Biology subjects

Fang, F. C.

Publications and source records attributed to Fang, F. C..

7 recordsLinked to original sources

bioRxiv2026

Impaired acid stress resistance in Salmonella Typhi Ty2

Salmonella enterica encounters acid stress during gastrointestinal transit and within the phagosomal environment of macrophages. Acid stress resistance has been well characterized in Salmonella enterica serovar Typhimurium, but comparative studies in the human-adapted Salmonella enterica serovar Typhi are limited. We compared the growth of S. Typhimurium 14028s and S. Typhi Ty2 at pH values ranging from 3-8 and observed that Salmonella enterica serovar Typhimurium exhibits enhanced growth at pH 4.5 compared to S. Typhi. Comparative transcriptomic profiling of S. Typhimurium and S. Typhi at pH 4.5 and 7.5 identified numerous differentially expressed acid-induced genes (DEGs), including genes encoding membrane proteins (OmpC, PhoE, HydB), a transcriptional regulator (RpoS), and stress response proteins (YciG, STM14_1829, YmdF). Targeted deletion of selected genes in S. Typhimurium significantly suppressed growth at acidic pH, confirming their role in acid stress resistance. These resistance mechanisms are compromised in S. Typhi due to pseudogenization. Heterologous expression of pseudogenized genes in S. Typhi restored acid tolerance. Collectively, these findings suggest that S. Typhi has lost the ability to withstand acid stress due to genomic decay and the loss of multiple genes essential for acid survival in S. Typhimurium, reflecting divergent evolutionary paths in these two serovars. ImportanceSalmonella Typhimurium must adapt to acidic pH conditions in the intestinal tract and the intracellular environment to cause infection. In this study, we show that the enteric fever serovar Salmonella Typhi exhibits impaired growth at pH 4.5, in comparison to Salmonella Typhimurium. We further show that the loss of specific membrane proteins, a transcriptional regulator, and a family of stress response proteins in Salmonella Typhi are responsible for this difference. Collectively, these observations suggest that Salmonella Typhi has evolutionarily lost the ability to withstand acid stress due to differences in its interaction with the human host. This has important implications for the pathogenesis of typhoid fever.

microbiology↗

bioRxiv2025

The MarR Family Transcription Factor SlyASenses Iron and Respiratory Status in Enteric Bacteria

SlyA and its homologs are conserved essential transcription factors in enteric bacteria, including Salmonella enterica and Yersinia pestis, in which they upregulate horizontally-acquired virulence genes. As members of the MarR family of transcription factors, they possess a small molecule binding pocket that allows the protein to undergo a conformational change upon ligand interaction that abrogates DNA binding. Although the original discovery of MarR was based on its ability to recognize xenobiotic compounds and promote their efflux, the conservation of the MarR family throughout Bacteria and Archaea suggests a more general function. Because SlyA is known to bind xenobiotic aromatic carboxylates, we performed a targeted analysis of aromatic metabolic genes in S. Typhimurium to identify potential endogenous ligands, including genes involved in essential cellular processes including iron metabolism, respiration, and aromatic amino acid and folate biosynthesis. We found that SlyA is promiscuously inhibited by multiple aromatic carboxylates including 2,3-dihydroxybenzoate, a precursor of iron-scavenging catecholate siderophores, and 4-hydroxybenzoate, a precursor of quinone-based electron-carriers, which allows it to sense changes in iron availability, respiration and growth on succinate. We suggest that SlyA and other MarR proteins sense bacterial metabolic status via the flux of aromatic carboxylates in biosynthetic pathways, allowing SlyA to function as a counter-silencer of horizontally-acquired genes that is exquisitely responsive to the metabolic state of the cell. SIGNIFICANCEMarR proteins comprise an ancient group of transcription factors that emerged before the divergence of Archaea and Bacteria. First identified as regulators of antibiotic efflux, they have also been suggested to sense and regulate concentrations of endogenous intracellular metabolites, but such metabolites have not previously been identified. Here we show that SlyA, a conserved and essential MarR family virulence gene regulator in enteric pathogens, binds to and is inhibited by aromatic metabolites required for many essential cellular processes. Our findings show how SlyA integrates metabolic status into bacterial transcriptional networks that control both molecular efflux and virulence.

