Biology subjects

Farah, C. S.

Publications and source records attributed to Farah, C. S..

13 recordsLinked to original sources

bioRxiv2026

To Kill or not to Kill: A Conserved trans-intoxication protection factor Blocks X-T4SS-Mediated Fratricide through Interaction with VirB5

Bacteria can outcompete rivals by using specialized secretion systems to deliver toxic effectors into prey cells. How these systems distinguish prey from kin remains a fundamental unanswered question. In many Xanthomonadales (Lysobacterales) species, the antibacterial type IV secretion system (X-T4SS) mediates cell-cell contact-dependent killing of competing bacteria. Here, we identified XAC2611, a chromosomally encoded, cysteine-rich DUF4189 protein, as essential for preventing X-T4SS-mediated fratricide among sibling cells in Xanthomonas citri. XAC2611 homologs are found within or proximal to the genomic loci coding almost all identified X-T4SS. Live-cell microscopy and biochemical data reveal that XAC2611 is abundantly produced and widely distributed throughout the periplasm of recipient cells and is required to prevent X. citri cells from intoxicating each other in a contact-dependent manner. We also show that XAC2611 homologs from Stenotrophomonas maltophilia protect X. citri cells from attack by S. maltophilia. Protein-protein interaction assays show that XAC2611 interacts directly with the VirB5 subunit. Since VirB5 is predicted to be localized at the tip of the X-T4SS pilus, its interaction with XAC2611 in a neighboring sister cell could block X-T4SS-mediated effector delivery. We therefore name this family of proteins trans-intoxication protection factors (Tpfs).

microbiology↗

bioRxiv2026

Cryo-EM structure analysis of phage {Phi}Xacm4-11 that infects the phytopathogen Xanthomonas citri

Very few bacteriophages that infect Xanthomonas species have been characterized genetically and only one 3D structure, the capsid of a siphovirus that infects the phytopathogen Xanthomonas citri, has been determined at high resolution. This study presents the annotated DNA sequence and detailed structural analysis of {Phi}Xacm4-11, a podovirus that infects Xanthomonas citri, shedding light on its unique architecture and functional attributes, providing insights into the molecular mechanisms underlying host recognition and infection. Annotation of the genome revealed conserved features among related phages, but also distinct genetic elements that may contribute to {Phi}Xacm4-11s specificity toward X. citri. Genes associated with host recognition and infection were identified, including the genes potentially coding for the receptor-binding proteins (RBPs) at the tail fibre tip, offering insights into their role in bacterial attachment. Using high-resolution cryo-electron microscopy, we resolved the architecture of the mature, pre-released virion, revealing a T7-like head-tail assembly with a well-defined portal-tail complex embedded at a unique fivefold vertex. Our findings provide a detailed view of the structural and functional components of {Phi}Xacm4-11, furthering our understanding of its molecular interactions with X. citri and its potential application in phage therapy against phytopathogens. SIGNIFICANCE STATEMENTBacteriophages are increasingly recognized as powerful tools to control bacterial pathogens in medicine and agriculture, yet the structural basis of host recognition and genome delivery remains poorly understood for most phages. Here, we present a comprehensive structural and functional analysis of {Phi}Xacm4-11, a podovirus that infects the plant pathogen Xanthomonas citri. By combining genome annotation, proteomics, and high-resolution cryo-electron microscopy, we reveal the complete architecture of the mature virion and its specialized portal-tail machinery. Our results show how this short-tailed phage deploys an internal injection device to penetrate the bacterial cell envelope and highlight structural features linked to type IV pilus-dependent infection. These findings provide insights into phage entry mechanisms and establish {Phi}Xacm4-11 as a model for engineering biocontrol strategies.

biochemistry↗

bioRxiv2025

The single-particle structures of a Bacterial Cyanide Dihydratase and a Fungal Cyanide Hydratase

Cyanide is widely used in industries due to its strong affinity for metals, a property that also underlies its potent toxicity. Industries therefore must reduce cyanide concentration in wastewater final disposal. Physical, chemical, and biological methods have been developed for this purpose; however, knowledge about the structure of enzymes involved in cyanide degradation remains limited. Structural characterization of these proteins could facilitate the development of more efficient enzymes with enhanced bioremediation potential. Here, we present the single-particle cryo-electron microscopy structures of a cyanide dihydratase from Bacillus safensis and a cyanide hydratase from Gloeocercospora sorghi at 2.2 [A] and 2.0 [A] resolution, respectively. We provide a comprehensive description and comparative analysis of these structures alongside all previously experimentally determined nitrilase structures. Importantly, our full-length structures reveal new structural features in the C-terminal as well as specific intermolecular interactions between protomer interfaces and within the helix lumen. Finally, our findings offer insights into the possible reaction mechanisms of these two enzymes.

