Biology subjects

Zhang, C.-C.

Publications and source records attributed to Zhang, C.-C..

10 recordsLinked to original sources

bioRxiv2026

A complex two-component system CdgKA-CdgSH fine-tunes c-di-GMP homeostasis in a Cyanobacterium

The second messenger c-di-GMP plays a critical role in regulating cell size and growth in the cyanobacterium Anabaena sp. PCC 7120. While all 16 c-di-GMP metabolic enzymes and the primary receptor CdgR have been identified, how metabolic enzyme activity is controlled to maintain c-di-GMP homeostasis remains largely unexplored. Here, using a suppressor-screening approach based on c-di-GMP-deficient mutants, we identify All0729 (CdgKA) as a regulator that orchestrates c-di-GMP homeostasis and cell size regulation. Genetic and quantitative analyses demonstrate that CdgKA acts upstream of All2306 (CdgSHA), the reported major c-di-GMP hydrolase, to modulate the activity of the latter. While c-di-GMP synthesis mutants displayed reduced c-di-GMP levels and decreased cell size, inactivation of cdgKA or cdgSHA in these mutant backgrounds rescued both the c-di-GMP levels and cell size. We propose that CdgKA and CdgSHA form a complex two-component system, and the phosphorylation of CdgSHA enhances its c-di-GMP-degrading activity. While the previously identified two-component system composed of CdgK-CdgS regulates c-di-GMP synthesis, the CdgKA-CdgSHA system controls its degradation. Together, they constitute a dual TCS network that precisely tunes c-di-GMP levels and cell size, establishing a regulatory link between two-component signaling and second messenger homeostasis in cyanobacteria.

microbiology↗

bioRxiv2026

Regulation of cyanobacterial type IV pilus-dependent functions by interaction between a c-di-GMP receptor and two transcription factors

Cyanobacteria utilize type IV pili for many behavioural responses, such as phototaxis, aggregation, floating, and DNA uptake. Type IV pilus-dependent functions are regulated by the nucleotide second messengers, c-di-GMP and cAMP. In this study, we investigated the role of a recently identified c-di-GMP receptor (CdgR) in cyanobacteria that harbours a ComFB domain. ComFB-domain proteins are widespread in cyanobacteria and are also present in heterotrophic bacteria. We demonstrated that the CdgR homolog from the cyanobacterium Synechocystis sp. PCC 6803, a model organism for studying type IV pilus-dependent functions, specifically binds to c-di-GMP. Genetic and phenotypic analyses revealed that Synechocystis CdgR is involved in phototactic motility and natural competence. Inactivation of cdgR resulted in altered expression of specific sets of minor pilins, which are essential for motility or natural competence. We identified interactions between CdgR and the CRP-family transcription factors, SyCRP1 and SyCRP2. Disruption of these CdgR-SyCRP1 and CdgR/SyCRP2 complexes is initiated by elevated c-di-GMP levels. Moreover, the assembly and stability of these complexes are influenced by other cyclic nucleotides, such as cAMP and c-di-AMP. These observed interactions imply a complex regulatory mechanism by which CdgR influences gene expression in response to cyclic nucleotide messenger signalling, particularly c-di-GMP. The present findings highlight the importance of CdgR in c-di-GMP signalling and its role in regulating type IV pilus-dependent functions in Synechocystis. The modulation of the expression of specific minor pilin genes by CdgR, through interactions with the transcription factors SyCRP1 and SyCRP2, contributes to the establishment of multiple type IV pilus functions and adaptive behaviours of cyanobacteria.

microbiology↗

bioRxiv2026

Bacillus velezensis GFZF-23 Alleviates Colitis through Microbiome Restoration and β-Sitosterol-Mediated Metabolic Reprogramming