microbiology↗

bioRxiv2025

Evasion of serum antibodies and complement by Salmonella Typhi and Paratyphi A

Nontyphoidal and enteric fever serovars of Salmonella enterica display distinctive interactions with serum antibodies and the complement system, which initiate the host immune response to invading microbes. This study examines the contributions of lipopolysaccharide O-antigen and the S. Typhi Vi polysaccharide capsule to serum resistance, complement activation and deposition, and immunoglobulin (Ig) binding in nontyphoidal S. enterica serovar Typhimurium and the enteric fever serovars S. Typhi and S. Paratyphi A. Although all three serovars are resistant to serum killing, S. Typhi and S. Paratyphi A exhibit lower levels of Ig binding, complement binding and complement activation compared to S. Typhimurium. In S. Typhimurium, WzzB-dependent long O-antigen production and FepE-dependent very long O-antigen production are required for serum resistance but do not prevent IgM binding or complement deposition. S. Typhi lacks very long O-antigen, but its production of Vi capsule inhibits IgM binding and complement deposition, while acting in concert with long O-antigen to resist serum killing. In S. Paratyphi A, long O-antigen production is deficient due to a hypofunctional WzzB protein, but this is compensated by greater quantities of very long O-antigen, which are required for serum resistance. Restoration of WzzB function by exchange with the S. Typhimurium or S. Typhi wzzB alleles can restore long O-antigen production in S. Paratyphi A but decreases very long O-antigen production, resulting in increased IgM binding. Replacement of the S. Paratyphi A O2-type polysaccharide with the S. Typhi O9 polysaccharide further increases IgM binding of S. Paratyphi A, which enhances complement activation but not complement deposition. Lastly, a gene duplication of rfbV in S. Paratyphi A is necessary for higher levels of very long O-antigen and resistance to complement deposition and antibody binding. Collectively, these observations demonstrate fundamental differences between nontyphoidal and enteric fever Salmonella serovars in their interactions with innate immune effectors. Author SummaryEnteric fever acquired by ingestion of food or water contaminated with Salmonella Typhi or Paratyphi A is a significant cause of morbidity and mortality in low- and middle-income countries. In this study, we dissect the different mechanisms by which these bacteria avoid binding by serum proteins that are required for the initiation of protective immune responses. This is in contrast to the nontyphoidal serovar Salmonella Typhimurium, a common cause of gastroenteritis, which does not avoid complement activation nor antibody binding but instead exploits host inflammation. Our observations provide new insights into the mechanisms responsible for the distinctive immunological features of human enteric fever and can inform the development of Salmonella vaccines that target the Salmonella cell envelope.

microbiology↗

bioRxiv2024

A cytochrome bd repressed by a MarR family regulator confers resistance to metals, nitric oxide, sulfide, and cyanide in Chromobacterium violaceum

Chromobacterium violaceum is a ubiquitous environmental pathogen. Despite its remarkable adaptability, little is known about the mechanisms of stress resistance in this bacterium. Here, in a screen for iron-susceptible transposon mutants, we identified a cytochrome bd that protects C. violaceum against multiple stresses. The two subunits of this cytochrome bd (CioAB) are encoded by the cioRAB operon, which also encodes a GbsR-type MarR family transcription factor (CioR). A {Delta}cioAB mutant strain was sensitive to iron and the iron-requiring antibiotic streptonigrin and showed a decrease in siderophore production. Growth curves and survival assays revealed that the {Delta}cioAB strain was also sensitive to zinc, hydrogen peroxide, nitric oxide, sulfide, and cyanide. Expression analysis showed that the promoter activity of the cioRAB operon and the transcript levels of the cioAB genes were increased in a {Delta}cioR mutant. CioR bound the promoter region of the cio operon in vitro, indicating that CioR is a direct repressor of its own operon. Expression of the cio operon increased at high cell density and was dependent on the quorum-sensing regulator CviR. As cyanide is also a signal for cio expression, and production of endogenous cyanide is known to be a quorum sensing-regulated trait in C. violaceum, we suggest that CioAB is a cyanide-insensitive terminal oxidase that allow respiration under cyanogenic growth conditions. Our findings indicate that the cytochrome bd CioAB protects C. violaceum against multiple stress agents that are potentially produced endogenously or during interactions with a host. IMPORTANCEThe terminal oxidases of bacterial respiratory chains rely on heme-copper (heme-copper oxidases) or heme (cytochrome bd) to catalyze reduction of molecular oxygen to water. Chromobacterium violaceum is a facultative anaerobic bacterium that uses oxygen and other electron acceptors for respiration under conditions of varying oxygen availability. The C. violaceum genome encodes multiple respiratory terminal oxidases, but their role and regulation remain unexplored. Here, we demonstrate that CioAB, the single cytochrome bd from C. violaceum, protects this bacterium against multiple stressors that are inhibitors of heme-copper oxidases, including nitric oxide, sulfide, and cyanide. CioAB also confers C. violaceum resistance to iron, zinc, and hydrogen peroxide. This cytochrome bd is encoded by the cioRAB operon, which is under direct repression by the MarR-type regulator CioR. In addition, the cioRAB operon responds to quorum sensing and to cyanide, suggesting a protective mechanism of increasing CioAB in the setting of high endogenous cyanide production.