biochemistry↗

bioRxiv2023

The protective function of an immunity protein against the cis-toxic effects of a Xanthomonas Type IV Secretion System Effector

Many bacterial species use specialized secretion systems to translocate proteinaceous toxic effectors into target bacterial cells. In most cases, effectors are encoded in bicistronic operons with their cognate immunity proteins. The current model is that immunity proteins could, in principle, provide protection in two different ways: i) by avoiding self-intoxication (suicide or cis-intoxication) or ii) by inhibiting intoxication due to "friendly-fire" translocation from neighboring sister cells (fratricide or trans-intoxication). Here, we set out to distinguish between these two protection mechanisms in the case of the bactericidal Xanthomonas citri Type IV Secretion System (X-T4SS), where killing is due to the action of a cocktail of secreted effectors (X-Tfes) that are inhibited by their cognate immunity proteins (X-Tfis). We use a set of X. citri mutants lacking multiple X-Tfe/X-Tfi pairs to show that X-Tfis are not absolutely required to protect against trans-intoxication. Our investigation then focused on the in vivo function of the lysozyme-like effector X-TfeXAC2609 and its cognate immunity protein X-TfiXAC2610. We observe the accumulation of damage in the X. citri cell envelope and inhibition of biofilm formation due to the action of X-TfeXAC2609 in the absence of X-TfiXAC2610. We show that X-TfeXAC2609 toxicity is independent of an active X-T4SS and that X-TfiXAC2610 protects the cell colony against X-TfeXAC2609-induced cis-intoxication via autolysis. In vitro assays employing X-TfiXAC2610 mutants were used to test and validate an AlphaFold2-derived model of the X-TfeXAC2609-X-TfiXAC2610 complex which presents topological similarities with the distantly related Tse1/Tsi1 complex from P. aeruginosa and the the i-type lysozyme from Meretrix lusoria (MI-iLys) in complex with PliI-Ah from Aeromonas hydrophila. While immunity proteins in other systems have been shown to protect against attacks by sister cells (trans-intoxication), this is the first description of an antibacterial secretion system in which the immunity proteins are dedicated to protecting cells against cis-intoxication.

biochemistry↗

bioRxiv2023

Uncovering the association mechanism between two intrinsically flexible proteins

The understanding of protein-protein interaction mechanisms is key to the atomistic description of cell signalling pathways and for the development of new drugs. In this context, the mechanism of intrinsically disordered proteins folding upon binding has attracted attention. The VirB9 C-terminal domain (VirB9Ct) and the VirB7 N-terminal motif (VirB7Nt) associate with VirB10 to form the outer membrane core complex of the Type IV Secretion System injectisome. Despite forming a stable and rigid complex, VirB7Nt behaves as a random coil while VirB9Ct is intrinsically dynamic in the free state. Here we combined NMR, stopped-flow fluorescence and computer simulations using structure-based models to characterize the VirB9Ct-VirB7Nt coupled folding and binding mechanism. Our data indicated that VirB9Ct binds to VirB7Nt by way of a conformational selection mechanism. However, at higher temperatures energy barriers between different VirB9Ct conformations are more easily surpassed. Under these conditions the formation of non-native initial encounter complexes may not be neglected, providing alternative pathways towards the native complex conformation. These observations highlight the intimate relationship between folding and binding, calling attention to the fact that the two molecular partners must search for the most favored intramolecular and intermolecular interactions on a rugged and funnelled conformational energy landscape, along which multiple intermediates may lead to the final native state.

biophysics↗

bioRxiv2021

Antibacterial T6SS effectors with a VRR-Nuc domain induce target cell death via DNA Double-Strand Breaks