BackgroundA major hurdle in probiotic development for inflammatory bowel disease (IBD) is the inability to disentangle their direct effects on the host from those mediated through the resident microbiota. Here, we establish a reverse screening platform in gnotobiotic zebrafish to overcome this limitation. ResultsWe isolated Bacillus velezensis (B. velezensis) GFZF-23 from long-surviving gnotobiotic zebrafish and demonstrated its potent protective effects against DSS-induced colitis. The strain significantly attenuated intestinal damage and inflammatory responses in both germ-free and conventional hosts. Multi-omics analysis revealed that B. velezensis GFZF-23 employs environment-specific strategies. In the presence of a microbiome, it restored community homeostasis by enriching beneficial taxa, such as Faecalibacterium. Strikingly, in germ-free conditions, GFZF-23 did not simply reverse disease-associated markers but actively reprogrammed host metabolism, with particular enrichment in the linoleic acid pathway. Functional assays confirmed that {beta}-sitosterol serves as a critical effector metabolite driving this protection. ConclusionsThis work establishes B. velezensis as a promising therapeutic candidate and provides a robust framework for deconvoluting the direct and indirect effects of potential probiotics. Our findings highlight metabolic reprogramming as a vital, underappreciated mechanism in precision microbiome therapeutics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/710680v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@10868e6org.highwire.dtl.DTLVardef@11f1532org.highwire.dtl.DTLVardef@1a88631org.highwire.dtl.DTLVardef@1020b33_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

An Electromechanical Relay-like Multi-enzymatic System Gates c-di-GMP-Dependent Cell Fate in a Cyanobacterium

Cyclic-di-GMP is a ubiquitous bacterial second messenger that regulates diverse cellular processes. Although many bacteria harbor multiple enzymes for metabolism, the mechanisms underlying coordinated regulation remain unclear. Using the cyanobacterium Anabaena PCC 7120, we generate mutant strains with varying numbers of c-di-GMP metabolic genes deleted, including cdg0 (all degradation genes deleted) and cdgmax (all synthesis genes deleted). We found that cyclic-di-GMP is essential for both cell viability and size regulation. Quantitative analysis identified two critical physiological thresholds: one for maintaining normal cell size and a lower, lethal threshold required for survival. The 16 cyclic-di-GMP metabolic enzymes function as an electromechanical-like dual relay system, where different enzyme groups maintain cyclic-di-GMP homeostasis or activate SOS-like alarm responses when cyclic-di-GMP concentrations drop below the lethal threshold. These regulatory effects are mediated by the cyclic-di-GMP receptor CdgR, depending on the fraction of apo-CdgR form. This dual-threshold system enables dynamic cellular adaptation while preventing lethal consequences, representing a fundamental growth-survival trade-off strategy in living organisms.

microbiology↗

bioRxiv2025

Carbon metabolism shapes FtsZ levels and cell division in a cyanobacterium

Cyanobacteria, as photoautotrophs, play key ecological roles and are widely used in synthetic biology research. While metabolism profoundly influences cellular processes like cell division, the regulatory mechanisms linking these pathways remain poorly understood in cyanobacteria. Here, we engineered the model cyanobacterium Anabaena sp. PCC 7120 by introducing an extra carboxylation module into the TCA pathway, perturbing this central metabolic pathway. This modification alters the division protein FtsZ levels, impairing cell division under varying light conditions. We found that 2-oxoglutarate, which is known as a metabolic signal, regulates ftsZ expression via the transcription factor NtcA. Furthermore, metabolic status modulates cell division in an NtcA-dependent manner, revealing a direct integration of metabolic control and cell division. Our findings uncover a coordination mechanism between metabolism and cell division in cyanobacteria, providing mechanistic insights for synthetic biology engineering and the understanding of metabolic regulation.

microbiology↗

bioRxiv2024

16S rRNA gene sequencing for bacterial identification and infectious disease diagnosis

16S rRNA gene sequence is the most common housekeeping genetic marker to study bacterial phylogeny and taxonomy. Therefore, 16S rRNA gene sequencing has the potential to identify novel bacteria and diagnose bacteria. This study compared 16S rRNA gene sequencing with conventional PCR for bacterial identification and disease diagnosis. The bacterial community in healthy and diseased hosts was analyzed by 16S rRNA gene sequencing. 16S rRNA gene sequencing is more sensitive than conventional PCR in detecting bacteria. Moreover, 16S rRNA gene sequencing is adequate to identify novel bacteria. 16S rRNA gene sequencing demonstrated that most pathogenic bacteria persist in diseased or healthy hosts in different abundance. Pathogenic bacteria, such as well-known chicken pathogen Avibacterium paragallinarum, Ornithobacterium rhinotracheale, and Gallibacterium anatis, were identified as indicator species of diseased samples. Alpha diversity analysis showed that the healthy group species is significantly higher than in the diseased groups. Beta diversity analysis also demonstrated differences between healthy and infected groups. The study concluded that 16S rRNA gene sequencing is a more sensitive method for detecting pathogens, and microbiota analysis can distinguish between healthy and diseased samples. Eventually, 16S rRNA gene sequencing has represented the potential in human and animal clinical diagnosis and novel bacterial identification.

