Biology subjects

Zhang, Y. E.

Publications and source records attributed to Zhang, Y. E..

8 recordsLinked to original sources

bioRxiv2023

cCMP and cUMP stimulate the acid phosphatase activity of AphA in Haemophilus influenzae

We recently detailed the competitive inhibition of cyclic AMP (cAMP) on three periplasmic enzymes, AphA, NadN, and Hel, in Haemophilus influenzae Rd KW20. This inhibitory effect is vital for orchestrating the nutritional growth and competence development in KW20. Here, we extended the study to the three other second messengers, i.e., cyclic GMP, cyclic UMP, and cyclic CMP, each sharing structural similarities with cAMP. Notably, cGMP competitively inhibits AphAs acid phosphatase activity akin to cAMP. In contrast, both cUMP and cCMP stimulate AphAs phosphatase activity in a dose-dependent manner. This novel finding underscores the intriguing opposing effects of cyclic purine and pyrimidine nucleotides on AphA, suggesting potential intricate biological crosstalk among these second messengers.

biochemistry↗

bioRxiv2023

Substrate promiscuity of the Escherichia coli xanthine oxidase

PpnN is a cytosolic nucleosidase that cleaves nucleotide monophosphates to nucleobases and ribose-5-phosphate and plays a crucial role in regulating bacterial competitive fitness and persistence. To quantify the PpnN reaction, here we developed an enzyme-coupled assay, wherein PpnN hydrolyzes IMP to hypoxanthine, which is then converted by xanthine oxidase (XO) into xanthine, uric acid and hydrogen peroxide. The detection of hydrogen peroxide via horseradish peroxidase and Amplex Red provides a measure of PpnN enzymatic activity. Surprisingly, we found that in addition to IMP, other nucleotides like GMP significantly increased the signal, suggesting that the corresponding nucleobases might also be substrates for XO. Direct tests by using guanine confirmed XOs capacity to use it as a substrate, albeit less effectively than hypoxanthine. These findings suggest a potential guanine aminohydrolase activity of E. coli XO and broaden our understanding of nucleobase metabolism in bacterial systems.

biochemistry↗

bioRxiv2023

Escherichia coli acid phosphatase AphA expression is upregulated under carbon and phosphate starvations and inhibited by CytR

This study investigates the regulation of E. coli aphA expression under nutrient starvation. Using transcriptional reporters with truncated aphA promoter sequences, we found that starvation of carbon and phosphate, but not amino acid, stimulated aphA expression through distinct promoter regions. Deletions of crp or cyaA reduced aphA expression, confirming their importance in aphA regulation during carbon starvation. Conversely, CytR deletion increased aphA expression, suggesting CytRs role as a repressor of aphA expression. Collectively, these data imply a potential connection between CytR, aphA expression, and the broader context of natural competence evolution and bacterial nutrient absorption.

microbiology↗

bioRxiv2023

Cholinergic stimulation increases cortical spine formation via local inhibitory circuit

Basal forebrain (BF) cholinergic projections densely innervate the neocortex, releasing acetylcholine (ACh) to modulate neuronal excitability, thereby influencing sensory processing and cognitive functions. However, the synaptic basis of such ACh-induced effects in vivo remains elusive. To investigate how ACh release from BF regulates synaptic dynamics in the neocortex, we selectively stimulated BF cholinergic neurons in mice, and used two-photon microscopy to track structural changes of dendritic spines on cortical pyramidal neurons. We found that optogenetic and chemogenetic stimulation of BF cholinergic neurons rapidly induced spine formation in layer 5 pyramidal neurons in the auditory cortex and the posterior parietal cortex. Selective blockage of ACh receptors (AChRs) demonstrated that nicotinic AChRs are required for the ACh-induced spine formation. We also found that Ach-induced spine formation of pyramidal neurons requires the activity of cortical somatostatin-expressing inhibitory interneurons. Together, our study revealed ACh-induced synaptic plasticity in the cortical microcircuit in vivo, providing a synaptic mechanism for cortical neuronal plasticity and functional changes associated with BF ACh release.

neuroscience↗

bioRxiv2023

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations1. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution2, 3. However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive7. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity7.

genomics↗

bioRxiv2020

AlphaTracker: A Multi-Animal Tracking and Behavioral Analysis Tool

The advancement of behavioral analysis in neuroscience has been aided by the development of computational tools1,2. Specifically, computer vision algorithms have emerged as a powerful tool to elevate behavioral research3,4. Yet fully automatic analysis of social behavior remains challenging in two ways. First, existing tools to track and analyze behavior often focus on single animals, not multiple, interacting animals. Second, many available tools are not developed for novice users and require programming experience to run. Here, we unveil a computer vision pipeline called AlphaTracker, which requires minimal hardware requirements and produces reliable tracking of multiple unmarked animals. An easy-to-use user interface further enables manual inspection and curation of results. We demonstrate the practical, real-time advantages of AlphaTracker through the study of multiple, socially-interacting mice.

animal behavior and cognition↗

bioRxiv2020

New Genes in Drosophila Quickly Evolved Essential Functions in Viability During Development

It is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development of Drosophila. The recent progress in the analyses of gene effects and improvements in the computational identification of new genes, which has led to large sample sizes of new genes, open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including the dating of gene ages, the interpretation of RNAi data that may confuse false positive/false negative rates, and the potential confounding impact of compensation and developmental effects that were not considered during previous CRISPR knockout experiments. We further analyzed new data from knockdowns of 702 new genes (~66% of total 1,070 Drosophila melanogaster new genes), revealing a similarly high proportion of essential genes from recent evolution, compared to those found in distant ancestors of D. melanogaster. Knockout of a few young genes detected analogous essentiality. Furthermore, our experimentally determined distribution and comparison of knockdown efficiency in different RNAi libraries provided valuable data for general functional analyses of genes. Taken together, these data, along with an improved understanding of the phenotypic effect analyses of new genes, provide further evidence to the conclusion that new genes in Drosophila quickly evolved essential functions in viability during development.

developmental biology↗

bioRxiv2020

The mutational load in natural populations is significantly affected by high primary rates of retroposition

Gene retroposition is known to contribute to patterns of gene evolution and adaptations. However, possible negative effects of gene retroposition remain largely unexplored, since most previous studies have focussed on between-species comparisons where negatively selected copies are mostly not observed, as they are quickly lost from the populations. Here, we show for natural house mouse populations that the primary rate of retroposition is orders of magnitude higher than previously thought. Comparisons with SNP distribution patterns in the same populations show that most retroposition events are deleterious. Transcriptomic profiling analysis shows that new retroposed copies become easily subject to transcription and have an influence on the expression level of their parental genes, especially when transcribed in the antisense direction. Our results imply that the impact of retroposition on the mutational load in natural populations has been highly underestimated, which has also implications for strategies of disease allele detection in humans. Significance statementThe phenomenon or retroposition (re-integration of reverse transcribed RNA into the genome), has been well studied in comparisons between genomes and has been identified as a source of evolutionary innovation. However, the negative effects of retroposition have been overlooked so far. Our study makes use of a unique population genomic dataset from natural mouse populations. It shows that the retroposition rate is magnitudes higher than previously suspected. We show that most of the newly transposed retrocopies have a deleterious impact through modifying the expression of their parental genes. In humans, this effect is expected to cause disease alleles and we propose that genetic screening needs to take into account the search for newly transposed retrocopies.

genomics↗