The T6SS (Type VI secretion System) secretes antibacterial effectors into target competitors. Salmonella spp. encode five phylogenetically distinct T6SSs. Here we characterize the function of the SPI-22 T6SS of S. bongori, showing that it has antibacterial activity. We identify a group of antibacterial T6SS effectors (TseV1-4) containing an N-terminal PAAR-like domain and a C-terminal VRR-Nuc domain encoded next to cognate immunity proteins that contain the DUF3396 domain (TsiV1-4). TseV2 and TseV3 are toxic when expressed in Escherichia coli and bacterial competition assays confirm that TseV2 and TseV3 are secreted by the SPI-22 T6SS. Phylogenetic analysis reveals that TseV1-4 are evolutionarily related to enzymes involved in DNA repair. TseV2 and TseV3 maintained the ability to bind DNA, but instead cause specific DNA double-strand breaks and induce the SOS response in target cells. The crystal structure of the TseV3:TsiV3 complex reveals that the immunity protein likely blocks the effector interaction with the DNA substrate. These results expand our knowledge on the function of Salmonella pathogenicity islands, the evolution of toxins used in biological conflicts, and the endogenous mechanism regulating the activity of these toxins.

microbiology↗

bioRxiv2021

Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide- degrading enzyme CynD

Cyanide is widely used in industry as a potent lixiviant due to its capacity to tightly bind metals. This property imparts cyanide enormous toxicity to all known organisms. Thus, industries that utilize this compound must reduce its concentration in recycled or waste waters. Physical, chemical, and biological treatments have been used for cyanide remediation; however, none of them meet all the desired characteristics: efficiency, low cost and low environmental impact. A better understanding of metabolic pathways and biochemistry of enzymes involved in cyanide degradation is a necessary step to improve cyanide bioremediation efficacy to satisfy the industry requirements. Here, we used several approaches to explore this topic. We have isolated three cyanide-degrading Bacillus strains from water in contact with mine tailings from Lima, Peru, and classified them as Bacillus safensis PER-URP-08, Bacillus licheniformis PER-URP-12, and Bacillus subtilis PER-URP-17 based on 16S rRNA gene sequencing and core genome analyses. Additionally, core genome analyses of 132 publicly available genomes of Bacillus pumilus group including B. safensis and B. altitudinis allowed us to reclassify some strains and identify two strains that did not match with any known species of the Bacillus pumilus group. We searched for possible routes of cyanide-degradation in the genomes of these three strains and identified putative B. licheniformis PER-URP-12 and B. subtilis PER-URP-17 rhodaneses and B. safensis PER-URP-08 cyanide dihydratase (CynD) sequences possibly involved cyanide degradation. We identified characteristic C-terminal residues that differentiate CynD from B. pumilus and B. safensis, and showed that, differently from CynD from B. pumilus C1, recombinant CynD from the Bacillus safensis PER-URP-08 strain remains active up to pH 9 and presents a distinct oligomerization pattern at pH 8 and 9. Moreover, transcripts of B. safensis PER-URP-08 CynD (CynDPER-URP-08) are strongly induced in the presence of cyanide. Our results warrant further investigation of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tools for cyanide-bioremediation.

microbiology↗

bioRxiv2021

Resource sharing by outer membrane vesicles from a citrus pathogen

The causative agent of citrus canker disease, Xanthomonas citri pv. citri, was found to produce copious amounts of outer membrane vesicles (OMVs), frequently forming long membranous tubes under different culture conditions. Lipidomic analysis revealed significant differences in lipid composition between purified vesicles in relation to whole cells. The results suggest an enrichment in saturated cardiolipins and a decrease in unsaturated lipids in the OMV samples, possibly granting them a more rigid structure while allowing their high degree of curvature caused by their small diameters. The vesicles proteome was found to be significantly enriched in TonB-dependent receptors related to the acquisition of different nutrients. These proteins are known to transport siderophores, which were evidenced to be present in purified X. citri OMVs, along with essential metals including iron, zinc, and manganese quantified by elemental analysis. The availability of vesicle-associated nutrients to be incorporated by cells was demonstrated by the use of OMVs as the sole carbon source for bacterial growth. At last, the vesicles also presented esterase and protease activities, which have been associated with virulence in phytopathogens. These evidences point that X. citri cells can use OMVs to share resources within microbial communities, which has potential implications for microbial interactions and plant colonization, affecting their survival and persistence on the host and in the environment. ImportanceThe shedding of outer membrane vesicles appears to be universal in Gram-negative bacteria and effectively constitutes a unique secretion pathway for diverse molecules and proteins. To study their possible functions in the citrus pathogen Xanthomonas citri, purified vesicles from this bacterium were studied by omics and functional approaches. Nutrient transporters were found associated to these structures, which were evidenced to contain siderophores and essential metals. The availability of these nutrients to be incorporated by cells was then demonstrated by showing that purified vesicles can be used as sole carbon sources for microbial growth. Additionally, the samples also presented esterase and protease activities which can contribute to the release of substrates from plant host tissues. These observations help to establish the developing idea of vesicles as shared bacterial resources which can participate in shaping host-associated microbial communities in contrast to other interactions such as bacterial competition.

