletion of AvcI is not sufficient to confer protection against some phage. Rather, our results support that phage with a longer lysis time like T5 are sensitive to AvcID-mediated protection while those with a shorter lysis time like T7 are resistant. AUTHORS SUMMARYNumerous diverse antiphage defense systems have been discovered in the past several years, but the mechanisms of how these systems are activated upon phage infection and why these systems protect against some phage but not others are poorly understood. The AvcID toxin-antitoxin phage defense system depletes nucleotides of the dC pool inside the host upon phage infection. We show that phage inhibition of host cell transcription activates this system by depleting the AvcI inhibitory sRNA, which inhibits production of phage and leads to the formation of defective virions. Additionally, we determined that phage lysis time is a key factor that influences sensitivity to AvcID with faster replicating phage exhibiting resistance to its effects. This study has implications for understanding the factors that influence bacterial host/phage dynamics.

microbiology↗

bioRxiv2021

A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection

The El Tor biotype of Vibrio cholerae is responsible for perpetuating the longest cholera pandemic in recorded history (1961-current). The genomic islands VSP-1 and -2 are two understudied genetic features that distinguish El Tor from previous pandemics. To understand their utility, we calculated the co-occurrence of VSP genes across bacterial genomes. This analysis predicted the previously uncharacterized vc0175, herein renamed deoxycytidylate deaminase Vibrio (dcdV), is in a gene network with dncV, a cyclic GMP-AMP synthase involved in phage defense. DcdV consists of two domains, a P-loop kinase and a deoxycytidylate deaminase, that are required for the deamination of dCTP and dCMP, inhibiting phage predation by corrupting cellular nucleotide concentrations. Additionally, DcdV is post-translationally inhibited by a unique noncoding RNA encoded 5 of the dcdV locus. DcdV homologs are conserved in bacteria and eukaryotes and our results identify V. cholerae DcdV as the founding member of a previously undescribed bacterial phage defense system.

microbiology↗

bioRxiv2021

CloudReg: Automatic Terabyte-Scale Cross-Modal Brain Volume Registration

Quantifying terabyte-scale multi-modal human and animal imaging data requires scalable analysis tools. We developed CloudReg, an open-source, automatic, terabyte-scale, cloud-based image analysis pipeline that pre-processes and registers cross-modal volumetric datasets with artifacts via spatially-varying polynomial intensity transform. CloudReg accurately registers the following datasets to their respective atlases: in vivo human and ex vivo macaque brain magnetic resonance imaging, ex vivo mouse brain micro-computed tomography, and cleared murine brain light-sheet microscopy.

bioengineering↗

bioRxiv2020

VIBRIO CHOLERAE ADAPTS TO SESSILE AND MOTILE LIFESTYLES BY CYCLIC DI-GMP REGULATION OF CELL SHAPE

The cell morphology of rod-shaped bacteria is determined by the rigid net of peptidoglycan forming the cell wall. While V. cholerae grows into a curved shape under most conditions, straight rods have been observed. However, the signals and regulatory pathways controlling cell shape transitions in V. cholerae and the benefits of switching between rod and curved shape have not been determined. We demonstrate that cell shape in V. cholerae is regulated by the bacterial second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) by repressing expression of crvA, a gene encoding an intermediate filament-like protein necessary for curvature formation in V. cholerae. This regulation is mediated by the transcriptional cascade that also induces production of biofilm matrix components, indicating that cell shape is coregulated with V. choleraes induction of sessility. Wild-type V. cholerae cells adhering to a surface lose their characteristic curved shape to become as straight as cells lacking crvA while genetically engineering cells to maintain high curvature reduced microcolony formation and biofilm density. Conversely, straight V. cholerae mutants have reduced speed when swimming using flagellar motility in liquid. Our results demonstrate regulation of cell shape in bacteria is a mechanism to increase fitness in planktonic or biofilm lifestyles.

microbiology↗