microbiology↗

bioRxiv2024

A detailed analysis of 16S rRNA gene sequencing and conventional PCR-based testing for the diagnosis of bacterial pathogens and discovery of novel bacteria

This study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence of Avibacterium paragallinarum (APG) and Ornithobacterium rhinotracheale (ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7% to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1% to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited to Gallibacterium anatis, Riemerella columbina, Enterococcus cecorum, Mycoplasma synoviae, Helicobacter hepaticus, and Staphylococcus lentus. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.

microbiology↗

bioRxiv2023

Nonribosomal peptide synthetases require dynamic interaction between modular domains

Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two newly identified conformations in the NRPS catalytic cycle. Our data reveals that the dynamic interaction between the C and the A domains in these modules are mediated by the conserved "RXGR" motif, and this interaction is important for the adenylation activity. Furthermore, the "RXGR" motif-mediated dynamic interaction and its functional regulation is prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insight into the catalytic mechanism of NRPSs and should inspire novel ideas in NRPS enzyme engineering in synthetic biology.

biochemistry↗

bioRxiv2023

A conserved protein inhibitor brings under check the activity of RNase E in cyanobacteria

RNase E is a major ribonuclease for RNA metabolism in bacteria. Because it has a large substrate spectrum and poor substrate specificity, its activity must be well controlled under different conditions. Only a few regulators of RNase E are known in bacteria, limiting our understanding on the posttranscriptional regulatory mechanisms operating in these organisms. Here we show that, RebA, a protein universally present in cyanobacteria, interacts with RNase E in the filamentous cyanobacterium Anabaena PCC 7120. Distinct from those known regulators of RNase E, RebA interacts with the 5 sensor domain in the catalytic region of RNase E, and suppresses the cleavage activities of RNase E for all tested RNA substrates irrespective of their 5-end status. Consistent with the inhibitory function of RebA on RNase E, conditional depletion of RNase E and overproduction of RebA caused formation of elongated cells, whereas the absence of RebA and overproduction of RNase E resulted in a shorter-cell phenotype. We further showed that the morphological changes caused by altered levels of RNase E or RebA are dependent on their physical interaction. The action of RebA represents a new mechanism, highly conserved in cyanobacteria, for RNase E regulation. Our findings provide insights into the regulation and the function of RNase E, and demonstrate the importance of balanced RNA metabolism in bacteria.

microbiology↗

bioRxiv2020

HetF protein is a new divisome component in a filamentous and developmental cyanobacterium

Bacterial cell division, with a few exceptions, is driven by FtsZ through a treadmilling mechanism to remodel and constrict the rigid peptidoglycan (PG) layer. Yet, different organisms may differ in the composition of the cell-division complex (divisome). In the filamentous cyanobacterium Anabaena PCC 7120, hetF is required for the initiation of the differentiation of heterocysts, cells specialized in N2-fixing cells under combined nitrogen deprivation. In this study, we demonstrate that hetF is expressed in vegetative cells and necessary for cell division in a conditional manner. Under non-permissive conditions, cells of a {Delta}hetF mutant stop dividing, consistent with increased level of HetF under similar conditions in the wild type. Furthermore, HetF is a membrane protein located at midcell and cell-cell junctions. In the absence of HetF, FtsZ rings are still present in the elongated cells; however, PG remodelling is abolished. This phenotype is similar to that observed with the inhibition of septal PG synthase FtsI. We further reveal that HetF is recruited to or stabilized at the divisome by interacting with FtsI and this interaction is necessary for HetF function in cell division. Our results indicate that HetF is a member of the divisome, and reveal distinct features of the cell-division machinery in cyanobacteria that are of high ecological and environmental importance. Significance StatementCyanobacteria shaped the Earths evolutionary history, and are still playing important roles for elementary cycles in different environments. They are consisted of highly diverse species with different cell shape, size and morphology. Although these properties are strongly affected by the process of cytokinesis, the mechanism remains largely unexplored. Using different approaches, we demonstrate that HetF is a new component of the cell division machinery in the filamentous cyanobacterium Anabaena PCC 7120. The common and diverged characteristics of cell division in prokaryotes reflect the evolutionary history of different bacteria, as an adaptive measure to proliferate under certain environmental conditions. As a protein for cell differentiation, the recruitment of HetF to the septum illustrates such an adaptive mechanism for cyanobacteria.

microbiology↗