microbiology↗

bioRxiv2020

Molecular and functional basis of a novel Amazonian Dark Earth Esterase 1 (Ade1) with hysteresis behavior and quorum-quenching activity

Amazon Dark Earth (ADE) soil is rich in organic compounds and its fertility has been associated with a high diversity of microorganisms. Herein, we investigate the biochemical and functional features of a novel esterase, Ade1, obtained from a metagenomic library of Amazonian Dark Earth soils of the Amazonian Rainforest, in Brazil. The esterases cleave ester bonds to form a carboxylic and an alcohol group. Esterases and lipases are enzymes found in almost all living organisms, demonstrating their biological relevance. We reported that Ade1 belongs to an /{beta}-hydrolase superfamily. We suggest that Ade1 is a moonlighting enzyme with hysteresis behavior and quorum-quenching activity, which may play a key role in the metabolism of a Gram-negative proteobacteria. In addition, molecular dynamics simulations reveal that the hysteresis behavior is directly associated with structural properties of the cap domain. Our findings reveal details of the molecular basis, catalytic and structural mechanisms of a novel /{beta}-hydrolase, which may be applied to other esterases of biotechnological, food, and/or pharmaceutical interest. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biochemistry↗

bioRxiv2020

Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction

Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. We produced a recombinant N-terminal fraction of the Spike SARS-CoV-2 protein and injected it into adult female zebrafish. The specimens generated humoral immunity and passed the antibodies to the eggs. However, they presented adverse reactions and inflammatory responses similar to severe cases of human COVID-19. The analysis of the structure and function of zebrafish and human Angiotensin-converting enzyme 2, the main human receptor for virus infection, presented remarkable sequence similarities. Moreover, bioinformatic analysis predicted protein-protein interaction of the Spike SARS-CoV-2 fragment and the Toll-like receptor pathway. It might help in the choice of future therapeutic pharmaceutical drugs to be studied. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus.

immunology↗

bioRxiv2020

Molecular dynamics reveals complex compensatory effects of ionic strength on the SARS-CoV-2 Spike/hACE-2 interaction

The SARS-CoV-2 pandemic has already killed more than 800,000 people worldwide. To gain entry, the virus uses its spike protein to bind to host hACE-2 receptors on the host cell surface and mediate fusion between viral and cell membranes. As initial steps leading to virus entry involves significant changes in protein conformation as well as in the electrostatic environment in the vicinity of the spike-hACE-2 complex, we explored the sensitivity of the interaction to changes in ionic strength through computational simulations and surface plasmon resonance. We identified two regions in the receptor-binding domain (RBD), E1 and E2, which interact differently with hACE-2. At high salt concentration, E2-mediated interactions are weakened but are compensated by strengthening E1-mediated hydrophobic interactions. These results provide a detailed molecular understanding of spike RBD/hACE-2 complex formation and stability under a wide range of ionic strengths. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/267351v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1a7dc02org.highwire.dtl.DTLVardef@15d3c78org.highwire.dtl.DTLVardef@2d09c1org.highwire.dtl.DTLVardef@db78a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