microbiology↗

bioRxiv2018

The Evolution of SlyA/RovA Transcription Factors From Repressors to Counter-Silencers in Enterobacteriaceae

Gene duplication and subsequent evolutionary divergence have allowed conserved proteins to develop unique roles. The MarR family of transcription factors (TFs) has undergone extensive duplication and diversification in bacteria, where they act as environmentally-responsive repressors of genes encoding efflux pumps that confer resistance to xenobiotics, including many antimicrobial agents. We have performed structural, functional, and genetic analyses of representative members of the SlyA/RovA lineage of MarR TFs, which retain some ancestral functions, including repression of their own expression and that of divergently-transcribed multidrug efflux pumps, as well as allosteric inhibition by aromatic carboxylate compounds. However, SlyA and RovA have acquired the ability to counter-silence horizontally-acquired genes, which has greatly facilitated the evolution of Enterobacteriaceae by horizontal gene transfer. SlyA/RovA TFs in different species have independently evolved novel regulatory circuits to provide the enhanced levels of expression required for their new role. Moreover, in contrast to MarR, SlyA is not responsive to copper. These observations demonstrate the ability of TFs to acquire new functions as a result of evolutionary divergence of both cis-regulatory sequences and in trans interactions with modulatory ligands.

microbiology↗

bioRxiv2018

Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience

The present study analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009-2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 42 corrections, 5 retractions and 12 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, ~10% of papers with inappropriate image duplications in MCB were retracted. If this proportion is representative, then as many as 35,000 papers in the literature are candidates for retraction due to image duplication. The resolution of inappropriate image duplication concerns after publication required an average of 6 h of journal staff time per published paper. MCB instituted a pilot program to screen images of accepted papers prior to publication that identified 12 manuscripts (14.5% out of 83) with image concerns in two months. The screening and correction of papers before publication required an average of 30 min of staff time per problematic paper. Image screening can identify papers with problematic images prior to publication, reduces post-publication problems and requires significantly less staff time than the correction of problems after publication.

scientific communication and education↗

bioRxiv2017

Why Do Scientists Fabricate And Falsify Data? A Matched-Control Analysis Of Papers Containing Problematic Image Duplications

It is commonly hypothesized that scientists are more likely to engage in data falsification and fabrication when they are subject to pressures to publish, when they are not restrained by forms of social control, when they work in countries lacking policies to tackle scientific misconduct, and when they are male. Evidence to test these hypotheses, however, is inconclusive due to the difficulties of obtaining unbiased data.\n\nHere we report a pre-registered test of these four hypotheses, conducted on papers that were identified in a previous study as containing problematic image duplications through a systematic screening of the journal PLoS ONE. Image duplications were classified into three categories based on their complexity, with category 1 being most likely to reflect unintentional error and category 3 being most likely to reflect intentional fabrication. Multiple parameters connected to the hypotheses above were tested with a matched-control paradigm, by collecting two controls for each paper containing duplications.\n\nCategory 1 duplications were mostly not associated with any of the parameters tested, in accordance with the assumption that these duplications were mostly not due to misconduct. Category 2 and 3, however, exhibited numerous statistically significant associations. Results of univariable and multivariable analyses support the hypotheses that academic culture, peer control, cash-based publication incentives and national misconduct policies might affect scientific integrity. Significant correlations between the risk of image duplication and individual publication rates or gender, however, were only observed in secondary and exploratory analyses.\n\nCountry-level parameters generally exhibited effects of larger magnitude than individual-level parameters, because a subset of countries was significantly more likely to produce problematic image duplications. Promoting good research practices in all countries should be a priority for the international research integrity agenda.

scientific communication and education↗