Biology subjects

Shih, Y.-L.

Publications and source records attributed to Shih, Y.-L..

5 recordsLinked to original sources

bioRxiv2023

Growth-dependent concentration gradient of the oscillating Min system in Escherichia coli

The Min system contributes to the spatiotemporal regulation of division sites in Escherichia coli. The MinD and MinE proteins of this system self-organize into oscillatory waves in the form of concentration gradients. How the intracellular Min protein concentration gradients are coordinated with cell growth to achieve spatiotemporal accuracy of cell division is unknown. Here, we report that the MinD concentration gradient becomes progressively steeper as cells elongate, suggesting that the division inhibitory activity at the midcell also decreases with cell growth. Interestingly, the oscillation period appears relatively stable across different cell lengths. Similar features were found in cells under carbon stress conditions, but the gradient was even steeper, likely favoring division at shorter cell lengths. The length-dependent variation of the concentration gradient was further examined in silico using a reaction-diffusion model, which not only supported the above features, but also revealed a decrease in the midcell concentration as the shape of the gradient becomes steeper in growing cells. This growth-dependent regulation of the midcell concentration of MinD may be coupled with the FtsZ ring formation through the MinD-interacting protein MinC. We found that the variable concentration gradients occur by coordinating the reaction rates of the recruitment of MinD and MinE to the membrane and the recharging of MinD with ATP in the cytoplasm. In conclusion, this work uncovers the plasticity of MinD concentration gradients during interpolar oscillations throughout cell growth, an intrinsic property integrated during cell division.

cell biology↗

bioRxiv2023

Two classes of His-Me finger superfamily nuclease effectors exerting synergy for Agrobacterium T6SS-mediated interbacterial competition

Type VI secretion system (T6SS) assembles into a contractile nanomachine to inject effectors across bacterial membranes for secretion. Agrobacterium tumefaciens species complex is a group of soil inhabitants and phytopathogens that deploys T6SS as an antibacterial weapon against bacterial competitors at both inter-species and intra-species levels. A. tumefaciens strain 1D1609 genome encodes one main T6SS gene cluster and four vrgG genes (i.e. vgrGa-d), each encoding a spike protein as an effector carrier. Previous study reported that vgrGa-associated gene 2, named as v2a, encodes a His-Me finger nuclease toxin (also named as HNH/ENDO VII nuclease) contributing to DNase-mediated antibacterial activity. However, the functions and roles of other putative effectors remain unknown. In this study, we identified vgrGc- associated gene 2 (v2c) that encodes another His-Me finger nuclease but with distinct SHH motif differed from AHH motif of V2a. We demonstrated that the ectopic expression of V2c caused growth inhibition, plasmid DNA degradation, and cell elongation in Escherichia coli. The cognate immunity protein, V3c, neutralizes the DNase activity and rescues phenotypes of the growth inhibition and cell elongation. Ectopic expression of V2c DNase-inactive variants retains the cell elongation phenotype while V2a induced cell elongation in a DNase-mediated manner. We also showed that the amino acids of conserved SHH and HNH motifs are responsible for the V2c DNase activity in vivo and in vitro. Notably, V2c also mediated the DNA degradation and cell elongation of target cell in the context of interbacterial competition. Importantly, V2a and V2c exhibit different capacities against different bacterial species and function synergistically to exert stronger antibacterial activity against the soft rot phytopathogen, Dickeya dadantii.

microbiology↗

bioRxiv2021

Chromatin state transition underlies the temporal changes in gene expression during cardiomyocyte maturation

Congenital heart disease (CHD) is often rooted in gene expression anomalies that occur during heart development. As cells commit to a specific lineage, chromatin dynamics and developmental plasticity generally become more limited. However, it remains unclear how differentiated cardiomyocytes (CMs) undergo morphological and functional adaptations to the postnatal environment during their maturation. In this work, we sought to identify the regulatory mechanisms controlling postnatal cardiac gene networks. A time-series transcriptomic analysis of postnatal hearts revealed an integrated, time-ordered transcriptional network that regulates CM maturation. Remarkably, depletion of histone H2B ubiquitin ligase RNF20 after formation of the four-chamber heart disrupted these highly coordinated gene networks. Its ablation also caused early-onset cardiomyopathy, a phenotype reminiscent of CHD. Furthermore, we found that dynamic RNF20-mediated modulation of chromatin accessibility during CM maturation was necessary for the operative binding of cardiac transcription factors known to drive transcriptional gene networks. Together, our results reveal how epigenetic-mediated chromatin state transitions modulate time-ordered gene expression during CM maturation.

developmental biology↗

bioRxiv2019

Effector loading onto VgrG spike proteins is critical for the assembly of the type VI secretion system in Agrobacterium tumefaciens

The type VI secretion system (T6SS) is used by many bacteria to engage in social behaviors with others and can directly or indirectly affect the health of plants and animals. Because activities associated with T6SS are often costly, the assembly and activation of the T6SS must be highly regulated. However, our knowledge regarding how T6SS assembly and contraction are regulated remains limited. Here we show that the loading of effectors onto their cognate carriers is critical for the assembly of a functional T6SS in Agrobacterium tumefaciens. A. tumefaciens strain C58 encodes one T6SS and two Tde DNase toxin effectors used as major weapons for interbacterial competition. We found that loading of Tde effectors onto their cognate carrier, the VgrG spike, is required for active T6SS secretion. Our data also suggest the assembly of the TssBC contractile sheath occurs only after Tde effectors are loaded onto the VgrG spike. The requirement of effector loading for efficient T6SS secretion was also validated in other A. tumefaciens strains. Such a mechanism may be used by bacteria as a strategy for efficacious T6SS firing. Given the prevalence of T6SS-encoding loci in host-associated bacteria, these findings inform on mechanisms that influence the composition of microbial communities and the services provided to hosts.

microbiology↗

bioRxiv2018

Active Transport of Membrane Components by Self-Organization of the Min Proteins

Heterogeneous distribution of components in the biological membrane is critical in the process of cell polarization. However, little is known about the mechanisms that can generate and maintain the heterogeneous distribution of the membrane components. Here we report that the propagating wave patterns of the bacterial Min proteins can impose corresponding steric pressure on the membrane to establish a directional accumulation of the membrane components, resulting in segregation of the components in the membrane. The diffusivity, influenced by the membrane anchor of the component, and the repulsed ability, influenced by the steric property of the soluble region of the component and molecular crowding, determine the differential spatial distribution of the component in the membrane. Thus, transportation of the membrane components by the Min proteins follows a simple physical principle, which resembles a linear peristaltic pumping process, to selectively segregate and maintain heterogeneous distribution of materials in the membrane.

biophysics↗