Bactericidal Type IV Secretion System Homeostasis in Xanthomonas citri

Several Xanthomonas species have a type IV secretion system (T4SS) that injects a cocktail of antibacterial proteins into neighbouring Gram-negative bacteria, often leading to rapid lysis upon cell contact. This capability represents an obvious fitness benefit since it can eliminate competition while the liberated contents of the lysed bacteria could provide an increase in the local availability of nutrients. However, the production of this Mega Dalton-sized T4SS, with over a hundred subunits, also imposes a significant metabolic cost. Here we show that the chromosomal virB operon, which encodes the entirety of structural genes of the T4SS in X. citri, is regulated by the global regulator CsrA. Relieving CsrA repression from the virB operon produced a greater number of T4SSs in the cell envelope and an increased efficiency in contact dependent lysis of target cells. However, this was also accompanied by a physiological cost leading to reduced fitness when in co-culture with wild-type X. citri. We show that T4SS production is constitutive despite being downregulated by CsrA. Cells subjected to a wide range of rich and poor growth conditions maintain a constant density of T4SSs in the cell envelope and concomitant interbacterial competitiveness. These results show that CsrA provides a constant though partial repression on the virB operon, independent of the tested growth conditions, in this way controlling T4SS-related costs while at the same time maintaining X. citris aggressive posture when confronted by competitors.\n\nAuthor SummaryXanthomonas citri is a member of a family of phytopathogenic bacteria that can cause substantial losses in crops. At different stages of the infection cycle, these cells will encounter other bacterial species with whom they will have to compete for space and nutrients. One mechanism which improves a cells chance to survive these encounters is a type IV secretion system that transfers a cocktail of antimicrobial effector proteins into other Gram-negative bacteria in a contact-dependent manner. Here, we show that this system is constitutively produced at a low basal level, even during low nutrient conditions, despite representing a significant metabolic burden to the cell. The conserved global regulator, CsrA, provides a constant, nutrient-independent, repression on the production T4SS components, thereby holding production costs to a minimum while at the same time ensuring X. citris competitiveness during encounters with bacterial rivals.

microbiology↗

bioRxiv2019

The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing

Bacterial type IV secretion systems (T4SS) are a highly diversified but evolutionarily related family of macromolecule transporters that can secrete proteins and DNA into the extracellular medium or into target cells. They have been long known to play a fundamental role in bacterial conjugation and virulence of several species. It was recently shown that a subtype of T4SS harboured by the plant pathogenic bacterium Xanthomonas citri transfers toxins into other bacteria cells resulting in cell death. In this study, we show that a similar T4SS from the multi-drug-resistant global opportunistic pathogen Stenotrophomonas maltophilia is proficient in killing competitor bacterial species. T4SS-dependent duelling between S. maltophilia and X. citri was observed by time-lapse fluorescence microscopy. A bioinformatic search of the S. maltophilia K279a genome for proteins containing a C-terminal domain (XVIPCD) conserved in X. citri T4SS effectors identified eleven putative effectors secreted by the S. maltophilia T4SS. Six of these effectors have no recognizable domain except for the XVIPCD. We selected one of these new effectors (Smlt3024) and its cognate inhibitor (Smlt3025) for further characterization and confirmed that Smlt3024 is indeed secreted in a T4SS-dependent manner by S. maltophilia when in contact with a target bacterial species. Expression of Smlt3024 in the periplasm of E. coli resulted in greatly reduced growth rate and cell size, which could be counteracted by co-expression with its cognate periplasmic inhibitor, Smlt3025. This work expands our current knowledge about the diverse function of T4SSs subtypes and increases the panel of effectors known to be involved in T4SS-mediated interbacterial competition. Further elucidation of the mechanism of these antibacterial proteins could lead to the discovery of new antibacterial targets. The study also adds information about the molecular mechanisms possibly contributing to the establishment of S. maltophilia in different biotic and abiotic surfaces in both clinical and environmental settings. Author SummaryCompetition between microorganisms for nutrients and space determines which species will emerge and dominate or be eradicated from a specific habitat. Bacteria use a series of mechanisms to kill or prevent multiplication of competitor species. Recently, it was reported that a subtype of type IV secretion system (T4SS) works as a weapon to kill competitor bacterial species. In this study, we show that an important human opportunistic pathogen, Stenotrophomonas maltophilia, harbours a T4SS that promotes killing of competitor species. We also identified a series of new toxic proteins secreted by S. maltophilia via its T4SS to poison competitor species. We showed that two different bacterial species that harbour a bacteria-killing T4SS can kill each other; most likely due to differences in effector-immunity protein pairs. This work expands our current knowledge about the bacterial arsenal used in competitions with other species and expands the repertoire of antibacterial ammunition fired by T4SSs. In addition, the work contributes with knowledge on the possible mechanisms used by S. maltophilia to establish communities in different biotic and abiotic surfaces in both clinical and environmental settings.

microbiology↗